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cell lines h1 hescs wicell wa01 h1 klf17 gfp reporter line  (WiCell Research Institute Inc)


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    WiCell Research Institute Inc cell lines h1 hescs wicell wa01 h1 klf17 gfp reporter line
    Cell Lines H1 Hescs Wicell Wa01 H1 Klf17 Gfp Reporter Line, supplied by WiCell Research Institute Inc, used in various techniques. Bioz Stars score: 99/100, based on 963 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/cell+lines+h1+hesc+wicell+wa01/WA01/10__1016_slash_j__xpro__2025__104164-72-7-11
    Average 99 stars, based on 963 article reviews
    cell lines h1 hescs wicell wa01 h1 klf17 gfp reporter line - by Bioz Stars, 2026-09
    99/100 stars

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    Recombinant:

    Article Title: HiCAR is a robust and sensitive method to analyze open-chromatin-associated genome organization.
    Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-CD31-Alexa Fluor 488 BioLegend Cat# 303110; RRID: AB_493074 Anti-CD34-FITC BioLegend Cat# 343503; RRID: AB_1731923 Anti-CD29-APC BioLegend Cat# 303008; RRID: AB_314324 Anti-NCAM-Biotin BioLegend Cat# 318319; RRID: AB_893392 Biological samples Lower extremity human skeletal muscle samples (collected from a female, 67-year-old individual) Duke University Medical Center N/A Chemicals, peptides, and recombinant proteins Matrigel Corning 354230 mTeSR Plus STEMCELL Technologies 05825 Accutase BioLegend 423201 Chitin column Bio-Rad 7372522 Amicon Ultracel 30K Millipore UFC903024 Dialysis membrane tube Spectra/Por D1614-11 NEBuffer 3.1 NEB B7203S CviQI NEB R0639L T4 DNA ligase (400U/ml) NEB M0202S 20mg/ml BSA NEB B9000S Proteinase K Thermo Fisher AM2546 Phenol:Chloroform:Isoamyl Alcohol (25:24:1, v/v,) Spectrum 136112-00-0 T4 DNA polymerase NEB M0203L NlaIII NEB R0125L SPRI beads Beckman B23319 DNA clean & concentrator kit Zymo D4013 Gel extraction using DNA recovery kit Zymo D4002 Roche Complete Protease Inhibitor Sigma 5056489001 PmeI NEB R0560L RNaseOUT Invitrogen 10777-019 Q5 High-Fidelity DNA Polymerase NEB m0491L FuGENE HD Transfection Reagent Promega E2311 Anza 13 Esp3I Invitrogen IVGN0136 Critical commercial assays iTaq Universal SYBR Green Supermix Bio-Rad 1725122 Dual-Luciferase Reporter Assay System Promega E1910 Deposited data HiCAR H1 This study GEO: GSE162819 HiCAR GM12878 This study GEO: GSE162819 HiCAR human muscle stem cells This study Under the Synapse ID: syn26841404 For published genomics datasets, see Table S3 Table S3 N/A Experimental models: Cell lines H1 hESC WiCell WA01; RRID: CVCL_9771 Human lymphoblastoid cell lines Coriell Institute GM12878; RRID: CVCL_7526 (Continued on next page) Molecular Cell 82, 1225–1238.e1–e6, March 17, 2022 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Oligonucleotides Custom primers for HiCAR, see Table S1 Table S1 N/A sgRNA Oligos, see Table S1 Table S1 N/A Recombinant DNA pTXB1-Tn5 Addgene RRID: Addgene_60240 Lentiguide-puro Addgene RRID: Addgene_52963 Lenti-dCas9-KRAB-blast Addgene RRID: Addgene_89567 Lenti dCAS-VP64_Blast Addgene RRID: Addgene_61425 pGL3-Promoter Promega E1761 pRL-SV40 Promega E2231 Software and algorithms BWA (Li and Durbin, 2010) http://bio-bwa.sourceforge.net/bwa.shtml; RRID:SCR_010910 Pairtools Python package https://github.com/mirnylab/pairtools HiGlass (Kerpedjiev et al., 2018) https://github.com/higlass EnrichedHeatmap (Gu et al., 2018) https://github.com/jokergoo/EnrichedHeatmap Cooltools Python package https://github.com/open2c/cooltools HiCRep (Yang et al., 2017) https://github.com/qunhualilab/hicrep Pairsqc (Lee et al., 2022) https://github.com/4dn-dcic/pairsqc MACS2 (Zhang et al., 2008) https://github.com/macs3-project/MACS; RRID:SCR_013291 Chip-R (Newell et al., 2021) https://github.com/rhysnewell/ChIP-R/ Gimme (van Heeringen and Veenstra, 2011) https://github.com/vanheeringen-lab/ gimmemotifs; RRID:SCR_001146 MAPS (Juric et al., 2019) https://github.com/ijuric/MAPS Juicer:HiCCUPS (Durand et al., 2016) https://github.com/aidenlab/juicer; RRID:SCR_017226 FitHiC2 (Kaul et al., 2020) https://github.com/ay-lab/fithic HiCAR nextflow pipeline (Ou et al., 2022) DOI: 10.5281/zenodo.5889172 Clusterprofile (Yu et al., 2012) https://bioconductor.org/packages/release/ bioc/html/clusterProfiler.html Other Detailed protocol for the preparation of HiCAR library In this study See supplemental information and Method S1

    Membrane:

    Article Title: HiCAR is a robust and sensitive method to analyze open-chromatin-associated genome organization.
    Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-CD31-Alexa Fluor 488 BioLegend Cat# 303110; RRID: AB_493074 Anti-CD34-FITC BioLegend Cat# 343503; RRID: AB_1731923 Anti-CD29-APC BioLegend Cat# 303008; RRID: AB_314324 Anti-NCAM-Biotin BioLegend Cat# 318319; RRID: AB_893392 Biological samples Lower extremity human skeletal muscle samples (collected from a female, 67-year-old individual) Duke University Medical Center N/A Chemicals, peptides, and recombinant proteins Matrigel Corning 354230 mTeSR Plus STEMCELL Technologies 05825 Accutase BioLegend 423201 Chitin column Bio-Rad 7372522 Amicon Ultracel 30K Millipore UFC903024 Dialysis membrane tube Spectra/Por D1614-11 NEBuffer 3.1 NEB B7203S CviQI NEB R0639L T4 DNA ligase (400U/ml) NEB M0202S 20mg/ml BSA NEB B9000S Proteinase K Thermo Fisher AM2546 Phenol:Chloroform:Isoamyl Alcohol (25:24:1, v/v,) Spectrum 136112-00-0 T4 DNA polymerase NEB M0203L NlaIII NEB R0125L SPRI beads Beckman B23319 DNA clean & concentrator kit Zymo D4013 Gel extraction using DNA recovery kit Zymo D4002 Roche Complete Protease Inhibitor Sigma 5056489001 PmeI NEB R0560L RNaseOUT Invitrogen 10777-019 Q5 High-Fidelity DNA Polymerase NEB m0491L FuGENE HD Transfection Reagent Promega E2311 Anza 13 Esp3I Invitrogen IVGN0136 Critical commercial assays iTaq Universal SYBR Green Supermix Bio-Rad 1725122 Dual-Luciferase Reporter Assay System Promega E1910 Deposited data HiCAR H1 This study GEO: GSE162819 HiCAR GM12878 This study GEO: GSE162819 HiCAR human muscle stem cells This study Under the Synapse ID: syn26841404 For published genomics datasets, see Table S3 Table S3 N/A Experimental models: Cell lines H1 hESC WiCell WA01; RRID: CVCL_9771 Human lymphoblastoid cell lines Coriell Institute GM12878; RRID: CVCL_7526 (Continued on next page) Molecular Cell 82, 1225–1238.e1–e6, March 17, 2022 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Oligonucleotides Custom primers for HiCAR, see Table S1 Table S1 N/A sgRNA Oligos, see Table S1 Table S1 N/A Recombinant DNA pTXB1-Tn5 Addgene RRID: Addgene_60240 Lentiguide-puro Addgene RRID: Addgene_52963 Lenti-dCas9-KRAB-blast Addgene RRID: Addgene_89567 Lenti dCAS-VP64_Blast Addgene RRID: Addgene_61425 pGL3-Promoter Promega E1761 pRL-SV40 Promega E2231 Software and algorithms BWA (Li and Durbin, 2010) http://bio-bwa.sourceforge.net/bwa.shtml; RRID:SCR_010910 Pairtools Python package https://github.com/mirnylab/pairtools HiGlass (Kerpedjiev et al., 2018) https://github.com/higlass EnrichedHeatmap (Gu et al., 2018) https://github.com/jokergoo/EnrichedHeatmap Cooltools Python package https://github.com/open2c/cooltools HiCRep (Yang et al., 2017) https://github.com/qunhualilab/hicrep Pairsqc (Lee et al., 2022) https://github.com/4dn-dcic/pairsqc MACS2 (Zhang et al., 2008) https://github.com/macs3-project/MACS; RRID:SCR_013291 Chip-R (Newell et al., 2021) https://github.com/rhysnewell/ChIP-R/ Gimme (van Heeringen and Veenstra, 2011) https://github.com/vanheeringen-lab/ gimmemotifs; RRID:SCR_001146 MAPS (Juric et al., 2019) https://github.com/ijuric/MAPS Juicer:HiCCUPS (Durand et al., 2016) https://github.com/aidenlab/juicer; RRID:SCR_017226 FitHiC2 (Kaul et al., 2020) https://github.com/ay-lab/fithic HiCAR nextflow pipeline (Ou et al., 2022) DOI: 10.5281/zenodo.5889172 Clusterprofile (Yu et al., 2012) https://bioconductor.org/packages/release/ bioc/html/clusterProfiler.html Other Detailed protocol for the preparation of HiCAR library In this study See supplemental information and Method S1

    Gel Extraction:

    Article Title: HiCAR is a robust and sensitive method to analyze open-chromatin-associated genome organization.
    Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-CD31-Alexa Fluor 488 BioLegend Cat# 303110; RRID: AB_493074 Anti-CD34-FITC BioLegend Cat# 343503; RRID: AB_1731923 Anti-CD29-APC BioLegend Cat# 303008; RRID: AB_314324 Anti-NCAM-Biotin BioLegend Cat# 318319; RRID: AB_893392 Biological samples Lower extremity human skeletal muscle samples (collected from a female, 67-year-old individual) Duke University Medical Center N/A Chemicals, peptides, and recombinant proteins Matrigel Corning 354230 mTeSR Plus STEMCELL Technologies 05825 Accutase BioLegend 423201 Chitin column Bio-Rad 7372522 Amicon Ultracel 30K Millipore UFC903024 Dialysis membrane tube Spectra/Por D1614-11 NEBuffer 3.1 NEB B7203S CviQI NEB R0639L T4 DNA ligase (400U/ml) NEB M0202S 20mg/ml BSA NEB B9000S Proteinase K Thermo Fisher AM2546 Phenol:Chloroform:Isoamyl Alcohol (25:24:1, v/v,) Spectrum 136112-00-0 T4 DNA polymerase NEB M0203L NlaIII NEB R0125L SPRI beads Beckman B23319 DNA clean & concentrator kit Zymo D4013 Gel extraction using DNA recovery kit Zymo D4002 Roche Complete Protease Inhibitor Sigma 5056489001 PmeI NEB R0560L RNaseOUT Invitrogen 10777-019 Q5 High-Fidelity DNA Polymerase NEB m0491L FuGENE HD Transfection Reagent Promega E2311 Anza 13 Esp3I Invitrogen IVGN0136 Critical commercial assays iTaq Universal SYBR Green Supermix Bio-Rad 1725122 Dual-Luciferase Reporter Assay System Promega E1910 Deposited data HiCAR H1 This study GEO: GSE162819 HiCAR GM12878 This study GEO: GSE162819 HiCAR human muscle stem cells This study Under the Synapse ID: syn26841404 For published genomics datasets, see Table S3 Table S3 N/A Experimental models: Cell lines H1 hESC WiCell WA01; RRID: CVCL_9771 Human lymphoblastoid cell lines Coriell Institute GM12878; RRID: CVCL_7526 (Continued on next page) Molecular Cell 82, 1225–1238.e1–e6, March 17, 2022 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Oligonucleotides Custom primers for HiCAR, see Table S1 Table S1 N/A sgRNA Oligos, see Table S1 Table S1 N/A Recombinant DNA pTXB1-Tn5 Addgene RRID: Addgene_60240 Lentiguide-puro Addgene RRID: Addgene_52963 Lenti-dCas9-KRAB-blast Addgene RRID: Addgene_89567 Lenti dCAS-VP64_Blast Addgene RRID: Addgene_61425 pGL3-Promoter Promega E1761 pRL-SV40 Promega E2231 Software and algorithms BWA (Li and Durbin, 2010) http://bio-bwa.sourceforge.net/bwa.shtml; RRID:SCR_010910 Pairtools Python package https://github.com/mirnylab/pairtools HiGlass (Kerpedjiev et al., 2018) https://github.com/higlass EnrichedHeatmap (Gu et al., 2018) https://github.com/jokergoo/EnrichedHeatmap Cooltools Python package https://github.com/open2c/cooltools HiCRep (Yang et al., 2017) https://github.com/qunhualilab/hicrep Pairsqc (Lee et al., 2022) https://github.com/4dn-dcic/pairsqc MACS2 (Zhang et al., 2008) https://github.com/macs3-project/MACS; RRID:SCR_013291 Chip-R (Newell et al., 2021) https://github.com/rhysnewell/ChIP-R/ Gimme (van Heeringen and Veenstra, 2011) https://github.com/vanheeringen-lab/ gimmemotifs; RRID:SCR_001146 MAPS (Juric et al., 2019) https://github.com/ijuric/MAPS Juicer:HiCCUPS (Durand et al., 2016) https://github.com/aidenlab/juicer; RRID:SCR_017226 FitHiC2 (Kaul et al., 2020) https://github.com/ay-lab/fithic HiCAR nextflow pipeline (Ou et al., 2022) DOI: 10.5281/zenodo.5889172 Clusterprofile (Yu et al., 2012) https://bioconductor.org/packages/release/ bioc/html/clusterProfiler.html Other Detailed protocol for the preparation of HiCAR library In this study See supplemental information and Method S1

    Protease Inhibitor:

    Article Title: HiCAR is a robust and sensitive method to analyze open-chromatin-associated genome organization.
    Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-CD31-Alexa Fluor 488 BioLegend Cat# 303110; RRID: AB_493074 Anti-CD34-FITC BioLegend Cat# 343503; RRID: AB_1731923 Anti-CD29-APC BioLegend Cat# 303008; RRID: AB_314324 Anti-NCAM-Biotin BioLegend Cat# 318319; RRID: AB_893392 Biological samples Lower extremity human skeletal muscle samples (collected from a female, 67-year-old individual) Duke University Medical Center N/A Chemicals, peptides, and recombinant proteins Matrigel Corning 354230 mTeSR Plus STEMCELL Technologies 05825 Accutase BioLegend 423201 Chitin column Bio-Rad 7372522 Amicon Ultracel 30K Millipore UFC903024 Dialysis membrane tube Spectra/Por D1614-11 NEBuffer 3.1 NEB B7203S CviQI NEB R0639L T4 DNA ligase (400U/ml) NEB M0202S 20mg/ml BSA NEB B9000S Proteinase K Thermo Fisher AM2546 Phenol:Chloroform:Isoamyl Alcohol (25:24:1, v/v,) Spectrum 136112-00-0 T4 DNA polymerase NEB M0203L NlaIII NEB R0125L SPRI beads Beckman B23319 DNA clean & concentrator kit Zymo D4013 Gel extraction using DNA recovery kit Zymo D4002 Roche Complete Protease Inhibitor Sigma 5056489001 PmeI NEB R0560L RNaseOUT Invitrogen 10777-019 Q5 High-Fidelity DNA Polymerase NEB m0491L FuGENE HD Transfection Reagent Promega E2311 Anza 13 Esp3I Invitrogen IVGN0136 Critical commercial assays iTaq Universal SYBR Green Supermix Bio-Rad 1725122 Dual-Luciferase Reporter Assay System Promega E1910 Deposited data HiCAR H1 This study GEO: GSE162819 HiCAR GM12878 This study GEO: GSE162819 HiCAR human muscle stem cells This study Under the Synapse ID: syn26841404 For published genomics datasets, see Table S3 Table S3 N/A Experimental models: Cell lines H1 hESC WiCell WA01; RRID: CVCL_9771 Human lymphoblastoid cell lines Coriell Institute GM12878; RRID: CVCL_7526 (Continued on next page) Molecular Cell 82, 1225–1238.e1–e6, March 17, 2022 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Oligonucleotides Custom primers for HiCAR, see Table S1 Table S1 N/A sgRNA Oligos, see Table S1 Table S1 N/A Recombinant DNA pTXB1-Tn5 Addgene RRID: Addgene_60240 Lentiguide-puro Addgene RRID: Addgene_52963 Lenti-dCas9-KRAB-blast Addgene RRID: Addgene_89567 Lenti dCAS-VP64_Blast Addgene RRID: Addgene_61425 pGL3-Promoter Promega E1761 pRL-SV40 Promega E2231 Software and algorithms BWA (Li and Durbin, 2010) http://bio-bwa.sourceforge.net/bwa.shtml; RRID:SCR_010910 Pairtools Python package https://github.com/mirnylab/pairtools HiGlass (Kerpedjiev et al., 2018) https://github.com/higlass EnrichedHeatmap (Gu et al., 2018) https://github.com/jokergoo/EnrichedHeatmap Cooltools Python package https://github.com/open2c/cooltools HiCRep (Yang et al., 2017) https://github.com/qunhualilab/hicrep Pairsqc (Lee et al., 2022) https://github.com/4dn-dcic/pairsqc MACS2 (Zhang et al., 2008) https://github.com/macs3-project/MACS; RRID:SCR_013291 Chip-R (Newell et al., 2021) https://github.com/rhysnewell/ChIP-R/ Gimme (van Heeringen and Veenstra, 2011) https://github.com/vanheeringen-lab/ gimmemotifs; RRID:SCR_001146 MAPS (Juric et al., 2019) https://github.com/ijuric/MAPS Juicer:HiCCUPS (Durand et al., 2016) https://github.com/aidenlab/juicer; RRID:SCR_017226 FitHiC2 (Kaul et al., 2020) https://github.com/ay-lab/fithic HiCAR nextflow pipeline (Ou et al., 2022) DOI: 10.5281/zenodo.5889172 Clusterprofile (Yu et al., 2012) https://bioconductor.org/packages/release/ bioc/html/clusterProfiler.html Other Detailed protocol for the preparation of HiCAR library In this study See supplemental information and Method S1

    Transfection:

    Article Title: HiCAR is a robust and sensitive method to analyze open-chromatin-associated genome organization.
    Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-CD31-Alexa Fluor 488 BioLegend Cat# 303110; RRID: AB_493074 Anti-CD34-FITC BioLegend Cat# 343503; RRID: AB_1731923 Anti-CD29-APC BioLegend Cat# 303008; RRID: AB_314324 Anti-NCAM-Biotin BioLegend Cat# 318319; RRID: AB_893392 Biological samples Lower extremity human skeletal muscle samples (collected from a female, 67-year-old individual) Duke University Medical Center N/A Chemicals, peptides, and recombinant proteins Matrigel Corning 354230 mTeSR Plus STEMCELL Technologies 05825 Accutase BioLegend 423201 Chitin column Bio-Rad 7372522 Amicon Ultracel 30K Millipore UFC903024 Dialysis membrane tube Spectra/Por D1614-11 NEBuffer 3.1 NEB B7203S CviQI NEB R0639L T4 DNA ligase (400U/ml) NEB M0202S 20mg/ml BSA NEB B9000S Proteinase K Thermo Fisher AM2546 Phenol:Chloroform:Isoamyl Alcohol (25:24:1, v/v,) Spectrum 136112-00-0 T4 DNA polymerase NEB M0203L NlaIII NEB R0125L SPRI beads Beckman B23319 DNA clean & concentrator kit Zymo D4013 Gel extraction using DNA recovery kit Zymo D4002 Roche Complete Protease Inhibitor Sigma 5056489001 PmeI NEB R0560L RNaseOUT Invitrogen 10777-019 Q5 High-Fidelity DNA Polymerase NEB m0491L FuGENE HD Transfection Reagent Promega E2311 Anza 13 Esp3I Invitrogen IVGN0136 Critical commercial assays iTaq Universal SYBR Green Supermix Bio-Rad 1725122 Dual-Luciferase Reporter Assay System Promega E1910 Deposited data HiCAR H1 This study GEO: GSE162819 HiCAR GM12878 This study GEO: GSE162819 HiCAR human muscle stem cells This study Under the Synapse ID: syn26841404 For published genomics datasets, see Table S3 Table S3 N/A Experimental models: Cell lines H1 hESC WiCell WA01; RRID: CVCL_9771 Human lymphoblastoid cell lines Coriell Institute GM12878; RRID: CVCL_7526 (Continued on next page) Molecular Cell 82, 1225–1238.e1–e6, March 17, 2022 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Oligonucleotides Custom primers for HiCAR, see Table S1 Table S1 N/A sgRNA Oligos, see Table S1 Table S1 N/A Recombinant DNA pTXB1-Tn5 Addgene RRID: Addgene_60240 Lentiguide-puro Addgene RRID: Addgene_52963 Lenti-dCas9-KRAB-blast Addgene RRID: Addgene_89567 Lenti dCAS-VP64_Blast Addgene RRID: Addgene_61425 pGL3-Promoter Promega E1761 pRL-SV40 Promega E2231 Software and algorithms BWA (Li and Durbin, 2010) http://bio-bwa.sourceforge.net/bwa.shtml; RRID:SCR_010910 Pairtools Python package https://github.com/mirnylab/pairtools HiGlass (Kerpedjiev et al., 2018) https://github.com/higlass EnrichedHeatmap (Gu et al., 2018) https://github.com/jokergoo/EnrichedHeatmap Cooltools Python package https://github.com/open2c/cooltools HiCRep (Yang et al., 2017) https://github.com/qunhualilab/hicrep Pairsqc (Lee et al., 2022) https://github.com/4dn-dcic/pairsqc MACS2 (Zhang et al., 2008) https://github.com/macs3-project/MACS; RRID:SCR_013291 Chip-R (Newell et al., 2021) https://github.com/rhysnewell/ChIP-R/ Gimme (van Heeringen and Veenstra, 2011) https://github.com/vanheeringen-lab/ gimmemotifs; RRID:SCR_001146 MAPS (Juric et al., 2019) https://github.com/ijuric/MAPS Juicer:HiCCUPS (Durand et al., 2016) https://github.com/aidenlab/juicer; RRID:SCR_017226 FitHiC2 (Kaul et al., 2020) https://github.com/ay-lab/fithic HiCAR nextflow pipeline (Ou et al., 2022) DOI: 10.5281/zenodo.5889172 Clusterprofile (Yu et al., 2012) https://bioconductor.org/packages/release/ bioc/html/clusterProfiler.html Other Detailed protocol for the preparation of HiCAR library In this study See supplemental information and Method S1

    SYBR Green Assay:

    Article Title: HiCAR is a robust and sensitive method to analyze open-chromatin-associated genome organization.
    Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-CD31-Alexa Fluor 488 BioLegend Cat# 303110; RRID: AB_493074 Anti-CD34-FITC BioLegend Cat# 343503; RRID: AB_1731923 Anti-CD29-APC BioLegend Cat# 303008; RRID: AB_314324 Anti-NCAM-Biotin BioLegend Cat# 318319; RRID: AB_893392 Biological samples Lower extremity human skeletal muscle samples (collected from a female, 67-year-old individual) Duke University Medical Center N/A Chemicals, peptides, and recombinant proteins Matrigel Corning 354230 mTeSR Plus STEMCELL Technologies 05825 Accutase BioLegend 423201 Chitin column Bio-Rad 7372522 Amicon Ultracel 30K Millipore UFC903024 Dialysis membrane tube Spectra/Por D1614-11 NEBuffer 3.1 NEB B7203S CviQI NEB R0639L T4 DNA ligase (400U/ml) NEB M0202S 20mg/ml BSA NEB B9000S Proteinase K Thermo Fisher AM2546 Phenol:Chloroform:Isoamyl Alcohol (25:24:1, v/v,) Spectrum 136112-00-0 T4 DNA polymerase NEB M0203L NlaIII NEB R0125L SPRI beads Beckman B23319 DNA clean & concentrator kit Zymo D4013 Gel extraction using DNA recovery kit Zymo D4002 Roche Complete Protease Inhibitor Sigma 5056489001 PmeI NEB R0560L RNaseOUT Invitrogen 10777-019 Q5 High-Fidelity DNA Polymerase NEB m0491L FuGENE HD Transfection Reagent Promega E2311 Anza 13 Esp3I Invitrogen IVGN0136 Critical commercial assays iTaq Universal SYBR Green Supermix Bio-Rad 1725122 Dual-Luciferase Reporter Assay System Promega E1910 Deposited data HiCAR H1 This study GEO: GSE162819 HiCAR GM12878 This study GEO: GSE162819 HiCAR human muscle stem cells This study Under the Synapse ID: syn26841404 For published genomics datasets, see Table S3 Table S3 N/A Experimental models: Cell lines H1 hESC WiCell WA01; RRID: CVCL_9771 Human lymphoblastoid cell lines Coriell Institute GM12878; RRID: CVCL_7526 (Continued on next page) Molecular Cell 82, 1225–1238.e1–e6, March 17, 2022 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Oligonucleotides Custom primers for HiCAR, see Table S1 Table S1 N/A sgRNA Oligos, see Table S1 Table S1 N/A Recombinant DNA pTXB1-Tn5 Addgene RRID: Addgene_60240 Lentiguide-puro Addgene RRID: Addgene_52963 Lenti-dCas9-KRAB-blast Addgene RRID: Addgene_89567 Lenti dCAS-VP64_Blast Addgene RRID: Addgene_61425 pGL3-Promoter Promega E1761 pRL-SV40 Promega E2231 Software and algorithms BWA (Li and Durbin, 2010) http://bio-bwa.sourceforge.net/bwa.shtml; RRID:SCR_010910 Pairtools Python package https://github.com/mirnylab/pairtools HiGlass (Kerpedjiev et al., 2018) https://github.com/higlass EnrichedHeatmap (Gu et al., 2018) https://github.com/jokergoo/EnrichedHeatmap Cooltools Python package https://github.com/open2c/cooltools HiCRep (Yang et al., 2017) https://github.com/qunhualilab/hicrep Pairsqc (Lee et al., 2022) https://github.com/4dn-dcic/pairsqc MACS2 (Zhang et al., 2008) https://github.com/macs3-project/MACS; RRID:SCR_013291 Chip-R (Newell et al., 2021) https://github.com/rhysnewell/ChIP-R/ Gimme (van Heeringen and Veenstra, 2011) https://github.com/vanheeringen-lab/ gimmemotifs; RRID:SCR_001146 MAPS (Juric et al., 2019) https://github.com/ijuric/MAPS Juicer:HiCCUPS (Durand et al., 2016) https://github.com/aidenlab/juicer; RRID:SCR_017226 FitHiC2 (Kaul et al., 2020) https://github.com/ay-lab/fithic HiCAR nextflow pipeline (Ou et al., 2022) DOI: 10.5281/zenodo.5889172 Clusterprofile (Yu et al., 2012) https://bioconductor.org/packages/release/ bioc/html/clusterProfiler.html Other Detailed protocol for the preparation of HiCAR library In this study See supplemental information and Method S1

    Reporter Assay:

    Article Title: HiCAR is a robust and sensitive method to analyze open-chromatin-associated genome organization.
    Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-CD31-Alexa Fluor 488 BioLegend Cat# 303110; RRID: AB_493074 Anti-CD34-FITC BioLegend Cat# 343503; RRID: AB_1731923 Anti-CD29-APC BioLegend Cat# 303008; RRID: AB_314324 Anti-NCAM-Biotin BioLegend Cat# 318319; RRID: AB_893392 Biological samples Lower extremity human skeletal muscle samples (collected from a female, 67-year-old individual) Duke University Medical Center N/A Chemicals, peptides, and recombinant proteins Matrigel Corning 354230 mTeSR Plus STEMCELL Technologies 05825 Accutase BioLegend 423201 Chitin column Bio-Rad 7372522 Amicon Ultracel 30K Millipore UFC903024 Dialysis membrane tube Spectra/Por D1614-11 NEBuffer 3.1 NEB B7203S CviQI NEB R0639L T4 DNA ligase (400U/ml) NEB M0202S 20mg/ml BSA NEB B9000S Proteinase K Thermo Fisher AM2546 Phenol:Chloroform:Isoamyl Alcohol (25:24:1, v/v,) Spectrum 136112-00-0 T4 DNA polymerase NEB M0203L NlaIII NEB R0125L SPRI beads Beckman B23319 DNA clean & concentrator kit Zymo D4013 Gel extraction using DNA recovery kit Zymo D4002 Roche Complete Protease Inhibitor Sigma 5056489001 PmeI NEB R0560L RNaseOUT Invitrogen 10777-019 Q5 High-Fidelity DNA Polymerase NEB m0491L FuGENE HD Transfection Reagent Promega E2311 Anza 13 Esp3I Invitrogen IVGN0136 Critical commercial assays iTaq Universal SYBR Green Supermix Bio-Rad 1725122 Dual-Luciferase Reporter Assay System Promega E1910 Deposited data HiCAR H1 This study GEO: GSE162819 HiCAR GM12878 This study GEO: GSE162819 HiCAR human muscle stem cells This study Under the Synapse ID: syn26841404 For published genomics datasets, see Table S3 Table S3 N/A Experimental models: Cell lines H1 hESC WiCell WA01; RRID: CVCL_9771 Human lymphoblastoid cell lines Coriell Institute GM12878; RRID: CVCL_7526 (Continued on next page) Molecular Cell 82, 1225–1238.e1–e6, March 17, 2022 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Oligonucleotides Custom primers for HiCAR, see Table S1 Table S1 N/A sgRNA Oligos, see Table S1 Table S1 N/A Recombinant DNA pTXB1-Tn5 Addgene RRID: Addgene_60240 Lentiguide-puro Addgene RRID: Addgene_52963 Lenti-dCas9-KRAB-blast Addgene RRID: Addgene_89567 Lenti dCAS-VP64_Blast Addgene RRID: Addgene_61425 pGL3-Promoter Promega E1761 pRL-SV40 Promega E2231 Software and algorithms BWA (Li and Durbin, 2010) http://bio-bwa.sourceforge.net/bwa.shtml; RRID:SCR_010910 Pairtools Python package https://github.com/mirnylab/pairtools HiGlass (Kerpedjiev et al., 2018) https://github.com/higlass EnrichedHeatmap (Gu et al., 2018) https://github.com/jokergoo/EnrichedHeatmap Cooltools Python package https://github.com/open2c/cooltools HiCRep (Yang et al., 2017) https://github.com/qunhualilab/hicrep Pairsqc (Lee et al., 2022) https://github.com/4dn-dcic/pairsqc MACS2 (Zhang et al., 2008) https://github.com/macs3-project/MACS; RRID:SCR_013291 Chip-R (Newell et al., 2021) https://github.com/rhysnewell/ChIP-R/ Gimme (van Heeringen and Veenstra, 2011) https://github.com/vanheeringen-lab/ gimmemotifs; RRID:SCR_001146 MAPS (Juric et al., 2019) https://github.com/ijuric/MAPS Juicer:HiCCUPS (Durand et al., 2016) https://github.com/aidenlab/juicer; RRID:SCR_017226 FitHiC2 (Kaul et al., 2020) https://github.com/ay-lab/fithic HiCAR nextflow pipeline (Ou et al., 2022) DOI: 10.5281/zenodo.5889172 Clusterprofile (Yu et al., 2012) https://bioconductor.org/packages/release/ bioc/html/clusterProfiler.html Other Detailed protocol for the preparation of HiCAR library In this study See supplemental information and Method S1



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