Recombinant:Article Title: Modeling high-risk Wilms tumors enables the discovery of therapeutic vulnerability.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-Ki67 Abcam Cat# ab15580; RRID: AB_443209 Anti-SIX2 Proteintech Cat# 11562-1-AP; RRID: AB_2189084 Anti-NCAM1 Thermo Cat# 701379; RRID: AB_2532477 Anti-EZH2 Cell signaling technology Cat# 5246; RRID: AB_10694683 Anti-Vimentin Cell signaling technology Cat# 5741; RRID: AB_10695459 Anti-HLAB Cell signaling technology Cat# 41915; RRID: AB_3224414 Anti-human mitochondria Thermo Cat# MA5-12017; RRID: AB_10983622 Anti-Snail2 Proteintech Cat# 12129-1-AP; RRID: AB_2191889 Anti-Keratin 18 Thermo Cat# MA5-12104; RRID: AB_10981680 Biological samples PDX226 Dr. Michael Dye38 SJWLM046152_X1 PDX207 Dr. Michael Dye38 SJWLM049191_X1 PDX253 Dr. Michael Dye38 SJWLM046157_X1 Chemicals, peptides, and recombinant proteins Panobinostat TargetMol CatT2383-CUST Romidepsin Medchem Express Cat#HY-15149 Doxorubicin TargetMol Cat#T1020-CUST Alisertib Medchem Express Cat#HY-10971 Cytarabine Medchem Express Cat#HY-13605 CY-10683 Medchem Express Cat#HY-N0931 RGFP966 Medchem Express Cat#HY-13909 BRD4354 Medchem Express Cat#HY-112719 CXD101 Medchem Express Cat#HY-100748 Critical commercial assays SMARTer Stranded RNA-Seq Kit Takara Bio Cat# 634839 E.Z.N.An HP Total RNA Extraction Kit Omega Cat# R6812 First-Strand cDNA Synthesis Kit Bio-Rad Cat# 1708841 SYBR Green Bio-Rad Cat# 1725121 Nucleofector kit R Lonza Cat# VCA-1001 Deposited data RNA-seq data This paper GEO: GSE246479 Experimental models: Cell lines WiT49 Prof. Herman Yeger RRID: CVCL_0583 HEK293T ATCC Cat# CRL-3216; RRID: CVCL_0063 Experimental models: Organisms/strains NSG mice Jackson Laboratory Strain code 5557 Oligonucleotides qRT-PCR sequences This paper See Table S2 Recombinant DNA pEP4 E02S EN2K Addgene Cat #20925 pCEP4-M2L Addgene Cat #20926 (Continued on next page) e1 Cell Reports Medicine 5, 101770, October 15, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER pEP4 E02S ET2K Addgene Cat #20927 pHAGE PGK-GFP-IRES-Luciferase Addgene Cat #46793 VSVG Addgene Cat #12259 psPAX2 Addgene Cat #12260 Software and algorithms GraphPad Prism8 GraphPad https://www.graphpad.com GSEA BROAD Institute https://www.gsea-msigdb.org/gsea/index.jsp Custom generated R scripts This paper https://github.com/chenlab-sj/WiT49_PRC R R project https://www.r-project.org/ edgeR (v3.40.2) R package https://bioconductor.org/packages/ release/bioc/html/edgeR.html STAR (version 2.5.2b) Dr. Alexander Dobin54 https://github.com/alexdobin/STAR BioRender BioRender https://www.biorender.com/
Article Title: Modeling high-risk Wilms tumors enables the discovery of therapeutic vulnerability
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-Ki67 Abcam Cat# ab15580; RRID: AB_443209 Anti-SIX2 Proteintech Cat# 11562-1-AP; RRID: AB_2189084 Anti-NCAM1 Thermo Cat# 701379; RRID: AB_2532477 Anti-EZH2 Cell signaling technology Cat# 5246; RRID: AB_10694683 Anti-Vimentin Cell signaling technology Cat# 5741; RRID: AB_10695459 Anti-HLAB Cell signaling technology Cat# 41915; RRID: AB_3224414 Anti-human mitochondria Thermo Cat# MA5-12017; RRID: AB_10983622 Anti-Snail2 Proteintech Cat# 12129-1-AP; RRID: AB_2191889 Anti-Keratin 18 Thermo Cat# MA5-12104; RRID: AB_10981680 Biological samples PDX226 Dr. Michael Dye38 SJWLM046152_X1 PDX207 Dr. Michael Dye38 SJWLM049191_X1 PDX253 Dr. Michael Dye38 SJWLM046157_X1 Chemicals, peptides, and recombinant proteins Panobinostat TargetMol CatT2383-CUST Romidepsin Medchem Express Cat#HY-15149 Doxorubicin TargetMol Cat#T1020-CUST Alisertib Medchem Express Cat#HY-10971 Cytarabine Medchem Express Cat#HY-13605 CY-10683 Medchem Express Cat#HY-N0931 RGFP966 Medchem Express Cat#HY-13909 BRD4354 Medchem Express Cat#HY-112719 CXD101 Medchem Express Cat#HY-100748 Critical commercial assays SMARTer Stranded RNA-Seq Kit Takara Bio Cat# 634839 E.Z.N.An HP Total RNA Extraction Kit Omega Cat# R6812 First-Strand cDNA Synthesis Kit Bio-Rad Cat# 1708841 SYBR Green Bio-Rad Cat# 1725121 Nucleofector kit R Lonza Cat# VCA-1001 Deposited data RNA-seq data This paper GEO: GSE246479 Experimental models: Cell lines WiT49 Prof. Herman Yeger RRID: CVCL_0583 HEK293T ATCC Cat# CRL-3216; RRID: CVCL_0063 Experimental models: Organisms/strains NSG mice Jackson Laboratory Strain code 5557 Oligonucleotides qRT-PCR sequences This paper See Table S2 Recombinant DNA pEP4 E02S EN2K Addgene Cat #20925 pCEP4-M2L Addgene Cat #20926 (Continued on next page) e1 Cell Reports Medicine 5, 101770, October 15, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER pEP4 E02S ET2K Addgene Cat #20927 pHAGE PGK-GFP-IRES-Luciferase Addgene Cat #46793 VSVG Addgene Cat #12259 psPAX2 Addgene Cat #12260 Software and algorithms GraphPad Prism8 GraphPad https://www.graphpad.com GSEA BROAD Institute https://www.gsea-msigdb.org/gsea/index.jsp Custom generated R scripts This paper https://github.com/chenlab-sj/WiT49_PRC R R project https://www.r-project.org/ edgeR (v3.40.2) R package https://bioconductor.org/packages/ release/bioc/html/edgeR.html STAR (version 2.5.2b) Dr. Alexander Dobin54 https://github.com/alexdobin/STAR BioRender BioRender https://www.biorender.com/ Article ll OPEN ACCESS
RNA sequencing:Article Title: Modeling high-risk Wilms tumors enables the discovery of therapeutic vulnerability.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-Ki67 Abcam Cat# ab15580; RRID: AB_443209 Anti-SIX2 Proteintech Cat# 11562-1-AP; RRID: AB_2189084 Anti-NCAM1 Thermo Cat# 701379; RRID: AB_2532477 Anti-EZH2 Cell signaling technology Cat# 5246; RRID: AB_10694683 Anti-Vimentin Cell signaling technology Cat# 5741; RRID: AB_10695459 Anti-HLAB Cell signaling technology Cat# 41915; RRID: AB_3224414 Anti-human mitochondria Thermo Cat# MA5-12017; RRID: AB_10983622 Anti-Snail2 Proteintech Cat# 12129-1-AP; RRID: AB_2191889 Anti-Keratin 18 Thermo Cat# MA5-12104; RRID: AB_10981680 Biological samples PDX226 Dr. Michael Dye38 SJWLM046152_X1 PDX207 Dr. Michael Dye38 SJWLM049191_X1 PDX253 Dr. Michael Dye38 SJWLM046157_X1 Chemicals, peptides, and recombinant proteins Panobinostat TargetMol CatT2383-CUST Romidepsin Medchem Express Cat#HY-15149 Doxorubicin TargetMol Cat#T1020-CUST Alisertib Medchem Express Cat#HY-10971 Cytarabine Medchem Express Cat#HY-13605 CY-10683 Medchem Express Cat#HY-N0931 RGFP966 Medchem Express Cat#HY-13909 BRD4354 Medchem Express Cat#HY-112719 CXD101 Medchem Express Cat#HY-100748 Critical commercial assays SMARTer Stranded RNA-Seq Kit Takara Bio Cat# 634839 E.Z.N.An HP Total RNA Extraction Kit Omega Cat# R6812 First-Strand cDNA Synthesis Kit Bio-Rad Cat# 1708841 SYBR Green Bio-Rad Cat# 1725121 Nucleofector kit R Lonza Cat# VCA-1001 Deposited data RNA-seq data This paper GEO: GSE246479 Experimental models: Cell lines WiT49 Prof. Herman Yeger RRID: CVCL_0583 HEK293T ATCC Cat# CRL-3216; RRID: CVCL_0063 Experimental models: Organisms/strains NSG mice Jackson Laboratory Strain code 5557 Oligonucleotides qRT-PCR sequences This paper See Table S2 Recombinant DNA pEP4 E02S EN2K Addgene Cat #20925 pCEP4-M2L Addgene Cat #20926 (Continued on next page) e1 Cell Reports Medicine 5, 101770, October 15, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER pEP4 E02S ET2K Addgene Cat #20927 pHAGE PGK-GFP-IRES-Luciferase Addgene Cat #46793 VSVG Addgene Cat #12259 psPAX2 Addgene Cat #12260 Software and algorithms GraphPad Prism8 GraphPad https://www.graphpad.com GSEA BROAD Institute https://www.gsea-msigdb.org/gsea/index.jsp Custom generated R scripts This paper https://github.com/chenlab-sj/WiT49_PRC R R project https://www.r-project.org/ edgeR (v3.40.2) R package https://bioconductor.org/packages/ release/bioc/html/edgeR.html STAR (version 2.5.2b) Dr. Alexander Dobin54 https://github.com/alexdobin/STAR BioRender BioRender https://www.biorender.com/
Article Title: Modeling high-risk Wilms tumors enables the discovery of therapeutic vulnerability
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-Ki67 Abcam Cat# ab15580; RRID: AB_443209 Anti-SIX2 Proteintech Cat# 11562-1-AP; RRID: AB_2189084 Anti-NCAM1 Thermo Cat# 701379; RRID: AB_2532477 Anti-EZH2 Cell signaling technology Cat# 5246; RRID: AB_10694683 Anti-Vimentin Cell signaling technology Cat# 5741; RRID: AB_10695459 Anti-HLAB Cell signaling technology Cat# 41915; RRID: AB_3224414 Anti-human mitochondria Thermo Cat# MA5-12017; RRID: AB_10983622 Anti-Snail2 Proteintech Cat# 12129-1-AP; RRID: AB_2191889 Anti-Keratin 18 Thermo Cat# MA5-12104; RRID: AB_10981680 Biological samples PDX226 Dr. Michael Dye38 SJWLM046152_X1 PDX207 Dr. Michael Dye38 SJWLM049191_X1 PDX253 Dr. Michael Dye38 SJWLM046157_X1 Chemicals, peptides, and recombinant proteins Panobinostat TargetMol CatT2383-CUST Romidepsin Medchem Express Cat#HY-15149 Doxorubicin TargetMol Cat#T1020-CUST Alisertib Medchem Express Cat#HY-10971 Cytarabine Medchem Express Cat#HY-13605 CY-10683 Medchem Express Cat#HY-N0931 RGFP966 Medchem Express Cat#HY-13909 BRD4354 Medchem Express Cat#HY-112719 CXD101 Medchem Express Cat#HY-100748 Critical commercial assays SMARTer Stranded RNA-Seq Kit Takara Bio Cat# 634839 E.Z.N.An HP Total RNA Extraction Kit Omega Cat# R6812 First-Strand cDNA Synthesis Kit Bio-Rad Cat# 1708841 SYBR Green Bio-Rad Cat# 1725121 Nucleofector kit R Lonza Cat# VCA-1001 Deposited data RNA-seq data This paper GEO: GSE246479 Experimental models: Cell lines WiT49 Prof. Herman Yeger RRID: CVCL_0583 HEK293T ATCC Cat# CRL-3216; RRID: CVCL_0063 Experimental models: Organisms/strains NSG mice Jackson Laboratory Strain code 5557 Oligonucleotides qRT-PCR sequences This paper See Table S2 Recombinant DNA pEP4 E02S EN2K Addgene Cat #20925 pCEP4-M2L Addgene Cat #20926 (Continued on next page) e1 Cell Reports Medicine 5, 101770, October 15, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER pEP4 E02S ET2K Addgene Cat #20927 pHAGE PGK-GFP-IRES-Luciferase Addgene Cat #46793 VSVG Addgene Cat #12259 psPAX2 Addgene Cat #12260 Software and algorithms GraphPad Prism8 GraphPad https://www.graphpad.com GSEA BROAD Institute https://www.gsea-msigdb.org/gsea/index.jsp Custom generated R scripts This paper https://github.com/chenlab-sj/WiT49_PRC R R project https://www.r-project.org/ edgeR (v3.40.2) R package https://bioconductor.org/packages/ release/bioc/html/edgeR.html STAR (version 2.5.2b) Dr. Alexander Dobin54 https://github.com/alexdobin/STAR BioRender BioRender https://www.biorender.com/ Article ll OPEN ACCESS
RNA Extraction:Article Title: Modeling high-risk Wilms tumors enables the discovery of therapeutic vulnerability.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-Ki67 Abcam Cat# ab15580; RRID: AB_443209 Anti-SIX2 Proteintech Cat# 11562-1-AP; RRID: AB_2189084 Anti-NCAM1 Thermo Cat# 701379; RRID: AB_2532477 Anti-EZH2 Cell signaling technology Cat# 5246; RRID: AB_10694683 Anti-Vimentin Cell signaling technology Cat# 5741; RRID: AB_10695459 Anti-HLAB Cell signaling technology Cat# 41915; RRID: AB_3224414 Anti-human mitochondria Thermo Cat# MA5-12017; RRID: AB_10983622 Anti-Snail2 Proteintech Cat# 12129-1-AP; RRID: AB_2191889 Anti-Keratin 18 Thermo Cat# MA5-12104; RRID: AB_10981680 Biological samples PDX226 Dr. Michael Dye38 SJWLM046152_X1 PDX207 Dr. Michael Dye38 SJWLM049191_X1 PDX253 Dr. Michael Dye38 SJWLM046157_X1 Chemicals, peptides, and recombinant proteins Panobinostat TargetMol CatT2383-CUST Romidepsin Medchem Express Cat#HY-15149 Doxorubicin TargetMol Cat#T1020-CUST Alisertib Medchem Express Cat#HY-10971 Cytarabine Medchem Express Cat#HY-13605 CY-10683 Medchem Express Cat#HY-N0931 RGFP966 Medchem Express Cat#HY-13909 BRD4354 Medchem Express Cat#HY-112719 CXD101 Medchem Express Cat#HY-100748 Critical commercial assays SMARTer Stranded RNA-Seq Kit Takara Bio Cat# 634839 E.Z.N.An HP Total RNA Extraction Kit Omega Cat# R6812 First-Strand cDNA Synthesis Kit Bio-Rad Cat# 1708841 SYBR Green Bio-Rad Cat# 1725121 Nucleofector kit R Lonza Cat# VCA-1001 Deposited data RNA-seq data This paper GEO: GSE246479 Experimental models: Cell lines WiT49 Prof. Herman Yeger RRID: CVCL_0583 HEK293T ATCC Cat# CRL-3216; RRID: CVCL_0063 Experimental models: Organisms/strains NSG mice Jackson Laboratory Strain code 5557 Oligonucleotides qRT-PCR sequences This paper See Table S2 Recombinant DNA pEP4 E02S EN2K Addgene Cat #20925 pCEP4-M2L Addgene Cat #20926 (Continued on next page) e1 Cell Reports Medicine 5, 101770, October 15, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER pEP4 E02S ET2K Addgene Cat #20927 pHAGE PGK-GFP-IRES-Luciferase Addgene Cat #46793 VSVG Addgene Cat #12259 psPAX2 Addgene Cat #12260 Software and algorithms GraphPad Prism8 GraphPad https://www.graphpad.com GSEA BROAD Institute https://www.gsea-msigdb.org/gsea/index.jsp Custom generated R scripts This paper https://github.com/chenlab-sj/WiT49_PRC R R project https://www.r-project.org/ edgeR (v3.40.2) R package https://bioconductor.org/packages/ release/bioc/html/edgeR.html STAR (version 2.5.2b) Dr. Alexander Dobin54 https://github.com/alexdobin/STAR BioRender BioRender https://www.biorender.com/
Article Title: Modeling high-risk Wilms tumors enables the discovery of therapeutic vulnerability
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-Ki67 Abcam Cat# ab15580; RRID: AB_443209 Anti-SIX2 Proteintech Cat# 11562-1-AP; RRID: AB_2189084 Anti-NCAM1 Thermo Cat# 701379; RRID: AB_2532477 Anti-EZH2 Cell signaling technology Cat# 5246; RRID: AB_10694683 Anti-Vimentin Cell signaling technology Cat# 5741; RRID: AB_10695459 Anti-HLAB Cell signaling technology Cat# 41915; RRID: AB_3224414 Anti-human mitochondria Thermo Cat# MA5-12017; RRID: AB_10983622 Anti-Snail2 Proteintech Cat# 12129-1-AP; RRID: AB_2191889 Anti-Keratin 18 Thermo Cat# MA5-12104; RRID: AB_10981680 Biological samples PDX226 Dr. Michael Dye38 SJWLM046152_X1 PDX207 Dr. Michael Dye38 SJWLM049191_X1 PDX253 Dr. Michael Dye38 SJWLM046157_X1 Chemicals, peptides, and recombinant proteins Panobinostat TargetMol CatT2383-CUST Romidepsin Medchem Express Cat#HY-15149 Doxorubicin TargetMol Cat#T1020-CUST Alisertib Medchem Express Cat#HY-10971 Cytarabine Medchem Express Cat#HY-13605 CY-10683 Medchem Express Cat#HY-N0931 RGFP966 Medchem Express Cat#HY-13909 BRD4354 Medchem Express Cat#HY-112719 CXD101 Medchem Express Cat#HY-100748 Critical commercial assays SMARTer Stranded RNA-Seq Kit Takara Bio Cat# 634839 E.Z.N.An HP Total RNA Extraction Kit Omega Cat# R6812 First-Strand cDNA Synthesis Kit Bio-Rad Cat# 1708841 SYBR Green Bio-Rad Cat# 1725121 Nucleofector kit R Lonza Cat# VCA-1001 Deposited data RNA-seq data This paper GEO: GSE246479 Experimental models: Cell lines WiT49 Prof. Herman Yeger RRID: CVCL_0583 HEK293T ATCC Cat# CRL-3216; RRID: CVCL_0063 Experimental models: Organisms/strains NSG mice Jackson Laboratory Strain code 5557 Oligonucleotides qRT-PCR sequences This paper See Table S2 Recombinant DNA pEP4 E02S EN2K Addgene Cat #20925 pCEP4-M2L Addgene Cat #20926 (Continued on next page) e1 Cell Reports Medicine 5, 101770, October 15, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER pEP4 E02S ET2K Addgene Cat #20927 pHAGE PGK-GFP-IRES-Luciferase Addgene Cat #46793 VSVG Addgene Cat #12259 psPAX2 Addgene Cat #12260 Software and algorithms GraphPad Prism8 GraphPad https://www.graphpad.com GSEA BROAD Institute https://www.gsea-msigdb.org/gsea/index.jsp Custom generated R scripts This paper https://github.com/chenlab-sj/WiT49_PRC R R project https://www.r-project.org/ edgeR (v3.40.2) R package https://bioconductor.org/packages/ release/bioc/html/edgeR.html STAR (version 2.5.2b) Dr. Alexander Dobin54 https://github.com/alexdobin/STAR BioRender BioRender https://www.biorender.com/ Article ll OPEN ACCESS
cDNA Synthesis:Article Title: Modeling high-risk Wilms tumors enables the discovery of therapeutic vulnerability.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-Ki67 Abcam Cat# ab15580; RRID: AB_443209 Anti-SIX2 Proteintech Cat# 11562-1-AP; RRID: AB_2189084 Anti-NCAM1 Thermo Cat# 701379; RRID: AB_2532477 Anti-EZH2 Cell signaling technology Cat# 5246; RRID: AB_10694683 Anti-Vimentin Cell signaling technology Cat# 5741; RRID: AB_10695459 Anti-HLAB Cell signaling technology Cat# 41915; RRID: AB_3224414 Anti-human mitochondria Thermo Cat# MA5-12017; RRID: AB_10983622 Anti-Snail2 Proteintech Cat# 12129-1-AP; RRID: AB_2191889 Anti-Keratin 18 Thermo Cat# MA5-12104; RRID: AB_10981680 Biological samples PDX226 Dr. Michael Dye38 SJWLM046152_X1 PDX207 Dr. Michael Dye38 SJWLM049191_X1 PDX253 Dr. Michael Dye38 SJWLM046157_X1 Chemicals, peptides, and recombinant proteins Panobinostat TargetMol CatT2383-CUST Romidepsin Medchem Express Cat#HY-15149 Doxorubicin TargetMol Cat#T1020-CUST Alisertib Medchem Express Cat#HY-10971 Cytarabine Medchem Express Cat#HY-13605 CY-10683 Medchem Express Cat#HY-N0931 RGFP966 Medchem Express Cat#HY-13909 BRD4354 Medchem Express Cat#HY-112719 CXD101 Medchem Express Cat#HY-100748 Critical commercial assays SMARTer Stranded RNA-Seq Kit Takara Bio Cat# 634839 E.Z.N.An HP Total RNA Extraction Kit Omega Cat# R6812 First-Strand cDNA Synthesis Kit Bio-Rad Cat# 1708841 SYBR Green Bio-Rad Cat# 1725121 Nucleofector kit R Lonza Cat# VCA-1001 Deposited data RNA-seq data This paper GEO: GSE246479 Experimental models: Cell lines WiT49 Prof. Herman Yeger RRID: CVCL_0583 HEK293T ATCC Cat# CRL-3216; RRID: CVCL_0063 Experimental models: Organisms/strains NSG mice Jackson Laboratory Strain code 5557 Oligonucleotides qRT-PCR sequences This paper See Table S2 Recombinant DNA pEP4 E02S EN2K Addgene Cat #20925 pCEP4-M2L Addgene Cat #20926 (Continued on next page) e1 Cell Reports Medicine 5, 101770, October 15, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER pEP4 E02S ET2K Addgene Cat #20927 pHAGE PGK-GFP-IRES-Luciferase Addgene Cat #46793 VSVG Addgene Cat #12259 psPAX2 Addgene Cat #12260 Software and algorithms GraphPad Prism8 GraphPad https://www.graphpad.com GSEA BROAD Institute https://www.gsea-msigdb.org/gsea/index.jsp Custom generated R scripts This paper https://github.com/chenlab-sj/WiT49_PRC R R project https://www.r-project.org/ edgeR (v3.40.2) R package https://bioconductor.org/packages/ release/bioc/html/edgeR.html STAR (version 2.5.2b) Dr. Alexander Dobin54 https://github.com/alexdobin/STAR BioRender BioRender https://www.biorender.com/
Article Title: Modeling high-risk Wilms tumors enables the discovery of therapeutic vulnerability
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-Ki67 Abcam Cat# ab15580; RRID: AB_443209 Anti-SIX2 Proteintech Cat# 11562-1-AP; RRID: AB_2189084 Anti-NCAM1 Thermo Cat# 701379; RRID: AB_2532477 Anti-EZH2 Cell signaling technology Cat# 5246; RRID: AB_10694683 Anti-Vimentin Cell signaling technology Cat# 5741; RRID: AB_10695459 Anti-HLAB Cell signaling technology Cat# 41915; RRID: AB_3224414 Anti-human mitochondria Thermo Cat# MA5-12017; RRID: AB_10983622 Anti-Snail2 Proteintech Cat# 12129-1-AP; RRID: AB_2191889 Anti-Keratin 18 Thermo Cat# MA5-12104; RRID: AB_10981680 Biological samples PDX226 Dr. Michael Dye38 SJWLM046152_X1 PDX207 Dr. Michael Dye38 SJWLM049191_X1 PDX253 Dr. Michael Dye38 SJWLM046157_X1 Chemicals, peptides, and recombinant proteins Panobinostat TargetMol CatT2383-CUST Romidepsin Medchem Express Cat#HY-15149 Doxorubicin TargetMol Cat#T1020-CUST Alisertib Medchem Express Cat#HY-10971 Cytarabine Medchem Express Cat#HY-13605 CY-10683 Medchem Express Cat#HY-N0931 RGFP966 Medchem Express Cat#HY-13909 BRD4354 Medchem Express Cat#HY-112719 CXD101 Medchem Express Cat#HY-100748 Critical commercial assays SMARTer Stranded RNA-Seq Kit Takara Bio Cat# 634839 E.Z.N.An HP Total RNA Extraction Kit Omega Cat# R6812 First-Strand cDNA Synthesis Kit Bio-Rad Cat# 1708841 SYBR Green Bio-Rad Cat# 1725121 Nucleofector kit R Lonza Cat# VCA-1001 Deposited data RNA-seq data This paper GEO: GSE246479 Experimental models: Cell lines WiT49 Prof. Herman Yeger RRID: CVCL_0583 HEK293T ATCC Cat# CRL-3216; RRID: CVCL_0063 Experimental models: Organisms/strains NSG mice Jackson Laboratory Strain code 5557 Oligonucleotides qRT-PCR sequences This paper See Table S2 Recombinant DNA pEP4 E02S EN2K Addgene Cat #20925 pCEP4-M2L Addgene Cat #20926 (Continued on next page) e1 Cell Reports Medicine 5, 101770, October 15, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER pEP4 E02S ET2K Addgene Cat #20927 pHAGE PGK-GFP-IRES-Luciferase Addgene Cat #46793 VSVG Addgene Cat #12259 psPAX2 Addgene Cat #12260 Software and algorithms GraphPad Prism8 GraphPad https://www.graphpad.com GSEA BROAD Institute https://www.gsea-msigdb.org/gsea/index.jsp Custom generated R scripts This paper https://github.com/chenlab-sj/WiT49_PRC R R project https://www.r-project.org/ edgeR (v3.40.2) R package https://bioconductor.org/packages/ release/bioc/html/edgeR.html STAR (version 2.5.2b) Dr. Alexander Dobin54 https://github.com/alexdobin/STAR BioRender BioRender https://www.biorender.com/ Article ll OPEN ACCESS
SYBR Green Assay:Article Title: Modeling high-risk Wilms tumors enables the discovery of therapeutic vulnerability.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-Ki67 Abcam Cat# ab15580; RRID: AB_443209 Anti-SIX2 Proteintech Cat# 11562-1-AP; RRID: AB_2189084 Anti-NCAM1 Thermo Cat# 701379; RRID: AB_2532477 Anti-EZH2 Cell signaling technology Cat# 5246; RRID: AB_10694683 Anti-Vimentin Cell signaling technology Cat# 5741; RRID: AB_10695459 Anti-HLAB Cell signaling technology Cat# 41915; RRID: AB_3224414 Anti-human mitochondria Thermo Cat# MA5-12017; RRID: AB_10983622 Anti-Snail2 Proteintech Cat# 12129-1-AP; RRID: AB_2191889 Anti-Keratin 18 Thermo Cat# MA5-12104; RRID: AB_10981680 Biological samples PDX226 Dr. Michael Dye38 SJWLM046152_X1 PDX207 Dr. Michael Dye38 SJWLM049191_X1 PDX253 Dr. Michael Dye38 SJWLM046157_X1 Chemicals, peptides, and recombinant proteins Panobinostat TargetMol CatT2383-CUST Romidepsin Medchem Express Cat#HY-15149 Doxorubicin TargetMol Cat#T1020-CUST Alisertib Medchem Express Cat#HY-10971 Cytarabine Medchem Express Cat#HY-13605 CY-10683 Medchem Express Cat#HY-N0931 RGFP966 Medchem Express Cat#HY-13909 BRD4354 Medchem Express Cat#HY-112719 CXD101 Medchem Express Cat#HY-100748 Critical commercial assays SMARTer Stranded RNA-Seq Kit Takara Bio Cat# 634839 E.Z.N.An HP Total RNA Extraction Kit Omega Cat# R6812 First-Strand cDNA Synthesis Kit Bio-Rad Cat# 1708841 SYBR Green Bio-Rad Cat# 1725121 Nucleofector kit R Lonza Cat# VCA-1001 Deposited data RNA-seq data This paper GEO: GSE246479 Experimental models: Cell lines WiT49 Prof. Herman Yeger RRID: CVCL_0583 HEK293T ATCC Cat# CRL-3216; RRID: CVCL_0063 Experimental models: Organisms/strains NSG mice Jackson Laboratory Strain code 5557 Oligonucleotides qRT-PCR sequences This paper See Table S2 Recombinant DNA pEP4 E02S EN2K Addgene Cat #20925 pCEP4-M2L Addgene Cat #20926 (Continued on next page) e1 Cell Reports Medicine 5, 101770, October 15, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER pEP4 E02S ET2K Addgene Cat #20927 pHAGE PGK-GFP-IRES-Luciferase Addgene Cat #46793 VSVG Addgene Cat #12259 psPAX2 Addgene Cat #12260 Software and algorithms GraphPad Prism8 GraphPad https://www.graphpad.com GSEA BROAD Institute https://www.gsea-msigdb.org/gsea/index.jsp Custom generated R scripts This paper https://github.com/chenlab-sj/WiT49_PRC R R project https://www.r-project.org/ edgeR (v3.40.2) R package https://bioconductor.org/packages/ release/bioc/html/edgeR.html STAR (version 2.5.2b) Dr. Alexander Dobin54 https://github.com/alexdobin/STAR BioRender BioRender https://www.biorender.com/
Article Title: Modeling high-risk Wilms tumors enables the discovery of therapeutic vulnerability
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-Ki67 Abcam Cat# ab15580; RRID: AB_443209 Anti-SIX2 Proteintech Cat# 11562-1-AP; RRID: AB_2189084 Anti-NCAM1 Thermo Cat# 701379; RRID: AB_2532477 Anti-EZH2 Cell signaling technology Cat# 5246; RRID: AB_10694683 Anti-Vimentin Cell signaling technology Cat# 5741; RRID: AB_10695459 Anti-HLAB Cell signaling technology Cat# 41915; RRID: AB_3224414 Anti-human mitochondria Thermo Cat# MA5-12017; RRID: AB_10983622 Anti-Snail2 Proteintech Cat# 12129-1-AP; RRID: AB_2191889 Anti-Keratin 18 Thermo Cat# MA5-12104; RRID: AB_10981680 Biological samples PDX226 Dr. Michael Dye38 SJWLM046152_X1 PDX207 Dr. Michael Dye38 SJWLM049191_X1 PDX253 Dr. Michael Dye38 SJWLM046157_X1 Chemicals, peptides, and recombinant proteins Panobinostat TargetMol CatT2383-CUST Romidepsin Medchem Express Cat#HY-15149 Doxorubicin TargetMol Cat#T1020-CUST Alisertib Medchem Express Cat#HY-10971 Cytarabine Medchem Express Cat#HY-13605 CY-10683 Medchem Express Cat#HY-N0931 RGFP966 Medchem Express Cat#HY-13909 BRD4354 Medchem Express Cat#HY-112719 CXD101 Medchem Express Cat#HY-100748 Critical commercial assays SMARTer Stranded RNA-Seq Kit Takara Bio Cat# 634839 E.Z.N.An HP Total RNA Extraction Kit Omega Cat# R6812 First-Strand cDNA Synthesis Kit Bio-Rad Cat# 1708841 SYBR Green Bio-Rad Cat# 1725121 Nucleofector kit R Lonza Cat# VCA-1001 Deposited data RNA-seq data This paper GEO: GSE246479 Experimental models: Cell lines WiT49 Prof. Herman Yeger RRID: CVCL_0583 HEK293T ATCC Cat# CRL-3216; RRID: CVCL_0063 Experimental models: Organisms/strains NSG mice Jackson Laboratory Strain code 5557 Oligonucleotides qRT-PCR sequences This paper See Table S2 Recombinant DNA pEP4 E02S EN2K Addgene Cat #20925 pCEP4-M2L Addgene Cat #20926 (Continued on next page) e1 Cell Reports Medicine 5, 101770, October 15, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER pEP4 E02S ET2K Addgene Cat #20927 pHAGE PGK-GFP-IRES-Luciferase Addgene Cat #46793 VSVG Addgene Cat #12259 psPAX2 Addgene Cat #12260 Software and algorithms GraphPad Prism8 GraphPad https://www.graphpad.com GSEA BROAD Institute https://www.gsea-msigdb.org/gsea/index.jsp Custom generated R scripts This paper https://github.com/chenlab-sj/WiT49_PRC R R project https://www.r-project.org/ edgeR (v3.40.2) R package https://bioconductor.org/packages/ release/bioc/html/edgeR.html STAR (version 2.5.2b) Dr. Alexander Dobin54 https://github.com/alexdobin/STAR BioRender BioRender https://www.biorender.com/ Article ll OPEN ACCESS
RNA Sequencing:Article Title: Modeling high-risk Wilms tumors enables the discovery of therapeutic vulnerability.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-Ki67 Abcam Cat# ab15580; RRID: AB_443209 Anti-SIX2 Proteintech Cat# 11562-1-AP; RRID: AB_2189084 Anti-NCAM1 Thermo Cat# 701379; RRID: AB_2532477 Anti-EZH2 Cell signaling technology Cat# 5246; RRID: AB_10694683 Anti-Vimentin Cell signaling technology Cat# 5741; RRID: AB_10695459 Anti-HLAB Cell signaling technology Cat# 41915; RRID: AB_3224414 Anti-human mitochondria Thermo Cat# MA5-12017; RRID: AB_10983622 Anti-Snail2 Proteintech Cat# 12129-1-AP; RRID: AB_2191889 Anti-Keratin 18 Thermo Cat# MA5-12104; RRID: AB_10981680 Biological samples PDX226 Dr. Michael Dye38 SJWLM046152_X1 PDX207 Dr. Michael Dye38 SJWLM049191_X1 PDX253 Dr. Michael Dye38 SJWLM046157_X1 Chemicals, peptides, and recombinant proteins Panobinostat TargetMol CatT2383-CUST Romidepsin Medchem Express Cat#HY-15149 Doxorubicin TargetMol Cat#T1020-CUST Alisertib Medchem Express Cat#HY-10971 Cytarabine Medchem Express Cat#HY-13605 CY-10683 Medchem Express Cat#HY-N0931 RGFP966 Medchem Express Cat#HY-13909 BRD4354 Medchem Express Cat#HY-112719 CXD101 Medchem Express Cat#HY-100748 Critical commercial assays SMARTer Stranded RNA-Seq Kit Takara Bio Cat# 634839 E.Z.N.An HP Total RNA Extraction Kit Omega Cat# R6812 First-Strand cDNA Synthesis Kit Bio-Rad Cat# 1708841 SYBR Green Bio-Rad Cat# 1725121 Nucleofector kit R Lonza Cat# VCA-1001 Deposited data RNA-seq data This paper GEO: GSE246479 Experimental models: Cell lines WiT49 Prof. Herman Yeger RRID: CVCL_0583 HEK293T ATCC Cat# CRL-3216; RRID: CVCL_0063 Experimental models: Organisms/strains NSG mice Jackson Laboratory Strain code 5557 Oligonucleotides qRT-PCR sequences This paper See Table S2 Recombinant DNA pEP4 E02S EN2K Addgene Cat #20925 pCEP4-M2L Addgene Cat #20926 (Continued on next page) e1 Cell Reports Medicine 5, 101770, October 15, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER pEP4 E02S ET2K Addgene Cat #20927 pHAGE PGK-GFP-IRES-Luciferase Addgene Cat #46793 VSVG Addgene Cat #12259 psPAX2 Addgene Cat #12260 Software and algorithms GraphPad Prism8 GraphPad https://www.graphpad.com GSEA BROAD Institute https://www.gsea-msigdb.org/gsea/index.jsp Custom generated R scripts This paper https://github.com/chenlab-sj/WiT49_PRC R R project https://www.r-project.org/ edgeR (v3.40.2) R package https://bioconductor.org/packages/ release/bioc/html/edgeR.html STAR (version 2.5.2b) Dr. Alexander Dobin54 https://github.com/alexdobin/STAR BioRender BioRender https://www.biorender.com/
Article Title: Modeling high-risk Wilms tumors enables the discovery of therapeutic vulnerability
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-Ki67 Abcam Cat# ab15580; RRID: AB_443209 Anti-SIX2 Proteintech Cat# 11562-1-AP; RRID: AB_2189084 Anti-NCAM1 Thermo Cat# 701379; RRID: AB_2532477 Anti-EZH2 Cell signaling technology Cat# 5246; RRID: AB_10694683 Anti-Vimentin Cell signaling technology Cat# 5741; RRID: AB_10695459 Anti-HLAB Cell signaling technology Cat# 41915; RRID: AB_3224414 Anti-human mitochondria Thermo Cat# MA5-12017; RRID: AB_10983622 Anti-Snail2 Proteintech Cat# 12129-1-AP; RRID: AB_2191889 Anti-Keratin 18 Thermo Cat# MA5-12104; RRID: AB_10981680 Biological samples PDX226 Dr. Michael Dye38 SJWLM046152_X1 PDX207 Dr. Michael Dye38 SJWLM049191_X1 PDX253 Dr. Michael Dye38 SJWLM046157_X1 Chemicals, peptides, and recombinant proteins Panobinostat TargetMol CatT2383-CUST Romidepsin Medchem Express Cat#HY-15149 Doxorubicin TargetMol Cat#T1020-CUST Alisertib Medchem Express Cat#HY-10971 Cytarabine Medchem Express Cat#HY-13605 CY-10683 Medchem Express Cat#HY-N0931 RGFP966 Medchem Express Cat#HY-13909 BRD4354 Medchem Express Cat#HY-112719 CXD101 Medchem Express Cat#HY-100748 Critical commercial assays SMARTer Stranded RNA-Seq Kit Takara Bio Cat# 634839 E.Z.N.An HP Total RNA Extraction Kit Omega Cat# R6812 First-Strand cDNA Synthesis Kit Bio-Rad Cat# 1708841 SYBR Green Bio-Rad Cat# 1725121 Nucleofector kit R Lonza Cat# VCA-1001 Deposited data RNA-seq data This paper GEO: GSE246479 Experimental models: Cell lines WiT49 Prof. Herman Yeger RRID: CVCL_0583 HEK293T ATCC Cat# CRL-3216; RRID: CVCL_0063 Experimental models: Organisms/strains NSG mice Jackson Laboratory Strain code 5557 Oligonucleotides qRT-PCR sequences This paper See Table S2 Recombinant DNA pEP4 E02S EN2K Addgene Cat #20925 pCEP4-M2L Addgene Cat #20926 (Continued on next page) e1 Cell Reports Medicine 5, 101770, October 15, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER pEP4 E02S ET2K Addgene Cat #20927 pHAGE PGK-GFP-IRES-Luciferase Addgene Cat #46793 VSVG Addgene Cat #12259 psPAX2 Addgene Cat #12260 Software and algorithms GraphPad Prism8 GraphPad https://www.graphpad.com GSEA BROAD Institute https://www.gsea-msigdb.org/gsea/index.jsp Custom generated R scripts This paper https://github.com/chenlab-sj/WiT49_PRC R R project https://www.r-project.org/ edgeR (v3.40.2) R package https://bioconductor.org/packages/ release/bioc/html/edgeR.html STAR (version 2.5.2b) Dr. Alexander Dobin54 https://github.com/alexdobin/STAR BioRender BioRender https://www.biorender.com/ Article ll OPEN ACCESS
Quantitative RT-PCR:Article Title: Modeling high-risk Wilms tumors enables the discovery of therapeutic vulnerability.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-Ki67 Abcam Cat# ab15580; RRID: AB_443209 Anti-SIX2 Proteintech Cat# 11562-1-AP; RRID: AB_2189084 Anti-NCAM1 Thermo Cat# 701379; RRID: AB_2532477 Anti-EZH2 Cell signaling technology Cat# 5246; RRID: AB_10694683 Anti-Vimentin Cell signaling technology Cat# 5741; RRID: AB_10695459 Anti-HLAB Cell signaling technology Cat# 41915; RRID: AB_3224414 Anti-human mitochondria Thermo Cat# MA5-12017; RRID: AB_10983622 Anti-Snail2 Proteintech Cat# 12129-1-AP; RRID: AB_2191889 Anti-Keratin 18 Thermo Cat# MA5-12104; RRID: AB_10981680 Biological samples PDX226 Dr. Michael Dye38 SJWLM046152_X1 PDX207 Dr. Michael Dye38 SJWLM049191_X1 PDX253 Dr. Michael Dye38 SJWLM046157_X1 Chemicals, peptides, and recombinant proteins Panobinostat TargetMol CatT2383-CUST Romidepsin Medchem Express Cat#HY-15149 Doxorubicin TargetMol Cat#T1020-CUST Alisertib Medchem Express Cat#HY-10971 Cytarabine Medchem Express Cat#HY-13605 CY-10683 Medchem Express Cat#HY-N0931 RGFP966 Medchem Express Cat#HY-13909 BRD4354 Medchem Express Cat#HY-112719 CXD101 Medchem Express Cat#HY-100748 Critical commercial assays SMARTer Stranded RNA-Seq Kit Takara Bio Cat# 634839 E.Z.N.An HP Total RNA Extraction Kit Omega Cat# R6812 First-Strand cDNA Synthesis Kit Bio-Rad Cat# 1708841 SYBR Green Bio-Rad Cat# 1725121 Nucleofector kit R Lonza Cat# VCA-1001 Deposited data RNA-seq data This paper GEO: GSE246479 Experimental models: Cell lines WiT49 Prof. Herman Yeger RRID: CVCL_0583 HEK293T ATCC Cat# CRL-3216; RRID: CVCL_0063 Experimental models: Organisms/strains NSG mice Jackson Laboratory Strain code 5557 Oligonucleotides qRT-PCR sequences This paper See Table S2 Recombinant DNA pEP4 E02S EN2K Addgene Cat #20925 pCEP4-M2L Addgene Cat #20926 (Continued on next page) e1 Cell Reports Medicine 5, 101770, October 15, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER pEP4 E02S ET2K Addgene Cat #20927 pHAGE PGK-GFP-IRES-Luciferase Addgene Cat #46793 VSVG Addgene Cat #12259 psPAX2 Addgene Cat #12260 Software and algorithms GraphPad Prism8 GraphPad https://www.graphpad.com GSEA BROAD Institute https://www.gsea-msigdb.org/gsea/index.jsp Custom generated R scripts This paper https://github.com/chenlab-sj/WiT49_PRC R R project https://www.r-project.org/ edgeR (v3.40.2) R package https://bioconductor.org/packages/ release/bioc/html/edgeR.html STAR (version 2.5.2b) Dr. Alexander Dobin54 https://github.com/alexdobin/STAR BioRender BioRender https://www.biorender.com/
Article Title: Modeling high-risk Wilms tumors enables the discovery of therapeutic vulnerability
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-Ki67 Abcam Cat# ab15580; RRID: AB_443209 Anti-SIX2 Proteintech Cat# 11562-1-AP; RRID: AB_2189084 Anti-NCAM1 Thermo Cat# 701379; RRID: AB_2532477 Anti-EZH2 Cell signaling technology Cat# 5246; RRID: AB_10694683 Anti-Vimentin Cell signaling technology Cat# 5741; RRID: AB_10695459 Anti-HLAB Cell signaling technology Cat# 41915; RRID: AB_3224414 Anti-human mitochondria Thermo Cat# MA5-12017; RRID: AB_10983622 Anti-Snail2 Proteintech Cat# 12129-1-AP; RRID: AB_2191889 Anti-Keratin 18 Thermo Cat# MA5-12104; RRID: AB_10981680 Biological samples PDX226 Dr. Michael Dye38 SJWLM046152_X1 PDX207 Dr. Michael Dye38 SJWLM049191_X1 PDX253 Dr. Michael Dye38 SJWLM046157_X1 Chemicals, peptides, and recombinant proteins Panobinostat TargetMol CatT2383-CUST Romidepsin Medchem Express Cat#HY-15149 Doxorubicin TargetMol Cat#T1020-CUST Alisertib Medchem Express Cat#HY-10971 Cytarabine Medchem Express Cat#HY-13605 CY-10683 Medchem Express Cat#HY-N0931 RGFP966 Medchem Express Cat#HY-13909 BRD4354 Medchem Express Cat#HY-112719 CXD101 Medchem Express Cat#HY-100748 Critical commercial assays SMARTer Stranded RNA-Seq Kit Takara Bio Cat# 634839 E.Z.N.An HP Total RNA Extraction Kit Omega Cat# R6812 First-Strand cDNA Synthesis Kit Bio-Rad Cat# 1708841 SYBR Green Bio-Rad Cat# 1725121 Nucleofector kit R Lonza Cat# VCA-1001 Deposited data RNA-seq data This paper GEO: GSE246479 Experimental models: Cell lines WiT49 Prof. Herman Yeger RRID: CVCL_0583 HEK293T ATCC Cat# CRL-3216; RRID: CVCL_0063 Experimental models: Organisms/strains NSG mice Jackson Laboratory Strain code 5557 Oligonucleotides qRT-PCR sequences This paper See Table S2 Recombinant DNA pEP4 E02S EN2K Addgene Cat #20925 pCEP4-M2L Addgene Cat #20926 (Continued on next page) e1 Cell Reports Medicine 5, 101770, October 15, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER pEP4 E02S ET2K Addgene Cat #20927 pHAGE PGK-GFP-IRES-Luciferase Addgene Cat #46793 VSVG Addgene Cat #12259 psPAX2 Addgene Cat #12260 Software and algorithms GraphPad Prism8 GraphPad https://www.graphpad.com GSEA BROAD Institute https://www.gsea-msigdb.org/gsea/index.jsp Custom generated R scripts This paper https://github.com/chenlab-sj/WiT49_PRC R R project https://www.r-project.org/ edgeR (v3.40.2) R package https://bioconductor.org/packages/ release/bioc/html/edgeR.html STAR (version 2.5.2b) Dr. Alexander Dobin54 https://github.com/alexdobin/STAR BioRender BioRender https://www.biorender.com/ Article ll OPEN ACCESS
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