SYBR Green Assay:Article Title: Genome-wide R-loop Landscapes during Cell Differentiation and Reprogramming.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER hLIF Millipore Cat# LIF1050 Dorsomorphin Sigma-Aldrich Cat# P5499 Compound E EMD Chemicals Inc. Cat# 565790 Hoechst 33342 Thermo Fisher Scientific Cat# H3570 iTaq Universal SYBR Green Super mix Bio-Rad Cat# QPS-201 Triton X-100 Sigma-Aldrich Cat# T9284 TRIzol Reagent Thermo Fisher Scientific Cat# 15596018 NP-40 Dingguo Cat# DH218 Proteinase K NEB Cat# P8107S MboI NEB Cat# R0147L AluI NEB Cat# R0137L DdeI NEB Cat# R0175L MseI NEB Cat# R0525L RNase A TAKARA Cat# 2158 EDTA Sigma-Aldrich Cat# EDS-500G Critical Commercial Assays Cell Meter JC-10 Mitochondrial MembranePotential Assay Kit AAT Bioquest, Inc. Cat# 22801 Seahorse XF Glycolysis Stress Test Kit Seahorse Bioscience Cat# 103020-100 ACCEL-NGS 1S plus DNA Library Ki Swift Biosciences Cat# 10096 NEBNext DNA Library Prep Reagent Set for Illumina NEB Cat# # E6000 DNeasy Blood & Tissue Kits QIAGEN Cat# 69506 Deposited Data Raw data files for ssDRIP-seq This study GSE145964 Raw data files for ChIP-seq This study GSE145964 Raw data files for WGBS This study GSE145964 Raw data files for RNA-seq and ATAC-seq Zhang et al., 2020 PRJCA002454 Experimental Models: Cell Lines Wildtype hESCs (Line H9) WiCell Research Cat# WA09 Human vascular endothelial cells derived from hESCs This paper N/A Human vascular smooth muscle cells derived from hESCs This paper N/A Humanmesenchymal stem cells derived from hESCs This paper N/A Human neural stem cells derived from hESCs This paper N/A Human induced pluripotent stem cells derived from hNSCs This paper N/A Oligonucleotides Primers for RT-qPCR, see Table S7 This paper N/A Software and Algorithms FlowJo Flowjo, LLC https://www.flowjo.com/ Leica LAS AF Lite (version 2.6.0) Leica https://leica-las-af-lite.updatestar.com/ GraphPadPrism (version 6.0) GraphPad Software Inc. https://www.graphpad.com/ Seahorse Wave Controller (version 2.6) Agilent https://www.agilent.com/ TrimGalore (version 0.4.5) Babraham Bioinformatics https://github.com/FelixKrueger/TrimGalore Bowtie2 (version 2.2.9) Langmead and Salzberg, 2012 http://bowtie-bio.sourceforge.net/bowtie2/ index.shtml (Continued on next page) e2 Cell Reports 32, 107870, July 7, 2020 .. REAGENT or RESOURCE SOURCE IDENTIFIER hLIF Millipore Cat# LIF1050 Dorsomorphin Sigma-Aldrich Cat# P5499 Compound E EMD Chemicals Inc. Cat# 565790 Hoechst 33342 Thermo Fisher Scientific Cat# H3570 iTaq Universal SYBR Green Super mix Bio-Rad Cat# QPS-201 Triton X-100 Sigma-Aldrich Cat# T9284 TRIzol Reagent Thermo Fisher Scientific Cat# 15596018 NP-40 Dingguo Cat# DH218 Proteinase K NEB Cat# P8107S MboI NEB Cat# R0147L AluI NEB Cat# R0137L DdeI NEB Cat# R0175L MseI NEB Cat# R0525L RNase A TAKARA Cat# 2158 EDTA Sigma-Aldrich Cat# EDS-500G Critical Commercial Assays Cell Meter JC-10 Mitochondrial MembranePotential Assay Kit AAT Bioquest, Inc. Cat# 22801 Seahorse XF Glycolysis Stress Test Kit Seahorse Bioscience Cat# 103020-100 ACCEL-NGS 1S plus DNA Library Ki Swift Biosciences Cat# 10096 NEBNext DNA Library Prep Reagent Set for Illumina NEB Cat# # E6000 DNeasy Blood & Tissue Kits QIAGEN Cat# 69506 Deposited Data Raw data files for ssDRIP-seq This study GSE145964 Raw data files for ChIP-seq This study GSE145964 Raw data files for WGBS This study GSE145964 Raw data files for RNA-seq and ATAC-seq Zhang et al., 2020 PRJCA002454 Experimental Models: Cell Lines Wildtype hESCs (Line H9) WiCell Research Cat# WA09 Human vascular endothelial cells derived from hESCs This paper N/A Human vascular smooth muscle cells derived from hESCs This paper N/A Humanmesenchymal stem cells derived from hESCs This paper N/A Human neural stem cells derived from hESCs This paper N/A Human induced pluripotent stem cells derived from hNSCs This paper N/A Oligonucleotides Primers for RT-qPCR, see Table S7 This paper N/A Software and Algorithms FlowJo Flowjo, LLC https://www.flowjo.com/ Leica LAS AF Lite (version 2.6.0) Leica https://leica-las-af-lite.updatestar.com/ GraphPadPrism (version 6.0) GraphPad Software Inc. https://www.graphpad.com/ Seahorse Wave Controller (version 2.6) Agilent https://www.agilent.com/ TrimGalore (version 0.4.5) Babraham Bioinformatics https://github.com/FelixKrueger/TrimGalore Bowtie2 (version 2.2.9) Langmead and Salzberg, 2012 http://bowtie-bio.sourceforge.net/bowtie2/ index.shtml (Continued on next page) e2 Cell Reports 32, 107870, July 7, 2020
Chromatin Immunoprecipitation:Article Title: Genome-wide R-loop Landscapes during Cell Differentiation and Reprogramming.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER hLIF Millipore Cat# LIF1050 Dorsomorphin Sigma-Aldrich Cat# P5499 Compound E EMD Chemicals Inc. Cat# 565790 Hoechst 33342 Thermo Fisher Scientific Cat# H3570 iTaq Universal SYBR Green Super mix Bio-Rad Cat# QPS-201 Triton X-100 Sigma-Aldrich Cat# T9284 TRIzol Reagent Thermo Fisher Scientific Cat# 15596018 NP-40 Dingguo Cat# DH218 Proteinase K NEB Cat# P8107S MboI NEB Cat# R0147L AluI NEB Cat# R0137L DdeI NEB Cat# R0175L MseI NEB Cat# R0525L RNase A TAKARA Cat# 2158 EDTA Sigma-Aldrich Cat# EDS-500G Critical Commercial Assays Cell Meter JC-10 Mitochondrial MembranePotential Assay Kit AAT Bioquest, Inc. Cat# 22801 Seahorse XF Glycolysis Stress Test Kit Seahorse Bioscience Cat# 103020-100 ACCEL-NGS 1S plus DNA Library Ki Swift Biosciences Cat# 10096 NEBNext DNA Library Prep Reagent Set for Illumina NEB Cat# # E6000 DNeasy Blood & Tissue Kits QIAGEN Cat# 69506 Deposited Data Raw data files for ssDRIP-seq This study GSE145964 Raw data files for ChIP-seq This study GSE145964 Raw data files for WGBS This study GSE145964 Raw data files for RNA-seq and ATAC-seq Zhang et al., 2020 PRJCA002454 Experimental Models: Cell Lines Wildtype hESCs (Line H9) WiCell Research Cat# WA09 Human vascular endothelial cells derived from hESCs This paper N/A Human vascular smooth muscle cells derived from hESCs This paper N/A Humanmesenchymal stem cells derived from hESCs This paper N/A Human neural stem cells derived from hESCs This paper N/A Human induced pluripotent stem cells derived from hNSCs This paper N/A Oligonucleotides Primers for RT-qPCR, see Table S7 This paper N/A Software and Algorithms FlowJo Flowjo, LLC https://www.flowjo.com/ Leica LAS AF Lite (version 2.6.0) Leica https://leica-las-af-lite.updatestar.com/ GraphPadPrism (version 6.0) GraphPad Software Inc. https://www.graphpad.com/ Seahorse Wave Controller (version 2.6) Agilent https://www.agilent.com/ TrimGalore (version 0.4.5) Babraham Bioinformatics https://github.com/FelixKrueger/TrimGalore Bowtie2 (version 2.2.9) Langmead and Salzberg, 2012 http://bowtie-bio.sourceforge.net/bowtie2/ index.shtml (Continued on next page) e2 Cell Reports 32, 107870, July 7, 2020 .. REAGENT or RESOURCE SOURCE IDENTIFIER hLIF Millipore Cat# LIF1050 Dorsomorphin Sigma-Aldrich Cat# P5499 Compound E EMD Chemicals Inc. Cat# 565790 Hoechst 33342 Thermo Fisher Scientific Cat# H3570 iTaq Universal SYBR Green Super mix Bio-Rad Cat# QPS-201 Triton X-100 Sigma-Aldrich Cat# T9284 TRIzol Reagent Thermo Fisher Scientific Cat# 15596018 NP-40 Dingguo Cat# DH218 Proteinase K NEB Cat# P8107S MboI NEB Cat# R0147L AluI NEB Cat# R0137L DdeI NEB Cat# R0175L MseI NEB Cat# R0525L RNase A TAKARA Cat# 2158 EDTA Sigma-Aldrich Cat# EDS-500G Critical Commercial Assays Cell Meter JC-10 Mitochondrial MembranePotential Assay Kit AAT Bioquest, Inc. Cat# 22801 Seahorse XF Glycolysis Stress Test Kit Seahorse Bioscience Cat# 103020-100 ACCEL-NGS 1S plus DNA Library Ki Swift Biosciences Cat# 10096 NEBNext DNA Library Prep Reagent Set for Illumina NEB Cat# # E6000 DNeasy Blood & Tissue Kits QIAGEN Cat# 69506 Deposited Data Raw data files for ssDRIP-seq This study GSE145964 Raw data files for ChIP-seq This study GSE145964 Raw data files for WGBS This study GSE145964 Raw data files for RNA-seq and ATAC-seq Zhang et al., 2020 PRJCA002454 Experimental Models: Cell Lines Wildtype hESCs (Line H9) WiCell Research Cat# WA09 Human vascular endothelial cells derived from hESCs This paper N/A Human vascular smooth muscle cells derived from hESCs This paper N/A Humanmesenchymal stem cells derived from hESCs This paper N/A Human neural stem cells derived from hESCs This paper N/A Human induced pluripotent stem cells derived from hNSCs This paper N/A Oligonucleotides Primers for RT-qPCR, see Table S7 This paper N/A Software and Algorithms FlowJo Flowjo, LLC https://www.flowjo.com/ Leica LAS AF Lite (version 2.6.0) Leica https://leica-las-af-lite.updatestar.com/ GraphPadPrism (version 6.0) GraphPad Software Inc. https://www.graphpad.com/ Seahorse Wave Controller (version 2.6) Agilent https://www.agilent.com/ TrimGalore (version 0.4.5) Babraham Bioinformatics https://github.com/FelixKrueger/TrimGalore Bowtie2 (version 2.2.9) Langmead and Salzberg, 2012 http://bowtie-bio.sourceforge.net/bowtie2/ index.shtml (Continued on next page) e2 Cell Reports 32, 107870, July 7, 2020
RNA Sequencing:Article Title: Genome-wide R-loop Landscapes during Cell Differentiation and Reprogramming.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER hLIF Millipore Cat# LIF1050 Dorsomorphin Sigma-Aldrich Cat# P5499 Compound E EMD Chemicals Inc. Cat# 565790 Hoechst 33342 Thermo Fisher Scientific Cat# H3570 iTaq Universal SYBR Green Super mix Bio-Rad Cat# QPS-201 Triton X-100 Sigma-Aldrich Cat# T9284 TRIzol Reagent Thermo Fisher Scientific Cat# 15596018 NP-40 Dingguo Cat# DH218 Proteinase K NEB Cat# P8107S MboI NEB Cat# R0147L AluI NEB Cat# R0137L DdeI NEB Cat# R0175L MseI NEB Cat# R0525L RNase A TAKARA Cat# 2158 EDTA Sigma-Aldrich Cat# EDS-500G Critical Commercial Assays Cell Meter JC-10 Mitochondrial MembranePotential Assay Kit AAT Bioquest, Inc. Cat# 22801 Seahorse XF Glycolysis Stress Test Kit Seahorse Bioscience Cat# 103020-100 ACCEL-NGS 1S plus DNA Library Ki Swift Biosciences Cat# 10096 NEBNext DNA Library Prep Reagent Set for Illumina NEB Cat# # E6000 DNeasy Blood & Tissue Kits QIAGEN Cat# 69506 Deposited Data Raw data files for ssDRIP-seq This study GSE145964 Raw data files for ChIP-seq This study GSE145964 Raw data files for WGBS This study GSE145964 Raw data files for RNA-seq and ATAC-seq Zhang et al., 2020 PRJCA002454 Experimental Models: Cell Lines Wildtype hESCs (Line H9) WiCell Research Cat# WA09 Human vascular endothelial cells derived from hESCs This paper N/A Human vascular smooth muscle cells derived from hESCs This paper N/A Humanmesenchymal stem cells derived from hESCs This paper N/A Human neural stem cells derived from hESCs This paper N/A Human induced pluripotent stem cells derived from hNSCs This paper N/A Oligonucleotides Primers for RT-qPCR, see Table S7 This paper N/A Software and Algorithms FlowJo Flowjo, LLC https://www.flowjo.com/ Leica LAS AF Lite (version 2.6.0) Leica https://leica-las-af-lite.updatestar.com/ GraphPadPrism (version 6.0) GraphPad Software Inc. https://www.graphpad.com/ Seahorse Wave Controller (version 2.6) Agilent https://www.agilent.com/ TrimGalore (version 0.4.5) Babraham Bioinformatics https://github.com/FelixKrueger/TrimGalore Bowtie2 (version 2.2.9) Langmead and Salzberg, 2012 http://bowtie-bio.sourceforge.net/bowtie2/ index.shtml (Continued on next page) e2 Cell Reports 32, 107870, July 7, 2020 .. REAGENT or RESOURCE SOURCE IDENTIFIER hLIF Millipore Cat# LIF1050 Dorsomorphin Sigma-Aldrich Cat# P5499 Compound E EMD Chemicals Inc. Cat# 565790 Hoechst 33342 Thermo Fisher Scientific Cat# H3570 iTaq Universal SYBR Green Super mix Bio-Rad Cat# QPS-201 Triton X-100 Sigma-Aldrich Cat# T9284 TRIzol Reagent Thermo Fisher Scientific Cat# 15596018 NP-40 Dingguo Cat# DH218 Proteinase K NEB Cat# P8107S MboI NEB Cat# R0147L AluI NEB Cat# R0137L DdeI NEB Cat# R0175L MseI NEB Cat# R0525L RNase A TAKARA Cat# 2158 EDTA Sigma-Aldrich Cat# EDS-500G Critical Commercial Assays Cell Meter JC-10 Mitochondrial MembranePotential Assay Kit AAT Bioquest, Inc. Cat# 22801 Seahorse XF Glycolysis Stress Test Kit Seahorse Bioscience Cat# 103020-100 ACCEL-NGS 1S plus DNA Library Ki Swift Biosciences Cat# 10096 NEBNext DNA Library Prep Reagent Set for Illumina NEB Cat# # E6000 DNeasy Blood & Tissue Kits QIAGEN Cat# 69506 Deposited Data Raw data files for ssDRIP-seq This study GSE145964 Raw data files for ChIP-seq This study GSE145964 Raw data files for WGBS This study GSE145964 Raw data files for RNA-seq and ATAC-seq Zhang et al., 2020 PRJCA002454 Experimental Models: Cell Lines Wildtype hESCs (Line H9) WiCell Research Cat# WA09 Human vascular endothelial cells derived from hESCs This paper N/A Human vascular smooth muscle cells derived from hESCs This paper N/A Humanmesenchymal stem cells derived from hESCs This paper N/A Human neural stem cells derived from hESCs This paper N/A Human induced pluripotent stem cells derived from hNSCs This paper N/A Oligonucleotides Primers for RT-qPCR, see Table S7 This paper N/A Software and Algorithms FlowJo Flowjo, LLC https://www.flowjo.com/ Leica LAS AF Lite (version 2.6.0) Leica https://leica-las-af-lite.updatestar.com/ GraphPadPrism (version 6.0) GraphPad Software Inc. https://www.graphpad.com/ Seahorse Wave Controller (version 2.6) Agilent https://www.agilent.com/ TrimGalore (version 0.4.5) Babraham Bioinformatics https://github.com/FelixKrueger/TrimGalore Bowtie2 (version 2.2.9) Langmead and Salzberg, 2012 http://bowtie-bio.sourceforge.net/bowtie2/ index.shtml (Continued on next page) e2 Cell Reports 32, 107870, July 7, 2020
Derivative Assay:Article Title: Genome-wide R-loop Landscapes during Cell Differentiation and Reprogramming.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER hLIF Millipore Cat# LIF1050 Dorsomorphin Sigma-Aldrich Cat# P5499 Compound E EMD Chemicals Inc. Cat# 565790 Hoechst 33342 Thermo Fisher Scientific Cat# H3570 iTaq Universal SYBR Green Super mix Bio-Rad Cat# QPS-201 Triton X-100 Sigma-Aldrich Cat# T9284 TRIzol Reagent Thermo Fisher Scientific Cat# 15596018 NP-40 Dingguo Cat# DH218 Proteinase K NEB Cat# P8107S MboI NEB Cat# R0147L AluI NEB Cat# R0137L DdeI NEB Cat# R0175L MseI NEB Cat# R0525L RNase A TAKARA Cat# 2158 EDTA Sigma-Aldrich Cat# EDS-500G Critical Commercial Assays Cell Meter JC-10 Mitochondrial MembranePotential Assay Kit AAT Bioquest, Inc. Cat# 22801 Seahorse XF Glycolysis Stress Test Kit Seahorse Bioscience Cat# 103020-100 ACCEL-NGS 1S plus DNA Library Ki Swift Biosciences Cat# 10096 NEBNext DNA Library Prep Reagent Set for Illumina NEB Cat# # E6000 DNeasy Blood & Tissue Kits QIAGEN Cat# 69506 Deposited Data Raw data files for ssDRIP-seq This study GSE145964 Raw data files for ChIP-seq This study GSE145964 Raw data files for WGBS This study GSE145964 Raw data files for RNA-seq and ATAC-seq Zhang et al., 2020 PRJCA002454 Experimental Models: Cell Lines Wildtype hESCs (Line H9) WiCell Research Cat# WA09 Human vascular endothelial cells derived from hESCs This paper N/A Human vascular smooth muscle cells derived from hESCs This paper N/A Humanmesenchymal stem cells derived from hESCs This paper N/A Human neural stem cells derived from hESCs This paper N/A Human induced pluripotent stem cells derived from hNSCs This paper N/A Oligonucleotides Primers for RT-qPCR, see Table S7 This paper N/A Software and Algorithms FlowJo Flowjo, LLC https://www.flowjo.com/ Leica LAS AF Lite (version 2.6.0) Leica https://leica-las-af-lite.updatestar.com/ GraphPadPrism (version 6.0) GraphPad Software Inc. https://www.graphpad.com/ Seahorse Wave Controller (version 2.6) Agilent https://www.agilent.com/ TrimGalore (version 0.4.5) Babraham Bioinformatics https://github.com/FelixKrueger/TrimGalore Bowtie2 (version 2.2.9) Langmead and Salzberg, 2012 http://bowtie-bio.sourceforge.net/bowtie2/ index.shtml (Continued on next page) e2 Cell Reports 32, 107870, July 7, 2020 .. REAGENT or RESOURCE SOURCE IDENTIFIER hLIF Millipore Cat# LIF1050 Dorsomorphin Sigma-Aldrich Cat# P5499 Compound E EMD Chemicals Inc. Cat# 565790 Hoechst 33342 Thermo Fisher Scientific Cat# H3570 iTaq Universal SYBR Green Super mix Bio-Rad Cat# QPS-201 Triton X-100 Sigma-Aldrich Cat# T9284 TRIzol Reagent Thermo Fisher Scientific Cat# 15596018 NP-40 Dingguo Cat# DH218 Proteinase K NEB Cat# P8107S MboI NEB Cat# R0147L AluI NEB Cat# R0137L DdeI NEB Cat# R0175L MseI NEB Cat# R0525L RNase A TAKARA Cat# 2158 EDTA Sigma-Aldrich Cat# EDS-500G Critical Commercial Assays Cell Meter JC-10 Mitochondrial MembranePotential Assay Kit AAT Bioquest, Inc. Cat# 22801 Seahorse XF Glycolysis Stress Test Kit Seahorse Bioscience Cat# 103020-100 ACCEL-NGS 1S plus DNA Library Ki Swift Biosciences Cat# 10096 NEBNext DNA Library Prep Reagent Set for Illumina NEB Cat# # E6000 DNeasy Blood & Tissue Kits QIAGEN Cat# 69506 Deposited Data Raw data files for ssDRIP-seq This study GSE145964 Raw data files for ChIP-seq This study GSE145964 Raw data files for WGBS This study GSE145964 Raw data files for RNA-seq and ATAC-seq Zhang et al., 2020 PRJCA002454 Experimental Models: Cell Lines Wildtype hESCs (Line H9) WiCell Research Cat# WA09 Human vascular endothelial cells derived from hESCs This paper N/A Human vascular smooth muscle cells derived from hESCs This paper N/A Humanmesenchymal stem cells derived from hESCs This paper N/A Human neural stem cells derived from hESCs This paper N/A Human induced pluripotent stem cells derived from hNSCs This paper N/A Oligonucleotides Primers for RT-qPCR, see Table S7 This paper N/A Software and Algorithms FlowJo Flowjo, LLC https://www.flowjo.com/ Leica LAS AF Lite (version 2.6.0) Leica https://leica-las-af-lite.updatestar.com/ GraphPadPrism (version 6.0) GraphPad Software Inc. https://www.graphpad.com/ Seahorse Wave Controller (version 2.6) Agilent https://www.agilent.com/ TrimGalore (version 0.4.5) Babraham Bioinformatics https://github.com/FelixKrueger/TrimGalore Bowtie2 (version 2.2.9) Langmead and Salzberg, 2012 http://bowtie-bio.sourceforge.net/bowtie2/ index.shtml (Continued on next page) e2 Cell Reports 32, 107870, July 7, 2020
Software:Article Title: Genome-wide R-loop Landscapes during Cell Differentiation and Reprogramming.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER hLIF Millipore Cat# LIF1050 Dorsomorphin Sigma-Aldrich Cat# P5499 Compound E EMD Chemicals Inc. Cat# 565790 Hoechst 33342 Thermo Fisher Scientific Cat# H3570 iTaq Universal SYBR Green Super mix Bio-Rad Cat# QPS-201 Triton X-100 Sigma-Aldrich Cat# T9284 TRIzol Reagent Thermo Fisher Scientific Cat# 15596018 NP-40 Dingguo Cat# DH218 Proteinase K NEB Cat# P8107S MboI NEB Cat# R0147L AluI NEB Cat# R0137L DdeI NEB Cat# R0175L MseI NEB Cat# R0525L RNase A TAKARA Cat# 2158 EDTA Sigma-Aldrich Cat# EDS-500G Critical Commercial Assays Cell Meter JC-10 Mitochondrial MembranePotential Assay Kit AAT Bioquest, Inc. Cat# 22801 Seahorse XF Glycolysis Stress Test Kit Seahorse Bioscience Cat# 103020-100 ACCEL-NGS 1S plus DNA Library Ki Swift Biosciences Cat# 10096 NEBNext DNA Library Prep Reagent Set for Illumina NEB Cat# # E6000 DNeasy Blood & Tissue Kits QIAGEN Cat# 69506 Deposited Data Raw data files for ssDRIP-seq This study GSE145964 Raw data files for ChIP-seq This study GSE145964 Raw data files for WGBS This study GSE145964 Raw data files for RNA-seq and ATAC-seq Zhang et al., 2020 PRJCA002454 Experimental Models: Cell Lines Wildtype hESCs (Line H9) WiCell Research Cat# WA09 Human vascular endothelial cells derived from hESCs This paper N/A Human vascular smooth muscle cells derived from hESCs This paper N/A Humanmesenchymal stem cells derived from hESCs This paper N/A Human neural stem cells derived from hESCs This paper N/A Human induced pluripotent stem cells derived from hNSCs This paper N/A Oligonucleotides Primers for RT-qPCR, see Table S7 This paper N/A Software and Algorithms FlowJo Flowjo, LLC https://www.flowjo.com/ Leica LAS AF Lite (version 2.6.0) Leica https://leica-las-af-lite.updatestar.com/ GraphPadPrism (version 6.0) GraphPad Software Inc. https://www.graphpad.com/ Seahorse Wave Controller (version 2.6) Agilent https://www.agilent.com/ TrimGalore (version 0.4.5) Babraham Bioinformatics https://github.com/FelixKrueger/TrimGalore Bowtie2 (version 2.2.9) Langmead and Salzberg, 2012 http://bowtie-bio.sourceforge.net/bowtie2/ index.shtml (Continued on next page) e2 Cell Reports 32, 107870, July 7, 2020 .. REAGENT or RESOURCE SOURCE IDENTIFIER hLIF Millipore Cat# LIF1050 Dorsomorphin Sigma-Aldrich Cat# P5499 Compound E EMD Chemicals Inc. Cat# 565790 Hoechst 33342 Thermo Fisher Scientific Cat# H3570 iTaq Universal SYBR Green Super mix Bio-Rad Cat# QPS-201 Triton X-100 Sigma-Aldrich Cat# T9284 TRIzol Reagent Thermo Fisher Scientific Cat# 15596018 NP-40 Dingguo Cat# DH218 Proteinase K NEB Cat# P8107S MboI NEB Cat# R0147L AluI NEB Cat# R0137L DdeI NEB Cat# R0175L MseI NEB Cat# R0525L RNase A TAKARA Cat# 2158 EDTA Sigma-Aldrich Cat# EDS-500G Critical Commercial Assays Cell Meter JC-10 Mitochondrial MembranePotential Assay Kit AAT Bioquest, Inc. Cat# 22801 Seahorse XF Glycolysis Stress Test Kit Seahorse Bioscience Cat# 103020-100 ACCEL-NGS 1S plus DNA Library Ki Swift Biosciences Cat# 10096 NEBNext DNA Library Prep Reagent Set for Illumina NEB Cat# # E6000 DNeasy Blood & Tissue Kits QIAGEN Cat# 69506 Deposited Data Raw data files for ssDRIP-seq This study GSE145964 Raw data files for ChIP-seq This study GSE145964 Raw data files for WGBS This study GSE145964 Raw data files for RNA-seq and ATAC-seq Zhang et al., 2020 PRJCA002454 Experimental Models: Cell Lines Wildtype hESCs (Line H9) WiCell Research Cat# WA09 Human vascular endothelial cells derived from hESCs This paper N/A Human vascular smooth muscle cells derived from hESCs This paper N/A Humanmesenchymal stem cells derived from hESCs This paper N/A Human neural stem cells derived from hESCs This paper N/A Human induced pluripotent stem cells derived from hNSCs This paper N/A Oligonucleotides Primers for RT-qPCR, see Table S7 This paper N/A Software and Algorithms FlowJo Flowjo, LLC https://www.flowjo.com/ Leica LAS AF Lite (version 2.6.0) Leica https://leica-las-af-lite.updatestar.com/ GraphPadPrism (version 6.0) GraphPad Software Inc. https://www.graphpad.com/ Seahorse Wave Controller (version 2.6) Agilent https://www.agilent.com/ TrimGalore (version 0.4.5) Babraham Bioinformatics https://github.com/FelixKrueger/TrimGalore Bowtie2 (version 2.2.9) Langmead and Salzberg, 2012 http://bowtie-bio.sourceforge.net/bowtie2/ index.shtml (Continued on next page) e2 Cell Reports 32, 107870, July 7, 2020
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