Recombinant:
Article Title: CTCF DNA-binding domain undergoes dynamic and selective protein-protein interactions.
Article Snippet: Antibodies Rabbit polyclonal anti-CTCF Millipore Cat# 07-729; RRID: AB_441965 Rabbit polyclonal anti-CTCF Abcam Cat# ab128873; RRID: AB_11144295 Rabbit polyclonal anti-CTCF Active motif Cat# 61311; RRID: AB_2614975 Rabbit polyclonal anti-HaloTag Promega Cat# G9281; RRID: AB_713650 Rabbit monoclonal anti-FLAG Sigma-Aldrich Cat# F1804; RRID: AB_262044 Rabbit monoclonal anti-BRD2 Cell Signaling Technology Cat# 5848; RRID: AB_10835146 Mouse monoclonal anti-GAPDH Proteintech Cat# 60004-1-Ig; RRID: AB_2107436 Mouse monoclonal anti-Actin Proteintech Cat# 66009-1-Ig; RRID: AB_2687938 Donkey anti-Rabbit IgG, Alexa Fluor 488 Invitrogen Cat# A-21206; RRID: AB_2535792 Donkey anti-Rabbit IgG, Alexa Fluor 568 Invitrogen Cat# A-10042; RRID: AB_2534017 Rabbit IgG HRP Linked Whole Ab Sigma-Aldrich Cat# GENA934-1ML; RRID: AB_2722659 Mouse IgG HRP Linked Whole Ab Sigma-Aldrich Cat# GENXA931-1ML; RRID: AB_772209 .. Chemicals, peptides, and recombinant proteins Halotag-JF549 ligand Promega Cat# GA1110 Indole-3-acetic acid Sigma-Aldrich Cat# I5148 GSK3b inhibitor CHIR99021 Selleck Chemicals Cat# S2924 MEK inhibitor PD0325901 Selleck Chemicals Cat# S1036 YOYO-1 Thermo Fisher Cat# Y3601 SYBR Safe Thermo Fisher Cat# S33102 mLIF Millipore Cat# ESG1107 ..
Article Title: Ligand-receptor promiscuity enables cellular addressing.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Chemicals, Peptides, and Recombinant Proteins BMP2 R&D Systems Cat# 355-BM BMP9 R&D Systems Cat# 5566-BP BMP10 R&D Systems Cat# 6038-BP Fetal Bovine Serum Clontech Cat# 631367 Fetal Bovine Serum, ES Cell Qualified Gibco Cat# 16141 Leukemia Inhibitory Factor MilliporeSigma Cat# ESG1107 Trypsin Gibco Cat# 25200 Accutase Gibco Cat# A11105 Deposited Data Optimization and simulation results This paper https://doi.org/10.22002/D1.1692 Experimental measurements of BMP responses in multiple cell lines This paper https://doi.org/10.22002/D1.1692 Experimental Models: Cell Lines NMuMG sensor line Klumpe et al., 2022 N/A NMuMG sensor line with ACVR1 knockdown Klumpe et al., 2022 N/A NMuMG sensor line with BMPR2 knockdown Klumpe et al., 2022 N/A NMuMG sensor line with ACVRL1 overexpression Klumpe et al., 2022 N/A mESC sensor line Antebi et al., 2017 N/A Software and Algorithms MATLAB MathWorks N/A Python Python Software Foundation N/A Equilibrium Toolkit (EQTK) (Python) Bois, 2020 https://github.com/justinbois/eqtk and https://doi.org/10.22002/D1.1430 PromiSys (Python) This paper https://github.com/christinasu/PromiSys and https://doi.org/10.22002/D1.20047 Simulation and analysis code (Python) This paper https://github.com/christinasu/PromiSys and https://doi.org/10.22002/D1.20047 EasyFlow (MATLAB) Antebi et al., 2017 https://github.com/AntebiLab/easyflow ..
Article Title: A mouse model with high clonal barcode diversity for joint lineage, transcriptomic, and epigenomic profiling in single cells.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies FC Receptor Block eBioscience Cat# 156604 biotin-conjugated lineage antibody cocktail Miltenyi Biotec Cat# 130-090-858 Streptavidin eFluor 450 eBioscience Cat# 48-4317-82 Streptavidin PE-Cy7 eBioscience Cat# 25-4317-82; RRID: AB_10116480 APC anti-mouse CD117 (c-kit) [ACK2] BioLegend Cat# 135108; RRID: AB_2028407 PE anti-mouse Ly-6A/E (Sca-1) [D7] eBioscience Cat# 12-5981-83; RRID: AB_466087 PE-Cy7 anti-mouse Ly-6A/E (Sca-1) [D7] eBioscience Cat# 25-5981-82; RRID: AB_469669 APC-Cy7 anti-mouse CD48 [HM48-1] BD Pharmingen Cat# 561242 PE-Cy5 anti-mouse CD150 [TC15-12F12.2] BioLegend Cat# 115912; RRID: AB_493598 BV605 anti-mouse CD41 [MWReg30] BioLegend Cat# 133921; RRID: AB_2563933 APC anti-mouse/human CD45R/B220 [RA3-6B2] BioLegend Cat# 17-0452-83 PE anti-mouse Ly-6G [1A8] BioLegend Cat# 127608; RRID: AB_1186099 APC-Cy7 anti-mouse CD11b (Mac1) [M1/70] BD Pharmingen Cat# 557657 PE-Cyanine5 anti-mouse Ter-119 [TER-119] eBioscience Cat# 15-5921-83; RRID: AB_468811 Brilliant Violet 605 anti-mouse CD45 Antibody [30-F11] BioLegend Cat# 103140; RRID: AB_2562342 PerCP/Cy5.5 anti-mouse CD31 [MEC13.3] BioLegend Cat# 102522; RRID: AB_2566761 Anti-SSEA-1 Mouse Monoclonal Antibody (Biotin) [clone: MC-480] BioLegend Cat# 125604; RRID: AB_1089194 DAPI (4’,6-Diamidino-2-Phenylindole, Dihydrochloride) Invitrogen Cat# D1306; RRID: AB_2629482 Chemicals, Peptides, and Recombinant Proteins Doxycycline Sigma Cat# D9891 Knock-Out DMEM GIBCO Cat# 10829018 ESC US Qualified FBS GIBCO Cat# 16141079 LIF EMD Millipore Cat# ESG1107 Chiron Sigma Cat# SML1046 Mirdametinib Selleck Chemicals Cat# S1036 Non-essential amino acids GIBCO Cat# 11140-050 L-Glutamine GIBCO Cat# 25030164 Penicillin-Streptomycin GIBCO Cat# 15140-163 MEM NEAA GIBCO Cat# 11140050 b-Mercaptoethanol GIBCO Cat# 21985023 Mitomycin C Santa-Cruz Cat# CAS 50-07-7 Hygromycin GIBCO Cat# 10687010 Puromycin Sigma-Aldrich Cat# P9620 fetal bovine serum (FBS) Gibco Cat# A3160401 Trypsin-EDTA (0.05%) GIBCO Cat# 25300120 Collagenase Sigma-Aldrich Cat# C0130 Trizol Invitrogen Cat# 15596018 Qiagen protease Qiagen Cat# 19155 Superscript III Reverse Transcriptase Invitrogen Cat# 18080-044 (Continued on next page) e1 Cell 186, 5183–5199.e1–e11, November 9, 2023 .. REAGENT or RESOURCE SOURCE IDENTIFIER Q5 polymerase New England Biolabs (NEB) Cat# M0491 KAPA HiFi HotStart ReadyMix Roche Applied Science Cat# 07958935001 dNTPs New England Biolabs (NEB) Cat# N0446 SuperScript II Reverse Transcriptase Thermo Scientific Cat# 18064014 GpC Methyltransferase (M.CviPI) New England Biolabs (NEB) Cat# M0227L PhiX Control v3 Illumina Cat# FC-110-3001 Critical Commercial Assays Nebuilder HiFi DNA Assembly New England Biolabs (NEB) Cat# E5520S Endotoxin-free plasmid maxiprep kit Takara Cat# 740424.10 Mouse Nucleofector Kit Lonza Cat# VPH-1001 MACS Separation Columns Miltenyi Biotec Cat# 130-042-401 AMPure XP beads Beckman Coulter Cat# A63881 SPRIselect reagent Beckman Coulter Cat# B23318 Dynabeads Myone Carboxylic Acid Invitrogen Cat# 65011 Chromium Next GEM Single Cell 30 Kit v3.1 10X Genomics Cat# PN-1000268 Dual Index Kit TT Set A 10x Genomics Cat# PN-1000215 EZ-96 DNA Methylation-Direct MagPrep Zymo Research Cat# D5044 Klenow Fragment (30-50 exo-) New England Biolabs (NEB) Cat# M0212L KAPA Library Quantification Kit Kappa Biosystems Cat# KK4835 MiSeq Reagent Kit v2 (500 cycles) Illumina Cat# MS-102-2003 Deposited data Raw and processed data This paper GEO: GSE222486 Experimental Models: Cell Lines DR4-MEFs ATCC SCRC-1045 KH2 mESCs Beard et al.39 N/A JM8A3 mESCs Pettitt et al.65 N/A Cas9–TdT mESCs This paper N/A Cas9-TdT-gRNAs mESCs This paper N/A Tigre-target-array (TA) mESCs This paper N/A Rosa26-target-array (RA) mESCs This paper N/A Cas9-TdT-gRNAs-TA mESCs This paper N/A Experimental Models: Organisms/Strains Mouse: B6;129S4-Gt(ROSA) 26Sortm1(rtTA*M2)Jae Col1a1tm1(tetO-cas9)Sho/J Stuart H. Orkin Cat# JAX:029415; RRID: IMSR_JAX:029415 Col1a1-target-array mouse: B6;129S4Col1a1tm4(CAG-EGFP)Fcam/Mmjax Fernando Camargo MMRRC Strain #067061-JAX; RRID: MMRRC_067061-JAX Cas9-TdT mouse: B6;129S4-Gt(ROSA) 26Sortm1(rtTA*M2)Jae Col1a1tm1(Cas9-TdT) This paper N/A Cas9-TdT-gRNA mouse: B6;129S4Gt(ROSA)26Sortm1(rtTA*M2)Jae Col1a1tm5(tetO-Cas9/Dntt*)Fcam/J This paper Cat# JAX:038749 CA-TA-RA mouse: B6;129S4-Gt(ROSA) 26Sortm1(UBC-GFP)Fcam Igs7em1(CAG-mCherry)Fcam Col1a1tm4(CAG-EGFP) Fcam/J This paper Cat# JAX:038750 Oligonucleotides Primers, see Table S1 IDT N/A Recombinant DNA Plasmid: pCAG-Cas9 Addgene Cat# 48138; RRID: Addgene_48138 (Continued on next page) ll Cell 186, 5183–5199.e1–e11, November 9, 2023 e2 Resource
Knock-Out:Article Title: Combinatorial single molecule analysis of chromatin
Article Snippet: Mouse embryonic stem cells (ESCs) from a male mouse embryo (v6.5, NBP1-41162, Novus, USA) were cultured on mitotically inactivated mouse embryonic fibroblasts (MEFs, Globalstem, USA). .. ESCs were maintained in medium containing Knockout DMEM (Gibco, USA), 15% Fetal Bovine serum, 1% Pen/Strep (Gibco, USA), 1% Non-essential amino acids (Gibco, USA), 1% Glutamax (Gibco, USA), 0.01% LIF (ESG1107, Millipore, USA) and 0.0004% beta-mercaptoethanol. .. Mouse lung fibroblasts were purchased from ATCC (CCL-206) and grown in Eagle's Minimum Essential Medium (ATCC, 30-2003) with 10% Fetal Bovine serum.
Article Title: A mouse model with high clonal barcode diversity for joint lineage, transcriptomic, and epigenomic profiling in single cells.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies FC Receptor Block eBioscience Cat# 156604 biotin-conjugated lineage antibody cocktail Miltenyi Biotec Cat# 130-090-858 Streptavidin eFluor 450 eBioscience Cat# 48-4317-82 Streptavidin PE-Cy7 eBioscience Cat# 25-4317-82; RRID: AB_10116480 APC anti-mouse CD117 (c-kit) [ACK2] BioLegend Cat# 135108; RRID: AB_2028407 PE anti-mouse Ly-6A/E (Sca-1) [D7] eBioscience Cat# 12-5981-83; RRID: AB_466087 PE-Cy7 anti-mouse Ly-6A/E (Sca-1) [D7] eBioscience Cat# 25-5981-82; RRID: AB_469669 APC-Cy7 anti-mouse CD48 [HM48-1] BD Pharmingen Cat# 561242 PE-Cy5 anti-mouse CD150 [TC15-12F12.2] BioLegend Cat# 115912; RRID: AB_493598 BV605 anti-mouse CD41 [MWReg30] BioLegend Cat# 133921; RRID: AB_2563933 APC anti-mouse/human CD45R/B220 [RA3-6B2] BioLegend Cat# 17-0452-83 PE anti-mouse Ly-6G [1A8] BioLegend Cat# 127608; RRID: AB_1186099 APC-Cy7 anti-mouse CD11b (Mac1) [M1/70] BD Pharmingen Cat# 557657 PE-Cyanine5 anti-mouse Ter-119 [TER-119] eBioscience Cat# 15-5921-83; RRID: AB_468811 Brilliant Violet 605 anti-mouse CD45 Antibody [30-F11] BioLegend Cat# 103140; RRID: AB_2562342 PerCP/Cy5.5 anti-mouse CD31 [MEC13.3] BioLegend Cat# 102522; RRID: AB_2566761 Anti-SSEA-1 Mouse Monoclonal Antibody (Biotin) [clone: MC-480] BioLegend Cat# 125604; RRID: AB_1089194 DAPI (4’,6-Diamidino-2-Phenylindole, Dihydrochloride) Invitrogen Cat# D1306; RRID: AB_2629482 Chemicals, Peptides, and Recombinant Proteins Doxycycline Sigma Cat# D9891 Knock-Out DMEM GIBCO Cat# 10829018 ESC US Qualified FBS GIBCO Cat# 16141079 LIF EMD Millipore Cat# ESG1107 Chiron Sigma Cat# SML1046 Mirdametinib Selleck Chemicals Cat# S1036 Non-essential amino acids GIBCO Cat# 11140-050 L-Glutamine GIBCO Cat# 25030164 Penicillin-Streptomycin GIBCO Cat# 15140-163 MEM NEAA GIBCO Cat# 11140050 b-Mercaptoethanol GIBCO Cat# 21985023 Mitomycin C Santa-Cruz Cat# CAS 50-07-7 Hygromycin GIBCO Cat# 10687010 Puromycin Sigma-Aldrich Cat# P9620 fetal bovine serum (FBS) Gibco Cat# A3160401 Trypsin-EDTA (0.05%) GIBCO Cat# 25300120 Collagenase Sigma-Aldrich Cat# C0130 Trizol Invitrogen Cat# 15596018 Qiagen protease Qiagen Cat# 19155 Superscript III Reverse Transcriptase Invitrogen Cat# 18080-044 (Continued on next page) e1 Cell 186, 5183–5199.e1–e11, November 9, 2023 .. REAGENT or RESOURCE SOURCE IDENTIFIER Q5 polymerase New England Biolabs (NEB) Cat# M0491 KAPA HiFi HotStart ReadyMix Roche Applied Science Cat# 07958935001 dNTPs New England Biolabs (NEB) Cat# N0446 SuperScript II Reverse Transcriptase Thermo Scientific Cat# 18064014 GpC Methyltransferase (M.CviPI) New England Biolabs (NEB) Cat# M0227L PhiX Control v3 Illumina Cat# FC-110-3001 Critical Commercial Assays Nebuilder HiFi DNA Assembly New England Biolabs (NEB) Cat# E5520S Endotoxin-free plasmid maxiprep kit Takara Cat# 740424.10 Mouse Nucleofector Kit Lonza Cat# VPH-1001 MACS Separation Columns Miltenyi Biotec Cat# 130-042-401 AMPure XP beads Beckman Coulter Cat# A63881 SPRIselect reagent Beckman Coulter Cat# B23318 Dynabeads Myone Carboxylic Acid Invitrogen Cat# 65011 Chromium Next GEM Single Cell 30 Kit v3.1 10X Genomics Cat# PN-1000268 Dual Index Kit TT Set A 10x Genomics Cat# PN-1000215 EZ-96 DNA Methylation-Direct MagPrep Zymo Research Cat# D5044 Klenow Fragment (30-50 exo-) New England Biolabs (NEB) Cat# M0212L KAPA Library Quantification Kit Kappa Biosystems Cat# KK4835 MiSeq Reagent Kit v2 (500 cycles) Illumina Cat# MS-102-2003 Deposited data Raw and processed data This paper GEO: GSE222486 Experimental Models: Cell Lines DR4-MEFs ATCC SCRC-1045 KH2 mESCs Beard et al.39 N/A JM8A3 mESCs Pettitt et al.65 N/A Cas9–TdT mESCs This paper N/A Cas9-TdT-gRNAs mESCs This paper N/A Tigre-target-array (TA) mESCs This paper N/A Rosa26-target-array (RA) mESCs This paper N/A Cas9-TdT-gRNAs-TA mESCs This paper N/A Experimental Models: Organisms/Strains Mouse: B6;129S4-Gt(ROSA) 26Sortm1(rtTA*M2)Jae Col1a1tm1(tetO-cas9)Sho/J Stuart H. Orkin Cat# JAX:029415; RRID: IMSR_JAX:029415 Col1a1-target-array mouse: B6;129S4Col1a1tm4(CAG-EGFP)Fcam/Mmjax Fernando Camargo MMRRC Strain #067061-JAX; RRID: MMRRC_067061-JAX Cas9-TdT mouse: B6;129S4-Gt(ROSA) 26Sortm1(rtTA*M2)Jae Col1a1tm1(Cas9-TdT) This paper N/A Cas9-TdT-gRNA mouse: B6;129S4Gt(ROSA)26Sortm1(rtTA*M2)Jae Col1a1tm5(tetO-Cas9/Dntt*)Fcam/J This paper Cat# JAX:038749 CA-TA-RA mouse: B6;129S4-Gt(ROSA) 26Sortm1(UBC-GFP)Fcam Igs7em1(CAG-mCherry)Fcam Col1a1tm4(CAG-EGFP) Fcam/J This paper Cat# JAX:038750 Oligonucleotides Primers, see Table S1 IDT N/A Recombinant DNA Plasmid: pCAG-Cas9 Addgene Cat# 48138; RRID: Addgene_48138 (Continued on next page) ll Cell 186, 5183–5199.e1–e11, November 9, 2023 e2 Resource
Knockdown:Article Title: Ligand-receptor promiscuity enables cellular addressing.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Chemicals, Peptides, and Recombinant Proteins BMP2 R&D Systems Cat# 355-BM BMP9 R&D Systems Cat# 5566-BP BMP10 R&D Systems Cat# 6038-BP Fetal Bovine Serum Clontech Cat# 631367 Fetal Bovine Serum, ES Cell Qualified Gibco Cat# 16141 Leukemia Inhibitory Factor MilliporeSigma Cat# ESG1107 Trypsin Gibco Cat# 25200 Accutase Gibco Cat# A11105 Deposited Data Optimization and simulation results This paper https://doi.org/10.22002/D1.1692 Experimental measurements of BMP responses in multiple cell lines This paper https://doi.org/10.22002/D1.1692 Experimental Models: Cell Lines NMuMG sensor line Klumpe et al., 2022 N/A NMuMG sensor line with ACVR1 knockdown Klumpe et al., 2022 N/A NMuMG sensor line with BMPR2 knockdown Klumpe et al., 2022 N/A NMuMG sensor line with ACVRL1 overexpression Klumpe et al., 2022 N/A mESC sensor line Antebi et al., 2017 N/A Software and Algorithms MATLAB MathWorks N/A Python Python Software Foundation N/A Equilibrium Toolkit (EQTK) (Python) Bois, 2020 https://github.com/justinbois/eqtk and https://doi.org/10.22002/D1.1430 PromiSys (Python) This paper https://github.com/christinasu/PromiSys and https://doi.org/10.22002/D1.20047 Simulation and analysis code (Python) This paper https://github.com/christinasu/PromiSys and https://doi.org/10.22002/D1.20047 EasyFlow (MATLAB) Antebi et al., 2017 https://github.com/AntebiLab/easyflow ..
Over Expression:Article Title: Ligand-receptor promiscuity enables cellular addressing.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Chemicals, Peptides, and Recombinant Proteins BMP2 R&D Systems Cat# 355-BM BMP9 R&D Systems Cat# 5566-BP BMP10 R&D Systems Cat# 6038-BP Fetal Bovine Serum Clontech Cat# 631367 Fetal Bovine Serum, ES Cell Qualified Gibco Cat# 16141 Leukemia Inhibitory Factor MilliporeSigma Cat# ESG1107 Trypsin Gibco Cat# 25200 Accutase Gibco Cat# A11105 Deposited Data Optimization and simulation results This paper https://doi.org/10.22002/D1.1692 Experimental measurements of BMP responses in multiple cell lines This paper https://doi.org/10.22002/D1.1692 Experimental Models: Cell Lines NMuMG sensor line Klumpe et al., 2022 N/A NMuMG sensor line with ACVR1 knockdown Klumpe et al., 2022 N/A NMuMG sensor line with BMPR2 knockdown Klumpe et al., 2022 N/A NMuMG sensor line with ACVRL1 overexpression Klumpe et al., 2022 N/A mESC sensor line Antebi et al., 2017 N/A Software and Algorithms MATLAB MathWorks N/A Python Python Software Foundation N/A Equilibrium Toolkit (EQTK) (Python) Bois, 2020 https://github.com/justinbois/eqtk and https://doi.org/10.22002/D1.1430 PromiSys (Python) This paper https://github.com/christinasu/PromiSys and https://doi.org/10.22002/D1.20047 Simulation and analysis code (Python) This paper https://github.com/christinasu/PromiSys and https://doi.org/10.22002/D1.20047 EasyFlow (MATLAB) Antebi et al., 2017 https://github.com/AntebiLab/easyflow ..
Software:Article Title: Ligand-receptor promiscuity enables cellular addressing.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Chemicals, Peptides, and Recombinant Proteins BMP2 R&D Systems Cat# 355-BM BMP9 R&D Systems Cat# 5566-BP BMP10 R&D Systems Cat# 6038-BP Fetal Bovine Serum Clontech Cat# 631367 Fetal Bovine Serum, ES Cell Qualified Gibco Cat# 16141 Leukemia Inhibitory Factor MilliporeSigma Cat# ESG1107 Trypsin Gibco Cat# 25200 Accutase Gibco Cat# A11105 Deposited Data Optimization and simulation results This paper https://doi.org/10.22002/D1.1692 Experimental measurements of BMP responses in multiple cell lines This paper https://doi.org/10.22002/D1.1692 Experimental Models: Cell Lines NMuMG sensor line Klumpe et al., 2022 N/A NMuMG sensor line with ACVR1 knockdown Klumpe et al., 2022 N/A NMuMG sensor line with BMPR2 knockdown Klumpe et al., 2022 N/A NMuMG sensor line with ACVRL1 overexpression Klumpe et al., 2022 N/A mESC sensor line Antebi et al., 2017 N/A Software and Algorithms MATLAB MathWorks N/A Python Python Software Foundation N/A Equilibrium Toolkit (EQTK) (Python) Bois, 2020 https://github.com/justinbois/eqtk and https://doi.org/10.22002/D1.1430 PromiSys (Python) This paper https://github.com/christinasu/PromiSys and https://doi.org/10.22002/D1.20047 Simulation and analysis code (Python) This paper https://github.com/christinasu/PromiSys and https://doi.org/10.22002/D1.20047 EasyFlow (MATLAB) Antebi et al., 2017 https://github.com/AntebiLab/easyflow ..
other:Article Title: Single-Cell Multiomics Sequencing Reveals Prevalent Genomic Alterations in Tumor Stromal Cells of Human Colorectal Cancer.
Article Snippet: Mouse embryonic stem cells (mESCs) were maintained on gelatinized dishes without feeders in 2i [1 mM PD0325901 (Selleckchem, S1036), 3 mM CHIR99021 (Selleckchem, S1263)] media in the presence of 1,000 U/ml leukemia inhibitory factor (LIF, Millipore, ESG1107), 0.53 N-2 (Gibco, 17502048), 0.53 B-27 (Gibco, 10889038), 50 mg/ml Bovine Serum Albumin (BSA, Sigma-Aldrich, A3311), 2 mM L-Glutamine (Gibco, 2503081), 0.1 mM b-Mercaptoethanol (Sigma-Aldrich, M7522), 13 MEM Non-Essential Amino Acids Solution (NEAA, Gibco, 11140050), 100 U/ml Penicillin and 0.1mg/ml Streptomycin (Gibco, 15140122) in equal volume of Dulbecco’s modified eagle’s medium (DMEM/F-12, Gibco, 11320033) and Neurobasal Medium (Gibco, 21103049) for routine passage.
Article Title: Repurposing an adenine riboswitch into a fluorogenic imaging and sensing tag
Article Snippet: The −2i imaging media (without methionine and threonine) was prepared mixing these two media in 1:1 ratio and supplemented with 10 % dialyzed FBS (Gemini, no. 100–108), 1x GlutaMAX (Life Technologies, no. 35050–061), β-ME (55 μM final), and 1000 units/mL of LIF (Millipore Sigma no. ESG1107).
Blocking Assay:Article Title: A mouse model with high clonal barcode diversity for joint lineage, transcriptomic, and epigenomic profiling in single cells.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies FC Receptor Block eBioscience Cat# 156604 biotin-conjugated lineage antibody cocktail Miltenyi Biotec Cat# 130-090-858 Streptavidin eFluor 450 eBioscience Cat# 48-4317-82 Streptavidin PE-Cy7 eBioscience Cat# 25-4317-82; RRID: AB_10116480 APC anti-mouse CD117 (c-kit) [ACK2] BioLegend Cat# 135108; RRID: AB_2028407 PE anti-mouse Ly-6A/E (Sca-1) [D7] eBioscience Cat# 12-5981-83; RRID: AB_466087 PE-Cy7 anti-mouse Ly-6A/E (Sca-1) [D7] eBioscience Cat# 25-5981-82; RRID: AB_469669 APC-Cy7 anti-mouse CD48 [HM48-1] BD Pharmingen Cat# 561242 PE-Cy5 anti-mouse CD150 [TC15-12F12.2] BioLegend Cat# 115912; RRID: AB_493598 BV605 anti-mouse CD41 [MWReg30] BioLegend Cat# 133921; RRID: AB_2563933 APC anti-mouse/human CD45R/B220 [RA3-6B2] BioLegend Cat# 17-0452-83 PE anti-mouse Ly-6G [1A8] BioLegend Cat# 127608; RRID: AB_1186099 APC-Cy7 anti-mouse CD11b (Mac1) [M1/70] BD Pharmingen Cat# 557657 PE-Cyanine5 anti-mouse Ter-119 [TER-119] eBioscience Cat# 15-5921-83; RRID: AB_468811 Brilliant Violet 605 anti-mouse CD45 Antibody [30-F11] BioLegend Cat# 103140; RRID: AB_2562342 PerCP/Cy5.5 anti-mouse CD31 [MEC13.3] BioLegend Cat# 102522; RRID: AB_2566761 Anti-SSEA-1 Mouse Monoclonal Antibody (Biotin) [clone: MC-480] BioLegend Cat# 125604; RRID: AB_1089194 DAPI (4’,6-Diamidino-2-Phenylindole, Dihydrochloride) Invitrogen Cat# D1306; RRID: AB_2629482 Chemicals, Peptides, and Recombinant Proteins Doxycycline Sigma Cat# D9891 Knock-Out DMEM GIBCO Cat# 10829018 ESC US Qualified FBS GIBCO Cat# 16141079 LIF EMD Millipore Cat# ESG1107 Chiron Sigma Cat# SML1046 Mirdametinib Selleck Chemicals Cat# S1036 Non-essential amino acids GIBCO Cat# 11140-050 L-Glutamine GIBCO Cat# 25030164 Penicillin-Streptomycin GIBCO Cat# 15140-163 MEM NEAA GIBCO Cat# 11140050 b-Mercaptoethanol GIBCO Cat# 21985023 Mitomycin C Santa-Cruz Cat# CAS 50-07-7 Hygromycin GIBCO Cat# 10687010 Puromycin Sigma-Aldrich Cat# P9620 fetal bovine serum (FBS) Gibco Cat# A3160401 Trypsin-EDTA (0.05%) GIBCO Cat# 25300120 Collagenase Sigma-Aldrich Cat# C0130 Trizol Invitrogen Cat# 15596018 Qiagen protease Qiagen Cat# 19155 Superscript III Reverse Transcriptase Invitrogen Cat# 18080-044 (Continued on next page) e1 Cell 186, 5183–5199.e1–e11, November 9, 2023 .. REAGENT or RESOURCE SOURCE IDENTIFIER Q5 polymerase New England Biolabs (NEB) Cat# M0491 KAPA HiFi HotStart ReadyMix Roche Applied Science Cat# 07958935001 dNTPs New England Biolabs (NEB) Cat# N0446 SuperScript II Reverse Transcriptase Thermo Scientific Cat# 18064014 GpC Methyltransferase (M.CviPI) New England Biolabs (NEB) Cat# M0227L PhiX Control v3 Illumina Cat# FC-110-3001 Critical Commercial Assays Nebuilder HiFi DNA Assembly New England Biolabs (NEB) Cat# E5520S Endotoxin-free plasmid maxiprep kit Takara Cat# 740424.10 Mouse Nucleofector Kit Lonza Cat# VPH-1001 MACS Separation Columns Miltenyi Biotec Cat# 130-042-401 AMPure XP beads Beckman Coulter Cat# A63881 SPRIselect reagent Beckman Coulter Cat# B23318 Dynabeads Myone Carboxylic Acid Invitrogen Cat# 65011 Chromium Next GEM Single Cell 30 Kit v3.1 10X Genomics Cat# PN-1000268 Dual Index Kit TT Set A 10x Genomics Cat# PN-1000215 EZ-96 DNA Methylation-Direct MagPrep Zymo Research Cat# D5044 Klenow Fragment (30-50 exo-) New England Biolabs (NEB) Cat# M0212L KAPA Library Quantification Kit Kappa Biosystems Cat# KK4835 MiSeq Reagent Kit v2 (500 cycles) Illumina Cat# MS-102-2003 Deposited data Raw and processed data This paper GEO: GSE222486 Experimental Models: Cell Lines DR4-MEFs ATCC SCRC-1045 KH2 mESCs Beard et al.39 N/A JM8A3 mESCs Pettitt et al.65 N/A Cas9–TdT mESCs This paper N/A Cas9-TdT-gRNAs mESCs This paper N/A Tigre-target-array (TA) mESCs This paper N/A Rosa26-target-array (RA) mESCs This paper N/A Cas9-TdT-gRNAs-TA mESCs This paper N/A Experimental Models: Organisms/Strains Mouse: B6;129S4-Gt(ROSA) 26Sortm1(rtTA*M2)Jae Col1a1tm1(tetO-cas9)Sho/J Stuart H. Orkin Cat# JAX:029415; RRID: IMSR_JAX:029415 Col1a1-target-array mouse: B6;129S4Col1a1tm4(CAG-EGFP)Fcam/Mmjax Fernando Camargo MMRRC Strain #067061-JAX; RRID: MMRRC_067061-JAX Cas9-TdT mouse: B6;129S4-Gt(ROSA) 26Sortm1(rtTA*M2)Jae Col1a1tm1(Cas9-TdT) This paper N/A Cas9-TdT-gRNA mouse: B6;129S4Gt(ROSA)26Sortm1(rtTA*M2)Jae Col1a1tm5(tetO-Cas9/Dntt*)Fcam/J This paper Cat# JAX:038749 CA-TA-RA mouse: B6;129S4-Gt(ROSA) 26Sortm1(UBC-GFP)Fcam Igs7em1(CAG-mCherry)Fcam Col1a1tm4(CAG-EGFP) Fcam/J This paper Cat# JAX:038750 Oligonucleotides Primers, see Table S1 IDT N/A Recombinant DNA Plasmid: pCAG-Cas9 Addgene Cat# 48138; RRID: Addgene_48138 (Continued on next page) ll Cell 186, 5183–5199.e1–e11, November 9, 2023 e2 Resource
Reverse Transcription:Article Title: A mouse model with high clonal barcode diversity for joint lineage, transcriptomic, and epigenomic profiling in single cells.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies FC Receptor Block eBioscience Cat# 156604 biotin-conjugated lineage antibody cocktail Miltenyi Biotec Cat# 130-090-858 Streptavidin eFluor 450 eBioscience Cat# 48-4317-82 Streptavidin PE-Cy7 eBioscience Cat# 25-4317-82; RRID: AB_10116480 APC anti-mouse CD117 (c-kit) [ACK2] BioLegend Cat# 135108; RRID: AB_2028407 PE anti-mouse Ly-6A/E (Sca-1) [D7] eBioscience Cat# 12-5981-83; RRID: AB_466087 PE-Cy7 anti-mouse Ly-6A/E (Sca-1) [D7] eBioscience Cat# 25-5981-82; RRID: AB_469669 APC-Cy7 anti-mouse CD48 [HM48-1] BD Pharmingen Cat# 561242 PE-Cy5 anti-mouse CD150 [TC15-12F12.2] BioLegend Cat# 115912; RRID: AB_493598 BV605 anti-mouse CD41 [MWReg30] BioLegend Cat# 133921; RRID: AB_2563933 APC anti-mouse/human CD45R/B220 [RA3-6B2] BioLegend Cat# 17-0452-83 PE anti-mouse Ly-6G [1A8] BioLegend Cat# 127608; RRID: AB_1186099 APC-Cy7 anti-mouse CD11b (Mac1) [M1/70] BD Pharmingen Cat# 557657 PE-Cyanine5 anti-mouse Ter-119 [TER-119] eBioscience Cat# 15-5921-83; RRID: AB_468811 Brilliant Violet 605 anti-mouse CD45 Antibody [30-F11] BioLegend Cat# 103140; RRID: AB_2562342 PerCP/Cy5.5 anti-mouse CD31 [MEC13.3] BioLegend Cat# 102522; RRID: AB_2566761 Anti-SSEA-1 Mouse Monoclonal Antibody (Biotin) [clone: MC-480] BioLegend Cat# 125604; RRID: AB_1089194 DAPI (4’,6-Diamidino-2-Phenylindole, Dihydrochloride) Invitrogen Cat# D1306; RRID: AB_2629482 Chemicals, Peptides, and Recombinant Proteins Doxycycline Sigma Cat# D9891 Knock-Out DMEM GIBCO Cat# 10829018 ESC US Qualified FBS GIBCO Cat# 16141079 LIF EMD Millipore Cat# ESG1107 Chiron Sigma Cat# SML1046 Mirdametinib Selleck Chemicals Cat# S1036 Non-essential amino acids GIBCO Cat# 11140-050 L-Glutamine GIBCO Cat# 25030164 Penicillin-Streptomycin GIBCO Cat# 15140-163 MEM NEAA GIBCO Cat# 11140050 b-Mercaptoethanol GIBCO Cat# 21985023 Mitomycin C Santa-Cruz Cat# CAS 50-07-7 Hygromycin GIBCO Cat# 10687010 Puromycin Sigma-Aldrich Cat# P9620 fetal bovine serum (FBS) Gibco Cat# A3160401 Trypsin-EDTA (0.05%) GIBCO Cat# 25300120 Collagenase Sigma-Aldrich Cat# C0130 Trizol Invitrogen Cat# 15596018 Qiagen protease Qiagen Cat# 19155 Superscript III Reverse Transcriptase Invitrogen Cat# 18080-044 (Continued on next page) e1 Cell 186, 5183–5199.e1–e11, November 9, 2023 .. REAGENT or RESOURCE SOURCE IDENTIFIER Q5 polymerase New England Biolabs (NEB) Cat# M0491 KAPA HiFi HotStart ReadyMix Roche Applied Science Cat# 07958935001 dNTPs New England Biolabs (NEB) Cat# N0446 SuperScript II Reverse Transcriptase Thermo Scientific Cat# 18064014 GpC Methyltransferase (M.CviPI) New England Biolabs (NEB) Cat# M0227L PhiX Control v3 Illumina Cat# FC-110-3001 Critical Commercial Assays Nebuilder HiFi DNA Assembly New England Biolabs (NEB) Cat# E5520S Endotoxin-free plasmid maxiprep kit Takara Cat# 740424.10 Mouse Nucleofector Kit Lonza Cat# VPH-1001 MACS Separation Columns Miltenyi Biotec Cat# 130-042-401 AMPure XP beads Beckman Coulter Cat# A63881 SPRIselect reagent Beckman Coulter Cat# B23318 Dynabeads Myone Carboxylic Acid Invitrogen Cat# 65011 Chromium Next GEM Single Cell 30 Kit v3.1 10X Genomics Cat# PN-1000268 Dual Index Kit TT Set A 10x Genomics Cat# PN-1000215 EZ-96 DNA Methylation-Direct MagPrep Zymo Research Cat# D5044 Klenow Fragment (30-50 exo-) New England Biolabs (NEB) Cat# M0212L KAPA Library Quantification Kit Kappa Biosystems Cat# KK4835 MiSeq Reagent Kit v2 (500 cycles) Illumina Cat# MS-102-2003 Deposited data Raw and processed data This paper GEO: GSE222486 Experimental Models: Cell Lines DR4-MEFs ATCC SCRC-1045 KH2 mESCs Beard et al.39 N/A JM8A3 mESCs Pettitt et al.65 N/A Cas9–TdT mESCs This paper N/A Cas9-TdT-gRNAs mESCs This paper N/A Tigre-target-array (TA) mESCs This paper N/A Rosa26-target-array (RA) mESCs This paper N/A Cas9-TdT-gRNAs-TA mESCs This paper N/A Experimental Models: Organisms/Strains Mouse: B6;129S4-Gt(ROSA) 26Sortm1(rtTA*M2)Jae Col1a1tm1(tetO-cas9)Sho/J Stuart H. Orkin Cat# JAX:029415; RRID: IMSR_JAX:029415 Col1a1-target-array mouse: B6;129S4Col1a1tm4(CAG-EGFP)Fcam/Mmjax Fernando Camargo MMRRC Strain #067061-JAX; RRID: MMRRC_067061-JAX Cas9-TdT mouse: B6;129S4-Gt(ROSA) 26Sortm1(rtTA*M2)Jae Col1a1tm1(Cas9-TdT) This paper N/A Cas9-TdT-gRNA mouse: B6;129S4Gt(ROSA)26Sortm1(rtTA*M2)Jae Col1a1tm5(tetO-Cas9/Dntt*)Fcam/J This paper Cat# JAX:038749 CA-TA-RA mouse: B6;129S4-Gt(ROSA) 26Sortm1(UBC-GFP)Fcam Igs7em1(CAG-mCherry)Fcam Col1a1tm4(CAG-EGFP) Fcam/J This paper Cat# JAX:038750 Oligonucleotides Primers, see Table S1 IDT N/A Recombinant DNA Plasmid: pCAG-Cas9 Addgene Cat# 48138; RRID: Addgene_48138 (Continued on next page) ll Cell 186, 5183–5199.e1–e11, November 9, 2023 e2 Resource
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