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    Addgene inc px330s 2 pitch addgene
    Px330s 2 Pitch Addgene, supplied by Addgene inc, used in various techniques. Bioz Stars score: 93/100, based on 38 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/px330s+2+addgene/pX330S-2-PITCh+(Plasmid+%2363670)/pm41344331-297-247-248
    Average 93 stars, based on 38 article reviews
    px330s 2 pitch addgene - by Bioz Stars, 2026-09
    93/100 stars

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    Related Articles

    Chromatin Immunoprecipitation:

    Article Title: Systematic dissection of sequence features affecting binding specificity of a pioneer factor reveals binding synergy between FOXA1 and AP-1.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-FOXA1, rabbit polyclonal GeneTex Cat#GTX100308; RRID: AB_1240823 Anti-Fra2, rabbit monoclonal Cell Signaling Technology Cat#19967S; RRID: AB_2722526 Anti-H3K9me3, rabbit polyclonal Abcam Cat#ab8898; RRID: AB_306848 Anti-H3K27me3, mouse monoclonal Abcam Cat#ab6002; RRID: AB_305237 Anti-FLAG, mouse monoclonal Millipore-Sigma Cat#F1804; RRID: AB_262044 Anti-FOSL1, mouse monoclonal Santa Cruz Biotechnology Cat#sc-28310; RRID: AB_627632 Goat anti-mouse IgG(H+L), Alexa Fluor 594 ThermoFisher Cat#A-11005; RRID: AB_2534073 Goat anti-rabbit IgG(H+L), Alexa Fluor 488 ThermoFisher Cat#A-11008; RRID: AB_143165 Bacterial and virus strains NEB 5-alpha competent E. coli NEB Cat#C2987 5-alpha electrocompetent E. coli NEB Cat#C2989 BL21(DE3)pLysS E. coli Novagen Cat#69388-3 Rosetta2(DE3)pLysS E. coli Novagen Cat#70951 Chemicals, peptides, and recombinant proteins Ham’s F-12K (Kaighn’s) Medium Gibco Cat#21127022 Dulbecco’s Modified Eagle Medium (DMEM) Gibco Cat#10569044 FBS Gibco Cat#16000044 Penicillin-Streptomycin Gibco Cat#15070063 NEBNext Ultra II Q5 master mix NEB Cat#M0544S T4 DNA ligase NEB Cat#M0202S AMPure XP beads Beckman Coulter Cat#MSPP-A63880 E.Z.N.A. cycle pure kit Omega Cat#D6492-02 E.Z.N.A. plasmid DNA maxi kit Omega Cat#D6922-02 Lipofectamine 3000 reagent ThermoFisher Cat#L3000015 37% formaldehyde Ricca Chemical Company Cat#RSOF0010250A Protease inhibitor cocktail Sigma-Aldrich Cat#P8340 Magna ChIP Protein A+G Magnetic Beads Sigma-Aldrich Cat#16-663 NEBNext ultra II DNA library prep kit NEB Cat#E7103L Illumina Stranded mRNA Prep kit Illumina Cat#20040532 Trizol ThermoFisher Cat#15596026 RNeasy kit Qiagen Cat#74104 Ni-NTA chromatography GoldBio Cat#H-350-25 Source S cation-exchange chromatography Cytiva Cat#17-0944-01 cobalt metal-affinity chromatography Clontech Cat#635652 7.5% non-denaturing polyacrylamide gel Bio-Rad Cat#4561026 Ethidium Bromide Invitrogen Cat#15585011 QIAGEN QIAquick Gel Extraction Kit QIAGEN Cat#28704 G418 Gibco Cat#10131035 Doxycycline Sigma-Aldrich Cat#D5207 Blasticidin S HCl Gibco Cat#A11139 Fluoromount-G Mounting Medium ThermoFisher Cat#00-4958-02 Mouse FOXA1 (UniProtKB: P35582) This study N/A (Continued on next page) e1 Molecular Cell 84, 2838–2855.e1–e10, August 8, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER Human c-Fos (UniprotKB: P01100) This study N/A Human c-Jun (UniprotKB: P05412) This study N/A Deposited data ChIP-ISO datasets This study (GEO) GEO: GSE247411 ChIP–seq datasets This study (GEO) GEO: GSE247412 RNA-seq datasets This study (GEO) GEO: GSE247414 EMSA-seq datasets This study (GEO) GEO: GSE247431 ENCODE datasets ENCODE (Table S2) N/A Other published datasets Other publications (Table S2) N/A Raw images (immunostaining) This paper; Mendeley Data Mendeley Data: https://data.mendeley.com/ datasets/x6z25n3z2z/1 Experimental models: Cell lines A549 Dr. Yanming Wang N/A HepG2 ATCC Cat#HB-8065 MCF-7 ATCC Cat#HTB-22 A549-HK1 This study (Table S3) N/A A549-HK2 This study (Table S3) N/A A549 ePB tet-on A-FOS This study (Table S3) N/A A549-CX1 This study (Table S3) N/A A549-CX2 This study (Table S3) N/A A549-CX3 This study (Table S3) N/A A549-CX4 This study (Table S3) N/A Oligonucleotides Synthetic oligo library Agilent Cat#G7220A Primers This study (Table S3) N/A gBlocks This study (Table S3) N/A Recombinant DNA pAAVS1-Nst-MCS Addgene Cat#80487 eSpCas9(1.1) Addgene Cat#71814 pXAT2 Addgene Cat#80494 CMV500 A-FOS Addgene Cat#33353 Xlone-GFP Addgene Cat#96930 pGEP179_pX330K Addgene Cat#137882 pX330S-2 Addgene Cat1000000055 pGEP163 Addgene Cat#137881 pT077 Addgene Cat#137879 AAVS1 TALEN L Addgene Cat#59025 AAVS1 TALEN R Addgene Cat#59026 Super piggyBac transposase plasmid System Biosciences Cat#PB210PA-1 pCX1.4 This study (Table S3) N/A pCX1.5 This study (Table S3) N/A pCX1.16 This study (Table S3) N/A pCX1.17 This study (Table S3) N/A pCX1.10 This study (Table S3) N/A pCX3.10 This study (Table S3) N/A pCX4.1 This study (Table S3) N/A pGEP163_CCND1_U2_D4 This study (Table S3) N/A (Continued on next page) Molecular Cell 84, 2838–2855.e1–e10, August 8, 2024 e2 .. REAGENT or RESOURCE SOURCE IDENTIFIER Software and algorithms OligoDesign3 Chen et al.65 N/A FIMO (Version 5.5.4) MEME N/A Intersect intervals (Version 2.30.0) BEDTools N/A AME (Version 5.5.4) MEME N/A getfasta (Version 2.30.0) BEDTools N/A fastp (Version 0.23.2) Chen et al.66 N/A cutadapt (Version 4.4) Martin67 N/A NGmerge (Version 0.1) Gaspar68 N/A BWA-MEM2 (Version 2.2.1) Vasimuddin et al.69 N/A BAMtools (Version 2.4.0) Barnett et al.70 N/A SAMtools (Version 1.8) Li et al.71 N/A bamCoverage (Version 3.5.1) deepTools2 N/A MACS2 callpeak (Version 2.1.1.20160309) Zhang et al.72 N/A computeMatrix (Version 3.5.4) deepTools2 N/A plotHeatmap (Version 3.5.4) deepTools2 N/A plotProfile (Version 3.5.4) deepTools2 N/A DiffBind (Version 3.18) Ross-Innes et al.73 N/A T-Gene (Version 5.5.4) MEME N/A Metascape (Version 3.5.20230501) Zhou et al.74 N/A edgeR (Version 3.34.0) Robinson et al.75 N/A SHAP Lundberg and Lee40 N/A Tomtom (Version 5.5.4) MEME N/A DNAShapeR Chiu et al.76 N/A Zeiss Bio Apps Gene Expression tool Zeiss N/A

    RNA Sequencing:

    Article Title: Systematic dissection of sequence features affecting binding specificity of a pioneer factor reveals binding synergy between FOXA1 and AP-1.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-FOXA1, rabbit polyclonal GeneTex Cat#GTX100308; RRID: AB_1240823 Anti-Fra2, rabbit monoclonal Cell Signaling Technology Cat#19967S; RRID: AB_2722526 Anti-H3K9me3, rabbit polyclonal Abcam Cat#ab8898; RRID: AB_306848 Anti-H3K27me3, mouse monoclonal Abcam Cat#ab6002; RRID: AB_305237 Anti-FLAG, mouse monoclonal Millipore-Sigma Cat#F1804; RRID: AB_262044 Anti-FOSL1, mouse monoclonal Santa Cruz Biotechnology Cat#sc-28310; RRID: AB_627632 Goat anti-mouse IgG(H+L), Alexa Fluor 594 ThermoFisher Cat#A-11005; RRID: AB_2534073 Goat anti-rabbit IgG(H+L), Alexa Fluor 488 ThermoFisher Cat#A-11008; RRID: AB_143165 Bacterial and virus strains NEB 5-alpha competent E. coli NEB Cat#C2987 5-alpha electrocompetent E. coli NEB Cat#C2989 BL21(DE3)pLysS E. coli Novagen Cat#69388-3 Rosetta2(DE3)pLysS E. coli Novagen Cat#70951 Chemicals, peptides, and recombinant proteins Ham’s F-12K (Kaighn’s) Medium Gibco Cat#21127022 Dulbecco’s Modified Eagle Medium (DMEM) Gibco Cat#10569044 FBS Gibco Cat#16000044 Penicillin-Streptomycin Gibco Cat#15070063 NEBNext Ultra II Q5 master mix NEB Cat#M0544S T4 DNA ligase NEB Cat#M0202S AMPure XP beads Beckman Coulter Cat#MSPP-A63880 E.Z.N.A. cycle pure kit Omega Cat#D6492-02 E.Z.N.A. plasmid DNA maxi kit Omega Cat#D6922-02 Lipofectamine 3000 reagent ThermoFisher Cat#L3000015 37% formaldehyde Ricca Chemical Company Cat#RSOF0010250A Protease inhibitor cocktail Sigma-Aldrich Cat#P8340 Magna ChIP Protein A+G Magnetic Beads Sigma-Aldrich Cat#16-663 NEBNext ultra II DNA library prep kit NEB Cat#E7103L Illumina Stranded mRNA Prep kit Illumina Cat#20040532 Trizol ThermoFisher Cat#15596026 RNeasy kit Qiagen Cat#74104 Ni-NTA chromatography GoldBio Cat#H-350-25 Source S cation-exchange chromatography Cytiva Cat#17-0944-01 cobalt metal-affinity chromatography Clontech Cat#635652 7.5% non-denaturing polyacrylamide gel Bio-Rad Cat#4561026 Ethidium Bromide Invitrogen Cat#15585011 QIAGEN QIAquick Gel Extraction Kit QIAGEN Cat#28704 G418 Gibco Cat#10131035 Doxycycline Sigma-Aldrich Cat#D5207 Blasticidin S HCl Gibco Cat#A11139 Fluoromount-G Mounting Medium ThermoFisher Cat#00-4958-02 Mouse FOXA1 (UniProtKB: P35582) This study N/A (Continued on next page) e1 Molecular Cell 84, 2838–2855.e1–e10, August 8, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER Human c-Fos (UniprotKB: P01100) This study N/A Human c-Jun (UniprotKB: P05412) This study N/A Deposited data ChIP-ISO datasets This study (GEO) GEO: GSE247411 ChIP–seq datasets This study (GEO) GEO: GSE247412 RNA-seq datasets This study (GEO) GEO: GSE247414 EMSA-seq datasets This study (GEO) GEO: GSE247431 ENCODE datasets ENCODE (Table S2) N/A Other published datasets Other publications (Table S2) N/A Raw images (immunostaining) This paper; Mendeley Data Mendeley Data: https://data.mendeley.com/ datasets/x6z25n3z2z/1 Experimental models: Cell lines A549 Dr. Yanming Wang N/A HepG2 ATCC Cat#HB-8065 MCF-7 ATCC Cat#HTB-22 A549-HK1 This study (Table S3) N/A A549-HK2 This study (Table S3) N/A A549 ePB tet-on A-FOS This study (Table S3) N/A A549-CX1 This study (Table S3) N/A A549-CX2 This study (Table S3) N/A A549-CX3 This study (Table S3) N/A A549-CX4 This study (Table S3) N/A Oligonucleotides Synthetic oligo library Agilent Cat#G7220A Primers This study (Table S3) N/A gBlocks This study (Table S3) N/A Recombinant DNA pAAVS1-Nst-MCS Addgene Cat#80487 eSpCas9(1.1) Addgene Cat#71814 pXAT2 Addgene Cat#80494 CMV500 A-FOS Addgene Cat#33353 Xlone-GFP Addgene Cat#96930 pGEP179_pX330K Addgene Cat#137882 pX330S-2 Addgene Cat1000000055 pGEP163 Addgene Cat#137881 pT077 Addgene Cat#137879 AAVS1 TALEN L Addgene Cat#59025 AAVS1 TALEN R Addgene Cat#59026 Super piggyBac transposase plasmid System Biosciences Cat#PB210PA-1 pCX1.4 This study (Table S3) N/A pCX1.5 This study (Table S3) N/A pCX1.16 This study (Table S3) N/A pCX1.17 This study (Table S3) N/A pCX1.10 This study (Table S3) N/A pCX3.10 This study (Table S3) N/A pCX4.1 This study (Table S3) N/A pGEP163_CCND1_U2_D4 This study (Table S3) N/A (Continued on next page) Molecular Cell 84, 2838–2855.e1–e10, August 8, 2024 e2 .. REAGENT or RESOURCE SOURCE IDENTIFIER Software and algorithms OligoDesign3 Chen et al.65 N/A FIMO (Version 5.5.4) MEME N/A Intersect intervals (Version 2.30.0) BEDTools N/A AME (Version 5.5.4) MEME N/A getfasta (Version 2.30.0) BEDTools N/A fastp (Version 0.23.2) Chen et al.66 N/A cutadapt (Version 4.4) Martin67 N/A NGmerge (Version 0.1) Gaspar68 N/A BWA-MEM2 (Version 2.2.1) Vasimuddin et al.69 N/A BAMtools (Version 2.4.0) Barnett et al.70 N/A SAMtools (Version 1.8) Li et al.71 N/A bamCoverage (Version 3.5.1) deepTools2 N/A MACS2 callpeak (Version 2.1.1.20160309) Zhang et al.72 N/A computeMatrix (Version 3.5.4) deepTools2 N/A plotHeatmap (Version 3.5.4) deepTools2 N/A plotProfile (Version 3.5.4) deepTools2 N/A DiffBind (Version 3.18) Ross-Innes et al.73 N/A T-Gene (Version 5.5.4) MEME N/A Metascape (Version 3.5.20230501) Zhou et al.74 N/A edgeR (Version 3.34.0) Robinson et al.75 N/A SHAP Lundberg and Lee40 N/A Tomtom (Version 5.5.4) MEME N/A DNAShapeR Chiu et al.76 N/A Zeiss Bio Apps Gene Expression tool Zeiss N/A

    Immunostaining:

    Article Title: Systematic dissection of sequence features affecting binding specificity of a pioneer factor reveals binding synergy between FOXA1 and AP-1.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-FOXA1, rabbit polyclonal GeneTex Cat#GTX100308; RRID: AB_1240823 Anti-Fra2, rabbit monoclonal Cell Signaling Technology Cat#19967S; RRID: AB_2722526 Anti-H3K9me3, rabbit polyclonal Abcam Cat#ab8898; RRID: AB_306848 Anti-H3K27me3, mouse monoclonal Abcam Cat#ab6002; RRID: AB_305237 Anti-FLAG, mouse monoclonal Millipore-Sigma Cat#F1804; RRID: AB_262044 Anti-FOSL1, mouse monoclonal Santa Cruz Biotechnology Cat#sc-28310; RRID: AB_627632 Goat anti-mouse IgG(H+L), Alexa Fluor 594 ThermoFisher Cat#A-11005; RRID: AB_2534073 Goat anti-rabbit IgG(H+L), Alexa Fluor 488 ThermoFisher Cat#A-11008; RRID: AB_143165 Bacterial and virus strains NEB 5-alpha competent E. coli NEB Cat#C2987 5-alpha electrocompetent E. coli NEB Cat#C2989 BL21(DE3)pLysS E. coli Novagen Cat#69388-3 Rosetta2(DE3)pLysS E. coli Novagen Cat#70951 Chemicals, peptides, and recombinant proteins Ham’s F-12K (Kaighn’s) Medium Gibco Cat#21127022 Dulbecco’s Modified Eagle Medium (DMEM) Gibco Cat#10569044 FBS Gibco Cat#16000044 Penicillin-Streptomycin Gibco Cat#15070063 NEBNext Ultra II Q5 master mix NEB Cat#M0544S T4 DNA ligase NEB Cat#M0202S AMPure XP beads Beckman Coulter Cat#MSPP-A63880 E.Z.N.A. cycle pure kit Omega Cat#D6492-02 E.Z.N.A. plasmid DNA maxi kit Omega Cat#D6922-02 Lipofectamine 3000 reagent ThermoFisher Cat#L3000015 37% formaldehyde Ricca Chemical Company Cat#RSOF0010250A Protease inhibitor cocktail Sigma-Aldrich Cat#P8340 Magna ChIP Protein A+G Magnetic Beads Sigma-Aldrich Cat#16-663 NEBNext ultra II DNA library prep kit NEB Cat#E7103L Illumina Stranded mRNA Prep kit Illumina Cat#20040532 Trizol ThermoFisher Cat#15596026 RNeasy kit Qiagen Cat#74104 Ni-NTA chromatography GoldBio Cat#H-350-25 Source S cation-exchange chromatography Cytiva Cat#17-0944-01 cobalt metal-affinity chromatography Clontech Cat#635652 7.5% non-denaturing polyacrylamide gel Bio-Rad Cat#4561026 Ethidium Bromide Invitrogen Cat#15585011 QIAGEN QIAquick Gel Extraction Kit QIAGEN Cat#28704 G418 Gibco Cat#10131035 Doxycycline Sigma-Aldrich Cat#D5207 Blasticidin S HCl Gibco Cat#A11139 Fluoromount-G Mounting Medium ThermoFisher Cat#00-4958-02 Mouse FOXA1 (UniProtKB: P35582) This study N/A (Continued on next page) e1 Molecular Cell 84, 2838–2855.e1–e10, August 8, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER Human c-Fos (UniprotKB: P01100) This study N/A Human c-Jun (UniprotKB: P05412) This study N/A Deposited data ChIP-ISO datasets This study (GEO) GEO: GSE247411 ChIP–seq datasets This study (GEO) GEO: GSE247412 RNA-seq datasets This study (GEO) GEO: GSE247414 EMSA-seq datasets This study (GEO) GEO: GSE247431 ENCODE datasets ENCODE (Table S2) N/A Other published datasets Other publications (Table S2) N/A Raw images (immunostaining) This paper; Mendeley Data Mendeley Data: https://data.mendeley.com/ datasets/x6z25n3z2z/1 Experimental models: Cell lines A549 Dr. Yanming Wang N/A HepG2 ATCC Cat#HB-8065 MCF-7 ATCC Cat#HTB-22 A549-HK1 This study (Table S3) N/A A549-HK2 This study (Table S3) N/A A549 ePB tet-on A-FOS This study (Table S3) N/A A549-CX1 This study (Table S3) N/A A549-CX2 This study (Table S3) N/A A549-CX3 This study (Table S3) N/A A549-CX4 This study (Table S3) N/A Oligonucleotides Synthetic oligo library Agilent Cat#G7220A Primers This study (Table S3) N/A gBlocks This study (Table S3) N/A Recombinant DNA pAAVS1-Nst-MCS Addgene Cat#80487 eSpCas9(1.1) Addgene Cat#71814 pXAT2 Addgene Cat#80494 CMV500 A-FOS Addgene Cat#33353 Xlone-GFP Addgene Cat#96930 pGEP179_pX330K Addgene Cat#137882 pX330S-2 Addgene Cat1000000055 pGEP163 Addgene Cat#137881 pT077 Addgene Cat#137879 AAVS1 TALEN L Addgene Cat#59025 AAVS1 TALEN R Addgene Cat#59026 Super piggyBac transposase plasmid System Biosciences Cat#PB210PA-1 pCX1.4 This study (Table S3) N/A pCX1.5 This study (Table S3) N/A pCX1.16 This study (Table S3) N/A pCX1.17 This study (Table S3) N/A pCX1.10 This study (Table S3) N/A pCX3.10 This study (Table S3) N/A pCX4.1 This study (Table S3) N/A pGEP163_CCND1_U2_D4 This study (Table S3) N/A (Continued on next page) Molecular Cell 84, 2838–2855.e1–e10, August 8, 2024 e2 .. REAGENT or RESOURCE SOURCE IDENTIFIER Software and algorithms OligoDesign3 Chen et al.65 N/A FIMO (Version 5.5.4) MEME N/A Intersect intervals (Version 2.30.0) BEDTools N/A AME (Version 5.5.4) MEME N/A getfasta (Version 2.30.0) BEDTools N/A fastp (Version 0.23.2) Chen et al.66 N/A cutadapt (Version 4.4) Martin67 N/A NGmerge (Version 0.1) Gaspar68 N/A BWA-MEM2 (Version 2.2.1) Vasimuddin et al.69 N/A BAMtools (Version 2.4.0) Barnett et al.70 N/A SAMtools (Version 1.8) Li et al.71 N/A bamCoverage (Version 3.5.1) deepTools2 N/A MACS2 callpeak (Version 2.1.1.20160309) Zhang et al.72 N/A computeMatrix (Version 3.5.4) deepTools2 N/A plotHeatmap (Version 3.5.4) deepTools2 N/A plotProfile (Version 3.5.4) deepTools2 N/A DiffBind (Version 3.18) Ross-Innes et al.73 N/A T-Gene (Version 5.5.4) MEME N/A Metascape (Version 3.5.20230501) Zhou et al.74 N/A edgeR (Version 3.34.0) Robinson et al.75 N/A SHAP Lundberg and Lee40 N/A Tomtom (Version 5.5.4) MEME N/A DNAShapeR Chiu et al.76 N/A Zeiss Bio Apps Gene Expression tool Zeiss N/A

    Recombinant:

    Article Title: Systematic dissection of sequence features affecting binding specificity of a pioneer factor reveals binding synergy between FOXA1 and AP-1.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-FOXA1, rabbit polyclonal GeneTex Cat#GTX100308; RRID: AB_1240823 Anti-Fra2, rabbit monoclonal Cell Signaling Technology Cat#19967S; RRID: AB_2722526 Anti-H3K9me3, rabbit polyclonal Abcam Cat#ab8898; RRID: AB_306848 Anti-H3K27me3, mouse monoclonal Abcam Cat#ab6002; RRID: AB_305237 Anti-FLAG, mouse monoclonal Millipore-Sigma Cat#F1804; RRID: AB_262044 Anti-FOSL1, mouse monoclonal Santa Cruz Biotechnology Cat#sc-28310; RRID: AB_627632 Goat anti-mouse IgG(H+L), Alexa Fluor 594 ThermoFisher Cat#A-11005; RRID: AB_2534073 Goat anti-rabbit IgG(H+L), Alexa Fluor 488 ThermoFisher Cat#A-11008; RRID: AB_143165 Bacterial and virus strains NEB 5-alpha competent E. coli NEB Cat#C2987 5-alpha electrocompetent E. coli NEB Cat#C2989 BL21(DE3)pLysS E. coli Novagen Cat#69388-3 Rosetta2(DE3)pLysS E. coli Novagen Cat#70951 Chemicals, peptides, and recombinant proteins Ham’s F-12K (Kaighn’s) Medium Gibco Cat#21127022 Dulbecco’s Modified Eagle Medium (DMEM) Gibco Cat#10569044 FBS Gibco Cat#16000044 Penicillin-Streptomycin Gibco Cat#15070063 NEBNext Ultra II Q5 master mix NEB Cat#M0544S T4 DNA ligase NEB Cat#M0202S AMPure XP beads Beckman Coulter Cat#MSPP-A63880 E.Z.N.A. cycle pure kit Omega Cat#D6492-02 E.Z.N.A. plasmid DNA maxi kit Omega Cat#D6922-02 Lipofectamine 3000 reagent ThermoFisher Cat#L3000015 37% formaldehyde Ricca Chemical Company Cat#RSOF0010250A Protease inhibitor cocktail Sigma-Aldrich Cat#P8340 Magna ChIP Protein A+G Magnetic Beads Sigma-Aldrich Cat#16-663 NEBNext ultra II DNA library prep kit NEB Cat#E7103L Illumina Stranded mRNA Prep kit Illumina Cat#20040532 Trizol ThermoFisher Cat#15596026 RNeasy kit Qiagen Cat#74104 Ni-NTA chromatography GoldBio Cat#H-350-25 Source S cation-exchange chromatography Cytiva Cat#17-0944-01 cobalt metal-affinity chromatography Clontech Cat#635652 7.5% non-denaturing polyacrylamide gel Bio-Rad Cat#4561026 Ethidium Bromide Invitrogen Cat#15585011 QIAGEN QIAquick Gel Extraction Kit QIAGEN Cat#28704 G418 Gibco Cat#10131035 Doxycycline Sigma-Aldrich Cat#D5207 Blasticidin S HCl Gibco Cat#A11139 Fluoromount-G Mounting Medium ThermoFisher Cat#00-4958-02 Mouse FOXA1 (UniProtKB: P35582) This study N/A (Continued on next page) e1 Molecular Cell 84, 2838–2855.e1–e10, August 8, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER Human c-Fos (UniprotKB: P01100) This study N/A Human c-Jun (UniprotKB: P05412) This study N/A Deposited data ChIP-ISO datasets This study (GEO) GEO: GSE247411 ChIP–seq datasets This study (GEO) GEO: GSE247412 RNA-seq datasets This study (GEO) GEO: GSE247414 EMSA-seq datasets This study (GEO) GEO: GSE247431 ENCODE datasets ENCODE (Table S2) N/A Other published datasets Other publications (Table S2) N/A Raw images (immunostaining) This paper; Mendeley Data Mendeley Data: https://data.mendeley.com/ datasets/x6z25n3z2z/1 Experimental models: Cell lines A549 Dr. Yanming Wang N/A HepG2 ATCC Cat#HB-8065 MCF-7 ATCC Cat#HTB-22 A549-HK1 This study (Table S3) N/A A549-HK2 This study (Table S3) N/A A549 ePB tet-on A-FOS This study (Table S3) N/A A549-CX1 This study (Table S3) N/A A549-CX2 This study (Table S3) N/A A549-CX3 This study (Table S3) N/A A549-CX4 This study (Table S3) N/A Oligonucleotides Synthetic oligo library Agilent Cat#G7220A Primers This study (Table S3) N/A gBlocks This study (Table S3) N/A Recombinant DNA pAAVS1-Nst-MCS Addgene Cat#80487 eSpCas9(1.1) Addgene Cat#71814 pXAT2 Addgene Cat#80494 CMV500 A-FOS Addgene Cat#33353 Xlone-GFP Addgene Cat#96930 pGEP179_pX330K Addgene Cat#137882 pX330S-2 Addgene Cat1000000055 pGEP163 Addgene Cat#137881 pT077 Addgene Cat#137879 AAVS1 TALEN L Addgene Cat#59025 AAVS1 TALEN R Addgene Cat#59026 Super piggyBac transposase plasmid System Biosciences Cat#PB210PA-1 pCX1.4 This study (Table S3) N/A pCX1.5 This study (Table S3) N/A pCX1.16 This study (Table S3) N/A pCX1.17 This study (Table S3) N/A pCX1.10 This study (Table S3) N/A pCX3.10 This study (Table S3) N/A pCX4.1 This study (Table S3) N/A pGEP163_CCND1_U2_D4 This study (Table S3) N/A (Continued on next page) Molecular Cell 84, 2838–2855.e1–e10, August 8, 2024 e2 .. REAGENT or RESOURCE SOURCE IDENTIFIER Software and algorithms OligoDesign3 Chen et al.65 N/A FIMO (Version 5.5.4) MEME N/A Intersect intervals (Version 2.30.0) BEDTools N/A AME (Version 5.5.4) MEME N/A getfasta (Version 2.30.0) BEDTools N/A fastp (Version 0.23.2) Chen et al.66 N/A cutadapt (Version 4.4) Martin67 N/A NGmerge (Version 0.1) Gaspar68 N/A BWA-MEM2 (Version 2.2.1) Vasimuddin et al.69 N/A BAMtools (Version 2.4.0) Barnett et al.70 N/A SAMtools (Version 1.8) Li et al.71 N/A bamCoverage (Version 3.5.1) deepTools2 N/A MACS2 callpeak (Version 2.1.1.20160309) Zhang et al.72 N/A computeMatrix (Version 3.5.4) deepTools2 N/A plotHeatmap (Version 3.5.4) deepTools2 N/A plotProfile (Version 3.5.4) deepTools2 N/A DiffBind (Version 3.18) Ross-Innes et al.73 N/A T-Gene (Version 5.5.4) MEME N/A Metascape (Version 3.5.20230501) Zhou et al.74 N/A edgeR (Version 3.34.0) Robinson et al.75 N/A SHAP Lundberg and Lee40 N/A Tomtom (Version 5.5.4) MEME N/A DNAShapeR Chiu et al.76 N/A Zeiss Bio Apps Gene Expression tool Zeiss N/A

    Plasmid Preparation:

    Article Title: Systematic dissection of sequence features affecting binding specificity of a pioneer factor reveals binding synergy between FOXA1 and AP-1.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-FOXA1, rabbit polyclonal GeneTex Cat#GTX100308; RRID: AB_1240823 Anti-Fra2, rabbit monoclonal Cell Signaling Technology Cat#19967S; RRID: AB_2722526 Anti-H3K9me3, rabbit polyclonal Abcam Cat#ab8898; RRID: AB_306848 Anti-H3K27me3, mouse monoclonal Abcam Cat#ab6002; RRID: AB_305237 Anti-FLAG, mouse monoclonal Millipore-Sigma Cat#F1804; RRID: AB_262044 Anti-FOSL1, mouse monoclonal Santa Cruz Biotechnology Cat#sc-28310; RRID: AB_627632 Goat anti-mouse IgG(H+L), Alexa Fluor 594 ThermoFisher Cat#A-11005; RRID: AB_2534073 Goat anti-rabbit IgG(H+L), Alexa Fluor 488 ThermoFisher Cat#A-11008; RRID: AB_143165 Bacterial and virus strains NEB 5-alpha competent E. coli NEB Cat#C2987 5-alpha electrocompetent E. coli NEB Cat#C2989 BL21(DE3)pLysS E. coli Novagen Cat#69388-3 Rosetta2(DE3)pLysS E. coli Novagen Cat#70951 Chemicals, peptides, and recombinant proteins Ham’s F-12K (Kaighn’s) Medium Gibco Cat#21127022 Dulbecco’s Modified Eagle Medium (DMEM) Gibco Cat#10569044 FBS Gibco Cat#16000044 Penicillin-Streptomycin Gibco Cat#15070063 NEBNext Ultra II Q5 master mix NEB Cat#M0544S T4 DNA ligase NEB Cat#M0202S AMPure XP beads Beckman Coulter Cat#MSPP-A63880 E.Z.N.A. cycle pure kit Omega Cat#D6492-02 E.Z.N.A. plasmid DNA maxi kit Omega Cat#D6922-02 Lipofectamine 3000 reagent ThermoFisher Cat#L3000015 37% formaldehyde Ricca Chemical Company Cat#RSOF0010250A Protease inhibitor cocktail Sigma-Aldrich Cat#P8340 Magna ChIP Protein A+G Magnetic Beads Sigma-Aldrich Cat#16-663 NEBNext ultra II DNA library prep kit NEB Cat#E7103L Illumina Stranded mRNA Prep kit Illumina Cat#20040532 Trizol ThermoFisher Cat#15596026 RNeasy kit Qiagen Cat#74104 Ni-NTA chromatography GoldBio Cat#H-350-25 Source S cation-exchange chromatography Cytiva Cat#17-0944-01 cobalt metal-affinity chromatography Clontech Cat#635652 7.5% non-denaturing polyacrylamide gel Bio-Rad Cat#4561026 Ethidium Bromide Invitrogen Cat#15585011 QIAGEN QIAquick Gel Extraction Kit QIAGEN Cat#28704 G418 Gibco Cat#10131035 Doxycycline Sigma-Aldrich Cat#D5207 Blasticidin S HCl Gibco Cat#A11139 Fluoromount-G Mounting Medium ThermoFisher Cat#00-4958-02 Mouse FOXA1 (UniProtKB: P35582) This study N/A (Continued on next page) e1 Molecular Cell 84, 2838–2855.e1–e10, August 8, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER Human c-Fos (UniprotKB: P01100) This study N/A Human c-Jun (UniprotKB: P05412) This study N/A Deposited data ChIP-ISO datasets This study (GEO) GEO: GSE247411 ChIP–seq datasets This study (GEO) GEO: GSE247412 RNA-seq datasets This study (GEO) GEO: GSE247414 EMSA-seq datasets This study (GEO) GEO: GSE247431 ENCODE datasets ENCODE (Table S2) N/A Other published datasets Other publications (Table S2) N/A Raw images (immunostaining) This paper; Mendeley Data Mendeley Data: https://data.mendeley.com/ datasets/x6z25n3z2z/1 Experimental models: Cell lines A549 Dr. Yanming Wang N/A HepG2 ATCC Cat#HB-8065 MCF-7 ATCC Cat#HTB-22 A549-HK1 This study (Table S3) N/A A549-HK2 This study (Table S3) N/A A549 ePB tet-on A-FOS This study (Table S3) N/A A549-CX1 This study (Table S3) N/A A549-CX2 This study (Table S3) N/A A549-CX3 This study (Table S3) N/A A549-CX4 This study (Table S3) N/A Oligonucleotides Synthetic oligo library Agilent Cat#G7220A Primers This study (Table S3) N/A gBlocks This study (Table S3) N/A Recombinant DNA pAAVS1-Nst-MCS Addgene Cat#80487 eSpCas9(1.1) Addgene Cat#71814 pXAT2 Addgene Cat#80494 CMV500 A-FOS Addgene Cat#33353 Xlone-GFP Addgene Cat#96930 pGEP179_pX330K Addgene Cat#137882 pX330S-2 Addgene Cat1000000055 pGEP163 Addgene Cat#137881 pT077 Addgene Cat#137879 AAVS1 TALEN L Addgene Cat#59025 AAVS1 TALEN R Addgene Cat#59026 Super piggyBac transposase plasmid System Biosciences Cat#PB210PA-1 pCX1.4 This study (Table S3) N/A pCX1.5 This study (Table S3) N/A pCX1.16 This study (Table S3) N/A pCX1.17 This study (Table S3) N/A pCX1.10 This study (Table S3) N/A pCX3.10 This study (Table S3) N/A pCX4.1 This study (Table S3) N/A pGEP163_CCND1_U2_D4 This study (Table S3) N/A (Continued on next page) Molecular Cell 84, 2838–2855.e1–e10, August 8, 2024 e2 .. REAGENT or RESOURCE SOURCE IDENTIFIER Software and algorithms OligoDesign3 Chen et al.65 N/A FIMO (Version 5.5.4) MEME N/A Intersect intervals (Version 2.30.0) BEDTools N/A AME (Version 5.5.4) MEME N/A getfasta (Version 2.30.0) BEDTools N/A fastp (Version 0.23.2) Chen et al.66 N/A cutadapt (Version 4.4) Martin67 N/A NGmerge (Version 0.1) Gaspar68 N/A BWA-MEM2 (Version 2.2.1) Vasimuddin et al.69 N/A BAMtools (Version 2.4.0) Barnett et al.70 N/A SAMtools (Version 1.8) Li et al.71 N/A bamCoverage (Version 3.5.1) deepTools2 N/A MACS2 callpeak (Version 2.1.1.20160309) Zhang et al.72 N/A computeMatrix (Version 3.5.4) deepTools2 N/A plotHeatmap (Version 3.5.4) deepTools2 N/A plotProfile (Version 3.5.4) deepTools2 N/A DiffBind (Version 3.18) Ross-Innes et al.73 N/A T-Gene (Version 5.5.4) MEME N/A Metascape (Version 3.5.20230501) Zhou et al.74 N/A edgeR (Version 3.34.0) Robinson et al.75 N/A SHAP Lundberg and Lee40 N/A Tomtom (Version 5.5.4) MEME N/A DNAShapeR Chiu et al.76 N/A Zeiss Bio Apps Gene Expression tool Zeiss N/A



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