Concentration Assay:Article Title: Lentiviral vectors for hematopoietic stem cell gene therapy restore α-globin expression in α-thalassemia red blood cells.
Article Snippet: .. Cells were maintained at a concentration of 3E5 cells per mL in REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies hCD45 (V450) BD HorizonCAT #560367 RRID: AB_1645573 hCD34 (APC) BD PharmingenCAT #555824 RRID: AB_398614 hCD34 (APC) BioLegend CAT #343509 RRID: AB_1877154 hCD19 (Pe-Cy7) BioLegendCAT # 302216 RRID: AB_314246 hCD56 (PE) BD PharmingenCAT #555516 RRID: AB_395906 hCD3 (APC-Cy7) BioLegendCAT #300318; RRID: AB_314053 hCD33 (BV711) BioLegendCAT #303424 RRID: AB_2565775 Bacterial and virus strains NEB® Stable Competent E. coli (High Efficiency) New England BioLabs C3040I Biological samples Mobilized CD34+ Stem/Progenitor Cells; GCSF; 1 × 10e6 cells, Cryo Charles River Laboratories N/A Human Bone Marrow Mononuclear Cells, Frozen STEMCELL CAT #70001.2 Human Cord Blood Mononuclear Cells, Frozen STEMCELL CAT #70007.1 Human Fetal Liver Mononuclear Cells, Frozen UCLA N/A Critical commercial assays PureLinkTM Genomic DNA Mini Kit ThermoFisher K182001 RNeasy Kits for RNA Purification Qiagen 74104 QIAGEN Plasmid Kits for Plasmid DNA Extraction Qiagen 12162 SuperScriptTM III First-Strand Synthesis System ThermoFisher 18080051 Deposited data RNA-seq For reviewers: GSE292575: Go to https://www.ncbi.nlm.nih.gov/ geo/query/acc.cgi?acc=GSE292575 Enter token ipkfemkwtnwnvev into the box. .. Accession number: GEO: GSE292575 Vector Integration Site VMHDS core, University of Pennsylvania http://github.com/BushmanLab/INSPIIRED RRID:SCR_02243320 accession number: PRJNA122524119,20 Experimental models: Cell lines HUDEP-2 https://doi.org/10.1371/journal.pone.0059890 N/A Experimental models: Organisms/strains NSG mice (NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ) Jackson Laboratories Cat# 005557 Software and algorithms SnapGene SnapGene 7.2.1 GraphPad Prism GraphPad 10.4.1 Loupe Browser Loupe Browser 8.0.0 R software www.r_project.org R.4.4.1 Cell Reports Medicine 6, 102362, October 21, 2025 e1 OPEN ACCESS StemSpan SFEM medium, supplemented with 1 μM dexamethasone and 1% glutamine, penicillin, streptomycin.
Virus:Article Title: Lentiviral vectors for hematopoietic stem cell gene therapy restore α-globin expression in α-thalassemia red blood cells.
Article Snippet: .. Cells were maintained at a concentration of 3E5 cells per mL in REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies hCD45 (V450) BD HorizonCAT #560367 RRID: AB_1645573 hCD34 (APC) BD PharmingenCAT #555824 RRID: AB_398614 hCD34 (APC) BioLegend CAT #343509 RRID: AB_1877154 hCD19 (Pe-Cy7) BioLegendCAT # 302216 RRID: AB_314246 hCD56 (PE) BD PharmingenCAT #555516 RRID: AB_395906 hCD3 (APC-Cy7) BioLegendCAT #300318; RRID: AB_314053 hCD33 (BV711) BioLegendCAT #303424 RRID: AB_2565775 Bacterial and virus strains NEB® Stable Competent E. coli (High Efficiency) New England BioLabs C3040I Biological samples Mobilized CD34+ Stem/Progenitor Cells; GCSF; 1 × 10e6 cells, Cryo Charles River Laboratories N/A Human Bone Marrow Mononuclear Cells, Frozen STEMCELL CAT #70001.2 Human Cord Blood Mononuclear Cells, Frozen STEMCELL CAT #70007.1 Human Fetal Liver Mononuclear Cells, Frozen UCLA N/A Critical commercial assays PureLinkTM Genomic DNA Mini Kit ThermoFisher K182001 RNeasy Kits for RNA Purification Qiagen 74104 QIAGEN Plasmid Kits for Plasmid DNA Extraction Qiagen 12162 SuperScriptTM III First-Strand Synthesis System ThermoFisher 18080051 Deposited data RNA-seq For reviewers: GSE292575: Go to https://www.ncbi.nlm.nih.gov/ geo/query/acc.cgi?acc=GSE292575 Enter token ipkfemkwtnwnvev into the box. .. Accession number: GEO: GSE292575 Vector Integration Site VMHDS core, University of Pennsylvania http://github.com/BushmanLab/INSPIIRED RRID:SCR_02243320 accession number: PRJNA122524119,20 Experimental models: Cell lines HUDEP-2 https://doi.org/10.1371/journal.pone.0059890 N/A Experimental models: Organisms/strains NSG mice (NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ) Jackson Laboratories Cat# 005557 Software and algorithms SnapGene SnapGene 7.2.1 GraphPad Prism GraphPad 10.4.1 Loupe Browser Loupe Browser 8.0.0 R software www.r_project.org R.4.4.1 Cell Reports Medicine 6, 102362, October 21, 2025 e1 OPEN ACCESS StemSpan SFEM medium, supplemented with 1 μM dexamethasone and 1% glutamine, penicillin, streptomycin.
Article Title: Alanine catabolism as a targetable vulnerability for MYC-driven liver cancer.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies α-GPT2 Sigma Cat# HPA051514; RRID: AB_2681516 α-GPT1 Abcam Cat# ab202083; RRID: AB_2915976 α-c-MYC, clone Y69 Abcam Cat# ab32072; RRID: AB_731658 α-β-actin-HRP Santa Cruz Cat# sc-47778; RRID: AB_2714189 α-Vinculin Cell Signaling Technologies Cat# 13901; RRID: AB_2728768 α-ATF4 Cell Signaling Technologies Cat# 11815; RRID: AB_2616025 α-eIF2α Cell Signaling Technologies Cat# 9722; RRID: AB_2230924 α-P-eIF2α Cell Signaling Technologies Cat# 3597; RRID: AB_390740 α-Rabbit IgG-HRP Promega Cat# W4011; RRID: AB_430833 Bacterial and virus strains NEB® Stable Competent E. coli (High Efficiency) New England Biolabs Cat# C3040H Chemicals, peptides, and recombinant proteins Doxycycline Fisher Scientific Cat# BP2653-5 L-Cycloserine MedChemExpress Cat# HY-B1122 Trypan blue Invitrogen Cat# T10282 DTT Fisher Scientific Cat# BP172-25G Heparin McKesson Cat# NDC 63739-931-14 Lipofectamine RNAi MAX Invitrogen Cat# AM9938 13C3; 15N-alanine Cambridge Isotopes Cat# CNLM-534-H-PK Trifluoromethanesulfonate Sigma Cat# 422843-5G Water; LC-MS grade Fisher Scientific Cat# W6-212 Methanol; LC-MS grade Fisher Scientific Cat# A456-500 Acetonitrile; LC-MS grade Fisher Scientific Cat# A955-4 Non-essential amino acids UCSF Cell Culture Facility Cat# CCFGA001-22BU01 L-Alanine Sigma Cat# A7627-100G L-Glutamine Sigma Cat# G3126-100G D-(+)-Glucose solution Sigma Cat# G8769-100ML Methyl-pruvate Thermo scientific Cat# A13966.14 Dimethyl-glutamate Thermo scientific Cat# L03764.06 Hoechst 33342 Biotium Cat# 40046 Propidium Iodide Invitrogen Cat# P3566 Critical commercial assays Alanine Transaminase Activity Assay Kit Abcam Cat# ab105134 DC protein assay kit Biorad Cat# 5000111 QIAshredder Kit Qiagen Cat# 79656 CYQUANT cell proliferation assay ThermoFisher Cat# C7026 Rneasy Mini Kit Qiagen Cat# 74106 High Capacity RNA-to-cDNA Kit Applied Biosystems Cat# 4387406 TaqMan Fast Advanced Master Mix Applied Biosystems Cat# 4444557 Mouse Gpt2 taqman probe Thermo fisher Cat# Mm00558028_m1 Gpt2 Mouse Actb taqman probe Thermo fisher Cat# Mm02619580_g1 Actb Mouse Gpt2 taqman probe Thermo fisher Cat# Hs99999903_m1 ACTB (Continued on next page) Cell Reports 45, 117107, April 28, 2026 13 .. REAGENT or RESOURCE SOURCE IDENTIFIER Mouse Actb taqman probe Thermo fisher Cat# Hs00370287_m1 GPT2 Deposited data The Cancer Genome Atlas (HCC) Ally et al.5 https://gdc.cancer.gov/; https:// www.cbioportal.org/study/ summary?id=lihc_tcga RNA sequencing and ChIP sequencing in the LT2-MYC model Kress et al.18 GEO: GSE76078 LT2-MYC metabolomics data Anderton et al.15 https://pmc.ncbi.nlm.nih.gov/articles/ PMC5376764/#embr201643068sup-0003 13C3; 15N-alanine tracing in the LT2-MYC model https://doi.org/10.21228/M8TK1K NMDR: ST004169 Experimental models: Cell lines EC4 Cao et al.50 N/A HepG2 ATCC HB-8065; RRID: CVCL_0027 Tong Xin Chen (University of Hawai’i Cancer Center) RRID: CVCL_V640 PLC5 Xin Chen (University of Hawai’i Cancer Center) CRL-8024; RRID: CVCL_0485 SNU475 Xin Chen (University of Hawai’i Cancer Center) CRL-2236; RRID: CVCL_0497 Experimental models: Organisms/strains C57BL/6 mice JAX Cat# 000664 Nude mice JAX Cat# 002019 LT2-MYC mice Shachaf et al.51 N/A GPT2 FLOX mice Martino et al.10 N/A Recombinant DNA pT3-MYC-IRES-CRE This study.
Article Title: FAME-CRISPR improves CRISPR-Cas9 genome editing via HDAC inhibition and engineered virus-like particle delivery.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Histone H3ac (pan-acetyl) Polyclonal antibody Thermo Fisher Scientific Cat# 39139; RRID: AB_2687871 Monoclonal ANTI-FLAG® M2 Sigma-Aldrich Cat# F3165-2MG; RRID: AB_259529 beta Actin Monoclonal antibody (AC-15) Thermo Fisher Scientific Cat# AM4302; RRID: AB_437394 Anti-GAPDH antibody [6C5] - Loading Control Abcam Cat# ab8245; RRID: AB_2107448 GFP tag Polyclonal antibody Proteintech Cat# 50430-2-AP; RRID: AB_11042881 Caspase-3 antibody Cell signaling Cat# 9662; RRID:AB_331439 Cleaved Caspase-3 (Asp175) (5A1E) antibody Cell signaling Cat# 9664; RRID: AB_2070042 ANTI-FLAG® M2 Magnetic Beads Sigma-Aldrich Cat# M8823-1ML; RRID: AB_2637089 γH2AX Abcam Cat# ab26350; RRID: AB_470861 Alexa Fluor 633 Invitrogen Cat# A-21050; RRID: AB_2535718 Bacterial and virus strains NEB® Stable Competent E. coli (High Efficiency) New England Biolabs # C3040I NEB® 5-alpha Competent E. coli (Subcloning Efficiency) New England Biolabs # C2988J Recombinant 3 rd generation Lentivirus – N/A 5 th generation engineered Virus-Like Particles (eVLPs) Raguram et al. 49 N/A Chemicals, peptides, and recombinant proteins LBH589 (Panobinostat) Sigma-Aldrich # SML3060-10MG Belinostat Sigma-Aldrich # SML3010-10MG SB505124 Sigma-Aldrich # S4696-5MG PCI-24781 Sigma-Aldrich # SML4043-5MG Valproic acid Sigma-Aldrich # P4543-10G DMSO Sigma-Aldrich # D2650-100ML Polybrene Sigma-Aldrich # TR-1003-50UL Lipofectamine 3000 Thermo Fisher Scientific # L3000015 Critical commercial assays AlamarBlue TM Cell Viability Reagents Thermo Fisher Scientific # DAL1100 Deposited data Raw Sanger Sequencing data This paper https://doi.org/10.17632/33tm3dd9dw.1 Raw immunofluorescent microscopy data This paper https://doi.org/10.17632/33tm3dd9dw.1 Uncropped gel images This paper https://doi.org/10.17632/33tm3dd9dw.1 Experimental models: Cell lines HeLa ATCC # CCL-2 HepG2 ATCC # HB-8065 .. MDA-MB-231 ATCC # HTB-26
Article Title: The structure of human sweetness.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies DYKDDDDK Tag Polyclonal Antibody Thermo Fisher Scientific Cat# PA1-984B; RRID: AB_347227 HA-Tag (C29F4) Rabbit mAb Cell Signaling Technology Cat# 3724; RRID: AB_1549585 GAPDH (14C10) Rabbit mAb Cell Signaling Technology Cat# 2118; RRID: AB_561053 Anti-Rabbit IgG - Alkaline Phosphatase antibody produced in goat Sigma-Aldrich Cat# A3687; RRID: AB_258103 Bacterial and virus strains NEB® Stable Competent E. coli (High Efficiency) New England Biolabs C3040H MAX EfficiencyTM DH10Bac Competent Cells Thermo Fisher Scientific 10361012 BL21(DE3) Competent E. coli New England Biolabs C2527H Chemicals, peptides, and recombinant proteins Sucralose Sigma-Aldrich 69293 Aspartame Sigma-Aldrich 47135 (±)-2-(p-Methoxyphenoxy)propionic acid (Lactisole) Sigma-Aldrich M6546 Cholesteryl Hemisuccinate (CHS) Tris Salt Anatrace CH210 Lauryl Maltose Neopentyl Glycol (LMNG) Anatrace NG310 Glyco-diosgenin (GDN) Anatrace GDN101 PEG400 Sigma-Aldrich 91893 Ethylene glycol Sigma-Aldrich 324558 Expi293TM Expression Medium Thermo Fisher Scientific A1435102 Sf-900 II SFM Thermo Fisher Scientific 10902104 Fetal Bovine Serum (FBS) Thermo Fisher Scientific A5669502 DMEM, low glucose, pyruvate Thermo Fisher Scientific 11885076 ANTI-FLAG® M2 Affinity Gel Sigma-Aldrich A2220 FLAG peptide Peptide 2.0 N/A LipofectamineTM 3000 Transfection Reagent Invitrogen L3000015 CellfectinTM II Reagent Gibco 10362100 cOmpleteTM Protease Inhibitor Cocktail Sigma-Aldrich 4693116001 Isopropyl β-D-1-thiogalactopyranoside (IPTG) Sigma-Aldrich I5502-1G Bluo-Gal Sigma-Aldrich 15519028 Carbenicillin disodium salt Sigma-Aldrich C1389 Gentamicin Sigma-Aldrich G1397-10ML Kanamycin solution from Streptomyces kanamyceticus Sigma-Aldrich K0129-20ML Tetracycline Sigma-Aldrich 87128-25G HEPES, 1.0M buffer, pH 7.5 Thermo Scientific Chemicals J60712.AP Apyrase New England Biolabs M0398S Critical commercial assays FLIPR® Calcium 6 Assay Kits Molecular Devices R6133 Q5® Site-Directed Mutagenesis Kit New England Biolabs E0554S NEBuilder® HiFi DNA Assembly Master Mix New England Biolabs E2621S Superose 6 Increase 10/300 GL column Cytiva 29091596 ÄKTA goTM protein purification system Cytiva N/A Amicon® Ultra Centrifugal Filter, 100 kDa MWCO,15mL Sigma-Aldrich UFC910008 Amicon® Ultra Centrifugal Filter, 100 kDa MWCO, 0.5mL Sigma-Aldrich UFC510008 Centrifuge Filters - CentrexTM GVS Filter Technology 10467013 (Continued on next page) ll OPEN ACCESS e1 Cell 188, 1–13.e1–e6, July 24, 2025 Please cite this article in press as: Juen et al., The structure of human sweetness, Cell (2025), https://doi.org/10.1016/j.cell.2025.04.021 Article ..
Article Title: Protocol for enhancing CRISPR-Cas9 genome editing using histone deacetylase inhibition and engineered virus-like particle delivery.
Article Snippet: .. KEY RESOURCES TABLE REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Histone H3ac (pan-acetyl) Polyclonal antibody [1:1000] Thermo Fisher Scientific Cat# 39139; RRID: AB_2687871 Monoclonal ANTI-FLAG® M2 [1:5000] Sigma-Aldrich Cat# F3165-2MG; RRID: AB_259529 beta Actin Monoclonal antibody (AC-15) [1:10,000] Thermo Fisher Scientific Cat# AM4302; RRID: AB_437394 Anti-GAPDH antibody [6C5] - Loading Control [1:5000] Abcam Cat# ab8245; RRID: AB_2107448 GFP tag Polyclonal antibody [1:1000] Proteintech Cat# 50430-2-AP; RRID: AB_11042881 Caspase-3 antibody [1:1000] Cell signaling Cat# 9662; RRID:AB_331439 Cleaved Caspase-3 (Asp175) (5A1E) antibody [1:1000] Cell signaling Cat# 9664; RRID: AB_2070042 Bacterial and virus strains NEB® Stable Competent E. coli (High Efficiency) New England Biolabs #C3040I 16th generation engineered Virus-Like Particles (eVLPs) Raguram, A. et al 16 Not applicable Chemicals, peptides, and recombinant proteins LBH589 (Panobinostat) Sigma-Aldrich #SML3060-10MG Belinostat Sigma-Aldrich #SML3010-10MG DMSO Sigma-Aldrich #D2650-100ML Polybrene Sigma-Aldrich #TR-1003-50UL Lipofectamine 3000 Thermo Fisher Scientific #L3000015 Critical commercial assays AlamarBlueTM Cell Viability Reagents Thermo Fisher Scientific #DAL1100 Deposited data Raw Sanger Sequencing data Mendeley https://doi.org/10.17632/33tm3dd9dw.1 Raw immunofluorescent microscopy data Mendeley https://doi.org/10.17632/33tm3dd9dw.1 Uncropped gel images Mendeley https://doi.org/10.17632/33tm3dd9dw.1 Experimental models: Cell lines MDA-MB-231 ATCC #HTB-26 HEK-293 T ATCC #CRL-3216 Recombinant DNA psPAX2 Addgene #12260 pMD2.G Addgene #122259 MLV gag-pro-pol Addgene 16 #228466 MMLV gag-Cas9 Addgene 16 #228468 (Continued on next page) 4 STAR Protocols 7, 104493, June 19, 2026 ..
Article Title: Approaches for identification of 5' UTR mutations impacting translation and protein production from neurodevelopmental disorder genes.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies rabbit anti-RFP primary antibody Rockland 600-401-379; RRID: AB_2209751 chicken anti-eGFP primary antibody Aves Labs GFP-1020; RRID: AB_10000240 donkey anti-rabbit Alexa Fluor 568 secondary antibody Invitrogen A10042; RRID: AB_2534017 donkey anti-chicken Alexa Fluor 488 Jackson Immuno 703-545-155; RRID: AB_2340375 Mouse anti-EGFP(1) MSKCC Clone 19F7; RRID: AB_2716736 Mouse anti-EGFP(2) MSKCC Clone 19C8; RRID: AB_2716737 rabbit anti-MKRN1 primary antibody Abcam 72054; RRID: AB_1269434 mouse anti-SMC5 primary antibody Santa Cruz sc-393282 mouse anti-NSD2, clone29D1 Milipore Sigma MABE191 mouse anti-GAPDH Sigma-Aldrich G8795; RRID: AB_1078991 Bacterial and virus strains NEB® Stable Competent E. coli (High Efficiency) New England Biolabs C3040 Chemicals, peptides, and recombinant proteins AgeI-HF New England Biolabs R3552 KpnI-HF New England Biolabs R3142 BamHI-HF New England Biolabs R3136 SalI-HF New England Biolabs R3138 Proteinase K, Molecular Biology Grade New England Biolabs P8107 NEBNext® High-Fidelity 2× PCR Master Mix New England Biolabs M0541 Quick-Load® Taq 2× Master Mix New England Biolabs M0271 NEBNext® Ultra TM II Q5® Master Mix New England Biolabs M0544 Mag-Bind® TotalPure NGS Omega Bio-tek M1378 Plasmid Maxi Kit Qiagen 12162 DMEM/F-12 Gibco 11320033 DMEM Gibco 11965092 Penicillin-Streptomycin Gibco 15140163 Trypsin-EDTA (0.25%), phenol red Gibco 25200056 Fetal Bovine Serum R&D Systems S11150 Lipofectamine TM 2000 Transfection Reagent Invitrogen 11668027 RNasin® Ribonuclease Inhibitor Promega N2511 SUPERase⋅In TM RNase Inhibitor Invitrogen AM2696 cOmplete TM , EDTA-free Protease Inhibitor Cocktail Roche 04693132001 TRIzol TM LS Reagent Invitrogen 10296010 1M HEPES Corning 25-060-CI 2M KCl Invitrogen AM9640G 1M MgCl 2 Invitrogen AM9530G DTT Thermo Fisher Scientific N/A NP-40 Sigma 74385 Cycloheximide Sigma C1988-1G RNA Clean & Concentrator-5 Zymo R1014 (Continued on next page) Cell Reports Methods 5, 101247, December 15, 2025 e1 OPEN ACCESS .. REAGENT or RESOURCE SOURCE IDENTIFIER DNeasy Blood & Tissue Kit Qiagen 69504 Dynabeads TM MyOne TM Streptavidin T1 Invitrogen 65601 Pierce TM Recombinant Protein L, Biotinylated Thermo Scientific 29997 DHPC Avanti Polar Lipids 850306P OCT compound Thermo Fisher Scientific 23-730-571 SuperScript TM IV Reverse Transcriptase Invitrogen 18090050 PowerUp TM SYBR TM Green Master Mix for qPCR Applied Biosystems A25742 0.01% poly-L-lysine Sigma P4707 10× RIPA Buffer Cell Signaling 9806 2× Laemmli Sample Buffer Bio-Rad 1610737 Mini-Protean TGX gels Bio-Rad N/A Immun-Blot PVDF Membrane Bio-Rad 1620177 Clarity TM Western ECL Substrate Bio-Rad 1705060 Critical commercial assays Nano-Glo® Dual-Luciferase® Reporter Assay System Promega N1610 High Sensitivity D1000 ScreenTape Agilent 5067–5584 Pierce TM BCA Protein Assay Kit Thermo Scientific 23227 Deposited data Raw fastq files and processed count files GEO GSE246381 Experimental models: Cell lines Human: HEK This paper N/A Experimental models: Organisms/strains Mouse: ROSA26:LSL-eGFP-RPl10 Jackson Stock no. 022367 Mouse: Vglut1-IRES2-Cre-D Jackson Stock no. 023527 Oligonucleotides See Table S6 Integrated DNA Technologies N/A Recombinant DNA JD486 This paper N/A Software and algorithms umi_tools (v1.0.0) Smith et al. 59 https://github.com/CGATOxford/UMI-tools cutadapt (v2.1) Martin 60 https://github.com/marcelm/cutadapt bowtie2 (v2.3.5) Langmead and Salzberg 61 https://bowtie-bio.sourceforge.net/ bowtie2/index.shtml samtools (v1.9) Li et al. 62 https://www.htslib.org/doc/1.9/samtools. html subread (v2.0.0) Liao et al. 63 https://subread.sourceforge.net/ lme4 Bates et al. 64 https://cran.r-project.org/web/packages/ lme4/index.html qvalue Storey et al. 65 https://bioconductor.org/packages/ release/bioc/html/qvalue.html ViennaRNA (v2.4.17) Lorenz et al. 66 https://www.tbi.univie.ac.at/RNA/ RNAfold Gruber et al. 44 http://rna.tbi.univie.ac.at/ QGRS Mapper Kikin et al. 43 https://bioinformatics.ramapo.edu/QGRS/ index.php R R Core Team https://www.r-project.org/ Custom code This Paper https://bitbucket.org/jdlabteam/fiveprime_ mpra_pub/src/main/ https://doi.org/10.5281/zenodo.17459278 e2 Cell Reports Methods 5, 101247, December 15, 2025 OPEN ACCESS
Article Title: Physiological role and mechanisms of action for a long noncoding haplotype region.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Natriuretic Peptide Receptor C Antibody Novus Cat# NBP1-90163, RRID: AB_11017636 Anti-Rabbit IgG (whole molecule)– Peroxidase antibody Sigma-Aldrich Cat# A6154, RRID:AB_258284 Goat polyclonal anti-human/mouse OCT-4 antibody R&D Systems Cat# AF1759, RRID:AB_354975 Rabbit anti-mouse/human NANOG antibody Reprocell Cat# 09–0020, RRID:AB_2298294 Mouse monoclonal anti-human TRA-1 antibody Santa Cruz Biotechnology Cat# sc-21706, RRID:AB_628386 Mouse monoclonal anti-human SSEA4 antibody Santa Cruz Biotechnology Cat# sc-21704, RRID:AB_628289 Rabbit polyclonal anti-human vWF antibody Dako Cat# A0082, RRID:AB_2810304 Goat polyclonal anti-human VE-cadherin antibody R&D Systems Cat# AF938, RRID:AB_355726 Mouse monoclonal anti-human α-SMA antibody Santa Cruz Biotechnology Cat# sc-130616, RRID:AB_1561784 Rabbit monoclonal anti- human/mouse Myosin IIb antibody Cell Signaling Technology Cat# 8824S, RRID:AB_11217639 Donkey anti-Mouse IgG (H + L) Highly Cross-Adsorbed Secondary Antibody, Alexa Fluor TM 488 Invitrogen Cat# A-21202, RRID:AB_141607 Donkey anti-Goat IgG (H + L) CrossAdsorbed Secondary Antibody, Alexa Fluor TM 488 Invitrogen Cat# A-11055, RRID:AB_2534102 Donkey anti-Mouse IgG (H + L) Highly Cross-Adsorbed Secondary Antibody, Alexa Fluor TM 594 Invitrogen Cat# A-21203, RRID:AB_2535789 Donkey anti-Rabbit IgG (H + L) Highly Cross-Adsorbed Secondary Antibody, Alexa Fluor TM 594 Invitrogen Cat# A-21207, RRID:AB_141637 NPRC JAH84 antibody Alli lab N/A Bacterial and virus strains NEB Stable Competent E. coli (High Efficiency) NEB Cat# C3040I Chemicals, peptides, and recombinant proteins C-type Natriuretic Peptide (CNP) Sigma-Aldrich Cat# N8768 AP 811 Tocris Bioscience Cat# 5498 U46619 Cayman Chemical Cat# 16450 spCas9-2NLS Nuclease protein Synthego N/A Y-27632 (Rock inhibitor) Selleck Chemicals Cat# S1049 CHIR99021 (GSK-3 inhibitor) Selleck Chemicals Cat# S1263 2-Mercaptoethanol Gibco Cat# 21985023 BMP4 PeproTech (Gibco) Cat# 120-05-100UG VEGF PeproTech (Gibco) Cat# 100-20-1MG Forskolin Abcam Cat# ab120058 PDGF-BB PeproTech (Gibco) Cat# 100-14B-100UG (Continued on next page) 16 Cell Reports 44, 115805, June 24, 2025 .. REAGENT or RESOURCE SOURCE IDENTIFIER Activin A PeproTech (Gibco) Cat# 120-14E-500UG MEK-inhibitor (Mirdametinib) Selleck Chemicals Cat# S1036 Paraformaldehyde solution Electron Microscopy Sciences Cat# 15700 Triton X-100 Surfact-Amps Detergent Solution Thermo Scientific Cat# 85111 Tween 20 Bio-Rad Cat# 1706531 GoTaq G2 DNA Polymerase Promega Cat# M7841 Q5 Hi-fidelity DNA polymerase NEB Cat# M0491S 2.5% normal horse serum Vector Labs Cat# S-2012-50 Vectashield Vibrance anti-fade mounting media Vector Labs Cat# H-1800 Critical commercial assays ANP EIA Kit RayBiotech Cat# EIA-ANP BNP EIA Kit RayBiotech Cat# EIAM-BNP CNP-22 EIA Kit Phoenix Pharmaceuticals Cat# EKE-012-03 Dovetail® Micro-C kit Cantata Bio Dovetail® Hybridization Module Cantata Bio CP2-HM-001 Deposited data Omics data This paper GSE284940 at Gene Expression Omnibus (GEO) Omics data This paper GSE284945 at Gene Expression Omnibus (GEO) Experimental models: Cell lines iPSC Y4 This paper N/A iPSC Y4_Δ LD This paper N/A iPSC Y4_BP-lowering haplotype This paper N/A iPSC Y4_BP-elevating haplotype This paper N/A iPSC 39b This paper N/A iPSC 39b_Δ SNP This paper N/A iPSC 39b_BP-lowering allele This paper N/A iPSC 39b_BP-elevating allele This paper N/A iPSC 39b_Δ LD This paper N/A iPSC 39b_BP-lowering haplotype This paper N/A iPSC 39b_BP-elevating haplotype This paper N/A iPSC 39b_low-high BP haplotype This paper N/A iPSC 39b_high-low BP haplotype This paper N/A Experimental models: Organisms/strains SS-Δrs1173771LD − /− Medical College of Wisconsin RRID:RGD_401938598 Oligonucleotides Primer sequences for SSΔrs1173771LD − /− genotyping This paper Table S7 Primer sequences for PCR, cloning, and sequencing (IDT) This paper Table S7 Sequences of guide RNAs for rs1173771 haplotype region editing This paper Table S8 Primer sequences for qPCR This paper Table S9 Recombinant DNA Synthetic sgRNAs for rs1173771 single SNP editing (Synthego) This paper Table S6 (Continued on next page) Cell Reports 44, 115805, June 24, 2025 17
Article Title: Genomic copy-number variants drive apoptotic evasion underlying acquired resistance to immune checkpoint inhibitors.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies beta-2 Microglobulin Monoclonal Antibody (B2M-02) Invitrogen Cat# MA1-19413; RRID: AB_1070703 GSDMC Polyclonal Antibody Invitrogen Cat# PA5-116594; RRID: AB_2901225 Fas Recombinant Rabbit Monoclonal Antibody (JJ0942) Invitrogen Cat# MA5-32489; RRID: AB_2809766 DFFB Polyclonal Antibody Invitrogen Cat# PA5-115114; RRID: AB_2899750 Caspase 9 Monoclonal Antibody (LAP6 96-2-22) Invitrogen Cat# MA1-16842; RRID: AB_568482 Bad Antibody Cell Signaling Technology Cat# 9292; RRID: AB_331419 alpha-Tubulin Antibody Cell Signaling Technology Cat# 2144; RRID: AB_2210548 Bax (E4U1V) Rabbit mAb Cell Signaling Technology Cat# 41162; RRID: AB_2924730 DYKDDDDK Tag (D6W5B) Rabbit mAb Cell Signaling Technology Cat# 14793; RRID: AB_2572291 p53 (7F5) Rabbit mAb Cell Signaling Technology Cat# 2527; RRID: AB_10695803 TNF-R1 (C25C1) Rabbit mAb Cell Signaling Technology Cat# 3736; RRID: AB_2241018 TAP1 (E4T4F) Rabbit mAb Cell Signaling Technology Cat# 49671 TAP2 (E8G5I) Rabbit mAb Cell Signaling Technology Cat# 25657 IFNGR1 Antibody Cell Signaling Technology Cat# 34808; RRID: AB_2799061 FITC anti-human CD3 Antibody BioLegend Cat# 317306; RRID: AB_571907 PE anti-human TCR Vβ13.1 Antibody BioLegend Cat# 362410; RRID: AB_2750159 Goat anti-Mouse IgG (H+L) Highly CrossAdsorbed Secondary Antibody, Alexa FluorTM Plus 488 Invitrogen Cat# A32723; RRID: AB_2633275 Goat anti-Rabbit IgG (H+L) Highly CrossAdsorbed Secondary Antibody, Alexa FluorTM 555 Invitrogen Cat# A-21429; RRID: AB_2535850 Bacterial and virus strains NEB® Stable Competent E. coli (High Efficiency) New England Biolabs Cat# C3040H Biological samples Tumor and patient-matched normal tissues University of California, Los Angeles, Sutter Health, and the Vanderbilt-Ingram Cancer Center See Table S1 for details Peripheral blood mononuclear cells (PBMCs) UCLA virology core laboratory N/A Mouse syngeneic tumors Dr. Roger Lo N/A Chemicals, peptides, and recombinant proteins Anti-Mouse CD279 (PD-1) (Clone RMP1-14) Leinco Tech Cat# P362 InVivoMAb anti-mouse CTLA-4 (CD152) BioXcell Cat# BE0131 Venetoclax TargetMol Cat# T2119 PEG300 MedChemExpress Cat# HY-Y0873 Antigen Retrieval Buffer Abcam Cat# ab93684 DAPI MilliporeSigma Cat# D9542 Molecular ProbesTM ProLongTM Diamond Antifade Mountant Thermo Fisher Scientific Cat# P36965 BioT Bioland Scientific Cat# B01-00 (Continued on next page) Immunity 58, 1–14.e1–e9, November 11, 2025 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Sodium butyrate Thermo Fisher Scientific Cat# A11079.36 HEPES Thermo Fisher Scientific Cat# 15630080 Recombinant human IL-2 Miltenyi Biotec Cat# 130-097-748 DynabeadsTM Human T-Activator CD3/ CD28 for T Cell Expansion and Activation Gibco Cat# 11161D RetroNectin Takara Cat# T110A Cryostor CS10 cryopreservation medium Biolife Solutions Cat# 210102 G418 disulfate salt MilliporeSigma Cat# A1720-1G Blasticidin S HCl Gibco Cat# R21001 Puromycin MilliporeSigma Cat# P8833-25MG Hygromycin B Thermo Fisher Scientific Cat# AAJ6068103 Polybrene Infection / Transfection Reagent MilliporeSigma Cat# TR-1003-G RIPA Lysis and Extraction Buffer Thermo Fisher Scientific Cat# 89901 HaltTM Phosphatase Inhibitor Single-Use Cocktail Thermo Fisher Scientific Cat# 78428 PierceTM BCA Protein Assay Kits Thermo Fisher Scientific Cat# 23227 Tween 80 Thermo Fisher Scientific Cat# BP338-500 4% Paraformaldehyde in PBS Thermo Fisher Scientific Cat# J61899.AP Crystal violet solution MilliporeSigma Cat# V5256 Tris-HCl (PH7.4) MilliporeSigma Cat# T2194 Tween 20 Andwin Scientific Cat# NC9022994 Nonidet P40 Substitute MilliporeSigma Cat# 74385 NaCl Invitrogen Cat# AM9760G MgCl2 Invitrogen Cat# AM9530G Triton X-100 Thermo Fisher Scientific Cat# ICN19485483 QIAGEN Protease (30 AU) Qiagen Cat# 19157 0.5M EDTA Thermo Fisher Scientific Cat# R1021 Xylene Fisher Scientific Cat# X5-1 Ethyl Alcohol Sigma-Aldrich Cat# E7023 Critical commercial assays QIAGEN AllPrep DNA/RNA Mini Kit Qiagen Cat# 80204 QIAGEN QIAamp DNA FFPE Tissue Kit Qiagen Cat# 56404 QIAGEN FlexiGene DNA Kit Qiagen Cat# 51206 Pan T Cell Isolation Kit Miltenyi Biotec Cat# 130-096-535 Tumor Dissociation Kit, mouse Miltenyi Biotec Cat# 130-096-730 FFPE Tissue Dissociation Kit Miltenyi Biotec Cat# 130-118-052 Illumina Tagment DNA Enzyme and Buffer Large Kit Illumina Cat# 20034198 KAPA HotStart PCR Kit, with dNTPs Roche Cat# KK2502 Qubit dsDNA HS (High Sensitivity) Assay Kit Invitrogen Cat# Q32851 Qubit dsDNA BR (Broad-Range) Assay Kit Invitrogen Cat# Q32850 Deposited data WES This paper European Genome-phenome Archive (EGA): EGAS50000001055 WGS This paper EGA: EGAS50000001055 WES Zaretsky et al. 15 SRA: SRP076315 WES Hugo et al. 11 SRA: SRP067938, SRP090294 WES Liu et al., 13 Hugo et al., 44 Moriceau et al., 45 Shi et al. 46 SRA: SRP049746 Copy number profiles of TCGA-SKCM cohort TCGA, PanCancer Atlas https://www.cbioportal.org/ (Continued on next page) e2 Immunity 58, 1–14.e1–e9, November 11, 2025
Purification:Article Title: Lentiviral vectors for hematopoietic stem cell gene therapy restore α-globin expression in α-thalassemia red blood cells.
Article Snippet: .. Cells were maintained at a concentration of 3E5 cells per mL in REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies hCD45 (V450) BD HorizonCAT #560367 RRID: AB_1645573 hCD34 (APC) BD PharmingenCAT #555824 RRID: AB_398614 hCD34 (APC) BioLegend CAT #343509 RRID: AB_1877154 hCD19 (Pe-Cy7) BioLegendCAT # 302216 RRID: AB_314246 hCD56 (PE) BD PharmingenCAT #555516 RRID: AB_395906 hCD3 (APC-Cy7) BioLegendCAT #300318; RRID: AB_314053 hCD33 (BV711) BioLegendCAT #303424 RRID: AB_2565775 Bacterial and virus strains NEB® Stable Competent E. coli (High Efficiency) New England BioLabs C3040I Biological samples Mobilized CD34+ Stem/Progenitor Cells; GCSF; 1 × 10e6 cells, Cryo Charles River Laboratories N/A Human Bone Marrow Mononuclear Cells, Frozen STEMCELL CAT #70001.2 Human Cord Blood Mononuclear Cells, Frozen STEMCELL CAT #70007.1 Human Fetal Liver Mononuclear Cells, Frozen UCLA N/A Critical commercial assays PureLinkTM Genomic DNA Mini Kit ThermoFisher K182001 RNeasy Kits for RNA Purification Qiagen 74104 QIAGEN Plasmid Kits for Plasmid DNA Extraction Qiagen 12162 SuperScriptTM III First-Strand Synthesis System ThermoFisher 18080051 Deposited data RNA-seq For reviewers: GSE292575: Go to https://www.ncbi.nlm.nih.gov/ geo/query/acc.cgi?acc=GSE292575 Enter token ipkfemkwtnwnvev into the box. .. Accession number: GEO: GSE292575 Vector Integration Site VMHDS core, University of Pennsylvania http://github.com/BushmanLab/INSPIIRED RRID:SCR_02243320 accession number: PRJNA122524119,20 Experimental models: Cell lines HUDEP-2 https://doi.org/10.1371/journal.pone.0059890 N/A Experimental models: Organisms/strains NSG mice (NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ) Jackson Laboratories Cat# 005557 Software and algorithms SnapGene SnapGene 7.2.1 GraphPad Prism GraphPad 10.4.1 Loupe Browser Loupe Browser 8.0.0 R software www.r_project.org R.4.4.1 Cell Reports Medicine 6, 102362, October 21, 2025 e1 OPEN ACCESS StemSpan SFEM medium, supplemented with 1 μM dexamethasone and 1% glutamine, penicillin, streptomycin.
Plasmid Preparation:Article Title: Lentiviral vectors for hematopoietic stem cell gene therapy restore α-globin expression in α-thalassemia red blood cells.
Article Snippet: .. Cells were maintained at a concentration of 3E5 cells per mL in REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies hCD45 (V450) BD HorizonCAT #560367 RRID: AB_1645573 hCD34 (APC) BD PharmingenCAT #555824 RRID: AB_398614 hCD34 (APC) BioLegend CAT #343509 RRID: AB_1877154 hCD19 (Pe-Cy7) BioLegendCAT # 302216 RRID: AB_314246 hCD56 (PE) BD PharmingenCAT #555516 RRID: AB_395906 hCD3 (APC-Cy7) BioLegendCAT #300318; RRID: AB_314053 hCD33 (BV711) BioLegendCAT #303424 RRID: AB_2565775 Bacterial and virus strains NEB® Stable Competent E. coli (High Efficiency) New England BioLabs C3040I Biological samples Mobilized CD34+ Stem/Progenitor Cells; GCSF; 1 × 10e6 cells, Cryo Charles River Laboratories N/A Human Bone Marrow Mononuclear Cells, Frozen STEMCELL CAT #70001.2 Human Cord Blood Mononuclear Cells, Frozen STEMCELL CAT #70007.1 Human Fetal Liver Mononuclear Cells, Frozen UCLA N/A Critical commercial assays PureLinkTM Genomic DNA Mini Kit ThermoFisher K182001 RNeasy Kits for RNA Purification Qiagen 74104 QIAGEN Plasmid Kits for Plasmid DNA Extraction Qiagen 12162 SuperScriptTM III First-Strand Synthesis System ThermoFisher 18080051 Deposited data RNA-seq For reviewers: GSE292575: Go to https://www.ncbi.nlm.nih.gov/ geo/query/acc.cgi?acc=GSE292575 Enter token ipkfemkwtnwnvev into the box. .. Accession number: GEO: GSE292575 Vector Integration Site VMHDS core, University of Pennsylvania http://github.com/BushmanLab/INSPIIRED RRID:SCR_02243320 accession number: PRJNA122524119,20 Experimental models: Cell lines HUDEP-2 https://doi.org/10.1371/journal.pone.0059890 N/A Experimental models: Organisms/strains NSG mice (NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ) Jackson Laboratories Cat# 005557 Software and algorithms SnapGene SnapGene 7.2.1 GraphPad Prism GraphPad 10.4.1 Loupe Browser Loupe Browser 8.0.0 R software www.r_project.org R.4.4.1 Cell Reports Medicine 6, 102362, October 21, 2025 e1 OPEN ACCESS StemSpan SFEM medium, supplemented with 1 μM dexamethasone and 1% glutamine, penicillin, streptomycin.
Article Title: Approaches for identification of 5' UTR mutations impacting translation and protein production from neurodevelopmental disorder genes.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies rabbit anti-RFP primary antibody Rockland 600-401-379; RRID: AB_2209751 chicken anti-eGFP primary antibody Aves Labs GFP-1020; RRID: AB_10000240 donkey anti-rabbit Alexa Fluor 568 secondary antibody Invitrogen A10042; RRID: AB_2534017 donkey anti-chicken Alexa Fluor 488 Jackson Immuno 703-545-155; RRID: AB_2340375 Mouse anti-EGFP(1) MSKCC Clone 19F7; RRID: AB_2716736 Mouse anti-EGFP(2) MSKCC Clone 19C8; RRID: AB_2716737 rabbit anti-MKRN1 primary antibody Abcam 72054; RRID: AB_1269434 mouse anti-SMC5 primary antibody Santa Cruz sc-393282 mouse anti-NSD2, clone29D1 Milipore Sigma MABE191 mouse anti-GAPDH Sigma-Aldrich G8795; RRID: AB_1078991 Bacterial and virus strains NEB® Stable Competent E. coli (High Efficiency) New England Biolabs C3040 Chemicals, peptides, and recombinant proteins AgeI-HF New England Biolabs R3552 KpnI-HF New England Biolabs R3142 BamHI-HF New England Biolabs R3136 SalI-HF New England Biolabs R3138 Proteinase K, Molecular Biology Grade New England Biolabs P8107 NEBNext® High-Fidelity 2× PCR Master Mix New England Biolabs M0541 Quick-Load® Taq 2× Master Mix New England Biolabs M0271 NEBNext® Ultra TM II Q5® Master Mix New England Biolabs M0544 Mag-Bind® TotalPure NGS Omega Bio-tek M1378 Plasmid Maxi Kit Qiagen 12162 DMEM/F-12 Gibco 11320033 DMEM Gibco 11965092 Penicillin-Streptomycin Gibco 15140163 Trypsin-EDTA (0.25%), phenol red Gibco 25200056 Fetal Bovine Serum R&D Systems S11150 Lipofectamine TM 2000 Transfection Reagent Invitrogen 11668027 RNasin® Ribonuclease Inhibitor Promega N2511 SUPERase⋅In TM RNase Inhibitor Invitrogen AM2696 cOmplete TM , EDTA-free Protease Inhibitor Cocktail Roche 04693132001 TRIzol TM LS Reagent Invitrogen 10296010 1M HEPES Corning 25-060-CI 2M KCl Invitrogen AM9640G 1M MgCl 2 Invitrogen AM9530G DTT Thermo Fisher Scientific N/A NP-40 Sigma 74385 Cycloheximide Sigma C1988-1G RNA Clean & Concentrator-5 Zymo R1014 (Continued on next page) Cell Reports Methods 5, 101247, December 15, 2025 e1 OPEN ACCESS .. REAGENT or RESOURCE SOURCE IDENTIFIER DNeasy Blood & Tissue Kit Qiagen 69504 Dynabeads TM MyOne TM Streptavidin T1 Invitrogen 65601 Pierce TM Recombinant Protein L, Biotinylated Thermo Scientific 29997 DHPC Avanti Polar Lipids 850306P OCT compound Thermo Fisher Scientific 23-730-571 SuperScript TM IV Reverse Transcriptase Invitrogen 18090050 PowerUp TM SYBR TM Green Master Mix for qPCR Applied Biosystems A25742 0.01% poly-L-lysine Sigma P4707 10× RIPA Buffer Cell Signaling 9806 2× Laemmli Sample Buffer Bio-Rad 1610737 Mini-Protean TGX gels Bio-Rad N/A Immun-Blot PVDF Membrane Bio-Rad 1620177 Clarity TM Western ECL Substrate Bio-Rad 1705060 Critical commercial assays Nano-Glo® Dual-Luciferase® Reporter Assay System Promega N1610 High Sensitivity D1000 ScreenTape Agilent 5067–5584 Pierce TM BCA Protein Assay Kit Thermo Scientific 23227 Deposited data Raw fastq files and processed count files GEO GSE246381 Experimental models: Cell lines Human: HEK This paper N/A Experimental models: Organisms/strains Mouse: ROSA26:LSL-eGFP-RPl10 Jackson Stock no. 022367 Mouse: Vglut1-IRES2-Cre-D Jackson Stock no. 023527 Oligonucleotides See Table S6 Integrated DNA Technologies N/A Recombinant DNA JD486 This paper N/A Software and algorithms umi_tools (v1.0.0) Smith et al. 59 https://github.com/CGATOxford/UMI-tools cutadapt (v2.1) Martin 60 https://github.com/marcelm/cutadapt bowtie2 (v2.3.5) Langmead and Salzberg 61 https://bowtie-bio.sourceforge.net/ bowtie2/index.shtml samtools (v1.9) Li et al. 62 https://www.htslib.org/doc/1.9/samtools. html subread (v2.0.0) Liao et al. 63 https://subread.sourceforge.net/ lme4 Bates et al. 64 https://cran.r-project.org/web/packages/ lme4/index.html qvalue Storey et al. 65 https://bioconductor.org/packages/ release/bioc/html/qvalue.html ViennaRNA (v2.4.17) Lorenz et al. 66 https://www.tbi.univie.ac.at/RNA/ RNAfold Gruber et al. 44 http://rna.tbi.univie.ac.at/ QGRS Mapper Kikin et al. 43 https://bioinformatics.ramapo.edu/QGRS/ index.php R R Core Team https://www.r-project.org/ Custom code This Paper https://bitbucket.org/jdlabteam/fiveprime_ mpra_pub/src/main/ https://doi.org/10.5281/zenodo.17459278 e2 Cell Reports Methods 5, 101247, December 15, 2025 OPEN ACCESS
DNA Extraction:Article Title: Lentiviral vectors for hematopoietic stem cell gene therapy restore α-globin expression in α-thalassemia red blood cells.
Article Snippet: .. Cells were maintained at a concentration of 3E5 cells per mL in REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies hCD45 (V450) BD HorizonCAT #560367 RRID: AB_1645573 hCD34 (APC) BD PharmingenCAT #555824 RRID: AB_398614 hCD34 (APC) BioLegend CAT #343509 RRID: AB_1877154 hCD19 (Pe-Cy7) BioLegendCAT # 302216 RRID: AB_314246 hCD56 (PE) BD PharmingenCAT #555516 RRID: AB_395906 hCD3 (APC-Cy7) BioLegendCAT #300318; RRID: AB_314053 hCD33 (BV711) BioLegendCAT #303424 RRID: AB_2565775 Bacterial and virus strains NEB® Stable Competent E. coli (High Efficiency) New England BioLabs C3040I Biological samples Mobilized CD34+ Stem/Progenitor Cells; GCSF; 1 × 10e6 cells, Cryo Charles River Laboratories N/A Human Bone Marrow Mononuclear Cells, Frozen STEMCELL CAT #70001.2 Human Cord Blood Mononuclear Cells, Frozen STEMCELL CAT #70007.1 Human Fetal Liver Mononuclear Cells, Frozen UCLA N/A Critical commercial assays PureLinkTM Genomic DNA Mini Kit ThermoFisher K182001 RNeasy Kits for RNA Purification Qiagen 74104 QIAGEN Plasmid Kits for Plasmid DNA Extraction Qiagen 12162 SuperScriptTM III First-Strand Synthesis System ThermoFisher 18080051 Deposited data RNA-seq For reviewers: GSE292575: Go to https://www.ncbi.nlm.nih.gov/ geo/query/acc.cgi?acc=GSE292575 Enter token ipkfemkwtnwnvev into the box. .. Accession number: GEO: GSE292575 Vector Integration Site VMHDS core, University of Pennsylvania http://github.com/BushmanLab/INSPIIRED RRID:SCR_02243320 accession number: PRJNA122524119,20 Experimental models: Cell lines HUDEP-2 https://doi.org/10.1371/journal.pone.0059890 N/A Experimental models: Organisms/strains NSG mice (NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ) Jackson Laboratories Cat# 005557 Software and algorithms SnapGene SnapGene 7.2.1 GraphPad Prism GraphPad 10.4.1 Loupe Browser Loupe Browser 8.0.0 R software www.r_project.org R.4.4.1 Cell Reports Medicine 6, 102362, October 21, 2025 e1 OPEN ACCESS StemSpan SFEM medium, supplemented with 1 μM dexamethasone and 1% glutamine, penicillin, streptomycin.
RNA Sequencing:Article Title: Lentiviral vectors for hematopoietic stem cell gene therapy restore α-globin expression in α-thalassemia red blood cells.
Article Snippet: .. Cells were maintained at a concentration of 3E5 cells per mL in REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies hCD45 (V450) BD HorizonCAT #560367 RRID: AB_1645573 hCD34 (APC) BD PharmingenCAT #555824 RRID: AB_398614 hCD34 (APC) BioLegend CAT #343509 RRID: AB_1877154 hCD19 (Pe-Cy7) BioLegendCAT # 302216 RRID: AB_314246 hCD56 (PE) BD PharmingenCAT #555516 RRID: AB_395906 hCD3 (APC-Cy7) BioLegendCAT #300318; RRID: AB_314053 hCD33 (BV711) BioLegendCAT #303424 RRID: AB_2565775 Bacterial and virus strains NEB® Stable Competent E. coli (High Efficiency) New England BioLabs C3040I Biological samples Mobilized CD34+ Stem/Progenitor Cells; GCSF; 1 × 10e6 cells, Cryo Charles River Laboratories N/A Human Bone Marrow Mononuclear Cells, Frozen STEMCELL CAT #70001.2 Human Cord Blood Mononuclear Cells, Frozen STEMCELL CAT #70007.1 Human Fetal Liver Mononuclear Cells, Frozen UCLA N/A Critical commercial assays PureLinkTM Genomic DNA Mini Kit ThermoFisher K182001 RNeasy Kits for RNA Purification Qiagen 74104 QIAGEN Plasmid Kits for Plasmid DNA Extraction Qiagen 12162 SuperScriptTM III First-Strand Synthesis System ThermoFisher 18080051 Deposited data RNA-seq For reviewers: GSE292575: Go to https://www.ncbi.nlm.nih.gov/ geo/query/acc.cgi?acc=GSE292575 Enter token ipkfemkwtnwnvev into the box. .. Accession number: GEO: GSE292575 Vector Integration Site VMHDS core, University of Pennsylvania http://github.com/BushmanLab/INSPIIRED RRID:SCR_02243320 accession number: PRJNA122524119,20 Experimental models: Cell lines HUDEP-2 https://doi.org/10.1371/journal.pone.0059890 N/A Experimental models: Organisms/strains NSG mice (NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ) Jackson Laboratories Cat# 005557 Software and algorithms SnapGene SnapGene 7.2.1 GraphPad Prism GraphPad 10.4.1 Loupe Browser Loupe Browser 8.0.0 R software www.r_project.org R.4.4.1 Cell Reports Medicine 6, 102362, October 21, 2025 e1 OPEN ACCESS StemSpan SFEM medium, supplemented with 1 μM dexamethasone and 1% glutamine, penicillin, streptomycin.
Recombinant:Article Title: Alanine catabolism as a targetable vulnerability for MYC-driven liver cancer.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies α-GPT2 Sigma Cat# HPA051514; RRID: AB_2681516 α-GPT1 Abcam Cat# ab202083; RRID: AB_2915976 α-c-MYC, clone Y69 Abcam Cat# ab32072; RRID: AB_731658 α-β-actin-HRP Santa Cruz Cat# sc-47778; RRID: AB_2714189 α-Vinculin Cell Signaling Technologies Cat# 13901; RRID: AB_2728768 α-ATF4 Cell Signaling Technologies Cat# 11815; RRID: AB_2616025 α-eIF2α Cell Signaling Technologies Cat# 9722; RRID: AB_2230924 α-P-eIF2α Cell Signaling Technologies Cat# 3597; RRID: AB_390740 α-Rabbit IgG-HRP Promega Cat# W4011; RRID: AB_430833 Bacterial and virus strains NEB® Stable Competent E. coli (High Efficiency) New England Biolabs Cat# C3040H Chemicals, peptides, and recombinant proteins Doxycycline Fisher Scientific Cat# BP2653-5 L-Cycloserine MedChemExpress Cat# HY-B1122 Trypan blue Invitrogen Cat# T10282 DTT Fisher Scientific Cat# BP172-25G Heparin McKesson Cat# NDC 63739-931-14 Lipofectamine RNAi MAX Invitrogen Cat# AM9938 13C3; 15N-alanine Cambridge Isotopes Cat# CNLM-534-H-PK Trifluoromethanesulfonate Sigma Cat# 422843-5G Water; LC-MS grade Fisher Scientific Cat# W6-212 Methanol; LC-MS grade Fisher Scientific Cat# A456-500 Acetonitrile; LC-MS grade Fisher Scientific Cat# A955-4 Non-essential amino acids UCSF Cell Culture Facility Cat# CCFGA001-22BU01 L-Alanine Sigma Cat# A7627-100G L-Glutamine Sigma Cat# G3126-100G D-(+)-Glucose solution Sigma Cat# G8769-100ML Methyl-pruvate Thermo scientific Cat# A13966.14 Dimethyl-glutamate Thermo scientific Cat# L03764.06 Hoechst 33342 Biotium Cat# 40046 Propidium Iodide Invitrogen Cat# P3566 Critical commercial assays Alanine Transaminase Activity Assay Kit Abcam Cat# ab105134 DC protein assay kit Biorad Cat# 5000111 QIAshredder Kit Qiagen Cat# 79656 CYQUANT cell proliferation assay ThermoFisher Cat# C7026 Rneasy Mini Kit Qiagen Cat# 74106 High Capacity RNA-to-cDNA Kit Applied Biosystems Cat# 4387406 TaqMan Fast Advanced Master Mix Applied Biosystems Cat# 4444557 Mouse Gpt2 taqman probe Thermo fisher Cat# Mm00558028_m1 Gpt2 Mouse Actb taqman probe Thermo fisher Cat# Mm02619580_g1 Actb Mouse Gpt2 taqman probe Thermo fisher Cat# Hs99999903_m1 ACTB (Continued on next page) Cell Reports 45, 117107, April 28, 2026 13 .. REAGENT or RESOURCE SOURCE IDENTIFIER Mouse Actb taqman probe Thermo fisher Cat# Hs00370287_m1 GPT2 Deposited data The Cancer Genome Atlas (HCC) Ally et al.5 https://gdc.cancer.gov/; https:// www.cbioportal.org/study/ summary?id=lihc_tcga RNA sequencing and ChIP sequencing in the LT2-MYC model Kress et al.18 GEO: GSE76078 LT2-MYC metabolomics data Anderton et al.15 https://pmc.ncbi.nlm.nih.gov/articles/ PMC5376764/#embr201643068sup-0003 13C3; 15N-alanine tracing in the LT2-MYC model https://doi.org/10.21228/M8TK1K NMDR: ST004169 Experimental models: Cell lines EC4 Cao et al.50 N/A HepG2 ATCC HB-8065; RRID: CVCL_0027 Tong Xin Chen (University of Hawai’i Cancer Center) RRID: CVCL_V640 PLC5 Xin Chen (University of Hawai’i Cancer Center) CRL-8024; RRID: CVCL_0485 SNU475 Xin Chen (University of Hawai’i Cancer Center) CRL-2236; RRID: CVCL_0497 Experimental models: Organisms/strains C57BL/6 mice JAX Cat# 000664 Nude mice JAX Cat# 002019 LT2-MYC mice Shachaf et al.51 N/A GPT2 FLOX mice Martino et al.10 N/A Recombinant DNA pT3-MYC-IRES-CRE This study.
Article Title: FAME-CRISPR improves CRISPR-Cas9 genome editing via HDAC inhibition and engineered virus-like particle delivery.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Histone H3ac (pan-acetyl) Polyclonal antibody Thermo Fisher Scientific Cat# 39139; RRID: AB_2687871 Monoclonal ANTI-FLAG® M2 Sigma-Aldrich Cat# F3165-2MG; RRID: AB_259529 beta Actin Monoclonal antibody (AC-15) Thermo Fisher Scientific Cat# AM4302; RRID: AB_437394 Anti-GAPDH antibody [6C5] - Loading Control Abcam Cat# ab8245; RRID: AB_2107448 GFP tag Polyclonal antibody Proteintech Cat# 50430-2-AP; RRID: AB_11042881 Caspase-3 antibody Cell signaling Cat# 9662; RRID:AB_331439 Cleaved Caspase-3 (Asp175) (5A1E) antibody Cell signaling Cat# 9664; RRID: AB_2070042 ANTI-FLAG® M2 Magnetic Beads Sigma-Aldrich Cat# M8823-1ML; RRID: AB_2637089 γH2AX Abcam Cat# ab26350; RRID: AB_470861 Alexa Fluor 633 Invitrogen Cat# A-21050; RRID: AB_2535718 Bacterial and virus strains NEB® Stable Competent E. coli (High Efficiency) New England Biolabs # C3040I NEB® 5-alpha Competent E. coli (Subcloning Efficiency) New England Biolabs # C2988J Recombinant 3 rd generation Lentivirus – N/A 5 th generation engineered Virus-Like Particles (eVLPs) Raguram et al. 49 N/A Chemicals, peptides, and recombinant proteins LBH589 (Panobinostat) Sigma-Aldrich # SML3060-10MG Belinostat Sigma-Aldrich # SML3010-10MG SB505124 Sigma-Aldrich # S4696-5MG PCI-24781 Sigma-Aldrich # SML4043-5MG Valproic acid Sigma-Aldrich # P4543-10G DMSO Sigma-Aldrich # D2650-100ML Polybrene Sigma-Aldrich # TR-1003-50UL Lipofectamine 3000 Thermo Fisher Scientific # L3000015 Critical commercial assays AlamarBlue TM Cell Viability Reagents Thermo Fisher Scientific # DAL1100 Deposited data Raw Sanger Sequencing data This paper https://doi.org/10.17632/33tm3dd9dw.1 Raw immunofluorescent microscopy data This paper https://doi.org/10.17632/33tm3dd9dw.1 Uncropped gel images This paper https://doi.org/10.17632/33tm3dd9dw.1 Experimental models: Cell lines HeLa ATCC # CCL-2 HepG2 ATCC # HB-8065 .. MDA-MB-231 ATCC # HTB-26
Article Title: The structure of human sweetness.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies DYKDDDDK Tag Polyclonal Antibody Thermo Fisher Scientific Cat# PA1-984B; RRID: AB_347227 HA-Tag (C29F4) Rabbit mAb Cell Signaling Technology Cat# 3724; RRID: AB_1549585 GAPDH (14C10) Rabbit mAb Cell Signaling Technology Cat# 2118; RRID: AB_561053 Anti-Rabbit IgG - Alkaline Phosphatase antibody produced in goat Sigma-Aldrich Cat# A3687; RRID: AB_258103 Bacterial and virus strains NEB® Stable Competent E. coli (High Efficiency) New England Biolabs C3040H MAX EfficiencyTM DH10Bac Competent Cells Thermo Fisher Scientific 10361012 BL21(DE3) Competent E. coli New England Biolabs C2527H Chemicals, peptides, and recombinant proteins Sucralose Sigma-Aldrich 69293 Aspartame Sigma-Aldrich 47135 (±)-2-(p-Methoxyphenoxy)propionic acid (Lactisole) Sigma-Aldrich M6546 Cholesteryl Hemisuccinate (CHS) Tris Salt Anatrace CH210 Lauryl Maltose Neopentyl Glycol (LMNG) Anatrace NG310 Glyco-diosgenin (GDN) Anatrace GDN101 PEG400 Sigma-Aldrich 91893 Ethylene glycol Sigma-Aldrich 324558 Expi293TM Expression Medium Thermo Fisher Scientific A1435102 Sf-900 II SFM Thermo Fisher Scientific 10902104 Fetal Bovine Serum (FBS) Thermo Fisher Scientific A5669502 DMEM, low glucose, pyruvate Thermo Fisher Scientific 11885076 ANTI-FLAG® M2 Affinity Gel Sigma-Aldrich A2220 FLAG peptide Peptide 2.0 N/A LipofectamineTM 3000 Transfection Reagent Invitrogen L3000015 CellfectinTM II Reagent Gibco 10362100 cOmpleteTM Protease Inhibitor Cocktail Sigma-Aldrich 4693116001 Isopropyl β-D-1-thiogalactopyranoside (IPTG) Sigma-Aldrich I5502-1G Bluo-Gal Sigma-Aldrich 15519028 Carbenicillin disodium salt Sigma-Aldrich C1389 Gentamicin Sigma-Aldrich G1397-10ML Kanamycin solution from Streptomyces kanamyceticus Sigma-Aldrich K0129-20ML Tetracycline Sigma-Aldrich 87128-25G HEPES, 1.0M buffer, pH 7.5 Thermo Scientific Chemicals J60712.AP Apyrase New England Biolabs M0398S Critical commercial assays FLIPR® Calcium 6 Assay Kits Molecular Devices R6133 Q5® Site-Directed Mutagenesis Kit New England Biolabs E0554S NEBuilder® HiFi DNA Assembly Master Mix New England Biolabs E2621S Superose 6 Increase 10/300 GL column Cytiva 29091596 ÄKTA goTM protein purification system Cytiva N/A Amicon® Ultra Centrifugal Filter, 100 kDa MWCO,15mL Sigma-Aldrich UFC910008 Amicon® Ultra Centrifugal Filter, 100 kDa MWCO, 0.5mL Sigma-Aldrich UFC510008 Centrifuge Filters - CentrexTM GVS Filter Technology 10467013 (Continued on next page) ll OPEN ACCESS e1 Cell 188, 1–13.e1–e6, July 24, 2025 Please cite this article in press as: Juen et al., The structure of human sweetness, Cell (2025), https://doi.org/10.1016/j.cell.2025.04.021 Article ..
Article Title: Protocol for enhancing CRISPR-Cas9 genome editing using histone deacetylase inhibition and engineered virus-like particle delivery.
Article Snippet: .. KEY RESOURCES TABLE REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Histone H3ac (pan-acetyl) Polyclonal antibody [1:1000] Thermo Fisher Scientific Cat# 39139; RRID: AB_2687871 Monoclonal ANTI-FLAG® M2 [1:5000] Sigma-Aldrich Cat# F3165-2MG; RRID: AB_259529 beta Actin Monoclonal antibody (AC-15) [1:10,000] Thermo Fisher Scientific Cat# AM4302; RRID: AB_437394 Anti-GAPDH antibody [6C5] - Loading Control [1:5000] Abcam Cat# ab8245; RRID: AB_2107448 GFP tag Polyclonal antibody [1:1000] Proteintech Cat# 50430-2-AP; RRID: AB_11042881 Caspase-3 antibody [1:1000] Cell signaling Cat# 9662; RRID:AB_331439 Cleaved Caspase-3 (Asp175) (5A1E) antibody [1:1000] Cell signaling Cat# 9664; RRID: AB_2070042 Bacterial and virus strains NEB® Stable Competent E. coli (High Efficiency) New England Biolabs #C3040I 16th generation engineered Virus-Like Particles (eVLPs) Raguram, A. et al 16 Not applicable Chemicals, peptides, and recombinant proteins LBH589 (Panobinostat) Sigma-Aldrich #SML3060-10MG Belinostat Sigma-Aldrich #SML3010-10MG DMSO Sigma-Aldrich #D2650-100ML Polybrene Sigma-Aldrich #TR-1003-50UL Lipofectamine 3000 Thermo Fisher Scientific #L3000015 Critical commercial assays AlamarBlueTM Cell Viability Reagents Thermo Fisher Scientific #DAL1100 Deposited data Raw Sanger Sequencing data Mendeley https://doi.org/10.17632/33tm3dd9dw.1 Raw immunofluorescent microscopy data Mendeley https://doi.org/10.17632/33tm3dd9dw.1 Uncropped gel images Mendeley https://doi.org/10.17632/33tm3dd9dw.1 Experimental models: Cell lines MDA-MB-231 ATCC #HTB-26 HEK-293 T ATCC #CRL-3216 Recombinant DNA psPAX2 Addgene #12260 pMD2.G Addgene #122259 MLV gag-pro-pol Addgene 16 #228466 MMLV gag-Cas9 Addgene 16 #228468 (Continued on next page) 4 STAR Protocols 7, 104493, June 19, 2026 ..
Article Title: Approaches for identification of 5' UTR mutations impacting translation and protein production from neurodevelopmental disorder genes.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies rabbit anti-RFP primary antibody Rockland 600-401-379; RRID: AB_2209751 chicken anti-eGFP primary antibody Aves Labs GFP-1020; RRID: AB_10000240 donkey anti-rabbit Alexa Fluor 568 secondary antibody Invitrogen A10042; RRID: AB_2534017 donkey anti-chicken Alexa Fluor 488 Jackson Immuno 703-545-155; RRID: AB_2340375 Mouse anti-EGFP(1) MSKCC Clone 19F7; RRID: AB_2716736 Mouse anti-EGFP(2) MSKCC Clone 19C8; RRID: AB_2716737 rabbit anti-MKRN1 primary antibody Abcam 72054; RRID: AB_1269434 mouse anti-SMC5 primary antibody Santa Cruz sc-393282 mouse anti-NSD2, clone29D1 Milipore Sigma MABE191 mouse anti-GAPDH Sigma-Aldrich G8795; RRID: AB_1078991 Bacterial and virus strains NEB® Stable Competent E. coli (High Efficiency) New England Biolabs C3040 Chemicals, peptides, and recombinant proteins AgeI-HF New England Biolabs R3552 KpnI-HF New England Biolabs R3142 BamHI-HF New England Biolabs R3136 SalI-HF New England Biolabs R3138 Proteinase K, Molecular Biology Grade New England Biolabs P8107 NEBNext® High-Fidelity 2× PCR Master Mix New England Biolabs M0541 Quick-Load® Taq 2× Master Mix New England Biolabs M0271 NEBNext® Ultra TM II Q5® Master Mix New England Biolabs M0544 Mag-Bind® TotalPure NGS Omega Bio-tek M1378 Plasmid Maxi Kit Qiagen 12162 DMEM/F-12 Gibco 11320033 DMEM Gibco 11965092 Penicillin-Streptomycin Gibco 15140163 Trypsin-EDTA (0.25%), phenol red Gibco 25200056 Fetal Bovine Serum R&D Systems S11150 Lipofectamine TM 2000 Transfection Reagent Invitrogen 11668027 RNasin® Ribonuclease Inhibitor Promega N2511 SUPERase⋅In TM RNase Inhibitor Invitrogen AM2696 cOmplete TM , EDTA-free Protease Inhibitor Cocktail Roche 04693132001 TRIzol TM LS Reagent Invitrogen 10296010 1M HEPES Corning 25-060-CI 2M KCl Invitrogen AM9640G 1M MgCl 2 Invitrogen AM9530G DTT Thermo Fisher Scientific N/A NP-40 Sigma 74385 Cycloheximide Sigma C1988-1G RNA Clean & Concentrator-5 Zymo R1014 (Continued on next page) Cell Reports Methods 5, 101247, December 15, 2025 e1 OPEN ACCESS .. REAGENT or RESOURCE SOURCE IDENTIFIER DNeasy Blood & Tissue Kit Qiagen 69504 Dynabeads TM MyOne TM Streptavidin T1 Invitrogen 65601 Pierce TM Recombinant Protein L, Biotinylated Thermo Scientific 29997 DHPC Avanti Polar Lipids 850306P OCT compound Thermo Fisher Scientific 23-730-571 SuperScript TM IV Reverse Transcriptase Invitrogen 18090050 PowerUp TM SYBR TM Green Master Mix for qPCR Applied Biosystems A25742 0.01% poly-L-lysine Sigma P4707 10× RIPA Buffer Cell Signaling 9806 2× Laemmli Sample Buffer Bio-Rad 1610737 Mini-Protean TGX gels Bio-Rad N/A Immun-Blot PVDF Membrane Bio-Rad 1620177 Clarity TM Western ECL Substrate Bio-Rad 1705060 Critical commercial assays Nano-Glo® Dual-Luciferase® Reporter Assay System Promega N1610 High Sensitivity D1000 ScreenTape Agilent 5067–5584 Pierce TM BCA Protein Assay Kit Thermo Scientific 23227 Deposited data Raw fastq files and processed count files GEO GSE246381 Experimental models: Cell lines Human: HEK This paper N/A Experimental models: Organisms/strains Mouse: ROSA26:LSL-eGFP-RPl10 Jackson Stock no. 022367 Mouse: Vglut1-IRES2-Cre-D Jackson Stock no. 023527 Oligonucleotides See Table S6 Integrated DNA Technologies N/A Recombinant DNA JD486 This paper N/A Software and algorithms umi_tools (v1.0.0) Smith et al. 59 https://github.com/CGATOxford/UMI-tools cutadapt (v2.1) Martin 60 https://github.com/marcelm/cutadapt bowtie2 (v2.3.5) Langmead and Salzberg 61 https://bowtie-bio.sourceforge.net/ bowtie2/index.shtml samtools (v1.9) Li et al. 62 https://www.htslib.org/doc/1.9/samtools. html subread (v2.0.0) Liao et al. 63 https://subread.sourceforge.net/ lme4 Bates et al. 64 https://cran.r-project.org/web/packages/ lme4/index.html qvalue Storey et al. 65 https://bioconductor.org/packages/ release/bioc/html/qvalue.html ViennaRNA (v2.4.17) Lorenz et al. 66 https://www.tbi.univie.ac.at/RNA/ RNAfold Gruber et al. 44 http://rna.tbi.univie.ac.at/ QGRS Mapper Kikin et al. 43 https://bioinformatics.ramapo.edu/QGRS/ index.php R R Core Team https://www.r-project.org/ Custom code This Paper https://bitbucket.org/jdlabteam/fiveprime_ mpra_pub/src/main/ https://doi.org/10.5281/zenodo.17459278 e2 Cell Reports Methods 5, 101247, December 15, 2025 OPEN ACCESS
Article Title: Physiological role and mechanisms of action for a long noncoding haplotype region.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Natriuretic Peptide Receptor C Antibody Novus Cat# NBP1-90163, RRID: AB_11017636 Anti-Rabbit IgG (whole molecule)– Peroxidase antibody Sigma-Aldrich Cat# A6154, RRID:AB_258284 Goat polyclonal anti-human/mouse OCT-4 antibody R&D Systems Cat# AF1759, RRID:AB_354975 Rabbit anti-mouse/human NANOG antibody Reprocell Cat# 09–0020, RRID:AB_2298294 Mouse monoclonal anti-human TRA-1 antibody Santa Cruz Biotechnology Cat# sc-21706, RRID:AB_628386 Mouse monoclonal anti-human SSEA4 antibody Santa Cruz Biotechnology Cat# sc-21704, RRID:AB_628289 Rabbit polyclonal anti-human vWF antibody Dako Cat# A0082, RRID:AB_2810304 Goat polyclonal anti-human VE-cadherin antibody R&D Systems Cat# AF938, RRID:AB_355726 Mouse monoclonal anti-human α-SMA antibody Santa Cruz Biotechnology Cat# sc-130616, RRID:AB_1561784 Rabbit monoclonal anti- human/mouse Myosin IIb antibody Cell Signaling Technology Cat# 8824S, RRID:AB_11217639 Donkey anti-Mouse IgG (H + L) Highly Cross-Adsorbed Secondary Antibody, Alexa Fluor TM 488 Invitrogen Cat# A-21202, RRID:AB_141607 Donkey anti-Goat IgG (H + L) CrossAdsorbed Secondary Antibody, Alexa Fluor TM 488 Invitrogen Cat# A-11055, RRID:AB_2534102 Donkey anti-Mouse IgG (H + L) Highly Cross-Adsorbed Secondary Antibody, Alexa Fluor TM 594 Invitrogen Cat# A-21203, RRID:AB_2535789 Donkey anti-Rabbit IgG (H + L) Highly Cross-Adsorbed Secondary Antibody, Alexa Fluor TM 594 Invitrogen Cat# A-21207, RRID:AB_141637 NPRC JAH84 antibody Alli lab N/A Bacterial and virus strains NEB Stable Competent E. coli (High Efficiency) NEB Cat# C3040I Chemicals, peptides, and recombinant proteins C-type Natriuretic Peptide (CNP) Sigma-Aldrich Cat# N8768 AP 811 Tocris Bioscience Cat# 5498 U46619 Cayman Chemical Cat# 16450 spCas9-2NLS Nuclease protein Synthego N/A Y-27632 (Rock inhibitor) Selleck Chemicals Cat# S1049 CHIR99021 (GSK-3 inhibitor) Selleck Chemicals Cat# S1263 2-Mercaptoethanol Gibco Cat# 21985023 BMP4 PeproTech (Gibco) Cat# 120-05-100UG VEGF PeproTech (Gibco) Cat# 100-20-1MG Forskolin Abcam Cat# ab120058 PDGF-BB PeproTech (Gibco) Cat# 100-14B-100UG (Continued on next page) 16 Cell Reports 44, 115805, June 24, 2025 .. REAGENT or RESOURCE SOURCE IDENTIFIER Activin A PeproTech (Gibco) Cat# 120-14E-500UG MEK-inhibitor (Mirdametinib) Selleck Chemicals Cat# S1036 Paraformaldehyde solution Electron Microscopy Sciences Cat# 15700 Triton X-100 Surfact-Amps Detergent Solution Thermo Scientific Cat# 85111 Tween 20 Bio-Rad Cat# 1706531 GoTaq G2 DNA Polymerase Promega Cat# M7841 Q5 Hi-fidelity DNA polymerase NEB Cat# M0491S 2.5% normal horse serum Vector Labs Cat# S-2012-50 Vectashield Vibrance anti-fade mounting media Vector Labs Cat# H-1800 Critical commercial assays ANP EIA Kit RayBiotech Cat# EIA-ANP BNP EIA Kit RayBiotech Cat# EIAM-BNP CNP-22 EIA Kit Phoenix Pharmaceuticals Cat# EKE-012-03 Dovetail® Micro-C kit Cantata Bio Dovetail® Hybridization Module Cantata Bio CP2-HM-001 Deposited data Omics data This paper GSE284940 at Gene Expression Omnibus (GEO) Omics data This paper GSE284945 at Gene Expression Omnibus (GEO) Experimental models: Cell lines iPSC Y4 This paper N/A iPSC Y4_Δ LD This paper N/A iPSC Y4_BP-lowering haplotype This paper N/A iPSC Y4_BP-elevating haplotype This paper N/A iPSC 39b This paper N/A iPSC 39b_Δ SNP This paper N/A iPSC 39b_BP-lowering allele This paper N/A iPSC 39b_BP-elevating allele This paper N/A iPSC 39b_Δ LD This paper N/A iPSC 39b_BP-lowering haplotype This paper N/A iPSC 39b_BP-elevating haplotype This paper N/A iPSC 39b_low-high BP haplotype This paper N/A iPSC 39b_high-low BP haplotype This paper N/A Experimental models: Organisms/strains SS-Δrs1173771LD − /− Medical College of Wisconsin RRID:RGD_401938598 Oligonucleotides Primer sequences for SSΔrs1173771LD − /− genotyping This paper Table S7 Primer sequences for PCR, cloning, and sequencing (IDT) This paper Table S7 Sequences of guide RNAs for rs1173771 haplotype region editing This paper Table S8 Primer sequences for qPCR This paper Table S9 Recombinant DNA Synthetic sgRNAs for rs1173771 single SNP editing (Synthego) This paper Table S6 (Continued on next page) Cell Reports 44, 115805, June 24, 2025 17
Article Title: Genomic copy-number variants drive apoptotic evasion underlying acquired resistance to immune checkpoint inhibitors.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies beta-2 Microglobulin Monoclonal Antibody (B2M-02) Invitrogen Cat# MA1-19413; RRID: AB_1070703 GSDMC Polyclonal Antibody Invitrogen Cat# PA5-116594; RRID: AB_2901225 Fas Recombinant Rabbit Monoclonal Antibody (JJ0942) Invitrogen Cat# MA5-32489; RRID: AB_2809766 DFFB Polyclonal Antibody Invitrogen Cat# PA5-115114; RRID: AB_2899750 Caspase 9 Monoclonal Antibody (LAP6 96-2-22) Invitrogen Cat# MA1-16842; RRID: AB_568482 Bad Antibody Cell Signaling Technology Cat# 9292; RRID: AB_331419 alpha-Tubulin Antibody Cell Signaling Technology Cat# 2144; RRID: AB_2210548 Bax (E4U1V) Rabbit mAb Cell Signaling Technology Cat# 41162; RRID: AB_2924730 DYKDDDDK Tag (D6W5B) Rabbit mAb Cell Signaling Technology Cat# 14793; RRID: AB_2572291 p53 (7F5) Rabbit mAb Cell Signaling Technology Cat# 2527; RRID: AB_10695803 TNF-R1 (C25C1) Rabbit mAb Cell Signaling Technology Cat# 3736; RRID: AB_2241018 TAP1 (E4T4F) Rabbit mAb Cell Signaling Technology Cat# 49671 TAP2 (E8G5I) Rabbit mAb Cell Signaling Technology Cat# 25657 IFNGR1 Antibody Cell Signaling Technology Cat# 34808; RRID: AB_2799061 FITC anti-human CD3 Antibody BioLegend Cat# 317306; RRID: AB_571907 PE anti-human TCR Vβ13.1 Antibody BioLegend Cat# 362410; RRID: AB_2750159 Goat anti-Mouse IgG (H+L) Highly CrossAdsorbed Secondary Antibody, Alexa FluorTM Plus 488 Invitrogen Cat# A32723; RRID: AB_2633275 Goat anti-Rabbit IgG (H+L) Highly CrossAdsorbed Secondary Antibody, Alexa FluorTM 555 Invitrogen Cat# A-21429; RRID: AB_2535850 Bacterial and virus strains NEB® Stable Competent E. coli (High Efficiency) New England Biolabs Cat# C3040H Biological samples Tumor and patient-matched normal tissues University of California, Los Angeles, Sutter Health, and the Vanderbilt-Ingram Cancer Center See Table S1 for details Peripheral blood mononuclear cells (PBMCs) UCLA virology core laboratory N/A Mouse syngeneic tumors Dr. Roger Lo N/A Chemicals, peptides, and recombinant proteins Anti-Mouse CD279 (PD-1) (Clone RMP1-14) Leinco Tech Cat# P362 InVivoMAb anti-mouse CTLA-4 (CD152) BioXcell Cat# BE0131 Venetoclax TargetMol Cat# T2119 PEG300 MedChemExpress Cat# HY-Y0873 Antigen Retrieval Buffer Abcam Cat# ab93684 DAPI MilliporeSigma Cat# D9542 Molecular ProbesTM ProLongTM Diamond Antifade Mountant Thermo Fisher Scientific Cat# P36965 BioT Bioland Scientific Cat# B01-00 (Continued on next page) Immunity 58, 1–14.e1–e9, November 11, 2025 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Sodium butyrate Thermo Fisher Scientific Cat# A11079.36 HEPES Thermo Fisher Scientific Cat# 15630080 Recombinant human IL-2 Miltenyi Biotec Cat# 130-097-748 DynabeadsTM Human T-Activator CD3/ CD28 for T Cell Expansion and Activation Gibco Cat# 11161D RetroNectin Takara Cat# T110A Cryostor CS10 cryopreservation medium Biolife Solutions Cat# 210102 G418 disulfate salt MilliporeSigma Cat# A1720-1G Blasticidin S HCl Gibco Cat# R21001 Puromycin MilliporeSigma Cat# P8833-25MG Hygromycin B Thermo Fisher Scientific Cat# AAJ6068103 Polybrene Infection / Transfection Reagent MilliporeSigma Cat# TR-1003-G RIPA Lysis and Extraction Buffer Thermo Fisher Scientific Cat# 89901 HaltTM Phosphatase Inhibitor Single-Use Cocktail Thermo Fisher Scientific Cat# 78428 PierceTM BCA Protein Assay Kits Thermo Fisher Scientific Cat# 23227 Tween 80 Thermo Fisher Scientific Cat# BP338-500 4% Paraformaldehyde in PBS Thermo Fisher Scientific Cat# J61899.AP Crystal violet solution MilliporeSigma Cat# V5256 Tris-HCl (PH7.4) MilliporeSigma Cat# T2194 Tween 20 Andwin Scientific Cat# NC9022994 Nonidet P40 Substitute MilliporeSigma Cat# 74385 NaCl Invitrogen Cat# AM9760G MgCl2 Invitrogen Cat# AM9530G Triton X-100 Thermo Fisher Scientific Cat# ICN19485483 QIAGEN Protease (30 AU) Qiagen Cat# 19157 0.5M EDTA Thermo Fisher Scientific Cat# R1021 Xylene Fisher Scientific Cat# X5-1 Ethyl Alcohol Sigma-Aldrich Cat# E7023 Critical commercial assays QIAGEN AllPrep DNA/RNA Mini Kit Qiagen Cat# 80204 QIAGEN QIAamp DNA FFPE Tissue Kit Qiagen Cat# 56404 QIAGEN FlexiGene DNA Kit Qiagen Cat# 51206 Pan T Cell Isolation Kit Miltenyi Biotec Cat# 130-096-535 Tumor Dissociation Kit, mouse Miltenyi Biotec Cat# 130-096-730 FFPE Tissue Dissociation Kit Miltenyi Biotec Cat# 130-118-052 Illumina Tagment DNA Enzyme and Buffer Large Kit Illumina Cat# 20034198 KAPA HotStart PCR Kit, with dNTPs Roche Cat# KK2502 Qubit dsDNA HS (High Sensitivity) Assay Kit Invitrogen Cat# Q32851 Qubit dsDNA BR (Broad-Range) Assay Kit Invitrogen Cat# Q32850 Deposited data WES This paper European Genome-phenome Archive (EGA): EGAS50000001055 WGS This paper EGA: EGAS50000001055 WES Zaretsky et al. 15 SRA: SRP076315 WES Hugo et al. 11 SRA: SRP067938, SRP090294 WES Liu et al., 13 Hugo et al., 44 Moriceau et al., 45 Shi et al. 46 SRA: SRP049746 Copy number profiles of TCGA-SKCM cohort TCGA, PanCancer Atlas https://www.cbioportal.org/ (Continued on next page) e2 Immunity 58, 1–14.e1–e9, November 11, 2025
Liquid Chromatography with Mass Spectroscopy:Article Title: Alanine catabolism as a targetable vulnerability for MYC-driven liver cancer.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies α-GPT2 Sigma Cat# HPA051514; RRID: AB_2681516 α-GPT1 Abcam Cat# ab202083; RRID: AB_2915976 α-c-MYC, clone Y69 Abcam Cat# ab32072; RRID: AB_731658 α-β-actin-HRP Santa Cruz Cat# sc-47778; RRID: AB_2714189 α-Vinculin Cell Signaling Technologies Cat# 13901; RRID: AB_2728768 α-ATF4 Cell Signaling Technologies Cat# 11815; RRID: AB_2616025 α-eIF2α Cell Signaling Technologies Cat# 9722; RRID: AB_2230924 α-P-eIF2α Cell Signaling Technologies Cat# 3597; RRID: AB_390740 α-Rabbit IgG-HRP Promega Cat# W4011; RRID: AB_430833 Bacterial and virus strains NEB® Stable Competent E. coli (High Efficiency) New England Biolabs Cat# C3040H Chemicals, peptides, and recombinant proteins Doxycycline Fisher Scientific Cat# BP2653-5 L-Cycloserine MedChemExpress Cat# HY-B1122 Trypan blue Invitrogen Cat# T10282 DTT Fisher Scientific Cat# BP172-25G Heparin McKesson Cat# NDC 63739-931-14 Lipofectamine RNAi MAX Invitrogen Cat# AM9938 13C3; 15N-alanine Cambridge Isotopes Cat# CNLM-534-H-PK Trifluoromethanesulfonate Sigma Cat# 422843-5G Water; LC-MS grade Fisher Scientific Cat# W6-212 Methanol; LC-MS grade Fisher Scientific Cat# A456-500 Acetonitrile; LC-MS grade Fisher Scientific Cat# A955-4 Non-essential amino acids UCSF Cell Culture Facility Cat# CCFGA001-22BU01 L-Alanine Sigma Cat# A7627-100G L-Glutamine Sigma Cat# G3126-100G D-(+)-Glucose solution Sigma Cat# G8769-100ML Methyl-pruvate Thermo scientific Cat# A13966.14 Dimethyl-glutamate Thermo scientific Cat# L03764.06 Hoechst 33342 Biotium Cat# 40046 Propidium Iodide Invitrogen Cat# P3566 Critical commercial assays Alanine Transaminase Activity Assay Kit Abcam Cat# ab105134 DC protein assay kit Biorad Cat# 5000111 QIAshredder Kit Qiagen Cat# 79656 CYQUANT cell proliferation assay ThermoFisher Cat# C7026 Rneasy Mini Kit Qiagen Cat# 74106 High Capacity RNA-to-cDNA Kit Applied Biosystems Cat# 4387406 TaqMan Fast Advanced Master Mix Applied Biosystems Cat# 4444557 Mouse Gpt2 taqman probe Thermo fisher Cat# Mm00558028_m1 Gpt2 Mouse Actb taqman probe Thermo fisher Cat# Mm02619580_g1 Actb Mouse Gpt2 taqman probe Thermo fisher Cat# Hs99999903_m1 ACTB (Continued on next page) Cell Reports 45, 117107, April 28, 2026 13 .. REAGENT or RESOURCE SOURCE IDENTIFIER Mouse Actb taqman probe Thermo fisher Cat# Hs00370287_m1 GPT2 Deposited data The Cancer Genome Atlas (HCC) Ally et al.5 https://gdc.cancer.gov/; https:// www.cbioportal.org/study/ summary?id=lihc_tcga RNA sequencing and ChIP sequencing in the LT2-MYC model Kress et al.18 GEO: GSE76078 LT2-MYC metabolomics data Anderton et al.15 https://pmc.ncbi.nlm.nih.gov/articles/ PMC5376764/#embr201643068sup-0003 13C3; 15N-alanine tracing in the LT2-MYC model https://doi.org/10.21228/M8TK1K NMDR: ST004169 Experimental models: Cell lines EC4 Cao et al.50 N/A HepG2 ATCC HB-8065; RRID: CVCL_0027 Tong Xin Chen (University of Hawai’i Cancer Center) RRID: CVCL_V640 PLC5 Xin Chen (University of Hawai’i Cancer Center) CRL-8024; RRID: CVCL_0485 SNU475 Xin Chen (University of Hawai’i Cancer Center) CRL-2236; RRID: CVCL_0497 Experimental models: Organisms/strains C57BL/6 mice JAX Cat# 000664 Nude mice JAX Cat# 002019 LT2-MYC mice Shachaf et al.51 N/A GPT2 FLOX mice Martino et al.10 N/A Recombinant DNA pT3-MYC-IRES-CRE This study.
Cell Culture:Article Title: Alanine catabolism as a targetable vulnerability for MYC-driven liver cancer.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies α-GPT2 Sigma Cat# HPA051514; RRID: AB_2681516 α-GPT1 Abcam Cat# ab202083; RRID: AB_2915976 α-c-MYC, clone Y69 Abcam Cat# ab32072; RRID: AB_731658 α-β-actin-HRP Santa Cruz Cat# sc-47778; RRID: AB_2714189 α-Vinculin Cell Signaling Technologies Cat# 13901; RRID: AB_2728768 α-ATF4 Cell Signaling Technologies Cat# 11815; RRID: AB_2616025 α-eIF2α Cell Signaling Technologies Cat# 9722; RRID: AB_2230924 α-P-eIF2α Cell Signaling Technologies Cat# 3597; RRID: AB_390740 α-Rabbit IgG-HRP Promega Cat# W4011; RRID: AB_430833 Bacterial and virus strains NEB® Stable Competent E. coli (High Efficiency) New England Biolabs Cat# C3040H Chemicals, peptides, and recombinant proteins Doxycycline Fisher Scientific Cat# BP2653-5 L-Cycloserine MedChemExpress Cat# HY-B1122 Trypan blue Invitrogen Cat# T10282 DTT Fisher Scientific Cat# BP172-25G Heparin McKesson Cat# NDC 63739-931-14 Lipofectamine RNAi MAX Invitrogen Cat# AM9938 13C3; 15N-alanine Cambridge Isotopes Cat# CNLM-534-H-PK Trifluoromethanesulfonate Sigma Cat# 422843-5G Water; LC-MS grade Fisher Scientific Cat# W6-212 Methanol; LC-MS grade Fisher Scientific Cat# A456-500 Acetonitrile; LC-MS grade Fisher Scientific Cat# A955-4 Non-essential amino acids UCSF Cell Culture Facility Cat# CCFGA001-22BU01 L-Alanine Sigma Cat# A7627-100G L-Glutamine Sigma Cat# G3126-100G D-(+)-Glucose solution Sigma Cat# G8769-100ML Methyl-pruvate Thermo scientific Cat# A13966.14 Dimethyl-glutamate Thermo scientific Cat# L03764.06 Hoechst 33342 Biotium Cat# 40046 Propidium Iodide Invitrogen Cat# P3566 Critical commercial assays Alanine Transaminase Activity Assay Kit Abcam Cat# ab105134 DC protein assay kit Biorad Cat# 5000111 QIAshredder Kit Qiagen Cat# 79656 CYQUANT cell proliferation assay ThermoFisher Cat# C7026 Rneasy Mini Kit Qiagen Cat# 74106 High Capacity RNA-to-cDNA Kit Applied Biosystems Cat# 4387406 TaqMan Fast Advanced Master Mix Applied Biosystems Cat# 4444557 Mouse Gpt2 taqman probe Thermo fisher Cat# Mm00558028_m1 Gpt2 Mouse Actb taqman probe Thermo fisher Cat# Mm02619580_g1 Actb Mouse Gpt2 taqman probe Thermo fisher Cat# Hs99999903_m1 ACTB (Continued on next page) Cell Reports 45, 117107, April 28, 2026 13 .. REAGENT or RESOURCE SOURCE IDENTIFIER Mouse Actb taqman probe Thermo fisher Cat# Hs00370287_m1 GPT2 Deposited data The Cancer Genome Atlas (HCC) Ally et al.5 https://gdc.cancer.gov/; https:// www.cbioportal.org/study/ summary?id=lihc_tcga RNA sequencing and ChIP sequencing in the LT2-MYC model Kress et al.18 GEO: GSE76078 LT2-MYC metabolomics data Anderton et al.15 https://pmc.ncbi.nlm.nih.gov/articles/ PMC5376764/#embr201643068sup-0003 13C3; 15N-alanine tracing in the LT2-MYC model https://doi.org/10.21228/M8TK1K NMDR: ST004169 Experimental models: Cell lines EC4 Cao et al.50 N/A HepG2 ATCC HB-8065; RRID: CVCL_0027 Tong Xin Chen (University of Hawai’i Cancer Center) RRID: CVCL_V640 PLC5 Xin Chen (University of Hawai’i Cancer Center) CRL-8024; RRID: CVCL_0485 SNU475 Xin Chen (University of Hawai’i Cancer Center) CRL-2236; RRID: CVCL_0497 Experimental models: Organisms/strains C57BL/6 mice JAX Cat# 000664 Nude mice JAX Cat# 002019 LT2-MYC mice Shachaf et al.51 N/A GPT2 FLOX mice Martino et al.10 N/A Recombinant DNA pT3-MYC-IRES-CRE This study.
Activity Assay:Article Title: Alanine catabolism as a targetable vulnerability for MYC-driven liver cancer.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies α-GPT2 Sigma Cat# HPA051514; RRID: AB_2681516 α-GPT1 Abcam Cat# ab202083; RRID: AB_2915976 α-c-MYC, clone Y69 Abcam Cat# ab32072; RRID: AB_731658 α-β-actin-HRP Santa Cruz Cat# sc-47778; RRID: AB_2714189 α-Vinculin Cell Signaling Technologies Cat# 13901; RRID: AB_2728768 α-ATF4 Cell Signaling Technologies Cat# 11815; RRID: AB_2616025 α-eIF2α Cell Signaling Technologies Cat# 9722; RRID: AB_2230924 α-P-eIF2α Cell Signaling Technologies Cat# 3597; RRID: AB_390740 α-Rabbit IgG-HRP Promega Cat# W4011; RRID: AB_430833 Bacterial and virus strains NEB® Stable Competent E. coli (High Efficiency) New England Biolabs Cat# C3040H Chemicals, peptides, and recombinant proteins Doxycycline Fisher Scientific Cat# BP2653-5 L-Cycloserine MedChemExpress Cat# HY-B1122 Trypan blue Invitrogen Cat# T10282 DTT Fisher Scientific Cat# BP172-25G Heparin McKesson Cat# NDC 63739-931-14 Lipofectamine RNAi MAX Invitrogen Cat# AM9938 13C3; 15N-alanine Cambridge Isotopes Cat# CNLM-534-H-PK Trifluoromethanesulfonate Sigma Cat# 422843-5G Water; LC-MS grade Fisher Scientific Cat# W6-212 Methanol; LC-MS grade Fisher Scientific Cat# A456-500 Acetonitrile; LC-MS grade Fisher Scientific Cat# A955-4 Non-essential amino acids UCSF Cell Culture Facility Cat# CCFGA001-22BU01 L-Alanine Sigma Cat# A7627-100G L-Glutamine Sigma Cat# G3126-100G D-(+)-Glucose solution Sigma Cat# G8769-100ML Methyl-pruvate Thermo scientific Cat# A13966.14 Dimethyl-glutamate Thermo scientific Cat# L03764.06 Hoechst 33342 Biotium Cat# 40046 Propidium Iodide Invitrogen Cat# P3566 Critical commercial assays Alanine Transaminase Activity Assay Kit Abcam Cat# ab105134 DC protein assay kit Biorad Cat# 5000111 QIAshredder Kit Qiagen Cat# 79656 CYQUANT cell proliferation assay ThermoFisher Cat# C7026 Rneasy Mini Kit Qiagen Cat# 74106 High Capacity RNA-to-cDNA Kit Applied Biosystems Cat# 4387406 TaqMan Fast Advanced Master Mix Applied Biosystems Cat# 4444557 Mouse Gpt2 taqman probe Thermo fisher Cat# Mm00558028_m1 Gpt2 Mouse Actb taqman probe Thermo fisher Cat# Mm02619580_g1 Actb Mouse Gpt2 taqman probe Thermo fisher Cat# Hs99999903_m1 ACTB (Continued on next page) Cell Reports 45, 117107, April 28, 2026 13 .. REAGENT or RESOURCE SOURCE IDENTIFIER Mouse Actb taqman probe Thermo fisher Cat# Hs00370287_m1 GPT2 Deposited data The Cancer Genome Atlas (HCC) Ally et al.5 https://gdc.cancer.gov/; https:// www.cbioportal.org/study/ summary?id=lihc_tcga RNA sequencing and ChIP sequencing in the LT2-MYC model Kress et al.18 GEO: GSE76078 LT2-MYC metabolomics data Anderton et al.15 https://pmc.ncbi.nlm.nih.gov/articles/ PMC5376764/#embr201643068sup-0003 13C3; 15N-alanine tracing in the LT2-MYC model https://doi.org/10.21228/M8TK1K NMDR: ST004169 Experimental models: Cell lines EC4 Cao et al.50 N/A HepG2 ATCC HB-8065; RRID: CVCL_0027 Tong Xin Chen (University of Hawai’i Cancer Center) RRID: CVCL_V640 PLC5 Xin Chen (University of Hawai’i Cancer Center) CRL-8024; RRID: CVCL_0485 SNU475 Xin Chen (University of Hawai’i Cancer Center) CRL-2236; RRID: CVCL_0497 Experimental models: Organisms/strains C57BL/6 mice JAX Cat# 000664 Nude mice JAX Cat# 002019 LT2-MYC mice Shachaf et al.51 N/A GPT2 FLOX mice Martino et al.10 N/A Recombinant DNA pT3-MYC-IRES-CRE This study.
DC Protein Assay:Article Title: Alanine catabolism as a targetable vulnerability for MYC-driven liver cancer.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies α-GPT2 Sigma Cat# HPA051514; RRID: AB_2681516 α-GPT1 Abcam Cat# ab202083; RRID: AB_2915976 α-c-MYC, clone Y69 Abcam Cat# ab32072; RRID: AB_731658 α-β-actin-HRP Santa Cruz Cat# sc-47778; RRID: AB_2714189 α-Vinculin Cell Signaling Technologies Cat# 13901; RRID: AB_2728768 α-ATF4 Cell Signaling Technologies Cat# 11815; RRID: AB_2616025 α-eIF2α Cell Signaling Technologies Cat# 9722; RRID: AB_2230924 α-P-eIF2α Cell Signaling Technologies Cat# 3597; RRID: AB_390740 α-Rabbit IgG-HRP Promega Cat# W4011; RRID: AB_430833 Bacterial and virus strains NEB® Stable Competent E. coli (High Efficiency) New England Biolabs Cat# C3040H Chemicals, peptides, and recombinant proteins Doxycycline Fisher Scientific Cat# BP2653-5 L-Cycloserine MedChemExpress Cat# HY-B1122 Trypan blue Invitrogen Cat# T10282 DTT Fisher Scientific Cat# BP172-25G Heparin McKesson Cat# NDC 63739-931-14 Lipofectamine RNAi MAX Invitrogen Cat# AM9938 13C3; 15N-alanine Cambridge Isotopes Cat# CNLM-534-H-PK Trifluoromethanesulfonate Sigma Cat# 422843-5G Water; LC-MS grade Fisher Scientific Cat# W6-212 Methanol; LC-MS grade Fisher Scientific Cat# A456-500 Acetonitrile; LC-MS grade Fisher Scientific Cat# A955-4 Non-essential amino acids UCSF Cell Culture Facility Cat# CCFGA001-22BU01 L-Alanine Sigma Cat# A7627-100G L-Glutamine Sigma Cat# G3126-100G D-(+)-Glucose solution Sigma Cat# G8769-100ML Methyl-pruvate Thermo scientific Cat# A13966.14 Dimethyl-glutamate Thermo scientific Cat# L03764.06 Hoechst 33342 Biotium Cat# 40046 Propidium Iodide Invitrogen Cat# P3566 Critical commercial assays Alanine Transaminase Activity Assay Kit Abcam Cat# ab105134 DC protein assay kit Biorad Cat# 5000111 QIAshredder Kit Qiagen Cat# 79656 CYQUANT cell proliferation assay ThermoFisher Cat# C7026 Rneasy Mini Kit Qiagen Cat# 74106 High Capacity RNA-to-cDNA Kit Applied Biosystems Cat# 4387406 TaqMan Fast Advanced Master Mix Applied Biosystems Cat# 4444557 Mouse Gpt2 taqman probe Thermo fisher Cat# Mm00558028_m1 Gpt2 Mouse Actb taqman probe Thermo fisher Cat# Mm02619580_g1 Actb Mouse Gpt2 taqman probe Thermo fisher Cat# Hs99999903_m1 ACTB (Continued on next page) Cell Reports 45, 117107, April 28, 2026 13 .. REAGENT or RESOURCE SOURCE IDENTIFIER Mouse Actb taqman probe Thermo fisher Cat# Hs00370287_m1 GPT2 Deposited data The Cancer Genome Atlas (HCC) Ally et al.5 https://gdc.cancer.gov/; https:// www.cbioportal.org/study/ summary?id=lihc_tcga RNA sequencing and ChIP sequencing in the LT2-MYC model Kress et al.18 GEO: GSE76078 LT2-MYC metabolomics data Anderton et al.15 https://pmc.ncbi.nlm.nih.gov/articles/ PMC5376764/#embr201643068sup-0003 13C3; 15N-alanine tracing in the LT2-MYC model https://doi.org/10.21228/M8TK1K NMDR: ST004169 Experimental models: Cell lines EC4 Cao et al.50 N/A HepG2 ATCC HB-8065; RRID: CVCL_0027 Tong Xin Chen (University of Hawai’i Cancer Center) RRID: CVCL_V640 PLC5 Xin Chen (University of Hawai’i Cancer Center) CRL-8024; RRID: CVCL_0485 SNU475 Xin Chen (University of Hawai’i Cancer Center) CRL-2236; RRID: CVCL_0497 Experimental models: Organisms/strains C57BL/6 mice JAX Cat# 000664 Nude mice JAX Cat# 002019 LT2-MYC mice Shachaf et al.51 N/A GPT2 FLOX mice Martino et al.10 N/A Recombinant DNA pT3-MYC-IRES-CRE This study.
CyQUANT Assay:Article Title: Alanine catabolism as a targetable vulnerability for MYC-driven liver cancer.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies α-GPT2 Sigma Cat# HPA051514; RRID: AB_2681516 α-GPT1 Abcam Cat# ab202083; RRID: AB_2915976 α-c-MYC, clone Y69 Abcam Cat# ab32072; RRID: AB_731658 α-β-actin-HRP Santa Cruz Cat# sc-47778; RRID: AB_2714189 α-Vinculin Cell Signaling Technologies Cat# 13901; RRID: AB_2728768 α-ATF4 Cell Signaling Technologies Cat# 11815; RRID: AB_2616025 α-eIF2α Cell Signaling Technologies Cat# 9722; RRID: AB_2230924 α-P-eIF2α Cell Signaling Technologies Cat# 3597; RRID: AB_390740 α-Rabbit IgG-HRP Promega Cat# W4011; RRID: AB_430833 Bacterial and virus strains NEB® Stable Competent E. coli (High Efficiency) New England Biolabs Cat# C3040H Chemicals, peptides, and recombinant proteins Doxycycline Fisher Scientific Cat# BP2653-5 L-Cycloserine MedChemExpress Cat# HY-B1122 Trypan blue Invitrogen Cat# T10282 DTT Fisher Scientific Cat# BP172-25G Heparin McKesson Cat# NDC 63739-931-14 Lipofectamine RNAi MAX Invitrogen Cat# AM9938 13C3; 15N-alanine Cambridge Isotopes Cat# CNLM-534-H-PK Trifluoromethanesulfonate Sigma Cat# 422843-5G Water; LC-MS grade Fisher Scientific Cat# W6-212 Methanol; LC-MS grade Fisher Scientific Cat# A456-500 Acetonitrile; LC-MS grade Fisher Scientific Cat# A955-4 Non-essential amino acids UCSF Cell Culture Facility Cat# CCFGA001-22BU01 L-Alanine Sigma Cat# A7627-100G L-Glutamine Sigma Cat# G3126-100G D-(+)-Glucose solution Sigma Cat# G8769-100ML Methyl-pruvate Thermo scientific Cat# A13966.14 Dimethyl-glutamate Thermo scientific Cat# L03764.06 Hoechst 33342 Biotium Cat# 40046 Propidium Iodide Invitrogen Cat# P3566 Critical commercial assays Alanine Transaminase Activity Assay Kit Abcam Cat# ab105134 DC protein assay kit Biorad Cat# 5000111 QIAshredder Kit Qiagen Cat# 79656 CYQUANT cell proliferation assay ThermoFisher Cat# C7026 Rneasy Mini Kit Qiagen Cat# 74106 High Capacity RNA-to-cDNA Kit Applied Biosystems Cat# 4387406 TaqMan Fast Advanced Master Mix Applied Biosystems Cat# 4444557 Mouse Gpt2 taqman probe Thermo fisher Cat# Mm00558028_m1 Gpt2 Mouse Actb taqman probe Thermo fisher Cat# Mm02619580_g1 Actb Mouse Gpt2 taqman probe Thermo fisher Cat# Hs99999903_m1 ACTB (Continued on next page) Cell Reports 45, 117107, April 28, 2026 13 .. REAGENT or RESOURCE SOURCE IDENTIFIER Mouse Actb taqman probe Thermo fisher Cat# Hs00370287_m1 GPT2 Deposited data The Cancer Genome Atlas (HCC) Ally et al.5 https://gdc.cancer.gov/; https:// www.cbioportal.org/study/ summary?id=lihc_tcga RNA sequencing and ChIP sequencing in the LT2-MYC model Kress et al.18 GEO: GSE76078 LT2-MYC metabolomics data Anderton et al.15 https://pmc.ncbi.nlm.nih.gov/articles/ PMC5376764/#embr201643068sup-0003 13C3; 15N-alanine tracing in the LT2-MYC model https://doi.org/10.21228/M8TK1K NMDR: ST004169 Experimental models: Cell lines EC4 Cao et al.50 N/A HepG2 ATCC HB-8065; RRID: CVCL_0027 Tong Xin Chen (University of Hawai’i Cancer Center) RRID: CVCL_V640 PLC5 Xin Chen (University of Hawai’i Cancer Center) CRL-8024; RRID: CVCL_0485 SNU475 Xin Chen (University of Hawai’i Cancer Center) CRL-2236; RRID: CVCL_0497 Experimental models: Organisms/strains C57BL/6 mice JAX Cat# 000664 Nude mice JAX Cat# 002019 LT2-MYC mice Shachaf et al.51 N/A GPT2 FLOX mice Martino et al.10 N/A Recombinant DNA pT3-MYC-IRES-CRE This study.
Proliferation Assay:Article Title: Alanine catabolism as a targetable vulnerability for MYC-driven liver cancer.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies α-GPT2 Sigma Cat# HPA051514; RRID: AB_2681516 α-GPT1 Abcam Cat# ab202083; RRID: AB_2915976 α-c-MYC, clone Y69 Abcam Cat# ab32072; RRID: AB_731658 α-β-actin-HRP Santa Cruz Cat# sc-47778; RRID: AB_2714189 α-Vinculin Cell Signaling Technologies Cat# 13901; RRID: AB_2728768 α-ATF4 Cell Signaling Technologies Cat# 11815; RRID: AB_2616025 α-eIF2α Cell Signaling Technologies Cat# 9722; RRID: AB_2230924 α-P-eIF2α Cell Signaling Technologies Cat# 3597; RRID: AB_390740 α-Rabbit IgG-HRP Promega Cat# W4011; RRID: AB_430833 Bacterial and virus strains NEB® Stable Competent E. coli (High Efficiency) New England Biolabs Cat# C3040H Chemicals, peptides, and recombinant proteins Doxycycline Fisher Scientific Cat# BP2653-5 L-Cycloserine MedChemExpress Cat# HY-B1122 Trypan blue Invitrogen Cat# T10282 DTT Fisher Scientific Cat# BP172-25G Heparin McKesson Cat# NDC 63739-931-14 Lipofectamine RNAi MAX Invitrogen Cat# AM9938 13C3; 15N-alanine Cambridge Isotopes Cat# CNLM-534-H-PK Trifluoromethanesulfonate Sigma Cat# 422843-5G Water; LC-MS grade Fisher Scientific Cat# W6-212 Methanol; LC-MS grade Fisher Scientific Cat# A456-500 Acetonitrile; LC-MS grade Fisher Scientific Cat# A955-4 Non-essential amino acids UCSF Cell Culture Facility Cat# CCFGA001-22BU01 L-Alanine Sigma Cat# A7627-100G L-Glutamine Sigma Cat# G3126-100G D-(+)-Glucose solution Sigma Cat# G8769-100ML Methyl-pruvate Thermo scientific Cat# A13966.14 Dimethyl-glutamate Thermo scientific Cat# L03764.06 Hoechst 33342 Biotium Cat# 40046 Propidium Iodide Invitrogen Cat# P3566 Critical commercial assays Alanine Transaminase Activity Assay Kit Abcam Cat# ab105134 DC protein assay kit Biorad Cat# 5000111 QIAshredder Kit Qiagen Cat# 79656 CYQUANT cell proliferation assay ThermoFisher Cat# C7026 Rneasy Mini Kit Qiagen Cat# 74106 High Capacity RNA-to-cDNA Kit Applied Biosystems Cat# 4387406 TaqMan Fast Advanced Master Mix Applied Biosystems Cat# 4444557 Mouse Gpt2 taqman probe Thermo fisher Cat# Mm00558028_m1 Gpt2 Mouse Actb taqman probe Thermo fisher Cat# Mm02619580_g1 Actb Mouse Gpt2 taqman probe Thermo fisher Cat# Hs99999903_m1 ACTB (Continued on next page) Cell Reports 45, 117107, April 28, 2026 13 .. REAGENT or RESOURCE SOURCE IDENTIFIER Mouse Actb taqman probe Thermo fisher Cat# Hs00370287_m1 GPT2 Deposited data The Cancer Genome Atlas (HCC) Ally et al.5 https://gdc.cancer.gov/; https:// www.cbioportal.org/study/ summary?id=lihc_tcga RNA sequencing and ChIP sequencing in the LT2-MYC model Kress et al.18 GEO: GSE76078 LT2-MYC metabolomics data Anderton et al.15 https://pmc.ncbi.nlm.nih.gov/articles/ PMC5376764/#embr201643068sup-0003 13C3; 15N-alanine tracing in the LT2-MYC model https://doi.org/10.21228/M8TK1K NMDR: ST004169 Experimental models: Cell lines EC4 Cao et al.50 N/A HepG2 ATCC HB-8065; RRID: CVCL_0027 Tong Xin Chen (University of Hawai’i Cancer Center) RRID: CVCL_V640 PLC5 Xin Chen (University of Hawai’i Cancer Center) CRL-8024; RRID: CVCL_0485 SNU475 Xin Chen (University of Hawai’i Cancer Center) CRL-2236; RRID: CVCL_0497 Experimental models: Organisms/strains C57BL/6 mice JAX Cat# 000664 Nude mice JAX Cat# 002019 LT2-MYC mice Shachaf et al.51 N/A GPT2 FLOX mice Martino et al.10 N/A Recombinant DNA pT3-MYC-IRES-CRE This study.
Control:Article Title: FAME-CRISPR improves CRISPR-Cas9 genome editing via HDAC inhibition and engineered virus-like particle delivery.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Histone H3ac (pan-acetyl) Polyclonal antibody Thermo Fisher Scientific Cat# 39139; RRID: AB_2687871 Monoclonal ANTI-FLAG® M2 Sigma-Aldrich Cat# F3165-2MG; RRID: AB_259529 beta Actin Monoclonal antibody (AC-15) Thermo Fisher Scientific Cat# AM4302; RRID: AB_437394 Anti-GAPDH antibody [6C5] - Loading Control Abcam Cat# ab8245; RRID: AB_2107448 GFP tag Polyclonal antibody Proteintech Cat# 50430-2-AP; RRID: AB_11042881 Caspase-3 antibody Cell signaling Cat# 9662; RRID:AB_331439 Cleaved Caspase-3 (Asp175) (5A1E) antibody Cell signaling Cat# 9664; RRID: AB_2070042 ANTI-FLAG® M2 Magnetic Beads Sigma-Aldrich Cat# M8823-1ML; RRID: AB_2637089 γH2AX Abcam Cat# ab26350; RRID: AB_470861 Alexa Fluor 633 Invitrogen Cat# A-21050; RRID: AB_2535718 Bacterial and virus strains NEB® Stable Competent E. coli (High Efficiency) New England Biolabs # C3040I NEB® 5-alpha Competent E. coli (Subcloning Efficiency) New England Biolabs # C2988J Recombinant 3 rd generation Lentivirus – N/A 5 th generation engineered Virus-Like Particles (eVLPs) Raguram et al. 49 N/A Chemicals, peptides, and recombinant proteins LBH589 (Panobinostat) Sigma-Aldrich # SML3060-10MG Belinostat Sigma-Aldrich # SML3010-10MG SB505124 Sigma-Aldrich # S4696-5MG PCI-24781 Sigma-Aldrich # SML4043-5MG Valproic acid Sigma-Aldrich # P4543-10G DMSO Sigma-Aldrich # D2650-100ML Polybrene Sigma-Aldrich # TR-1003-50UL Lipofectamine 3000 Thermo Fisher Scientific # L3000015 Critical commercial assays AlamarBlue TM Cell Viability Reagents Thermo Fisher Scientific # DAL1100 Deposited data Raw Sanger Sequencing data This paper https://doi.org/10.17632/33tm3dd9dw.1 Raw immunofluorescent microscopy data This paper https://doi.org/10.17632/33tm3dd9dw.1 Uncropped gel images This paper https://doi.org/10.17632/33tm3dd9dw.1 Experimental models: Cell lines HeLa ATCC # CCL-2 HepG2 ATCC # HB-8065 .. MDA-MB-231 ATCC # HTB-26
Article Title: Protocol for enhancing CRISPR-Cas9 genome editing using histone deacetylase inhibition and engineered virus-like particle delivery.
Article Snippet: .. KEY RESOURCES TABLE REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Histone H3ac (pan-acetyl) Polyclonal antibody [1:1000] Thermo Fisher Scientific Cat# 39139; RRID: AB_2687871 Monoclonal ANTI-FLAG® M2 [1:5000] Sigma-Aldrich Cat# F3165-2MG; RRID: AB_259529 beta Actin Monoclonal antibody (AC-15) [1:10,000] Thermo Fisher Scientific Cat# AM4302; RRID: AB_437394 Anti-GAPDH antibody [6C5] - Loading Control [1:5000] Abcam Cat# ab8245; RRID: AB_2107448 GFP tag Polyclonal antibody [1:1000] Proteintech Cat# 50430-2-AP; RRID: AB_11042881 Caspase-3 antibody [1:1000] Cell signaling Cat# 9662; RRID:AB_331439 Cleaved Caspase-3 (Asp175) (5A1E) antibody [1:1000] Cell signaling Cat# 9664; RRID: AB_2070042 Bacterial and virus strains NEB® Stable Competent E. coli (High Efficiency) New England Biolabs #C3040I 16th generation engineered Virus-Like Particles (eVLPs) Raguram, A. et al 16 Not applicable Chemicals, peptides, and recombinant proteins LBH589 (Panobinostat) Sigma-Aldrich #SML3060-10MG Belinostat Sigma-Aldrich #SML3010-10MG DMSO Sigma-Aldrich #D2650-100ML Polybrene Sigma-Aldrich #TR-1003-50UL Lipofectamine 3000 Thermo Fisher Scientific #L3000015 Critical commercial assays AlamarBlueTM Cell Viability Reagents Thermo Fisher Scientific #DAL1100 Deposited data Raw Sanger Sequencing data Mendeley https://doi.org/10.17632/33tm3dd9dw.1 Raw immunofluorescent microscopy data Mendeley https://doi.org/10.17632/33tm3dd9dw.1 Uncropped gel images Mendeley https://doi.org/10.17632/33tm3dd9dw.1 Experimental models: Cell lines MDA-MB-231 ATCC #HTB-26 HEK-293 T ATCC #CRL-3216 Recombinant DNA psPAX2 Addgene #12260 pMD2.G Addgene #122259 MLV gag-pro-pol Addgene 16 #228466 MMLV gag-Cas9 Addgene 16 #228468 (Continued on next page) 4 STAR Protocols 7, 104493, June 19, 2026 ..
Magnetic Beads:Article Title: FAME-CRISPR improves CRISPR-Cas9 genome editing via HDAC inhibition and engineered virus-like particle delivery.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Histone H3ac (pan-acetyl) Polyclonal antibody Thermo Fisher Scientific Cat# 39139; RRID: AB_2687871 Monoclonal ANTI-FLAG® M2 Sigma-Aldrich Cat# F3165-2MG; RRID: AB_259529 beta Actin Monoclonal antibody (AC-15) Thermo Fisher Scientific Cat# AM4302; RRID: AB_437394 Anti-GAPDH antibody [6C5] - Loading Control Abcam Cat# ab8245; RRID: AB_2107448 GFP tag Polyclonal antibody Proteintech Cat# 50430-2-AP; RRID: AB_11042881 Caspase-3 antibody Cell signaling Cat# 9662; RRID:AB_331439 Cleaved Caspase-3 (Asp175) (5A1E) antibody Cell signaling Cat# 9664; RRID: AB_2070042 ANTI-FLAG® M2 Magnetic Beads Sigma-Aldrich Cat# M8823-1ML; RRID: AB_2637089 γH2AX Abcam Cat# ab26350; RRID: AB_470861 Alexa Fluor 633 Invitrogen Cat# A-21050; RRID: AB_2535718 Bacterial and virus strains NEB® Stable Competent E. coli (High Efficiency) New England Biolabs # C3040I NEB® 5-alpha Competent E. coli (Subcloning Efficiency) New England Biolabs # C2988J Recombinant 3 rd generation Lentivirus – N/A 5 th generation engineered Virus-Like Particles (eVLPs) Raguram et al. 49 N/A Chemicals, peptides, and recombinant proteins LBH589 (Panobinostat) Sigma-Aldrich # SML3060-10MG Belinostat Sigma-Aldrich # SML3010-10MG SB505124 Sigma-Aldrich # S4696-5MG PCI-24781 Sigma-Aldrich # SML4043-5MG Valproic acid Sigma-Aldrich # P4543-10G DMSO Sigma-Aldrich # D2650-100ML Polybrene Sigma-Aldrich # TR-1003-50UL Lipofectamine 3000 Thermo Fisher Scientific # L3000015 Critical commercial assays AlamarBlue TM Cell Viability Reagents Thermo Fisher Scientific # DAL1100 Deposited data Raw Sanger Sequencing data This paper https://doi.org/10.17632/33tm3dd9dw.1 Raw immunofluorescent microscopy data This paper https://doi.org/10.17632/33tm3dd9dw.1 Uncropped gel images This paper https://doi.org/10.17632/33tm3dd9dw.1 Experimental models: Cell lines HeLa ATCC # CCL-2 HepG2 ATCC # HB-8065 .. MDA-MB-231 ATCC # HTB-26
Subcloning:Article Title: FAME-CRISPR improves CRISPR-Cas9 genome editing via HDAC inhibition and engineered virus-like particle delivery.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Histone H3ac (pan-acetyl) Polyclonal antibody Thermo Fisher Scientific Cat# 39139; RRID: AB_2687871 Monoclonal ANTI-FLAG® M2 Sigma-Aldrich Cat# F3165-2MG; RRID: AB_259529 beta Actin Monoclonal antibody (AC-15) Thermo Fisher Scientific Cat# AM4302; RRID: AB_437394 Anti-GAPDH antibody [6C5] - Loading Control Abcam Cat# ab8245; RRID: AB_2107448 GFP tag Polyclonal antibody Proteintech Cat# 50430-2-AP; RRID: AB_11042881 Caspase-3 antibody Cell signaling Cat# 9662; RRID:AB_331439 Cleaved Caspase-3 (Asp175) (5A1E) antibody Cell signaling Cat# 9664; RRID: AB_2070042 ANTI-FLAG® M2 Magnetic Beads Sigma-Aldrich Cat# M8823-1ML; RRID: AB_2637089 γH2AX Abcam Cat# ab26350; RRID: AB_470861 Alexa Fluor 633 Invitrogen Cat# A-21050; RRID: AB_2535718 Bacterial and virus strains NEB® Stable Competent E. coli (High Efficiency) New England Biolabs # C3040I NEB® 5-alpha Competent E. coli (Subcloning Efficiency) New England Biolabs # C2988J Recombinant 3 rd generation Lentivirus – N/A 5 th generation engineered Virus-Like Particles (eVLPs) Raguram et al. 49 N/A Chemicals, peptides, and recombinant proteins LBH589 (Panobinostat) Sigma-Aldrich # SML3060-10MG Belinostat Sigma-Aldrich # SML3010-10MG SB505124 Sigma-Aldrich # S4696-5MG PCI-24781 Sigma-Aldrich # SML4043-5MG Valproic acid Sigma-Aldrich # P4543-10G DMSO Sigma-Aldrich # D2650-100ML Polybrene Sigma-Aldrich # TR-1003-50UL Lipofectamine 3000 Thermo Fisher Scientific # L3000015 Critical commercial assays AlamarBlue TM Cell Viability Reagents Thermo Fisher Scientific # DAL1100 Deposited data Raw Sanger Sequencing data This paper https://doi.org/10.17632/33tm3dd9dw.1 Raw immunofluorescent microscopy data This paper https://doi.org/10.17632/33tm3dd9dw.1 Uncropped gel images This paper https://doi.org/10.17632/33tm3dd9dw.1 Experimental models: Cell lines HeLa ATCC # CCL-2 HepG2 ATCC # HB-8065 .. MDA-MB-231 ATCC # HTB-26
Sequencing:Article Title: FAME-CRISPR improves CRISPR-Cas9 genome editing via HDAC inhibition and engineered virus-like particle delivery.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Histone H3ac (pan-acetyl) Polyclonal antibody Thermo Fisher Scientific Cat# 39139; RRID: AB_2687871 Monoclonal ANTI-FLAG® M2 Sigma-Aldrich Cat# F3165-2MG; RRID: AB_259529 beta Actin Monoclonal antibody (AC-15) Thermo Fisher Scientific Cat# AM4302; RRID: AB_437394 Anti-GAPDH antibody [6C5] - Loading Control Abcam Cat# ab8245; RRID: AB_2107448 GFP tag Polyclonal antibody Proteintech Cat# 50430-2-AP; RRID: AB_11042881 Caspase-3 antibody Cell signaling Cat# 9662; RRID:AB_331439 Cleaved Caspase-3 (Asp175) (5A1E) antibody Cell signaling Cat# 9664; RRID: AB_2070042 ANTI-FLAG® M2 Magnetic Beads Sigma-Aldrich Cat# M8823-1ML; RRID: AB_2637089 γH2AX Abcam Cat# ab26350; RRID: AB_470861 Alexa Fluor 633 Invitrogen Cat# A-21050; RRID: AB_2535718 Bacterial and virus strains NEB® Stable Competent E. coli (High Efficiency) New England Biolabs # C3040I NEB® 5-alpha Competent E. coli (Subcloning Efficiency) New England Biolabs # C2988J Recombinant 3 rd generation Lentivirus – N/A 5 th generation engineered Virus-Like Particles (eVLPs) Raguram et al. 49 N/A Chemicals, peptides, and recombinant proteins LBH589 (Panobinostat) Sigma-Aldrich # SML3060-10MG Belinostat Sigma-Aldrich # SML3010-10MG SB505124 Sigma-Aldrich # S4696-5MG PCI-24781 Sigma-Aldrich # SML4043-5MG Valproic acid Sigma-Aldrich # P4543-10G DMSO Sigma-Aldrich # D2650-100ML Polybrene Sigma-Aldrich # TR-1003-50UL Lipofectamine 3000 Thermo Fisher Scientific # L3000015 Critical commercial assays AlamarBlue TM Cell Viability Reagents Thermo Fisher Scientific # DAL1100 Deposited data Raw Sanger Sequencing data This paper https://doi.org/10.17632/33tm3dd9dw.1 Raw immunofluorescent microscopy data This paper https://doi.org/10.17632/33tm3dd9dw.1 Uncropped gel images This paper https://doi.org/10.17632/33tm3dd9dw.1 Experimental models: Cell lines HeLa ATCC # CCL-2 HepG2 ATCC # HB-8065 .. MDA-MB-231 ATCC # HTB-26
Article Title: Protocol for enhancing CRISPR-Cas9 genome editing using histone deacetylase inhibition and engineered virus-like particle delivery.
Article Snippet: .. KEY RESOURCES TABLE REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Histone H3ac (pan-acetyl) Polyclonal antibody [1:1000] Thermo Fisher Scientific Cat# 39139; RRID: AB_2687871 Monoclonal ANTI-FLAG® M2 [1:5000] Sigma-Aldrich Cat# F3165-2MG; RRID: AB_259529 beta Actin Monoclonal antibody (AC-15) [1:10,000] Thermo Fisher Scientific Cat# AM4302; RRID: AB_437394 Anti-GAPDH antibody [6C5] - Loading Control [1:5000] Abcam Cat# ab8245; RRID: AB_2107448 GFP tag Polyclonal antibody [1:1000] Proteintech Cat# 50430-2-AP; RRID: AB_11042881 Caspase-3 antibody [1:1000] Cell signaling Cat# 9662; RRID:AB_331439 Cleaved Caspase-3 (Asp175) (5A1E) antibody [1:1000] Cell signaling Cat# 9664; RRID: AB_2070042 Bacterial and virus strains NEB® Stable Competent E. coli (High Efficiency) New England Biolabs #C3040I 16th generation engineered Virus-Like Particles (eVLPs) Raguram, A. et al 16 Not applicable Chemicals, peptides, and recombinant proteins LBH589 (Panobinostat) Sigma-Aldrich #SML3060-10MG Belinostat Sigma-Aldrich #SML3010-10MG DMSO Sigma-Aldrich #D2650-100ML Polybrene Sigma-Aldrich #TR-1003-50UL Lipofectamine 3000 Thermo Fisher Scientific #L3000015 Critical commercial assays AlamarBlueTM Cell Viability Reagents Thermo Fisher Scientific #DAL1100 Deposited data Raw Sanger Sequencing data Mendeley https://doi.org/10.17632/33tm3dd9dw.1 Raw immunofluorescent microscopy data Mendeley https://doi.org/10.17632/33tm3dd9dw.1 Uncropped gel images Mendeley https://doi.org/10.17632/33tm3dd9dw.1 Experimental models: Cell lines MDA-MB-231 ATCC #HTB-26 HEK-293 T ATCC #CRL-3216 Recombinant DNA psPAX2 Addgene #12260 pMD2.G Addgene #122259 MLV gag-pro-pol Addgene 16 #228466 MMLV gag-Cas9 Addgene 16 #228468 (Continued on next page) 4 STAR Protocols 7, 104493, June 19, 2026 ..
Microscopy:Article Title: FAME-CRISPR improves CRISPR-Cas9 genome editing via HDAC inhibition and engineered virus-like particle delivery.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Histone H3ac (pan-acetyl) Polyclonal antibody Thermo Fisher Scientific Cat# 39139; RRID: AB_2687871 Monoclonal ANTI-FLAG® M2 Sigma-Aldrich Cat# F3165-2MG; RRID: AB_259529 beta Actin Monoclonal antibody (AC-15) Thermo Fisher Scientific Cat# AM4302; RRID: AB_437394 Anti-GAPDH antibody [6C5] - Loading Control Abcam Cat# ab8245; RRID: AB_2107448 GFP tag Polyclonal antibody Proteintech Cat# 50430-2-AP; RRID: AB_11042881 Caspase-3 antibody Cell signaling Cat# 9662; RRID:AB_331439 Cleaved Caspase-3 (Asp175) (5A1E) antibody Cell signaling Cat# 9664; RRID: AB_2070042 ANTI-FLAG® M2 Magnetic Beads Sigma-Aldrich Cat# M8823-1ML; RRID: AB_2637089 γH2AX Abcam Cat# ab26350; RRID: AB_470861 Alexa Fluor 633 Invitrogen Cat# A-21050; RRID: AB_2535718 Bacterial and virus strains NEB® Stable Competent E. coli (High Efficiency) New England Biolabs # C3040I NEB® 5-alpha Competent E. coli (Subcloning Efficiency) New England Biolabs # C2988J Recombinant 3 rd generation Lentivirus – N/A 5 th generation engineered Virus-Like Particles (eVLPs) Raguram et al. 49 N/A Chemicals, peptides, and recombinant proteins LBH589 (Panobinostat) Sigma-Aldrich # SML3060-10MG Belinostat Sigma-Aldrich # SML3010-10MG SB505124 Sigma-Aldrich # S4696-5MG PCI-24781 Sigma-Aldrich # SML4043-5MG Valproic acid Sigma-Aldrich # P4543-10G DMSO Sigma-Aldrich # D2650-100ML Polybrene Sigma-Aldrich # TR-1003-50UL Lipofectamine 3000 Thermo Fisher Scientific # L3000015 Critical commercial assays AlamarBlue TM Cell Viability Reagents Thermo Fisher Scientific # DAL1100 Deposited data Raw Sanger Sequencing data This paper https://doi.org/10.17632/33tm3dd9dw.1 Raw immunofluorescent microscopy data This paper https://doi.org/10.17632/33tm3dd9dw.1 Uncropped gel images This paper https://doi.org/10.17632/33tm3dd9dw.1 Experimental models: Cell lines HeLa ATCC # CCL-2 HepG2 ATCC # HB-8065 .. MDA-MB-231 ATCC # HTB-26
Article Title: Protocol for enhancing CRISPR-Cas9 genome editing using histone deacetylase inhibition and engineered virus-like particle delivery.
Article Snippet: .. KEY RESOURCES TABLE REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Histone H3ac (pan-acetyl) Polyclonal antibody [1:1000] Thermo Fisher Scientific Cat# 39139; RRID: AB_2687871 Monoclonal ANTI-FLAG® M2 [1:5000] Sigma-Aldrich Cat# F3165-2MG; RRID: AB_259529 beta Actin Monoclonal antibody (AC-15) [1:10,000] Thermo Fisher Scientific Cat# AM4302; RRID: AB_437394 Anti-GAPDH antibody [6C5] - Loading Control [1:5000] Abcam Cat# ab8245; RRID: AB_2107448 GFP tag Polyclonal antibody [1:1000] Proteintech Cat# 50430-2-AP; RRID: AB_11042881 Caspase-3 antibody [1:1000] Cell signaling Cat# 9662; RRID:AB_331439 Cleaved Caspase-3 (Asp175) (5A1E) antibody [1:1000] Cell signaling Cat# 9664; RRID: AB_2070042 Bacterial and virus strains NEB® Stable Competent E. coli (High Efficiency) New England Biolabs #C3040I 16th generation engineered Virus-Like Particles (eVLPs) Raguram, A. et al 16 Not applicable Chemicals, peptides, and recombinant proteins LBH589 (Panobinostat) Sigma-Aldrich #SML3060-10MG Belinostat Sigma-Aldrich #SML3010-10MG DMSO Sigma-Aldrich #D2650-100ML Polybrene Sigma-Aldrich #TR-1003-50UL Lipofectamine 3000 Thermo Fisher Scientific #L3000015 Critical commercial assays AlamarBlueTM Cell Viability Reagents Thermo Fisher Scientific #DAL1100 Deposited data Raw Sanger Sequencing data Mendeley https://doi.org/10.17632/33tm3dd9dw.1 Raw immunofluorescent microscopy data Mendeley https://doi.org/10.17632/33tm3dd9dw.1 Uncropped gel images Mendeley https://doi.org/10.17632/33tm3dd9dw.1 Experimental models: Cell lines MDA-MB-231 ATCC #HTB-26 HEK-293 T ATCC #CRL-3216 Recombinant DNA psPAX2 Addgene #12260 pMD2.G Addgene #122259 MLV gag-pro-pol Addgene 16 #228466 MMLV gag-Cas9 Addgene 16 #228468 (Continued on next page) 4 STAR Protocols 7, 104493, June 19, 2026 ..
Produced:Article Title: The structure of human sweetness.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies DYKDDDDK Tag Polyclonal Antibody Thermo Fisher Scientific Cat# PA1-984B; RRID: AB_347227 HA-Tag (C29F4) Rabbit mAb Cell Signaling Technology Cat# 3724; RRID: AB_1549585 GAPDH (14C10) Rabbit mAb Cell Signaling Technology Cat# 2118; RRID: AB_561053 Anti-Rabbit IgG - Alkaline Phosphatase antibody produced in goat Sigma-Aldrich Cat# A3687; RRID: AB_258103 Bacterial and virus strains NEB® Stable Competent E. coli (High Efficiency) New England Biolabs C3040H MAX EfficiencyTM DH10Bac Competent Cells Thermo Fisher Scientific 10361012 BL21(DE3) Competent E. coli New England Biolabs C2527H Chemicals, peptides, and recombinant proteins Sucralose Sigma-Aldrich 69293 Aspartame Sigma-Aldrich 47135 (±)-2-(p-Methoxyphenoxy)propionic acid (Lactisole) Sigma-Aldrich M6546 Cholesteryl Hemisuccinate (CHS) Tris Salt Anatrace CH210 Lauryl Maltose Neopentyl Glycol (LMNG) Anatrace NG310 Glyco-diosgenin (GDN) Anatrace GDN101 PEG400 Sigma-Aldrich 91893 Ethylene glycol Sigma-Aldrich 324558 Expi293TM Expression Medium Thermo Fisher Scientific A1435102 Sf-900 II SFM Thermo Fisher Scientific 10902104 Fetal Bovine Serum (FBS) Thermo Fisher Scientific A5669502 DMEM, low glucose, pyruvate Thermo Fisher Scientific 11885076 ANTI-FLAG® M2 Affinity Gel Sigma-Aldrich A2220 FLAG peptide Peptide 2.0 N/A LipofectamineTM 3000 Transfection Reagent Invitrogen L3000015 CellfectinTM II Reagent Gibco 10362100 cOmpleteTM Protease Inhibitor Cocktail Sigma-Aldrich 4693116001 Isopropyl β-D-1-thiogalactopyranoside (IPTG) Sigma-Aldrich I5502-1G Bluo-Gal Sigma-Aldrich 15519028 Carbenicillin disodium salt Sigma-Aldrich C1389 Gentamicin Sigma-Aldrich G1397-10ML Kanamycin solution from Streptomyces kanamyceticus Sigma-Aldrich K0129-20ML Tetracycline Sigma-Aldrich 87128-25G HEPES, 1.0M buffer, pH 7.5 Thermo Scientific Chemicals J60712.AP Apyrase New England Biolabs M0398S Critical commercial assays FLIPR® Calcium 6 Assay Kits Molecular Devices R6133 Q5® Site-Directed Mutagenesis Kit New England Biolabs E0554S NEBuilder® HiFi DNA Assembly Master Mix New England Biolabs E2621S Superose 6 Increase 10/300 GL column Cytiva 29091596 ÄKTA goTM protein purification system Cytiva N/A Amicon® Ultra Centrifugal Filter, 100 kDa MWCO,15mL Sigma-Aldrich UFC910008 Amicon® Ultra Centrifugal Filter, 100 kDa MWCO, 0.5mL Sigma-Aldrich UFC510008 Centrifuge Filters - CentrexTM GVS Filter Technology 10467013 (Continued on next page) ll OPEN ACCESS e1 Cell 188, 1–13.e1–e6, July 24, 2025 Please cite this article in press as: Juen et al., The structure of human sweetness, Cell (2025), https://doi.org/10.1016/j.cell.2025.04.021 Article ..
Expressing:Article Title: The structure of human sweetness.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies DYKDDDDK Tag Polyclonal Antibody Thermo Fisher Scientific Cat# PA1-984B; RRID: AB_347227 HA-Tag (C29F4) Rabbit mAb Cell Signaling Technology Cat# 3724; RRID: AB_1549585 GAPDH (14C10) Rabbit mAb Cell Signaling Technology Cat# 2118; RRID: AB_561053 Anti-Rabbit IgG - Alkaline Phosphatase antibody produced in goat Sigma-Aldrich Cat# A3687; RRID: AB_258103 Bacterial and virus strains NEB® Stable Competent E. coli (High Efficiency) New England Biolabs C3040H MAX EfficiencyTM DH10Bac Competent Cells Thermo Fisher Scientific 10361012 BL21(DE3) Competent E. coli New England Biolabs C2527H Chemicals, peptides, and recombinant proteins Sucralose Sigma-Aldrich 69293 Aspartame Sigma-Aldrich 47135 (±)-2-(p-Methoxyphenoxy)propionic acid (Lactisole) Sigma-Aldrich M6546 Cholesteryl Hemisuccinate (CHS) Tris Salt Anatrace CH210 Lauryl Maltose Neopentyl Glycol (LMNG) Anatrace NG310 Glyco-diosgenin (GDN) Anatrace GDN101 PEG400 Sigma-Aldrich 91893 Ethylene glycol Sigma-Aldrich 324558 Expi293TM Expression Medium Thermo Fisher Scientific A1435102 Sf-900 II SFM Thermo Fisher Scientific 10902104 Fetal Bovine Serum (FBS) Thermo Fisher Scientific A5669502 DMEM, low glucose, pyruvate Thermo Fisher Scientific 11885076 ANTI-FLAG® M2 Affinity Gel Sigma-Aldrich A2220 FLAG peptide Peptide 2.0 N/A LipofectamineTM 3000 Transfection Reagent Invitrogen L3000015 CellfectinTM II Reagent Gibco 10362100 cOmpleteTM Protease Inhibitor Cocktail Sigma-Aldrich 4693116001 Isopropyl β-D-1-thiogalactopyranoside (IPTG) Sigma-Aldrich I5502-1G Bluo-Gal Sigma-Aldrich 15519028 Carbenicillin disodium salt Sigma-Aldrich C1389 Gentamicin Sigma-Aldrich G1397-10ML Kanamycin solution from Streptomyces kanamyceticus Sigma-Aldrich K0129-20ML Tetracycline Sigma-Aldrich 87128-25G HEPES, 1.0M buffer, pH 7.5 Thermo Scientific Chemicals J60712.AP Apyrase New England Biolabs M0398S Critical commercial assays FLIPR® Calcium 6 Assay Kits Molecular Devices R6133 Q5® Site-Directed Mutagenesis Kit New England Biolabs E0554S NEBuilder® HiFi DNA Assembly Master Mix New England Biolabs E2621S Superose 6 Increase 10/300 GL column Cytiva 29091596 ÄKTA goTM protein purification system Cytiva N/A Amicon® Ultra Centrifugal Filter, 100 kDa MWCO,15mL Sigma-Aldrich UFC910008 Amicon® Ultra Centrifugal Filter, 100 kDa MWCO, 0.5mL Sigma-Aldrich UFC510008 Centrifuge Filters - CentrexTM GVS Filter Technology 10467013 (Continued on next page) ll OPEN ACCESS e1 Cell 188, 1–13.e1–e6, July 24, 2025 Please cite this article in press as: Juen et al., The structure of human sweetness, Cell (2025), https://doi.org/10.1016/j.cell.2025.04.021 Article ..
Transfection:Article Title: The structure of human sweetness.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies DYKDDDDK Tag Polyclonal Antibody Thermo Fisher Scientific Cat# PA1-984B; RRID: AB_347227 HA-Tag (C29F4) Rabbit mAb Cell Signaling Technology Cat# 3724; RRID: AB_1549585 GAPDH (14C10) Rabbit mAb Cell Signaling Technology Cat# 2118; RRID: AB_561053 Anti-Rabbit IgG - Alkaline Phosphatase antibody produced in goat Sigma-Aldrich Cat# A3687; RRID: AB_258103 Bacterial and virus strains NEB® Stable Competent E. coli (High Efficiency) New England Biolabs C3040H MAX EfficiencyTM DH10Bac Competent Cells Thermo Fisher Scientific 10361012 BL21(DE3) Competent E. coli New England Biolabs C2527H Chemicals, peptides, and recombinant proteins Sucralose Sigma-Aldrich 69293 Aspartame Sigma-Aldrich 47135 (±)-2-(p-Methoxyphenoxy)propionic acid (Lactisole) Sigma-Aldrich M6546 Cholesteryl Hemisuccinate (CHS) Tris Salt Anatrace CH210 Lauryl Maltose Neopentyl Glycol (LMNG) Anatrace NG310 Glyco-diosgenin (GDN) Anatrace GDN101 PEG400 Sigma-Aldrich 91893 Ethylene glycol Sigma-Aldrich 324558 Expi293TM Expression Medium Thermo Fisher Scientific A1435102 Sf-900 II SFM Thermo Fisher Scientific 10902104 Fetal Bovine Serum (FBS) Thermo Fisher Scientific A5669502 DMEM, low glucose, pyruvate Thermo Fisher Scientific 11885076 ANTI-FLAG® M2 Affinity Gel Sigma-Aldrich A2220 FLAG peptide Peptide 2.0 N/A LipofectamineTM 3000 Transfection Reagent Invitrogen L3000015 CellfectinTM II Reagent Gibco 10362100 cOmpleteTM Protease Inhibitor Cocktail Sigma-Aldrich 4693116001 Isopropyl β-D-1-thiogalactopyranoside (IPTG) Sigma-Aldrich I5502-1G Bluo-Gal Sigma-Aldrich 15519028 Carbenicillin disodium salt Sigma-Aldrich C1389 Gentamicin Sigma-Aldrich G1397-10ML Kanamycin solution from Streptomyces kanamyceticus Sigma-Aldrich K0129-20ML Tetracycline Sigma-Aldrich 87128-25G HEPES, 1.0M buffer, pH 7.5 Thermo Scientific Chemicals J60712.AP Apyrase New England Biolabs M0398S Critical commercial assays FLIPR® Calcium 6 Assay Kits Molecular Devices R6133 Q5® Site-Directed Mutagenesis Kit New England Biolabs E0554S NEBuilder® HiFi DNA Assembly Master Mix New England Biolabs E2621S Superose 6 Increase 10/300 GL column Cytiva 29091596 ÄKTA goTM protein purification system Cytiva N/A Amicon® Ultra Centrifugal Filter, 100 kDa MWCO,15mL Sigma-Aldrich UFC910008 Amicon® Ultra Centrifugal Filter, 100 kDa MWCO, 0.5mL Sigma-Aldrich UFC510008 Centrifuge Filters - CentrexTM GVS Filter Technology 10467013 (Continued on next page) ll OPEN ACCESS e1 Cell 188, 1–13.e1–e6, July 24, 2025 Please cite this article in press as: Juen et al., The structure of human sweetness, Cell (2025), https://doi.org/10.1016/j.cell.2025.04.021 Article ..
Article Title: Approaches for identification of 5' UTR mutations impacting translation and protein production from neurodevelopmental disorder genes.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies rabbit anti-RFP primary antibody Rockland 600-401-379; RRID: AB_2209751 chicken anti-eGFP primary antibody Aves Labs GFP-1020; RRID: AB_10000240 donkey anti-rabbit Alexa Fluor 568 secondary antibody Invitrogen A10042; RRID: AB_2534017 donkey anti-chicken Alexa Fluor 488 Jackson Immuno 703-545-155; RRID: AB_2340375 Mouse anti-EGFP(1) MSKCC Clone 19F7; RRID: AB_2716736 Mouse anti-EGFP(2) MSKCC Clone 19C8; RRID: AB_2716737 rabbit anti-MKRN1 primary antibody Abcam 72054; RRID: AB_1269434 mouse anti-SMC5 primary antibody Santa Cruz sc-393282 mouse anti-NSD2, clone29D1 Milipore Sigma MABE191 mouse anti-GAPDH Sigma-Aldrich G8795; RRID: AB_1078991 Bacterial and virus strains NEB® Stable Competent E. coli (High Efficiency) New England Biolabs C3040 Chemicals, peptides, and recombinant proteins AgeI-HF New England Biolabs R3552 KpnI-HF New England Biolabs R3142 BamHI-HF New England Biolabs R3136 SalI-HF New England Biolabs R3138 Proteinase K, Molecular Biology Grade New England Biolabs P8107 NEBNext® High-Fidelity 2× PCR Master Mix New England Biolabs M0541 Quick-Load® Taq 2× Master Mix New England Biolabs M0271 NEBNext® Ultra TM II Q5® Master Mix New England Biolabs M0544 Mag-Bind® TotalPure NGS Omega Bio-tek M1378 Plasmid Maxi Kit Qiagen 12162 DMEM/F-12 Gibco 11320033 DMEM Gibco 11965092 Penicillin-Streptomycin Gibco 15140163 Trypsin-EDTA (0.25%), phenol red Gibco 25200056 Fetal Bovine Serum R&D Systems S11150 Lipofectamine TM 2000 Transfection Reagent Invitrogen 11668027 RNasin® Ribonuclease Inhibitor Promega N2511 SUPERase⋅In TM RNase Inhibitor Invitrogen AM2696 cOmplete TM , EDTA-free Protease Inhibitor Cocktail Roche 04693132001 TRIzol TM LS Reagent Invitrogen 10296010 1M HEPES Corning 25-060-CI 2M KCl Invitrogen AM9640G 1M MgCl 2 Invitrogen AM9530G DTT Thermo Fisher Scientific N/A NP-40 Sigma 74385 Cycloheximide Sigma C1988-1G RNA Clean & Concentrator-5 Zymo R1014 (Continued on next page) Cell Reports Methods 5, 101247, December 15, 2025 e1 OPEN ACCESS .. REAGENT or RESOURCE SOURCE IDENTIFIER DNeasy Blood & Tissue Kit Qiagen 69504 Dynabeads TM MyOne TM Streptavidin T1 Invitrogen 65601 Pierce TM Recombinant Protein L, Biotinylated Thermo Scientific 29997 DHPC Avanti Polar Lipids 850306P OCT compound Thermo Fisher Scientific 23-730-571 SuperScript TM IV Reverse Transcriptase Invitrogen 18090050 PowerUp TM SYBR TM Green Master Mix for qPCR Applied Biosystems A25742 0.01% poly-L-lysine Sigma P4707 10× RIPA Buffer Cell Signaling 9806 2× Laemmli Sample Buffer Bio-Rad 1610737 Mini-Protean TGX gels Bio-Rad N/A Immun-Blot PVDF Membrane Bio-Rad 1620177 Clarity TM Western ECL Substrate Bio-Rad 1705060 Critical commercial assays Nano-Glo® Dual-Luciferase® Reporter Assay System Promega N1610 High Sensitivity D1000 ScreenTape Agilent 5067–5584 Pierce TM BCA Protein Assay Kit Thermo Scientific 23227 Deposited data Raw fastq files and processed count files GEO GSE246381 Experimental models: Cell lines Human: HEK This paper N/A Experimental models: Organisms/strains Mouse: ROSA26:LSL-eGFP-RPl10 Jackson Stock no. 022367 Mouse: Vglut1-IRES2-Cre-D Jackson Stock no. 023527 Oligonucleotides See Table S6 Integrated DNA Technologies N/A Recombinant DNA JD486 This paper N/A Software and algorithms umi_tools (v1.0.0) Smith et al. 59 https://github.com/CGATOxford/UMI-tools cutadapt (v2.1) Martin 60 https://github.com/marcelm/cutadapt bowtie2 (v2.3.5) Langmead and Salzberg 61 https://bowtie-bio.sourceforge.net/ bowtie2/index.shtml samtools (v1.9) Li et al. 62 https://www.htslib.org/doc/1.9/samtools. html subread (v2.0.0) Liao et al. 63 https://subread.sourceforge.net/ lme4 Bates et al. 64 https://cran.r-project.org/web/packages/ lme4/index.html qvalue Storey et al. 65 https://bioconductor.org/packages/ release/bioc/html/qvalue.html ViennaRNA (v2.4.17) Lorenz et al. 66 https://www.tbi.univie.ac.at/RNA/ RNAfold Gruber et al. 44 http://rna.tbi.univie.ac.at/ QGRS Mapper Kikin et al. 43 https://bioinformatics.ramapo.edu/QGRS/ index.php R R Core Team https://www.r-project.org/ Custom code This Paper https://bitbucket.org/jdlabteam/fiveprime_ mpra_pub/src/main/ https://doi.org/10.5281/zenodo.17459278 e2 Cell Reports Methods 5, 101247, December 15, 2025 OPEN ACCESS
Protease Inhibitor:Article Title: The structure of human sweetness.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies DYKDDDDK Tag Polyclonal Antibody Thermo Fisher Scientific Cat# PA1-984B; RRID: AB_347227 HA-Tag (C29F4) Rabbit mAb Cell Signaling Technology Cat# 3724; RRID: AB_1549585 GAPDH (14C10) Rabbit mAb Cell Signaling Technology Cat# 2118; RRID: AB_561053 Anti-Rabbit IgG - Alkaline Phosphatase antibody produced in goat Sigma-Aldrich Cat# A3687; RRID: AB_258103 Bacterial and virus strains NEB® Stable Competent E. coli (High Efficiency) New England Biolabs C3040H MAX EfficiencyTM DH10Bac Competent Cells Thermo Fisher Scientific 10361012 BL21(DE3) Competent E. coli New England Biolabs C2527H Chemicals, peptides, and recombinant proteins Sucralose Sigma-Aldrich 69293 Aspartame Sigma-Aldrich 47135 (±)-2-(p-Methoxyphenoxy)propionic acid (Lactisole) Sigma-Aldrich M6546 Cholesteryl Hemisuccinate (CHS) Tris Salt Anatrace CH210 Lauryl Maltose Neopentyl Glycol (LMNG) Anatrace NG310 Glyco-diosgenin (GDN) Anatrace GDN101 PEG400 Sigma-Aldrich 91893 Ethylene glycol Sigma-Aldrich 324558 Expi293TM Expression Medium Thermo Fisher Scientific A1435102 Sf-900 II SFM Thermo Fisher Scientific 10902104 Fetal Bovine Serum (FBS) Thermo Fisher Scientific A5669502 DMEM, low glucose, pyruvate Thermo Fisher Scientific 11885076 ANTI-FLAG® M2 Affinity Gel Sigma-Aldrich A2220 FLAG peptide Peptide 2.0 N/A LipofectamineTM 3000 Transfection Reagent Invitrogen L3000015 CellfectinTM II Reagent Gibco 10362100 cOmpleteTM Protease Inhibitor Cocktail Sigma-Aldrich 4693116001 Isopropyl β-D-1-thiogalactopyranoside (IPTG) Sigma-Aldrich I5502-1G Bluo-Gal Sigma-Aldrich 15519028 Carbenicillin disodium salt Sigma-Aldrich C1389 Gentamicin Sigma-Aldrich G1397-10ML Kanamycin solution from Streptomyces kanamyceticus Sigma-Aldrich K0129-20ML Tetracycline Sigma-Aldrich 87128-25G HEPES, 1.0M buffer, pH 7.5 Thermo Scientific Chemicals J60712.AP Apyrase New England Biolabs M0398S Critical commercial assays FLIPR® Calcium 6 Assay Kits Molecular Devices R6133 Q5® Site-Directed Mutagenesis Kit New England Biolabs E0554S NEBuilder® HiFi DNA Assembly Master Mix New England Biolabs E2621S Superose 6 Increase 10/300 GL column Cytiva 29091596 ÄKTA goTM protein purification system Cytiva N/A Amicon® Ultra Centrifugal Filter, 100 kDa MWCO,15mL Sigma-Aldrich UFC910008 Amicon® Ultra Centrifugal Filter, 100 kDa MWCO, 0.5mL Sigma-Aldrich UFC510008 Centrifuge Filters - CentrexTM GVS Filter Technology 10467013 (Continued on next page) ll OPEN ACCESS e1 Cell 188, 1–13.e1–e6, July 24, 2025 Please cite this article in press as: Juen et al., The structure of human sweetness, Cell (2025), https://doi.org/10.1016/j.cell.2025.04.021 Article ..
Article Title: Approaches for identification of 5' UTR mutations impacting translation and protein production from neurodevelopmental disorder genes.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies rabbit anti-RFP primary antibody Rockland 600-401-379; RRID: AB_2209751 chicken anti-eGFP primary antibody Aves Labs GFP-1020; RRID: AB_10000240 donkey anti-rabbit Alexa Fluor 568 secondary antibody Invitrogen A10042; RRID: AB_2534017 donkey anti-chicken Alexa Fluor 488 Jackson Immuno 703-545-155; RRID: AB_2340375 Mouse anti-EGFP(1) MSKCC Clone 19F7; RRID: AB_2716736 Mouse anti-EGFP(2) MSKCC Clone 19C8; RRID: AB_2716737 rabbit anti-MKRN1 primary antibody Abcam 72054; RRID: AB_1269434 mouse anti-SMC5 primary antibody Santa Cruz sc-393282 mouse anti-NSD2, clone29D1 Milipore Sigma MABE191 mouse anti-GAPDH Sigma-Aldrich G8795; RRID: AB_1078991 Bacterial and virus strains NEB® Stable Competent E. coli (High Efficiency) New England Biolabs C3040 Chemicals, peptides, and recombinant proteins AgeI-HF New England Biolabs R3552 KpnI-HF New England Biolabs R3142 BamHI-HF New England Biolabs R3136 SalI-HF New England Biolabs R3138 Proteinase K, Molecular Biology Grade New England Biolabs P8107 NEBNext® High-Fidelity 2× PCR Master Mix New England Biolabs M0541 Quick-Load® Taq 2× Master Mix New England Biolabs M0271 NEBNext® Ultra TM II Q5® Master Mix New England Biolabs M0544 Mag-Bind® TotalPure NGS Omega Bio-tek M1378 Plasmid Maxi Kit Qiagen 12162 DMEM/F-12 Gibco 11320033 DMEM Gibco 11965092 Penicillin-Streptomycin Gibco 15140163 Trypsin-EDTA (0.25%), phenol red Gibco 25200056 Fetal Bovine Serum R&D Systems S11150 Lipofectamine TM 2000 Transfection Reagent Invitrogen 11668027 RNasin® Ribonuclease Inhibitor Promega N2511 SUPERase⋅In TM RNase Inhibitor Invitrogen AM2696 cOmplete TM , EDTA-free Protease Inhibitor Cocktail Roche 04693132001 TRIzol TM LS Reagent Invitrogen 10296010 1M HEPES Corning 25-060-CI 2M KCl Invitrogen AM9640G 1M MgCl 2 Invitrogen AM9530G DTT Thermo Fisher Scientific N/A NP-40 Sigma 74385 Cycloheximide Sigma C1988-1G RNA Clean & Concentrator-5 Zymo R1014 (Continued on next page) Cell Reports Methods 5, 101247, December 15, 2025 e1 OPEN ACCESS .. REAGENT or RESOURCE SOURCE IDENTIFIER DNeasy Blood & Tissue Kit Qiagen 69504 Dynabeads TM MyOne TM Streptavidin T1 Invitrogen 65601 Pierce TM Recombinant Protein L, Biotinylated Thermo Scientific 29997 DHPC Avanti Polar Lipids 850306P OCT compound Thermo Fisher Scientific 23-730-571 SuperScript TM IV Reverse Transcriptase Invitrogen 18090050 PowerUp TM SYBR TM Green Master Mix for qPCR Applied Biosystems A25742 0.01% poly-L-lysine Sigma P4707 10× RIPA Buffer Cell Signaling 9806 2× Laemmli Sample Buffer Bio-Rad 1610737 Mini-Protean TGX gels Bio-Rad N/A Immun-Blot PVDF Membrane Bio-Rad 1620177 Clarity TM Western ECL Substrate Bio-Rad 1705060 Critical commercial assays Nano-Glo® Dual-Luciferase® Reporter Assay System Promega N1610 High Sensitivity D1000 ScreenTape Agilent 5067–5584 Pierce TM BCA Protein Assay Kit Thermo Scientific 23227 Deposited data Raw fastq files and processed count files GEO GSE246381 Experimental models: Cell lines Human: HEK This paper N/A Experimental models: Organisms/strains Mouse: ROSA26:LSL-eGFP-RPl10 Jackson Stock no. 022367 Mouse: Vglut1-IRES2-Cre-D Jackson Stock no. 023527 Oligonucleotides See Table S6 Integrated DNA Technologies N/A Recombinant DNA JD486 This paper N/A Software and algorithms umi_tools (v1.0.0) Smith et al. 59 https://github.com/CGATOxford/UMI-tools cutadapt (v2.1) Martin 60 https://github.com/marcelm/cutadapt bowtie2 (v2.3.5) Langmead and Salzberg 61 https://bowtie-bio.sourceforge.net/ bowtie2/index.shtml samtools (v1.9) Li et al. 62 https://www.htslib.org/doc/1.9/samtools. html subread (v2.0.0) Liao et al. 63 https://subread.sourceforge.net/ lme4 Bates et al. 64 https://cran.r-project.org/web/packages/ lme4/index.html qvalue Storey et al. 65 https://bioconductor.org/packages/ release/bioc/html/qvalue.html ViennaRNA (v2.4.17) Lorenz et al. 66 https://www.tbi.univie.ac.at/RNA/ RNAfold Gruber et al. 44 http://rna.tbi.univie.ac.at/ QGRS Mapper Kikin et al. 43 https://bioinformatics.ramapo.edu/QGRS/ index.php R R Core Team https://www.r-project.org/ Custom code This Paper https://bitbucket.org/jdlabteam/fiveprime_ mpra_pub/src/main/ https://doi.org/10.5281/zenodo.17459278 e2 Cell Reports Methods 5, 101247, December 15, 2025 OPEN ACCESS
Mutagenesis:Article Title: The structure of human sweetness.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies DYKDDDDK Tag Polyclonal Antibody Thermo Fisher Scientific Cat# PA1-984B; RRID: AB_347227 HA-Tag (C29F4) Rabbit mAb Cell Signaling Technology Cat# 3724; RRID: AB_1549585 GAPDH (14C10) Rabbit mAb Cell Signaling Technology Cat# 2118; RRID: AB_561053 Anti-Rabbit IgG - Alkaline Phosphatase antibody produced in goat Sigma-Aldrich Cat# A3687; RRID: AB_258103 Bacterial and virus strains NEB® Stable Competent E. coli (High Efficiency) New England Biolabs C3040H MAX EfficiencyTM DH10Bac Competent Cells Thermo Fisher Scientific 10361012 BL21(DE3) Competent E. coli New England Biolabs C2527H Chemicals, peptides, and recombinant proteins Sucralose Sigma-Aldrich 69293 Aspartame Sigma-Aldrich 47135 (±)-2-(p-Methoxyphenoxy)propionic acid (Lactisole) Sigma-Aldrich M6546 Cholesteryl Hemisuccinate (CHS) Tris Salt Anatrace CH210 Lauryl Maltose Neopentyl Glycol (LMNG) Anatrace NG310 Glyco-diosgenin (GDN) Anatrace GDN101 PEG400 Sigma-Aldrich 91893 Ethylene glycol Sigma-Aldrich 324558 Expi293TM Expression Medium Thermo Fisher Scientific A1435102 Sf-900 II SFM Thermo Fisher Scientific 10902104 Fetal Bovine Serum (FBS) Thermo Fisher Scientific A5669502 DMEM, low glucose, pyruvate Thermo Fisher Scientific 11885076 ANTI-FLAG® M2 Affinity Gel Sigma-Aldrich A2220 FLAG peptide Peptide 2.0 N/A LipofectamineTM 3000 Transfection Reagent Invitrogen L3000015 CellfectinTM II Reagent Gibco 10362100 cOmpleteTM Protease Inhibitor Cocktail Sigma-Aldrich 4693116001 Isopropyl β-D-1-thiogalactopyranoside (IPTG) Sigma-Aldrich I5502-1G Bluo-Gal Sigma-Aldrich 15519028 Carbenicillin disodium salt Sigma-Aldrich C1389 Gentamicin Sigma-Aldrich G1397-10ML Kanamycin solution from Streptomyces kanamyceticus Sigma-Aldrich K0129-20ML Tetracycline Sigma-Aldrich 87128-25G HEPES, 1.0M buffer, pH 7.5 Thermo Scientific Chemicals J60712.AP Apyrase New England Biolabs M0398S Critical commercial assays FLIPR® Calcium 6 Assay Kits Molecular Devices R6133 Q5® Site-Directed Mutagenesis Kit New England Biolabs E0554S NEBuilder® HiFi DNA Assembly Master Mix New England Biolabs E2621S Superose 6 Increase 10/300 GL column Cytiva 29091596 ÄKTA goTM protein purification system Cytiva N/A Amicon® Ultra Centrifugal Filter, 100 kDa MWCO,15mL Sigma-Aldrich UFC910008 Amicon® Ultra Centrifugal Filter, 100 kDa MWCO, 0.5mL Sigma-Aldrich UFC510008 Centrifuge Filters - CentrexTM GVS Filter Technology 10467013 (Continued on next page) ll OPEN ACCESS e1 Cell 188, 1–13.e1–e6, July 24, 2025 Please cite this article in press as: Juen et al., The structure of human sweetness, Cell (2025), https://doi.org/10.1016/j.cell.2025.04.021 Article ..
Protein Purification:Article Title: The structure of human sweetness.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies DYKDDDDK Tag Polyclonal Antibody Thermo Fisher Scientific Cat# PA1-984B; RRID: AB_347227 HA-Tag (C29F4) Rabbit mAb Cell Signaling Technology Cat# 3724; RRID: AB_1549585 GAPDH (14C10) Rabbit mAb Cell Signaling Technology Cat# 2118; RRID: AB_561053 Anti-Rabbit IgG - Alkaline Phosphatase antibody produced in goat Sigma-Aldrich Cat# A3687; RRID: AB_258103 Bacterial and virus strains NEB® Stable Competent E. coli (High Efficiency) New England Biolabs C3040H MAX EfficiencyTM DH10Bac Competent Cells Thermo Fisher Scientific 10361012 BL21(DE3) Competent E. coli New England Biolabs C2527H Chemicals, peptides, and recombinant proteins Sucralose Sigma-Aldrich 69293 Aspartame Sigma-Aldrich 47135 (±)-2-(p-Methoxyphenoxy)propionic acid (Lactisole) Sigma-Aldrich M6546 Cholesteryl Hemisuccinate (CHS) Tris Salt Anatrace CH210 Lauryl Maltose Neopentyl Glycol (LMNG) Anatrace NG310 Glyco-diosgenin (GDN) Anatrace GDN101 PEG400 Sigma-Aldrich 91893 Ethylene glycol Sigma-Aldrich 324558 Expi293TM Expression Medium Thermo Fisher Scientific A1435102 Sf-900 II SFM Thermo Fisher Scientific 10902104 Fetal Bovine Serum (FBS) Thermo Fisher Scientific A5669502 DMEM, low glucose, pyruvate Thermo Fisher Scientific 11885076 ANTI-FLAG® M2 Affinity Gel Sigma-Aldrich A2220 FLAG peptide Peptide 2.0 N/A LipofectamineTM 3000 Transfection Reagent Invitrogen L3000015 CellfectinTM II Reagent Gibco 10362100 cOmpleteTM Protease Inhibitor Cocktail Sigma-Aldrich 4693116001 Isopropyl β-D-1-thiogalactopyranoside (IPTG) Sigma-Aldrich I5502-1G Bluo-Gal Sigma-Aldrich 15519028 Carbenicillin disodium salt Sigma-Aldrich C1389 Gentamicin Sigma-Aldrich G1397-10ML Kanamycin solution from Streptomyces kanamyceticus Sigma-Aldrich K0129-20ML Tetracycline Sigma-Aldrich 87128-25G HEPES, 1.0M buffer, pH 7.5 Thermo Scientific Chemicals J60712.AP Apyrase New England Biolabs M0398S Critical commercial assays FLIPR® Calcium 6 Assay Kits Molecular Devices R6133 Q5® Site-Directed Mutagenesis Kit New England Biolabs E0554S NEBuilder® HiFi DNA Assembly Master Mix New England Biolabs E2621S Superose 6 Increase 10/300 GL column Cytiva 29091596 ÄKTA goTM protein purification system Cytiva N/A Amicon® Ultra Centrifugal Filter, 100 kDa MWCO,15mL Sigma-Aldrich UFC910008 Amicon® Ultra Centrifugal Filter, 100 kDa MWCO, 0.5mL Sigma-Aldrich UFC510008 Centrifuge Filters - CentrexTM GVS Filter Technology 10467013 (Continued on next page) ll OPEN ACCESS e1 Cell 188, 1–13.e1–e6, July 24, 2025 Please cite this article in press as: Juen et al., The structure of human sweetness, Cell (2025), https://doi.org/10.1016/j.cell.2025.04.021 Article ..
Multiple Displacement Amplification:Article Title: Protocol for enhancing CRISPR-Cas9 genome editing using histone deacetylase inhibition and engineered virus-like particle delivery.
Article Snippet: .. KEY RESOURCES TABLE REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Histone H3ac (pan-acetyl) Polyclonal antibody [1:1000] Thermo Fisher Scientific Cat# 39139; RRID: AB_2687871 Monoclonal ANTI-FLAG® M2 [1:5000] Sigma-Aldrich Cat# F3165-2MG; RRID: AB_259529 beta Actin Monoclonal antibody (AC-15) [1:10,000] Thermo Fisher Scientific Cat# AM4302; RRID: AB_437394 Anti-GAPDH antibody [6C5] - Loading Control [1:5000] Abcam Cat# ab8245; RRID: AB_2107448 GFP tag Polyclonal antibody [1:1000] Proteintech Cat# 50430-2-AP; RRID: AB_11042881 Caspase-3 antibody [1:1000] Cell signaling Cat# 9662; RRID:AB_331439 Cleaved Caspase-3 (Asp175) (5A1E) antibody [1:1000] Cell signaling Cat# 9664; RRID: AB_2070042 Bacterial and virus strains NEB® Stable Competent E. coli (High Efficiency) New England Biolabs #C3040I 16th generation engineered Virus-Like Particles (eVLPs) Raguram, A. et al 16 Not applicable Chemicals, peptides, and recombinant proteins LBH589 (Panobinostat) Sigma-Aldrich #SML3060-10MG Belinostat Sigma-Aldrich #SML3010-10MG DMSO Sigma-Aldrich #D2650-100ML Polybrene Sigma-Aldrich #TR-1003-50UL Lipofectamine 3000 Thermo Fisher Scientific #L3000015 Critical commercial assays AlamarBlueTM Cell Viability Reagents Thermo Fisher Scientific #DAL1100 Deposited data Raw Sanger Sequencing data Mendeley https://doi.org/10.17632/33tm3dd9dw.1 Raw immunofluorescent microscopy data Mendeley https://doi.org/10.17632/33tm3dd9dw.1 Uncropped gel images Mendeley https://doi.org/10.17632/33tm3dd9dw.1 Experimental models: Cell lines MDA-MB-231 ATCC #HTB-26 HEK-293 T ATCC #CRL-3216 Recombinant DNA psPAX2 Addgene #12260 pMD2.G Addgene #122259 MLV gag-pro-pol Addgene 16 #228466 MMLV gag-Cas9 Addgene 16 #228468 (Continued on next page) 4 STAR Protocols 7, 104493, June 19, 2026 ..
Polymerase Chain Reaction:Article Title: Approaches for identification of 5' UTR mutations impacting translation and protein production from neurodevelopmental disorder genes.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies rabbit anti-RFP primary antibody Rockland 600-401-379; RRID: AB_2209751 chicken anti-eGFP primary antibody Aves Labs GFP-1020; RRID: AB_10000240 donkey anti-rabbit Alexa Fluor 568 secondary antibody Invitrogen A10042; RRID: AB_2534017 donkey anti-chicken Alexa Fluor 488 Jackson Immuno 703-545-155; RRID: AB_2340375 Mouse anti-EGFP(1) MSKCC Clone 19F7; RRID: AB_2716736 Mouse anti-EGFP(2) MSKCC Clone 19C8; RRID: AB_2716737 rabbit anti-MKRN1 primary antibody Abcam 72054; RRID: AB_1269434 mouse anti-SMC5 primary antibody Santa Cruz sc-393282 mouse anti-NSD2, clone29D1 Milipore Sigma MABE191 mouse anti-GAPDH Sigma-Aldrich G8795; RRID: AB_1078991 Bacterial and virus strains NEB® Stable Competent E. coli (High Efficiency) New England Biolabs C3040 Chemicals, peptides, and recombinant proteins AgeI-HF New England Biolabs R3552 KpnI-HF New England Biolabs R3142 BamHI-HF New England Biolabs R3136 SalI-HF New England Biolabs R3138 Proteinase K, Molecular Biology Grade New England Biolabs P8107 NEBNext® High-Fidelity 2× PCR Master Mix New England Biolabs M0541 Quick-Load® Taq 2× Master Mix New England Biolabs M0271 NEBNext® Ultra TM II Q5® Master Mix New England Biolabs M0544 Mag-Bind® TotalPure NGS Omega Bio-tek M1378 Plasmid Maxi Kit Qiagen 12162 DMEM/F-12 Gibco 11320033 DMEM Gibco 11965092 Penicillin-Streptomycin Gibco 15140163 Trypsin-EDTA (0.25%), phenol red Gibco 25200056 Fetal Bovine Serum R&D Systems S11150 Lipofectamine TM 2000 Transfection Reagent Invitrogen 11668027 RNasin® Ribonuclease Inhibitor Promega N2511 SUPERase⋅In TM RNase Inhibitor Invitrogen AM2696 cOmplete TM , EDTA-free Protease Inhibitor Cocktail Roche 04693132001 TRIzol TM LS Reagent Invitrogen 10296010 1M HEPES Corning 25-060-CI 2M KCl Invitrogen AM9640G 1M MgCl 2 Invitrogen AM9530G DTT Thermo Fisher Scientific N/A NP-40 Sigma 74385 Cycloheximide Sigma C1988-1G RNA Clean & Concentrator-5 Zymo R1014 (Continued on next page) Cell Reports Methods 5, 101247, December 15, 2025 e1 OPEN ACCESS .. REAGENT or RESOURCE SOURCE IDENTIFIER DNeasy Blood & Tissue Kit Qiagen 69504 Dynabeads TM MyOne TM Streptavidin T1 Invitrogen 65601 Pierce TM Recombinant Protein L, Biotinylated Thermo Scientific 29997 DHPC Avanti Polar Lipids 850306P OCT compound Thermo Fisher Scientific 23-730-571 SuperScript TM IV Reverse Transcriptase Invitrogen 18090050 PowerUp TM SYBR TM Green Master Mix for qPCR Applied Biosystems A25742 0.01% poly-L-lysine Sigma P4707 10× RIPA Buffer Cell Signaling 9806 2× Laemmli Sample Buffer Bio-Rad 1610737 Mini-Protean TGX gels Bio-Rad N/A Immun-Blot PVDF Membrane Bio-Rad 1620177 Clarity TM Western ECL Substrate Bio-Rad 1705060 Critical commercial assays Nano-Glo® Dual-Luciferase® Reporter Assay System Promega N1610 High Sensitivity D1000 ScreenTape Agilent 5067–5584 Pierce TM BCA Protein Assay Kit Thermo Scientific 23227 Deposited data Raw fastq files and processed count files GEO GSE246381 Experimental models: Cell lines Human: HEK This paper N/A Experimental models: Organisms/strains Mouse: ROSA26:LSL-eGFP-RPl10 Jackson Stock no. 022367 Mouse: Vglut1-IRES2-Cre-D Jackson Stock no. 023527 Oligonucleotides See Table S6 Integrated DNA Technologies N/A Recombinant DNA JD486 This paper N/A Software and algorithms umi_tools (v1.0.0) Smith et al. 59 https://github.com/CGATOxford/UMI-tools cutadapt (v2.1) Martin 60 https://github.com/marcelm/cutadapt bowtie2 (v2.3.5) Langmead and Salzberg 61 https://bowtie-bio.sourceforge.net/ bowtie2/index.shtml samtools (v1.9) Li et al. 62 https://www.htslib.org/doc/1.9/samtools. html subread (v2.0.0) Liao et al. 63 https://subread.sourceforge.net/ lme4 Bates et al. 64 https://cran.r-project.org/web/packages/ lme4/index.html qvalue Storey et al. 65 https://bioconductor.org/packages/ release/bioc/html/qvalue.html ViennaRNA (v2.4.17) Lorenz et al. 66 https://www.tbi.univie.ac.at/RNA/ RNAfold Gruber et al. 44 http://rna.tbi.univie.ac.at/ QGRS Mapper Kikin et al. 43 https://bioinformatics.ramapo.edu/QGRS/ index.php R R Core Team https://www.r-project.org/ Custom code This Paper https://bitbucket.org/jdlabteam/fiveprime_ mpra_pub/src/main/ https://doi.org/10.5281/zenodo.17459278 e2 Cell Reports Methods 5, 101247, December 15, 2025 OPEN ACCESS
Next-Generation Sequencing:Article Title: Approaches for identification of 5' UTR mutations impacting translation and protein production from neurodevelopmental disorder genes.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies rabbit anti-RFP primary antibody Rockland 600-401-379; RRID: AB_2209751 chicken anti-eGFP primary antibody Aves Labs GFP-1020; RRID: AB_10000240 donkey anti-rabbit Alexa Fluor 568 secondary antibody Invitrogen A10042; RRID: AB_2534017 donkey anti-chicken Alexa Fluor 488 Jackson Immuno 703-545-155; RRID: AB_2340375 Mouse anti-EGFP(1) MSKCC Clone 19F7; RRID: AB_2716736 Mouse anti-EGFP(2) MSKCC Clone 19C8; RRID: AB_2716737 rabbit anti-MKRN1 primary antibody Abcam 72054; RRID: AB_1269434 mouse anti-SMC5 primary antibody Santa Cruz sc-393282 mouse anti-NSD2, clone29D1 Milipore Sigma MABE191 mouse anti-GAPDH Sigma-Aldrich G8795; RRID: AB_1078991 Bacterial and virus strains NEB® Stable Competent E. coli (High Efficiency) New England Biolabs C3040 Chemicals, peptides, and recombinant proteins AgeI-HF New England Biolabs R3552 KpnI-HF New England Biolabs R3142 BamHI-HF New England Biolabs R3136 SalI-HF New England Biolabs R3138 Proteinase K, Molecular Biology Grade New England Biolabs P8107 NEBNext® High-Fidelity 2× PCR Master Mix New England Biolabs M0541 Quick-Load® Taq 2× Master Mix New England Biolabs M0271 NEBNext® Ultra TM II Q5® Master Mix New England Biolabs M0544 Mag-Bind® TotalPure NGS Omega Bio-tek M1378 Plasmid Maxi Kit Qiagen 12162 DMEM/F-12 Gibco 11320033 DMEM Gibco 11965092 Penicillin-Streptomycin Gibco 15140163 Trypsin-EDTA (0.25%), phenol red Gibco 25200056 Fetal Bovine Serum R&D Systems S11150 Lipofectamine TM 2000 Transfection Reagent Invitrogen 11668027 RNasin® Ribonuclease Inhibitor Promega N2511 SUPERase⋅In TM RNase Inhibitor Invitrogen AM2696 cOmplete TM , EDTA-free Protease Inhibitor Cocktail Roche 04693132001 TRIzol TM LS Reagent Invitrogen 10296010 1M HEPES Corning 25-060-CI 2M KCl Invitrogen AM9640G 1M MgCl 2 Invitrogen AM9530G DTT Thermo Fisher Scientific N/A NP-40 Sigma 74385 Cycloheximide Sigma C1988-1G RNA Clean & Concentrator-5 Zymo R1014 (Continued on next page) Cell Reports Methods 5, 101247, December 15, 2025 e1 OPEN ACCESS .. REAGENT or RESOURCE SOURCE IDENTIFIER DNeasy Blood & Tissue Kit Qiagen 69504 Dynabeads TM MyOne TM Streptavidin T1 Invitrogen 65601 Pierce TM Recombinant Protein L, Biotinylated Thermo Scientific 29997 DHPC Avanti Polar Lipids 850306P OCT compound Thermo Fisher Scientific 23-730-571 SuperScript TM IV Reverse Transcriptase Invitrogen 18090050 PowerUp TM SYBR TM Green Master Mix for qPCR Applied Biosystems A25742 0.01% poly-L-lysine Sigma P4707 10× RIPA Buffer Cell Signaling 9806 2× Laemmli Sample Buffer Bio-Rad 1610737 Mini-Protean TGX gels Bio-Rad N/A Immun-Blot PVDF Membrane Bio-Rad 1620177 Clarity TM Western ECL Substrate Bio-Rad 1705060 Critical commercial assays Nano-Glo® Dual-Luciferase® Reporter Assay System Promega N1610 High Sensitivity D1000 ScreenTape Agilent 5067–5584 Pierce TM BCA Protein Assay Kit Thermo Scientific 23227 Deposited data Raw fastq files and processed count files GEO GSE246381 Experimental models: Cell lines Human: HEK This paper N/A Experimental models: Organisms/strains Mouse: ROSA26:LSL-eGFP-RPl10 Jackson Stock no. 022367 Mouse: Vglut1-IRES2-Cre-D Jackson Stock no. 023527 Oligonucleotides See Table S6 Integrated DNA Technologies N/A Recombinant DNA JD486 This paper N/A Software and algorithms umi_tools (v1.0.0) Smith et al. 59 https://github.com/CGATOxford/UMI-tools cutadapt (v2.1) Martin 60 https://github.com/marcelm/cutadapt bowtie2 (v2.3.5) Langmead and Salzberg 61 https://bowtie-bio.sourceforge.net/ bowtie2/index.shtml samtools (v1.9) Li et al. 62 https://www.htslib.org/doc/1.9/samtools. html subread (v2.0.0) Liao et al. 63 https://subread.sourceforge.net/ lme4 Bates et al. 64 https://cran.r-project.org/web/packages/ lme4/index.html qvalue Storey et al. 65 https://bioconductor.org/packages/ release/bioc/html/qvalue.html ViennaRNA (v2.4.17) Lorenz et al. 66 https://www.tbi.univie.ac.at/RNA/ RNAfold Gruber et al. 44 http://rna.tbi.univie.ac.at/ QGRS Mapper Kikin et al. 43 https://bioinformatics.ramapo.edu/QGRS/ index.php R R Core Team https://www.r-project.org/ Custom code This Paper https://bitbucket.org/jdlabteam/fiveprime_ mpra_pub/src/main/ https://doi.org/10.5281/zenodo.17459278 e2 Cell Reports Methods 5, 101247, December 15, 2025 OPEN ACCESS
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