cDNA Synthesis:Article Title: Interface-guided phenotyping of coding variants in the transcription factor RUNX1.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies RUNX1 Antibody (A-2), mouse monoclonal Santa Cruz Biotechnologies Cat#sc-365644; RRID:AB_10843207 Anti-b-Actin Antibody (AC-15), mouse monoclonal Millipore Sigma Cat#A1978; RRID:AB_476692 Anti-Mouse IgG, HRP-linked Antibody Cell Signaling Technology Cat#7076P2; RRID:AB_330924 IRDye 680RD Goat anti-Mouse IgG Secondary Antibody Li-Cor Bio Cat#926–68070; RRID:AB_10956588 Bacterial and virus strains Stbl3 Thermo Fisher Cat#C737303 Chemicals, peptides, and recombinant proteins NheI-HF New England Biolabs Cat#R3131S SalI-HF New England Biolabs Cat#R3138S AflII New England Biolabs Cat#R0520S Gibson Assembly Master Mix New England Biolabs Cat#E2611S KAPA HiFi HotStart ReadyMix Roche Cat#KK2601 OneTaq 2X Master Mix New England Biolabs Cat#M0482S AMPure XP Beads Beckman Coulter Cat#A63880 DMEM ThermoFisher Scientific Cat#10566016 .05% Trypsin-EDTA Gibco Cat#25300062 OptiMEM ThermoFisher Scientific Cat#31985062 RPMI Medium 1640 Gibco Cat#11875-093 FBS Gibco Cat#A52568 Anti-anti Gibco Cat#15240-062 Lipofectamine 2000 ThermoFisher Scientific Cat#11668030 Doxycycline hyclate Sigma Cat#D5207 Hygromycin Invitrogen Cat#10687010 Puromycin Gibco Cat#A11138-03 Polybrene Millipore-Sigma Cat#TR-1003-G PBS, pH 7.4 Gibco Cat#10010023 Tn5 Illumina Cat#20034198 RIPA Buffer Cell Signaling Technologies Cat#9806 Pierce Protease Inhibitor Tablets ThermoFisher Scientific Cat#A32963 4X Laemmli Sample Buffer Bio-Rad Cat#1610747 4-20% Mini-PROTEAN TGX gel Bio-Rad Cat#4561094 10X Tris/Glycine/SDS Buffer Bio-Rad Cat#1610732 Nonfat Dry Milk Apex Bioresearch Cat#20-241 TBST Cell Signaling Technology Cat#9997 BSA, Fraction V, Fatty Acid-Free Millipore Sigma Cat#126575 SuperSignal West Pico Plus Chemiluminescent Substrate ThermoFisher Scientific Cat#34577 Carbenicillin Teknova Cat#C2199 iTaq Universal SYBR Green Master Mix Bio-Rad Cat#1725120 Critical commercial assays Pierce BCA Protein Assay kit ThermoFisher Scientific Cat#23227 RNeasy Mini Kit Qiagen Cat#74104 DNeasy Blood and Tissue Kit Qiagen Cat#69504 (Continued on next page) 20 Cell Reports 43, 114436, July 23, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER Protoscript II First Strand cDNA Synthesis Kit New England BioLabs CatE6560S QIAquick PCR Purification Kit Qiagen Cat#28104 Nucleofector Solution Set SF Lonza Cat#PBC2-00675 Chromium Single Cell 30 v3 10X Genomics Cat# PN- 1000128 NEBNext Ultra RNA Library Prep Kit New England Biolabs Cat#E7530 Deposited data Raw data: scRNA-seq This paper SRA: PRJNA1033389 Raw data: bulk RNA-seq This paper SRA: PRJNA1121326 Raw data: ATAC-seq This paper SRA: PRJNA1121327 RUNX1-CBFB-DNA structures Protein DataBank PDB: 1ljm, 1e50, 1h9d Human reference genome NCBI build 38, GRCh38–3.0.0 Genome Reference Consortium http://www.ncbi.nlm.nih.gov/projects/ genome/assembly/grc/human/ ATAC-seq data for K562 ENCODE ENCSR868FGK ChromHMM states for K562 Roadmap Epigenomics Project https://egg2.wustl.edu/roadmap/web_portal/ Hi-C chromatin loop data for K562 NCBI GEO: GSM1551620 Experimental models: Cell lines K-562 ATCC Cat#CCL-243; RRID:CVCL_0004 HEK293T ATCC Cat#CRL-3216; RRID:CVCL_0063 Oligonucleotides RUNX1 library variants Twist Bioscience https://www.twistbioscience.com Primers for qPCR, Sanger Sequencing, & oligopool amplification, see Table S10 This Paper N/A NEBNext Multiplex Oligos for Illumina New England Biolabs Cat#E7335S Recombinant DNA EF1a_mCherry_P2A_Hygro_Barcode (Parekh et al.)12 Addgene #120426 PB-TRE-dCas9-VPR (Chavez et al.)108 Addgene #63800 pHR-SFFV-KRAB-dCas9-P2A-mCherry (Gilbert et al.)109 Addgene #60954 pMD2.G N/A Addgene #12259 pCMV delta R8.2 N/A Addgene #12263 Software and algorithms Code related to analyses of RUNX1 mutations This paper https://github.com/cartercompbio/ RUNX1_SEUSS; https://doi.org/ 10.5281/zenodo.11580866 CellRanger 3.1.0 10X Genomics https://support.10xgenomics.com genotyping-matrices (Parekh et al.)12 https://github.com/yanwu2014/ genotyping-matrices MAGeCK (W. Li et al.)110 https://sourceforge.net/p/mageck/ wiki/Home/ PRISM (Baspinar et al.)60 https://cosbi.ku.edu.tr/prism/ VEST (Carter et al.)62 http://www.cravat.us/CRAVAT/ FoldX (Schymkowitz et al.)63 http://foldx.crg.es/ Seurat 4.1.0 (Macosko et al.)111 https://satijalab.org/seurat/ CoGAPS (Fertig et al.)72 http://www.bioconductor.org/packages/ release/bioc/html/CoGAPS.html EnrichR (Kuleshov et al.)112 https://github.com/wjawaid/enrichR STAR 2.7.1a (Dobin et al.)113 https://github.com/alexdobin/STAR RSEM 1.3.1 N/A http://deweylab.biostat.wisc.edu/rsem/ limma (Ritchie et al.)114 http://bioinf.wehi.edu.au/limma/ (Continued on next page) Cell Reports 43, 114436, July 23, 2024 21 ..
Polymerase Chain Reaction:Article Title: Interface-guided phenotyping of coding variants in the transcription factor RUNX1.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies RUNX1 Antibody (A-2), mouse monoclonal Santa Cruz Biotechnologies Cat#sc-365644; RRID:AB_10843207 Anti-b-Actin Antibody (AC-15), mouse monoclonal Millipore Sigma Cat#A1978; RRID:AB_476692 Anti-Mouse IgG, HRP-linked Antibody Cell Signaling Technology Cat#7076P2; RRID:AB_330924 IRDye 680RD Goat anti-Mouse IgG Secondary Antibody Li-Cor Bio Cat#926–68070; RRID:AB_10956588 Bacterial and virus strains Stbl3 Thermo Fisher Cat#C737303 Chemicals, peptides, and recombinant proteins NheI-HF New England Biolabs Cat#R3131S SalI-HF New England Biolabs Cat#R3138S AflII New England Biolabs Cat#R0520S Gibson Assembly Master Mix New England Biolabs Cat#E2611S KAPA HiFi HotStart ReadyMix Roche Cat#KK2601 OneTaq 2X Master Mix New England Biolabs Cat#M0482S AMPure XP Beads Beckman Coulter Cat#A63880 DMEM ThermoFisher Scientific Cat#10566016 .05% Trypsin-EDTA Gibco Cat#25300062 OptiMEM ThermoFisher Scientific Cat#31985062 RPMI Medium 1640 Gibco Cat#11875-093 FBS Gibco Cat#A52568 Anti-anti Gibco Cat#15240-062 Lipofectamine 2000 ThermoFisher Scientific Cat#11668030 Doxycycline hyclate Sigma Cat#D5207 Hygromycin Invitrogen Cat#10687010 Puromycin Gibco Cat#A11138-03 Polybrene Millipore-Sigma Cat#TR-1003-G PBS, pH 7.4 Gibco Cat#10010023 Tn5 Illumina Cat#20034198 RIPA Buffer Cell Signaling Technologies Cat#9806 Pierce Protease Inhibitor Tablets ThermoFisher Scientific Cat#A32963 4X Laemmli Sample Buffer Bio-Rad Cat#1610747 4-20% Mini-PROTEAN TGX gel Bio-Rad Cat#4561094 10X Tris/Glycine/SDS Buffer Bio-Rad Cat#1610732 Nonfat Dry Milk Apex Bioresearch Cat#20-241 TBST Cell Signaling Technology Cat#9997 BSA, Fraction V, Fatty Acid-Free Millipore Sigma Cat#126575 SuperSignal West Pico Plus Chemiluminescent Substrate ThermoFisher Scientific Cat#34577 Carbenicillin Teknova Cat#C2199 iTaq Universal SYBR Green Master Mix Bio-Rad Cat#1725120 Critical commercial assays Pierce BCA Protein Assay kit ThermoFisher Scientific Cat#23227 RNeasy Mini Kit Qiagen Cat#74104 DNeasy Blood and Tissue Kit Qiagen Cat#69504 (Continued on next page) 20 Cell Reports 43, 114436, July 23, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER Protoscript II First Strand cDNA Synthesis Kit New England BioLabs CatE6560S QIAquick PCR Purification Kit Qiagen Cat#28104 Nucleofector Solution Set SF Lonza Cat#PBC2-00675 Chromium Single Cell 30 v3 10X Genomics Cat# PN- 1000128 NEBNext Ultra RNA Library Prep Kit New England Biolabs Cat#E7530 Deposited data Raw data: scRNA-seq This paper SRA: PRJNA1033389 Raw data: bulk RNA-seq This paper SRA: PRJNA1121326 Raw data: ATAC-seq This paper SRA: PRJNA1121327 RUNX1-CBFB-DNA structures Protein DataBank PDB: 1ljm, 1e50, 1h9d Human reference genome NCBI build 38, GRCh38–3.0.0 Genome Reference Consortium http://www.ncbi.nlm.nih.gov/projects/ genome/assembly/grc/human/ ATAC-seq data for K562 ENCODE ENCSR868FGK ChromHMM states for K562 Roadmap Epigenomics Project https://egg2.wustl.edu/roadmap/web_portal/ Hi-C chromatin loop data for K562 NCBI GEO: GSM1551620 Experimental models: Cell lines K-562 ATCC Cat#CCL-243; RRID:CVCL_0004 HEK293T ATCC Cat#CRL-3216; RRID:CVCL_0063 Oligonucleotides RUNX1 library variants Twist Bioscience https://www.twistbioscience.com Primers for qPCR, Sanger Sequencing, & oligopool amplification, see Table S10 This Paper N/A NEBNext Multiplex Oligos for Illumina New England Biolabs Cat#E7335S Recombinant DNA EF1a_mCherry_P2A_Hygro_Barcode (Parekh et al.)12 Addgene #120426 PB-TRE-dCas9-VPR (Chavez et al.)108 Addgene #63800 pHR-SFFV-KRAB-dCas9-P2A-mCherry (Gilbert et al.)109 Addgene #60954 pMD2.G N/A Addgene #12259 pCMV delta R8.2 N/A Addgene #12263 Software and algorithms Code related to analyses of RUNX1 mutations This paper https://github.com/cartercompbio/ RUNX1_SEUSS; https://doi.org/ 10.5281/zenodo.11580866 CellRanger 3.1.0 10X Genomics https://support.10xgenomics.com genotyping-matrices (Parekh et al.)12 https://github.com/yanwu2014/ genotyping-matrices MAGeCK (W. Li et al.)110 https://sourceforge.net/p/mageck/ wiki/Home/ PRISM (Baspinar et al.)60 https://cosbi.ku.edu.tr/prism/ VEST (Carter et al.)62 http://www.cravat.us/CRAVAT/ FoldX (Schymkowitz et al.)63 http://foldx.crg.es/ Seurat 4.1.0 (Macosko et al.)111 https://satijalab.org/seurat/ CoGAPS (Fertig et al.)72 http://www.bioconductor.org/packages/ release/bioc/html/CoGAPS.html EnrichR (Kuleshov et al.)112 https://github.com/wjawaid/enrichR STAR 2.7.1a (Dobin et al.)113 https://github.com/alexdobin/STAR RSEM 1.3.1 N/A http://deweylab.biostat.wisc.edu/rsem/ limma (Ritchie et al.)114 http://bioinf.wehi.edu.au/limma/ (Continued on next page) Cell Reports 43, 114436, July 23, 2024 21 ..
Article Title: Protocol for mapping the three-dimensional organization of dinoflagellate genomes.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Chemicals and recombinant proteins Nuclease-free H2O Thermo Fisher Scientific AM9916 1 M Tris-HCl pH 7.5 Thermo Fisher Scientific 15567027 1 M Tris-HCl pH 8.0 Thermo Fisher Scientific 15568025 1 M MgCl2 Thermo Fisher Scientific AM9530G 5 M NaCl Thermo Fisher Scientific AM9759 0.5 M EDTA, pH 8.0 Thermo Fisher Scientific 15575020 20% SDS Thermo Fisher Scientific AM9820 1x PBS buffer solution pH 7.4 Thermo Fisher Scientific 10010023 1x TE buffer Thermo Fisher Scientific 12090015 IGEPAL CA-630 detergent Sigma I8896-50ML Tween 20 detergent 10% Sigma 11332465001 10% Triton X-100 Sigma 93443 37% formaldehyde Sigma 252549-100ML 0.1 M NaHCO3 Sigma S6014-1KG Glycine Sigma 1005901000 MboI restriction enzyme NEB R0147 10x CutSmart buffer NEB B7204 0.4 mM biotin-14-dATP Thermo Fisher Scientific 19524-016 100 mM dCTP/dGTP/dTTP Promega U1330 DNA polymerase I large (Klenow) fragment NEB M0210 10x NEB T4 DNA ligase buffer NEB B0202 Bovine serum albumin (BSA) 100x NEB B9000 T4 DNA ligase NEB M0202 Proteinase K Promega MC5005 Dynabeads MyOne Streptavidin T1 Thermo Fisher Scientific 65602 AMPure XP beads Beckman Coulter A63881 100% EtOH Sigma 493546-1L 200-mL PCR tubes Thermo Fisher Scientific AB1182 1.5-mL DNA LoBind microcentrifuge tubes Eppendorf 022431021 (Continued on next page) 2 STAR Protocols 5, 102941, June 21, 2024 Continued REAGENT or RESOURCE SOURCE IDENTIFIER 15/50 mL tubes Critical commercial assays NEBNext Ultra II DNA Library Prep Kit for Illumina NEB E7645L NEBNext Multiplex Oligos for Illumina NEB E7600S MinElute PCR Purification Kit QIAGEN 28004/28006 Covaris milliTUBE 1 mL Covaris 520135 QuBit tubes Thermo Fisher Scientific Q32856 QuBit dsDNA HS Assay Kit Thermo Fisher Scientific Q32854 TapeStation D1000 tape Agilent 5067-5582 TapeStation D1000 reagents Agilent 5067-5583 Equipment TapeStation Agilent G2991BA Covaris E220 Covaris SKU500239 QuBit fluorometer Thermo Fisher Scientific Q33327 Tabletop centrifuge Thermomixer Eppendorf 5382000023 PCR thermocycler Magnetic rack Tube rotator Software and algorithms Juicer (version 1.6 used) Durand et al.4 https://github.com/aidenlab/juicer Juicebox (version 1.11.08 used) Durand et al.5 https://github.com/aidenlab/Juicebox 3D-DNA (version 180419 used) Dudchenko et al.6 https://github.com/aidenlab/3d-dna bwa (version 0.7.5a used) Li & Durbin7 https://github.com/lh3/bwa sra-tools (version 2.11.0 used) https://github.com/ncbi/sra-tools Deposited data Fugacium kawagutii Hi-C SRA: SRR25948349 and SRR25948348 Fugacium kawagutii draft assembly (V3) http://sampgr.org.cn/index.php/download ..
Article Title: LDB1 establishes multi-enhancer networks to regulate gene expression.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Mouse monoclonal anti-LDB1 CLIM-2 (C-9) Santa Cruz Biotechnology Cat#sc-365074; RRID: AB_10848267 Rabbit polyclonal anti-LDB1 Lot# VI3089586A Thermo Fisher Scientific Cat#PA5-56948; RRID: AB_2643320 Mouse monoclonal anti-GAPDH Lot# A1822 (6C5) Santa Cruz Biotechnology Cat#sc-32233; RRID: AB_627679 Rabbit monoclonal anti-RPB1 (Pol2) (D8L4Y) Cell Signaling Technology Cat#14958; RRID: AB_2687876 Rabbit polyclonal anti-YY1 Active Motif Cat#61779; RRID: AB_2793763 Rabbit polyclonal anti-CTCF Millipore Cat#07-729; RRID: AB_441965 Rabbit polyclonal anti-RAD21 Abcam Cat#ab992; RRID: AB_2176601 Mouse monoclonal anti-pMPM2 Millipore Cat# 05-368; RRID: AB_309698 F(ab’)2-Goat anti-Mouse IgG (H+L) Secondary Antibody, APC, eBioscience Thermo Fisher Scientific Cat#17-4010-82; RRID: AB_2573203 Chemicals, peptides, and recombinant proteins AMPure XP Beckman Coulter Cat#A63880 Indole-3-acetic acid sodium salt (auxin) Sigma Aldrich Cat#I5148 estradiol Sigma Aldrich Cat#E2758 iSCRIPT Reverse Transcription Supermix Bio Rad Cat#1708840 Power SYBR Green PCR Master Mix Thermo Fisher Scientific Cat#4367660 Protein A agarose beads Thermo Fisher Scientific Cat#15918014 Protein G agarose beads Thermo Fisher Scientific Cat#15920010 DSG crosslinker ProteoChem Cat#c1104-1gm cOmplete Mini, EDTA-free Millipore Sigma Cat#11836170001 MNase Worthington Biochemical Cat#LS004798 rSAP New England Biolabs Cat#M0371S T4 PNK New England Biolabs Cat#M0201S Large (Klenow) Fragment New England Biolabs Cat#M0210S Biotin-11-dCTP Jena Bioscience Cat#NU-809-BIOX-S Biotin-14-dATP Jena Bioscience Cat#NU-835-BIO14-S Biotin-14-dATP Active Motif Cat#14138 T4 DNA Ligase New England Biolabs Cat#M0202S T4 DNA Ligase buffer New England Biolabs Cat#B0202S Dynabeads MyOne Streptavidin C1 Thermo Fisher Scientific Cat#65001 KAPA HiFi HotStart ReadyMix Roche Cat#08202940001 Herculase II Fusion DNA Polymerase Agilent Cat#600675 Mouse Cot-1 DNA Thermo Fisher Scientific Cat#18440016 Twist Universal Blockers Twist Bioscience Cat#100578 Twist Binding and Purification Beads Twist Bioscience Cat#100983 Dynabeads M-270 Streptavidn Thermo Fisher Scientic Cat#65305 NlaIII New England Biolabs Cat#R0125L NEB Buffer 2 New England Biolabs Cat#7002S NEB Buffer 3.1 New England Biolabs Cat#B7203S DpnII New England Biolabs Cat#R0543M VAHTS DNA Clean Beads Vazyme Cat#N411 (Continued on next page) e1 Molecular Cell 85, 376–393.e1–e9, January 16, 2025 .. REAGENT or RESOURCE SOURCE IDENTIFIER T4 DNA polymerase New England Biolabs CatM0203S 4-thiouridine (4SU) MedChemExpress Cat#HY-W011793 TRIzol Reagent Invitrogen Cat#15596026 MTSEA-biotin Biotium Cat# 90064 Critical commercial assays KAPA HyperCapture Reagent Kit Roche Cat#9075810001 Twist Hybridization and Wash Kit with Amplification Mix, 12 Reactions Twist Bioscience Cat#104178 RNeasy Mini Kit QIAGEN Cat#74104 QIAshredder QIAGEN Cat#79656 NEBNext Ultra II DNA Library Prep Kit for Illumina New England Biolabs Cat#E7645S NEBNext Multiplex Oligos for Illumina (96 Unique Dual Index Primer Pairs) New England Biolabs Cat#E6440S TruSeq Stranded mRNA kit Illumina Cat#20020594 Illumina Stranded Total RNA Prep Illumina Cat# 20040525 Qubit dsDNA Quantification Assay Kits Thermo Fisher Scientific Cat#Q32850 In-Fusion HD Cloning kit Takara Cat#639648 QIAquick PCR Purification Kit QIAGEN Cat#28104 QIAquick Gel Extraction Kit QIAGEN Cat#28704 AHTS Universal DNA Library Prep Kit Vazyme Cat#ND627-01 Deposited data LDB1-AID Micro-C This paper GSE254373 LDB1-AID RCMC This paper GSE266450 LDB1-AID TT-seq This paper GSE264584 LDB1-AID Tri-C This paper GSE254372 LDB1-AID RNA-seq This paper GSE264455 SMC3-AID Hi-C Zhao et al.103 GSE228402 CTCF-AID Hi-C Zhang et al.26 GSE168251 YY1-AID Micro-C Lam et al.84 GSE247254 Mitotic Hi-C Zhang et al.38 GSE129997 Mitotic ChIP-seq (CTCF/RAD21) Zhang et al.38 GSE129997 H3K27ac ChIP-seq Dogan et al.104 GSE61349 LDB1-AID ChIP-seq This paper GSE254377 SMC3-AID ChIP-seq This paper GSE254377 Original western blot data This paper, Mendeley Data https://doi.org/10.17632/mf78pvcrkk.2 Experimental models: Cell lines G1E-ER4 Mitchell J. Weiss lab Weiss et al.82 LDB1-AID This paper N/A YY1-AID Gerd Blobel Lab Lam et al.84 SMC3-AID Haoyue Zhang Lab Zhao et al.103 CTCF-AID Gerd A. Blobel lab Zhang et al.26 Oligonucleotides See Table S2 for oligonucleotides used in this study This paper Table S2 Recombinant DNA pX458-GFP Addgene 48138 md-mCherry Gerd A. Blobel lab Zhang et al.38 OsTiR-IRES-GFP Gerd A. Blobel lab Zhang et al.38 (Continued on next page) Molecular Cell 85, 376–393.e1–e9, January 16, 2025 e2 ..
Purification:Article Title: Interface-guided phenotyping of coding variants in the transcription factor RUNX1.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies RUNX1 Antibody (A-2), mouse monoclonal Santa Cruz Biotechnologies Cat#sc-365644; RRID:AB_10843207 Anti-b-Actin Antibody (AC-15), mouse monoclonal Millipore Sigma Cat#A1978; RRID:AB_476692 Anti-Mouse IgG, HRP-linked Antibody Cell Signaling Technology Cat#7076P2; RRID:AB_330924 IRDye 680RD Goat anti-Mouse IgG Secondary Antibody Li-Cor Bio Cat#926–68070; RRID:AB_10956588 Bacterial and virus strains Stbl3 Thermo Fisher Cat#C737303 Chemicals, peptides, and recombinant proteins NheI-HF New England Biolabs Cat#R3131S SalI-HF New England Biolabs Cat#R3138S AflII New England Biolabs Cat#R0520S Gibson Assembly Master Mix New England Biolabs Cat#E2611S KAPA HiFi HotStart ReadyMix Roche Cat#KK2601 OneTaq 2X Master Mix New England Biolabs Cat#M0482S AMPure XP Beads Beckman Coulter Cat#A63880 DMEM ThermoFisher Scientific Cat#10566016 .05% Trypsin-EDTA Gibco Cat#25300062 OptiMEM ThermoFisher Scientific Cat#31985062 RPMI Medium 1640 Gibco Cat#11875-093 FBS Gibco Cat#A52568 Anti-anti Gibco Cat#15240-062 Lipofectamine 2000 ThermoFisher Scientific Cat#11668030 Doxycycline hyclate Sigma Cat#D5207 Hygromycin Invitrogen Cat#10687010 Puromycin Gibco Cat#A11138-03 Polybrene Millipore-Sigma Cat#TR-1003-G PBS, pH 7.4 Gibco Cat#10010023 Tn5 Illumina Cat#20034198 RIPA Buffer Cell Signaling Technologies Cat#9806 Pierce Protease Inhibitor Tablets ThermoFisher Scientific Cat#A32963 4X Laemmli Sample Buffer Bio-Rad Cat#1610747 4-20% Mini-PROTEAN TGX gel Bio-Rad Cat#4561094 10X Tris/Glycine/SDS Buffer Bio-Rad Cat#1610732 Nonfat Dry Milk Apex Bioresearch Cat#20-241 TBST Cell Signaling Technology Cat#9997 BSA, Fraction V, Fatty Acid-Free Millipore Sigma Cat#126575 SuperSignal West Pico Plus Chemiluminescent Substrate ThermoFisher Scientific Cat#34577 Carbenicillin Teknova Cat#C2199 iTaq Universal SYBR Green Master Mix Bio-Rad Cat#1725120 Critical commercial assays Pierce BCA Protein Assay kit ThermoFisher Scientific Cat#23227 RNeasy Mini Kit Qiagen Cat#74104 DNeasy Blood and Tissue Kit Qiagen Cat#69504 (Continued on next page) 20 Cell Reports 43, 114436, July 23, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER Protoscript II First Strand cDNA Synthesis Kit New England BioLabs CatE6560S QIAquick PCR Purification Kit Qiagen Cat#28104 Nucleofector Solution Set SF Lonza Cat#PBC2-00675 Chromium Single Cell 30 v3 10X Genomics Cat# PN- 1000128 NEBNext Ultra RNA Library Prep Kit New England Biolabs Cat#E7530 Deposited data Raw data: scRNA-seq This paper SRA: PRJNA1033389 Raw data: bulk RNA-seq This paper SRA: PRJNA1121326 Raw data: ATAC-seq This paper SRA: PRJNA1121327 RUNX1-CBFB-DNA structures Protein DataBank PDB: 1ljm, 1e50, 1h9d Human reference genome NCBI build 38, GRCh38–3.0.0 Genome Reference Consortium http://www.ncbi.nlm.nih.gov/projects/ genome/assembly/grc/human/ ATAC-seq data for K562 ENCODE ENCSR868FGK ChromHMM states for K562 Roadmap Epigenomics Project https://egg2.wustl.edu/roadmap/web_portal/ Hi-C chromatin loop data for K562 NCBI GEO: GSM1551620 Experimental models: Cell lines K-562 ATCC Cat#CCL-243; RRID:CVCL_0004 HEK293T ATCC Cat#CRL-3216; RRID:CVCL_0063 Oligonucleotides RUNX1 library variants Twist Bioscience https://www.twistbioscience.com Primers for qPCR, Sanger Sequencing, & oligopool amplification, see Table S10 This Paper N/A NEBNext Multiplex Oligos for Illumina New England Biolabs Cat#E7335S Recombinant DNA EF1a_mCherry_P2A_Hygro_Barcode (Parekh et al.)12 Addgene #120426 PB-TRE-dCas9-VPR (Chavez et al.)108 Addgene #63800 pHR-SFFV-KRAB-dCas9-P2A-mCherry (Gilbert et al.)109 Addgene #60954 pMD2.G N/A Addgene #12259 pCMV delta R8.2 N/A Addgene #12263 Software and algorithms Code related to analyses of RUNX1 mutations This paper https://github.com/cartercompbio/ RUNX1_SEUSS; https://doi.org/ 10.5281/zenodo.11580866 CellRanger 3.1.0 10X Genomics https://support.10xgenomics.com genotyping-matrices (Parekh et al.)12 https://github.com/yanwu2014/ genotyping-matrices MAGeCK (W. Li et al.)110 https://sourceforge.net/p/mageck/ wiki/Home/ PRISM (Baspinar et al.)60 https://cosbi.ku.edu.tr/prism/ VEST (Carter et al.)62 http://www.cravat.us/CRAVAT/ FoldX (Schymkowitz et al.)63 http://foldx.crg.es/ Seurat 4.1.0 (Macosko et al.)111 https://satijalab.org/seurat/ CoGAPS (Fertig et al.)72 http://www.bioconductor.org/packages/ release/bioc/html/CoGAPS.html EnrichR (Kuleshov et al.)112 https://github.com/wjawaid/enrichR STAR 2.7.1a (Dobin et al.)113 https://github.com/alexdobin/STAR RSEM 1.3.1 N/A http://deweylab.biostat.wisc.edu/rsem/ limma (Ritchie et al.)114 http://bioinf.wehi.edu.au/limma/ (Continued on next page) Cell Reports 43, 114436, July 23, 2024 21 ..
Article Title: Protocol for mapping the three-dimensional organization of dinoflagellate genomes.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Chemicals and recombinant proteins Nuclease-free H2O Thermo Fisher Scientific AM9916 1 M Tris-HCl pH 7.5 Thermo Fisher Scientific 15567027 1 M Tris-HCl pH 8.0 Thermo Fisher Scientific 15568025 1 M MgCl2 Thermo Fisher Scientific AM9530G 5 M NaCl Thermo Fisher Scientific AM9759 0.5 M EDTA, pH 8.0 Thermo Fisher Scientific 15575020 20% SDS Thermo Fisher Scientific AM9820 1x PBS buffer solution pH 7.4 Thermo Fisher Scientific 10010023 1x TE buffer Thermo Fisher Scientific 12090015 IGEPAL CA-630 detergent Sigma I8896-50ML Tween 20 detergent 10% Sigma 11332465001 10% Triton X-100 Sigma 93443 37% formaldehyde Sigma 252549-100ML 0.1 M NaHCO3 Sigma S6014-1KG Glycine Sigma 1005901000 MboI restriction enzyme NEB R0147 10x CutSmart buffer NEB B7204 0.4 mM biotin-14-dATP Thermo Fisher Scientific 19524-016 100 mM dCTP/dGTP/dTTP Promega U1330 DNA polymerase I large (Klenow) fragment NEB M0210 10x NEB T4 DNA ligase buffer NEB B0202 Bovine serum albumin (BSA) 100x NEB B9000 T4 DNA ligase NEB M0202 Proteinase K Promega MC5005 Dynabeads MyOne Streptavidin T1 Thermo Fisher Scientific 65602 AMPure XP beads Beckman Coulter A63881 100% EtOH Sigma 493546-1L 200-mL PCR tubes Thermo Fisher Scientific AB1182 1.5-mL DNA LoBind microcentrifuge tubes Eppendorf 022431021 (Continued on next page) 2 STAR Protocols 5, 102941, June 21, 2024 Continued REAGENT or RESOURCE SOURCE IDENTIFIER 15/50 mL tubes Critical commercial assays NEBNext Ultra II DNA Library Prep Kit for Illumina NEB E7645L NEBNext Multiplex Oligos for Illumina NEB E7600S MinElute PCR Purification Kit QIAGEN 28004/28006 Covaris milliTUBE 1 mL Covaris 520135 QuBit tubes Thermo Fisher Scientific Q32856 QuBit dsDNA HS Assay Kit Thermo Fisher Scientific Q32854 TapeStation D1000 tape Agilent 5067-5582 TapeStation D1000 reagents Agilent 5067-5583 Equipment TapeStation Agilent G2991BA Covaris E220 Covaris SKU500239 QuBit fluorometer Thermo Fisher Scientific Q33327 Tabletop centrifuge Thermomixer Eppendorf 5382000023 PCR thermocycler Magnetic rack Tube rotator Software and algorithms Juicer (version 1.6 used) Durand et al.4 https://github.com/aidenlab/juicer Juicebox (version 1.11.08 used) Durand et al.5 https://github.com/aidenlab/Juicebox 3D-DNA (version 180419 used) Dudchenko et al.6 https://github.com/aidenlab/3d-dna bwa (version 0.7.5a used) Li & Durbin7 https://github.com/lh3/bwa sra-tools (version 2.11.0 used) https://github.com/ncbi/sra-tools Deposited data Fugacium kawagutii Hi-C SRA: SRR25948349 and SRR25948348 Fugacium kawagutii draft assembly (V3) http://sampgr.org.cn/index.php/download ..
Article Title: LDB1 establishes multi-enhancer networks to regulate gene expression.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Mouse monoclonal anti-LDB1 CLIM-2 (C-9) Santa Cruz Biotechnology Cat#sc-365074; RRID: AB_10848267 Rabbit polyclonal anti-LDB1 Lot# VI3089586A Thermo Fisher Scientific Cat#PA5-56948; RRID: AB_2643320 Mouse monoclonal anti-GAPDH Lot# A1822 (6C5) Santa Cruz Biotechnology Cat#sc-32233; RRID: AB_627679 Rabbit monoclonal anti-RPB1 (Pol2) (D8L4Y) Cell Signaling Technology Cat#14958; RRID: AB_2687876 Rabbit polyclonal anti-YY1 Active Motif Cat#61779; RRID: AB_2793763 Rabbit polyclonal anti-CTCF Millipore Cat#07-729; RRID: AB_441965 Rabbit polyclonal anti-RAD21 Abcam Cat#ab992; RRID: AB_2176601 Mouse monoclonal anti-pMPM2 Millipore Cat# 05-368; RRID: AB_309698 F(ab’)2-Goat anti-Mouse IgG (H+L) Secondary Antibody, APC, eBioscience Thermo Fisher Scientific Cat#17-4010-82; RRID: AB_2573203 Chemicals, peptides, and recombinant proteins AMPure XP Beckman Coulter Cat#A63880 Indole-3-acetic acid sodium salt (auxin) Sigma Aldrich Cat#I5148 estradiol Sigma Aldrich Cat#E2758 iSCRIPT Reverse Transcription Supermix Bio Rad Cat#1708840 Power SYBR Green PCR Master Mix Thermo Fisher Scientific Cat#4367660 Protein A agarose beads Thermo Fisher Scientific Cat#15918014 Protein G agarose beads Thermo Fisher Scientific Cat#15920010 DSG crosslinker ProteoChem Cat#c1104-1gm cOmplete Mini, EDTA-free Millipore Sigma Cat#11836170001 MNase Worthington Biochemical Cat#LS004798 rSAP New England Biolabs Cat#M0371S T4 PNK New England Biolabs Cat#M0201S Large (Klenow) Fragment New England Biolabs Cat#M0210S Biotin-11-dCTP Jena Bioscience Cat#NU-809-BIOX-S Biotin-14-dATP Jena Bioscience Cat#NU-835-BIO14-S Biotin-14-dATP Active Motif Cat#14138 T4 DNA Ligase New England Biolabs Cat#M0202S T4 DNA Ligase buffer New England Biolabs Cat#B0202S Dynabeads MyOne Streptavidin C1 Thermo Fisher Scientific Cat#65001 KAPA HiFi HotStart ReadyMix Roche Cat#08202940001 Herculase II Fusion DNA Polymerase Agilent Cat#600675 Mouse Cot-1 DNA Thermo Fisher Scientific Cat#18440016 Twist Universal Blockers Twist Bioscience Cat#100578 Twist Binding and Purification Beads Twist Bioscience Cat#100983 Dynabeads M-270 Streptavidn Thermo Fisher Scientic Cat#65305 NlaIII New England Biolabs Cat#R0125L NEB Buffer 2 New England Biolabs Cat#7002S NEB Buffer 3.1 New England Biolabs Cat#B7203S DpnII New England Biolabs Cat#R0543M VAHTS DNA Clean Beads Vazyme Cat#N411 (Continued on next page) e1 Molecular Cell 85, 376–393.e1–e9, January 16, 2025 .. REAGENT or RESOURCE SOURCE IDENTIFIER T4 DNA polymerase New England Biolabs CatM0203S 4-thiouridine (4SU) MedChemExpress Cat#HY-W011793 TRIzol Reagent Invitrogen Cat#15596026 MTSEA-biotin Biotium Cat# 90064 Critical commercial assays KAPA HyperCapture Reagent Kit Roche Cat#9075810001 Twist Hybridization and Wash Kit with Amplification Mix, 12 Reactions Twist Bioscience Cat#104178 RNeasy Mini Kit QIAGEN Cat#74104 QIAshredder QIAGEN Cat#79656 NEBNext Ultra II DNA Library Prep Kit for Illumina New England Biolabs Cat#E7645S NEBNext Multiplex Oligos for Illumina (96 Unique Dual Index Primer Pairs) New England Biolabs Cat#E6440S TruSeq Stranded mRNA kit Illumina Cat#20020594 Illumina Stranded Total RNA Prep Illumina Cat# 20040525 Qubit dsDNA Quantification Assay Kits Thermo Fisher Scientific Cat#Q32850 In-Fusion HD Cloning kit Takara Cat#639648 QIAquick PCR Purification Kit QIAGEN Cat#28104 QIAquick Gel Extraction Kit QIAGEN Cat#28704 AHTS Universal DNA Library Prep Kit Vazyme Cat#ND627-01 Deposited data LDB1-AID Micro-C This paper GSE254373 LDB1-AID RCMC This paper GSE266450 LDB1-AID TT-seq This paper GSE264584 LDB1-AID Tri-C This paper GSE254372 LDB1-AID RNA-seq This paper GSE264455 SMC3-AID Hi-C Zhao et al.103 GSE228402 CTCF-AID Hi-C Zhang et al.26 GSE168251 YY1-AID Micro-C Lam et al.84 GSE247254 Mitotic Hi-C Zhang et al.38 GSE129997 Mitotic ChIP-seq (CTCF/RAD21) Zhang et al.38 GSE129997 H3K27ac ChIP-seq Dogan et al.104 GSE61349 LDB1-AID ChIP-seq This paper GSE254377 SMC3-AID ChIP-seq This paper GSE254377 Original western blot data This paper, Mendeley Data https://doi.org/10.17632/mf78pvcrkk.2 Experimental models: Cell lines G1E-ER4 Mitchell J. Weiss lab Weiss et al.82 LDB1-AID This paper N/A YY1-AID Gerd Blobel Lab Lam et al.84 SMC3-AID Haoyue Zhang Lab Zhao et al.103 CTCF-AID Gerd A. Blobel lab Zhang et al.26 Oligonucleotides See Table S2 for oligonucleotides used in this study This paper Table S2 Recombinant DNA pX458-GFP Addgene 48138 md-mCherry Gerd A. Blobel lab Zhang et al.38 OsTiR-IRES-GFP Gerd A. Blobel lab Zhang et al.38 (Continued on next page) Molecular Cell 85, 376–393.e1–e9, January 16, 2025 e2 ..
Article Title: Graft-seq precisely maps RNA modifications via site-specific chemical grafting strategy.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-7-methylguanosine (m 7 G)-Cap mAb MBL life science Cat# RN016M; RRID: AB_2921296 Goat anti-Mouse IgG HRP HuaBio Cat# HA1006; RRID: AB_2819167 Chemicals, peptides, and recombinant proteins 3 M Sodium Acetate Solution, pH 5.2 Thermo Scientific Cat# R1181 3 ′ -Desthiobiotin-GTP; DTB-GTP New England Biolabs Cat# N0761 3-azido-1-propanol Sigma-Aldrich Cat# 776130 ADP-ribosylcyclase; ADPRC Sigma-Aldrich Cat# A9106 Alexa Fluor 488 Azide Invitrogen Cat# A10266 Ammonium iron(II) sulfate hexahydrate Sigma-Aldrich Cat# 09719 ATP New England Biolabs Cat# P0756S Biotin-Azide QIYUEBIO Cat# QY-24297 Blotting membranes, Amersham TM Hybond TM -N+ GE Healthcare Cat# RPN303B Bst 2.0 DNA polymerase New England Biolabs Cat# M0537S CleanCap Reagent M6 Trilink Cat# N-7453 Copper(II) sulfate pentahydrate Sigma-Aldrich Cat# C3036 D-biotin MedChemExpress Cat# HY-B0511 Dibenzocyclooctyne-maleimide Sigma-Aldrich Cat# 760668 DL-Dithiothreitol; DTT Sigma-Aldrich Cat# V900830 DMEM/high-glucose medium HyClone Cat# SH30243.01 DMF Sigma-Aldrich Cat# D4551 DMSO Sigma-Aldrich Cat# 41639 DNase I New England Biolabs Cat# M0303 dTTP (100 mM) Thermo Scientific Cat# R0171 EDTA (0.5 M),pH 8.0 Invitrogen Cat# AM9260G Fetal Bovine Serum Gibco Cat# 10270 Fetal Bovine Serum, Sterile(irradiated) Ausbian Cat# VS500T GlutaMAX Gibco Cat# 35050061 Glycogen Invitrogen Cat# AM9510 HEPES Sigma-Aldrich Cat# V900477 HRP-streptavidin Invitrogen Cat# 434323 L-Ascorbic acid Sigma-Aldrich Cat# 95209 m 6 ATP Trilink Cat# N-1013 Maxima H Minus Reverse Transcriptase Thermo Scientific Cat# EP0751 MEM Non-Essential Amino Acids Solution (100X) Gibco Cat# 11140 mRNA decapping enzyme New England Biolabs Cat# M0608S NAD Sigma-Aldrich Cat# N6522 Non-fat Powdered milk BBI Life Sciences Cat# A600669 Nuclease P1 Wako Cat# 145-08221 Penicillin/streptomycin Gibco Cat# 15140 Penicillin-Streptomycin HyClone Cat# SV30010 Phanta Max Super-Fidelity DNA Polymerase Vazyme Cat# P505 Potassium chloride Sigma-Aldrich Cat# P9541 PrimerScript II Reverse Transcriptase Takara Cat# 6210A PrimerScript Reverse Transcriptase Takara Cat# 6110A (Continued on next page) e1 Cell Reports Methods 5, 101103, July 21, 2025 OPEN ACCESS .. REAGENT or RESOURCE SOURCE IDENTIFIER Quick CIP New England Biolabs Cat# M0525 rCutSmart buffer New England Biolabs Cat# B6004V Recombinant Mouse LIF Protein Milipore Cat# ESG1107 Reverse Transcriptase, Recombinant HIV Worthington Biochemical Corporation Cat# LS05003 RevertAid Reverse Transcriptase Thermo Scientific Cat# EP0442 RNase inhibitor Vazyme Cat# R301 RppH New England Biolabs Cat# M0356 rSAP New England Biolabs Cat# M0371S SMARTScribe Reverse Transcriptase Clontech Cat# 639536 Sodium L-ascorbate Energy Chemical Cat# E082526 Sodium pyruvate Gibco Cat# 11360 SplintR ligase New England Biolabs Cat# M0375S SuperScript II Reverse Transcriptase Invitrogen Cat# 18064071 T4 Polynucleotide Kinase; T4 PNK New England Biolabs Cat# M0201 TGIRT III Reverse Transcriptase InGex Cat# CM0101 ThermoPol Reaction Buffer New England Biolabs Cat# B90004 Tris(3-hydroxypropyltriazolylmethyl)amine Sigma-Aldrich Cat# 762342 Trizol Invitrogen Cat# 10296010 Tween 20 Sigma-Aldrich Cat# V900548 Vaccinia Capping System New England Biolabs Cat# M2080S yDcpS New England Biolabs Cat# M0463S α-L-Ascorbic acid; α-KG Sigma-Aldrich Cat# 75890 β-mercaptoethanol Gibco Cat# 21985023 Critical commercial assays GenElute mRNA Purification Miniprep Kit Sigma-Aldrich Cat# MRN10-1KT NEBNext rRNA Depletion Kit New England Biolabs Cat# E7400 HiScribe T7 High Yield RNA Synthesis Kit New England Biolabs Cat# E2040 RNA Clean & Concentrator-25 kit Zymo Research Cat# R1017 RNA Clean & Concentrator-5 kit Zymo Research Cat# R1013 RNAClean XP beads Beckman Coulter Cat# A63987 QIAquick Gel Extraction Kit QIAGEN Cat# 28704 ABclonal Zero TOPO-TA/Blunt Cloning Kit ABclonal Cat# RK30130 AMPure XP beads Beckman Coulter Cat# A63881 NEBNext Magnesium RNA Fragmentation Module New England Biolabs Cat# E6150 Dynabeads Protein A Invitrogen Cat# 10002D Dynabeads MyOne Streptavidin C1 Invitrogen Cat# 65001 NEBNext Multiplex Small RNA Library Prep Kit for Illumina New England Biolabs Cat# E7560S ChamQ Universal SYBR qPCR Master Mix Vazyme Cat# Q711-03 SuperSignal West Pico PLUS Chemiluminescent Substrate Thermo Scientific Cat# 34577 Deposited data Raw data This paper GSA-Human: HRA009209; GSA: CRA020263 Experimental models: Cell lines HEK293T ATCC Cat# ATCC-CRL-3216 HeLa ATCC Cat# ATCC-CCL-2 mouse ESC E14 Lab of Li Shen (Zhejiang University) N/A (Continued on next page) Cell Reports Methods 5, 101103, July 21, 2025 e2 OPEN ACCESS ..
Article Title: Graft-seq precisely maps RNA modifications via site-specific chemical grafting strategy
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-7-methylguanosine (m7G)-Cap mAb MBL life science Cat# RN016M; RRID: AB_2921296 Goat anti-Mouse IgG HRP HuaBio Cat# HA1006; RRID: AB_2819167 Chemicals, peptides, and recombinant proteins 3 M Sodium Acetate Solution, pH 5.2 Thermo Scientific Cat# R1181 3′-Desthiobiotin-GTP; DTB-GTP New England Biolabs Cat# N0761 3-azido-1-propanol Sigma-Aldrich Cat# 776130 ADP-ribosylcyclase; ADPRC Sigma-Aldrich Cat# A9106 Alexa Fluor 488 Azide Invitrogen Cat# A10266 Ammonium iron(II) sulfate hexahydrate Sigma-Aldrich Cat# 09719 ATP New England Biolabs Cat# P0756S Biotin-Azide QIYUEBIO Cat# QY-24297 Blotting membranes, AmershamTM HybondTM-N+ GE Healthcare Cat# RPN303B Bst 2.0 DNA polymerase New England Biolabs Cat# M0537S CleanCap Reagent M6 Trilink Cat# N-7453 Copper(II) sulfate pentahydrate Sigma-Aldrich Cat# C3036 D-biotin MedChemExpress Cat# HY-B0511 Dibenzocyclooctyne-maleimide Sigma-Aldrich Cat# 760668 DL-Dithiothreitol; DTT Sigma-Aldrich Cat# V900830 DMEM/high-glucose medium HyClone Cat# SH30243.01 DMF Sigma-Aldrich Cat# D4551 DMSO Sigma-Aldrich Cat# 41639 DNase I New England Biolabs Cat# M0303 dTTP (100 mM) Thermo Scientific Cat# R0171 EDTA (0.5 M),pH 8.0 Invitrogen Cat# AM9260G Fetal Bovine Serum Gibco Cat# 10270 Fetal Bovine Serum, Sterile(irradiated) Ausbian Cat# VS500T GlutaMAX Gibco Cat# 35050061 Glycogen Invitrogen Cat# AM9510 HEPES Sigma-Aldrich Cat# V900477 HRP-streptavidin Invitrogen Cat# 434323 L-Ascorbic acid Sigma-Aldrich Cat# 95209 m6ATP Trilink Cat# N-1013 Maxima H Minus Reverse Transcriptase Thermo Scientific Cat# EP0751 MEM Non-Essential Amino Acids Solution (100X) Gibco Cat# 11140 mRNA decapping enzyme New England Biolabs Cat# M0608S NAD Sigma-Aldrich Cat# N6522 Non-fat Powdered milk BBI Life Sciences Cat# A600669 Nuclease P1 Wako Cat# 145-08221 Penicillin/streptomycin Gibco Cat# 15140 Penicillin-Streptomycin HyClone Cat# SV30010 Phanta Max Super-Fidelity DNA Polymerase Vazyme Cat# P505 Potassium chloride Sigma-Aldrich Cat# P9541 PrimerScript II Reverse Transcriptase Takara Cat# 6210A PrimerScript Reverse Transcriptase Takara Cat# 6110A (Continued on next page) e1 Cell Reports Methods 5, 101103, July 21, 2025 Article ll OPEN ACCESS .. REAGENT or RESOURCE SOURCE IDENTIFIER Quick CIP New England Biolabs Cat# M0525 rCutSmart buffer New England Biolabs Cat# B6004V Recombinant Mouse LIF Protein Milipore Cat# ESG1107 Reverse Transcriptase, Recombinant HIV Worthington Biochemical Corporation Cat# LS05003 RevertAid Reverse Transcriptase Thermo Scientific Cat# EP0442 RNase inhibitor Vazyme Cat# R301 RppH New England Biolabs Cat# M0356 rSAP New England Biolabs Cat# M0371S SMARTScribe Reverse Transcriptase Clontech Cat# 639536 Sodium L-ascorbate Energy Chemical Cat# E082526 Sodium pyruvate Gibco Cat# 11360 SplintR ligase New England Biolabs Cat# M0375S SuperScript II Reverse Transcriptase Invitrogen Cat# 18064071 T4 Polynucleotide Kinase; T4 PNK New England Biolabs Cat# M0201 TGIRT III Reverse Transcriptase InGex Cat# CM0101 ThermoPol Reaction Buffer New England Biolabs Cat# B90004 Tris(3-hydroxypropyltriazolylmethyl)amine Sigma-Aldrich Cat# 762342 Trizol Invitrogen Cat# 10296010 Tween 20 Sigma-Aldrich Cat# V900548 Vaccinia Capping System New England Biolabs Cat# M2080S yDcpS New England Biolabs Cat# M0463S α-L-Ascorbic acid; α-KG Sigma-Aldrich Cat# 75890 β-mercaptoethanol Gibco Cat# 21985023 Critical commercial assays GenElute mRNA Purification Miniprep Kit Sigma-Aldrich Cat# MRN10-1KT NEBNext rRNA Depletion Kit New England Biolabs Cat# E7400 HiScribe T7 High Yield RNA Synthesis Kit New England Biolabs Cat# E2040 RNA Clean & Concentrator-25 kit Zymo Research Cat# R1017 RNA Clean & Concentrator-5 kit Zymo Research Cat# R1013 RNAClean XP beads Beckman Coulter Cat# A63987 QIAquick Gel Extraction Kit QIAGEN Cat# 28704 ABclonal Zero TOPO-TA/Blunt Cloning Kit ABclonal Cat# RK30130 AMPure XP beads Beckman Coulter Cat# A63881 NEBNext Magnesium RNA Fragmentation Module New England Biolabs Cat# E6150 Dynabeads Protein A Invitrogen Cat# 10002D Dynabeads MyOne Streptavidin C1 Invitrogen Cat# 65001 NEBNext Multiplex Small RNA Library Prep Kit for Illumina New England Biolabs Cat# E7560S ChamQ Universal SYBR qPCR Master Mix Vazyme Cat# Q711-03 SuperSignal West Pico PLUS Chemiluminescent Substrate Thermo Scientific Cat# 34577 Deposited data Raw data This paper GSA-Human: HRA009209; GSA: CRA020263 Experimental models: Cell lines HEK293T ATCC Cat# ATCC-CRL-3216 HeLa ATCC Cat# ATCC-CCL-2 mouse ESC E14 Lab of Li Shen (Zhejiang University) N/A (Continued on next page) Cell Reports Methods 5, 101103, July 21, 2025 e2 Article ll OPEN ACCESS ..
Single Cell:Article Title: Interface-guided phenotyping of coding variants in the transcription factor RUNX1.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies RUNX1 Antibody (A-2), mouse monoclonal Santa Cruz Biotechnologies Cat#sc-365644; RRID:AB_10843207 Anti-b-Actin Antibody (AC-15), mouse monoclonal Millipore Sigma Cat#A1978; RRID:AB_476692 Anti-Mouse IgG, HRP-linked Antibody Cell Signaling Technology Cat#7076P2; RRID:AB_330924 IRDye 680RD Goat anti-Mouse IgG Secondary Antibody Li-Cor Bio Cat#926–68070; RRID:AB_10956588 Bacterial and virus strains Stbl3 Thermo Fisher Cat#C737303 Chemicals, peptides, and recombinant proteins NheI-HF New England Biolabs Cat#R3131S SalI-HF New England Biolabs Cat#R3138S AflII New England Biolabs Cat#R0520S Gibson Assembly Master Mix New England Biolabs Cat#E2611S KAPA HiFi HotStart ReadyMix Roche Cat#KK2601 OneTaq 2X Master Mix New England Biolabs Cat#M0482S AMPure XP Beads Beckman Coulter Cat#A63880 DMEM ThermoFisher Scientific Cat#10566016 .05% Trypsin-EDTA Gibco Cat#25300062 OptiMEM ThermoFisher Scientific Cat#31985062 RPMI Medium 1640 Gibco Cat#11875-093 FBS Gibco Cat#A52568 Anti-anti Gibco Cat#15240-062 Lipofectamine 2000 ThermoFisher Scientific Cat#11668030 Doxycycline hyclate Sigma Cat#D5207 Hygromycin Invitrogen Cat#10687010 Puromycin Gibco Cat#A11138-03 Polybrene Millipore-Sigma Cat#TR-1003-G PBS, pH 7.4 Gibco Cat#10010023 Tn5 Illumina Cat#20034198 RIPA Buffer Cell Signaling Technologies Cat#9806 Pierce Protease Inhibitor Tablets ThermoFisher Scientific Cat#A32963 4X Laemmli Sample Buffer Bio-Rad Cat#1610747 4-20% Mini-PROTEAN TGX gel Bio-Rad Cat#4561094 10X Tris/Glycine/SDS Buffer Bio-Rad Cat#1610732 Nonfat Dry Milk Apex Bioresearch Cat#20-241 TBST Cell Signaling Technology Cat#9997 BSA, Fraction V, Fatty Acid-Free Millipore Sigma Cat#126575 SuperSignal West Pico Plus Chemiluminescent Substrate ThermoFisher Scientific Cat#34577 Carbenicillin Teknova Cat#C2199 iTaq Universal SYBR Green Master Mix Bio-Rad Cat#1725120 Critical commercial assays Pierce BCA Protein Assay kit ThermoFisher Scientific Cat#23227 RNeasy Mini Kit Qiagen Cat#74104 DNeasy Blood and Tissue Kit Qiagen Cat#69504 (Continued on next page) 20 Cell Reports 43, 114436, July 23, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER Protoscript II First Strand cDNA Synthesis Kit New England BioLabs CatE6560S QIAquick PCR Purification Kit Qiagen Cat#28104 Nucleofector Solution Set SF Lonza Cat#PBC2-00675 Chromium Single Cell 30 v3 10X Genomics Cat# PN- 1000128 NEBNext Ultra RNA Library Prep Kit New England Biolabs Cat#E7530 Deposited data Raw data: scRNA-seq This paper SRA: PRJNA1033389 Raw data: bulk RNA-seq This paper SRA: PRJNA1121326 Raw data: ATAC-seq This paper SRA: PRJNA1121327 RUNX1-CBFB-DNA structures Protein DataBank PDB: 1ljm, 1e50, 1h9d Human reference genome NCBI build 38, GRCh38–3.0.0 Genome Reference Consortium http://www.ncbi.nlm.nih.gov/projects/ genome/assembly/grc/human/ ATAC-seq data for K562 ENCODE ENCSR868FGK ChromHMM states for K562 Roadmap Epigenomics Project https://egg2.wustl.edu/roadmap/web_portal/ Hi-C chromatin loop data for K562 NCBI GEO: GSM1551620 Experimental models: Cell lines K-562 ATCC Cat#CCL-243; RRID:CVCL_0004 HEK293T ATCC Cat#CRL-3216; RRID:CVCL_0063 Oligonucleotides RUNX1 library variants Twist Bioscience https://www.twistbioscience.com Primers for qPCR, Sanger Sequencing, & oligopool amplification, see Table S10 This Paper N/A NEBNext Multiplex Oligos for Illumina New England Biolabs Cat#E7335S Recombinant DNA EF1a_mCherry_P2A_Hygro_Barcode (Parekh et al.)12 Addgene #120426 PB-TRE-dCas9-VPR (Chavez et al.)108 Addgene #63800 pHR-SFFV-KRAB-dCas9-P2A-mCherry (Gilbert et al.)109 Addgene #60954 pMD2.G N/A Addgene #12259 pCMV delta R8.2 N/A Addgene #12263 Software and algorithms Code related to analyses of RUNX1 mutations This paper https://github.com/cartercompbio/ RUNX1_SEUSS; https://doi.org/ 10.5281/zenodo.11580866 CellRanger 3.1.0 10X Genomics https://support.10xgenomics.com genotyping-matrices (Parekh et al.)12 https://github.com/yanwu2014/ genotyping-matrices MAGeCK (W. Li et al.)110 https://sourceforge.net/p/mageck/ wiki/Home/ PRISM (Baspinar et al.)60 https://cosbi.ku.edu.tr/prism/ VEST (Carter et al.)62 http://www.cravat.us/CRAVAT/ FoldX (Schymkowitz et al.)63 http://foldx.crg.es/ Seurat 4.1.0 (Macosko et al.)111 https://satijalab.org/seurat/ CoGAPS (Fertig et al.)72 http://www.bioconductor.org/packages/ release/bioc/html/CoGAPS.html EnrichR (Kuleshov et al.)112 https://github.com/wjawaid/enrichR STAR 2.7.1a (Dobin et al.)113 https://github.com/alexdobin/STAR RSEM 1.3.1 N/A http://deweylab.biostat.wisc.edu/rsem/ limma (Ritchie et al.)114 http://bioinf.wehi.edu.au/limma/ (Continued on next page) Cell Reports 43, 114436, July 23, 2024 21 ..
Article Title: The primitive endoderm supports lineage plasticity to enable regulative development.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies See Table S6 for antibodies used in this study N/A N/A Chemicals, peptides, and recombinant proteins Leukemia inhibitory factor (LIF) Made in house N/A CHIR99021 (GSKb inhibitor) Axon Medchem Cat#1386 PD0325901 (PD03, MEK inhibitor) Sigma Aldrich Cat#PZ0162 Activin A Peprotech Cat#120-14E Doxycycline (Dox) Sigma Aldrich Cat#D9891 4-hydroxytamoxifen (4OHT) Sigma Aldrich Cat#H7904 BMP4 Peprotech Cat#120-05ET A83-01 Sigma-Aldrich Cat#SML0788 Y-27632 (ROCK inhibitor) Tocris Cat#1254 Retinoic acid Sigma Aldrich Cat#R2625 2-mercaptoethanol Sigma Aldrich Cat#M6250 L-glutamine Thermo Fisher Cat#25030024 B-27 Supplement (50X) Gibco Cat#17504001 B-27 Supplement (50X), minus insulin Gibco Cat#A1895601 N-2 Supplement (100X) Gibco Cat#17502048 Neurobasal Medium Gibco Cat#21103049 DMEM/F12 Medium Gibco Cat#12634010 RPMI 1640 Medium, GlutaMAX Supplement Gibco Cat#61870036 MEM non-essential amino acids (100X) Gibco Cat#11140050 Sodium pyruvate (100mM) Gibco Cat#11360070 Accutase Sigma Aldrich Cat#A6964 16% Formaldehyde Thermo Fisher Cat#PI28906 Donkey Serum Sigma Aldrich Cat#D9663 EmbryoMax KSOM Medium (1X) Sigma Aldrich Cat#MR-106 Polyvinylpyrrolidine (PVP) Sigma Aldrich Cat#P0930 Triton X-100 Sigma Aldrich Cat#T8787 Anti-mouse rabbit serum Sigma Aldrich Cat#M5774 Guinea pig complement Sigma-Aldrich Cat#234395 Acidic Tyrode’s solution Sigma Aldrich Cat#T1788 Bovine Serum Albumin Gibco Cat#15260037 Tween20 Sigma-Aldrich Cat#P1379 Anti-Adherence Rinsing Solution STEMCELL Technologies Cat#07010 M2 medium Sigma Aldrich Cat#M7167 PMSG Sigma Aldrich Cat#G4527 hCG (Chorulon) Intervet N/A Critical commercial assays RNeasy Mini Kit Qiagen Cat#74106 RNeasy Micro Kit Qiagen Cat#74004 RNase-Free DNase Set Qiagen Cat#79256 SuperScript III Reverse Transcriptase Thermo Fisher Cat#18080051 Universal ProbeLibrary Roche N/A (Continued on next page) Cell 187, 1–20.e1–e6, July 25, 2024 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER NEBNext Ultra II DNA Library Prep Kit for Illumina New England Biolabs Cat# E7645L Chromium Next GEM Single Cell 3’ Kit v3.1 10x Genomics Cat#1000269 Chromium Next GEM Chip G Single Cell Kit 10x Genomics Cat#1000127 NEBNext Ultra II Directional RNA Library Prep kit New England Biolabs Cat#E7765 NEBNext Multiplex Oligos for Illumina New England Biolabs Cat#E6440 Qubit dsDNA Quantification Assay Kits Invitrogen Cat#Q32851 Deposited data Raw and analysed data This study GEO:GSE232926 External re-analysed mouse embryo scRNA-seq dataset Nowotschin et al.53 GEO:GSE123046 External re-analysed mouse reprogramming scRNA-seq dataset Zhao et al.77 GEO:GSE114952 Experimental models: Cell lines SOX2-GFP/ GATA6-mCherry (SGGC) ESCs Redó-Riveiro et al.48 N/A OCT4-mCherry ESCs Hashmi et al.58 N/A OCT4-mCherry-H2B-Venus This study N/A Esrrb KO with tetON-Esrrb transgene (EKOiE) ESCs Festuccia et al.82 N/A E14JU ESCs (E14Tg2a 129/Ola subclone) Hamilton and Brickman117 N/A DR4 mouse embryonic fibroblasts (MEFs) Tucker et al.118 N/A Experimental models: Organisms/strains C57BL/6N Taconic RRID:MGI:2159965 Rosa26mT/mG Muzumdar et al.45 RRID:IMSR_JAX:007576 Pdgfra-CreERT2 Chung et al.44 RRID:IMSR_JAX:032770 Oligonucleotides See Table S6 for primer sequences used in this study N/A N/A Software and algorithms BD FACSDiva BD Biosciences RRID:SCR_001456 FCS Express v7 De Novo Software RRID:SCR_016431 Prism v10.1.1 GraphPad RRID:SCR_002798 R v4.3.1 R Core Team RRID:SCR_001905 Cell Ranger v6.1.12 10x Genomics RRID:SCR_017344 scVelo v0.2.5 and v0.17.1 Bergen et al.54 N/A scvi-tools Gayoso et al.74 N/A scanpy v1.8.2 and 1.9.1 Wolf et al.119 RRID:SCR_018139 Seurat v4.3.0 Hao et al.120 RRID:SCR_007322 BEDtools Quinlan and Hall121 RRID:SCR_006646 SEACR Meers et al.122 N/A DiffBind Ross-Innes et al.123 RRID:SCR_012918 deeptools Ramı́rez et al.124 RRID:SCR_016366 SAMtools Danecek et al.125 RRID:SCR_002105 IGV v2.16.2 Robinson et al.126 RRID:SCR_011793 pyGenomeTracks Lopez-Delisle et al.127 N/A HOMER Heinz et al.128 RRID:SCR_010881 DESeq2 v1.40.2 Love et al.129 RRID:SCR_015687 FIJI (ImageJ) v2.14.0 Schindelin et al.130 RRID: SCR_002285 CellProfiler v4.2.5 Stirling et al.131 RRID:SCR_007358 Imaris v9.9.1 Oxford Instruments RRID:SCR_007370 (Continued on next page) ll e2 Cell 187, 1–20.e1–e6, July 25, 2024 Please cite this article in press as: Linneberg-Agerholm et al., The primitive endoderm supports lineage plasticity to enable regulative development, Cell (2024), https://doi.org/10.1016/j.cell.2024.05.051 Article ..
RNA Sequencing:Article Title: Interface-guided phenotyping of coding variants in the transcription factor RUNX1.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies RUNX1 Antibody (A-2), mouse monoclonal Santa Cruz Biotechnologies Cat#sc-365644; RRID:AB_10843207 Anti-b-Actin Antibody (AC-15), mouse monoclonal Millipore Sigma Cat#A1978; RRID:AB_476692 Anti-Mouse IgG, HRP-linked Antibody Cell Signaling Technology Cat#7076P2; RRID:AB_330924 IRDye 680RD Goat anti-Mouse IgG Secondary Antibody Li-Cor Bio Cat#926–68070; RRID:AB_10956588 Bacterial and virus strains Stbl3 Thermo Fisher Cat#C737303 Chemicals, peptides, and recombinant proteins NheI-HF New England Biolabs Cat#R3131S SalI-HF New England Biolabs Cat#R3138S AflII New England Biolabs Cat#R0520S Gibson Assembly Master Mix New England Biolabs Cat#E2611S KAPA HiFi HotStart ReadyMix Roche Cat#KK2601 OneTaq 2X Master Mix New England Biolabs Cat#M0482S AMPure XP Beads Beckman Coulter Cat#A63880 DMEM ThermoFisher Scientific Cat#10566016 .05% Trypsin-EDTA Gibco Cat#25300062 OptiMEM ThermoFisher Scientific Cat#31985062 RPMI Medium 1640 Gibco Cat#11875-093 FBS Gibco Cat#A52568 Anti-anti Gibco Cat#15240-062 Lipofectamine 2000 ThermoFisher Scientific Cat#11668030 Doxycycline hyclate Sigma Cat#D5207 Hygromycin Invitrogen Cat#10687010 Puromycin Gibco Cat#A11138-03 Polybrene Millipore-Sigma Cat#TR-1003-G PBS, pH 7.4 Gibco Cat#10010023 Tn5 Illumina Cat#20034198 RIPA Buffer Cell Signaling Technologies Cat#9806 Pierce Protease Inhibitor Tablets ThermoFisher Scientific Cat#A32963 4X Laemmli Sample Buffer Bio-Rad Cat#1610747 4-20% Mini-PROTEAN TGX gel Bio-Rad Cat#4561094 10X Tris/Glycine/SDS Buffer Bio-Rad Cat#1610732 Nonfat Dry Milk Apex Bioresearch Cat#20-241 TBST Cell Signaling Technology Cat#9997 BSA, Fraction V, Fatty Acid-Free Millipore Sigma Cat#126575 SuperSignal West Pico Plus Chemiluminescent Substrate ThermoFisher Scientific Cat#34577 Carbenicillin Teknova Cat#C2199 iTaq Universal SYBR Green Master Mix Bio-Rad Cat#1725120 Critical commercial assays Pierce BCA Protein Assay kit ThermoFisher Scientific Cat#23227 RNeasy Mini Kit Qiagen Cat#74104 DNeasy Blood and Tissue Kit Qiagen Cat#69504 (Continued on next page) 20 Cell Reports 43, 114436, July 23, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER Protoscript II First Strand cDNA Synthesis Kit New England BioLabs CatE6560S QIAquick PCR Purification Kit Qiagen Cat#28104 Nucleofector Solution Set SF Lonza Cat#PBC2-00675 Chromium Single Cell 30 v3 10X Genomics Cat# PN- 1000128 NEBNext Ultra RNA Library Prep Kit New England Biolabs Cat#E7530 Deposited data Raw data: scRNA-seq This paper SRA: PRJNA1033389 Raw data: bulk RNA-seq This paper SRA: PRJNA1121326 Raw data: ATAC-seq This paper SRA: PRJNA1121327 RUNX1-CBFB-DNA structures Protein DataBank PDB: 1ljm, 1e50, 1h9d Human reference genome NCBI build 38, GRCh38–3.0.0 Genome Reference Consortium http://www.ncbi.nlm.nih.gov/projects/ genome/assembly/grc/human/ ATAC-seq data for K562 ENCODE ENCSR868FGK ChromHMM states for K562 Roadmap Epigenomics Project https://egg2.wustl.edu/roadmap/web_portal/ Hi-C chromatin loop data for K562 NCBI GEO: GSM1551620 Experimental models: Cell lines K-562 ATCC Cat#CCL-243; RRID:CVCL_0004 HEK293T ATCC Cat#CRL-3216; RRID:CVCL_0063 Oligonucleotides RUNX1 library variants Twist Bioscience https://www.twistbioscience.com Primers for qPCR, Sanger Sequencing, & oligopool amplification, see Table S10 This Paper N/A NEBNext Multiplex Oligos for Illumina New England Biolabs Cat#E7335S Recombinant DNA EF1a_mCherry_P2A_Hygro_Barcode (Parekh et al.)12 Addgene #120426 PB-TRE-dCas9-VPR (Chavez et al.)108 Addgene #63800 pHR-SFFV-KRAB-dCas9-P2A-mCherry (Gilbert et al.)109 Addgene #60954 pMD2.G N/A Addgene #12259 pCMV delta R8.2 N/A Addgene #12263 Software and algorithms Code related to analyses of RUNX1 mutations This paper https://github.com/cartercompbio/ RUNX1_SEUSS; https://doi.org/ 10.5281/zenodo.11580866 CellRanger 3.1.0 10X Genomics https://support.10xgenomics.com genotyping-matrices (Parekh et al.)12 https://github.com/yanwu2014/ genotyping-matrices MAGeCK (W. Li et al.)110 https://sourceforge.net/p/mageck/ wiki/Home/ PRISM (Baspinar et al.)60 https://cosbi.ku.edu.tr/prism/ VEST (Carter et al.)62 http://www.cravat.us/CRAVAT/ FoldX (Schymkowitz et al.)63 http://foldx.crg.es/ Seurat 4.1.0 (Macosko et al.)111 https://satijalab.org/seurat/ CoGAPS (Fertig et al.)72 http://www.bioconductor.org/packages/ release/bioc/html/CoGAPS.html EnrichR (Kuleshov et al.)112 https://github.com/wjawaid/enrichR STAR 2.7.1a (Dobin et al.)113 https://github.com/alexdobin/STAR RSEM 1.3.1 N/A http://deweylab.biostat.wisc.edu/rsem/ limma (Ritchie et al.)114 http://bioinf.wehi.edu.au/limma/ (Continued on next page) Cell Reports 43, 114436, July 23, 2024 21 ..
Article Title: LDB1 establishes multi-enhancer networks to regulate gene expression.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Mouse monoclonal anti-LDB1 CLIM-2 (C-9) Santa Cruz Biotechnology Cat#sc-365074; RRID: AB_10848267 Rabbit polyclonal anti-LDB1 Lot# VI3089586A Thermo Fisher Scientific Cat#PA5-56948; RRID: AB_2643320 Mouse monoclonal anti-GAPDH Lot# A1822 (6C5) Santa Cruz Biotechnology Cat#sc-32233; RRID: AB_627679 Rabbit monoclonal anti-RPB1 (Pol2) (D8L4Y) Cell Signaling Technology Cat#14958; RRID: AB_2687876 Rabbit polyclonal anti-YY1 Active Motif Cat#61779; RRID: AB_2793763 Rabbit polyclonal anti-CTCF Millipore Cat#07-729; RRID: AB_441965 Rabbit polyclonal anti-RAD21 Abcam Cat#ab992; RRID: AB_2176601 Mouse monoclonal anti-pMPM2 Millipore Cat# 05-368; RRID: AB_309698 F(ab’)2-Goat anti-Mouse IgG (H+L) Secondary Antibody, APC, eBioscience Thermo Fisher Scientific Cat#17-4010-82; RRID: AB_2573203 Chemicals, peptides, and recombinant proteins AMPure XP Beckman Coulter Cat#A63880 Indole-3-acetic acid sodium salt (auxin) Sigma Aldrich Cat#I5148 estradiol Sigma Aldrich Cat#E2758 iSCRIPT Reverse Transcription Supermix Bio Rad Cat#1708840 Power SYBR Green PCR Master Mix Thermo Fisher Scientific Cat#4367660 Protein A agarose beads Thermo Fisher Scientific Cat#15918014 Protein G agarose beads Thermo Fisher Scientific Cat#15920010 DSG crosslinker ProteoChem Cat#c1104-1gm cOmplete Mini, EDTA-free Millipore Sigma Cat#11836170001 MNase Worthington Biochemical Cat#LS004798 rSAP New England Biolabs Cat#M0371S T4 PNK New England Biolabs Cat#M0201S Large (Klenow) Fragment New England Biolabs Cat#M0210S Biotin-11-dCTP Jena Bioscience Cat#NU-809-BIOX-S Biotin-14-dATP Jena Bioscience Cat#NU-835-BIO14-S Biotin-14-dATP Active Motif Cat#14138 T4 DNA Ligase New England Biolabs Cat#M0202S T4 DNA Ligase buffer New England Biolabs Cat#B0202S Dynabeads MyOne Streptavidin C1 Thermo Fisher Scientific Cat#65001 KAPA HiFi HotStart ReadyMix Roche Cat#08202940001 Herculase II Fusion DNA Polymerase Agilent Cat#600675 Mouse Cot-1 DNA Thermo Fisher Scientific Cat#18440016 Twist Universal Blockers Twist Bioscience Cat#100578 Twist Binding and Purification Beads Twist Bioscience Cat#100983 Dynabeads M-270 Streptavidn Thermo Fisher Scientic Cat#65305 NlaIII New England Biolabs Cat#R0125L NEB Buffer 2 New England Biolabs Cat#7002S NEB Buffer 3.1 New England Biolabs Cat#B7203S DpnII New England Biolabs Cat#R0543M VAHTS DNA Clean Beads Vazyme Cat#N411 (Continued on next page) e1 Molecular Cell 85, 376–393.e1–e9, January 16, 2025 .. REAGENT or RESOURCE SOURCE IDENTIFIER T4 DNA polymerase New England Biolabs CatM0203S 4-thiouridine (4SU) MedChemExpress Cat#HY-W011793 TRIzol Reagent Invitrogen Cat#15596026 MTSEA-biotin Biotium Cat# 90064 Critical commercial assays KAPA HyperCapture Reagent Kit Roche Cat#9075810001 Twist Hybridization and Wash Kit with Amplification Mix, 12 Reactions Twist Bioscience Cat#104178 RNeasy Mini Kit QIAGEN Cat#74104 QIAshredder QIAGEN Cat#79656 NEBNext Ultra II DNA Library Prep Kit for Illumina New England Biolabs Cat#E7645S NEBNext Multiplex Oligos for Illumina (96 Unique Dual Index Primer Pairs) New England Biolabs Cat#E6440S TruSeq Stranded mRNA kit Illumina Cat#20020594 Illumina Stranded Total RNA Prep Illumina Cat# 20040525 Qubit dsDNA Quantification Assay Kits Thermo Fisher Scientific Cat#Q32850 In-Fusion HD Cloning kit Takara Cat#639648 QIAquick PCR Purification Kit QIAGEN Cat#28104 QIAquick Gel Extraction Kit QIAGEN Cat#28704 AHTS Universal DNA Library Prep Kit Vazyme Cat#ND627-01 Deposited data LDB1-AID Micro-C This paper GSE254373 LDB1-AID RCMC This paper GSE266450 LDB1-AID TT-seq This paper GSE264584 LDB1-AID Tri-C This paper GSE254372 LDB1-AID RNA-seq This paper GSE264455 SMC3-AID Hi-C Zhao et al.103 GSE228402 CTCF-AID Hi-C Zhang et al.26 GSE168251 YY1-AID Micro-C Lam et al.84 GSE247254 Mitotic Hi-C Zhang et al.38 GSE129997 Mitotic ChIP-seq (CTCF/RAD21) Zhang et al.38 GSE129997 H3K27ac ChIP-seq Dogan et al.104 GSE61349 LDB1-AID ChIP-seq This paper GSE254377 SMC3-AID ChIP-seq This paper GSE254377 Original western blot data This paper, Mendeley Data https://doi.org/10.17632/mf78pvcrkk.2 Experimental models: Cell lines G1E-ER4 Mitchell J. Weiss lab Weiss et al.82 LDB1-AID This paper N/A YY1-AID Gerd Blobel Lab Lam et al.84 SMC3-AID Haoyue Zhang Lab Zhao et al.103 CTCF-AID Gerd A. Blobel lab Zhang et al.26 Oligonucleotides See Table S2 for oligonucleotides used in this study This paper Table S2 Recombinant DNA pX458-GFP Addgene 48138 md-mCherry Gerd A. Blobel lab Zhang et al.38 OsTiR-IRES-GFP Gerd A. Blobel lab Zhang et al.38 (Continued on next page) Molecular Cell 85, 376–393.e1–e9, January 16, 2025 e2 ..
Hi-C:Article Title: Interface-guided phenotyping of coding variants in the transcription factor RUNX1.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies RUNX1 Antibody (A-2), mouse monoclonal Santa Cruz Biotechnologies Cat#sc-365644; RRID:AB_10843207 Anti-b-Actin Antibody (AC-15), mouse monoclonal Millipore Sigma Cat#A1978; RRID:AB_476692 Anti-Mouse IgG, HRP-linked Antibody Cell Signaling Technology Cat#7076P2; RRID:AB_330924 IRDye 680RD Goat anti-Mouse IgG Secondary Antibody Li-Cor Bio Cat#926–68070; RRID:AB_10956588 Bacterial and virus strains Stbl3 Thermo Fisher Cat#C737303 Chemicals, peptides, and recombinant proteins NheI-HF New England Biolabs Cat#R3131S SalI-HF New England Biolabs Cat#R3138S AflII New England Biolabs Cat#R0520S Gibson Assembly Master Mix New England Biolabs Cat#E2611S KAPA HiFi HotStart ReadyMix Roche Cat#KK2601 OneTaq 2X Master Mix New England Biolabs Cat#M0482S AMPure XP Beads Beckman Coulter Cat#A63880 DMEM ThermoFisher Scientific Cat#10566016 .05% Trypsin-EDTA Gibco Cat#25300062 OptiMEM ThermoFisher Scientific Cat#31985062 RPMI Medium 1640 Gibco Cat#11875-093 FBS Gibco Cat#A52568 Anti-anti Gibco Cat#15240-062 Lipofectamine 2000 ThermoFisher Scientific Cat#11668030 Doxycycline hyclate Sigma Cat#D5207 Hygromycin Invitrogen Cat#10687010 Puromycin Gibco Cat#A11138-03 Polybrene Millipore-Sigma Cat#TR-1003-G PBS, pH 7.4 Gibco Cat#10010023 Tn5 Illumina Cat#20034198 RIPA Buffer Cell Signaling Technologies Cat#9806 Pierce Protease Inhibitor Tablets ThermoFisher Scientific Cat#A32963 4X Laemmli Sample Buffer Bio-Rad Cat#1610747 4-20% Mini-PROTEAN TGX gel Bio-Rad Cat#4561094 10X Tris/Glycine/SDS Buffer Bio-Rad Cat#1610732 Nonfat Dry Milk Apex Bioresearch Cat#20-241 TBST Cell Signaling Technology Cat#9997 BSA, Fraction V, Fatty Acid-Free Millipore Sigma Cat#126575 SuperSignal West Pico Plus Chemiluminescent Substrate ThermoFisher Scientific Cat#34577 Carbenicillin Teknova Cat#C2199 iTaq Universal SYBR Green Master Mix Bio-Rad Cat#1725120 Critical commercial assays Pierce BCA Protein Assay kit ThermoFisher Scientific Cat#23227 RNeasy Mini Kit Qiagen Cat#74104 DNeasy Blood and Tissue Kit Qiagen Cat#69504 (Continued on next page) 20 Cell Reports 43, 114436, July 23, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER Protoscript II First Strand cDNA Synthesis Kit New England BioLabs CatE6560S QIAquick PCR Purification Kit Qiagen Cat#28104 Nucleofector Solution Set SF Lonza Cat#PBC2-00675 Chromium Single Cell 30 v3 10X Genomics Cat# PN- 1000128 NEBNext Ultra RNA Library Prep Kit New England Biolabs Cat#E7530 Deposited data Raw data: scRNA-seq This paper SRA: PRJNA1033389 Raw data: bulk RNA-seq This paper SRA: PRJNA1121326 Raw data: ATAC-seq This paper SRA: PRJNA1121327 RUNX1-CBFB-DNA structures Protein DataBank PDB: 1ljm, 1e50, 1h9d Human reference genome NCBI build 38, GRCh38–3.0.0 Genome Reference Consortium http://www.ncbi.nlm.nih.gov/projects/ genome/assembly/grc/human/ ATAC-seq data for K562 ENCODE ENCSR868FGK ChromHMM states for K562 Roadmap Epigenomics Project https://egg2.wustl.edu/roadmap/web_portal/ Hi-C chromatin loop data for K562 NCBI GEO: GSM1551620 Experimental models: Cell lines K-562 ATCC Cat#CCL-243; RRID:CVCL_0004 HEK293T ATCC Cat#CRL-3216; RRID:CVCL_0063 Oligonucleotides RUNX1 library variants Twist Bioscience https://www.twistbioscience.com Primers for qPCR, Sanger Sequencing, & oligopool amplification, see Table S10 This Paper N/A NEBNext Multiplex Oligos for Illumina New England Biolabs Cat#E7335S Recombinant DNA EF1a_mCherry_P2A_Hygro_Barcode (Parekh et al.)12 Addgene #120426 PB-TRE-dCas9-VPR (Chavez et al.)108 Addgene #63800 pHR-SFFV-KRAB-dCas9-P2A-mCherry (Gilbert et al.)109 Addgene #60954 pMD2.G N/A Addgene #12259 pCMV delta R8.2 N/A Addgene #12263 Software and algorithms Code related to analyses of RUNX1 mutations This paper https://github.com/cartercompbio/ RUNX1_SEUSS; https://doi.org/ 10.5281/zenodo.11580866 CellRanger 3.1.0 10X Genomics https://support.10xgenomics.com genotyping-matrices (Parekh et al.)12 https://github.com/yanwu2014/ genotyping-matrices MAGeCK (W. Li et al.)110 https://sourceforge.net/p/mageck/ wiki/Home/ PRISM (Baspinar et al.)60 https://cosbi.ku.edu.tr/prism/ VEST (Carter et al.)62 http://www.cravat.us/CRAVAT/ FoldX (Schymkowitz et al.)63 http://foldx.crg.es/ Seurat 4.1.0 (Macosko et al.)111 https://satijalab.org/seurat/ CoGAPS (Fertig et al.)72 http://www.bioconductor.org/packages/ release/bioc/html/CoGAPS.html EnrichR (Kuleshov et al.)112 https://github.com/wjawaid/enrichR STAR 2.7.1a (Dobin et al.)113 https://github.com/alexdobin/STAR RSEM 1.3.1 N/A http://deweylab.biostat.wisc.edu/rsem/ limma (Ritchie et al.)114 http://bioinf.wehi.edu.au/limma/ (Continued on next page) Cell Reports 43, 114436, July 23, 2024 21 ..
Article Title: Protocol for mapping the three-dimensional organization of dinoflagellate genomes.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Chemicals and recombinant proteins Nuclease-free H2O Thermo Fisher Scientific AM9916 1 M Tris-HCl pH 7.5 Thermo Fisher Scientific 15567027 1 M Tris-HCl pH 8.0 Thermo Fisher Scientific 15568025 1 M MgCl2 Thermo Fisher Scientific AM9530G 5 M NaCl Thermo Fisher Scientific AM9759 0.5 M EDTA, pH 8.0 Thermo Fisher Scientific 15575020 20% SDS Thermo Fisher Scientific AM9820 1x PBS buffer solution pH 7.4 Thermo Fisher Scientific 10010023 1x TE buffer Thermo Fisher Scientific 12090015 IGEPAL CA-630 detergent Sigma I8896-50ML Tween 20 detergent 10% Sigma 11332465001 10% Triton X-100 Sigma 93443 37% formaldehyde Sigma 252549-100ML 0.1 M NaHCO3 Sigma S6014-1KG Glycine Sigma 1005901000 MboI restriction enzyme NEB R0147 10x CutSmart buffer NEB B7204 0.4 mM biotin-14-dATP Thermo Fisher Scientific 19524-016 100 mM dCTP/dGTP/dTTP Promega U1330 DNA polymerase I large (Klenow) fragment NEB M0210 10x NEB T4 DNA ligase buffer NEB B0202 Bovine serum albumin (BSA) 100x NEB B9000 T4 DNA ligase NEB M0202 Proteinase K Promega MC5005 Dynabeads MyOne Streptavidin T1 Thermo Fisher Scientific 65602 AMPure XP beads Beckman Coulter A63881 100% EtOH Sigma 493546-1L 200-mL PCR tubes Thermo Fisher Scientific AB1182 1.5-mL DNA LoBind microcentrifuge tubes Eppendorf 022431021 (Continued on next page) 2 STAR Protocols 5, 102941, June 21, 2024 Continued REAGENT or RESOURCE SOURCE IDENTIFIER 15/50 mL tubes Critical commercial assays NEBNext Ultra II DNA Library Prep Kit for Illumina NEB E7645L NEBNext Multiplex Oligos for Illumina NEB E7600S MinElute PCR Purification Kit QIAGEN 28004/28006 Covaris milliTUBE 1 mL Covaris 520135 QuBit tubes Thermo Fisher Scientific Q32856 QuBit dsDNA HS Assay Kit Thermo Fisher Scientific Q32854 TapeStation D1000 tape Agilent 5067-5582 TapeStation D1000 reagents Agilent 5067-5583 Equipment TapeStation Agilent G2991BA Covaris E220 Covaris SKU500239 QuBit fluorometer Thermo Fisher Scientific Q33327 Tabletop centrifuge Thermomixer Eppendorf 5382000023 PCR thermocycler Magnetic rack Tube rotator Software and algorithms Juicer (version 1.6 used) Durand et al.4 https://github.com/aidenlab/juicer Juicebox (version 1.11.08 used) Durand et al.5 https://github.com/aidenlab/Juicebox 3D-DNA (version 180419 used) Dudchenko et al.6 https://github.com/aidenlab/3d-dna bwa (version 0.7.5a used) Li & Durbin7 https://github.com/lh3/bwa sra-tools (version 2.11.0 used) https://github.com/ncbi/sra-tools Deposited data Fugacium kawagutii Hi-C SRA: SRR25948349 and SRR25948348 Fugacium kawagutii draft assembly (V3) http://sampgr.org.cn/index.php/download ..
Article Title: LDB1 establishes multi-enhancer networks to regulate gene expression.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Mouse monoclonal anti-LDB1 CLIM-2 (C-9) Santa Cruz Biotechnology Cat#sc-365074; RRID: AB_10848267 Rabbit polyclonal anti-LDB1 Lot# VI3089586A Thermo Fisher Scientific Cat#PA5-56948; RRID: AB_2643320 Mouse monoclonal anti-GAPDH Lot# A1822 (6C5) Santa Cruz Biotechnology Cat#sc-32233; RRID: AB_627679 Rabbit monoclonal anti-RPB1 (Pol2) (D8L4Y) Cell Signaling Technology Cat#14958; RRID: AB_2687876 Rabbit polyclonal anti-YY1 Active Motif Cat#61779; RRID: AB_2793763 Rabbit polyclonal anti-CTCF Millipore Cat#07-729; RRID: AB_441965 Rabbit polyclonal anti-RAD21 Abcam Cat#ab992; RRID: AB_2176601 Mouse monoclonal anti-pMPM2 Millipore Cat# 05-368; RRID: AB_309698 F(ab’)2-Goat anti-Mouse IgG (H+L) Secondary Antibody, APC, eBioscience Thermo Fisher Scientific Cat#17-4010-82; RRID: AB_2573203 Chemicals, peptides, and recombinant proteins AMPure XP Beckman Coulter Cat#A63880 Indole-3-acetic acid sodium salt (auxin) Sigma Aldrich Cat#I5148 estradiol Sigma Aldrich Cat#E2758 iSCRIPT Reverse Transcription Supermix Bio Rad Cat#1708840 Power SYBR Green PCR Master Mix Thermo Fisher Scientific Cat#4367660 Protein A agarose beads Thermo Fisher Scientific Cat#15918014 Protein G agarose beads Thermo Fisher Scientific Cat#15920010 DSG crosslinker ProteoChem Cat#c1104-1gm cOmplete Mini, EDTA-free Millipore Sigma Cat#11836170001 MNase Worthington Biochemical Cat#LS004798 rSAP New England Biolabs Cat#M0371S T4 PNK New England Biolabs Cat#M0201S Large (Klenow) Fragment New England Biolabs Cat#M0210S Biotin-11-dCTP Jena Bioscience Cat#NU-809-BIOX-S Biotin-14-dATP Jena Bioscience Cat#NU-835-BIO14-S Biotin-14-dATP Active Motif Cat#14138 T4 DNA Ligase New England Biolabs Cat#M0202S T4 DNA Ligase buffer New England Biolabs Cat#B0202S Dynabeads MyOne Streptavidin C1 Thermo Fisher Scientific Cat#65001 KAPA HiFi HotStart ReadyMix Roche Cat#08202940001 Herculase II Fusion DNA Polymerase Agilent Cat#600675 Mouse Cot-1 DNA Thermo Fisher Scientific Cat#18440016 Twist Universal Blockers Twist Bioscience Cat#100578 Twist Binding and Purification Beads Twist Bioscience Cat#100983 Dynabeads M-270 Streptavidn Thermo Fisher Scientic Cat#65305 NlaIII New England Biolabs Cat#R0125L NEB Buffer 2 New England Biolabs Cat#7002S NEB Buffer 3.1 New England Biolabs Cat#B7203S DpnII New England Biolabs Cat#R0543M VAHTS DNA Clean Beads Vazyme Cat#N411 (Continued on next page) e1 Molecular Cell 85, 376–393.e1–e9, January 16, 2025 .. REAGENT or RESOURCE SOURCE IDENTIFIER T4 DNA polymerase New England Biolabs CatM0203S 4-thiouridine (4SU) MedChemExpress Cat#HY-W011793 TRIzol Reagent Invitrogen Cat#15596026 MTSEA-biotin Biotium Cat# 90064 Critical commercial assays KAPA HyperCapture Reagent Kit Roche Cat#9075810001 Twist Hybridization and Wash Kit with Amplification Mix, 12 Reactions Twist Bioscience Cat#104178 RNeasy Mini Kit QIAGEN Cat#74104 QIAshredder QIAGEN Cat#79656 NEBNext Ultra II DNA Library Prep Kit for Illumina New England Biolabs Cat#E7645S NEBNext Multiplex Oligos for Illumina (96 Unique Dual Index Primer Pairs) New England Biolabs Cat#E6440S TruSeq Stranded mRNA kit Illumina Cat#20020594 Illumina Stranded Total RNA Prep Illumina Cat# 20040525 Qubit dsDNA Quantification Assay Kits Thermo Fisher Scientific Cat#Q32850 In-Fusion HD Cloning kit Takara Cat#639648 QIAquick PCR Purification Kit QIAGEN Cat#28104 QIAquick Gel Extraction Kit QIAGEN Cat#28704 AHTS Universal DNA Library Prep Kit Vazyme Cat#ND627-01 Deposited data LDB1-AID Micro-C This paper GSE254373 LDB1-AID RCMC This paper GSE266450 LDB1-AID TT-seq This paper GSE264584 LDB1-AID Tri-C This paper GSE254372 LDB1-AID RNA-seq This paper GSE264455 SMC3-AID Hi-C Zhao et al.103 GSE228402 CTCF-AID Hi-C Zhang et al.26 GSE168251 YY1-AID Micro-C Lam et al.84 GSE247254 Mitotic Hi-C Zhang et al.38 GSE129997 Mitotic ChIP-seq (CTCF/RAD21) Zhang et al.38 GSE129997 H3K27ac ChIP-seq Dogan et al.104 GSE61349 LDB1-AID ChIP-seq This paper GSE254377 SMC3-AID ChIP-seq This paper GSE254377 Original western blot data This paper, Mendeley Data https://doi.org/10.17632/mf78pvcrkk.2 Experimental models: Cell lines G1E-ER4 Mitchell J. Weiss lab Weiss et al.82 LDB1-AID This paper N/A YY1-AID Gerd Blobel Lab Lam et al.84 SMC3-AID Haoyue Zhang Lab Zhao et al.103 CTCF-AID Gerd A. Blobel lab Zhang et al.26 Oligonucleotides See Table S2 for oligonucleotides used in this study This paper Table S2 Recombinant DNA pX458-GFP Addgene 48138 md-mCherry Gerd A. Blobel lab Zhang et al.38 OsTiR-IRES-GFP Gerd A. Blobel lab Zhang et al.38 (Continued on next page) Molecular Cell 85, 376–393.e1–e9, January 16, 2025 e2 ..
Real-time Polymerase Chain Reaction:Article Title: Interface-guided phenotyping of coding variants in the transcription factor RUNX1.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies RUNX1 Antibody (A-2), mouse monoclonal Santa Cruz Biotechnologies Cat#sc-365644; RRID:AB_10843207 Anti-b-Actin Antibody (AC-15), mouse monoclonal Millipore Sigma Cat#A1978; RRID:AB_476692 Anti-Mouse IgG, HRP-linked Antibody Cell Signaling Technology Cat#7076P2; RRID:AB_330924 IRDye 680RD Goat anti-Mouse IgG Secondary Antibody Li-Cor Bio Cat#926–68070; RRID:AB_10956588 Bacterial and virus strains Stbl3 Thermo Fisher Cat#C737303 Chemicals, peptides, and recombinant proteins NheI-HF New England Biolabs Cat#R3131S SalI-HF New England Biolabs Cat#R3138S AflII New England Biolabs Cat#R0520S Gibson Assembly Master Mix New England Biolabs Cat#E2611S KAPA HiFi HotStart ReadyMix Roche Cat#KK2601 OneTaq 2X Master Mix New England Biolabs Cat#M0482S AMPure XP Beads Beckman Coulter Cat#A63880 DMEM ThermoFisher Scientific Cat#10566016 .05% Trypsin-EDTA Gibco Cat#25300062 OptiMEM ThermoFisher Scientific Cat#31985062 RPMI Medium 1640 Gibco Cat#11875-093 FBS Gibco Cat#A52568 Anti-anti Gibco Cat#15240-062 Lipofectamine 2000 ThermoFisher Scientific Cat#11668030 Doxycycline hyclate Sigma Cat#D5207 Hygromycin Invitrogen Cat#10687010 Puromycin Gibco Cat#A11138-03 Polybrene Millipore-Sigma Cat#TR-1003-G PBS, pH 7.4 Gibco Cat#10010023 Tn5 Illumina Cat#20034198 RIPA Buffer Cell Signaling Technologies Cat#9806 Pierce Protease Inhibitor Tablets ThermoFisher Scientific Cat#A32963 4X Laemmli Sample Buffer Bio-Rad Cat#1610747 4-20% Mini-PROTEAN TGX gel Bio-Rad Cat#4561094 10X Tris/Glycine/SDS Buffer Bio-Rad Cat#1610732 Nonfat Dry Milk Apex Bioresearch Cat#20-241 TBST Cell Signaling Technology Cat#9997 BSA, Fraction V, Fatty Acid-Free Millipore Sigma Cat#126575 SuperSignal West Pico Plus Chemiluminescent Substrate ThermoFisher Scientific Cat#34577 Carbenicillin Teknova Cat#C2199 iTaq Universal SYBR Green Master Mix Bio-Rad Cat#1725120 Critical commercial assays Pierce BCA Protein Assay kit ThermoFisher Scientific Cat#23227 RNeasy Mini Kit Qiagen Cat#74104 DNeasy Blood and Tissue Kit Qiagen Cat#69504 (Continued on next page) 20 Cell Reports 43, 114436, July 23, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER Protoscript II First Strand cDNA Synthesis Kit New England BioLabs CatE6560S QIAquick PCR Purification Kit Qiagen Cat#28104 Nucleofector Solution Set SF Lonza Cat#PBC2-00675 Chromium Single Cell 30 v3 10X Genomics Cat# PN- 1000128 NEBNext Ultra RNA Library Prep Kit New England Biolabs Cat#E7530 Deposited data Raw data: scRNA-seq This paper SRA: PRJNA1033389 Raw data: bulk RNA-seq This paper SRA: PRJNA1121326 Raw data: ATAC-seq This paper SRA: PRJNA1121327 RUNX1-CBFB-DNA structures Protein DataBank PDB: 1ljm, 1e50, 1h9d Human reference genome NCBI build 38, GRCh38–3.0.0 Genome Reference Consortium http://www.ncbi.nlm.nih.gov/projects/ genome/assembly/grc/human/ ATAC-seq data for K562 ENCODE ENCSR868FGK ChromHMM states for K562 Roadmap Epigenomics Project https://egg2.wustl.edu/roadmap/web_portal/ Hi-C chromatin loop data for K562 NCBI GEO: GSM1551620 Experimental models: Cell lines K-562 ATCC Cat#CCL-243; RRID:CVCL_0004 HEK293T ATCC Cat#CRL-3216; RRID:CVCL_0063 Oligonucleotides RUNX1 library variants Twist Bioscience https://www.twistbioscience.com Primers for qPCR, Sanger Sequencing, & oligopool amplification, see Table S10 This Paper N/A NEBNext Multiplex Oligos for Illumina New England Biolabs Cat#E7335S Recombinant DNA EF1a_mCherry_P2A_Hygro_Barcode (Parekh et al.)12 Addgene #120426 PB-TRE-dCas9-VPR (Chavez et al.)108 Addgene #63800 pHR-SFFV-KRAB-dCas9-P2A-mCherry (Gilbert et al.)109 Addgene #60954 pMD2.G N/A Addgene #12259 pCMV delta R8.2 N/A Addgene #12263 Software and algorithms Code related to analyses of RUNX1 mutations This paper https://github.com/cartercompbio/ RUNX1_SEUSS; https://doi.org/ 10.5281/zenodo.11580866 CellRanger 3.1.0 10X Genomics https://support.10xgenomics.com genotyping-matrices (Parekh et al.)12 https://github.com/yanwu2014/ genotyping-matrices MAGeCK (W. Li et al.)110 https://sourceforge.net/p/mageck/ wiki/Home/ PRISM (Baspinar et al.)60 https://cosbi.ku.edu.tr/prism/ VEST (Carter et al.)62 http://www.cravat.us/CRAVAT/ FoldX (Schymkowitz et al.)63 http://foldx.crg.es/ Seurat 4.1.0 (Macosko et al.)111 https://satijalab.org/seurat/ CoGAPS (Fertig et al.)72 http://www.bioconductor.org/packages/ release/bioc/html/CoGAPS.html EnrichR (Kuleshov et al.)112 https://github.com/wjawaid/enrichR STAR 2.7.1a (Dobin et al.)113 https://github.com/alexdobin/STAR RSEM 1.3.1 N/A http://deweylab.biostat.wisc.edu/rsem/ limma (Ritchie et al.)114 http://bioinf.wehi.edu.au/limma/ (Continued on next page) Cell Reports 43, 114436, July 23, 2024 21 ..
Article Title: Graft-seq precisely maps RNA modifications via site-specific chemical grafting strategy.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-7-methylguanosine (m 7 G)-Cap mAb MBL life science Cat# RN016M; RRID: AB_2921296 Goat anti-Mouse IgG HRP HuaBio Cat# HA1006; RRID: AB_2819167 Chemicals, peptides, and recombinant proteins 3 M Sodium Acetate Solution, pH 5.2 Thermo Scientific Cat# R1181 3 ′ -Desthiobiotin-GTP; DTB-GTP New England Biolabs Cat# N0761 3-azido-1-propanol Sigma-Aldrich Cat# 776130 ADP-ribosylcyclase; ADPRC Sigma-Aldrich Cat# A9106 Alexa Fluor 488 Azide Invitrogen Cat# A10266 Ammonium iron(II) sulfate hexahydrate Sigma-Aldrich Cat# 09719 ATP New England Biolabs Cat# P0756S Biotin-Azide QIYUEBIO Cat# QY-24297 Blotting membranes, Amersham TM Hybond TM -N+ GE Healthcare Cat# RPN303B Bst 2.0 DNA polymerase New England Biolabs Cat# M0537S CleanCap Reagent M6 Trilink Cat# N-7453 Copper(II) sulfate pentahydrate Sigma-Aldrich Cat# C3036 D-biotin MedChemExpress Cat# HY-B0511 Dibenzocyclooctyne-maleimide Sigma-Aldrich Cat# 760668 DL-Dithiothreitol; DTT Sigma-Aldrich Cat# V900830 DMEM/high-glucose medium HyClone Cat# SH30243.01 DMF Sigma-Aldrich Cat# D4551 DMSO Sigma-Aldrich Cat# 41639 DNase I New England Biolabs Cat# M0303 dTTP (100 mM) Thermo Scientific Cat# R0171 EDTA (0.5 M),pH 8.0 Invitrogen Cat# AM9260G Fetal Bovine Serum Gibco Cat# 10270 Fetal Bovine Serum, Sterile(irradiated) Ausbian Cat# VS500T GlutaMAX Gibco Cat# 35050061 Glycogen Invitrogen Cat# AM9510 HEPES Sigma-Aldrich Cat# V900477 HRP-streptavidin Invitrogen Cat# 434323 L-Ascorbic acid Sigma-Aldrich Cat# 95209 m 6 ATP Trilink Cat# N-1013 Maxima H Minus Reverse Transcriptase Thermo Scientific Cat# EP0751 MEM Non-Essential Amino Acids Solution (100X) Gibco Cat# 11140 mRNA decapping enzyme New England Biolabs Cat# M0608S NAD Sigma-Aldrich Cat# N6522 Non-fat Powdered milk BBI Life Sciences Cat# A600669 Nuclease P1 Wako Cat# 145-08221 Penicillin/streptomycin Gibco Cat# 15140 Penicillin-Streptomycin HyClone Cat# SV30010 Phanta Max Super-Fidelity DNA Polymerase Vazyme Cat# P505 Potassium chloride Sigma-Aldrich Cat# P9541 PrimerScript II Reverse Transcriptase Takara Cat# 6210A PrimerScript Reverse Transcriptase Takara Cat# 6110A (Continued on next page) e1 Cell Reports Methods 5, 101103, July 21, 2025 OPEN ACCESS .. REAGENT or RESOURCE SOURCE IDENTIFIER Quick CIP New England Biolabs Cat# M0525 rCutSmart buffer New England Biolabs Cat# B6004V Recombinant Mouse LIF Protein Milipore Cat# ESG1107 Reverse Transcriptase, Recombinant HIV Worthington Biochemical Corporation Cat# LS05003 RevertAid Reverse Transcriptase Thermo Scientific Cat# EP0442 RNase inhibitor Vazyme Cat# R301 RppH New England Biolabs Cat# M0356 rSAP New England Biolabs Cat# M0371S SMARTScribe Reverse Transcriptase Clontech Cat# 639536 Sodium L-ascorbate Energy Chemical Cat# E082526 Sodium pyruvate Gibco Cat# 11360 SplintR ligase New England Biolabs Cat# M0375S SuperScript II Reverse Transcriptase Invitrogen Cat# 18064071 T4 Polynucleotide Kinase; T4 PNK New England Biolabs Cat# M0201 TGIRT III Reverse Transcriptase InGex Cat# CM0101 ThermoPol Reaction Buffer New England Biolabs Cat# B90004 Tris(3-hydroxypropyltriazolylmethyl)amine Sigma-Aldrich Cat# 762342 Trizol Invitrogen Cat# 10296010 Tween 20 Sigma-Aldrich Cat# V900548 Vaccinia Capping System New England Biolabs Cat# M2080S yDcpS New England Biolabs Cat# M0463S α-L-Ascorbic acid; α-KG Sigma-Aldrich Cat# 75890 β-mercaptoethanol Gibco Cat# 21985023 Critical commercial assays GenElute mRNA Purification Miniprep Kit Sigma-Aldrich Cat# MRN10-1KT NEBNext rRNA Depletion Kit New England Biolabs Cat# E7400 HiScribe T7 High Yield RNA Synthesis Kit New England Biolabs Cat# E2040 RNA Clean & Concentrator-25 kit Zymo Research Cat# R1017 RNA Clean & Concentrator-5 kit Zymo Research Cat# R1013 RNAClean XP beads Beckman Coulter Cat# A63987 QIAquick Gel Extraction Kit QIAGEN Cat# 28704 ABclonal Zero TOPO-TA/Blunt Cloning Kit ABclonal Cat# RK30130 AMPure XP beads Beckman Coulter Cat# A63881 NEBNext Magnesium RNA Fragmentation Module New England Biolabs Cat# E6150 Dynabeads Protein A Invitrogen Cat# 10002D Dynabeads MyOne Streptavidin C1 Invitrogen Cat# 65001 NEBNext Multiplex Small RNA Library Prep Kit for Illumina New England Biolabs Cat# E7560S ChamQ Universal SYBR qPCR Master Mix Vazyme Cat# Q711-03 SuperSignal West Pico PLUS Chemiluminescent Substrate Thermo Scientific Cat# 34577 Deposited data Raw data This paper GSA-Human: HRA009209; GSA: CRA020263 Experimental models: Cell lines HEK293T ATCC Cat# ATCC-CRL-3216 HeLa ATCC Cat# ATCC-CCL-2 mouse ESC E14 Lab of Li Shen (Zhejiang University) N/A (Continued on next page) Cell Reports Methods 5, 101103, July 21, 2025 e2 OPEN ACCESS ..
Article Title: Graft-seq precisely maps RNA modifications via site-specific chemical grafting strategy
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-7-methylguanosine (m7G)-Cap mAb MBL life science Cat# RN016M; RRID: AB_2921296 Goat anti-Mouse IgG HRP HuaBio Cat# HA1006; RRID: AB_2819167 Chemicals, peptides, and recombinant proteins 3 M Sodium Acetate Solution, pH 5.2 Thermo Scientific Cat# R1181 3′-Desthiobiotin-GTP; DTB-GTP New England Biolabs Cat# N0761 3-azido-1-propanol Sigma-Aldrich Cat# 776130 ADP-ribosylcyclase; ADPRC Sigma-Aldrich Cat# A9106 Alexa Fluor 488 Azide Invitrogen Cat# A10266 Ammonium iron(II) sulfate hexahydrate Sigma-Aldrich Cat# 09719 ATP New England Biolabs Cat# P0756S Biotin-Azide QIYUEBIO Cat# QY-24297 Blotting membranes, AmershamTM HybondTM-N+ GE Healthcare Cat# RPN303B Bst 2.0 DNA polymerase New England Biolabs Cat# M0537S CleanCap Reagent M6 Trilink Cat# N-7453 Copper(II) sulfate pentahydrate Sigma-Aldrich Cat# C3036 D-biotin MedChemExpress Cat# HY-B0511 Dibenzocyclooctyne-maleimide Sigma-Aldrich Cat# 760668 DL-Dithiothreitol; DTT Sigma-Aldrich Cat# V900830 DMEM/high-glucose medium HyClone Cat# SH30243.01 DMF Sigma-Aldrich Cat# D4551 DMSO Sigma-Aldrich Cat# 41639 DNase I New England Biolabs Cat# M0303 dTTP (100 mM) Thermo Scientific Cat# R0171 EDTA (0.5 M),pH 8.0 Invitrogen Cat# AM9260G Fetal Bovine Serum Gibco Cat# 10270 Fetal Bovine Serum, Sterile(irradiated) Ausbian Cat# VS500T GlutaMAX Gibco Cat# 35050061 Glycogen Invitrogen Cat# AM9510 HEPES Sigma-Aldrich Cat# V900477 HRP-streptavidin Invitrogen Cat# 434323 L-Ascorbic acid Sigma-Aldrich Cat# 95209 m6ATP Trilink Cat# N-1013 Maxima H Minus Reverse Transcriptase Thermo Scientific Cat# EP0751 MEM Non-Essential Amino Acids Solution (100X) Gibco Cat# 11140 mRNA decapping enzyme New England Biolabs Cat# M0608S NAD Sigma-Aldrich Cat# N6522 Non-fat Powdered milk BBI Life Sciences Cat# A600669 Nuclease P1 Wako Cat# 145-08221 Penicillin/streptomycin Gibco Cat# 15140 Penicillin-Streptomycin HyClone Cat# SV30010 Phanta Max Super-Fidelity DNA Polymerase Vazyme Cat# P505 Potassium chloride Sigma-Aldrich Cat# P9541 PrimerScript II Reverse Transcriptase Takara Cat# 6210A PrimerScript Reverse Transcriptase Takara Cat# 6110A (Continued on next page) e1 Cell Reports Methods 5, 101103, July 21, 2025 Article ll OPEN ACCESS .. REAGENT or RESOURCE SOURCE IDENTIFIER Quick CIP New England Biolabs Cat# M0525 rCutSmart buffer New England Biolabs Cat# B6004V Recombinant Mouse LIF Protein Milipore Cat# ESG1107 Reverse Transcriptase, Recombinant HIV Worthington Biochemical Corporation Cat# LS05003 RevertAid Reverse Transcriptase Thermo Scientific Cat# EP0442 RNase inhibitor Vazyme Cat# R301 RppH New England Biolabs Cat# M0356 rSAP New England Biolabs Cat# M0371S SMARTScribe Reverse Transcriptase Clontech Cat# 639536 Sodium L-ascorbate Energy Chemical Cat# E082526 Sodium pyruvate Gibco Cat# 11360 SplintR ligase New England Biolabs Cat# M0375S SuperScript II Reverse Transcriptase Invitrogen Cat# 18064071 T4 Polynucleotide Kinase; T4 PNK New England Biolabs Cat# M0201 TGIRT III Reverse Transcriptase InGex Cat# CM0101 ThermoPol Reaction Buffer New England Biolabs Cat# B90004 Tris(3-hydroxypropyltriazolylmethyl)amine Sigma-Aldrich Cat# 762342 Trizol Invitrogen Cat# 10296010 Tween 20 Sigma-Aldrich Cat# V900548 Vaccinia Capping System New England Biolabs Cat# M2080S yDcpS New England Biolabs Cat# M0463S α-L-Ascorbic acid; α-KG Sigma-Aldrich Cat# 75890 β-mercaptoethanol Gibco Cat# 21985023 Critical commercial assays GenElute mRNA Purification Miniprep Kit Sigma-Aldrich Cat# MRN10-1KT NEBNext rRNA Depletion Kit New England Biolabs Cat# E7400 HiScribe T7 High Yield RNA Synthesis Kit New England Biolabs Cat# E2040 RNA Clean & Concentrator-25 kit Zymo Research Cat# R1017 RNA Clean & Concentrator-5 kit Zymo Research Cat# R1013 RNAClean XP beads Beckman Coulter Cat# A63987 QIAquick Gel Extraction Kit QIAGEN Cat# 28704 ABclonal Zero TOPO-TA/Blunt Cloning Kit ABclonal Cat# RK30130 AMPure XP beads Beckman Coulter Cat# A63881 NEBNext Magnesium RNA Fragmentation Module New England Biolabs Cat# E6150 Dynabeads Protein A Invitrogen Cat# 10002D Dynabeads MyOne Streptavidin C1 Invitrogen Cat# 65001 NEBNext Multiplex Small RNA Library Prep Kit for Illumina New England Biolabs Cat# E7560S ChamQ Universal SYBR qPCR Master Mix Vazyme Cat# Q711-03 SuperSignal West Pico PLUS Chemiluminescent Substrate Thermo Scientific Cat# 34577 Deposited data Raw data This paper GSA-Human: HRA009209; GSA: CRA020263 Experimental models: Cell lines HEK293T ATCC Cat# ATCC-CRL-3216 HeLa ATCC Cat# ATCC-CCL-2 mouse ESC E14 Lab of Li Shen (Zhejiang University) N/A (Continued on next page) Cell Reports Methods 5, 101103, July 21, 2025 e2 Article ll OPEN ACCESS ..
Sequencing:Article Title: Interface-guided phenotyping of coding variants in the transcription factor RUNX1.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies RUNX1 Antibody (A-2), mouse monoclonal Santa Cruz Biotechnologies Cat#sc-365644; RRID:AB_10843207 Anti-b-Actin Antibody (AC-15), mouse monoclonal Millipore Sigma Cat#A1978; RRID:AB_476692 Anti-Mouse IgG, HRP-linked Antibody Cell Signaling Technology Cat#7076P2; RRID:AB_330924 IRDye 680RD Goat anti-Mouse IgG Secondary Antibody Li-Cor Bio Cat#926–68070; RRID:AB_10956588 Bacterial and virus strains Stbl3 Thermo Fisher Cat#C737303 Chemicals, peptides, and recombinant proteins NheI-HF New England Biolabs Cat#R3131S SalI-HF New England Biolabs Cat#R3138S AflII New England Biolabs Cat#R0520S Gibson Assembly Master Mix New England Biolabs Cat#E2611S KAPA HiFi HotStart ReadyMix Roche Cat#KK2601 OneTaq 2X Master Mix New England Biolabs Cat#M0482S AMPure XP Beads Beckman Coulter Cat#A63880 DMEM ThermoFisher Scientific Cat#10566016 .05% Trypsin-EDTA Gibco Cat#25300062 OptiMEM ThermoFisher Scientific Cat#31985062 RPMI Medium 1640 Gibco Cat#11875-093 FBS Gibco Cat#A52568 Anti-anti Gibco Cat#15240-062 Lipofectamine 2000 ThermoFisher Scientific Cat#11668030 Doxycycline hyclate Sigma Cat#D5207 Hygromycin Invitrogen Cat#10687010 Puromycin Gibco Cat#A11138-03 Polybrene Millipore-Sigma Cat#TR-1003-G PBS, pH 7.4 Gibco Cat#10010023 Tn5 Illumina Cat#20034198 RIPA Buffer Cell Signaling Technologies Cat#9806 Pierce Protease Inhibitor Tablets ThermoFisher Scientific Cat#A32963 4X Laemmli Sample Buffer Bio-Rad Cat#1610747 4-20% Mini-PROTEAN TGX gel Bio-Rad Cat#4561094 10X Tris/Glycine/SDS Buffer Bio-Rad Cat#1610732 Nonfat Dry Milk Apex Bioresearch Cat#20-241 TBST Cell Signaling Technology Cat#9997 BSA, Fraction V, Fatty Acid-Free Millipore Sigma Cat#126575 SuperSignal West Pico Plus Chemiluminescent Substrate ThermoFisher Scientific Cat#34577 Carbenicillin Teknova Cat#C2199 iTaq Universal SYBR Green Master Mix Bio-Rad Cat#1725120 Critical commercial assays Pierce BCA Protein Assay kit ThermoFisher Scientific Cat#23227 RNeasy Mini Kit Qiagen Cat#74104 DNeasy Blood and Tissue Kit Qiagen Cat#69504 (Continued on next page) 20 Cell Reports 43, 114436, July 23, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER Protoscript II First Strand cDNA Synthesis Kit New England BioLabs CatE6560S QIAquick PCR Purification Kit Qiagen Cat#28104 Nucleofector Solution Set SF Lonza Cat#PBC2-00675 Chromium Single Cell 30 v3 10X Genomics Cat# PN- 1000128 NEBNext Ultra RNA Library Prep Kit New England Biolabs Cat#E7530 Deposited data Raw data: scRNA-seq This paper SRA: PRJNA1033389 Raw data: bulk RNA-seq This paper SRA: PRJNA1121326 Raw data: ATAC-seq This paper SRA: PRJNA1121327 RUNX1-CBFB-DNA structures Protein DataBank PDB: 1ljm, 1e50, 1h9d Human reference genome NCBI build 38, GRCh38–3.0.0 Genome Reference Consortium http://www.ncbi.nlm.nih.gov/projects/ genome/assembly/grc/human/ ATAC-seq data for K562 ENCODE ENCSR868FGK ChromHMM states for K562 Roadmap Epigenomics Project https://egg2.wustl.edu/roadmap/web_portal/ Hi-C chromatin loop data for K562 NCBI GEO: GSM1551620 Experimental models: Cell lines K-562 ATCC Cat#CCL-243; RRID:CVCL_0004 HEK293T ATCC Cat#CRL-3216; RRID:CVCL_0063 Oligonucleotides RUNX1 library variants Twist Bioscience https://www.twistbioscience.com Primers for qPCR, Sanger Sequencing, & oligopool amplification, see Table S10 This Paper N/A NEBNext Multiplex Oligos for Illumina New England Biolabs Cat#E7335S Recombinant DNA EF1a_mCherry_P2A_Hygro_Barcode (Parekh et al.)12 Addgene #120426 PB-TRE-dCas9-VPR (Chavez et al.)108 Addgene #63800 pHR-SFFV-KRAB-dCas9-P2A-mCherry (Gilbert et al.)109 Addgene #60954 pMD2.G N/A Addgene #12259 pCMV delta R8.2 N/A Addgene #12263 Software and algorithms Code related to analyses of RUNX1 mutations This paper https://github.com/cartercompbio/ RUNX1_SEUSS; https://doi.org/ 10.5281/zenodo.11580866 CellRanger 3.1.0 10X Genomics https://support.10xgenomics.com genotyping-matrices (Parekh et al.)12 https://github.com/yanwu2014/ genotyping-matrices MAGeCK (W. Li et al.)110 https://sourceforge.net/p/mageck/ wiki/Home/ PRISM (Baspinar et al.)60 https://cosbi.ku.edu.tr/prism/ VEST (Carter et al.)62 http://www.cravat.us/CRAVAT/ FoldX (Schymkowitz et al.)63 http://foldx.crg.es/ Seurat 4.1.0 (Macosko et al.)111 https://satijalab.org/seurat/ CoGAPS (Fertig et al.)72 http://www.bioconductor.org/packages/ release/bioc/html/CoGAPS.html EnrichR (Kuleshov et al.)112 https://github.com/wjawaid/enrichR STAR 2.7.1a (Dobin et al.)113 https://github.com/alexdobin/STAR RSEM 1.3.1 N/A http://deweylab.biostat.wisc.edu/rsem/ limma (Ritchie et al.)114 http://bioinf.wehi.edu.au/limma/ (Continued on next page) Cell Reports 43, 114436, July 23, 2024 21 ..
Amplification:Article Title: Interface-guided phenotyping of coding variants in the transcription factor RUNX1.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies RUNX1 Antibody (A-2), mouse monoclonal Santa Cruz Biotechnologies Cat#sc-365644; RRID:AB_10843207 Anti-b-Actin Antibody (AC-15), mouse monoclonal Millipore Sigma Cat#A1978; RRID:AB_476692 Anti-Mouse IgG, HRP-linked Antibody Cell Signaling Technology Cat#7076P2; RRID:AB_330924 IRDye 680RD Goat anti-Mouse IgG Secondary Antibody Li-Cor Bio Cat#926–68070; RRID:AB_10956588 Bacterial and virus strains Stbl3 Thermo Fisher Cat#C737303 Chemicals, peptides, and recombinant proteins NheI-HF New England Biolabs Cat#R3131S SalI-HF New England Biolabs Cat#R3138S AflII New England Biolabs Cat#R0520S Gibson Assembly Master Mix New England Biolabs Cat#E2611S KAPA HiFi HotStart ReadyMix Roche Cat#KK2601 OneTaq 2X Master Mix New England Biolabs Cat#M0482S AMPure XP Beads Beckman Coulter Cat#A63880 DMEM ThermoFisher Scientific Cat#10566016 .05% Trypsin-EDTA Gibco Cat#25300062 OptiMEM ThermoFisher Scientific Cat#31985062 RPMI Medium 1640 Gibco Cat#11875-093 FBS Gibco Cat#A52568 Anti-anti Gibco Cat#15240-062 Lipofectamine 2000 ThermoFisher Scientific Cat#11668030 Doxycycline hyclate Sigma Cat#D5207 Hygromycin Invitrogen Cat#10687010 Puromycin Gibco Cat#A11138-03 Polybrene Millipore-Sigma Cat#TR-1003-G PBS, pH 7.4 Gibco Cat#10010023 Tn5 Illumina Cat#20034198 RIPA Buffer Cell Signaling Technologies Cat#9806 Pierce Protease Inhibitor Tablets ThermoFisher Scientific Cat#A32963 4X Laemmli Sample Buffer Bio-Rad Cat#1610747 4-20% Mini-PROTEAN TGX gel Bio-Rad Cat#4561094 10X Tris/Glycine/SDS Buffer Bio-Rad Cat#1610732 Nonfat Dry Milk Apex Bioresearch Cat#20-241 TBST Cell Signaling Technology Cat#9997 BSA, Fraction V, Fatty Acid-Free Millipore Sigma Cat#126575 SuperSignal West Pico Plus Chemiluminescent Substrate ThermoFisher Scientific Cat#34577 Carbenicillin Teknova Cat#C2199 iTaq Universal SYBR Green Master Mix Bio-Rad Cat#1725120 Critical commercial assays Pierce BCA Protein Assay kit ThermoFisher Scientific Cat#23227 RNeasy Mini Kit Qiagen Cat#74104 DNeasy Blood and Tissue Kit Qiagen Cat#69504 (Continued on next page) 20 Cell Reports 43, 114436, July 23, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER Protoscript II First Strand cDNA Synthesis Kit New England BioLabs CatE6560S QIAquick PCR Purification Kit Qiagen Cat#28104 Nucleofector Solution Set SF Lonza Cat#PBC2-00675 Chromium Single Cell 30 v3 10X Genomics Cat# PN- 1000128 NEBNext Ultra RNA Library Prep Kit New England Biolabs Cat#E7530 Deposited data Raw data: scRNA-seq This paper SRA: PRJNA1033389 Raw data: bulk RNA-seq This paper SRA: PRJNA1121326 Raw data: ATAC-seq This paper SRA: PRJNA1121327 RUNX1-CBFB-DNA structures Protein DataBank PDB: 1ljm, 1e50, 1h9d Human reference genome NCBI build 38, GRCh38–3.0.0 Genome Reference Consortium http://www.ncbi.nlm.nih.gov/projects/ genome/assembly/grc/human/ ATAC-seq data for K562 ENCODE ENCSR868FGK ChromHMM states for K562 Roadmap Epigenomics Project https://egg2.wustl.edu/roadmap/web_portal/ Hi-C chromatin loop data for K562 NCBI GEO: GSM1551620 Experimental models: Cell lines K-562 ATCC Cat#CCL-243; RRID:CVCL_0004 HEK293T ATCC Cat#CRL-3216; RRID:CVCL_0063 Oligonucleotides RUNX1 library variants Twist Bioscience https://www.twistbioscience.com Primers for qPCR, Sanger Sequencing, & oligopool amplification, see Table S10 This Paper N/A NEBNext Multiplex Oligos for Illumina New England Biolabs Cat#E7335S Recombinant DNA EF1a_mCherry_P2A_Hygro_Barcode (Parekh et al.)12 Addgene #120426 PB-TRE-dCas9-VPR (Chavez et al.)108 Addgene #63800 pHR-SFFV-KRAB-dCas9-P2A-mCherry (Gilbert et al.)109 Addgene #60954 pMD2.G N/A Addgene #12259 pCMV delta R8.2 N/A Addgene #12263 Software and algorithms Code related to analyses of RUNX1 mutations This paper https://github.com/cartercompbio/ RUNX1_SEUSS; https://doi.org/ 10.5281/zenodo.11580866 CellRanger 3.1.0 10X Genomics https://support.10xgenomics.com genotyping-matrices (Parekh et al.)12 https://github.com/yanwu2014/ genotyping-matrices MAGeCK (W. Li et al.)110 https://sourceforge.net/p/mageck/ wiki/Home/ PRISM (Baspinar et al.)60 https://cosbi.ku.edu.tr/prism/ VEST (Carter et al.)62 http://www.cravat.us/CRAVAT/ FoldX (Schymkowitz et al.)63 http://foldx.crg.es/ Seurat 4.1.0 (Macosko et al.)111 https://satijalab.org/seurat/ CoGAPS (Fertig et al.)72 http://www.bioconductor.org/packages/ release/bioc/html/CoGAPS.html EnrichR (Kuleshov et al.)112 https://github.com/wjawaid/enrichR STAR 2.7.1a (Dobin et al.)113 https://github.com/alexdobin/STAR RSEM 1.3.1 N/A http://deweylab.biostat.wisc.edu/rsem/ limma (Ritchie et al.)114 http://bioinf.wehi.edu.au/limma/ (Continued on next page) Cell Reports 43, 114436, July 23, 2024 21 ..
Article Title: LDB1 establishes multi-enhancer networks to regulate gene expression.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Mouse monoclonal anti-LDB1 CLIM-2 (C-9) Santa Cruz Biotechnology Cat#sc-365074; RRID: AB_10848267 Rabbit polyclonal anti-LDB1 Lot# VI3089586A Thermo Fisher Scientific Cat#PA5-56948; RRID: AB_2643320 Mouse monoclonal anti-GAPDH Lot# A1822 (6C5) Santa Cruz Biotechnology Cat#sc-32233; RRID: AB_627679 Rabbit monoclonal anti-RPB1 (Pol2) (D8L4Y) Cell Signaling Technology Cat#14958; RRID: AB_2687876 Rabbit polyclonal anti-YY1 Active Motif Cat#61779; RRID: AB_2793763 Rabbit polyclonal anti-CTCF Millipore Cat#07-729; RRID: AB_441965 Rabbit polyclonal anti-RAD21 Abcam Cat#ab992; RRID: AB_2176601 Mouse monoclonal anti-pMPM2 Millipore Cat# 05-368; RRID: AB_309698 F(ab’)2-Goat anti-Mouse IgG (H+L) Secondary Antibody, APC, eBioscience Thermo Fisher Scientific Cat#17-4010-82; RRID: AB_2573203 Chemicals, peptides, and recombinant proteins AMPure XP Beckman Coulter Cat#A63880 Indole-3-acetic acid sodium salt (auxin) Sigma Aldrich Cat#I5148 estradiol Sigma Aldrich Cat#E2758 iSCRIPT Reverse Transcription Supermix Bio Rad Cat#1708840 Power SYBR Green PCR Master Mix Thermo Fisher Scientific Cat#4367660 Protein A agarose beads Thermo Fisher Scientific Cat#15918014 Protein G agarose beads Thermo Fisher Scientific Cat#15920010 DSG crosslinker ProteoChem Cat#c1104-1gm cOmplete Mini, EDTA-free Millipore Sigma Cat#11836170001 MNase Worthington Biochemical Cat#LS004798 rSAP New England Biolabs Cat#M0371S T4 PNK New England Biolabs Cat#M0201S Large (Klenow) Fragment New England Biolabs Cat#M0210S Biotin-11-dCTP Jena Bioscience Cat#NU-809-BIOX-S Biotin-14-dATP Jena Bioscience Cat#NU-835-BIO14-S Biotin-14-dATP Active Motif Cat#14138 T4 DNA Ligase New England Biolabs Cat#M0202S T4 DNA Ligase buffer New England Biolabs Cat#B0202S Dynabeads MyOne Streptavidin C1 Thermo Fisher Scientific Cat#65001 KAPA HiFi HotStart ReadyMix Roche Cat#08202940001 Herculase II Fusion DNA Polymerase Agilent Cat#600675 Mouse Cot-1 DNA Thermo Fisher Scientific Cat#18440016 Twist Universal Blockers Twist Bioscience Cat#100578 Twist Binding and Purification Beads Twist Bioscience Cat#100983 Dynabeads M-270 Streptavidn Thermo Fisher Scientic Cat#65305 NlaIII New England Biolabs Cat#R0125L NEB Buffer 2 New England Biolabs Cat#7002S NEB Buffer 3.1 New England Biolabs Cat#B7203S DpnII New England Biolabs Cat#R0543M VAHTS DNA Clean Beads Vazyme Cat#N411 (Continued on next page) e1 Molecular Cell 85, 376–393.e1–e9, January 16, 2025 .. REAGENT or RESOURCE SOURCE IDENTIFIER T4 DNA polymerase New England Biolabs CatM0203S 4-thiouridine (4SU) MedChemExpress Cat#HY-W011793 TRIzol Reagent Invitrogen Cat#15596026 MTSEA-biotin Biotium Cat# 90064 Critical commercial assays KAPA HyperCapture Reagent Kit Roche Cat#9075810001 Twist Hybridization and Wash Kit with Amplification Mix, 12 Reactions Twist Bioscience Cat#104178 RNeasy Mini Kit QIAGEN Cat#74104 QIAshredder QIAGEN Cat#79656 NEBNext Ultra II DNA Library Prep Kit for Illumina New England Biolabs Cat#E7645S NEBNext Multiplex Oligos for Illumina (96 Unique Dual Index Primer Pairs) New England Biolabs Cat#E6440S TruSeq Stranded mRNA kit Illumina Cat#20020594 Illumina Stranded Total RNA Prep Illumina Cat# 20040525 Qubit dsDNA Quantification Assay Kits Thermo Fisher Scientific Cat#Q32850 In-Fusion HD Cloning kit Takara Cat#639648 QIAquick PCR Purification Kit QIAGEN Cat#28104 QIAquick Gel Extraction Kit QIAGEN Cat#28704 AHTS Universal DNA Library Prep Kit Vazyme Cat#ND627-01 Deposited data LDB1-AID Micro-C This paper GSE254373 LDB1-AID RCMC This paper GSE266450 LDB1-AID TT-seq This paper GSE264584 LDB1-AID Tri-C This paper GSE254372 LDB1-AID RNA-seq This paper GSE264455 SMC3-AID Hi-C Zhao et al.103 GSE228402 CTCF-AID Hi-C Zhang et al.26 GSE168251 YY1-AID Micro-C Lam et al.84 GSE247254 Mitotic Hi-C Zhang et al.38 GSE129997 Mitotic ChIP-seq (CTCF/RAD21) Zhang et al.38 GSE129997 H3K27ac ChIP-seq Dogan et al.104 GSE61349 LDB1-AID ChIP-seq This paper GSE254377 SMC3-AID ChIP-seq This paper GSE254377 Original western blot data This paper, Mendeley Data https://doi.org/10.17632/mf78pvcrkk.2 Experimental models: Cell lines G1E-ER4 Mitchell J. Weiss lab Weiss et al.82 LDB1-AID This paper N/A YY1-AID Gerd Blobel Lab Lam et al.84 SMC3-AID Haoyue Zhang Lab Zhao et al.103 CTCF-AID Gerd A. Blobel lab Zhang et al.26 Oligonucleotides See Table S2 for oligonucleotides used in this study This paper Table S2 Recombinant DNA pX458-GFP Addgene 48138 md-mCherry Gerd A. Blobel lab Zhang et al.38 OsTiR-IRES-GFP Gerd A. Blobel lab Zhang et al.38 (Continued on next page) Molecular Cell 85, 376–393.e1–e9, January 16, 2025 e2 ..
Multiplex Assay:Article Title: Interface-guided phenotyping of coding variants in the transcription factor RUNX1.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies RUNX1 Antibody (A-2), mouse monoclonal Santa Cruz Biotechnologies Cat#sc-365644; RRID:AB_10843207 Anti-b-Actin Antibody (AC-15), mouse monoclonal Millipore Sigma Cat#A1978; RRID:AB_476692 Anti-Mouse IgG, HRP-linked Antibody Cell Signaling Technology Cat#7076P2; RRID:AB_330924 IRDye 680RD Goat anti-Mouse IgG Secondary Antibody Li-Cor Bio Cat#926–68070; RRID:AB_10956588 Bacterial and virus strains Stbl3 Thermo Fisher Cat#C737303 Chemicals, peptides, and recombinant proteins NheI-HF New England Biolabs Cat#R3131S SalI-HF New England Biolabs Cat#R3138S AflII New England Biolabs Cat#R0520S Gibson Assembly Master Mix New England Biolabs Cat#E2611S KAPA HiFi HotStart ReadyMix Roche Cat#KK2601 OneTaq 2X Master Mix New England Biolabs Cat#M0482S AMPure XP Beads Beckman Coulter Cat#A63880 DMEM ThermoFisher Scientific Cat#10566016 .05% Trypsin-EDTA Gibco Cat#25300062 OptiMEM ThermoFisher Scientific Cat#31985062 RPMI Medium 1640 Gibco Cat#11875-093 FBS Gibco Cat#A52568 Anti-anti Gibco Cat#15240-062 Lipofectamine 2000 ThermoFisher Scientific Cat#11668030 Doxycycline hyclate Sigma Cat#D5207 Hygromycin Invitrogen Cat#10687010 Puromycin Gibco Cat#A11138-03 Polybrene Millipore-Sigma Cat#TR-1003-G PBS, pH 7.4 Gibco Cat#10010023 Tn5 Illumina Cat#20034198 RIPA Buffer Cell Signaling Technologies Cat#9806 Pierce Protease Inhibitor Tablets ThermoFisher Scientific Cat#A32963 4X Laemmli Sample Buffer Bio-Rad Cat#1610747 4-20% Mini-PROTEAN TGX gel Bio-Rad Cat#4561094 10X Tris/Glycine/SDS Buffer Bio-Rad Cat#1610732 Nonfat Dry Milk Apex Bioresearch Cat#20-241 TBST Cell Signaling Technology Cat#9997 BSA, Fraction V, Fatty Acid-Free Millipore Sigma Cat#126575 SuperSignal West Pico Plus Chemiluminescent Substrate ThermoFisher Scientific Cat#34577 Carbenicillin Teknova Cat#C2199 iTaq Universal SYBR Green Master Mix Bio-Rad Cat#1725120 Critical commercial assays Pierce BCA Protein Assay kit ThermoFisher Scientific Cat#23227 RNeasy Mini Kit Qiagen Cat#74104 DNeasy Blood and Tissue Kit Qiagen Cat#69504 (Continued on next page) 20 Cell Reports 43, 114436, July 23, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER Protoscript II First Strand cDNA Synthesis Kit New England BioLabs CatE6560S QIAquick PCR Purification Kit Qiagen Cat#28104 Nucleofector Solution Set SF Lonza Cat#PBC2-00675 Chromium Single Cell 30 v3 10X Genomics Cat# PN- 1000128 NEBNext Ultra RNA Library Prep Kit New England Biolabs Cat#E7530 Deposited data Raw data: scRNA-seq This paper SRA: PRJNA1033389 Raw data: bulk RNA-seq This paper SRA: PRJNA1121326 Raw data: ATAC-seq This paper SRA: PRJNA1121327 RUNX1-CBFB-DNA structures Protein DataBank PDB: 1ljm, 1e50, 1h9d Human reference genome NCBI build 38, GRCh38–3.0.0 Genome Reference Consortium http://www.ncbi.nlm.nih.gov/projects/ genome/assembly/grc/human/ ATAC-seq data for K562 ENCODE ENCSR868FGK ChromHMM states for K562 Roadmap Epigenomics Project https://egg2.wustl.edu/roadmap/web_portal/ Hi-C chromatin loop data for K562 NCBI GEO: GSM1551620 Experimental models: Cell lines K-562 ATCC Cat#CCL-243; RRID:CVCL_0004 HEK293T ATCC Cat#CRL-3216; RRID:CVCL_0063 Oligonucleotides RUNX1 library variants Twist Bioscience https://www.twistbioscience.com Primers for qPCR, Sanger Sequencing, & oligopool amplification, see Table S10 This Paper N/A NEBNext Multiplex Oligos for Illumina New England Biolabs Cat#E7335S Recombinant DNA EF1a_mCherry_P2A_Hygro_Barcode (Parekh et al.)12 Addgene #120426 PB-TRE-dCas9-VPR (Chavez et al.)108 Addgene #63800 pHR-SFFV-KRAB-dCas9-P2A-mCherry (Gilbert et al.)109 Addgene #60954 pMD2.G N/A Addgene #12259 pCMV delta R8.2 N/A Addgene #12263 Software and algorithms Code related to analyses of RUNX1 mutations This paper https://github.com/cartercompbio/ RUNX1_SEUSS; https://doi.org/ 10.5281/zenodo.11580866 CellRanger 3.1.0 10X Genomics https://support.10xgenomics.com genotyping-matrices (Parekh et al.)12 https://github.com/yanwu2014/ genotyping-matrices MAGeCK (W. Li et al.)110 https://sourceforge.net/p/mageck/ wiki/Home/ PRISM (Baspinar et al.)60 https://cosbi.ku.edu.tr/prism/ VEST (Carter et al.)62 http://www.cravat.us/CRAVAT/ FoldX (Schymkowitz et al.)63 http://foldx.crg.es/ Seurat 4.1.0 (Macosko et al.)111 https://satijalab.org/seurat/ CoGAPS (Fertig et al.)72 http://www.bioconductor.org/packages/ release/bioc/html/CoGAPS.html EnrichR (Kuleshov et al.)112 https://github.com/wjawaid/enrichR STAR 2.7.1a (Dobin et al.)113 https://github.com/alexdobin/STAR RSEM 1.3.1 N/A http://deweylab.biostat.wisc.edu/rsem/ limma (Ritchie et al.)114 http://bioinf.wehi.edu.au/limma/ (Continued on next page) Cell Reports 43, 114436, July 23, 2024 21 ..
Article Title: Protocol for mapping the three-dimensional organization of dinoflagellate genomes.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Chemicals and recombinant proteins Nuclease-free H2O Thermo Fisher Scientific AM9916 1 M Tris-HCl pH 7.5 Thermo Fisher Scientific 15567027 1 M Tris-HCl pH 8.0 Thermo Fisher Scientific 15568025 1 M MgCl2 Thermo Fisher Scientific AM9530G 5 M NaCl Thermo Fisher Scientific AM9759 0.5 M EDTA, pH 8.0 Thermo Fisher Scientific 15575020 20% SDS Thermo Fisher Scientific AM9820 1x PBS buffer solution pH 7.4 Thermo Fisher Scientific 10010023 1x TE buffer Thermo Fisher Scientific 12090015 IGEPAL CA-630 detergent Sigma I8896-50ML Tween 20 detergent 10% Sigma 11332465001 10% Triton X-100 Sigma 93443 37% formaldehyde Sigma 252549-100ML 0.1 M NaHCO3 Sigma S6014-1KG Glycine Sigma 1005901000 MboI restriction enzyme NEB R0147 10x CutSmart buffer NEB B7204 0.4 mM biotin-14-dATP Thermo Fisher Scientific 19524-016 100 mM dCTP/dGTP/dTTP Promega U1330 DNA polymerase I large (Klenow) fragment NEB M0210 10x NEB T4 DNA ligase buffer NEB B0202 Bovine serum albumin (BSA) 100x NEB B9000 T4 DNA ligase NEB M0202 Proteinase K Promega MC5005 Dynabeads MyOne Streptavidin T1 Thermo Fisher Scientific 65602 AMPure XP beads Beckman Coulter A63881 100% EtOH Sigma 493546-1L 200-mL PCR tubes Thermo Fisher Scientific AB1182 1.5-mL DNA LoBind microcentrifuge tubes Eppendorf 022431021 (Continued on next page) 2 STAR Protocols 5, 102941, June 21, 2024 Continued REAGENT or RESOURCE SOURCE IDENTIFIER 15/50 mL tubes Critical commercial assays NEBNext Ultra II DNA Library Prep Kit for Illumina NEB E7645L NEBNext Multiplex Oligos for Illumina NEB E7600S MinElute PCR Purification Kit QIAGEN 28004/28006 Covaris milliTUBE 1 mL Covaris 520135 QuBit tubes Thermo Fisher Scientific Q32856 QuBit dsDNA HS Assay Kit Thermo Fisher Scientific Q32854 TapeStation D1000 tape Agilent 5067-5582 TapeStation D1000 reagents Agilent 5067-5583 Equipment TapeStation Agilent G2991BA Covaris E220 Covaris SKU500239 QuBit fluorometer Thermo Fisher Scientific Q33327 Tabletop centrifuge Thermomixer Eppendorf 5382000023 PCR thermocycler Magnetic rack Tube rotator Software and algorithms Juicer (version 1.6 used) Durand et al.4 https://github.com/aidenlab/juicer Juicebox (version 1.11.08 used) Durand et al.5 https://github.com/aidenlab/Juicebox 3D-DNA (version 180419 used) Dudchenko et al.6 https://github.com/aidenlab/3d-dna bwa (version 0.7.5a used) Li & Durbin7 https://github.com/lh3/bwa sra-tools (version 2.11.0 used) https://github.com/ncbi/sra-tools Deposited data Fugacium kawagutii Hi-C SRA: SRR25948349 and SRR25948348 Fugacium kawagutii draft assembly (V3) http://sampgr.org.cn/index.php/download ..
Article Title: LDB1 establishes multi-enhancer networks to regulate gene expression.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Mouse monoclonal anti-LDB1 CLIM-2 (C-9) Santa Cruz Biotechnology Cat#sc-365074; RRID: AB_10848267 Rabbit polyclonal anti-LDB1 Lot# VI3089586A Thermo Fisher Scientific Cat#PA5-56948; RRID: AB_2643320 Mouse monoclonal anti-GAPDH Lot# A1822 (6C5) Santa Cruz Biotechnology Cat#sc-32233; RRID: AB_627679 Rabbit monoclonal anti-RPB1 (Pol2) (D8L4Y) Cell Signaling Technology Cat#14958; RRID: AB_2687876 Rabbit polyclonal anti-YY1 Active Motif Cat#61779; RRID: AB_2793763 Rabbit polyclonal anti-CTCF Millipore Cat#07-729; RRID: AB_441965 Rabbit polyclonal anti-RAD21 Abcam Cat#ab992; RRID: AB_2176601 Mouse monoclonal anti-pMPM2 Millipore Cat# 05-368; RRID: AB_309698 F(ab’)2-Goat anti-Mouse IgG (H+L) Secondary Antibody, APC, eBioscience Thermo Fisher Scientific Cat#17-4010-82; RRID: AB_2573203 Chemicals, peptides, and recombinant proteins AMPure XP Beckman Coulter Cat#A63880 Indole-3-acetic acid sodium salt (auxin) Sigma Aldrich Cat#I5148 estradiol Sigma Aldrich Cat#E2758 iSCRIPT Reverse Transcription Supermix Bio Rad Cat#1708840 Power SYBR Green PCR Master Mix Thermo Fisher Scientific Cat#4367660 Protein A agarose beads Thermo Fisher Scientific Cat#15918014 Protein G agarose beads Thermo Fisher Scientific Cat#15920010 DSG crosslinker ProteoChem Cat#c1104-1gm cOmplete Mini, EDTA-free Millipore Sigma Cat#11836170001 MNase Worthington Biochemical Cat#LS004798 rSAP New England Biolabs Cat#M0371S T4 PNK New England Biolabs Cat#M0201S Large (Klenow) Fragment New England Biolabs Cat#M0210S Biotin-11-dCTP Jena Bioscience Cat#NU-809-BIOX-S Biotin-14-dATP Jena Bioscience Cat#NU-835-BIO14-S Biotin-14-dATP Active Motif Cat#14138 T4 DNA Ligase New England Biolabs Cat#M0202S T4 DNA Ligase buffer New England Biolabs Cat#B0202S Dynabeads MyOne Streptavidin C1 Thermo Fisher Scientific Cat#65001 KAPA HiFi HotStart ReadyMix Roche Cat#08202940001 Herculase II Fusion DNA Polymerase Agilent Cat#600675 Mouse Cot-1 DNA Thermo Fisher Scientific Cat#18440016 Twist Universal Blockers Twist Bioscience Cat#100578 Twist Binding and Purification Beads Twist Bioscience Cat#100983 Dynabeads M-270 Streptavidn Thermo Fisher Scientic Cat#65305 NlaIII New England Biolabs Cat#R0125L NEB Buffer 2 New England Biolabs Cat#7002S NEB Buffer 3.1 New England Biolabs Cat#B7203S DpnII New England Biolabs Cat#R0543M VAHTS DNA Clean Beads Vazyme Cat#N411 (Continued on next page) e1 Molecular Cell 85, 376–393.e1–e9, January 16, 2025 .. REAGENT or RESOURCE SOURCE IDENTIFIER T4 DNA polymerase New England Biolabs CatM0203S 4-thiouridine (4SU) MedChemExpress Cat#HY-W011793 TRIzol Reagent Invitrogen Cat#15596026 MTSEA-biotin Biotium Cat# 90064 Critical commercial assays KAPA HyperCapture Reagent Kit Roche Cat#9075810001 Twist Hybridization and Wash Kit with Amplification Mix, 12 Reactions Twist Bioscience Cat#104178 RNeasy Mini Kit QIAGEN Cat#74104 QIAshredder QIAGEN Cat#79656 NEBNext Ultra II DNA Library Prep Kit for Illumina New England Biolabs Cat#E7645S NEBNext Multiplex Oligos for Illumina (96 Unique Dual Index Primer Pairs) New England Biolabs Cat#E6440S TruSeq Stranded mRNA kit Illumina Cat#20020594 Illumina Stranded Total RNA Prep Illumina Cat# 20040525 Qubit dsDNA Quantification Assay Kits Thermo Fisher Scientific Cat#Q32850 In-Fusion HD Cloning kit Takara Cat#639648 QIAquick PCR Purification Kit QIAGEN Cat#28104 QIAquick Gel Extraction Kit QIAGEN Cat#28704 AHTS Universal DNA Library Prep Kit Vazyme Cat#ND627-01 Deposited data LDB1-AID Micro-C This paper GSE254373 LDB1-AID RCMC This paper GSE266450 LDB1-AID TT-seq This paper GSE264584 LDB1-AID Tri-C This paper GSE254372 LDB1-AID RNA-seq This paper GSE264455 SMC3-AID Hi-C Zhao et al.103 GSE228402 CTCF-AID Hi-C Zhang et al.26 GSE168251 YY1-AID Micro-C Lam et al.84 GSE247254 Mitotic Hi-C Zhang et al.38 GSE129997 Mitotic ChIP-seq (CTCF/RAD21) Zhang et al.38 GSE129997 H3K27ac ChIP-seq Dogan et al.104 GSE61349 LDB1-AID ChIP-seq This paper GSE254377 SMC3-AID ChIP-seq This paper GSE254377 Original western blot data This paper, Mendeley Data https://doi.org/10.17632/mf78pvcrkk.2 Experimental models: Cell lines G1E-ER4 Mitchell J. Weiss lab Weiss et al.82 LDB1-AID This paper N/A YY1-AID Gerd Blobel Lab Lam et al.84 SMC3-AID Haoyue Zhang Lab Zhao et al.103 CTCF-AID Gerd A. Blobel lab Zhang et al.26 Oligonucleotides See Table S2 for oligonucleotides used in this study This paper Table S2 Recombinant DNA pX458-GFP Addgene 48138 md-mCherry Gerd A. Blobel lab Zhang et al.38 OsTiR-IRES-GFP Gerd A. Blobel lab Zhang et al.38 (Continued on next page) Molecular Cell 85, 376–393.e1–e9, January 16, 2025 e2 ..
Article Title: Graft-seq precisely maps RNA modifications via site-specific chemical grafting strategy.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-7-methylguanosine (m 7 G)-Cap mAb MBL life science Cat# RN016M; RRID: AB_2921296 Goat anti-Mouse IgG HRP HuaBio Cat# HA1006; RRID: AB_2819167 Chemicals, peptides, and recombinant proteins 3 M Sodium Acetate Solution, pH 5.2 Thermo Scientific Cat# R1181 3 ′ -Desthiobiotin-GTP; DTB-GTP New England Biolabs Cat# N0761 3-azido-1-propanol Sigma-Aldrich Cat# 776130 ADP-ribosylcyclase; ADPRC Sigma-Aldrich Cat# A9106 Alexa Fluor 488 Azide Invitrogen Cat# A10266 Ammonium iron(II) sulfate hexahydrate Sigma-Aldrich Cat# 09719 ATP New England Biolabs Cat# P0756S Biotin-Azide QIYUEBIO Cat# QY-24297 Blotting membranes, Amersham TM Hybond TM -N+ GE Healthcare Cat# RPN303B Bst 2.0 DNA polymerase New England Biolabs Cat# M0537S CleanCap Reagent M6 Trilink Cat# N-7453 Copper(II) sulfate pentahydrate Sigma-Aldrich Cat# C3036 D-biotin MedChemExpress Cat# HY-B0511 Dibenzocyclooctyne-maleimide Sigma-Aldrich Cat# 760668 DL-Dithiothreitol; DTT Sigma-Aldrich Cat# V900830 DMEM/high-glucose medium HyClone Cat# SH30243.01 DMF Sigma-Aldrich Cat# D4551 DMSO Sigma-Aldrich Cat# 41639 DNase I New England Biolabs Cat# M0303 dTTP (100 mM) Thermo Scientific Cat# R0171 EDTA (0.5 M),pH 8.0 Invitrogen Cat# AM9260G Fetal Bovine Serum Gibco Cat# 10270 Fetal Bovine Serum, Sterile(irradiated) Ausbian Cat# VS500T GlutaMAX Gibco Cat# 35050061 Glycogen Invitrogen Cat# AM9510 HEPES Sigma-Aldrich Cat# V900477 HRP-streptavidin Invitrogen Cat# 434323 L-Ascorbic acid Sigma-Aldrich Cat# 95209 m 6 ATP Trilink Cat# N-1013 Maxima H Minus Reverse Transcriptase Thermo Scientific Cat# EP0751 MEM Non-Essential Amino Acids Solution (100X) Gibco Cat# 11140 mRNA decapping enzyme New England Biolabs Cat# M0608S NAD Sigma-Aldrich Cat# N6522 Non-fat Powdered milk BBI Life Sciences Cat# A600669 Nuclease P1 Wako Cat# 145-08221 Penicillin/streptomycin Gibco Cat# 15140 Penicillin-Streptomycin HyClone Cat# SV30010 Phanta Max Super-Fidelity DNA Polymerase Vazyme Cat# P505 Potassium chloride Sigma-Aldrich Cat# P9541 PrimerScript II Reverse Transcriptase Takara Cat# 6210A PrimerScript Reverse Transcriptase Takara Cat# 6110A (Continued on next page) e1 Cell Reports Methods 5, 101103, July 21, 2025 OPEN ACCESS .. REAGENT or RESOURCE SOURCE IDENTIFIER Quick CIP New England Biolabs Cat# M0525 rCutSmart buffer New England Biolabs Cat# B6004V Recombinant Mouse LIF Protein Milipore Cat# ESG1107 Reverse Transcriptase, Recombinant HIV Worthington Biochemical Corporation Cat# LS05003 RevertAid Reverse Transcriptase Thermo Scientific Cat# EP0442 RNase inhibitor Vazyme Cat# R301 RppH New England Biolabs Cat# M0356 rSAP New England Biolabs Cat# M0371S SMARTScribe Reverse Transcriptase Clontech Cat# 639536 Sodium L-ascorbate Energy Chemical Cat# E082526 Sodium pyruvate Gibco Cat# 11360 SplintR ligase New England Biolabs Cat# M0375S SuperScript II Reverse Transcriptase Invitrogen Cat# 18064071 T4 Polynucleotide Kinase; T4 PNK New England Biolabs Cat# M0201 TGIRT III Reverse Transcriptase InGex Cat# CM0101 ThermoPol Reaction Buffer New England Biolabs Cat# B90004 Tris(3-hydroxypropyltriazolylmethyl)amine Sigma-Aldrich Cat# 762342 Trizol Invitrogen Cat# 10296010 Tween 20 Sigma-Aldrich Cat# V900548 Vaccinia Capping System New England Biolabs Cat# M2080S yDcpS New England Biolabs Cat# M0463S α-L-Ascorbic acid; α-KG Sigma-Aldrich Cat# 75890 β-mercaptoethanol Gibco Cat# 21985023 Critical commercial assays GenElute mRNA Purification Miniprep Kit Sigma-Aldrich Cat# MRN10-1KT NEBNext rRNA Depletion Kit New England Biolabs Cat# E7400 HiScribe T7 High Yield RNA Synthesis Kit New England Biolabs Cat# E2040 RNA Clean & Concentrator-25 kit Zymo Research Cat# R1017 RNA Clean & Concentrator-5 kit Zymo Research Cat# R1013 RNAClean XP beads Beckman Coulter Cat# A63987 QIAquick Gel Extraction Kit QIAGEN Cat# 28704 ABclonal Zero TOPO-TA/Blunt Cloning Kit ABclonal Cat# RK30130 AMPure XP beads Beckman Coulter Cat# A63881 NEBNext Magnesium RNA Fragmentation Module New England Biolabs Cat# E6150 Dynabeads Protein A Invitrogen Cat# 10002D Dynabeads MyOne Streptavidin C1 Invitrogen Cat# 65001 NEBNext Multiplex Small RNA Library Prep Kit for Illumina New England Biolabs Cat# E7560S ChamQ Universal SYBR qPCR Master Mix Vazyme Cat# Q711-03 SuperSignal West Pico PLUS Chemiluminescent Substrate Thermo Scientific Cat# 34577 Deposited data Raw data This paper GSA-Human: HRA009209; GSA: CRA020263 Experimental models: Cell lines HEK293T ATCC Cat# ATCC-CRL-3216 HeLa ATCC Cat# ATCC-CCL-2 mouse ESC E14 Lab of Li Shen (Zhejiang University) N/A (Continued on next page) Cell Reports Methods 5, 101103, July 21, 2025 e2 OPEN ACCESS ..
Article Title: Graft-seq precisely maps RNA modifications via site-specific chemical grafting strategy
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-7-methylguanosine (m7G)-Cap mAb MBL life science Cat# RN016M; RRID: AB_2921296 Goat anti-Mouse IgG HRP HuaBio Cat# HA1006; RRID: AB_2819167 Chemicals, peptides, and recombinant proteins 3 M Sodium Acetate Solution, pH 5.2 Thermo Scientific Cat# R1181 3′-Desthiobiotin-GTP; DTB-GTP New England Biolabs Cat# N0761 3-azido-1-propanol Sigma-Aldrich Cat# 776130 ADP-ribosylcyclase; ADPRC Sigma-Aldrich Cat# A9106 Alexa Fluor 488 Azide Invitrogen Cat# A10266 Ammonium iron(II) sulfate hexahydrate Sigma-Aldrich Cat# 09719 ATP New England Biolabs Cat# P0756S Biotin-Azide QIYUEBIO Cat# QY-24297 Blotting membranes, AmershamTM HybondTM-N+ GE Healthcare Cat# RPN303B Bst 2.0 DNA polymerase New England Biolabs Cat# M0537S CleanCap Reagent M6 Trilink Cat# N-7453 Copper(II) sulfate pentahydrate Sigma-Aldrich Cat# C3036 D-biotin MedChemExpress Cat# HY-B0511 Dibenzocyclooctyne-maleimide Sigma-Aldrich Cat# 760668 DL-Dithiothreitol; DTT Sigma-Aldrich Cat# V900830 DMEM/high-glucose medium HyClone Cat# SH30243.01 DMF Sigma-Aldrich Cat# D4551 DMSO Sigma-Aldrich Cat# 41639 DNase I New England Biolabs Cat# M0303 dTTP (100 mM) Thermo Scientific Cat# R0171 EDTA (0.5 M),pH 8.0 Invitrogen Cat# AM9260G Fetal Bovine Serum Gibco Cat# 10270 Fetal Bovine Serum, Sterile(irradiated) Ausbian Cat# VS500T GlutaMAX Gibco Cat# 35050061 Glycogen Invitrogen Cat# AM9510 HEPES Sigma-Aldrich Cat# V900477 HRP-streptavidin Invitrogen Cat# 434323 L-Ascorbic acid Sigma-Aldrich Cat# 95209 m6ATP Trilink Cat# N-1013 Maxima H Minus Reverse Transcriptase Thermo Scientific Cat# EP0751 MEM Non-Essential Amino Acids Solution (100X) Gibco Cat# 11140 mRNA decapping enzyme New England Biolabs Cat# M0608S NAD Sigma-Aldrich Cat# N6522 Non-fat Powdered milk BBI Life Sciences Cat# A600669 Nuclease P1 Wako Cat# 145-08221 Penicillin/streptomycin Gibco Cat# 15140 Penicillin-Streptomycin HyClone Cat# SV30010 Phanta Max Super-Fidelity DNA Polymerase Vazyme Cat# P505 Potassium chloride Sigma-Aldrich Cat# P9541 PrimerScript II Reverse Transcriptase Takara Cat# 6210A PrimerScript Reverse Transcriptase Takara Cat# 6110A (Continued on next page) e1 Cell Reports Methods 5, 101103, July 21, 2025 Article ll OPEN ACCESS .. REAGENT or RESOURCE SOURCE IDENTIFIER Quick CIP New England Biolabs Cat# M0525 rCutSmart buffer New England Biolabs Cat# B6004V Recombinant Mouse LIF Protein Milipore Cat# ESG1107 Reverse Transcriptase, Recombinant HIV Worthington Biochemical Corporation Cat# LS05003 RevertAid Reverse Transcriptase Thermo Scientific Cat# EP0442 RNase inhibitor Vazyme Cat# R301 RppH New England Biolabs Cat# M0356 rSAP New England Biolabs Cat# M0371S SMARTScribe Reverse Transcriptase Clontech Cat# 639536 Sodium L-ascorbate Energy Chemical Cat# E082526 Sodium pyruvate Gibco Cat# 11360 SplintR ligase New England Biolabs Cat# M0375S SuperScript II Reverse Transcriptase Invitrogen Cat# 18064071 T4 Polynucleotide Kinase; T4 PNK New England Biolabs Cat# M0201 TGIRT III Reverse Transcriptase InGex Cat# CM0101 ThermoPol Reaction Buffer New England Biolabs Cat# B90004 Tris(3-hydroxypropyltriazolylmethyl)amine Sigma-Aldrich Cat# 762342 Trizol Invitrogen Cat# 10296010 Tween 20 Sigma-Aldrich Cat# V900548 Vaccinia Capping System New England Biolabs Cat# M2080S yDcpS New England Biolabs Cat# M0463S α-L-Ascorbic acid; α-KG Sigma-Aldrich Cat# 75890 β-mercaptoethanol Gibco Cat# 21985023 Critical commercial assays GenElute mRNA Purification Miniprep Kit Sigma-Aldrich Cat# MRN10-1KT NEBNext rRNA Depletion Kit New England Biolabs Cat# E7400 HiScribe T7 High Yield RNA Synthesis Kit New England Biolabs Cat# E2040 RNA Clean & Concentrator-25 kit Zymo Research Cat# R1017 RNA Clean & Concentrator-5 kit Zymo Research Cat# R1013 RNAClean XP beads Beckman Coulter Cat# A63987 QIAquick Gel Extraction Kit QIAGEN Cat# 28704 ABclonal Zero TOPO-TA/Blunt Cloning Kit ABclonal Cat# RK30130 AMPure XP beads Beckman Coulter Cat# A63881 NEBNext Magnesium RNA Fragmentation Module New England Biolabs Cat# E6150 Dynabeads Protein A Invitrogen Cat# 10002D Dynabeads MyOne Streptavidin C1 Invitrogen Cat# 65001 NEBNext Multiplex Small RNA Library Prep Kit for Illumina New England Biolabs Cat# E7560S ChamQ Universal SYBR qPCR Master Mix Vazyme Cat# Q711-03 SuperSignal West Pico PLUS Chemiluminescent Substrate Thermo Scientific Cat# 34577 Deposited data Raw data This paper GSA-Human: HRA009209; GSA: CRA020263 Experimental models: Cell lines HEK293T ATCC Cat# ATCC-CRL-3216 HeLa ATCC Cat# ATCC-CCL-2 mouse ESC E14 Lab of Li Shen (Zhejiang University) N/A (Continued on next page) Cell Reports Methods 5, 101103, July 21, 2025 e2 Article ll OPEN ACCESS ..
Article Title: MicroRNAs are involved in ovarian physiology of greater amberjack (Seriola dumerili) under captivity.
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Article Title: The primitive endoderm supports lineage plasticity to enable regulative development.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies See Table S6 for antibodies used in this study N/A N/A Chemicals, peptides, and recombinant proteins Leukemia inhibitory factor (LIF) Made in house N/A CHIR99021 (GSKb inhibitor) Axon Medchem Cat#1386 PD0325901 (PD03, MEK inhibitor) Sigma Aldrich Cat#PZ0162 Activin A Peprotech Cat#120-14E Doxycycline (Dox) Sigma Aldrich Cat#D9891 4-hydroxytamoxifen (4OHT) Sigma Aldrich Cat#H7904 BMP4 Peprotech Cat#120-05ET A83-01 Sigma-Aldrich Cat#SML0788 Y-27632 (ROCK inhibitor) Tocris Cat#1254 Retinoic acid Sigma Aldrich Cat#R2625 2-mercaptoethanol Sigma Aldrich Cat#M6250 L-glutamine Thermo Fisher Cat#25030024 B-27 Supplement (50X) Gibco Cat#17504001 B-27 Supplement (50X), minus insulin Gibco Cat#A1895601 N-2 Supplement (100X) Gibco Cat#17502048 Neurobasal Medium Gibco Cat#21103049 DMEM/F12 Medium Gibco Cat#12634010 RPMI 1640 Medium, GlutaMAX Supplement Gibco Cat#61870036 MEM non-essential amino acids (100X) Gibco Cat#11140050 Sodium pyruvate (100mM) Gibco Cat#11360070 Accutase Sigma Aldrich Cat#A6964 16% Formaldehyde Thermo Fisher Cat#PI28906 Donkey Serum Sigma Aldrich Cat#D9663 EmbryoMax KSOM Medium (1X) Sigma Aldrich Cat#MR-106 Polyvinylpyrrolidine (PVP) Sigma Aldrich Cat#P0930 Triton X-100 Sigma Aldrich Cat#T8787 Anti-mouse rabbit serum Sigma Aldrich Cat#M5774 Guinea pig complement Sigma-Aldrich Cat#234395 Acidic Tyrode’s solution Sigma Aldrich Cat#T1788 Bovine Serum Albumin Gibco Cat#15260037 Tween20 Sigma-Aldrich Cat#P1379 Anti-Adherence Rinsing Solution STEMCELL Technologies Cat#07010 M2 medium Sigma Aldrich Cat#M7167 PMSG Sigma Aldrich Cat#G4527 hCG (Chorulon) Intervet N/A Critical commercial assays RNeasy Mini Kit Qiagen Cat#74106 RNeasy Micro Kit Qiagen Cat#74004 RNase-Free DNase Set Qiagen Cat#79256 SuperScript III Reverse Transcriptase Thermo Fisher Cat#18080051 Universal ProbeLibrary Roche N/A (Continued on next page) Cell 187, 1–20.e1–e6, July 25, 2024 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER NEBNext Ultra II DNA Library Prep Kit for Illumina New England Biolabs Cat# E7645L Chromium Next GEM Single Cell 3’ Kit v3.1 10x Genomics Cat#1000269 Chromium Next GEM Chip G Single Cell Kit 10x Genomics Cat#1000127 NEBNext Ultra II Directional RNA Library Prep kit New England Biolabs Cat#E7765 NEBNext Multiplex Oligos for Illumina New England Biolabs Cat#E6440 Qubit dsDNA Quantification Assay Kits Invitrogen Cat#Q32851 Deposited data Raw and analysed data This study GEO:GSE232926 External re-analysed mouse embryo scRNA-seq dataset Nowotschin et al.53 GEO:GSE123046 External re-analysed mouse reprogramming scRNA-seq dataset Zhao et al.77 GEO:GSE114952 Experimental models: Cell lines SOX2-GFP/ GATA6-mCherry (SGGC) ESCs Redó-Riveiro et al.48 N/A OCT4-mCherry ESCs Hashmi et al.58 N/A OCT4-mCherry-H2B-Venus This study N/A Esrrb KO with tetON-Esrrb transgene (EKOiE) ESCs Festuccia et al.82 N/A E14JU ESCs (E14Tg2a 129/Ola subclone) Hamilton and Brickman117 N/A DR4 mouse embryonic fibroblasts (MEFs) Tucker et al.118 N/A Experimental models: Organisms/strains C57BL/6N Taconic RRID:MGI:2159965 Rosa26mT/mG Muzumdar et al.45 RRID:IMSR_JAX:007576 Pdgfra-CreERT2 Chung et al.44 RRID:IMSR_JAX:032770 Oligonucleotides See Table S6 for primer sequences used in this study N/A N/A Software and algorithms BD FACSDiva BD Biosciences RRID:SCR_001456 FCS Express v7 De Novo Software RRID:SCR_016431 Prism v10.1.1 GraphPad RRID:SCR_002798 R v4.3.1 R Core Team RRID:SCR_001905 Cell Ranger v6.1.12 10x Genomics RRID:SCR_017344 scVelo v0.2.5 and v0.17.1 Bergen et al.54 N/A scvi-tools Gayoso et al.74 N/A scanpy v1.8.2 and 1.9.1 Wolf et al.119 RRID:SCR_018139 Seurat v4.3.0 Hao et al.120 RRID:SCR_007322 BEDtools Quinlan and Hall121 RRID:SCR_006646 SEACR Meers et al.122 N/A DiffBind Ross-Innes et al.123 RRID:SCR_012918 deeptools Ramı́rez et al.124 RRID:SCR_016366 SAMtools Danecek et al.125 RRID:SCR_002105 IGV v2.16.2 Robinson et al.126 RRID:SCR_011793 pyGenomeTracks Lopez-Delisle et al.127 N/A HOMER Heinz et al.128 RRID:SCR_010881 DESeq2 v1.40.2 Love et al.129 RRID:SCR_015687 FIJI (ImageJ) v2.14.0 Schindelin et al.130 RRID: SCR_002285 CellProfiler v4.2.5 Stirling et al.131 RRID:SCR_007358 Imaris v9.9.1 Oxford Instruments RRID:SCR_007370 (Continued on next page) ll e2 Cell 187, 1–20.e1–e6, July 25, 2024 Please cite this article in press as: Linneberg-Agerholm et al., The primitive endoderm supports lineage plasticity to enable regulative development, Cell (2024), https://doi.org/10.1016/j.cell.2024.05.051 Article ..
Recombinant:Article Title: Interface-guided phenotyping of coding variants in the transcription factor RUNX1.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies RUNX1 Antibody (A-2), mouse monoclonal Santa Cruz Biotechnologies Cat#sc-365644; RRID:AB_10843207 Anti-b-Actin Antibody (AC-15), mouse monoclonal Millipore Sigma Cat#A1978; RRID:AB_476692 Anti-Mouse IgG, HRP-linked Antibody Cell Signaling Technology Cat#7076P2; RRID:AB_330924 IRDye 680RD Goat anti-Mouse IgG Secondary Antibody Li-Cor Bio Cat#926–68070; RRID:AB_10956588 Bacterial and virus strains Stbl3 Thermo Fisher Cat#C737303 Chemicals, peptides, and recombinant proteins NheI-HF New England Biolabs Cat#R3131S SalI-HF New England Biolabs Cat#R3138S AflII New England Biolabs Cat#R0520S Gibson Assembly Master Mix New England Biolabs Cat#E2611S KAPA HiFi HotStart ReadyMix Roche Cat#KK2601 OneTaq 2X Master Mix New England Biolabs Cat#M0482S AMPure XP Beads Beckman Coulter Cat#A63880 DMEM ThermoFisher Scientific Cat#10566016 .05% Trypsin-EDTA Gibco Cat#25300062 OptiMEM ThermoFisher Scientific Cat#31985062 RPMI Medium 1640 Gibco Cat#11875-093 FBS Gibco Cat#A52568 Anti-anti Gibco Cat#15240-062 Lipofectamine 2000 ThermoFisher Scientific Cat#11668030 Doxycycline hyclate Sigma Cat#D5207 Hygromycin Invitrogen Cat#10687010 Puromycin Gibco Cat#A11138-03 Polybrene Millipore-Sigma Cat#TR-1003-G PBS, pH 7.4 Gibco Cat#10010023 Tn5 Illumina Cat#20034198 RIPA Buffer Cell Signaling Technologies Cat#9806 Pierce Protease Inhibitor Tablets ThermoFisher Scientific Cat#A32963 4X Laemmli Sample Buffer Bio-Rad Cat#1610747 4-20% Mini-PROTEAN TGX gel Bio-Rad Cat#4561094 10X Tris/Glycine/SDS Buffer Bio-Rad Cat#1610732 Nonfat Dry Milk Apex Bioresearch Cat#20-241 TBST Cell Signaling Technology Cat#9997 BSA, Fraction V, Fatty Acid-Free Millipore Sigma Cat#126575 SuperSignal West Pico Plus Chemiluminescent Substrate ThermoFisher Scientific Cat#34577 Carbenicillin Teknova Cat#C2199 iTaq Universal SYBR Green Master Mix Bio-Rad Cat#1725120 Critical commercial assays Pierce BCA Protein Assay kit ThermoFisher Scientific Cat#23227 RNeasy Mini Kit Qiagen Cat#74104 DNeasy Blood and Tissue Kit Qiagen Cat#69504 (Continued on next page) 20 Cell Reports 43, 114436, July 23, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER Protoscript II First Strand cDNA Synthesis Kit New England BioLabs CatE6560S QIAquick PCR Purification Kit Qiagen Cat#28104 Nucleofector Solution Set SF Lonza Cat#PBC2-00675 Chromium Single Cell 30 v3 10X Genomics Cat# PN- 1000128 NEBNext Ultra RNA Library Prep Kit New England Biolabs Cat#E7530 Deposited data Raw data: scRNA-seq This paper SRA: PRJNA1033389 Raw data: bulk RNA-seq This paper SRA: PRJNA1121326 Raw data: ATAC-seq This paper SRA: PRJNA1121327 RUNX1-CBFB-DNA structures Protein DataBank PDB: 1ljm, 1e50, 1h9d Human reference genome NCBI build 38, GRCh38–3.0.0 Genome Reference Consortium http://www.ncbi.nlm.nih.gov/projects/ genome/assembly/grc/human/ ATAC-seq data for K562 ENCODE ENCSR868FGK ChromHMM states for K562 Roadmap Epigenomics Project https://egg2.wustl.edu/roadmap/web_portal/ Hi-C chromatin loop data for K562 NCBI GEO: GSM1551620 Experimental models: Cell lines K-562 ATCC Cat#CCL-243; RRID:CVCL_0004 HEK293T ATCC Cat#CRL-3216; RRID:CVCL_0063 Oligonucleotides RUNX1 library variants Twist Bioscience https://www.twistbioscience.com Primers for qPCR, Sanger Sequencing, & oligopool amplification, see Table S10 This Paper N/A NEBNext Multiplex Oligos for Illumina New England Biolabs Cat#E7335S Recombinant DNA EF1a_mCherry_P2A_Hygro_Barcode (Parekh et al.)12 Addgene #120426 PB-TRE-dCas9-VPR (Chavez et al.)108 Addgene #63800 pHR-SFFV-KRAB-dCas9-P2A-mCherry (Gilbert et al.)109 Addgene #60954 pMD2.G N/A Addgene #12259 pCMV delta R8.2 N/A Addgene #12263 Software and algorithms Code related to analyses of RUNX1 mutations This paper https://github.com/cartercompbio/ RUNX1_SEUSS; https://doi.org/ 10.5281/zenodo.11580866 CellRanger 3.1.0 10X Genomics https://support.10xgenomics.com genotyping-matrices (Parekh et al.)12 https://github.com/yanwu2014/ genotyping-matrices MAGeCK (W. Li et al.)110 https://sourceforge.net/p/mageck/ wiki/Home/ PRISM (Baspinar et al.)60 https://cosbi.ku.edu.tr/prism/ VEST (Carter et al.)62 http://www.cravat.us/CRAVAT/ FoldX (Schymkowitz et al.)63 http://foldx.crg.es/ Seurat 4.1.0 (Macosko et al.)111 https://satijalab.org/seurat/ CoGAPS (Fertig et al.)72 http://www.bioconductor.org/packages/ release/bioc/html/CoGAPS.html EnrichR (Kuleshov et al.)112 https://github.com/wjawaid/enrichR STAR 2.7.1a (Dobin et al.)113 https://github.com/alexdobin/STAR RSEM 1.3.1 N/A http://deweylab.biostat.wisc.edu/rsem/ limma (Ritchie et al.)114 http://bioinf.wehi.edu.au/limma/ (Continued on next page) Cell Reports 43, 114436, July 23, 2024 21 ..
Article Title: Protocol for mapping the three-dimensional organization of dinoflagellate genomes.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Chemicals and recombinant proteins Nuclease-free H2O Thermo Fisher Scientific AM9916 1 M Tris-HCl pH 7.5 Thermo Fisher Scientific 15567027 1 M Tris-HCl pH 8.0 Thermo Fisher Scientific 15568025 1 M MgCl2 Thermo Fisher Scientific AM9530G 5 M NaCl Thermo Fisher Scientific AM9759 0.5 M EDTA, pH 8.0 Thermo Fisher Scientific 15575020 20% SDS Thermo Fisher Scientific AM9820 1x PBS buffer solution pH 7.4 Thermo Fisher Scientific 10010023 1x TE buffer Thermo Fisher Scientific 12090015 IGEPAL CA-630 detergent Sigma I8896-50ML Tween 20 detergent 10% Sigma 11332465001 10% Triton X-100 Sigma 93443 37% formaldehyde Sigma 252549-100ML 0.1 M NaHCO3 Sigma S6014-1KG Glycine Sigma 1005901000 MboI restriction enzyme NEB R0147 10x CutSmart buffer NEB B7204 0.4 mM biotin-14-dATP Thermo Fisher Scientific 19524-016 100 mM dCTP/dGTP/dTTP Promega U1330 DNA polymerase I large (Klenow) fragment NEB M0210 10x NEB T4 DNA ligase buffer NEB B0202 Bovine serum albumin (BSA) 100x NEB B9000 T4 DNA ligase NEB M0202 Proteinase K Promega MC5005 Dynabeads MyOne Streptavidin T1 Thermo Fisher Scientific 65602 AMPure XP beads Beckman Coulter A63881 100% EtOH Sigma 493546-1L 200-mL PCR tubes Thermo Fisher Scientific AB1182 1.5-mL DNA LoBind microcentrifuge tubes Eppendorf 022431021 (Continued on next page) 2 STAR Protocols 5, 102941, June 21, 2024 Continued REAGENT or RESOURCE SOURCE IDENTIFIER 15/50 mL tubes Critical commercial assays NEBNext Ultra II DNA Library Prep Kit for Illumina NEB E7645L NEBNext Multiplex Oligos for Illumina NEB E7600S MinElute PCR Purification Kit QIAGEN 28004/28006 Covaris milliTUBE 1 mL Covaris 520135 QuBit tubes Thermo Fisher Scientific Q32856 QuBit dsDNA HS Assay Kit Thermo Fisher Scientific Q32854 TapeStation D1000 tape Agilent 5067-5582 TapeStation D1000 reagents Agilent 5067-5583 Equipment TapeStation Agilent G2991BA Covaris E220 Covaris SKU500239 QuBit fluorometer Thermo Fisher Scientific Q33327 Tabletop centrifuge Thermomixer Eppendorf 5382000023 PCR thermocycler Magnetic rack Tube rotator Software and algorithms Juicer (version 1.6 used) Durand et al.4 https://github.com/aidenlab/juicer Juicebox (version 1.11.08 used) Durand et al.5 https://github.com/aidenlab/Juicebox 3D-DNA (version 180419 used) Dudchenko et al.6 https://github.com/aidenlab/3d-dna bwa (version 0.7.5a used) Li & Durbin7 https://github.com/lh3/bwa sra-tools (version 2.11.0 used) https://github.com/ncbi/sra-tools Deposited data Fugacium kawagutii Hi-C SRA: SRR25948349 and SRR25948348 Fugacium kawagutii draft assembly (V3) http://sampgr.org.cn/index.php/download ..
Article Title: LDB1 establishes multi-enhancer networks to regulate gene expression.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Mouse monoclonal anti-LDB1 CLIM-2 (C-9) Santa Cruz Biotechnology Cat#sc-365074; RRID: AB_10848267 Rabbit polyclonal anti-LDB1 Lot# VI3089586A Thermo Fisher Scientific Cat#PA5-56948; RRID: AB_2643320 Mouse monoclonal anti-GAPDH Lot# A1822 (6C5) Santa Cruz Biotechnology Cat#sc-32233; RRID: AB_627679 Rabbit monoclonal anti-RPB1 (Pol2) (D8L4Y) Cell Signaling Technology Cat#14958; RRID: AB_2687876 Rabbit polyclonal anti-YY1 Active Motif Cat#61779; RRID: AB_2793763 Rabbit polyclonal anti-CTCF Millipore Cat#07-729; RRID: AB_441965 Rabbit polyclonal anti-RAD21 Abcam Cat#ab992; RRID: AB_2176601 Mouse monoclonal anti-pMPM2 Millipore Cat# 05-368; RRID: AB_309698 F(ab’)2-Goat anti-Mouse IgG (H+L) Secondary Antibody, APC, eBioscience Thermo Fisher Scientific Cat#17-4010-82; RRID: AB_2573203 Chemicals, peptides, and recombinant proteins AMPure XP Beckman Coulter Cat#A63880 Indole-3-acetic acid sodium salt (auxin) Sigma Aldrich Cat#I5148 estradiol Sigma Aldrich Cat#E2758 iSCRIPT Reverse Transcription Supermix Bio Rad Cat#1708840 Power SYBR Green PCR Master Mix Thermo Fisher Scientific Cat#4367660 Protein A agarose beads Thermo Fisher Scientific Cat#15918014 Protein G agarose beads Thermo Fisher Scientific Cat#15920010 DSG crosslinker ProteoChem Cat#c1104-1gm cOmplete Mini, EDTA-free Millipore Sigma Cat#11836170001 MNase Worthington Biochemical Cat#LS004798 rSAP New England Biolabs Cat#M0371S T4 PNK New England Biolabs Cat#M0201S Large (Klenow) Fragment New England Biolabs Cat#M0210S Biotin-11-dCTP Jena Bioscience Cat#NU-809-BIOX-S Biotin-14-dATP Jena Bioscience Cat#NU-835-BIO14-S Biotin-14-dATP Active Motif Cat#14138 T4 DNA Ligase New England Biolabs Cat#M0202S T4 DNA Ligase buffer New England Biolabs Cat#B0202S Dynabeads MyOne Streptavidin C1 Thermo Fisher Scientific Cat#65001 KAPA HiFi HotStart ReadyMix Roche Cat#08202940001 Herculase II Fusion DNA Polymerase Agilent Cat#600675 Mouse Cot-1 DNA Thermo Fisher Scientific Cat#18440016 Twist Universal Blockers Twist Bioscience Cat#100578 Twist Binding and Purification Beads Twist Bioscience Cat#100983 Dynabeads M-270 Streptavidn Thermo Fisher Scientic Cat#65305 NlaIII New England Biolabs Cat#R0125L NEB Buffer 2 New England Biolabs Cat#7002S NEB Buffer 3.1 New England Biolabs Cat#B7203S DpnII New England Biolabs Cat#R0543M VAHTS DNA Clean Beads Vazyme Cat#N411 (Continued on next page) e1 Molecular Cell 85, 376–393.e1–e9, January 16, 2025 .. REAGENT or RESOURCE SOURCE IDENTIFIER T4 DNA polymerase New England Biolabs CatM0203S 4-thiouridine (4SU) MedChemExpress Cat#HY-W011793 TRIzol Reagent Invitrogen Cat#15596026 MTSEA-biotin Biotium Cat# 90064 Critical commercial assays KAPA HyperCapture Reagent Kit Roche Cat#9075810001 Twist Hybridization and Wash Kit with Amplification Mix, 12 Reactions Twist Bioscience Cat#104178 RNeasy Mini Kit QIAGEN Cat#74104 QIAshredder QIAGEN Cat#79656 NEBNext Ultra II DNA Library Prep Kit for Illumina New England Biolabs Cat#E7645S NEBNext Multiplex Oligos for Illumina (96 Unique Dual Index Primer Pairs) New England Biolabs Cat#E6440S TruSeq Stranded mRNA kit Illumina Cat#20020594 Illumina Stranded Total RNA Prep Illumina Cat# 20040525 Qubit dsDNA Quantification Assay Kits Thermo Fisher Scientific Cat#Q32850 In-Fusion HD Cloning kit Takara Cat#639648 QIAquick PCR Purification Kit QIAGEN Cat#28104 QIAquick Gel Extraction Kit QIAGEN Cat#28704 AHTS Universal DNA Library Prep Kit Vazyme Cat#ND627-01 Deposited data LDB1-AID Micro-C This paper GSE254373 LDB1-AID RCMC This paper GSE266450 LDB1-AID TT-seq This paper GSE264584 LDB1-AID Tri-C This paper GSE254372 LDB1-AID RNA-seq This paper GSE264455 SMC3-AID Hi-C Zhao et al.103 GSE228402 CTCF-AID Hi-C Zhang et al.26 GSE168251 YY1-AID Micro-C Lam et al.84 GSE247254 Mitotic Hi-C Zhang et al.38 GSE129997 Mitotic ChIP-seq (CTCF/RAD21) Zhang et al.38 GSE129997 H3K27ac ChIP-seq Dogan et al.104 GSE61349 LDB1-AID ChIP-seq This paper GSE254377 SMC3-AID ChIP-seq This paper GSE254377 Original western blot data This paper, Mendeley Data https://doi.org/10.17632/mf78pvcrkk.2 Experimental models: Cell lines G1E-ER4 Mitchell J. Weiss lab Weiss et al.82 LDB1-AID This paper N/A YY1-AID Gerd Blobel Lab Lam et al.84 SMC3-AID Haoyue Zhang Lab Zhao et al.103 CTCF-AID Gerd A. Blobel lab Zhang et al.26 Oligonucleotides See Table S2 for oligonucleotides used in this study This paper Table S2 Recombinant DNA pX458-GFP Addgene 48138 md-mCherry Gerd A. Blobel lab Zhang et al.38 OsTiR-IRES-GFP Gerd A. Blobel lab Zhang et al.38 (Continued on next page) Molecular Cell 85, 376–393.e1–e9, January 16, 2025 e2 ..
Article Title: Graft-seq precisely maps RNA modifications via site-specific chemical grafting strategy.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-7-methylguanosine (m 7 G)-Cap mAb MBL life science Cat# RN016M; RRID: AB_2921296 Goat anti-Mouse IgG HRP HuaBio Cat# HA1006; RRID: AB_2819167 Chemicals, peptides, and recombinant proteins 3 M Sodium Acetate Solution, pH 5.2 Thermo Scientific Cat# R1181 3 ′ -Desthiobiotin-GTP; DTB-GTP New England Biolabs Cat# N0761 3-azido-1-propanol Sigma-Aldrich Cat# 776130 ADP-ribosylcyclase; ADPRC Sigma-Aldrich Cat# A9106 Alexa Fluor 488 Azide Invitrogen Cat# A10266 Ammonium iron(II) sulfate hexahydrate Sigma-Aldrich Cat# 09719 ATP New England Biolabs Cat# P0756S Biotin-Azide QIYUEBIO Cat# QY-24297 Blotting membranes, Amersham TM Hybond TM -N+ GE Healthcare Cat# RPN303B Bst 2.0 DNA polymerase New England Biolabs Cat# M0537S CleanCap Reagent M6 Trilink Cat# N-7453 Copper(II) sulfate pentahydrate Sigma-Aldrich Cat# C3036 D-biotin MedChemExpress Cat# HY-B0511 Dibenzocyclooctyne-maleimide Sigma-Aldrich Cat# 760668 DL-Dithiothreitol; DTT Sigma-Aldrich Cat# V900830 DMEM/high-glucose medium HyClone Cat# SH30243.01 DMF Sigma-Aldrich Cat# D4551 DMSO Sigma-Aldrich Cat# 41639 DNase I New England Biolabs Cat# M0303 dTTP (100 mM) Thermo Scientific Cat# R0171 EDTA (0.5 M),pH 8.0 Invitrogen Cat# AM9260G Fetal Bovine Serum Gibco Cat# 10270 Fetal Bovine Serum, Sterile(irradiated) Ausbian Cat# VS500T GlutaMAX Gibco Cat# 35050061 Glycogen Invitrogen Cat# AM9510 HEPES Sigma-Aldrich Cat# V900477 HRP-streptavidin Invitrogen Cat# 434323 L-Ascorbic acid Sigma-Aldrich Cat# 95209 m 6 ATP Trilink Cat# N-1013 Maxima H Minus Reverse Transcriptase Thermo Scientific Cat# EP0751 MEM Non-Essential Amino Acids Solution (100X) Gibco Cat# 11140 mRNA decapping enzyme New England Biolabs Cat# M0608S NAD Sigma-Aldrich Cat# N6522 Non-fat Powdered milk BBI Life Sciences Cat# A600669 Nuclease P1 Wako Cat# 145-08221 Penicillin/streptomycin Gibco Cat# 15140 Penicillin-Streptomycin HyClone Cat# SV30010 Phanta Max Super-Fidelity DNA Polymerase Vazyme Cat# P505 Potassium chloride Sigma-Aldrich Cat# P9541 PrimerScript II Reverse Transcriptase Takara Cat# 6210A PrimerScript Reverse Transcriptase Takara Cat# 6110A (Continued on next page) e1 Cell Reports Methods 5, 101103, July 21, 2025 OPEN ACCESS .. REAGENT or RESOURCE SOURCE IDENTIFIER Quick CIP New England Biolabs Cat# M0525 rCutSmart buffer New England Biolabs Cat# B6004V Recombinant Mouse LIF Protein Milipore Cat# ESG1107 Reverse Transcriptase, Recombinant HIV Worthington Biochemical Corporation Cat# LS05003 RevertAid Reverse Transcriptase Thermo Scientific Cat# EP0442 RNase inhibitor Vazyme Cat# R301 RppH New England Biolabs Cat# M0356 rSAP New England Biolabs Cat# M0371S SMARTScribe Reverse Transcriptase Clontech Cat# 639536 Sodium L-ascorbate Energy Chemical Cat# E082526 Sodium pyruvate Gibco Cat# 11360 SplintR ligase New England Biolabs Cat# M0375S SuperScript II Reverse Transcriptase Invitrogen Cat# 18064071 T4 Polynucleotide Kinase; T4 PNK New England Biolabs Cat# M0201 TGIRT III Reverse Transcriptase InGex Cat# CM0101 ThermoPol Reaction Buffer New England Biolabs Cat# B90004 Tris(3-hydroxypropyltriazolylmethyl)amine Sigma-Aldrich Cat# 762342 Trizol Invitrogen Cat# 10296010 Tween 20 Sigma-Aldrich Cat# V900548 Vaccinia Capping System New England Biolabs Cat# M2080S yDcpS New England Biolabs Cat# M0463S α-L-Ascorbic acid; α-KG Sigma-Aldrich Cat# 75890 β-mercaptoethanol Gibco Cat# 21985023 Critical commercial assays GenElute mRNA Purification Miniprep Kit Sigma-Aldrich Cat# MRN10-1KT NEBNext rRNA Depletion Kit New England Biolabs Cat# E7400 HiScribe T7 High Yield RNA Synthesis Kit New England Biolabs Cat# E2040 RNA Clean & Concentrator-25 kit Zymo Research Cat# R1017 RNA Clean & Concentrator-5 kit Zymo Research Cat# R1013 RNAClean XP beads Beckman Coulter Cat# A63987 QIAquick Gel Extraction Kit QIAGEN Cat# 28704 ABclonal Zero TOPO-TA/Blunt Cloning Kit ABclonal Cat# RK30130 AMPure XP beads Beckman Coulter Cat# A63881 NEBNext Magnesium RNA Fragmentation Module New England Biolabs Cat# E6150 Dynabeads Protein A Invitrogen Cat# 10002D Dynabeads MyOne Streptavidin C1 Invitrogen Cat# 65001 NEBNext Multiplex Small RNA Library Prep Kit for Illumina New England Biolabs Cat# E7560S ChamQ Universal SYBR qPCR Master Mix Vazyme Cat# Q711-03 SuperSignal West Pico PLUS Chemiluminescent Substrate Thermo Scientific Cat# 34577 Deposited data Raw data This paper GSA-Human: HRA009209; GSA: CRA020263 Experimental models: Cell lines HEK293T ATCC Cat# ATCC-CRL-3216 HeLa ATCC Cat# ATCC-CCL-2 mouse ESC E14 Lab of Li Shen (Zhejiang University) N/A (Continued on next page) Cell Reports Methods 5, 101103, July 21, 2025 e2 OPEN ACCESS ..
Article Title: Graft-seq precisely maps RNA modifications via site-specific chemical grafting strategy
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-7-methylguanosine (m7G)-Cap mAb MBL life science Cat# RN016M; RRID: AB_2921296 Goat anti-Mouse IgG HRP HuaBio Cat# HA1006; RRID: AB_2819167 Chemicals, peptides, and recombinant proteins 3 M Sodium Acetate Solution, pH 5.2 Thermo Scientific Cat# R1181 3′-Desthiobiotin-GTP; DTB-GTP New England Biolabs Cat# N0761 3-azido-1-propanol Sigma-Aldrich Cat# 776130 ADP-ribosylcyclase; ADPRC Sigma-Aldrich Cat# A9106 Alexa Fluor 488 Azide Invitrogen Cat# A10266 Ammonium iron(II) sulfate hexahydrate Sigma-Aldrich Cat# 09719 ATP New England Biolabs Cat# P0756S Biotin-Azide QIYUEBIO Cat# QY-24297 Blotting membranes, AmershamTM HybondTM-N+ GE Healthcare Cat# RPN303B Bst 2.0 DNA polymerase New England Biolabs Cat# M0537S CleanCap Reagent M6 Trilink Cat# N-7453 Copper(II) sulfate pentahydrate Sigma-Aldrich Cat# C3036 D-biotin MedChemExpress Cat# HY-B0511 Dibenzocyclooctyne-maleimide Sigma-Aldrich Cat# 760668 DL-Dithiothreitol; DTT Sigma-Aldrich Cat# V900830 DMEM/high-glucose medium HyClone Cat# SH30243.01 DMF Sigma-Aldrich Cat# D4551 DMSO Sigma-Aldrich Cat# 41639 DNase I New England Biolabs Cat# M0303 dTTP (100 mM) Thermo Scientific Cat# R0171 EDTA (0.5 M),pH 8.0 Invitrogen Cat# AM9260G Fetal Bovine Serum Gibco Cat# 10270 Fetal Bovine Serum, Sterile(irradiated) Ausbian Cat# VS500T GlutaMAX Gibco Cat# 35050061 Glycogen Invitrogen Cat# AM9510 HEPES Sigma-Aldrich Cat# V900477 HRP-streptavidin Invitrogen Cat# 434323 L-Ascorbic acid Sigma-Aldrich Cat# 95209 m6ATP Trilink Cat# N-1013 Maxima H Minus Reverse Transcriptase Thermo Scientific Cat# EP0751 MEM Non-Essential Amino Acids Solution (100X) Gibco Cat# 11140 mRNA decapping enzyme New England Biolabs Cat# M0608S NAD Sigma-Aldrich Cat# N6522 Non-fat Powdered milk BBI Life Sciences Cat# A600669 Nuclease P1 Wako Cat# 145-08221 Penicillin/streptomycin Gibco Cat# 15140 Penicillin-Streptomycin HyClone Cat# SV30010 Phanta Max Super-Fidelity DNA Polymerase Vazyme Cat# P505 Potassium chloride Sigma-Aldrich Cat# P9541 PrimerScript II Reverse Transcriptase Takara Cat# 6210A PrimerScript Reverse Transcriptase Takara Cat# 6110A (Continued on next page) e1 Cell Reports Methods 5, 101103, July 21, 2025 Article ll OPEN ACCESS .. REAGENT or RESOURCE SOURCE IDENTIFIER Quick CIP New England Biolabs Cat# M0525 rCutSmart buffer New England Biolabs Cat# B6004V Recombinant Mouse LIF Protein Milipore Cat# ESG1107 Reverse Transcriptase, Recombinant HIV Worthington Biochemical Corporation Cat# LS05003 RevertAid Reverse Transcriptase Thermo Scientific Cat# EP0442 RNase inhibitor Vazyme Cat# R301 RppH New England Biolabs Cat# M0356 rSAP New England Biolabs Cat# M0371S SMARTScribe Reverse Transcriptase Clontech Cat# 639536 Sodium L-ascorbate Energy Chemical Cat# E082526 Sodium pyruvate Gibco Cat# 11360 SplintR ligase New England Biolabs Cat# M0375S SuperScript II Reverse Transcriptase Invitrogen Cat# 18064071 T4 Polynucleotide Kinase; T4 PNK New England Biolabs Cat# M0201 TGIRT III Reverse Transcriptase InGex Cat# CM0101 ThermoPol Reaction Buffer New England Biolabs Cat# B90004 Tris(3-hydroxypropyltriazolylmethyl)amine Sigma-Aldrich Cat# 762342 Trizol Invitrogen Cat# 10296010 Tween 20 Sigma-Aldrich Cat# V900548 Vaccinia Capping System New England Biolabs Cat# M2080S yDcpS New England Biolabs Cat# M0463S α-L-Ascorbic acid; α-KG Sigma-Aldrich Cat# 75890 β-mercaptoethanol Gibco Cat# 21985023 Critical commercial assays GenElute mRNA Purification Miniprep Kit Sigma-Aldrich Cat# MRN10-1KT NEBNext rRNA Depletion Kit New England Biolabs Cat# E7400 HiScribe T7 High Yield RNA Synthesis Kit New England Biolabs Cat# E2040 RNA Clean & Concentrator-25 kit Zymo Research Cat# R1017 RNA Clean & Concentrator-5 kit Zymo Research Cat# R1013 RNAClean XP beads Beckman Coulter Cat# A63987 QIAquick Gel Extraction Kit QIAGEN Cat# 28704 ABclonal Zero TOPO-TA/Blunt Cloning Kit ABclonal Cat# RK30130 AMPure XP beads Beckman Coulter Cat# A63881 NEBNext Magnesium RNA Fragmentation Module New England Biolabs Cat# E6150 Dynabeads Protein A Invitrogen Cat# 10002D Dynabeads MyOne Streptavidin C1 Invitrogen Cat# 65001 NEBNext Multiplex Small RNA Library Prep Kit for Illumina New England Biolabs Cat# E7560S ChamQ Universal SYBR qPCR Master Mix Vazyme Cat# Q711-03 SuperSignal West Pico PLUS Chemiluminescent Substrate Thermo Scientific Cat# 34577 Deposited data Raw data This paper GSA-Human: HRA009209; GSA: CRA020263 Experimental models: Cell lines HEK293T ATCC Cat# ATCC-CRL-3216 HeLa ATCC Cat# ATCC-CCL-2 mouse ESC E14 Lab of Li Shen (Zhejiang University) N/A (Continued on next page) Cell Reports Methods 5, 101103, July 21, 2025 e2 Article ll OPEN ACCESS ..
Software:Article Title: Interface-guided phenotyping of coding variants in the transcription factor RUNX1.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies RUNX1 Antibody (A-2), mouse monoclonal Santa Cruz Biotechnologies Cat#sc-365644; RRID:AB_10843207 Anti-b-Actin Antibody (AC-15), mouse monoclonal Millipore Sigma Cat#A1978; RRID:AB_476692 Anti-Mouse IgG, HRP-linked Antibody Cell Signaling Technology Cat#7076P2; RRID:AB_330924 IRDye 680RD Goat anti-Mouse IgG Secondary Antibody Li-Cor Bio Cat#926–68070; RRID:AB_10956588 Bacterial and virus strains Stbl3 Thermo Fisher Cat#C737303 Chemicals, peptides, and recombinant proteins NheI-HF New England Biolabs Cat#R3131S SalI-HF New England Biolabs Cat#R3138S AflII New England Biolabs Cat#R0520S Gibson Assembly Master Mix New England Biolabs Cat#E2611S KAPA HiFi HotStart ReadyMix Roche Cat#KK2601 OneTaq 2X Master Mix New England Biolabs Cat#M0482S AMPure XP Beads Beckman Coulter Cat#A63880 DMEM ThermoFisher Scientific Cat#10566016 .05% Trypsin-EDTA Gibco Cat#25300062 OptiMEM ThermoFisher Scientific Cat#31985062 RPMI Medium 1640 Gibco Cat#11875-093 FBS Gibco Cat#A52568 Anti-anti Gibco Cat#15240-062 Lipofectamine 2000 ThermoFisher Scientific Cat#11668030 Doxycycline hyclate Sigma Cat#D5207 Hygromycin Invitrogen Cat#10687010 Puromycin Gibco Cat#A11138-03 Polybrene Millipore-Sigma Cat#TR-1003-G PBS, pH 7.4 Gibco Cat#10010023 Tn5 Illumina Cat#20034198 RIPA Buffer Cell Signaling Technologies Cat#9806 Pierce Protease Inhibitor Tablets ThermoFisher Scientific Cat#A32963 4X Laemmli Sample Buffer Bio-Rad Cat#1610747 4-20% Mini-PROTEAN TGX gel Bio-Rad Cat#4561094 10X Tris/Glycine/SDS Buffer Bio-Rad Cat#1610732 Nonfat Dry Milk Apex Bioresearch Cat#20-241 TBST Cell Signaling Technology Cat#9997 BSA, Fraction V, Fatty Acid-Free Millipore Sigma Cat#126575 SuperSignal West Pico Plus Chemiluminescent Substrate ThermoFisher Scientific Cat#34577 Carbenicillin Teknova Cat#C2199 iTaq Universal SYBR Green Master Mix Bio-Rad Cat#1725120 Critical commercial assays Pierce BCA Protein Assay kit ThermoFisher Scientific Cat#23227 RNeasy Mini Kit Qiagen Cat#74104 DNeasy Blood and Tissue Kit Qiagen Cat#69504 (Continued on next page) 20 Cell Reports 43, 114436, July 23, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER Protoscript II First Strand cDNA Synthesis Kit New England BioLabs CatE6560S QIAquick PCR Purification Kit Qiagen Cat#28104 Nucleofector Solution Set SF Lonza Cat#PBC2-00675 Chromium Single Cell 30 v3 10X Genomics Cat# PN- 1000128 NEBNext Ultra RNA Library Prep Kit New England Biolabs Cat#E7530 Deposited data Raw data: scRNA-seq This paper SRA: PRJNA1033389 Raw data: bulk RNA-seq This paper SRA: PRJNA1121326 Raw data: ATAC-seq This paper SRA: PRJNA1121327 RUNX1-CBFB-DNA structures Protein DataBank PDB: 1ljm, 1e50, 1h9d Human reference genome NCBI build 38, GRCh38–3.0.0 Genome Reference Consortium http://www.ncbi.nlm.nih.gov/projects/ genome/assembly/grc/human/ ATAC-seq data for K562 ENCODE ENCSR868FGK ChromHMM states for K562 Roadmap Epigenomics Project https://egg2.wustl.edu/roadmap/web_portal/ Hi-C chromatin loop data for K562 NCBI GEO: GSM1551620 Experimental models: Cell lines K-562 ATCC Cat#CCL-243; RRID:CVCL_0004 HEK293T ATCC Cat#CRL-3216; RRID:CVCL_0063 Oligonucleotides RUNX1 library variants Twist Bioscience https://www.twistbioscience.com Primers for qPCR, Sanger Sequencing, & oligopool amplification, see Table S10 This Paper N/A NEBNext Multiplex Oligos for Illumina New England Biolabs Cat#E7335S Recombinant DNA EF1a_mCherry_P2A_Hygro_Barcode (Parekh et al.)12 Addgene #120426 PB-TRE-dCas9-VPR (Chavez et al.)108 Addgene #63800 pHR-SFFV-KRAB-dCas9-P2A-mCherry (Gilbert et al.)109 Addgene #60954 pMD2.G N/A Addgene #12259 pCMV delta R8.2 N/A Addgene #12263 Software and algorithms Code related to analyses of RUNX1 mutations This paper https://github.com/cartercompbio/ RUNX1_SEUSS; https://doi.org/ 10.5281/zenodo.11580866 CellRanger 3.1.0 10X Genomics https://support.10xgenomics.com genotyping-matrices (Parekh et al.)12 https://github.com/yanwu2014/ genotyping-matrices MAGeCK (W. Li et al.)110 https://sourceforge.net/p/mageck/ wiki/Home/ PRISM (Baspinar et al.)60 https://cosbi.ku.edu.tr/prism/ VEST (Carter et al.)62 http://www.cravat.us/CRAVAT/ FoldX (Schymkowitz et al.)63 http://foldx.crg.es/ Seurat 4.1.0 (Macosko et al.)111 https://satijalab.org/seurat/ CoGAPS (Fertig et al.)72 http://www.bioconductor.org/packages/ release/bioc/html/CoGAPS.html EnrichR (Kuleshov et al.)112 https://github.com/wjawaid/enrichR STAR 2.7.1a (Dobin et al.)113 https://github.com/alexdobin/STAR RSEM 1.3.1 N/A http://deweylab.biostat.wisc.edu/rsem/ limma (Ritchie et al.)114 http://bioinf.wehi.edu.au/limma/ (Continued on next page) Cell Reports 43, 114436, July 23, 2024 21 ..
Article Title: Protocol for mapping the three-dimensional organization of dinoflagellate genomes.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Chemicals and recombinant proteins Nuclease-free H2O Thermo Fisher Scientific AM9916 1 M Tris-HCl pH 7.5 Thermo Fisher Scientific 15567027 1 M Tris-HCl pH 8.0 Thermo Fisher Scientific 15568025 1 M MgCl2 Thermo Fisher Scientific AM9530G 5 M NaCl Thermo Fisher Scientific AM9759 0.5 M EDTA, pH 8.0 Thermo Fisher Scientific 15575020 20% SDS Thermo Fisher Scientific AM9820 1x PBS buffer solution pH 7.4 Thermo Fisher Scientific 10010023 1x TE buffer Thermo Fisher Scientific 12090015 IGEPAL CA-630 detergent Sigma I8896-50ML Tween 20 detergent 10% Sigma 11332465001 10% Triton X-100 Sigma 93443 37% formaldehyde Sigma 252549-100ML 0.1 M NaHCO3 Sigma S6014-1KG Glycine Sigma 1005901000 MboI restriction enzyme NEB R0147 10x CutSmart buffer NEB B7204 0.4 mM biotin-14-dATP Thermo Fisher Scientific 19524-016 100 mM dCTP/dGTP/dTTP Promega U1330 DNA polymerase I large (Klenow) fragment NEB M0210 10x NEB T4 DNA ligase buffer NEB B0202 Bovine serum albumin (BSA) 100x NEB B9000 T4 DNA ligase NEB M0202 Proteinase K Promega MC5005 Dynabeads MyOne Streptavidin T1 Thermo Fisher Scientific 65602 AMPure XP beads Beckman Coulter A63881 100% EtOH Sigma 493546-1L 200-mL PCR tubes Thermo Fisher Scientific AB1182 1.5-mL DNA LoBind microcentrifuge tubes Eppendorf 022431021 (Continued on next page) 2 STAR Protocols 5, 102941, June 21, 2024 Continued REAGENT or RESOURCE SOURCE IDENTIFIER 15/50 mL tubes Critical commercial assays NEBNext Ultra II DNA Library Prep Kit for Illumina NEB E7645L NEBNext Multiplex Oligos for Illumina NEB E7600S MinElute PCR Purification Kit QIAGEN 28004/28006 Covaris milliTUBE 1 mL Covaris 520135 QuBit tubes Thermo Fisher Scientific Q32856 QuBit dsDNA HS Assay Kit Thermo Fisher Scientific Q32854 TapeStation D1000 tape Agilent 5067-5582 TapeStation D1000 reagents Agilent 5067-5583 Equipment TapeStation Agilent G2991BA Covaris E220 Covaris SKU500239 QuBit fluorometer Thermo Fisher Scientific Q33327 Tabletop centrifuge Thermomixer Eppendorf 5382000023 PCR thermocycler Magnetic rack Tube rotator Software and algorithms Juicer (version 1.6 used) Durand et al.4 https://github.com/aidenlab/juicer Juicebox (version 1.11.08 used) Durand et al.5 https://github.com/aidenlab/Juicebox 3D-DNA (version 180419 used) Dudchenko et al.6 https://github.com/aidenlab/3d-dna bwa (version 0.7.5a used) Li & Durbin7 https://github.com/lh3/bwa sra-tools (version 2.11.0 used) https://github.com/ncbi/sra-tools Deposited data Fugacium kawagutii Hi-C SRA: SRR25948349 and SRR25948348 Fugacium kawagutii draft assembly (V3) http://sampgr.org.cn/index.php/download ..
Article Title: The primitive endoderm supports lineage plasticity to enable regulative development.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies See Table S6 for antibodies used in this study N/A N/A Chemicals, peptides, and recombinant proteins Leukemia inhibitory factor (LIF) Made in house N/A CHIR99021 (GSKb inhibitor) Axon Medchem Cat#1386 PD0325901 (PD03, MEK inhibitor) Sigma Aldrich Cat#PZ0162 Activin A Peprotech Cat#120-14E Doxycycline (Dox) Sigma Aldrich Cat#D9891 4-hydroxytamoxifen (4OHT) Sigma Aldrich Cat#H7904 BMP4 Peprotech Cat#120-05ET A83-01 Sigma-Aldrich Cat#SML0788 Y-27632 (ROCK inhibitor) Tocris Cat#1254 Retinoic acid Sigma Aldrich Cat#R2625 2-mercaptoethanol Sigma Aldrich Cat#M6250 L-glutamine Thermo Fisher Cat#25030024 B-27 Supplement (50X) Gibco Cat#17504001 B-27 Supplement (50X), minus insulin Gibco Cat#A1895601 N-2 Supplement (100X) Gibco Cat#17502048 Neurobasal Medium Gibco Cat#21103049 DMEM/F12 Medium Gibco Cat#12634010 RPMI 1640 Medium, GlutaMAX Supplement Gibco Cat#61870036 MEM non-essential amino acids (100X) Gibco Cat#11140050 Sodium pyruvate (100mM) Gibco Cat#11360070 Accutase Sigma Aldrich Cat#A6964 16% Formaldehyde Thermo Fisher Cat#PI28906 Donkey Serum Sigma Aldrich Cat#D9663 EmbryoMax KSOM Medium (1X) Sigma Aldrich Cat#MR-106 Polyvinylpyrrolidine (PVP) Sigma Aldrich Cat#P0930 Triton X-100 Sigma Aldrich Cat#T8787 Anti-mouse rabbit serum Sigma Aldrich Cat#M5774 Guinea pig complement Sigma-Aldrich Cat#234395 Acidic Tyrode’s solution Sigma Aldrich Cat#T1788 Bovine Serum Albumin Gibco Cat#15260037 Tween20 Sigma-Aldrich Cat#P1379 Anti-Adherence Rinsing Solution STEMCELL Technologies Cat#07010 M2 medium Sigma Aldrich Cat#M7167 PMSG Sigma Aldrich Cat#G4527 hCG (Chorulon) Intervet N/A Critical commercial assays RNeasy Mini Kit Qiagen Cat#74106 RNeasy Micro Kit Qiagen Cat#74004 RNase-Free DNase Set Qiagen Cat#79256 SuperScript III Reverse Transcriptase Thermo Fisher Cat#18080051 Universal ProbeLibrary Roche N/A (Continued on next page) Cell 187, 1–20.e1–e6, July 25, 2024 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER NEBNext Ultra II DNA Library Prep Kit for Illumina New England Biolabs Cat# E7645L Chromium Next GEM Single Cell 3’ Kit v3.1 10x Genomics Cat#1000269 Chromium Next GEM Chip G Single Cell Kit 10x Genomics Cat#1000127 NEBNext Ultra II Directional RNA Library Prep kit New England Biolabs Cat#E7765 NEBNext Multiplex Oligos for Illumina New England Biolabs Cat#E6440 Qubit dsDNA Quantification Assay Kits Invitrogen Cat#Q32851 Deposited data Raw and analysed data This study GEO:GSE232926 External re-analysed mouse embryo scRNA-seq dataset Nowotschin et al.53 GEO:GSE123046 External re-analysed mouse reprogramming scRNA-seq dataset Zhao et al.77 GEO:GSE114952 Experimental models: Cell lines SOX2-GFP/ GATA6-mCherry (SGGC) ESCs Redó-Riveiro et al.48 N/A OCT4-mCherry ESCs Hashmi et al.58 N/A OCT4-mCherry-H2B-Venus This study N/A Esrrb KO with tetON-Esrrb transgene (EKOiE) ESCs Festuccia et al.82 N/A E14JU ESCs (E14Tg2a 129/Ola subclone) Hamilton and Brickman117 N/A DR4 mouse embryonic fibroblasts (MEFs) Tucker et al.118 N/A Experimental models: Organisms/strains C57BL/6N Taconic RRID:MGI:2159965 Rosa26mT/mG Muzumdar et al.45 RRID:IMSR_JAX:007576 Pdgfra-CreERT2 Chung et al.44 RRID:IMSR_JAX:032770 Oligonucleotides See Table S6 for primer sequences used in this study N/A N/A Software and algorithms BD FACSDiva BD Biosciences RRID:SCR_001456 FCS Express v7 De Novo Software RRID:SCR_016431 Prism v10.1.1 GraphPad RRID:SCR_002798 R v4.3.1 R Core Team RRID:SCR_001905 Cell Ranger v6.1.12 10x Genomics RRID:SCR_017344 scVelo v0.2.5 and v0.17.1 Bergen et al.54 N/A scvi-tools Gayoso et al.74 N/A scanpy v1.8.2 and 1.9.1 Wolf et al.119 RRID:SCR_018139 Seurat v4.3.0 Hao et al.120 RRID:SCR_007322 BEDtools Quinlan and Hall121 RRID:SCR_006646 SEACR Meers et al.122 N/A DiffBind Ross-Innes et al.123 RRID:SCR_012918 deeptools Ramı́rez et al.124 RRID:SCR_016366 SAMtools Danecek et al.125 RRID:SCR_002105 IGV v2.16.2 Robinson et al.126 RRID:SCR_011793 pyGenomeTracks Lopez-Delisle et al.127 N/A HOMER Heinz et al.128 RRID:SCR_010881 DESeq2 v1.40.2 Love et al.129 RRID:SCR_015687 FIJI (ImageJ) v2.14.0 Schindelin et al.130 RRID: SCR_002285 CellProfiler v4.2.5 Stirling et al.131 RRID:SCR_007358 Imaris v9.9.1 Oxford Instruments RRID:SCR_007370 (Continued on next page) ll e2 Cell 187, 1–20.e1–e6, July 25, 2024 Please cite this article in press as: Linneberg-Agerholm et al., The primitive endoderm supports lineage plasticity to enable regulative development, Cell (2024), https://doi.org/10.1016/j.cell.2024.05.051 Article ..
Hybridization:Article Title: LDB1 establishes multi-enhancer networks to regulate gene expression.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Mouse monoclonal anti-LDB1 CLIM-2 (C-9) Santa Cruz Biotechnology Cat#sc-365074; RRID: AB_10848267 Rabbit polyclonal anti-LDB1 Lot# VI3089586A Thermo Fisher Scientific Cat#PA5-56948; RRID: AB_2643320 Mouse monoclonal anti-GAPDH Lot# A1822 (6C5) Santa Cruz Biotechnology Cat#sc-32233; RRID: AB_627679 Rabbit monoclonal anti-RPB1 (Pol2) (D8L4Y) Cell Signaling Technology Cat#14958; RRID: AB_2687876 Rabbit polyclonal anti-YY1 Active Motif Cat#61779; RRID: AB_2793763 Rabbit polyclonal anti-CTCF Millipore Cat#07-729; RRID: AB_441965 Rabbit polyclonal anti-RAD21 Abcam Cat#ab992; RRID: AB_2176601 Mouse monoclonal anti-pMPM2 Millipore Cat# 05-368; RRID: AB_309698 F(ab’)2-Goat anti-Mouse IgG (H+L) Secondary Antibody, APC, eBioscience Thermo Fisher Scientific Cat#17-4010-82; RRID: AB_2573203 Chemicals, peptides, and recombinant proteins AMPure XP Beckman Coulter Cat#A63880 Indole-3-acetic acid sodium salt (auxin) Sigma Aldrich Cat#I5148 estradiol Sigma Aldrich Cat#E2758 iSCRIPT Reverse Transcription Supermix Bio Rad Cat#1708840 Power SYBR Green PCR Master Mix Thermo Fisher Scientific Cat#4367660 Protein A agarose beads Thermo Fisher Scientific Cat#15918014 Protein G agarose beads Thermo Fisher Scientific Cat#15920010 DSG crosslinker ProteoChem Cat#c1104-1gm cOmplete Mini, EDTA-free Millipore Sigma Cat#11836170001 MNase Worthington Biochemical Cat#LS004798 rSAP New England Biolabs Cat#M0371S T4 PNK New England Biolabs Cat#M0201S Large (Klenow) Fragment New England Biolabs Cat#M0210S Biotin-11-dCTP Jena Bioscience Cat#NU-809-BIOX-S Biotin-14-dATP Jena Bioscience Cat#NU-835-BIO14-S Biotin-14-dATP Active Motif Cat#14138 T4 DNA Ligase New England Biolabs Cat#M0202S T4 DNA Ligase buffer New England Biolabs Cat#B0202S Dynabeads MyOne Streptavidin C1 Thermo Fisher Scientific Cat#65001 KAPA HiFi HotStart ReadyMix Roche Cat#08202940001 Herculase II Fusion DNA Polymerase Agilent Cat#600675 Mouse Cot-1 DNA Thermo Fisher Scientific Cat#18440016 Twist Universal Blockers Twist Bioscience Cat#100578 Twist Binding and Purification Beads Twist Bioscience Cat#100983 Dynabeads M-270 Streptavidn Thermo Fisher Scientic Cat#65305 NlaIII New England Biolabs Cat#R0125L NEB Buffer 2 New England Biolabs Cat#7002S NEB Buffer 3.1 New England Biolabs Cat#B7203S DpnII New England Biolabs Cat#R0543M VAHTS DNA Clean Beads Vazyme Cat#N411 (Continued on next page) e1 Molecular Cell 85, 376–393.e1–e9, January 16, 2025 .. REAGENT or RESOURCE SOURCE IDENTIFIER T4 DNA polymerase New England Biolabs CatM0203S 4-thiouridine (4SU) MedChemExpress Cat#HY-W011793 TRIzol Reagent Invitrogen Cat#15596026 MTSEA-biotin Biotium Cat# 90064 Critical commercial assays KAPA HyperCapture Reagent Kit Roche Cat#9075810001 Twist Hybridization and Wash Kit with Amplification Mix, 12 Reactions Twist Bioscience Cat#104178 RNeasy Mini Kit QIAGEN Cat#74104 QIAshredder QIAGEN Cat#79656 NEBNext Ultra II DNA Library Prep Kit for Illumina New England Biolabs Cat#E7645S NEBNext Multiplex Oligos for Illumina (96 Unique Dual Index Primer Pairs) New England Biolabs Cat#E6440S TruSeq Stranded mRNA kit Illumina Cat#20020594 Illumina Stranded Total RNA Prep Illumina Cat# 20040525 Qubit dsDNA Quantification Assay Kits Thermo Fisher Scientific Cat#Q32850 In-Fusion HD Cloning kit Takara Cat#639648 QIAquick PCR Purification Kit QIAGEN Cat#28104 QIAquick Gel Extraction Kit QIAGEN Cat#28704 AHTS Universal DNA Library Prep Kit Vazyme Cat#ND627-01 Deposited data LDB1-AID Micro-C This paper GSE254373 LDB1-AID RCMC This paper GSE266450 LDB1-AID TT-seq This paper GSE264584 LDB1-AID Tri-C This paper GSE254372 LDB1-AID RNA-seq This paper GSE264455 SMC3-AID Hi-C Zhao et al.103 GSE228402 CTCF-AID Hi-C Zhang et al.26 GSE168251 YY1-AID Micro-C Lam et al.84 GSE247254 Mitotic Hi-C Zhang et al.38 GSE129997 Mitotic ChIP-seq (CTCF/RAD21) Zhang et al.38 GSE129997 H3K27ac ChIP-seq Dogan et al.104 GSE61349 LDB1-AID ChIP-seq This paper GSE254377 SMC3-AID ChIP-seq This paper GSE254377 Original western blot data This paper, Mendeley Data https://doi.org/10.17632/mf78pvcrkk.2 Experimental models: Cell lines G1E-ER4 Mitchell J. Weiss lab Weiss et al.82 LDB1-AID This paper N/A YY1-AID Gerd Blobel Lab Lam et al.84 SMC3-AID Haoyue Zhang Lab Zhao et al.103 CTCF-AID Gerd A. Blobel lab Zhang et al.26 Oligonucleotides See Table S2 for oligonucleotides used in this study This paper Table S2 Recombinant DNA pX458-GFP Addgene 48138 md-mCherry Gerd A. Blobel lab Zhang et al.38 OsTiR-IRES-GFP Gerd A. Blobel lab Zhang et al.38 (Continued on next page) Molecular Cell 85, 376–393.e1–e9, January 16, 2025 e2 ..
Cloning:Article Title: LDB1 establishes multi-enhancer networks to regulate gene expression.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Mouse monoclonal anti-LDB1 CLIM-2 (C-9) Santa Cruz Biotechnology Cat#sc-365074; RRID: AB_10848267 Rabbit polyclonal anti-LDB1 Lot# VI3089586A Thermo Fisher Scientific Cat#PA5-56948; RRID: AB_2643320 Mouse monoclonal anti-GAPDH Lot# A1822 (6C5) Santa Cruz Biotechnology Cat#sc-32233; RRID: AB_627679 Rabbit monoclonal anti-RPB1 (Pol2) (D8L4Y) Cell Signaling Technology Cat#14958; RRID: AB_2687876 Rabbit polyclonal anti-YY1 Active Motif Cat#61779; RRID: AB_2793763 Rabbit polyclonal anti-CTCF Millipore Cat#07-729; RRID: AB_441965 Rabbit polyclonal anti-RAD21 Abcam Cat#ab992; RRID: AB_2176601 Mouse monoclonal anti-pMPM2 Millipore Cat# 05-368; RRID: AB_309698 F(ab’)2-Goat anti-Mouse IgG (H+L) Secondary Antibody, APC, eBioscience Thermo Fisher Scientific Cat#17-4010-82; RRID: AB_2573203 Chemicals, peptides, and recombinant proteins AMPure XP Beckman Coulter Cat#A63880 Indole-3-acetic acid sodium salt (auxin) Sigma Aldrich Cat#I5148 estradiol Sigma Aldrich Cat#E2758 iSCRIPT Reverse Transcription Supermix Bio Rad Cat#1708840 Power SYBR Green PCR Master Mix Thermo Fisher Scientific Cat#4367660 Protein A agarose beads Thermo Fisher Scientific Cat#15918014 Protein G agarose beads Thermo Fisher Scientific Cat#15920010 DSG crosslinker ProteoChem Cat#c1104-1gm cOmplete Mini, EDTA-free Millipore Sigma Cat#11836170001 MNase Worthington Biochemical Cat#LS004798 rSAP New England Biolabs Cat#M0371S T4 PNK New England Biolabs Cat#M0201S Large (Klenow) Fragment New England Biolabs Cat#M0210S Biotin-11-dCTP Jena Bioscience Cat#NU-809-BIOX-S Biotin-14-dATP Jena Bioscience Cat#NU-835-BIO14-S Biotin-14-dATP Active Motif Cat#14138 T4 DNA Ligase New England Biolabs Cat#M0202S T4 DNA Ligase buffer New England Biolabs Cat#B0202S Dynabeads MyOne Streptavidin C1 Thermo Fisher Scientific Cat#65001 KAPA HiFi HotStart ReadyMix Roche Cat#08202940001 Herculase II Fusion DNA Polymerase Agilent Cat#600675 Mouse Cot-1 DNA Thermo Fisher Scientific Cat#18440016 Twist Universal Blockers Twist Bioscience Cat#100578 Twist Binding and Purification Beads Twist Bioscience Cat#100983 Dynabeads M-270 Streptavidn Thermo Fisher Scientic Cat#65305 NlaIII New England Biolabs Cat#R0125L NEB Buffer 2 New England Biolabs Cat#7002S NEB Buffer 3.1 New England Biolabs Cat#B7203S DpnII New England Biolabs Cat#R0543M VAHTS DNA Clean Beads Vazyme Cat#N411 (Continued on next page) e1 Molecular Cell 85, 376–393.e1–e9, January 16, 2025 .. REAGENT or RESOURCE SOURCE IDENTIFIER T4 DNA polymerase New England Biolabs CatM0203S 4-thiouridine (4SU) MedChemExpress Cat#HY-W011793 TRIzol Reagent Invitrogen Cat#15596026 MTSEA-biotin Biotium Cat# 90064 Critical commercial assays KAPA HyperCapture Reagent Kit Roche Cat#9075810001 Twist Hybridization and Wash Kit with Amplification Mix, 12 Reactions Twist Bioscience Cat#104178 RNeasy Mini Kit QIAGEN Cat#74104 QIAshredder QIAGEN Cat#79656 NEBNext Ultra II DNA Library Prep Kit for Illumina New England Biolabs Cat#E7645S NEBNext Multiplex Oligos for Illumina (96 Unique Dual Index Primer Pairs) New England Biolabs Cat#E6440S TruSeq Stranded mRNA kit Illumina Cat#20020594 Illumina Stranded Total RNA Prep Illumina Cat# 20040525 Qubit dsDNA Quantification Assay Kits Thermo Fisher Scientific Cat#Q32850 In-Fusion HD Cloning kit Takara Cat#639648 QIAquick PCR Purification Kit QIAGEN Cat#28104 QIAquick Gel Extraction Kit QIAGEN Cat#28704 AHTS Universal DNA Library Prep Kit Vazyme Cat#ND627-01 Deposited data LDB1-AID Micro-C This paper GSE254373 LDB1-AID RCMC This paper GSE266450 LDB1-AID TT-seq This paper GSE264584 LDB1-AID Tri-C This paper GSE254372 LDB1-AID RNA-seq This paper GSE264455 SMC3-AID Hi-C Zhao et al.103 GSE228402 CTCF-AID Hi-C Zhang et al.26 GSE168251 YY1-AID Micro-C Lam et al.84 GSE247254 Mitotic Hi-C Zhang et al.38 GSE129997 Mitotic ChIP-seq (CTCF/RAD21) Zhang et al.38 GSE129997 H3K27ac ChIP-seq Dogan et al.104 GSE61349 LDB1-AID ChIP-seq This paper GSE254377 SMC3-AID ChIP-seq This paper GSE254377 Original western blot data This paper, Mendeley Data https://doi.org/10.17632/mf78pvcrkk.2 Experimental models: Cell lines G1E-ER4 Mitchell J. Weiss lab Weiss et al.82 LDB1-AID This paper N/A YY1-AID Gerd Blobel Lab Lam et al.84 SMC3-AID Haoyue Zhang Lab Zhao et al.103 CTCF-AID Gerd A. Blobel lab Zhang et al.26 Oligonucleotides See Table S2 for oligonucleotides used in this study This paper Table S2 Recombinant DNA pX458-GFP Addgene 48138 md-mCherry Gerd A. Blobel lab Zhang et al.38 OsTiR-IRES-GFP Gerd A. Blobel lab Zhang et al.38 (Continued on next page) Molecular Cell 85, 376–393.e1–e9, January 16, 2025 e2 ..
Article Title: Graft-seq precisely maps RNA modifications via site-specific chemical grafting strategy.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-7-methylguanosine (m 7 G)-Cap mAb MBL life science Cat# RN016M; RRID: AB_2921296 Goat anti-Mouse IgG HRP HuaBio Cat# HA1006; RRID: AB_2819167 Chemicals, peptides, and recombinant proteins 3 M Sodium Acetate Solution, pH 5.2 Thermo Scientific Cat# R1181 3 ′ -Desthiobiotin-GTP; DTB-GTP New England Biolabs Cat# N0761 3-azido-1-propanol Sigma-Aldrich Cat# 776130 ADP-ribosylcyclase; ADPRC Sigma-Aldrich Cat# A9106 Alexa Fluor 488 Azide Invitrogen Cat# A10266 Ammonium iron(II) sulfate hexahydrate Sigma-Aldrich Cat# 09719 ATP New England Biolabs Cat# P0756S Biotin-Azide QIYUEBIO Cat# QY-24297 Blotting membranes, Amersham TM Hybond TM -N+ GE Healthcare Cat# RPN303B Bst 2.0 DNA polymerase New England Biolabs Cat# M0537S CleanCap Reagent M6 Trilink Cat# N-7453 Copper(II) sulfate pentahydrate Sigma-Aldrich Cat# C3036 D-biotin MedChemExpress Cat# HY-B0511 Dibenzocyclooctyne-maleimide Sigma-Aldrich Cat# 760668 DL-Dithiothreitol; DTT Sigma-Aldrich Cat# V900830 DMEM/high-glucose medium HyClone Cat# SH30243.01 DMF Sigma-Aldrich Cat# D4551 DMSO Sigma-Aldrich Cat# 41639 DNase I New England Biolabs Cat# M0303 dTTP (100 mM) Thermo Scientific Cat# R0171 EDTA (0.5 M),pH 8.0 Invitrogen Cat# AM9260G Fetal Bovine Serum Gibco Cat# 10270 Fetal Bovine Serum, Sterile(irradiated) Ausbian Cat# VS500T GlutaMAX Gibco Cat# 35050061 Glycogen Invitrogen Cat# AM9510 HEPES Sigma-Aldrich Cat# V900477 HRP-streptavidin Invitrogen Cat# 434323 L-Ascorbic acid Sigma-Aldrich Cat# 95209 m 6 ATP Trilink Cat# N-1013 Maxima H Minus Reverse Transcriptase Thermo Scientific Cat# EP0751 MEM Non-Essential Amino Acids Solution (100X) Gibco Cat# 11140 mRNA decapping enzyme New England Biolabs Cat# M0608S NAD Sigma-Aldrich Cat# N6522 Non-fat Powdered milk BBI Life Sciences Cat# A600669 Nuclease P1 Wako Cat# 145-08221 Penicillin/streptomycin Gibco Cat# 15140 Penicillin-Streptomycin HyClone Cat# SV30010 Phanta Max Super-Fidelity DNA Polymerase Vazyme Cat# P505 Potassium chloride Sigma-Aldrich Cat# P9541 PrimerScript II Reverse Transcriptase Takara Cat# 6210A PrimerScript Reverse Transcriptase Takara Cat# 6110A (Continued on next page) e1 Cell Reports Methods 5, 101103, July 21, 2025 OPEN ACCESS .. REAGENT or RESOURCE SOURCE IDENTIFIER Quick CIP New England Biolabs Cat# M0525 rCutSmart buffer New England Biolabs Cat# B6004V Recombinant Mouse LIF Protein Milipore Cat# ESG1107 Reverse Transcriptase, Recombinant HIV Worthington Biochemical Corporation Cat# LS05003 RevertAid Reverse Transcriptase Thermo Scientific Cat# EP0442 RNase inhibitor Vazyme Cat# R301 RppH New England Biolabs Cat# M0356 rSAP New England Biolabs Cat# M0371S SMARTScribe Reverse Transcriptase Clontech Cat# 639536 Sodium L-ascorbate Energy Chemical Cat# E082526 Sodium pyruvate Gibco Cat# 11360 SplintR ligase New England Biolabs Cat# M0375S SuperScript II Reverse Transcriptase Invitrogen Cat# 18064071 T4 Polynucleotide Kinase; T4 PNK New England Biolabs Cat# M0201 TGIRT III Reverse Transcriptase InGex Cat# CM0101 ThermoPol Reaction Buffer New England Biolabs Cat# B90004 Tris(3-hydroxypropyltriazolylmethyl)amine Sigma-Aldrich Cat# 762342 Trizol Invitrogen Cat# 10296010 Tween 20 Sigma-Aldrich Cat# V900548 Vaccinia Capping System New England Biolabs Cat# M2080S yDcpS New England Biolabs Cat# M0463S α-L-Ascorbic acid; α-KG Sigma-Aldrich Cat# 75890 β-mercaptoethanol Gibco Cat# 21985023 Critical commercial assays GenElute mRNA Purification Miniprep Kit Sigma-Aldrich Cat# MRN10-1KT NEBNext rRNA Depletion Kit New England Biolabs Cat# E7400 HiScribe T7 High Yield RNA Synthesis Kit New England Biolabs Cat# E2040 RNA Clean & Concentrator-25 kit Zymo Research Cat# R1017 RNA Clean & Concentrator-5 kit Zymo Research Cat# R1013 RNAClean XP beads Beckman Coulter Cat# A63987 QIAquick Gel Extraction Kit QIAGEN Cat# 28704 ABclonal Zero TOPO-TA/Blunt Cloning Kit ABclonal Cat# RK30130 AMPure XP beads Beckman Coulter Cat# A63881 NEBNext Magnesium RNA Fragmentation Module New England Biolabs Cat# E6150 Dynabeads Protein A Invitrogen Cat# 10002D Dynabeads MyOne Streptavidin C1 Invitrogen Cat# 65001 NEBNext Multiplex Small RNA Library Prep Kit for Illumina New England Biolabs Cat# E7560S ChamQ Universal SYBR qPCR Master Mix Vazyme Cat# Q711-03 SuperSignal West Pico PLUS Chemiluminescent Substrate Thermo Scientific Cat# 34577 Deposited data Raw data This paper GSA-Human: HRA009209; GSA: CRA020263 Experimental models: Cell lines HEK293T ATCC Cat# ATCC-CRL-3216 HeLa ATCC Cat# ATCC-CCL-2 mouse ESC E14 Lab of Li Shen (Zhejiang University) N/A (Continued on next page) Cell Reports Methods 5, 101103, July 21, 2025 e2 OPEN ACCESS ..
Article Title: Graft-seq precisely maps RNA modifications via site-specific chemical grafting strategy
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-7-methylguanosine (m7G)-Cap mAb MBL life science Cat# RN016M; RRID: AB_2921296 Goat anti-Mouse IgG HRP HuaBio Cat# HA1006; RRID: AB_2819167 Chemicals, peptides, and recombinant proteins 3 M Sodium Acetate Solution, pH 5.2 Thermo Scientific Cat# R1181 3′-Desthiobiotin-GTP; DTB-GTP New England Biolabs Cat# N0761 3-azido-1-propanol Sigma-Aldrich Cat# 776130 ADP-ribosylcyclase; ADPRC Sigma-Aldrich Cat# A9106 Alexa Fluor 488 Azide Invitrogen Cat# A10266 Ammonium iron(II) sulfate hexahydrate Sigma-Aldrich Cat# 09719 ATP New England Biolabs Cat# P0756S Biotin-Azide QIYUEBIO Cat# QY-24297 Blotting membranes, AmershamTM HybondTM-N+ GE Healthcare Cat# RPN303B Bst 2.0 DNA polymerase New England Biolabs Cat# M0537S CleanCap Reagent M6 Trilink Cat# N-7453 Copper(II) sulfate pentahydrate Sigma-Aldrich Cat# C3036 D-biotin MedChemExpress Cat# HY-B0511 Dibenzocyclooctyne-maleimide Sigma-Aldrich Cat# 760668 DL-Dithiothreitol; DTT Sigma-Aldrich Cat# V900830 DMEM/high-glucose medium HyClone Cat# SH30243.01 DMF Sigma-Aldrich Cat# D4551 DMSO Sigma-Aldrich Cat# 41639 DNase I New England Biolabs Cat# M0303 dTTP (100 mM) Thermo Scientific Cat# R0171 EDTA (0.5 M),pH 8.0 Invitrogen Cat# AM9260G Fetal Bovine Serum Gibco Cat# 10270 Fetal Bovine Serum, Sterile(irradiated) Ausbian Cat# VS500T GlutaMAX Gibco Cat# 35050061 Glycogen Invitrogen Cat# AM9510 HEPES Sigma-Aldrich Cat# V900477 HRP-streptavidin Invitrogen Cat# 434323 L-Ascorbic acid Sigma-Aldrich Cat# 95209 m6ATP Trilink Cat# N-1013 Maxima H Minus Reverse Transcriptase Thermo Scientific Cat# EP0751 MEM Non-Essential Amino Acids Solution (100X) Gibco Cat# 11140 mRNA decapping enzyme New England Biolabs Cat# M0608S NAD Sigma-Aldrich Cat# N6522 Non-fat Powdered milk BBI Life Sciences Cat# A600669 Nuclease P1 Wako Cat# 145-08221 Penicillin/streptomycin Gibco Cat# 15140 Penicillin-Streptomycin HyClone Cat# SV30010 Phanta Max Super-Fidelity DNA Polymerase Vazyme Cat# P505 Potassium chloride Sigma-Aldrich Cat# P9541 PrimerScript II Reverse Transcriptase Takara Cat# 6210A PrimerScript Reverse Transcriptase Takara Cat# 6110A (Continued on next page) e1 Cell Reports Methods 5, 101103, July 21, 2025 Article ll OPEN ACCESS .. REAGENT or RESOURCE SOURCE IDENTIFIER Quick CIP New England Biolabs Cat# M0525 rCutSmart buffer New England Biolabs Cat# B6004V Recombinant Mouse LIF Protein Milipore Cat# ESG1107 Reverse Transcriptase, Recombinant HIV Worthington Biochemical Corporation Cat# LS05003 RevertAid Reverse Transcriptase Thermo Scientific Cat# EP0442 RNase inhibitor Vazyme Cat# R301 RppH New England Biolabs Cat# M0356 rSAP New England Biolabs Cat# M0371S SMARTScribe Reverse Transcriptase Clontech Cat# 639536 Sodium L-ascorbate Energy Chemical Cat# E082526 Sodium pyruvate Gibco Cat# 11360 SplintR ligase New England Biolabs Cat# M0375S SuperScript II Reverse Transcriptase Invitrogen Cat# 18064071 T4 Polynucleotide Kinase; T4 PNK New England Biolabs Cat# M0201 TGIRT III Reverse Transcriptase InGex Cat# CM0101 ThermoPol Reaction Buffer New England Biolabs Cat# B90004 Tris(3-hydroxypropyltriazolylmethyl)amine Sigma-Aldrich Cat# 762342 Trizol Invitrogen Cat# 10296010 Tween 20 Sigma-Aldrich Cat# V900548 Vaccinia Capping System New England Biolabs Cat# M2080S yDcpS New England Biolabs Cat# M0463S α-L-Ascorbic acid; α-KG Sigma-Aldrich Cat# 75890 β-mercaptoethanol Gibco Cat# 21985023 Critical commercial assays GenElute mRNA Purification Miniprep Kit Sigma-Aldrich Cat# MRN10-1KT NEBNext rRNA Depletion Kit New England Biolabs Cat# E7400 HiScribe T7 High Yield RNA Synthesis Kit New England Biolabs Cat# E2040 RNA Clean & Concentrator-25 kit Zymo Research Cat# R1017 RNA Clean & Concentrator-5 kit Zymo Research Cat# R1013 RNAClean XP beads Beckman Coulter Cat# A63987 QIAquick Gel Extraction Kit QIAGEN Cat# 28704 ABclonal Zero TOPO-TA/Blunt Cloning Kit ABclonal Cat# RK30130 AMPure XP beads Beckman Coulter Cat# A63881 NEBNext Magnesium RNA Fragmentation Module New England Biolabs Cat# E6150 Dynabeads Protein A Invitrogen Cat# 10002D Dynabeads MyOne Streptavidin C1 Invitrogen Cat# 65001 NEBNext Multiplex Small RNA Library Prep Kit for Illumina New England Biolabs Cat# E7560S ChamQ Universal SYBR qPCR Master Mix Vazyme Cat# Q711-03 SuperSignal West Pico PLUS Chemiluminescent Substrate Thermo Scientific Cat# 34577 Deposited data Raw data This paper GSA-Human: HRA009209; GSA: CRA020263 Experimental models: Cell lines HEK293T ATCC Cat# ATCC-CRL-3216 HeLa ATCC Cat# ATCC-CCL-2 mouse ESC E14 Lab of Li Shen (Zhejiang University) N/A (Continued on next page) Cell Reports Methods 5, 101103, July 21, 2025 e2 Article ll OPEN ACCESS ..
Gel Extraction:Article Title: LDB1 establishes multi-enhancer networks to regulate gene expression.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Mouse monoclonal anti-LDB1 CLIM-2 (C-9) Santa Cruz Biotechnology Cat#sc-365074; RRID: AB_10848267 Rabbit polyclonal anti-LDB1 Lot# VI3089586A Thermo Fisher Scientific Cat#PA5-56948; RRID: AB_2643320 Mouse monoclonal anti-GAPDH Lot# A1822 (6C5) Santa Cruz Biotechnology Cat#sc-32233; RRID: AB_627679 Rabbit monoclonal anti-RPB1 (Pol2) (D8L4Y) Cell Signaling Technology Cat#14958; RRID: AB_2687876 Rabbit polyclonal anti-YY1 Active Motif Cat#61779; RRID: AB_2793763 Rabbit polyclonal anti-CTCF Millipore Cat#07-729; RRID: AB_441965 Rabbit polyclonal anti-RAD21 Abcam Cat#ab992; RRID: AB_2176601 Mouse monoclonal anti-pMPM2 Millipore Cat# 05-368; RRID: AB_309698 F(ab’)2-Goat anti-Mouse IgG (H+L) Secondary Antibody, APC, eBioscience Thermo Fisher Scientific Cat#17-4010-82; RRID: AB_2573203 Chemicals, peptides, and recombinant proteins AMPure XP Beckman Coulter Cat#A63880 Indole-3-acetic acid sodium salt (auxin) Sigma Aldrich Cat#I5148 estradiol Sigma Aldrich Cat#E2758 iSCRIPT Reverse Transcription Supermix Bio Rad Cat#1708840 Power SYBR Green PCR Master Mix Thermo Fisher Scientific Cat#4367660 Protein A agarose beads Thermo Fisher Scientific Cat#15918014 Protein G agarose beads Thermo Fisher Scientific Cat#15920010 DSG crosslinker ProteoChem Cat#c1104-1gm cOmplete Mini, EDTA-free Millipore Sigma Cat#11836170001 MNase Worthington Biochemical Cat#LS004798 rSAP New England Biolabs Cat#M0371S T4 PNK New England Biolabs Cat#M0201S Large (Klenow) Fragment New England Biolabs Cat#M0210S Biotin-11-dCTP Jena Bioscience Cat#NU-809-BIOX-S Biotin-14-dATP Jena Bioscience Cat#NU-835-BIO14-S Biotin-14-dATP Active Motif Cat#14138 T4 DNA Ligase New England Biolabs Cat#M0202S T4 DNA Ligase buffer New England Biolabs Cat#B0202S Dynabeads MyOne Streptavidin C1 Thermo Fisher Scientific Cat#65001 KAPA HiFi HotStart ReadyMix Roche Cat#08202940001 Herculase II Fusion DNA Polymerase Agilent Cat#600675 Mouse Cot-1 DNA Thermo Fisher Scientific Cat#18440016 Twist Universal Blockers Twist Bioscience Cat#100578 Twist Binding and Purification Beads Twist Bioscience Cat#100983 Dynabeads M-270 Streptavidn Thermo Fisher Scientic Cat#65305 NlaIII New England Biolabs Cat#R0125L NEB Buffer 2 New England Biolabs Cat#7002S NEB Buffer 3.1 New England Biolabs Cat#B7203S DpnII New England Biolabs Cat#R0543M VAHTS DNA Clean Beads Vazyme Cat#N411 (Continued on next page) e1 Molecular Cell 85, 376–393.e1–e9, January 16, 2025 .. REAGENT or RESOURCE SOURCE IDENTIFIER T4 DNA polymerase New England Biolabs CatM0203S 4-thiouridine (4SU) MedChemExpress Cat#HY-W011793 TRIzol Reagent Invitrogen Cat#15596026 MTSEA-biotin Biotium Cat# 90064 Critical commercial assays KAPA HyperCapture Reagent Kit Roche Cat#9075810001 Twist Hybridization and Wash Kit with Amplification Mix, 12 Reactions Twist Bioscience Cat#104178 RNeasy Mini Kit QIAGEN Cat#74104 QIAshredder QIAGEN Cat#79656 NEBNext Ultra II DNA Library Prep Kit for Illumina New England Biolabs Cat#E7645S NEBNext Multiplex Oligos for Illumina (96 Unique Dual Index Primer Pairs) New England Biolabs Cat#E6440S TruSeq Stranded mRNA kit Illumina Cat#20020594 Illumina Stranded Total RNA Prep Illumina Cat# 20040525 Qubit dsDNA Quantification Assay Kits Thermo Fisher Scientific Cat#Q32850 In-Fusion HD Cloning kit Takara Cat#639648 QIAquick PCR Purification Kit QIAGEN Cat#28104 QIAquick Gel Extraction Kit QIAGEN Cat#28704 AHTS Universal DNA Library Prep Kit Vazyme Cat#ND627-01 Deposited data LDB1-AID Micro-C This paper GSE254373 LDB1-AID RCMC This paper GSE266450 LDB1-AID TT-seq This paper GSE264584 LDB1-AID Tri-C This paper GSE254372 LDB1-AID RNA-seq This paper GSE264455 SMC3-AID Hi-C Zhao et al.103 GSE228402 CTCF-AID Hi-C Zhang et al.26 GSE168251 YY1-AID Micro-C Lam et al.84 GSE247254 Mitotic Hi-C Zhang et al.38 GSE129997 Mitotic ChIP-seq (CTCF/RAD21) Zhang et al.38 GSE129997 H3K27ac ChIP-seq Dogan et al.104 GSE61349 LDB1-AID ChIP-seq This paper GSE254377 SMC3-AID ChIP-seq This paper GSE254377 Original western blot data This paper, Mendeley Data https://doi.org/10.17632/mf78pvcrkk.2 Experimental models: Cell lines G1E-ER4 Mitchell J. Weiss lab Weiss et al.82 LDB1-AID This paper N/A YY1-AID Gerd Blobel Lab Lam et al.84 SMC3-AID Haoyue Zhang Lab Zhao et al.103 CTCF-AID Gerd A. Blobel lab Zhang et al.26 Oligonucleotides See Table S2 for oligonucleotides used in this study This paper Table S2 Recombinant DNA pX458-GFP Addgene 48138 md-mCherry Gerd A. Blobel lab Zhang et al.38 OsTiR-IRES-GFP Gerd A. Blobel lab Zhang et al.38 (Continued on next page) Molecular Cell 85, 376–393.e1–e9, January 16, 2025 e2 ..
Article Title: Graft-seq precisely maps RNA modifications via site-specific chemical grafting strategy.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-7-methylguanosine (m 7 G)-Cap mAb MBL life science Cat# RN016M; RRID: AB_2921296 Goat anti-Mouse IgG HRP HuaBio Cat# HA1006; RRID: AB_2819167 Chemicals, peptides, and recombinant proteins 3 M Sodium Acetate Solution, pH 5.2 Thermo Scientific Cat# R1181 3 ′ -Desthiobiotin-GTP; DTB-GTP New England Biolabs Cat# N0761 3-azido-1-propanol Sigma-Aldrich Cat# 776130 ADP-ribosylcyclase; ADPRC Sigma-Aldrich Cat# A9106 Alexa Fluor 488 Azide Invitrogen Cat# A10266 Ammonium iron(II) sulfate hexahydrate Sigma-Aldrich Cat# 09719 ATP New England Biolabs Cat# P0756S Biotin-Azide QIYUEBIO Cat# QY-24297 Blotting membranes, Amersham TM Hybond TM -N+ GE Healthcare Cat# RPN303B Bst 2.0 DNA polymerase New England Biolabs Cat# M0537S CleanCap Reagent M6 Trilink Cat# N-7453 Copper(II) sulfate pentahydrate Sigma-Aldrich Cat# C3036 D-biotin MedChemExpress Cat# HY-B0511 Dibenzocyclooctyne-maleimide Sigma-Aldrich Cat# 760668 DL-Dithiothreitol; DTT Sigma-Aldrich Cat# V900830 DMEM/high-glucose medium HyClone Cat# SH30243.01 DMF Sigma-Aldrich Cat# D4551 DMSO Sigma-Aldrich Cat# 41639 DNase I New England Biolabs Cat# M0303 dTTP (100 mM) Thermo Scientific Cat# R0171 EDTA (0.5 M),pH 8.0 Invitrogen Cat# AM9260G Fetal Bovine Serum Gibco Cat# 10270 Fetal Bovine Serum, Sterile(irradiated) Ausbian Cat# VS500T GlutaMAX Gibco Cat# 35050061 Glycogen Invitrogen Cat# AM9510 HEPES Sigma-Aldrich Cat# V900477 HRP-streptavidin Invitrogen Cat# 434323 L-Ascorbic acid Sigma-Aldrich Cat# 95209 m 6 ATP Trilink Cat# N-1013 Maxima H Minus Reverse Transcriptase Thermo Scientific Cat# EP0751 MEM Non-Essential Amino Acids Solution (100X) Gibco Cat# 11140 mRNA decapping enzyme New England Biolabs Cat# M0608S NAD Sigma-Aldrich Cat# N6522 Non-fat Powdered milk BBI Life Sciences Cat# A600669 Nuclease P1 Wako Cat# 145-08221 Penicillin/streptomycin Gibco Cat# 15140 Penicillin-Streptomycin HyClone Cat# SV30010 Phanta Max Super-Fidelity DNA Polymerase Vazyme Cat# P505 Potassium chloride Sigma-Aldrich Cat# P9541 PrimerScript II Reverse Transcriptase Takara Cat# 6210A PrimerScript Reverse Transcriptase Takara Cat# 6110A (Continued on next page) e1 Cell Reports Methods 5, 101103, July 21, 2025 OPEN ACCESS .. REAGENT or RESOURCE SOURCE IDENTIFIER Quick CIP New England Biolabs Cat# M0525 rCutSmart buffer New England Biolabs Cat# B6004V Recombinant Mouse LIF Protein Milipore Cat# ESG1107 Reverse Transcriptase, Recombinant HIV Worthington Biochemical Corporation Cat# LS05003 RevertAid Reverse Transcriptase Thermo Scientific Cat# EP0442 RNase inhibitor Vazyme Cat# R301 RppH New England Biolabs Cat# M0356 rSAP New England Biolabs Cat# M0371S SMARTScribe Reverse Transcriptase Clontech Cat# 639536 Sodium L-ascorbate Energy Chemical Cat# E082526 Sodium pyruvate Gibco Cat# 11360 SplintR ligase New England Biolabs Cat# M0375S SuperScript II Reverse Transcriptase Invitrogen Cat# 18064071 T4 Polynucleotide Kinase; T4 PNK New England Biolabs Cat# M0201 TGIRT III Reverse Transcriptase InGex Cat# CM0101 ThermoPol Reaction Buffer New England Biolabs Cat# B90004 Tris(3-hydroxypropyltriazolylmethyl)amine Sigma-Aldrich Cat# 762342 Trizol Invitrogen Cat# 10296010 Tween 20 Sigma-Aldrich Cat# V900548 Vaccinia Capping System New England Biolabs Cat# M2080S yDcpS New England Biolabs Cat# M0463S α-L-Ascorbic acid; α-KG Sigma-Aldrich Cat# 75890 β-mercaptoethanol Gibco Cat# 21985023 Critical commercial assays GenElute mRNA Purification Miniprep Kit Sigma-Aldrich Cat# MRN10-1KT NEBNext rRNA Depletion Kit New England Biolabs Cat# E7400 HiScribe T7 High Yield RNA Synthesis Kit New England Biolabs Cat# E2040 RNA Clean & Concentrator-25 kit Zymo Research Cat# R1017 RNA Clean & Concentrator-5 kit Zymo Research Cat# R1013 RNAClean XP beads Beckman Coulter Cat# A63987 QIAquick Gel Extraction Kit QIAGEN Cat# 28704 ABclonal Zero TOPO-TA/Blunt Cloning Kit ABclonal Cat# RK30130 AMPure XP beads Beckman Coulter Cat# A63881 NEBNext Magnesium RNA Fragmentation Module New England Biolabs Cat# E6150 Dynabeads Protein A Invitrogen Cat# 10002D Dynabeads MyOne Streptavidin C1 Invitrogen Cat# 65001 NEBNext Multiplex Small RNA Library Prep Kit for Illumina New England Biolabs Cat# E7560S ChamQ Universal SYBR qPCR Master Mix Vazyme Cat# Q711-03 SuperSignal West Pico PLUS Chemiluminescent Substrate Thermo Scientific Cat# 34577 Deposited data Raw data This paper GSA-Human: HRA009209; GSA: CRA020263 Experimental models: Cell lines HEK293T ATCC Cat# ATCC-CRL-3216 HeLa ATCC Cat# ATCC-CCL-2 mouse ESC E14 Lab of Li Shen (Zhejiang University) N/A (Continued on next page) Cell Reports Methods 5, 101103, July 21, 2025 e2 OPEN ACCESS ..
Article Title: Graft-seq precisely maps RNA modifications via site-specific chemical grafting strategy
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-7-methylguanosine (m7G)-Cap mAb MBL life science Cat# RN016M; RRID: AB_2921296 Goat anti-Mouse IgG HRP HuaBio Cat# HA1006; RRID: AB_2819167 Chemicals, peptides, and recombinant proteins 3 M Sodium Acetate Solution, pH 5.2 Thermo Scientific Cat# R1181 3′-Desthiobiotin-GTP; DTB-GTP New England Biolabs Cat# N0761 3-azido-1-propanol Sigma-Aldrich Cat# 776130 ADP-ribosylcyclase; ADPRC Sigma-Aldrich Cat# A9106 Alexa Fluor 488 Azide Invitrogen Cat# A10266 Ammonium iron(II) sulfate hexahydrate Sigma-Aldrich Cat# 09719 ATP New England Biolabs Cat# P0756S Biotin-Azide QIYUEBIO Cat# QY-24297 Blotting membranes, AmershamTM HybondTM-N+ GE Healthcare Cat# RPN303B Bst 2.0 DNA polymerase New England Biolabs Cat# M0537S CleanCap Reagent M6 Trilink Cat# N-7453 Copper(II) sulfate pentahydrate Sigma-Aldrich Cat# C3036 D-biotin MedChemExpress Cat# HY-B0511 Dibenzocyclooctyne-maleimide Sigma-Aldrich Cat# 760668 DL-Dithiothreitol; DTT Sigma-Aldrich Cat# V900830 DMEM/high-glucose medium HyClone Cat# SH30243.01 DMF Sigma-Aldrich Cat# D4551 DMSO Sigma-Aldrich Cat# 41639 DNase I New England Biolabs Cat# M0303 dTTP (100 mM) Thermo Scientific Cat# R0171 EDTA (0.5 M),pH 8.0 Invitrogen Cat# AM9260G Fetal Bovine Serum Gibco Cat# 10270 Fetal Bovine Serum, Sterile(irradiated) Ausbian Cat# VS500T GlutaMAX Gibco Cat# 35050061 Glycogen Invitrogen Cat# AM9510 HEPES Sigma-Aldrich Cat# V900477 HRP-streptavidin Invitrogen Cat# 434323 L-Ascorbic acid Sigma-Aldrich Cat# 95209 m6ATP Trilink Cat# N-1013 Maxima H Minus Reverse Transcriptase Thermo Scientific Cat# EP0751 MEM Non-Essential Amino Acids Solution (100X) Gibco Cat# 11140 mRNA decapping enzyme New England Biolabs Cat# M0608S NAD Sigma-Aldrich Cat# N6522 Non-fat Powdered milk BBI Life Sciences Cat# A600669 Nuclease P1 Wako Cat# 145-08221 Penicillin/streptomycin Gibco Cat# 15140 Penicillin-Streptomycin HyClone Cat# SV30010 Phanta Max Super-Fidelity DNA Polymerase Vazyme Cat# P505 Potassium chloride Sigma-Aldrich Cat# P9541 PrimerScript II Reverse Transcriptase Takara Cat# 6210A PrimerScript Reverse Transcriptase Takara Cat# 6110A (Continued on next page) e1 Cell Reports Methods 5, 101103, July 21, 2025 Article ll OPEN ACCESS .. REAGENT or RESOURCE SOURCE IDENTIFIER Quick CIP New England Biolabs Cat# M0525 rCutSmart buffer New England Biolabs Cat# B6004V Recombinant Mouse LIF Protein Milipore Cat# ESG1107 Reverse Transcriptase, Recombinant HIV Worthington Biochemical Corporation Cat# LS05003 RevertAid Reverse Transcriptase Thermo Scientific Cat# EP0442 RNase inhibitor Vazyme Cat# R301 RppH New England Biolabs Cat# M0356 rSAP New England Biolabs Cat# M0371S SMARTScribe Reverse Transcriptase Clontech Cat# 639536 Sodium L-ascorbate Energy Chemical Cat# E082526 Sodium pyruvate Gibco Cat# 11360 SplintR ligase New England Biolabs Cat# M0375S SuperScript II Reverse Transcriptase Invitrogen Cat# 18064071 T4 Polynucleotide Kinase; T4 PNK New England Biolabs Cat# M0201 TGIRT III Reverse Transcriptase InGex Cat# CM0101 ThermoPol Reaction Buffer New England Biolabs Cat# B90004 Tris(3-hydroxypropyltriazolylmethyl)amine Sigma-Aldrich Cat# 762342 Trizol Invitrogen Cat# 10296010 Tween 20 Sigma-Aldrich Cat# V900548 Vaccinia Capping System New England Biolabs Cat# M2080S yDcpS New England Biolabs Cat# M0463S α-L-Ascorbic acid; α-KG Sigma-Aldrich Cat# 75890 β-mercaptoethanol Gibco Cat# 21985023 Critical commercial assays GenElute mRNA Purification Miniprep Kit Sigma-Aldrich Cat# MRN10-1KT NEBNext rRNA Depletion Kit New England Biolabs Cat# E7400 HiScribe T7 High Yield RNA Synthesis Kit New England Biolabs Cat# E2040 RNA Clean & Concentrator-25 kit Zymo Research Cat# R1017 RNA Clean & Concentrator-5 kit Zymo Research Cat# R1013 RNAClean XP beads Beckman Coulter Cat# A63987 QIAquick Gel Extraction Kit QIAGEN Cat# 28704 ABclonal Zero TOPO-TA/Blunt Cloning Kit ABclonal Cat# RK30130 AMPure XP beads Beckman Coulter Cat# A63881 NEBNext Magnesium RNA Fragmentation Module New England Biolabs Cat# E6150 Dynabeads Protein A Invitrogen Cat# 10002D Dynabeads MyOne Streptavidin C1 Invitrogen Cat# 65001 NEBNext Multiplex Small RNA Library Prep Kit for Illumina New England Biolabs Cat# E7560S ChamQ Universal SYBR qPCR Master Mix Vazyme Cat# Q711-03 SuperSignal West Pico PLUS Chemiluminescent Substrate Thermo Scientific Cat# 34577 Deposited data Raw data This paper GSA-Human: HRA009209; GSA: CRA020263 Experimental models: Cell lines HEK293T ATCC Cat# ATCC-CRL-3216 HeLa ATCC Cat# ATCC-CCL-2 mouse ESC E14 Lab of Li Shen (Zhejiang University) N/A (Continued on next page) Cell Reports Methods 5, 101103, July 21, 2025 e2 Article ll OPEN ACCESS ..
Chromatin Immunoprecipitation:Article Title: LDB1 establishes multi-enhancer networks to regulate gene expression.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Mouse monoclonal anti-LDB1 CLIM-2 (C-9) Santa Cruz Biotechnology Cat#sc-365074; RRID: AB_10848267 Rabbit polyclonal anti-LDB1 Lot# VI3089586A Thermo Fisher Scientific Cat#PA5-56948; RRID: AB_2643320 Mouse monoclonal anti-GAPDH Lot# A1822 (6C5) Santa Cruz Biotechnology Cat#sc-32233; RRID: AB_627679 Rabbit monoclonal anti-RPB1 (Pol2) (D8L4Y) Cell Signaling Technology Cat#14958; RRID: AB_2687876 Rabbit polyclonal anti-YY1 Active Motif Cat#61779; RRID: AB_2793763 Rabbit polyclonal anti-CTCF Millipore Cat#07-729; RRID: AB_441965 Rabbit polyclonal anti-RAD21 Abcam Cat#ab992; RRID: AB_2176601 Mouse monoclonal anti-pMPM2 Millipore Cat# 05-368; RRID: AB_309698 F(ab’)2-Goat anti-Mouse IgG (H+L) Secondary Antibody, APC, eBioscience Thermo Fisher Scientific Cat#17-4010-82; RRID: AB_2573203 Chemicals, peptides, and recombinant proteins AMPure XP Beckman Coulter Cat#A63880 Indole-3-acetic acid sodium salt (auxin) Sigma Aldrich Cat#I5148 estradiol Sigma Aldrich Cat#E2758 iSCRIPT Reverse Transcription Supermix Bio Rad Cat#1708840 Power SYBR Green PCR Master Mix Thermo Fisher Scientific Cat#4367660 Protein A agarose beads Thermo Fisher Scientific Cat#15918014 Protein G agarose beads Thermo Fisher Scientific Cat#15920010 DSG crosslinker ProteoChem Cat#c1104-1gm cOmplete Mini, EDTA-free Millipore Sigma Cat#11836170001 MNase Worthington Biochemical Cat#LS004798 rSAP New England Biolabs Cat#M0371S T4 PNK New England Biolabs Cat#M0201S Large (Klenow) Fragment New England Biolabs Cat#M0210S Biotin-11-dCTP Jena Bioscience Cat#NU-809-BIOX-S Biotin-14-dATP Jena Bioscience Cat#NU-835-BIO14-S Biotin-14-dATP Active Motif Cat#14138 T4 DNA Ligase New England Biolabs Cat#M0202S T4 DNA Ligase buffer New England Biolabs Cat#B0202S Dynabeads MyOne Streptavidin C1 Thermo Fisher Scientific Cat#65001 KAPA HiFi HotStart ReadyMix Roche Cat#08202940001 Herculase II Fusion DNA Polymerase Agilent Cat#600675 Mouse Cot-1 DNA Thermo Fisher Scientific Cat#18440016 Twist Universal Blockers Twist Bioscience Cat#100578 Twist Binding and Purification Beads Twist Bioscience Cat#100983 Dynabeads M-270 Streptavidn Thermo Fisher Scientic Cat#65305 NlaIII New England Biolabs Cat#R0125L NEB Buffer 2 New England Biolabs Cat#7002S NEB Buffer 3.1 New England Biolabs Cat#B7203S DpnII New England Biolabs Cat#R0543M VAHTS DNA Clean Beads Vazyme Cat#N411 (Continued on next page) e1 Molecular Cell 85, 376–393.e1–e9, January 16, 2025 .. REAGENT or RESOURCE SOURCE IDENTIFIER T4 DNA polymerase New England Biolabs CatM0203S 4-thiouridine (4SU) MedChemExpress Cat#HY-W011793 TRIzol Reagent Invitrogen Cat#15596026 MTSEA-biotin Biotium Cat# 90064 Critical commercial assays KAPA HyperCapture Reagent Kit Roche Cat#9075810001 Twist Hybridization and Wash Kit with Amplification Mix, 12 Reactions Twist Bioscience Cat#104178 RNeasy Mini Kit QIAGEN Cat#74104 QIAshredder QIAGEN Cat#79656 NEBNext Ultra II DNA Library Prep Kit for Illumina New England Biolabs Cat#E7645S NEBNext Multiplex Oligos for Illumina (96 Unique Dual Index Primer Pairs) New England Biolabs Cat#E6440S TruSeq Stranded mRNA kit Illumina Cat#20020594 Illumina Stranded Total RNA Prep Illumina Cat# 20040525 Qubit dsDNA Quantification Assay Kits Thermo Fisher Scientific Cat#Q32850 In-Fusion HD Cloning kit Takara Cat#639648 QIAquick PCR Purification Kit QIAGEN Cat#28104 QIAquick Gel Extraction Kit QIAGEN Cat#28704 AHTS Universal DNA Library Prep Kit Vazyme Cat#ND627-01 Deposited data LDB1-AID Micro-C This paper GSE254373 LDB1-AID RCMC This paper GSE266450 LDB1-AID TT-seq This paper GSE264584 LDB1-AID Tri-C This paper GSE254372 LDB1-AID RNA-seq This paper GSE264455 SMC3-AID Hi-C Zhao et al.103 GSE228402 CTCF-AID Hi-C Zhang et al.26 GSE168251 YY1-AID Micro-C Lam et al.84 GSE247254 Mitotic Hi-C Zhang et al.38 GSE129997 Mitotic ChIP-seq (CTCF/RAD21) Zhang et al.38 GSE129997 H3K27ac ChIP-seq Dogan et al.104 GSE61349 LDB1-AID ChIP-seq This paper GSE254377 SMC3-AID ChIP-seq This paper GSE254377 Original western blot data This paper, Mendeley Data https://doi.org/10.17632/mf78pvcrkk.2 Experimental models: Cell lines G1E-ER4 Mitchell J. Weiss lab Weiss et al.82 LDB1-AID This paper N/A YY1-AID Gerd Blobel Lab Lam et al.84 SMC3-AID Haoyue Zhang Lab Zhao et al.103 CTCF-AID Gerd A. Blobel lab Zhang et al.26 Oligonucleotides See Table S2 for oligonucleotides used in this study This paper Table S2 Recombinant DNA pX458-GFP Addgene 48138 md-mCherry Gerd A. Blobel lab Zhang et al.38 OsTiR-IRES-GFP Gerd A. Blobel lab Zhang et al.38 (Continued on next page) Molecular Cell 85, 376–393.e1–e9, January 16, 2025 e2 ..
Western Blot:Article Title: LDB1 establishes multi-enhancer networks to regulate gene expression.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Mouse monoclonal anti-LDB1 CLIM-2 (C-9) Santa Cruz Biotechnology Cat#sc-365074; RRID: AB_10848267 Rabbit polyclonal anti-LDB1 Lot# VI3089586A Thermo Fisher Scientific Cat#PA5-56948; RRID: AB_2643320 Mouse monoclonal anti-GAPDH Lot# A1822 (6C5) Santa Cruz Biotechnology Cat#sc-32233; RRID: AB_627679 Rabbit monoclonal anti-RPB1 (Pol2) (D8L4Y) Cell Signaling Technology Cat#14958; RRID: AB_2687876 Rabbit polyclonal anti-YY1 Active Motif Cat#61779; RRID: AB_2793763 Rabbit polyclonal anti-CTCF Millipore Cat#07-729; RRID: AB_441965 Rabbit polyclonal anti-RAD21 Abcam Cat#ab992; RRID: AB_2176601 Mouse monoclonal anti-pMPM2 Millipore Cat# 05-368; RRID: AB_309698 F(ab’)2-Goat anti-Mouse IgG (H+L) Secondary Antibody, APC, eBioscience Thermo Fisher Scientific Cat#17-4010-82; RRID: AB_2573203 Chemicals, peptides, and recombinant proteins AMPure XP Beckman Coulter Cat#A63880 Indole-3-acetic acid sodium salt (auxin) Sigma Aldrich Cat#I5148 estradiol Sigma Aldrich Cat#E2758 iSCRIPT Reverse Transcription Supermix Bio Rad Cat#1708840 Power SYBR Green PCR Master Mix Thermo Fisher Scientific Cat#4367660 Protein A agarose beads Thermo Fisher Scientific Cat#15918014 Protein G agarose beads Thermo Fisher Scientific Cat#15920010 DSG crosslinker ProteoChem Cat#c1104-1gm cOmplete Mini, EDTA-free Millipore Sigma Cat#11836170001 MNase Worthington Biochemical Cat#LS004798 rSAP New England Biolabs Cat#M0371S T4 PNK New England Biolabs Cat#M0201S Large (Klenow) Fragment New England Biolabs Cat#M0210S Biotin-11-dCTP Jena Bioscience Cat#NU-809-BIOX-S Biotin-14-dATP Jena Bioscience Cat#NU-835-BIO14-S Biotin-14-dATP Active Motif Cat#14138 T4 DNA Ligase New England Biolabs Cat#M0202S T4 DNA Ligase buffer New England Biolabs Cat#B0202S Dynabeads MyOne Streptavidin C1 Thermo Fisher Scientific Cat#65001 KAPA HiFi HotStart ReadyMix Roche Cat#08202940001 Herculase II Fusion DNA Polymerase Agilent Cat#600675 Mouse Cot-1 DNA Thermo Fisher Scientific Cat#18440016 Twist Universal Blockers Twist Bioscience Cat#100578 Twist Binding and Purification Beads Twist Bioscience Cat#100983 Dynabeads M-270 Streptavidn Thermo Fisher Scientic Cat#65305 NlaIII New England Biolabs Cat#R0125L NEB Buffer 2 New England Biolabs Cat#7002S NEB Buffer 3.1 New England Biolabs Cat#B7203S DpnII New England Biolabs Cat#R0543M VAHTS DNA Clean Beads Vazyme Cat#N411 (Continued on next page) e1 Molecular Cell 85, 376–393.e1–e9, January 16, 2025 .. REAGENT or RESOURCE SOURCE IDENTIFIER T4 DNA polymerase New England Biolabs CatM0203S 4-thiouridine (4SU) MedChemExpress Cat#HY-W011793 TRIzol Reagent Invitrogen Cat#15596026 MTSEA-biotin Biotium Cat# 90064 Critical commercial assays KAPA HyperCapture Reagent Kit Roche Cat#9075810001 Twist Hybridization and Wash Kit with Amplification Mix, 12 Reactions Twist Bioscience Cat#104178 RNeasy Mini Kit QIAGEN Cat#74104 QIAshredder QIAGEN Cat#79656 NEBNext Ultra II DNA Library Prep Kit for Illumina New England Biolabs Cat#E7645S NEBNext Multiplex Oligos for Illumina (96 Unique Dual Index Primer Pairs) New England Biolabs Cat#E6440S TruSeq Stranded mRNA kit Illumina Cat#20020594 Illumina Stranded Total RNA Prep Illumina Cat# 20040525 Qubit dsDNA Quantification Assay Kits Thermo Fisher Scientific Cat#Q32850 In-Fusion HD Cloning kit Takara Cat#639648 QIAquick PCR Purification Kit QIAGEN Cat#28104 QIAquick Gel Extraction Kit QIAGEN Cat#28704 AHTS Universal DNA Library Prep Kit Vazyme Cat#ND627-01 Deposited data LDB1-AID Micro-C This paper GSE254373 LDB1-AID RCMC This paper GSE266450 LDB1-AID TT-seq This paper GSE264584 LDB1-AID Tri-C This paper GSE254372 LDB1-AID RNA-seq This paper GSE264455 SMC3-AID Hi-C Zhao et al.103 GSE228402 CTCF-AID Hi-C Zhang et al.26 GSE168251 YY1-AID Micro-C Lam et al.84 GSE247254 Mitotic Hi-C Zhang et al.38 GSE129997 Mitotic ChIP-seq (CTCF/RAD21) Zhang et al.38 GSE129997 H3K27ac ChIP-seq Dogan et al.104 GSE61349 LDB1-AID ChIP-seq This paper GSE254377 SMC3-AID ChIP-seq This paper GSE254377 Original western blot data This paper, Mendeley Data https://doi.org/10.17632/mf78pvcrkk.2 Experimental models: Cell lines G1E-ER4 Mitchell J. Weiss lab Weiss et al.82 LDB1-AID This paper N/A YY1-AID Gerd Blobel Lab Lam et al.84 SMC3-AID Haoyue Zhang Lab Zhao et al.103 CTCF-AID Gerd A. Blobel lab Zhang et al.26 Oligonucleotides See Table S2 for oligonucleotides used in this study This paper Table S2 Recombinant DNA pX458-GFP Addgene 48138 md-mCherry Gerd A. Blobel lab Zhang et al.38 OsTiR-IRES-GFP Gerd A. Blobel lab Zhang et al.38 (Continued on next page) Molecular Cell 85, 376–393.e1–e9, January 16, 2025 e2 ..
Reverse Transcription:Article Title: Graft-seq precisely maps RNA modifications via site-specific chemical grafting strategy.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-7-methylguanosine (m 7 G)-Cap mAb MBL life science Cat# RN016M; RRID: AB_2921296 Goat anti-Mouse IgG HRP HuaBio Cat# HA1006; RRID: AB_2819167 Chemicals, peptides, and recombinant proteins 3 M Sodium Acetate Solution, pH 5.2 Thermo Scientific Cat# R1181 3 ′ -Desthiobiotin-GTP; DTB-GTP New England Biolabs Cat# N0761 3-azido-1-propanol Sigma-Aldrich Cat# 776130 ADP-ribosylcyclase; ADPRC Sigma-Aldrich Cat# A9106 Alexa Fluor 488 Azide Invitrogen Cat# A10266 Ammonium iron(II) sulfate hexahydrate Sigma-Aldrich Cat# 09719 ATP New England Biolabs Cat# P0756S Biotin-Azide QIYUEBIO Cat# QY-24297 Blotting membranes, Amersham TM Hybond TM -N+ GE Healthcare Cat# RPN303B Bst 2.0 DNA polymerase New England Biolabs Cat# M0537S CleanCap Reagent M6 Trilink Cat# N-7453 Copper(II) sulfate pentahydrate Sigma-Aldrich Cat# C3036 D-biotin MedChemExpress Cat# HY-B0511 Dibenzocyclooctyne-maleimide Sigma-Aldrich Cat# 760668 DL-Dithiothreitol; DTT Sigma-Aldrich Cat# V900830 DMEM/high-glucose medium HyClone Cat# SH30243.01 DMF Sigma-Aldrich Cat# D4551 DMSO Sigma-Aldrich Cat# 41639 DNase I New England Biolabs Cat# M0303 dTTP (100 mM) Thermo Scientific Cat# R0171 EDTA (0.5 M),pH 8.0 Invitrogen Cat# AM9260G Fetal Bovine Serum Gibco Cat# 10270 Fetal Bovine Serum, Sterile(irradiated) Ausbian Cat# VS500T GlutaMAX Gibco Cat# 35050061 Glycogen Invitrogen Cat# AM9510 HEPES Sigma-Aldrich Cat# V900477 HRP-streptavidin Invitrogen Cat# 434323 L-Ascorbic acid Sigma-Aldrich Cat# 95209 m 6 ATP Trilink Cat# N-1013 Maxima H Minus Reverse Transcriptase Thermo Scientific Cat# EP0751 MEM Non-Essential Amino Acids Solution (100X) Gibco Cat# 11140 mRNA decapping enzyme New England Biolabs Cat# M0608S NAD Sigma-Aldrich Cat# N6522 Non-fat Powdered milk BBI Life Sciences Cat# A600669 Nuclease P1 Wako Cat# 145-08221 Penicillin/streptomycin Gibco Cat# 15140 Penicillin-Streptomycin HyClone Cat# SV30010 Phanta Max Super-Fidelity DNA Polymerase Vazyme Cat# P505 Potassium chloride Sigma-Aldrich Cat# P9541 PrimerScript II Reverse Transcriptase Takara Cat# 6210A PrimerScript Reverse Transcriptase Takara Cat# 6110A (Continued on next page) e1 Cell Reports Methods 5, 101103, July 21, 2025 OPEN ACCESS .. REAGENT or RESOURCE SOURCE IDENTIFIER Quick CIP New England Biolabs Cat# M0525 rCutSmart buffer New England Biolabs Cat# B6004V Recombinant Mouse LIF Protein Milipore Cat# ESG1107 Reverse Transcriptase, Recombinant HIV Worthington Biochemical Corporation Cat# LS05003 RevertAid Reverse Transcriptase Thermo Scientific Cat# EP0442 RNase inhibitor Vazyme Cat# R301 RppH New England Biolabs Cat# M0356 rSAP New England Biolabs Cat# M0371S SMARTScribe Reverse Transcriptase Clontech Cat# 639536 Sodium L-ascorbate Energy Chemical Cat# E082526 Sodium pyruvate Gibco Cat# 11360 SplintR ligase New England Biolabs Cat# M0375S SuperScript II Reverse Transcriptase Invitrogen Cat# 18064071 T4 Polynucleotide Kinase; T4 PNK New England Biolabs Cat# M0201 TGIRT III Reverse Transcriptase InGex Cat# CM0101 ThermoPol Reaction Buffer New England Biolabs Cat# B90004 Tris(3-hydroxypropyltriazolylmethyl)amine Sigma-Aldrich Cat# 762342 Trizol Invitrogen Cat# 10296010 Tween 20 Sigma-Aldrich Cat# V900548 Vaccinia Capping System New England Biolabs Cat# M2080S yDcpS New England Biolabs Cat# M0463S α-L-Ascorbic acid; α-KG Sigma-Aldrich Cat# 75890 β-mercaptoethanol Gibco Cat# 21985023 Critical commercial assays GenElute mRNA Purification Miniprep Kit Sigma-Aldrich Cat# MRN10-1KT NEBNext rRNA Depletion Kit New England Biolabs Cat# E7400 HiScribe T7 High Yield RNA Synthesis Kit New England Biolabs Cat# E2040 RNA Clean & Concentrator-25 kit Zymo Research Cat# R1017 RNA Clean & Concentrator-5 kit Zymo Research Cat# R1013 RNAClean XP beads Beckman Coulter Cat# A63987 QIAquick Gel Extraction Kit QIAGEN Cat# 28704 ABclonal Zero TOPO-TA/Blunt Cloning Kit ABclonal Cat# RK30130 AMPure XP beads Beckman Coulter Cat# A63881 NEBNext Magnesium RNA Fragmentation Module New England Biolabs Cat# E6150 Dynabeads Protein A Invitrogen Cat# 10002D Dynabeads MyOne Streptavidin C1 Invitrogen Cat# 65001 NEBNext Multiplex Small RNA Library Prep Kit for Illumina New England Biolabs Cat# E7560S ChamQ Universal SYBR qPCR Master Mix Vazyme Cat# Q711-03 SuperSignal West Pico PLUS Chemiluminescent Substrate Thermo Scientific Cat# 34577 Deposited data Raw data This paper GSA-Human: HRA009209; GSA: CRA020263 Experimental models: Cell lines HEK293T ATCC Cat# ATCC-CRL-3216 HeLa ATCC Cat# ATCC-CCL-2 mouse ESC E14 Lab of Li Shen (Zhejiang University) N/A (Continued on next page) Cell Reports Methods 5, 101103, July 21, 2025 e2 OPEN ACCESS ..
Article Title: Graft-seq precisely maps RNA modifications via site-specific chemical grafting strategy
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-7-methylguanosine (m7G)-Cap mAb MBL life science Cat# RN016M; RRID: AB_2921296 Goat anti-Mouse IgG HRP HuaBio Cat# HA1006; RRID: AB_2819167 Chemicals, peptides, and recombinant proteins 3 M Sodium Acetate Solution, pH 5.2 Thermo Scientific Cat# R1181 3′-Desthiobiotin-GTP; DTB-GTP New England Biolabs Cat# N0761 3-azido-1-propanol Sigma-Aldrich Cat# 776130 ADP-ribosylcyclase; ADPRC Sigma-Aldrich Cat# A9106 Alexa Fluor 488 Azide Invitrogen Cat# A10266 Ammonium iron(II) sulfate hexahydrate Sigma-Aldrich Cat# 09719 ATP New England Biolabs Cat# P0756S Biotin-Azide QIYUEBIO Cat# QY-24297 Blotting membranes, AmershamTM HybondTM-N+ GE Healthcare Cat# RPN303B Bst 2.0 DNA polymerase New England Biolabs Cat# M0537S CleanCap Reagent M6 Trilink Cat# N-7453 Copper(II) sulfate pentahydrate Sigma-Aldrich Cat# C3036 D-biotin MedChemExpress Cat# HY-B0511 Dibenzocyclooctyne-maleimide Sigma-Aldrich Cat# 760668 DL-Dithiothreitol; DTT Sigma-Aldrich Cat# V900830 DMEM/high-glucose medium HyClone Cat# SH30243.01 DMF Sigma-Aldrich Cat# D4551 DMSO Sigma-Aldrich Cat# 41639 DNase I New England Biolabs Cat# M0303 dTTP (100 mM) Thermo Scientific Cat# R0171 EDTA (0.5 M),pH 8.0 Invitrogen Cat# AM9260G Fetal Bovine Serum Gibco Cat# 10270 Fetal Bovine Serum, Sterile(irradiated) Ausbian Cat# VS500T GlutaMAX Gibco Cat# 35050061 Glycogen Invitrogen Cat# AM9510 HEPES Sigma-Aldrich Cat# V900477 HRP-streptavidin Invitrogen Cat# 434323 L-Ascorbic acid Sigma-Aldrich Cat# 95209 m6ATP Trilink Cat# N-1013 Maxima H Minus Reverse Transcriptase Thermo Scientific Cat# EP0751 MEM Non-Essential Amino Acids Solution (100X) Gibco Cat# 11140 mRNA decapping enzyme New England Biolabs Cat# M0608S NAD Sigma-Aldrich Cat# N6522 Non-fat Powdered milk BBI Life Sciences Cat# A600669 Nuclease P1 Wako Cat# 145-08221 Penicillin/streptomycin Gibco Cat# 15140 Penicillin-Streptomycin HyClone Cat# SV30010 Phanta Max Super-Fidelity DNA Polymerase Vazyme Cat# P505 Potassium chloride Sigma-Aldrich Cat# P9541 PrimerScript II Reverse Transcriptase Takara Cat# 6210A PrimerScript Reverse Transcriptase Takara Cat# 6110A (Continued on next page) e1 Cell Reports Methods 5, 101103, July 21, 2025 Article ll OPEN ACCESS .. REAGENT or RESOURCE SOURCE IDENTIFIER Quick CIP New England Biolabs Cat# M0525 rCutSmart buffer New England Biolabs Cat# B6004V Recombinant Mouse LIF Protein Milipore Cat# ESG1107 Reverse Transcriptase, Recombinant HIV Worthington Biochemical Corporation Cat# LS05003 RevertAid Reverse Transcriptase Thermo Scientific Cat# EP0442 RNase inhibitor Vazyme Cat# R301 RppH New England Biolabs Cat# M0356 rSAP New England Biolabs Cat# M0371S SMARTScribe Reverse Transcriptase Clontech Cat# 639536 Sodium L-ascorbate Energy Chemical Cat# E082526 Sodium pyruvate Gibco Cat# 11360 SplintR ligase New England Biolabs Cat# M0375S SuperScript II Reverse Transcriptase Invitrogen Cat# 18064071 T4 Polynucleotide Kinase; T4 PNK New England Biolabs Cat# M0201 TGIRT III Reverse Transcriptase InGex Cat# CM0101 ThermoPol Reaction Buffer New England Biolabs Cat# B90004 Tris(3-hydroxypropyltriazolylmethyl)amine Sigma-Aldrich Cat# 762342 Trizol Invitrogen Cat# 10296010 Tween 20 Sigma-Aldrich Cat# V900548 Vaccinia Capping System New England Biolabs Cat# M2080S yDcpS New England Biolabs Cat# M0463S α-L-Ascorbic acid; α-KG Sigma-Aldrich Cat# 75890 β-mercaptoethanol Gibco Cat# 21985023 Critical commercial assays GenElute mRNA Purification Miniprep Kit Sigma-Aldrich Cat# MRN10-1KT NEBNext rRNA Depletion Kit New England Biolabs Cat# E7400 HiScribe T7 High Yield RNA Synthesis Kit New England Biolabs Cat# E2040 RNA Clean & Concentrator-25 kit Zymo Research Cat# R1017 RNA Clean & Concentrator-5 kit Zymo Research Cat# R1013 RNAClean XP beads Beckman Coulter Cat# A63987 QIAquick Gel Extraction Kit QIAGEN Cat# 28704 ABclonal Zero TOPO-TA/Blunt Cloning Kit ABclonal Cat# RK30130 AMPure XP beads Beckman Coulter Cat# A63881 NEBNext Magnesium RNA Fragmentation Module New England Biolabs Cat# E6150 Dynabeads Protein A Invitrogen Cat# 10002D Dynabeads MyOne Streptavidin C1 Invitrogen Cat# 65001 NEBNext Multiplex Small RNA Library Prep Kit for Illumina New England Biolabs Cat# E7560S ChamQ Universal SYBR qPCR Master Mix Vazyme Cat# Q711-03 SuperSignal West Pico PLUS Chemiluminescent Substrate Thermo Scientific Cat# 34577 Deposited data Raw data This paper GSA-Human: HRA009209; GSA: CRA020263 Experimental models: Cell lines HEK293T ATCC Cat# ATCC-CRL-3216 HeLa ATCC Cat# ATCC-CCL-2 mouse ESC E14 Lab of Li Shen (Zhejiang University) N/A (Continued on next page) Cell Reports Methods 5, 101103, July 21, 2025 e2 Article ll OPEN ACCESS ..
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