Virus:Article Title: Transcriptome-based chemical screens identify CDK8 as a common barrier in multiple cell reprogramming systems.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-hSOX17 R&D Systems Cat# AF1924; RRID:AB_355060 Anti-GATA-4 Santa Cruz Cat# sc-25310; RRID:AB_627667 Anti-Sall4 Abcam Cat# ab29112; RRID:AB_777810 Anti-FOXA2 Abcam Cat# ab108422; RRID:AB_11157157 Anti-Alb BETHYL Cat# A90-134A; RRID:AB_2891982 Donkey anti-Goat IgG (H + L) Cross-Adsorbed Secondary Antibody, Alexa FluorTM 555 Thermo Fisher Scientific Cat# A21432; RRID: AB_2535853 Donkey anti-Goat IgG (H + L) Cross-Adsorbed Secondary Antibody, Alexa FluorTM 488 Thermo Fisher Scientific Cat# A11055; RRID:AB_2534102 Donkey anti-Rabbit IgG (H + L) Highly Cross-Adsorbed Secondary Antibody, Alexa FluorTM 555 Thermo Fisher Scientific Cat# A31572; RRID:AB_162543 Donkey anti-Rabbit IgG (H + L) Highly Cross-Adsorbed Secondary Antibody, Alexa FluorTM 488 Thermo Fisher Scientific Cat# A21206; RRID:AB_2535792 Donkey anti-Goat IgG (H + L) Cross-Adsorbed Secondary Antibody, Alexa FluorTM 555 Thermo Fisher Scientific Cat# A21202; RRID:AB_141607 Bacterial and virus strains TransStbl3 Chemically Competent Cell TransGen Cat# CD521-01 Biological samples Human keloid samples Chinese Academy of Medical Sciences and Peking Union Medical College Ethics approval number: 2022-KY-043 Chemicals, peptides, and recombinant proteins Human FGF2 Dogesce Cat# TP750002 LIF Miltenyi Biotec Cat# 130-095-777 Human FGF4 Peprotech Cat# AF-100-31-25UG Human HGF Peprotech Cat# 100-39-2 EGF Peprotech Cat# 100-47 Human BMP4 Peprotech Cat# 120-05-100 CHIR99021 Selleck Cat# S2924; CAS: 252917-06-9 E-616452 TargetMol Cat# T6337; CAS 446859-33-2 Forskolin TargetMol Cat# T2939; CAS 66575-29-9 CH55 TargetMol Cat# T14946; CAS 110368-33-7 UNC0638 Selleck Cat# S8071; CAS: 1255580-76-7 EPZ00477 Selleck Cat# S7353; CAS: 1338466-77-5 AM580 Selleck Cat# S2933; CAS: 102121-60-8 Tranylcypromine Selleck Cat# S4246; CAS: 1986-47-6 DZNep Selleck Cat# S7120; CAS: 120964-45-6 SGC0946 Selleck Cat# S7079; CAS: 1561178-17-3 5-aza-dC Selleck Cat# S1200; CAS: 2353-33-5 PD0325901 Selleck Cat# S1036; CAS: 391210-10-9 Nicotinamide Selleck Cat# S4785; CAS: 1986-81-8 (Continued on next page) 16 Cell Reports 42, 112566, June 27, 2023 .. REAGENT or RESOURCE SOURCE IDENTIFIER Dexamethasone Selleck Cat# S5956; CAS: 2392-39-4 A-83-01 Selleck Cat# S7692; CAS: 909910-43-6 SB431542 Selleck Cat# S1067; CAS: 301836-41-9 LY364947 Selleck Cat# S2805; CAS: 396129-53-6 Y-27632 Selleck Cat# S6390; CAS: 146986-50-7 Hydrocortisone (cortisol) TargetMol Cat# T1614; CAS 50-23-7 Triiodothyronine TargetMol Cat# T29011; CAS 31135-55-4 Rosiglitazone TargetMol Cat# T0334; CAS 122320-73-4 BI-1347 TargetMol Cat# T5405; CAS 2163056-91-3 MSC2530818 TargetMol Cat# TQ0266; CAS 1883423-59-3 Kinase inhibitor library MedChemExpress Cat# HY-L00 Critical commercial assays EndoFree Maxi Plasmid Kit TIANGEN Cat# DP117 TIANprep Rapid Mini Plasmid Kit TIANGEN Cat# DP105 Universal DNA Purification Kit TIANGEN Cat# DP214-03 TransScript One-Step gDNA Removal and cDNA Synthesis SuperMix TransGen Cat# AT311-02 EasyPure RNA Kit TransGen Cat# ER101-01 TransStart FastPfu Fly DNA Polymerase TransGen Cat# AP231-02 pEASY-Uni Seamless Cloning and Assembly Kit TransGen Cat# CU101-02 KAPA HiFi PCR Kits KAPA BIOSYSTEMS Cat# KK2602 TruePrep DNA Library Prep Kit V2 for Illumina Vazyme Cat# TD502-01 Deposited data ATAC-Seq This paper GEO: GSE227566 Drug-seq2 This paper GEO: GSE227568 RNA-seq This paper GEO: GSE227569 Mouse reference genome mm10 UCSC https://hgdownload.soe.ucsc.edu/ goldenPath/mm10/bigZips/ Experimental models: Cell lines Mouse: mESC TT2 RIKEN BioResource Center Stock No.: AES0014 Experimental models: Organisms/strains Mouse: B6;CBA-Tg(Pou5f1-EGFP)2Mnn/J The Jackson Labratory RRID:IMSR_JAX:004654 Oligonucleotides Primers for quantitative real-time PCR, see Table S1 This paper N/A Recombinant DNA FU-tet-o-hOct4 (Maherali et al., 2008)37 Addgene PlasmidFU-tet-o- hOct4 Cat# 19778 FU-tet-o-GFP This paper N/A FU-tet-o-mCdk8-2HA This paper N/A FU-tet-o-mHnf4a This paper N/A FU-tet-o-mFoxa3 This paper N/A FU-tet-o-hCDK8 This paper N/A FU-tet-o-hCDK8-DFG This paper N/A FU-tet-o-hCDK8-15AA This paper N/A FU-tet-o-hCDK8-NMG This paper N/A pLKO.1-TRC cloning vector (Moffat et al., 2006)38 Addgene PlasmidpLKO.1-TRC cloning vector Cat# 10878 pLKO.1-scramble This paper N/A (Continued on next page) Cell Reports 42, 112566, June 27, 2023 17
Recombinant:Article Title: Transcriptome-based chemical screens identify CDK8 as a common barrier in multiple cell reprogramming systems.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-hSOX17 R&D Systems Cat# AF1924; RRID:AB_355060 Anti-GATA-4 Santa Cruz Cat# sc-25310; RRID:AB_627667 Anti-Sall4 Abcam Cat# ab29112; RRID:AB_777810 Anti-FOXA2 Abcam Cat# ab108422; RRID:AB_11157157 Anti-Alb BETHYL Cat# A90-134A; RRID:AB_2891982 Donkey anti-Goat IgG (H + L) Cross-Adsorbed Secondary Antibody, Alexa FluorTM 555 Thermo Fisher Scientific Cat# A21432; RRID: AB_2535853 Donkey anti-Goat IgG (H + L) Cross-Adsorbed Secondary Antibody, Alexa FluorTM 488 Thermo Fisher Scientific Cat# A11055; RRID:AB_2534102 Donkey anti-Rabbit IgG (H + L) Highly Cross-Adsorbed Secondary Antibody, Alexa FluorTM 555 Thermo Fisher Scientific Cat# A31572; RRID:AB_162543 Donkey anti-Rabbit IgG (H + L) Highly Cross-Adsorbed Secondary Antibody, Alexa FluorTM 488 Thermo Fisher Scientific Cat# A21206; RRID:AB_2535792 Donkey anti-Goat IgG (H + L) Cross-Adsorbed Secondary Antibody, Alexa FluorTM 555 Thermo Fisher Scientific Cat# A21202; RRID:AB_141607 Bacterial and virus strains TransStbl3 Chemically Competent Cell TransGen Cat# CD521-01 Biological samples Human keloid samples Chinese Academy of Medical Sciences and Peking Union Medical College Ethics approval number: 2022-KY-043 Chemicals, peptides, and recombinant proteins Human FGF2 Dogesce Cat# TP750002 LIF Miltenyi Biotec Cat# 130-095-777 Human FGF4 Peprotech Cat# AF-100-31-25UG Human HGF Peprotech Cat# 100-39-2 EGF Peprotech Cat# 100-47 Human BMP4 Peprotech Cat# 120-05-100 CHIR99021 Selleck Cat# S2924; CAS: 252917-06-9 E-616452 TargetMol Cat# T6337; CAS 446859-33-2 Forskolin TargetMol Cat# T2939; CAS 66575-29-9 CH55 TargetMol Cat# T14946; CAS 110368-33-7 UNC0638 Selleck Cat# S8071; CAS: 1255580-76-7 EPZ00477 Selleck Cat# S7353; CAS: 1338466-77-5 AM580 Selleck Cat# S2933; CAS: 102121-60-8 Tranylcypromine Selleck Cat# S4246; CAS: 1986-47-6 DZNep Selleck Cat# S7120; CAS: 120964-45-6 SGC0946 Selleck Cat# S7079; CAS: 1561178-17-3 5-aza-dC Selleck Cat# S1200; CAS: 2353-33-5 PD0325901 Selleck Cat# S1036; CAS: 391210-10-9 Nicotinamide Selleck Cat# S4785; CAS: 1986-81-8 (Continued on next page) 16 Cell Reports 42, 112566, June 27, 2023 .. REAGENT or RESOURCE SOURCE IDENTIFIER Dexamethasone Selleck Cat# S5956; CAS: 2392-39-4 A-83-01 Selleck Cat# S7692; CAS: 909910-43-6 SB431542 Selleck Cat# S1067; CAS: 301836-41-9 LY364947 Selleck Cat# S2805; CAS: 396129-53-6 Y-27632 Selleck Cat# S6390; CAS: 146986-50-7 Hydrocortisone (cortisol) TargetMol Cat# T1614; CAS 50-23-7 Triiodothyronine TargetMol Cat# T29011; CAS 31135-55-4 Rosiglitazone TargetMol Cat# T0334; CAS 122320-73-4 BI-1347 TargetMol Cat# T5405; CAS 2163056-91-3 MSC2530818 TargetMol Cat# TQ0266; CAS 1883423-59-3 Kinase inhibitor library MedChemExpress Cat# HY-L00 Critical commercial assays EndoFree Maxi Plasmid Kit TIANGEN Cat# DP117 TIANprep Rapid Mini Plasmid Kit TIANGEN Cat# DP105 Universal DNA Purification Kit TIANGEN Cat# DP214-03 TransScript One-Step gDNA Removal and cDNA Synthesis SuperMix TransGen Cat# AT311-02 EasyPure RNA Kit TransGen Cat# ER101-01 TransStart FastPfu Fly DNA Polymerase TransGen Cat# AP231-02 pEASY-Uni Seamless Cloning and Assembly Kit TransGen Cat# CU101-02 KAPA HiFi PCR Kits KAPA BIOSYSTEMS Cat# KK2602 TruePrep DNA Library Prep Kit V2 for Illumina Vazyme Cat# TD502-01 Deposited data ATAC-Seq This paper GEO: GSE227566 Drug-seq2 This paper GEO: GSE227568 RNA-seq This paper GEO: GSE227569 Mouse reference genome mm10 UCSC https://hgdownload.soe.ucsc.edu/ goldenPath/mm10/bigZips/ Experimental models: Cell lines Mouse: mESC TT2 RIKEN BioResource Center Stock No.: AES0014 Experimental models: Organisms/strains Mouse: B6;CBA-Tg(Pou5f1-EGFP)2Mnn/J The Jackson Labratory RRID:IMSR_JAX:004654 Oligonucleotides Primers for quantitative real-time PCR, see Table S1 This paper N/A Recombinant DNA FU-tet-o-hOct4 (Maherali et al., 2008)37 Addgene PlasmidFU-tet-o- hOct4 Cat# 19778 FU-tet-o-GFP This paper N/A FU-tet-o-mCdk8-2HA This paper N/A FU-tet-o-mHnf4a This paper N/A FU-tet-o-mFoxa3 This paper N/A FU-tet-o-hCDK8 This paper N/A FU-tet-o-hCDK8-DFG This paper N/A FU-tet-o-hCDK8-15AA This paper N/A FU-tet-o-hCDK8-NMG This paper N/A pLKO.1-TRC cloning vector (Moffat et al., 2006)38 Addgene PlasmidpLKO.1-TRC cloning vector Cat# 10878 pLKO.1-scramble This paper N/A (Continued on next page) Cell Reports 42, 112566, June 27, 2023 17
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