Data-independent acquisition:Article Title: Type I collagen deletion in αSMA + myofibroblasts augments immune suppression and accelerates progression of pancreatic cancer.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Goat Albumin Bethyl Cat# A90-134, RRID:AB_67120 Mouse aSMA DAKO Cat# M0851, RRID:AB_2223500 Rabbit CD206 (MRC1) Abcam Cat# ab64693, RRID:AB_1523910 Rabbit CD45R Abcam Cat# ab64100, RRID:AB_1140036 Rabbit CK19 Abcam Cat# ab52625, RRID:AB_2281020 Goat Collagen I SouthernBiotech Cat# 1310-01, RRID:AB_2753206 Rabbit Ki67 Abcam Cat# ab15580, RRID:AB_443209 Rabbit SOX9 Abcam Cat# ab185966, RRID:AB_2728660 Rabbit NG2 Chemicon/Millipore Cat# AB5320, RRID:AB_11213678 Rat CD31 Dianova Cat# DIA-310, RRID:AB_2631039 Goat Collagen IV Abcam Cat# ab6585, RRID:AB_305583 Rabbit FSP1 DAKO Cat# A5114, RRID:AB_2335679 Rabbit CD3 Abcam Cat# ab16669, RRID:AB_443425 Rabbit CD4 Cell Signaling Cat# 25229, RRID:AB_2798898 Rabbit CD8a Cell Signaling Cat# 98941, RRID:AB_2756376 Rat Cytokeratin 8 DSHB Cat# TROMA-I, RRID:AB_531826 Rat PDGFRa(CD140a)-PE BioLegend Cat# 135905, RRID:AB_1953268 Rat EpCAM(CD326)-AF488 BioLegend Cat# 118210, RRID:AB_1134099 Rat CD45-Pacific Blue BioLegend Cat# 103126, RRID:AB_493535 Rat CD3-AF700 eBioscience Cat# 56-0032-82, RRID:AB_529507 Rat CD11b-BV711 BD Cat# 563168, RRID:AB_2716860 Rat CD206-FITC BioLegend Cat# 141703, RRID:AB_10900988 Rat CD19-APC eBioscience Cat# 17-0193-82, RRID:AB_1659676 Biological Samples Tissue microarray sections of human PDAC MDACC IRB LAB05-0854 Chemicals, Peptides, and Recombinant Proteins RS 504393 Tocris Cat# 2517/10 SB 225002 Tocris Cat# 2725/10 Collagenase IV Gibco Cat# 17104019 Dispase II Gibco Cat# 17105041 Liberase Roche Cat# 5401020001 DNase I Roche Cat# 10104159001 Type I collagen solution from rat tail Sigma-Aldrich Cat# C3867 Critical Commercial Assays Direct-zol RNA Kit Zymo Research Cat# R2050 Reverse Transcription Kit Applied Biosystems Cat# 4368814 SYBR Green Master Mix Applied Biosystems Cat# 4367659 Cell Counting Kit-8 Abcam Cat# ab228554 Live-Dead-eFluor780 eBioscience Cat# 65-0865-14 Foxp3/Transcription Factor Staining Buffer Set eBioscience Cat# 00-5523-00 Gomori’s Trichrome Stain Kit Leica Biosystems Cat# 38016SS2 Chromium Single Cell 3’ Reagent Kits (v2) 10x Genomics Cat# PN-120237 ABC-Kit Vector Cat# PK-6100 (Continued on next page) e1 Cancer Cell 39, 548–565.e1–e6, April 12, 2021 .. REAGENT or RESOURCE SOURCE IDENTIFIER Stable DAB Invitrogen Cat# 750118 Direct Red 80 Sigma-Aldrich Cat# 365548 TruSeq Stranded mRNA Sample Prep Kit Illumina Cat# 20020594 Deposited Data KPPF and KPPF;Col1smaKO tumor RNA-sequencing This paper GEO: GSE131500 Single-cell RNA-sequencing This paper GEO: GSE166298 TCGA pancreatic adenocarcinoma cohort survival and gene expression data (GDAC Firehose PAAD) Broad Institute http://gdac.broadinstitute.org/runs/ stddata__2016_01_28/data/PAAD/ 20160128/ Experimental Models: Cell Lines Primary mouse KPPF;Col1smaKO cancer cells This paper N/A Experimental Models: Organisms/Strains Mouse: FSF-KrasG12D/+;Pdx1-Flp Schonhuber et al., 2014 N/A Mouse: Trp53frt/+ Lee et al., 2012 N/A Mouse: aSMA-Cre LeBleu et al., 2013 N/A Mouse: Fsp1-Cre Xue et al., 2003; Bhowmick et al., 2004 N/A Mouse: Rosa26-CAG-loxP-frt-Stop-frtFireflyLuc-EGFP-loxP-RenillaLuctdTomato Chen et al., 2018 N/A Mouse: Col1a1tm1a(EUCOMM)Wtsi EuMMCR https://www.mousephenotype.org/data/ alleles/MGI:88467/tm1a(EUCOMM)Wtsii Mouse: Col1a1loxP/loxP This study N/A Oligonucleotides Mouse Gapdh qRT-PCR F AGGTCGGTGTGAACGGATTTG This paper N/A Mouse Gapdh qRT-PCR R TGTAGACCATGTAGTTGAGGTCA This paper N/A Mouse Col1a1 qRT-PCR F GCTCCTCTTAGGGGCCACT This paper N/A Mouse Col1a1 qRT-PCR R CCACGTCTCACCATTGGGG This paper N/A Mouse Cxcl5 qRT-PCR F GTTCCATCTCGCCATTCATGC This paper N/A Mouse Cxcl5 qRT-PCR R GCGGCTATGACTGAGGAAGG This paper N/A Mouse Sox9 qRT-PCR F GAGCCGGATCTGAAGAGGGA This paper N/A Mouse Sox9 qRT-PCR R GCTTGACGTGTGGCTTGTTC This paper N/A Software and Algorithms Flowjo v10.7.1 Flowjo, L.L.C.
Microarray:Article Title: Type I collagen deletion in αSMA + myofibroblasts augments immune suppression and accelerates progression of pancreatic cancer.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Goat Albumin Bethyl Cat# A90-134, RRID:AB_67120 Mouse aSMA DAKO Cat# M0851, RRID:AB_2223500 Rabbit CD206 (MRC1) Abcam Cat# ab64693, RRID:AB_1523910 Rabbit CD45R Abcam Cat# ab64100, RRID:AB_1140036 Rabbit CK19 Abcam Cat# ab52625, RRID:AB_2281020 Goat Collagen I SouthernBiotech Cat# 1310-01, RRID:AB_2753206 Rabbit Ki67 Abcam Cat# ab15580, RRID:AB_443209 Rabbit SOX9 Abcam Cat# ab185966, RRID:AB_2728660 Rabbit NG2 Chemicon/Millipore Cat# AB5320, RRID:AB_11213678 Rat CD31 Dianova Cat# DIA-310, RRID:AB_2631039 Goat Collagen IV Abcam Cat# ab6585, RRID:AB_305583 Rabbit FSP1 DAKO Cat# A5114, RRID:AB_2335679 Rabbit CD3 Abcam Cat# ab16669, RRID:AB_443425 Rabbit CD4 Cell Signaling Cat# 25229, RRID:AB_2798898 Rabbit CD8a Cell Signaling Cat# 98941, RRID:AB_2756376 Rat Cytokeratin 8 DSHB Cat# TROMA-I, RRID:AB_531826 Rat PDGFRa(CD140a)-PE BioLegend Cat# 135905, RRID:AB_1953268 Rat EpCAM(CD326)-AF488 BioLegend Cat# 118210, RRID:AB_1134099 Rat CD45-Pacific Blue BioLegend Cat# 103126, RRID:AB_493535 Rat CD3-AF700 eBioscience Cat# 56-0032-82, RRID:AB_529507 Rat CD11b-BV711 BD Cat# 563168, RRID:AB_2716860 Rat CD206-FITC BioLegend Cat# 141703, RRID:AB_10900988 Rat CD19-APC eBioscience Cat# 17-0193-82, RRID:AB_1659676 Biological Samples Tissue microarray sections of human PDAC MDACC IRB LAB05-0854 Chemicals, Peptides, and Recombinant Proteins RS 504393 Tocris Cat# 2517/10 SB 225002 Tocris Cat# 2725/10 Collagenase IV Gibco Cat# 17104019 Dispase II Gibco Cat# 17105041 Liberase Roche Cat# 5401020001 DNase I Roche Cat# 10104159001 Type I collagen solution from rat tail Sigma-Aldrich Cat# C3867 Critical Commercial Assays Direct-zol RNA Kit Zymo Research Cat# R2050 Reverse Transcription Kit Applied Biosystems Cat# 4368814 SYBR Green Master Mix Applied Biosystems Cat# 4367659 Cell Counting Kit-8 Abcam Cat# ab228554 Live-Dead-eFluor780 eBioscience Cat# 65-0865-14 Foxp3/Transcription Factor Staining Buffer Set eBioscience Cat# 00-5523-00 Gomori’s Trichrome Stain Kit Leica Biosystems Cat# 38016SS2 Chromium Single Cell 3’ Reagent Kits (v2) 10x Genomics Cat# PN-120237 ABC-Kit Vector Cat# PK-6100 (Continued on next page) e1 Cancer Cell 39, 548–565.e1–e6, April 12, 2021 .. REAGENT or RESOURCE SOURCE IDENTIFIER Stable DAB Invitrogen Cat# 750118 Direct Red 80 Sigma-Aldrich Cat# 365548 TruSeq Stranded mRNA Sample Prep Kit Illumina Cat# 20020594 Deposited Data KPPF and KPPF;Col1smaKO tumor RNA-sequencing This paper GEO: GSE131500 Single-cell RNA-sequencing This paper GEO: GSE166298 TCGA pancreatic adenocarcinoma cohort survival and gene expression data (GDAC Firehose PAAD) Broad Institute http://gdac.broadinstitute.org/runs/ stddata__2016_01_28/data/PAAD/ 20160128/ Experimental Models: Cell Lines Primary mouse KPPF;Col1smaKO cancer cells This paper N/A Experimental Models: Organisms/Strains Mouse: FSF-KrasG12D/+;Pdx1-Flp Schonhuber et al., 2014 N/A Mouse: Trp53frt/+ Lee et al., 2012 N/A Mouse: aSMA-Cre LeBleu et al., 2013 N/A Mouse: Fsp1-Cre Xue et al., 2003; Bhowmick et al., 2004 N/A Mouse: Rosa26-CAG-loxP-frt-Stop-frtFireflyLuc-EGFP-loxP-RenillaLuctdTomato Chen et al., 2018 N/A Mouse: Col1a1tm1a(EUCOMM)Wtsi EuMMCR https://www.mousephenotype.org/data/ alleles/MGI:88467/tm1a(EUCOMM)Wtsii Mouse: Col1a1loxP/loxP This study N/A Oligonucleotides Mouse Gapdh qRT-PCR F AGGTCGGTGTGAACGGATTTG This paper N/A Mouse Gapdh qRT-PCR R TGTAGACCATGTAGTTGAGGTCA This paper N/A Mouse Col1a1 qRT-PCR F GCTCCTCTTAGGGGCCACT This paper N/A Mouse Col1a1 qRT-PCR R CCACGTCTCACCATTGGGG This paper N/A Mouse Cxcl5 qRT-PCR F GTTCCATCTCGCCATTCATGC This paper N/A Mouse Cxcl5 qRT-PCR R GCGGCTATGACTGAGGAAGG This paper N/A Mouse Sox9 qRT-PCR F GAGCCGGATCTGAAGAGGGA This paper N/A Mouse Sox9 qRT-PCR R GCTTGACGTGTGGCTTGTTC This paper N/A Software and Algorithms Flowjo v10.7.1 Flowjo, L.L.C.
Recombinant:Article Title: Type I collagen deletion in αSMA + myofibroblasts augments immune suppression and accelerates progression of pancreatic cancer.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Goat Albumin Bethyl Cat# A90-134, RRID:AB_67120 Mouse aSMA DAKO Cat# M0851, RRID:AB_2223500 Rabbit CD206 (MRC1) Abcam Cat# ab64693, RRID:AB_1523910 Rabbit CD45R Abcam Cat# ab64100, RRID:AB_1140036 Rabbit CK19 Abcam Cat# ab52625, RRID:AB_2281020 Goat Collagen I SouthernBiotech Cat# 1310-01, RRID:AB_2753206 Rabbit Ki67 Abcam Cat# ab15580, RRID:AB_443209 Rabbit SOX9 Abcam Cat# ab185966, RRID:AB_2728660 Rabbit NG2 Chemicon/Millipore Cat# AB5320, RRID:AB_11213678 Rat CD31 Dianova Cat# DIA-310, RRID:AB_2631039 Goat Collagen IV Abcam Cat# ab6585, RRID:AB_305583 Rabbit FSP1 DAKO Cat# A5114, RRID:AB_2335679 Rabbit CD3 Abcam Cat# ab16669, RRID:AB_443425 Rabbit CD4 Cell Signaling Cat# 25229, RRID:AB_2798898 Rabbit CD8a Cell Signaling Cat# 98941, RRID:AB_2756376 Rat Cytokeratin 8 DSHB Cat# TROMA-I, RRID:AB_531826 Rat PDGFRa(CD140a)-PE BioLegend Cat# 135905, RRID:AB_1953268 Rat EpCAM(CD326)-AF488 BioLegend Cat# 118210, RRID:AB_1134099 Rat CD45-Pacific Blue BioLegend Cat# 103126, RRID:AB_493535 Rat CD3-AF700 eBioscience Cat# 56-0032-82, RRID:AB_529507 Rat CD11b-BV711 BD Cat# 563168, RRID:AB_2716860 Rat CD206-FITC BioLegend Cat# 141703, RRID:AB_10900988 Rat CD19-APC eBioscience Cat# 17-0193-82, RRID:AB_1659676 Biological Samples Tissue microarray sections of human PDAC MDACC IRB LAB05-0854 Chemicals, Peptides, and Recombinant Proteins RS 504393 Tocris Cat# 2517/10 SB 225002 Tocris Cat# 2725/10 Collagenase IV Gibco Cat# 17104019 Dispase II Gibco Cat# 17105041 Liberase Roche Cat# 5401020001 DNase I Roche Cat# 10104159001 Type I collagen solution from rat tail Sigma-Aldrich Cat# C3867 Critical Commercial Assays Direct-zol RNA Kit Zymo Research Cat# R2050 Reverse Transcription Kit Applied Biosystems Cat# 4368814 SYBR Green Master Mix Applied Biosystems Cat# 4367659 Cell Counting Kit-8 Abcam Cat# ab228554 Live-Dead-eFluor780 eBioscience Cat# 65-0865-14 Foxp3/Transcription Factor Staining Buffer Set eBioscience Cat# 00-5523-00 Gomori’s Trichrome Stain Kit Leica Biosystems Cat# 38016SS2 Chromium Single Cell 3’ Reagent Kits (v2) 10x Genomics Cat# PN-120237 ABC-Kit Vector Cat# PK-6100 (Continued on next page) e1 Cancer Cell 39, 548–565.e1–e6, April 12, 2021 .. REAGENT or RESOURCE SOURCE IDENTIFIER Stable DAB Invitrogen Cat# 750118 Direct Red 80 Sigma-Aldrich Cat# 365548 TruSeq Stranded mRNA Sample Prep Kit Illumina Cat# 20020594 Deposited Data KPPF and KPPF;Col1smaKO tumor RNA-sequencing This paper GEO: GSE131500 Single-cell RNA-sequencing This paper GEO: GSE166298 TCGA pancreatic adenocarcinoma cohort survival and gene expression data (GDAC Firehose PAAD) Broad Institute http://gdac.broadinstitute.org/runs/ stddata__2016_01_28/data/PAAD/ 20160128/ Experimental Models: Cell Lines Primary mouse KPPF;Col1smaKO cancer cells This paper N/A Experimental Models: Organisms/Strains Mouse: FSF-KrasG12D/+;Pdx1-Flp Schonhuber et al., 2014 N/A Mouse: Trp53frt/+ Lee et al., 2012 N/A Mouse: aSMA-Cre LeBleu et al., 2013 N/A Mouse: Fsp1-Cre Xue et al., 2003; Bhowmick et al., 2004 N/A Mouse: Rosa26-CAG-loxP-frt-Stop-frtFireflyLuc-EGFP-loxP-RenillaLuctdTomato Chen et al., 2018 N/A Mouse: Col1a1tm1a(EUCOMM)Wtsi EuMMCR https://www.mousephenotype.org/data/ alleles/MGI:88467/tm1a(EUCOMM)Wtsii Mouse: Col1a1loxP/loxP This study N/A Oligonucleotides Mouse Gapdh qRT-PCR F AGGTCGGTGTGAACGGATTTG This paper N/A Mouse Gapdh qRT-PCR R TGTAGACCATGTAGTTGAGGTCA This paper N/A Mouse Col1a1 qRT-PCR F GCTCCTCTTAGGGGCCACT This paper N/A Mouse Col1a1 qRT-PCR R CCACGTCTCACCATTGGGG This paper N/A Mouse Cxcl5 qRT-PCR F GTTCCATCTCGCCATTCATGC This paper N/A Mouse Cxcl5 qRT-PCR R GCGGCTATGACTGAGGAAGG This paper N/A Mouse Sox9 qRT-PCR F GAGCCGGATCTGAAGAGGGA This paper N/A Mouse Sox9 qRT-PCR R GCTTGACGTGTGGCTTGTTC This paper N/A Software and Algorithms Flowjo v10.7.1 Flowjo, L.L.C.
Reverse Transcription:Article Title: Type I collagen deletion in αSMA + myofibroblasts augments immune suppression and accelerates progression of pancreatic cancer.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Goat Albumin Bethyl Cat# A90-134, RRID:AB_67120 Mouse aSMA DAKO Cat# M0851, RRID:AB_2223500 Rabbit CD206 (MRC1) Abcam Cat# ab64693, RRID:AB_1523910 Rabbit CD45R Abcam Cat# ab64100, RRID:AB_1140036 Rabbit CK19 Abcam Cat# ab52625, RRID:AB_2281020 Goat Collagen I SouthernBiotech Cat# 1310-01, RRID:AB_2753206 Rabbit Ki67 Abcam Cat# ab15580, RRID:AB_443209 Rabbit SOX9 Abcam Cat# ab185966, RRID:AB_2728660 Rabbit NG2 Chemicon/Millipore Cat# AB5320, RRID:AB_11213678 Rat CD31 Dianova Cat# DIA-310, RRID:AB_2631039 Goat Collagen IV Abcam Cat# ab6585, RRID:AB_305583 Rabbit FSP1 DAKO Cat# A5114, RRID:AB_2335679 Rabbit CD3 Abcam Cat# ab16669, RRID:AB_443425 Rabbit CD4 Cell Signaling Cat# 25229, RRID:AB_2798898 Rabbit CD8a Cell Signaling Cat# 98941, RRID:AB_2756376 Rat Cytokeratin 8 DSHB Cat# TROMA-I, RRID:AB_531826 Rat PDGFRa(CD140a)-PE BioLegend Cat# 135905, RRID:AB_1953268 Rat EpCAM(CD326)-AF488 BioLegend Cat# 118210, RRID:AB_1134099 Rat CD45-Pacific Blue BioLegend Cat# 103126, RRID:AB_493535 Rat CD3-AF700 eBioscience Cat# 56-0032-82, RRID:AB_529507 Rat CD11b-BV711 BD Cat# 563168, RRID:AB_2716860 Rat CD206-FITC BioLegend Cat# 141703, RRID:AB_10900988 Rat CD19-APC eBioscience Cat# 17-0193-82, RRID:AB_1659676 Biological Samples Tissue microarray sections of human PDAC MDACC IRB LAB05-0854 Chemicals, Peptides, and Recombinant Proteins RS 504393 Tocris Cat# 2517/10 SB 225002 Tocris Cat# 2725/10 Collagenase IV Gibco Cat# 17104019 Dispase II Gibco Cat# 17105041 Liberase Roche Cat# 5401020001 DNase I Roche Cat# 10104159001 Type I collagen solution from rat tail Sigma-Aldrich Cat# C3867 Critical Commercial Assays Direct-zol RNA Kit Zymo Research Cat# R2050 Reverse Transcription Kit Applied Biosystems Cat# 4368814 SYBR Green Master Mix Applied Biosystems Cat# 4367659 Cell Counting Kit-8 Abcam Cat# ab228554 Live-Dead-eFluor780 eBioscience Cat# 65-0865-14 Foxp3/Transcription Factor Staining Buffer Set eBioscience Cat# 00-5523-00 Gomori’s Trichrome Stain Kit Leica Biosystems Cat# 38016SS2 Chromium Single Cell 3’ Reagent Kits (v2) 10x Genomics Cat# PN-120237 ABC-Kit Vector Cat# PK-6100 (Continued on next page) e1 Cancer Cell 39, 548–565.e1–e6, April 12, 2021 .. REAGENT or RESOURCE SOURCE IDENTIFIER Stable DAB Invitrogen Cat# 750118 Direct Red 80 Sigma-Aldrich Cat# 365548 TruSeq Stranded mRNA Sample Prep Kit Illumina Cat# 20020594 Deposited Data KPPF and KPPF;Col1smaKO tumor RNA-sequencing This paper GEO: GSE131500 Single-cell RNA-sequencing This paper GEO: GSE166298 TCGA pancreatic adenocarcinoma cohort survival and gene expression data (GDAC Firehose PAAD) Broad Institute http://gdac.broadinstitute.org/runs/ stddata__2016_01_28/data/PAAD/ 20160128/ Experimental Models: Cell Lines Primary mouse KPPF;Col1smaKO cancer cells This paper N/A Experimental Models: Organisms/Strains Mouse: FSF-KrasG12D/+;Pdx1-Flp Schonhuber et al., 2014 N/A Mouse: Trp53frt/+ Lee et al., 2012 N/A Mouse: aSMA-Cre LeBleu et al., 2013 N/A Mouse: Fsp1-Cre Xue et al., 2003; Bhowmick et al., 2004 N/A Mouse: Rosa26-CAG-loxP-frt-Stop-frtFireflyLuc-EGFP-loxP-RenillaLuctdTomato Chen et al., 2018 N/A Mouse: Col1a1tm1a(EUCOMM)Wtsi EuMMCR https://www.mousephenotype.org/data/ alleles/MGI:88467/tm1a(EUCOMM)Wtsii Mouse: Col1a1loxP/loxP This study N/A Oligonucleotides Mouse Gapdh qRT-PCR F AGGTCGGTGTGAACGGATTTG This paper N/A Mouse Gapdh qRT-PCR R TGTAGACCATGTAGTTGAGGTCA This paper N/A Mouse Col1a1 qRT-PCR F GCTCCTCTTAGGGGCCACT This paper N/A Mouse Col1a1 qRT-PCR R CCACGTCTCACCATTGGGG This paper N/A Mouse Cxcl5 qRT-PCR F GTTCCATCTCGCCATTCATGC This paper N/A Mouse Cxcl5 qRT-PCR R GCGGCTATGACTGAGGAAGG This paper N/A Mouse Sox9 qRT-PCR F GAGCCGGATCTGAAGAGGGA This paper N/A Mouse Sox9 qRT-PCR R GCTTGACGTGTGGCTTGTTC This paper N/A Software and Algorithms Flowjo v10.7.1 Flowjo, L.L.C.
SYBR Green Assay:Article Title: Type I collagen deletion in αSMA + myofibroblasts augments immune suppression and accelerates progression of pancreatic cancer.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Goat Albumin Bethyl Cat# A90-134, RRID:AB_67120 Mouse aSMA DAKO Cat# M0851, RRID:AB_2223500 Rabbit CD206 (MRC1) Abcam Cat# ab64693, RRID:AB_1523910 Rabbit CD45R Abcam Cat# ab64100, RRID:AB_1140036 Rabbit CK19 Abcam Cat# ab52625, RRID:AB_2281020 Goat Collagen I SouthernBiotech Cat# 1310-01, RRID:AB_2753206 Rabbit Ki67 Abcam Cat# ab15580, RRID:AB_443209 Rabbit SOX9 Abcam Cat# ab185966, RRID:AB_2728660 Rabbit NG2 Chemicon/Millipore Cat# AB5320, RRID:AB_11213678 Rat CD31 Dianova Cat# DIA-310, RRID:AB_2631039 Goat Collagen IV Abcam Cat# ab6585, RRID:AB_305583 Rabbit FSP1 DAKO Cat# A5114, RRID:AB_2335679 Rabbit CD3 Abcam Cat# ab16669, RRID:AB_443425 Rabbit CD4 Cell Signaling Cat# 25229, RRID:AB_2798898 Rabbit CD8a Cell Signaling Cat# 98941, RRID:AB_2756376 Rat Cytokeratin 8 DSHB Cat# TROMA-I, RRID:AB_531826 Rat PDGFRa(CD140a)-PE BioLegend Cat# 135905, RRID:AB_1953268 Rat EpCAM(CD326)-AF488 BioLegend Cat# 118210, RRID:AB_1134099 Rat CD45-Pacific Blue BioLegend Cat# 103126, RRID:AB_493535 Rat CD3-AF700 eBioscience Cat# 56-0032-82, RRID:AB_529507 Rat CD11b-BV711 BD Cat# 563168, RRID:AB_2716860 Rat CD206-FITC BioLegend Cat# 141703, RRID:AB_10900988 Rat CD19-APC eBioscience Cat# 17-0193-82, RRID:AB_1659676 Biological Samples Tissue microarray sections of human PDAC MDACC IRB LAB05-0854 Chemicals, Peptides, and Recombinant Proteins RS 504393 Tocris Cat# 2517/10 SB 225002 Tocris Cat# 2725/10 Collagenase IV Gibco Cat# 17104019 Dispase II Gibco Cat# 17105041 Liberase Roche Cat# 5401020001 DNase I Roche Cat# 10104159001 Type I collagen solution from rat tail Sigma-Aldrich Cat# C3867 Critical Commercial Assays Direct-zol RNA Kit Zymo Research Cat# R2050 Reverse Transcription Kit Applied Biosystems Cat# 4368814 SYBR Green Master Mix Applied Biosystems Cat# 4367659 Cell Counting Kit-8 Abcam Cat# ab228554 Live-Dead-eFluor780 eBioscience Cat# 65-0865-14 Foxp3/Transcription Factor Staining Buffer Set eBioscience Cat# 00-5523-00 Gomori’s Trichrome Stain Kit Leica Biosystems Cat# 38016SS2 Chromium Single Cell 3’ Reagent Kits (v2) 10x Genomics Cat# PN-120237 ABC-Kit Vector Cat# PK-6100 (Continued on next page) e1 Cancer Cell 39, 548–565.e1–e6, April 12, 2021 .. REAGENT or RESOURCE SOURCE IDENTIFIER Stable DAB Invitrogen Cat# 750118 Direct Red 80 Sigma-Aldrich Cat# 365548 TruSeq Stranded mRNA Sample Prep Kit Illumina Cat# 20020594 Deposited Data KPPF and KPPF;Col1smaKO tumor RNA-sequencing This paper GEO: GSE131500 Single-cell RNA-sequencing This paper GEO: GSE166298 TCGA pancreatic adenocarcinoma cohort survival and gene expression data (GDAC Firehose PAAD) Broad Institute http://gdac.broadinstitute.org/runs/ stddata__2016_01_28/data/PAAD/ 20160128/ Experimental Models: Cell Lines Primary mouse KPPF;Col1smaKO cancer cells This paper N/A Experimental Models: Organisms/Strains Mouse: FSF-KrasG12D/+;Pdx1-Flp Schonhuber et al., 2014 N/A Mouse: Trp53frt/+ Lee et al., 2012 N/A Mouse: aSMA-Cre LeBleu et al., 2013 N/A Mouse: Fsp1-Cre Xue et al., 2003; Bhowmick et al., 2004 N/A Mouse: Rosa26-CAG-loxP-frt-Stop-frtFireflyLuc-EGFP-loxP-RenillaLuctdTomato Chen et al., 2018 N/A Mouse: Col1a1tm1a(EUCOMM)Wtsi EuMMCR https://www.mousephenotype.org/data/ alleles/MGI:88467/tm1a(EUCOMM)Wtsii Mouse: Col1a1loxP/loxP This study N/A Oligonucleotides Mouse Gapdh qRT-PCR F AGGTCGGTGTGAACGGATTTG This paper N/A Mouse Gapdh qRT-PCR R TGTAGACCATGTAGTTGAGGTCA This paper N/A Mouse Col1a1 qRT-PCR F GCTCCTCTTAGGGGCCACT This paper N/A Mouse Col1a1 qRT-PCR R CCACGTCTCACCATTGGGG This paper N/A Mouse Cxcl5 qRT-PCR F GTTCCATCTCGCCATTCATGC This paper N/A Mouse Cxcl5 qRT-PCR R GCGGCTATGACTGAGGAAGG This paper N/A Mouse Sox9 qRT-PCR F GAGCCGGATCTGAAGAGGGA This paper N/A Mouse Sox9 qRT-PCR R GCTTGACGTGTGGCTTGTTC This paper N/A Software and Algorithms Flowjo v10.7.1 Flowjo, L.L.C.
CCK-8 Assay:Article Title: Type I collagen deletion in αSMA + myofibroblasts augments immune suppression and accelerates progression of pancreatic cancer.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Goat Albumin Bethyl Cat# A90-134, RRID:AB_67120 Mouse aSMA DAKO Cat# M0851, RRID:AB_2223500 Rabbit CD206 (MRC1) Abcam Cat# ab64693, RRID:AB_1523910 Rabbit CD45R Abcam Cat# ab64100, RRID:AB_1140036 Rabbit CK19 Abcam Cat# ab52625, RRID:AB_2281020 Goat Collagen I SouthernBiotech Cat# 1310-01, RRID:AB_2753206 Rabbit Ki67 Abcam Cat# ab15580, RRID:AB_443209 Rabbit SOX9 Abcam Cat# ab185966, RRID:AB_2728660 Rabbit NG2 Chemicon/Millipore Cat# AB5320, RRID:AB_11213678 Rat CD31 Dianova Cat# DIA-310, RRID:AB_2631039 Goat Collagen IV Abcam Cat# ab6585, RRID:AB_305583 Rabbit FSP1 DAKO Cat# A5114, RRID:AB_2335679 Rabbit CD3 Abcam Cat# ab16669, RRID:AB_443425 Rabbit CD4 Cell Signaling Cat# 25229, RRID:AB_2798898 Rabbit CD8a Cell Signaling Cat# 98941, RRID:AB_2756376 Rat Cytokeratin 8 DSHB Cat# TROMA-I, RRID:AB_531826 Rat PDGFRa(CD140a)-PE BioLegend Cat# 135905, RRID:AB_1953268 Rat EpCAM(CD326)-AF488 BioLegend Cat# 118210, RRID:AB_1134099 Rat CD45-Pacific Blue BioLegend Cat# 103126, RRID:AB_493535 Rat CD3-AF700 eBioscience Cat# 56-0032-82, RRID:AB_529507 Rat CD11b-BV711 BD Cat# 563168, RRID:AB_2716860 Rat CD206-FITC BioLegend Cat# 141703, RRID:AB_10900988 Rat CD19-APC eBioscience Cat# 17-0193-82, RRID:AB_1659676 Biological Samples Tissue microarray sections of human PDAC MDACC IRB LAB05-0854 Chemicals, Peptides, and Recombinant Proteins RS 504393 Tocris Cat# 2517/10 SB 225002 Tocris Cat# 2725/10 Collagenase IV Gibco Cat# 17104019 Dispase II Gibco Cat# 17105041 Liberase Roche Cat# 5401020001 DNase I Roche Cat# 10104159001 Type I collagen solution from rat tail Sigma-Aldrich Cat# C3867 Critical Commercial Assays Direct-zol RNA Kit Zymo Research Cat# R2050 Reverse Transcription Kit Applied Biosystems Cat# 4368814 SYBR Green Master Mix Applied Biosystems Cat# 4367659 Cell Counting Kit-8 Abcam Cat# ab228554 Live-Dead-eFluor780 eBioscience Cat# 65-0865-14 Foxp3/Transcription Factor Staining Buffer Set eBioscience Cat# 00-5523-00 Gomori’s Trichrome Stain Kit Leica Biosystems Cat# 38016SS2 Chromium Single Cell 3’ Reagent Kits (v2) 10x Genomics Cat# PN-120237 ABC-Kit Vector Cat# PK-6100 (Continued on next page) e1 Cancer Cell 39, 548–565.e1–e6, April 12, 2021 .. REAGENT or RESOURCE SOURCE IDENTIFIER Stable DAB Invitrogen Cat# 750118 Direct Red 80 Sigma-Aldrich Cat# 365548 TruSeq Stranded mRNA Sample Prep Kit Illumina Cat# 20020594 Deposited Data KPPF and KPPF;Col1smaKO tumor RNA-sequencing This paper GEO: GSE131500 Single-cell RNA-sequencing This paper GEO: GSE166298 TCGA pancreatic adenocarcinoma cohort survival and gene expression data (GDAC Firehose PAAD) Broad Institute http://gdac.broadinstitute.org/runs/ stddata__2016_01_28/data/PAAD/ 20160128/ Experimental Models: Cell Lines Primary mouse KPPF;Col1smaKO cancer cells This paper N/A Experimental Models: Organisms/Strains Mouse: FSF-KrasG12D/+;Pdx1-Flp Schonhuber et al., 2014 N/A Mouse: Trp53frt/+ Lee et al., 2012 N/A Mouse: aSMA-Cre LeBleu et al., 2013 N/A Mouse: Fsp1-Cre Xue et al., 2003; Bhowmick et al., 2004 N/A Mouse: Rosa26-CAG-loxP-frt-Stop-frtFireflyLuc-EGFP-loxP-RenillaLuctdTomato Chen et al., 2018 N/A Mouse: Col1a1tm1a(EUCOMM)Wtsi EuMMCR https://www.mousephenotype.org/data/ alleles/MGI:88467/tm1a(EUCOMM)Wtsii Mouse: Col1a1loxP/loxP This study N/A Oligonucleotides Mouse Gapdh qRT-PCR F AGGTCGGTGTGAACGGATTTG This paper N/A Mouse Gapdh qRT-PCR R TGTAGACCATGTAGTTGAGGTCA This paper N/A Mouse Col1a1 qRT-PCR F GCTCCTCTTAGGGGCCACT This paper N/A Mouse Col1a1 qRT-PCR R CCACGTCTCACCATTGGGG This paper N/A Mouse Cxcl5 qRT-PCR F GTTCCATCTCGCCATTCATGC This paper N/A Mouse Cxcl5 qRT-PCR R GCGGCTATGACTGAGGAAGG This paper N/A Mouse Sox9 qRT-PCR F GAGCCGGATCTGAAGAGGGA This paper N/A Mouse Sox9 qRT-PCR R GCTTGACGTGTGGCTTGTTC This paper N/A Software and Algorithms Flowjo v10.7.1 Flowjo, L.L.C.
Staining:Article Title: Type I collagen deletion in αSMA + myofibroblasts augments immune suppression and accelerates progression of pancreatic cancer.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Goat Albumin Bethyl Cat# A90-134, RRID:AB_67120 Mouse aSMA DAKO Cat# M0851, RRID:AB_2223500 Rabbit CD206 (MRC1) Abcam Cat# ab64693, RRID:AB_1523910 Rabbit CD45R Abcam Cat# ab64100, RRID:AB_1140036 Rabbit CK19 Abcam Cat# ab52625, RRID:AB_2281020 Goat Collagen I SouthernBiotech Cat# 1310-01, RRID:AB_2753206 Rabbit Ki67 Abcam Cat# ab15580, RRID:AB_443209 Rabbit SOX9 Abcam Cat# ab185966, RRID:AB_2728660 Rabbit NG2 Chemicon/Millipore Cat# AB5320, RRID:AB_11213678 Rat CD31 Dianova Cat# DIA-310, RRID:AB_2631039 Goat Collagen IV Abcam Cat# ab6585, RRID:AB_305583 Rabbit FSP1 DAKO Cat# A5114, RRID:AB_2335679 Rabbit CD3 Abcam Cat# ab16669, RRID:AB_443425 Rabbit CD4 Cell Signaling Cat# 25229, RRID:AB_2798898 Rabbit CD8a Cell Signaling Cat# 98941, RRID:AB_2756376 Rat Cytokeratin 8 DSHB Cat# TROMA-I, RRID:AB_531826 Rat PDGFRa(CD140a)-PE BioLegend Cat# 135905, RRID:AB_1953268 Rat EpCAM(CD326)-AF488 BioLegend Cat# 118210, RRID:AB_1134099 Rat CD45-Pacific Blue BioLegend Cat# 103126, RRID:AB_493535 Rat CD3-AF700 eBioscience Cat# 56-0032-82, RRID:AB_529507 Rat CD11b-BV711 BD Cat# 563168, RRID:AB_2716860 Rat CD206-FITC BioLegend Cat# 141703, RRID:AB_10900988 Rat CD19-APC eBioscience Cat# 17-0193-82, RRID:AB_1659676 Biological Samples Tissue microarray sections of human PDAC MDACC IRB LAB05-0854 Chemicals, Peptides, and Recombinant Proteins RS 504393 Tocris Cat# 2517/10 SB 225002 Tocris Cat# 2725/10 Collagenase IV Gibco Cat# 17104019 Dispase II Gibco Cat# 17105041 Liberase Roche Cat# 5401020001 DNase I Roche Cat# 10104159001 Type I collagen solution from rat tail Sigma-Aldrich Cat# C3867 Critical Commercial Assays Direct-zol RNA Kit Zymo Research Cat# R2050 Reverse Transcription Kit Applied Biosystems Cat# 4368814 SYBR Green Master Mix Applied Biosystems Cat# 4367659 Cell Counting Kit-8 Abcam Cat# ab228554 Live-Dead-eFluor780 eBioscience Cat# 65-0865-14 Foxp3/Transcription Factor Staining Buffer Set eBioscience Cat# 00-5523-00 Gomori’s Trichrome Stain Kit Leica Biosystems Cat# 38016SS2 Chromium Single Cell 3’ Reagent Kits (v2) 10x Genomics Cat# PN-120237 ABC-Kit Vector Cat# PK-6100 (Continued on next page) e1 Cancer Cell 39, 548–565.e1–e6, April 12, 2021 .. REAGENT or RESOURCE SOURCE IDENTIFIER Stable DAB Invitrogen Cat# 750118 Direct Red 80 Sigma-Aldrich Cat# 365548 TruSeq Stranded mRNA Sample Prep Kit Illumina Cat# 20020594 Deposited Data KPPF and KPPF;Col1smaKO tumor RNA-sequencing This paper GEO: GSE131500 Single-cell RNA-sequencing This paper GEO: GSE166298 TCGA pancreatic adenocarcinoma cohort survival and gene expression data (GDAC Firehose PAAD) Broad Institute http://gdac.broadinstitute.org/runs/ stddata__2016_01_28/data/PAAD/ 20160128/ Experimental Models: Cell Lines Primary mouse KPPF;Col1smaKO cancer cells This paper N/A Experimental Models: Organisms/Strains Mouse: FSF-KrasG12D/+;Pdx1-Flp Schonhuber et al., 2014 N/A Mouse: Trp53frt/+ Lee et al., 2012 N/A Mouse: aSMA-Cre LeBleu et al., 2013 N/A Mouse: Fsp1-Cre Xue et al., 2003; Bhowmick et al., 2004 N/A Mouse: Rosa26-CAG-loxP-frt-Stop-frtFireflyLuc-EGFP-loxP-RenillaLuctdTomato Chen et al., 2018 N/A Mouse: Col1a1tm1a(EUCOMM)Wtsi EuMMCR https://www.mousephenotype.org/data/ alleles/MGI:88467/tm1a(EUCOMM)Wtsii Mouse: Col1a1loxP/loxP This study N/A Oligonucleotides Mouse Gapdh qRT-PCR F AGGTCGGTGTGAACGGATTTG This paper N/A Mouse Gapdh qRT-PCR R TGTAGACCATGTAGTTGAGGTCA This paper N/A Mouse Col1a1 qRT-PCR F GCTCCTCTTAGGGGCCACT This paper N/A Mouse Col1a1 qRT-PCR R CCACGTCTCACCATTGGGG This paper N/A Mouse Cxcl5 qRT-PCR F GTTCCATCTCGCCATTCATGC This paper N/A Mouse Cxcl5 qRT-PCR R GCGGCTATGACTGAGGAAGG This paper N/A Mouse Sox9 qRT-PCR F GAGCCGGATCTGAAGAGGGA This paper N/A Mouse Sox9 qRT-PCR R GCTTGACGTGTGGCTTGTTC This paper N/A Software and Algorithms Flowjo v10.7.1 Flowjo, L.L.C.
Single Cell:Article Title: Type I collagen deletion in αSMA + myofibroblasts augments immune suppression and accelerates progression of pancreatic cancer.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Goat Albumin Bethyl Cat# A90-134, RRID:AB_67120 Mouse aSMA DAKO Cat# M0851, RRID:AB_2223500 Rabbit CD206 (MRC1) Abcam Cat# ab64693, RRID:AB_1523910 Rabbit CD45R Abcam Cat# ab64100, RRID:AB_1140036 Rabbit CK19 Abcam Cat# ab52625, RRID:AB_2281020 Goat Collagen I SouthernBiotech Cat# 1310-01, RRID:AB_2753206 Rabbit Ki67 Abcam Cat# ab15580, RRID:AB_443209 Rabbit SOX9 Abcam Cat# ab185966, RRID:AB_2728660 Rabbit NG2 Chemicon/Millipore Cat# AB5320, RRID:AB_11213678 Rat CD31 Dianova Cat# DIA-310, RRID:AB_2631039 Goat Collagen IV Abcam Cat# ab6585, RRID:AB_305583 Rabbit FSP1 DAKO Cat# A5114, RRID:AB_2335679 Rabbit CD3 Abcam Cat# ab16669, RRID:AB_443425 Rabbit CD4 Cell Signaling Cat# 25229, RRID:AB_2798898 Rabbit CD8a Cell Signaling Cat# 98941, RRID:AB_2756376 Rat Cytokeratin 8 DSHB Cat# TROMA-I, RRID:AB_531826 Rat PDGFRa(CD140a)-PE BioLegend Cat# 135905, RRID:AB_1953268 Rat EpCAM(CD326)-AF488 BioLegend Cat# 118210, RRID:AB_1134099 Rat CD45-Pacific Blue BioLegend Cat# 103126, RRID:AB_493535 Rat CD3-AF700 eBioscience Cat# 56-0032-82, RRID:AB_529507 Rat CD11b-BV711 BD Cat# 563168, RRID:AB_2716860 Rat CD206-FITC BioLegend Cat# 141703, RRID:AB_10900988 Rat CD19-APC eBioscience Cat# 17-0193-82, RRID:AB_1659676 Biological Samples Tissue microarray sections of human PDAC MDACC IRB LAB05-0854 Chemicals, Peptides, and Recombinant Proteins RS 504393 Tocris Cat# 2517/10 SB 225002 Tocris Cat# 2725/10 Collagenase IV Gibco Cat# 17104019 Dispase II Gibco Cat# 17105041 Liberase Roche Cat# 5401020001 DNase I Roche Cat# 10104159001 Type I collagen solution from rat tail Sigma-Aldrich Cat# C3867 Critical Commercial Assays Direct-zol RNA Kit Zymo Research Cat# R2050 Reverse Transcription Kit Applied Biosystems Cat# 4368814 SYBR Green Master Mix Applied Biosystems Cat# 4367659 Cell Counting Kit-8 Abcam Cat# ab228554 Live-Dead-eFluor780 eBioscience Cat# 65-0865-14 Foxp3/Transcription Factor Staining Buffer Set eBioscience Cat# 00-5523-00 Gomori’s Trichrome Stain Kit Leica Biosystems Cat# 38016SS2 Chromium Single Cell 3’ Reagent Kits (v2) 10x Genomics Cat# PN-120237 ABC-Kit Vector Cat# PK-6100 (Continued on next page) e1 Cancer Cell 39, 548–565.e1–e6, April 12, 2021 .. REAGENT or RESOURCE SOURCE IDENTIFIER Stable DAB Invitrogen Cat# 750118 Direct Red 80 Sigma-Aldrich Cat# 365548 TruSeq Stranded mRNA Sample Prep Kit Illumina Cat# 20020594 Deposited Data KPPF and KPPF;Col1smaKO tumor RNA-sequencing This paper GEO: GSE131500 Single-cell RNA-sequencing This paper GEO: GSE166298 TCGA pancreatic adenocarcinoma cohort survival and gene expression data (GDAC Firehose PAAD) Broad Institute http://gdac.broadinstitute.org/runs/ stddata__2016_01_28/data/PAAD/ 20160128/ Experimental Models: Cell Lines Primary mouse KPPF;Col1smaKO cancer cells This paper N/A Experimental Models: Organisms/Strains Mouse: FSF-KrasG12D/+;Pdx1-Flp Schonhuber et al., 2014 N/A Mouse: Trp53frt/+ Lee et al., 2012 N/A Mouse: aSMA-Cre LeBleu et al., 2013 N/A Mouse: Fsp1-Cre Xue et al., 2003; Bhowmick et al., 2004 N/A Mouse: Rosa26-CAG-loxP-frt-Stop-frtFireflyLuc-EGFP-loxP-RenillaLuctdTomato Chen et al., 2018 N/A Mouse: Col1a1tm1a(EUCOMM)Wtsi EuMMCR https://www.mousephenotype.org/data/ alleles/MGI:88467/tm1a(EUCOMM)Wtsii Mouse: Col1a1loxP/loxP This study N/A Oligonucleotides Mouse Gapdh qRT-PCR F AGGTCGGTGTGAACGGATTTG This paper N/A Mouse Gapdh qRT-PCR R TGTAGACCATGTAGTTGAGGTCA This paper N/A Mouse Col1a1 qRT-PCR F GCTCCTCTTAGGGGCCACT This paper N/A Mouse Col1a1 qRT-PCR R CCACGTCTCACCATTGGGG This paper N/A Mouse Cxcl5 qRT-PCR F GTTCCATCTCGCCATTCATGC This paper N/A Mouse Cxcl5 qRT-PCR R GCGGCTATGACTGAGGAAGG This paper N/A Mouse Sox9 qRT-PCR F GAGCCGGATCTGAAGAGGGA This paper N/A Mouse Sox9 qRT-PCR R GCTTGACGTGTGGCTTGTTC This paper N/A Software and Algorithms Flowjo v10.7.1 Flowjo, L.L.C.
|