shRNA:Article Title: G9a Promotes Breast Cancer Recurrence through Repression of a Pro-inflammatory Program
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Human HCC202 Duke Cell Culture Facility RRID:CVCL_2062 Human MDA-MB-134 Duke Cell Culture Facility RRID:CVCL_0617 Human HCC1395 Duke Cell Culture Facility RRID:CVCL_1249 Human MDA-MB-361 Duke Cell Culture Facility RRID:CVCL_0620 Human HCC38 Duke Cell Culture Facility RRID:CVCL_1267 Human BT-483 Duke Cell Culture Facility RRID:CVCL_2319 Human HCC1954 Duke Cell Culture Facility RRID:CVCL_1259 Human MDA-MB-436 Duke Cell Culture Facility RRID:CVCL_0623 Human BT-549 Duke Cell Culture Facility RRID:CVCL_1092 Human HCC1569 Duke Cell Culture Facility RRID:CVCL_1255 Human ZR-75-1 Duke Cell Culture Facility RRID:CVCL_0588 Human UACC-812 Duke Cell Culture Facility RRID:CVCL_1781 Human BT-20 Duke Cell Culture Facility RRID:CVCL_0178 Human MDA-MB-157 Duke Cell Culture Facility RRID:CVCL_0618 Human HCC1419 Duke Cell Culture Facility RRID:CVCL_1251 Human HS578T Duke Cell Culture Facility RRID:CVCL_0332 Experimental Models: Organisms/Strains MMTV-rtTA;TetO-Her2/neu (MTB;TAN) on FVB Lewis Chodosh TetO-Her2/neu (TAN) on FVB Lewis Chodosh FVB mice Jackson laboratories Nu/nu female mice Duke University Breeding Core Oligonucleotides G9a cDNA overexpression plasmid generation Forward: 50-GTTAGGA TCCATGGCGGCGGCGGCGGGAGC-30 This paper N/A G9a cDNA overexpression plasmid generation Reverse: 50-GTTAGAATT CTTAAGAGTCCTCAGGTGTTG-30. .. This paper N/A sgG9a#1: 50-CGGCAGGCTCCAAG GAGTCG-30 This paper N/A sgG9a#2: 50-ACAGGCACCCCC CTTGCTGG-30 This paper N/A sgNT: 50-CCCGATCCCC TACCTAGCCG-30 This paper N/A sgP53: 50-GAAGTCACAGCACATGA CGG-30 This paper N/A shRNA scrambled control Addgene Cat1864 shRNA Ripk3#1 Dharmacon TRCN0000022534 shRNA Ripk3#2 Dharmacon TRCN0000022538 Primers used for H3K9me2 ChIP-qPCR see Table S5 This paper Taqman Cdkn1a probe ThermoFisher Scientific Cat#Mm00432448 Taqman Ehmt2 probe ThermoFisher Scientific Cat#Mm01132261 Taqman Tnf (mouse) probe ThermoFisher Scientific Cat#Mm00443258 Taqman Ripk3 (mouse) probe ThermoFisher Scientific Cat#Mm00444947 Taqman Actb probe ThermoFisher Scientific Cat#Mm02619580 Taqman 18 s (Mouse and Human) probe ThermoFisher Scientific Cat#4332641 Taqman Gadd45a probe ThermoFisher Scientific Cat#Mm00432802 Taqman Met probe ThermoFisher Scientific Cat#Mm01156972 (Continued on next page) e3 Cell Reports 33, 108341, November 3, 2020 Article ll OPEN ACCESS .. REAGENT or RESOURCE SOURCE IDENTIFIER Taqman TNF (Human) probe ThermoFisher Scientific Cat#Hs00174128 Taqman RIPK3 (Human) probe ThermoFisher Scientific Cat#Hs01011175 Taqman copy number Met probe ThermoFisher Scientific Cat#Mm00565151 Taqman copy number tnfr probe ThermoFisher Scientific Cat#4458366 Recombinant DNA Lenti-Cas9-blast Addgene Cat#52962 Lentiguide-puro Addgene Cat#52963 Full-length G9a cDNA Dharmacon Clone ID: 6822432 psPAX2 Addgene Cat#12260 pMDG.2 Addgene Cat#12559 pBABE-puro Addgene Cat#1764 Software and Algorithms Bowtie Langmead et al., 2009 MACS2 Feng et al., 2012 https://pypi.org/project/MACS2/ Diffbind Ross-Innes et al., 2012 https://bioconductor.org/packages/ release/bioc/html/DiffBind.html ChIPseeker Yu et al., 2015 http://bioconductor.org/packages/release/ bioc/html/ChIPseeker.html annotatr Cavalcante and Sartor, 2017 https://bioconductor.org/packages/ release/bioc/html/annotatr.html Deeptools2 Ramı́rez, et al., 2016 https://deeptools.readthedocs.io/en/ develop/content/installation.html ChIPpeakAnno Zhu et al., 2010 https://www.bioconductor.org/packages/ release/bioc/html/ChIPpeakAnno.html IGV desktop viewer (v2.3) Broad Institute http://software.broadinstitute.org/ software/igv/ ENCODE for H3K27ac and H3K4me1 in mouse fibroblasts Bing Ren from the ENCODE consortium GSM1000139 ; GSM769028 Rsubread Liao et al., 2019 http://subread.sourceforge.net/ pheatmap https://cran.r-project.org/web/packages/ pheatmap/index.html clusterProfiler Yu et al., 2012 https://bioconductor.org/packages/ release/bioc/html/clusterProfiler.html GSEA desktop viewer (v4.0) Broad Institute https://www.gsea-msigdb.org/gsea/ index.jsp DESeq2 Love et al., 2014 https://bioconductor.org/packages/ release/bioc/html/DESeq2.html Confidence Interval for IC50 calculator GraphPad Available from: https://www.graphpad. com/quickcalcs/errorProp1/?Format=SEM ImageStudio Lite (v5.0) Li-Cor https://www.licor.com/bio/ image-studio-lite/ FlowJo (v10) FlowJo Prism 7 Graphpad Article ll OPEN ACCESS
Control:Article Title: G9a Promotes Breast Cancer Recurrence through Repression of a Pro-inflammatory Program
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Human HCC202 Duke Cell Culture Facility RRID:CVCL_2062 Human MDA-MB-134 Duke Cell Culture Facility RRID:CVCL_0617 Human HCC1395 Duke Cell Culture Facility RRID:CVCL_1249 Human MDA-MB-361 Duke Cell Culture Facility RRID:CVCL_0620 Human HCC38 Duke Cell Culture Facility RRID:CVCL_1267 Human BT-483 Duke Cell Culture Facility RRID:CVCL_2319 Human HCC1954 Duke Cell Culture Facility RRID:CVCL_1259 Human MDA-MB-436 Duke Cell Culture Facility RRID:CVCL_0623 Human BT-549 Duke Cell Culture Facility RRID:CVCL_1092 Human HCC1569 Duke Cell Culture Facility RRID:CVCL_1255 Human ZR-75-1 Duke Cell Culture Facility RRID:CVCL_0588 Human UACC-812 Duke Cell Culture Facility RRID:CVCL_1781 Human BT-20 Duke Cell Culture Facility RRID:CVCL_0178 Human MDA-MB-157 Duke Cell Culture Facility RRID:CVCL_0618 Human HCC1419 Duke Cell Culture Facility RRID:CVCL_1251 Human HS578T Duke Cell Culture Facility RRID:CVCL_0332 Experimental Models: Organisms/Strains MMTV-rtTA;TetO-Her2/neu (MTB;TAN) on FVB Lewis Chodosh TetO-Her2/neu (TAN) on FVB Lewis Chodosh FVB mice Jackson laboratories Nu/nu female mice Duke University Breeding Core Oligonucleotides G9a cDNA overexpression plasmid generation Forward: 50-GTTAGGA TCCATGGCGGCGGCGGCGGGAGC-30 This paper N/A G9a cDNA overexpression plasmid generation Reverse: 50-GTTAGAATT CTTAAGAGTCCTCAGGTGTTG-30. .. This paper N/A sgG9a#1: 50-CGGCAGGCTCCAAG GAGTCG-30 This paper N/A sgG9a#2: 50-ACAGGCACCCCC CTTGCTGG-30 This paper N/A sgNT: 50-CCCGATCCCC TACCTAGCCG-30 This paper N/A sgP53: 50-GAAGTCACAGCACATGA CGG-30 This paper N/A shRNA scrambled control Addgene Cat1864 shRNA Ripk3#1 Dharmacon TRCN0000022534 shRNA Ripk3#2 Dharmacon TRCN0000022538 Primers used for H3K9me2 ChIP-qPCR see Table S5 This paper Taqman Cdkn1a probe ThermoFisher Scientific Cat#Mm00432448 Taqman Ehmt2 probe ThermoFisher Scientific Cat#Mm01132261 Taqman Tnf (mouse) probe ThermoFisher Scientific Cat#Mm00443258 Taqman Ripk3 (mouse) probe ThermoFisher Scientific Cat#Mm00444947 Taqman Actb probe ThermoFisher Scientific Cat#Mm02619580 Taqman 18 s (Mouse and Human) probe ThermoFisher Scientific Cat#4332641 Taqman Gadd45a probe ThermoFisher Scientific Cat#Mm00432802 Taqman Met probe ThermoFisher Scientific Cat#Mm01156972 (Continued on next page) e3 Cell Reports 33, 108341, November 3, 2020 Article ll OPEN ACCESS .. REAGENT or RESOURCE SOURCE IDENTIFIER Taqman TNF (Human) probe ThermoFisher Scientific Cat#Hs00174128 Taqman RIPK3 (Human) probe ThermoFisher Scientific Cat#Hs01011175 Taqman copy number Met probe ThermoFisher Scientific Cat#Mm00565151 Taqman copy number tnfr probe ThermoFisher Scientific Cat#4458366 Recombinant DNA Lenti-Cas9-blast Addgene Cat#52962 Lentiguide-puro Addgene Cat#52963 Full-length G9a cDNA Dharmacon Clone ID: 6822432 psPAX2 Addgene Cat#12260 pMDG.2 Addgene Cat#12559 pBABE-puro Addgene Cat#1764 Software and Algorithms Bowtie Langmead et al., 2009 MACS2 Feng et al., 2012 https://pypi.org/project/MACS2/ Diffbind Ross-Innes et al., 2012 https://bioconductor.org/packages/ release/bioc/html/DiffBind.html ChIPseeker Yu et al., 2015 http://bioconductor.org/packages/release/ bioc/html/ChIPseeker.html annotatr Cavalcante and Sartor, 2017 https://bioconductor.org/packages/ release/bioc/html/annotatr.html Deeptools2 Ramı́rez, et al., 2016 https://deeptools.readthedocs.io/en/ develop/content/installation.html ChIPpeakAnno Zhu et al., 2010 https://www.bioconductor.org/packages/ release/bioc/html/ChIPpeakAnno.html IGV desktop viewer (v2.3) Broad Institute http://software.broadinstitute.org/ software/igv/ ENCODE for H3K27ac and H3K4me1 in mouse fibroblasts Bing Ren from the ENCODE consortium GSM1000139 ; GSM769028 Rsubread Liao et al., 2019 http://subread.sourceforge.net/ pheatmap https://cran.r-project.org/web/packages/ pheatmap/index.html clusterProfiler Yu et al., 2012 https://bioconductor.org/packages/ release/bioc/html/clusterProfiler.html GSEA desktop viewer (v4.0) Broad Institute https://www.gsea-msigdb.org/gsea/ index.jsp DESeq2 Love et al., 2014 https://bioconductor.org/packages/ release/bioc/html/DESeq2.html Confidence Interval for IC50 calculator GraphPad Available from: https://www.graphpad. com/quickcalcs/errorProp1/?Format=SEM ImageStudio Lite (v5.0) Li-Cor https://www.licor.com/bio/ image-studio-lite/ FlowJo (v10) FlowJo Prism 7 Graphpad Article ll OPEN ACCESS
ChIP-qPCR:Article Title: G9a Promotes Breast Cancer Recurrence through Repression of a Pro-inflammatory Program
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Human HCC202 Duke Cell Culture Facility RRID:CVCL_2062 Human MDA-MB-134 Duke Cell Culture Facility RRID:CVCL_0617 Human HCC1395 Duke Cell Culture Facility RRID:CVCL_1249 Human MDA-MB-361 Duke Cell Culture Facility RRID:CVCL_0620 Human HCC38 Duke Cell Culture Facility RRID:CVCL_1267 Human BT-483 Duke Cell Culture Facility RRID:CVCL_2319 Human HCC1954 Duke Cell Culture Facility RRID:CVCL_1259 Human MDA-MB-436 Duke Cell Culture Facility RRID:CVCL_0623 Human BT-549 Duke Cell Culture Facility RRID:CVCL_1092 Human HCC1569 Duke Cell Culture Facility RRID:CVCL_1255 Human ZR-75-1 Duke Cell Culture Facility RRID:CVCL_0588 Human UACC-812 Duke Cell Culture Facility RRID:CVCL_1781 Human BT-20 Duke Cell Culture Facility RRID:CVCL_0178 Human MDA-MB-157 Duke Cell Culture Facility RRID:CVCL_0618 Human HCC1419 Duke Cell Culture Facility RRID:CVCL_1251 Human HS578T Duke Cell Culture Facility RRID:CVCL_0332 Experimental Models: Organisms/Strains MMTV-rtTA;TetO-Her2/neu (MTB;TAN) on FVB Lewis Chodosh TetO-Her2/neu (TAN) on FVB Lewis Chodosh FVB mice Jackson laboratories Nu/nu female mice Duke University Breeding Core Oligonucleotides G9a cDNA overexpression plasmid generation Forward: 50-GTTAGGA TCCATGGCGGCGGCGGCGGGAGC-30 This paper N/A G9a cDNA overexpression plasmid generation Reverse: 50-GTTAGAATT CTTAAGAGTCCTCAGGTGTTG-30. .. This paper N/A sgG9a#1: 50-CGGCAGGCTCCAAG GAGTCG-30 This paper N/A sgG9a#2: 50-ACAGGCACCCCC CTTGCTGG-30 This paper N/A sgNT: 50-CCCGATCCCC TACCTAGCCG-30 This paper N/A sgP53: 50-GAAGTCACAGCACATGA CGG-30 This paper N/A shRNA scrambled control Addgene Cat1864 shRNA Ripk3#1 Dharmacon TRCN0000022534 shRNA Ripk3#2 Dharmacon TRCN0000022538 Primers used for H3K9me2 ChIP-qPCR see Table S5 This paper Taqman Cdkn1a probe ThermoFisher Scientific Cat#Mm00432448 Taqman Ehmt2 probe ThermoFisher Scientific Cat#Mm01132261 Taqman Tnf (mouse) probe ThermoFisher Scientific Cat#Mm00443258 Taqman Ripk3 (mouse) probe ThermoFisher Scientific Cat#Mm00444947 Taqman Actb probe ThermoFisher Scientific Cat#Mm02619580 Taqman 18 s (Mouse and Human) probe ThermoFisher Scientific Cat#4332641 Taqman Gadd45a probe ThermoFisher Scientific Cat#Mm00432802 Taqman Met probe ThermoFisher Scientific Cat#Mm01156972 (Continued on next page) e3 Cell Reports 33, 108341, November 3, 2020 Article ll OPEN ACCESS .. REAGENT or RESOURCE SOURCE IDENTIFIER Taqman TNF (Human) probe ThermoFisher Scientific Cat#Hs00174128 Taqman RIPK3 (Human) probe ThermoFisher Scientific Cat#Hs01011175 Taqman copy number Met probe ThermoFisher Scientific Cat#Mm00565151 Taqman copy number tnfr probe ThermoFisher Scientific Cat#4458366 Recombinant DNA Lenti-Cas9-blast Addgene Cat#52962 Lentiguide-puro Addgene Cat#52963 Full-length G9a cDNA Dharmacon Clone ID: 6822432 psPAX2 Addgene Cat#12260 pMDG.2 Addgene Cat#12559 pBABE-puro Addgene Cat#1764 Software and Algorithms Bowtie Langmead et al., 2009 MACS2 Feng et al., 2012 https://pypi.org/project/MACS2/ Diffbind Ross-Innes et al., 2012 https://bioconductor.org/packages/ release/bioc/html/DiffBind.html ChIPseeker Yu et al., 2015 http://bioconductor.org/packages/release/ bioc/html/ChIPseeker.html annotatr Cavalcante and Sartor, 2017 https://bioconductor.org/packages/ release/bioc/html/annotatr.html Deeptools2 Ramı́rez, et al., 2016 https://deeptools.readthedocs.io/en/ develop/content/installation.html ChIPpeakAnno Zhu et al., 2010 https://www.bioconductor.org/packages/ release/bioc/html/ChIPpeakAnno.html IGV desktop viewer (v2.3) Broad Institute http://software.broadinstitute.org/ software/igv/ ENCODE for H3K27ac and H3K4me1 in mouse fibroblasts Bing Ren from the ENCODE consortium GSM1000139 ; GSM769028 Rsubread Liao et al., 2019 http://subread.sourceforge.net/ pheatmap https://cran.r-project.org/web/packages/ pheatmap/index.html clusterProfiler Yu et al., 2012 https://bioconductor.org/packages/ release/bioc/html/clusterProfiler.html GSEA desktop viewer (v4.0) Broad Institute https://www.gsea-msigdb.org/gsea/ index.jsp DESeq2 Love et al., 2014 https://bioconductor.org/packages/ release/bioc/html/DESeq2.html Confidence Interval for IC50 calculator GraphPad Available from: https://www.graphpad. com/quickcalcs/errorProp1/?Format=SEM ImageStudio Lite (v5.0) Li-Cor https://www.licor.com/bio/ image-studio-lite/ FlowJo (v10) FlowJo Prism 7 Graphpad Article ll OPEN ACCESS
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