Recombinant:Article Title: Batf Pioneers the Reorganization of Chromatin in Developing Effector T Cells via Ets1-Dependent Recruitment of Ctcf
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-Mouse CD4-APC/Cyanine7 (clone GK1.5) Biolegend Cat# 100414; RRID:AB_312699 Anti-Mouse CD25-APC (clone 3C7) Biolegend Cat#101910; RRID:AB_2280288 Anti-Mouse CD62L-PE/Cy7 (clone MEL-14) Biolegend Cat# 104417; RRID:AB_313102 Anti-Mouse CD44-FITC (clone IM7) Biolegend Cat#103006; RRID:AB_312957 Biotin Anti-Mouse CXCR5 (clone 2G8) BD Biosciences Cat#551960; RRID:AB_394301 Anti-Mouse PD-1-PE ((clone 29F.1A12) Biolegend Cat#135205; RRID:AB_1877232 Anti-Mouse CD69-PerCP/Cy5.5 (clone H1.2F3) Biolegend Cat#104522; RRID:AB_2260065 Anti-Mouse ICOS-FITC (clone 7E.17G9) eBioscience Cat#11-9942-82; RRID:AB_11218290 Streptavidin eFluor450 eBioscience Cat# 48-4317-82; RRID:AB_10359737 Anti-Mouse Batf-PE (clone 9B5A13) Biolegend Cat#654804; RRID:AB_2563517 Anti-Mouse CD3 (clone 145-2C11) BD Biosciences Cat#557306; RRID:AB_396632 Anti-Mouse CD28 (clone 37.51) BD Biosciences Cat#553295; RRID:AB_394764 Anti-Mouse IFN-g (clone XMG1.2) This paper N/A, generated in house Anti-Mouse IL-4 (clone 11B11) This paper N/A, generated in house Rabbit Anti-Mouse Irf4 Santa Cruz Cat#sc-28696X; RRID:AB_2127141 Rabbit Anti-Mouse Ets1 Santa Cruz Cat#sc-350X; RRID:AB_2100688 Normal rabbit IgG Millipore Cat#12-370; RRID:AB_145841 Rabbit Anti-Mouse H3K27me3 Millipore Cat#07-449; RRID:AB_310624 Rabbit Anti-Mouse H3K4me3 Millipore Cat#07-473; RRID:AB_1977252 Rabbit Anti-Mouse H3K27ac Abcam Cat#ab4729; RRID:AB_2118291 Rabbit Anti-Mouse Batf Schraml et al., 2009 N/A, generated in house Rabbit Anti-Mouse Med12 Bethyl Laboratory Cat#A300-774A; RRID:AB_669756 Rabbit Anti-Mouse Ctcf. .. Active Motif Cat#61311; RRID:AB_2614975 Chemicals, Peptides, and Recombinant Proteins Recombinant Human IL-2 Protein R&D Systems Cat# 202-IL-010 Recombinant Mouse IL-6 Protein R&D Systems Cat#406-ML-025 Recombinant Human TGF-b Protein R&D Systems Cat#240-B Recombinant Mouse IL-1b Protein R&D Systems Cat#401-ML-025 Phorbol 12-myristate 13-acetate Sigma-Aldrich Cat#P185-1MG Ionomycin EMD Bioscience Cat#4D7-952 Dynabeads M-280 Sheep Anti-Rabbit IgG ThermoFisher Scientific Cat#11203D Dynabeads MyOne Streptavidin C1 ThermoFisher Scientific Cat#65001 EcoRI-HF NEB Cat#R3101M HindIII-HF NEB Cat#R3104M NheI-HF NEB Cat#R3131L T4 DNA Ligase NEB Cat#0202M DNA Polymerase I, Large (Klenow) Fragment NEB Cat#0210M Deoxynucleotide (dNTP) Solution Set NEB Cat# N0446S Biotin-14-dCTP ThermoFisher Scientific Cat# 19518018 SsoAdvanced Universal SYBR Green Supermix Bio-Rad Cat#1725275 SsoAdvanced Universal Probes Supermix Bio-Rad Cat#1725285 iScript cDNA Synthesis Kit Biorad Cat# 1708891 Streptavidin BDBiosciences Cat#557598 (Continued on next page) Cell Reports 29, 1203–1220.e1–e7, October 29, 2019 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER FBS HyClone Cat#SH30109.03 RPMI-1640 Corning Cat#10-040-CM Penicillin/Streptomycin Corning Cat#30-002-Cl 2-Mercaptoethanol Sigma Cat# M3148 Non-Essential Amino Acids (MEM) Corning Cat#25025-Cl L-Glutamine Corning Cat#25-005-Cl HEPES Corning Cat#25-060-Cl Sodium Pyruvate Corning Cat#25-000-Cl Trizol ThermoFisher Cat# 15596018 RNaseA ThermoFisher Cat# EN0531 Critical Commercial Assays CD4+CD62L+ T Cell Isolation Kit, mouse Miltenyi Biotec Cat#130-106-643 QuikChange XL Site-Directed Mutagenesis Kit Agilent Technologies Cat# 200517 Nucleofector Kits for Mouse T Cells Lonza Cat#VPA-1006 Dual-Luciferase Reporter Assay System Promega Cat#E1910 NEBNext DNA Library Prep Master Mix Set for Illumina NEB Cat# E6040S NEBNext Ultra II DNA Library Prep Kit for Illumina NEB Cat#E7645S Nextera DNA Library Prep Kit (24 samples) Illumina Cat# FC-121-1030 Qubit dsDNA HS Assay Kit ThermoFisher Scientific Cat# Q32851 MinElute PCR Purification Kit QIAGEN Cat#28004 LS Columns Miltenyi Biotec Cat# 130-042-401 MS Columns Miltenyi Biotec Cat# 130-042-201 LIVE/DEAD Fixable Near-IR Dead Cell Stain Kit ThermoFisher Scientific Cat# L34976 Deposited Data ATAC-seq GEO database GSE: 123209 ChIP-seq GEO database GSE: 123209 Hi-C seq GEO database GSE: 123209 Experimental Models: Primary cells Mouse: primary T lymphocytes This paper N/A Experimental Models: Organisms/Strains Mouse: C57BL/6J The Jackson Laboratory Stock No: 000664 Mouse: Batf KO The Jackson Laboratory Stock No: 013758 Mouse: Irf4fl/fl The Jackson Laboratory Stock No: 009380 Mouse: Ets1fl/fl Zook et al., 2016 N/A Mouse: CD4-Cre The Jackson Laboratory Stock No: 022071 Recombinant DNA Mouse BAC DNA Il21 BACPAC Resources Center Cat#RP23-290D8 Mouse BAC DNA Il21 BACPAC Resources Center Cat#RP23-128L14 Mouse BAC DNA Gapdh BACPAC Resources Center Cat#RP23-410F11 MSCV-IRES-Thy1.1 Jabeen et al., 2013 N/A MSCV-IRES-Thy1.1 Batf Jabeen et al., 2013 N/A pCMV6-Ets1 Origene Cat#MR207015 MSCV-IRES-Thy1.1 Ets1 This paper N/A, generated in house pRL-TK Promega Cat#E2231 pGL3-Il2p This paper N/A, generated in house pGL3-Il2p 35 This paper N/A, generated in house pGL3-Il2p 47 This paper N/A, generated in house pGL3-Il2p 64 This paper N/A, generated in house (Continued on next page) e2 Cell Reports 29, 1203–1220.e1–e7, October 29, 2019
Article Title: Periostin Promotes Colorectal Tumorigenesis through Integrin-FAK-Src Pathway-Mediated YAP/TAZ Activation.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Chemicals, Peptides, and Recombinant Proteins Lipofectamine RNAi-MAX Reagent Invitrogen Cat# 13778030 STAT3 inhibitor Stattic Selleck Chemicals Cat# S7024 Src inhibitor PP2 Selleck Chemicals Cat# S7008 Src inhibitor dasatinib Selleck Chemicals Cat# S1021 AKT inhibitor LY294002 Selleck Chemicals Cat# S1105 RGD peptide PEPTIDES Cat# PCI-3661-PI Recombinant Human Periostin/OSF-2 Protein R&D Systems Cat# 3548-F2-050 Recombinant Mouse Periostin/OSF-2 Protein R&D Systems Cat# 2955-F2-050 Recombinant Mouse IL-6 Protein R&D Systems Cat# 406-ML-025 Azoxymethane (AOM) Sigma-Aldrich Cat# A5486 Dextran sulfate sodium salt (DSS) MP Biomedicals Cat# 160110 Lipofectamine 3000 Transfection Reagent Invitrogen Cat# L3000001 FAK inhibitor PF573228 Selleck Chemicals Cat# S2013 Critical Commercial Assays Mouse IL-6 ELISA Kit R&D Systems Cat# DY406 Mouse TNFa ELISA Kit R&D Systems Cat# DY410 Mouse IL-1b ELISA Kit R&D Systems Cat# DY401 Experimental Models: Cell Lines Mouse: CMT93 ATCC CCL-223 Human: DLD1 ATCC CCL-221 Mouse: CMF (colon myofibroblast) This paper N/A Mouse: CAF (cancer-associated fibroblast) This paper N/A Experimental Models: Organisms/Strains Mouse: B6.129-Postntm1Jmol/J Jackson Laboratory JAX: 009067 Mouse: C57BL/6 Nanjing Biomedical Research Institute of Nanjing University N000013 Mouse: C57BL/6J-ApcMin/J Jackson Laboratory JAX: 002020 Oligonucleotides siRNA targeting sequence: siYAP 1# GCAUGAGCAGCUACAGCAUTT This paper N/A siRNA targeting sequence: siYAP 2# GCUGAUGAAUUCUGCCUCATT This paper N/A siRNA targeting sequence: siYAP 3# GAUCCCUGAUGAUGUACCATT This paper N/A siRNA targeting sequence: siTAZ 1# GGAUUAGGAUGCGUCAAGATT Calvo et al., 2013 N/A siRNA targeting sequence: siLATS1 1# GCAAGUCACUCUGCUAAUUTT This paper N/A siRNA targeting sequence: siLATS1 2# GGUGAAGUCUGUCUAGCATT This paper N/A siRNA targeting sequence: siLATS2 1# GCCACAACUUACUCUGGAATT This paper N/A siRNA targeting sequence: siLATS2 2# GCCUCAAUGCUGACUUGUATT This paper N/A siRNA targeting sequence: siTAZ 2# CGAGAUGGAUACAGGUGAATT Calvo et al., 2013 N/A See Table S1 for qRT-PCR primer sequences This paper N/A (Continued on next page) e2 Cell Reports 30, 793–806.e1–e6, January 21, 2020 .. REAGENT or RESOURCE SOURCE IDENTIFIER Recombinant DNA Plasmid: pCMV5-Flag-YAP wild-type Liu et al., 2018 N/A Plasmid: pCMV5-Flag-YAP 5SA Liu et al., 2018 N/A Software and Algorithms GraphPad Prism 5 GraphPad Software https://www.graphpad.com/ Bio-Rad CFX Manager 3.0 CFX Manager Software http://www.advanceduninstaller.com
Article Title: Induction of a Timed Metabolic Collapse to Overcome Cancer Chemoresistance
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Pacific Blue Lineage cocktail BioLegend Cat#: 133310 RRID: AB_11150779 APC anti-cKit BioLegend Cat#: 135108 RRID: AB_2028407 Brilliant Violet 510 anti-Sca1 BioLegend Cat#: 108129 RRID: AB_2561593 eFluor 450 anti-CD34 eBioscience Cat#: 48-0341-82 RRID: AB_2043837 PE-Cy7 anti-CD45 BioLegend Cat#: 103114 RRID: AB_312979 PE-Cy7 anti-Ter-119 BioLegend Cat#: 116222 RRID: AB_2281408 PerCP-Cy5.5 anti-CD31 BioLegend Cat#: 102420 RRID: AB_10613644 APC anti-CD90.2 BioLegend Cat#: 105312 RRID: AB_313183 Pacific Blue anti-CD105 BioLegend Cat#: 120412 RRID: AB_2098890 Biotin anti-LepR R&D Systems Cat#: BAF497 RRID: AB_2296953 Anti-SLC1A3 (rabbit polyclonal) Novus Biologicals Cat#: NB100-1869 RRID: AB_531518 Anti-SLC38A1 (rabbit polyclonal) ThermoFisher Scientific Cat#: PA5-42420 RRID: AB_2605455 Alexa Fluor 647 anti-H2AX (pS139) (mouse monoclonal) BD Biosciences Cat#: 560447 RRID: AB_1645414 Anti-GOT1 (rabbit monoclonal) Abcam Cat#: ab170950 Anti-GOT2 (rabbit monoclonal) Abcam Cat#: ab171739 Anti-GLS (rabbit monoclonal) ThermoFisher Scientific Cat#: 701965 RRID: AB_2633041 Anti--actin (mouse monoclonal) Sigma-Aldrich Cat#: A2228 RRID: AB_476697 Alexa Fluor 546 anti-rabbit IgG (H+L) ThermoFisher Scientific Cat#: A11035 RRID: AB_2633041 IRDye 800CW anti-rabbit IgG (H + L) LI-COR Cat#: 925-32211 RRID: AB_2651127 IRDye 680RD anti-mouse IgG (H + L) LI-COR Cat#: 925-68070 RRID: AB_2651128 Chemicals, Peptides, and Recombinant Proteins Recombinant Mouse SCF Protein R&D Systems 455-MC Recombinant Mouse IL-3 Protein R&D Systems 403-ML Recombinant Mouse IL-6 Protein R&D Systems 406-ML D-luciferin GoldBio LUCK Cytarabine hydrochloride Sigma-Aldrich C6645 Doxorubicin hydrochloride Sigma-Aldrich D1515 Electronic copy available at: https://ssrn.com/abstract=3537802This preprint research paper has n t been peer reviewed. .. Electronic copy vailable at: https://ssrn.com/abstract=3537802 Pr ep rin t n ot p ee r r ev ie we d 24 6-Diazo-5-oxo-L-norleucine (DON) Sigma-Aldrich D2141 (2-Hydroxypropyl)-β-cyclodextrin Sigma-Aldrich H107 Solutol HS 15 Sigma-Aldrich 42966 AGI15280 Agios Pharmaceuticals N/A Poly(ethylene glycol)-400 Sigma-Aldrich 202398 Brequinar (BRQ) Broad Institute N/A 7-aminoactinomycin D (7-AAD) BD Biosciences 559925 BPTES Sigma-Aldrich SML0601 CB839 MedKoo Biosciences 206153 APC Annexin V BioLegend 640941 APC-eFluor 780 Streptavidin eBioscience 47-4317-82 CellROX Orange ThermoFisher Scientific C10443 Tetramethylrhodamine, Ethyl Ester (TMRE) ThermoFisher Scientific T669 RPMI 1640 Medium Lonza 12-167F DMEM Medium Lonza 12-614F Canonical Amino Acid Mix (13C-, 15N-labeled) Cambridge Isotope Laboratories MSK-CAA-1 L-Glutamine (13C5, 99%) Cambridge Isotope Laboratories CLM-1822-H L-Glutamine (15N2, 98%) Cambridge Isotope Laboratories NLM-1328 Critical Commercial Assays BD Cytofix/Cytoperm Kit BD Biosciences 554714 RNeasy Plus Mini Kit Qiagen 74134 MethoCult GF M3434 StemCell Technologies 03434 Deposited Data RNA sequencing of MLL-AF9 leukemia cells sorted from mice treated with or without iCT, at the moment of maximal response or after relapse GEO GSE139159 Single cell RNA sequencing of mouse bone marrow stromal cells GEO GSE128423 Experimental Models: Cell Lines MLL-AF9 mouse AML Sykes et al., 2016 N/A HoxA9/Meis1 mouse AML Sykes et al., 2016 N/A Experimental Models: Organisms/Strains C57Bl/6J mice Jackson Laboratories 000664 Recombinant DNA Mouse GLS shRNA (TRCN0000253167) Sigma-Aldrich SHCLNDNM_001081081 Mouse GOT1 shRNA (TRCN0000119792, TRCN0000119795) Sigma-Aldrich SHCLNDNM_010324 Mouse GOT2 shRNA (TRCN0000326018, TRCN0000326020) Sigma-Aldrich SHCLNDNM_010325 Software and Algorithms Compound Discoverer (version 3.0) ThermoFisher Scientific N/A TraceFinder (version 4.1) ThermoFisher Scientific N/A MassHunter (version B.08.00) Agilent N/A MetaboAnalyst (version 4.0) Chong et al., 2018 N/A Electronic copy available at: https://ssrn.com/abstract=3537802This preprint research paper has n t been peer reviewed.
Article Title: Transcription factor RORα enforces stability of the Th17 cell effector program by binding to a Rorc cis-regulatory element.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Flow Cytometry: anti-mouse IFNg (XM61.2) eFluor450 ThermoFisher Cat# 48-7311; RRID:AB_1834366 In vitro T cell differentiation: antihamster IgGs MP Biomedicals Catalog Cat# 55398 In vitro T cell differentiation: anti-mouse CD3ε (145-2C11) BioXCell Cat# BP0001-1 In vitro T cell differentiation: anti-mouse CD28 (37.51) BioXCell Cat# BE0015-1 In vitro T cell differentiation: anti-mouse IL-4 (11B11) BioXCell Cat# BP0045 In vitro T cell differentiation: anti-mouse IFNg (XMG1.2) BioXCell Cat# BP0055 RORa ChIP qPCR : polyclonal rabbit antimouse RORa This paper N/A Biological samples Fetal Bovine Serum Atlanta Biologicals Cat# S11195 Lot. .. A16003 Chemicals, peptides, and recombinant proteins EDTA, 0.5M, pH8.0 Ambion Cat# AM9260G TransIT -293 Transfection Reagent Mirus Cat# MIR2704 Collagenase D Roche Cat# 11088882001 Dispase Worthington Cat# LS02104 DNase I Sigma Cat# DN25 DTT Sigma Cat# D9779 Percoll GE Healthcare Life Sciences Cat# 45001747 Ficoll-Paque Premium GE Healthcare Life Sciences Cat# 17-5442-02 2-Mercaptoethanol (BME) ThermoFisher Cat# 21985023 Phorbol Myristate Acetate Sigma Cat# P1585 Ionomycin Sigma Cat# I0634 Recombinant Human IL-2 NIH AIDS Reagent Program Cat# 136 Recombinant Human TGFb Protein Peprotech Cat# 100-21-10ug Recombinant Mouse IL-6 Protein R&D systems Cat# 406-ML-200/CF Recombinant Mouse IL-23 Protein R&D systems Cat# 1887-ML Alt-R S.p. .. HiFi Cas9 Nuclease V3 Integrated DNA Technologies Lot #0000473804, 0000469029 Alt-R Cas9 Electroporation Enhancer Integrated DNA Technologies Lot #0000472336 Critical commercial assays LIVE/DEAD Fixable Blue Dead Cell Stain Kit ThermoFisher Cat# L34961 CountBright absolute counting beads ThermoFisher Cat# C36950 BD Cytofix/Cytoperm Plus Fixation/ Permeabilization Solution Kit BD Biosciences Cat# 554714 eBioscience Foxp3 / Transcription Factor Staining Buffer Set ThermoFisher Cat# 00-5523-00 LightCycler 480 SYBR Green I Master Roche Life Science Cat# 04707516001 SuperScript III First-Strand Synthesis System ThermoFisher Cat# 18080051 RNeasy Mini Kit QIAGEN Cat# 74104 RNeasy MinElute Cleanup Kit QIAGEN Cat# 74204 RNase-Free DNase Set QIAGEN Cat# 79254 TRIzol Reagent ThermoFisher Cat# 15596026 (Continued on next page) Immunity 55, 2027–2043.e1–e9, November 8, 2022 e2
SYBR Green Assay:Article Title: Batf Pioneers the Reorganization of Chromatin in Developing Effector T Cells via Ets1-Dependent Recruitment of Ctcf
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-Mouse CD4-APC/Cyanine7 (clone GK1.5) Biolegend Cat# 100414; RRID:AB_312699 Anti-Mouse CD25-APC (clone 3C7) Biolegend Cat#101910; RRID:AB_2280288 Anti-Mouse CD62L-PE/Cy7 (clone MEL-14) Biolegend Cat# 104417; RRID:AB_313102 Anti-Mouse CD44-FITC (clone IM7) Biolegend Cat#103006; RRID:AB_312957 Biotin Anti-Mouse CXCR5 (clone 2G8) BD Biosciences Cat#551960; RRID:AB_394301 Anti-Mouse PD-1-PE ((clone 29F.1A12) Biolegend Cat#135205; RRID:AB_1877232 Anti-Mouse CD69-PerCP/Cy5.5 (clone H1.2F3) Biolegend Cat#104522; RRID:AB_2260065 Anti-Mouse ICOS-FITC (clone 7E.17G9) eBioscience Cat#11-9942-82; RRID:AB_11218290 Streptavidin eFluor450 eBioscience Cat# 48-4317-82; RRID:AB_10359737 Anti-Mouse Batf-PE (clone 9B5A13) Biolegend Cat#654804; RRID:AB_2563517 Anti-Mouse CD3 (clone 145-2C11) BD Biosciences Cat#557306; RRID:AB_396632 Anti-Mouse CD28 (clone 37.51) BD Biosciences Cat#553295; RRID:AB_394764 Anti-Mouse IFN-g (clone XMG1.2) This paper N/A, generated in house Anti-Mouse IL-4 (clone 11B11) This paper N/A, generated in house Rabbit Anti-Mouse Irf4 Santa Cruz Cat#sc-28696X; RRID:AB_2127141 Rabbit Anti-Mouse Ets1 Santa Cruz Cat#sc-350X; RRID:AB_2100688 Normal rabbit IgG Millipore Cat#12-370; RRID:AB_145841 Rabbit Anti-Mouse H3K27me3 Millipore Cat#07-449; RRID:AB_310624 Rabbit Anti-Mouse H3K4me3 Millipore Cat#07-473; RRID:AB_1977252 Rabbit Anti-Mouse H3K27ac Abcam Cat#ab4729; RRID:AB_2118291 Rabbit Anti-Mouse Batf Schraml et al., 2009 N/A, generated in house Rabbit Anti-Mouse Med12 Bethyl Laboratory Cat#A300-774A; RRID:AB_669756 Rabbit Anti-Mouse Ctcf. .. Active Motif Cat#61311; RRID:AB_2614975 Chemicals, Peptides, and Recombinant Proteins Recombinant Human IL-2 Protein R&D Systems Cat# 202-IL-010 Recombinant Mouse IL-6 Protein R&D Systems Cat#406-ML-025 Recombinant Human TGF-b Protein R&D Systems Cat#240-B Recombinant Mouse IL-1b Protein R&D Systems Cat#401-ML-025 Phorbol 12-myristate 13-acetate Sigma-Aldrich Cat#P185-1MG Ionomycin EMD Bioscience Cat#4D7-952 Dynabeads M-280 Sheep Anti-Rabbit IgG ThermoFisher Scientific Cat#11203D Dynabeads MyOne Streptavidin C1 ThermoFisher Scientific Cat#65001 EcoRI-HF NEB Cat#R3101M HindIII-HF NEB Cat#R3104M NheI-HF NEB Cat#R3131L T4 DNA Ligase NEB Cat#0202M DNA Polymerase I, Large (Klenow) Fragment NEB Cat#0210M Deoxynucleotide (dNTP) Solution Set NEB Cat# N0446S Biotin-14-dCTP ThermoFisher Scientific Cat# 19518018 SsoAdvanced Universal SYBR Green Supermix Bio-Rad Cat#1725275 SsoAdvanced Universal Probes Supermix Bio-Rad Cat#1725285 iScript cDNA Synthesis Kit Biorad Cat# 1708891 Streptavidin BDBiosciences Cat#557598 (Continued on next page) Cell Reports 29, 1203–1220.e1–e7, October 29, 2019 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER FBS HyClone Cat#SH30109.03 RPMI-1640 Corning Cat#10-040-CM Penicillin/Streptomycin Corning Cat#30-002-Cl 2-Mercaptoethanol Sigma Cat# M3148 Non-Essential Amino Acids (MEM) Corning Cat#25025-Cl L-Glutamine Corning Cat#25-005-Cl HEPES Corning Cat#25-060-Cl Sodium Pyruvate Corning Cat#25-000-Cl Trizol ThermoFisher Cat# 15596018 RNaseA ThermoFisher Cat# EN0531 Critical Commercial Assays CD4+CD62L+ T Cell Isolation Kit, mouse Miltenyi Biotec Cat#130-106-643 QuikChange XL Site-Directed Mutagenesis Kit Agilent Technologies Cat# 200517 Nucleofector Kits for Mouse T Cells Lonza Cat#VPA-1006 Dual-Luciferase Reporter Assay System Promega Cat#E1910 NEBNext DNA Library Prep Master Mix Set for Illumina NEB Cat# E6040S NEBNext Ultra II DNA Library Prep Kit for Illumina NEB Cat#E7645S Nextera DNA Library Prep Kit (24 samples) Illumina Cat# FC-121-1030 Qubit dsDNA HS Assay Kit ThermoFisher Scientific Cat# Q32851 MinElute PCR Purification Kit QIAGEN Cat#28004 LS Columns Miltenyi Biotec Cat# 130-042-401 MS Columns Miltenyi Biotec Cat# 130-042-201 LIVE/DEAD Fixable Near-IR Dead Cell Stain Kit ThermoFisher Scientific Cat# L34976 Deposited Data ATAC-seq GEO database GSE: 123209 ChIP-seq GEO database GSE: 123209 Hi-C seq GEO database GSE: 123209 Experimental Models: Primary cells Mouse: primary T lymphocytes This paper N/A Experimental Models: Organisms/Strains Mouse: C57BL/6J The Jackson Laboratory Stock No: 000664 Mouse: Batf KO The Jackson Laboratory Stock No: 013758 Mouse: Irf4fl/fl The Jackson Laboratory Stock No: 009380 Mouse: Ets1fl/fl Zook et al., 2016 N/A Mouse: CD4-Cre The Jackson Laboratory Stock No: 022071 Recombinant DNA Mouse BAC DNA Il21 BACPAC Resources Center Cat#RP23-290D8 Mouse BAC DNA Il21 BACPAC Resources Center Cat#RP23-128L14 Mouse BAC DNA Gapdh BACPAC Resources Center Cat#RP23-410F11 MSCV-IRES-Thy1.1 Jabeen et al., 2013 N/A MSCV-IRES-Thy1.1 Batf Jabeen et al., 2013 N/A pCMV6-Ets1 Origene Cat#MR207015 MSCV-IRES-Thy1.1 Ets1 This paper N/A, generated in house pRL-TK Promega Cat#E2231 pGL3-Il2p This paper N/A, generated in house pGL3-Il2p 35 This paper N/A, generated in house pGL3-Il2p 47 This paper N/A, generated in house pGL3-Il2p 64 This paper N/A, generated in house (Continued on next page) e2 Cell Reports 29, 1203–1220.e1–e7, October 29, 2019
cDNA Synthesis:Article Title: Batf Pioneers the Reorganization of Chromatin in Developing Effector T Cells via Ets1-Dependent Recruitment of Ctcf
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-Mouse CD4-APC/Cyanine7 (clone GK1.5) Biolegend Cat# 100414; RRID:AB_312699 Anti-Mouse CD25-APC (clone 3C7) Biolegend Cat#101910; RRID:AB_2280288 Anti-Mouse CD62L-PE/Cy7 (clone MEL-14) Biolegend Cat# 104417; RRID:AB_313102 Anti-Mouse CD44-FITC (clone IM7) Biolegend Cat#103006; RRID:AB_312957 Biotin Anti-Mouse CXCR5 (clone 2G8) BD Biosciences Cat#551960; RRID:AB_394301 Anti-Mouse PD-1-PE ((clone 29F.1A12) Biolegend Cat#135205; RRID:AB_1877232 Anti-Mouse CD69-PerCP/Cy5.5 (clone H1.2F3) Biolegend Cat#104522; RRID:AB_2260065 Anti-Mouse ICOS-FITC (clone 7E.17G9) eBioscience Cat#11-9942-82; RRID:AB_11218290 Streptavidin eFluor450 eBioscience Cat# 48-4317-82; RRID:AB_10359737 Anti-Mouse Batf-PE (clone 9B5A13) Biolegend Cat#654804; RRID:AB_2563517 Anti-Mouse CD3 (clone 145-2C11) BD Biosciences Cat#557306; RRID:AB_396632 Anti-Mouse CD28 (clone 37.51) BD Biosciences Cat#553295; RRID:AB_394764 Anti-Mouse IFN-g (clone XMG1.2) This paper N/A, generated in house Anti-Mouse IL-4 (clone 11B11) This paper N/A, generated in house Rabbit Anti-Mouse Irf4 Santa Cruz Cat#sc-28696X; RRID:AB_2127141 Rabbit Anti-Mouse Ets1 Santa Cruz Cat#sc-350X; RRID:AB_2100688 Normal rabbit IgG Millipore Cat#12-370; RRID:AB_145841 Rabbit Anti-Mouse H3K27me3 Millipore Cat#07-449; RRID:AB_310624 Rabbit Anti-Mouse H3K4me3 Millipore Cat#07-473; RRID:AB_1977252 Rabbit Anti-Mouse H3K27ac Abcam Cat#ab4729; RRID:AB_2118291 Rabbit Anti-Mouse Batf Schraml et al., 2009 N/A, generated in house Rabbit Anti-Mouse Med12 Bethyl Laboratory Cat#A300-774A; RRID:AB_669756 Rabbit Anti-Mouse Ctcf. .. Active Motif Cat#61311; RRID:AB_2614975 Chemicals, Peptides, and Recombinant Proteins Recombinant Human IL-2 Protein R&D Systems Cat# 202-IL-010 Recombinant Mouse IL-6 Protein R&D Systems Cat#406-ML-025 Recombinant Human TGF-b Protein R&D Systems Cat#240-B Recombinant Mouse IL-1b Protein R&D Systems Cat#401-ML-025 Phorbol 12-myristate 13-acetate Sigma-Aldrich Cat#P185-1MG Ionomycin EMD Bioscience Cat#4D7-952 Dynabeads M-280 Sheep Anti-Rabbit IgG ThermoFisher Scientific Cat#11203D Dynabeads MyOne Streptavidin C1 ThermoFisher Scientific Cat#65001 EcoRI-HF NEB Cat#R3101M HindIII-HF NEB Cat#R3104M NheI-HF NEB Cat#R3131L T4 DNA Ligase NEB Cat#0202M DNA Polymerase I, Large (Klenow) Fragment NEB Cat#0210M Deoxynucleotide (dNTP) Solution Set NEB Cat# N0446S Biotin-14-dCTP ThermoFisher Scientific Cat# 19518018 SsoAdvanced Universal SYBR Green Supermix Bio-Rad Cat#1725275 SsoAdvanced Universal Probes Supermix Bio-Rad Cat#1725285 iScript cDNA Synthesis Kit Biorad Cat# 1708891 Streptavidin BDBiosciences Cat#557598 (Continued on next page) Cell Reports 29, 1203–1220.e1–e7, October 29, 2019 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER FBS HyClone Cat#SH30109.03 RPMI-1640 Corning Cat#10-040-CM Penicillin/Streptomycin Corning Cat#30-002-Cl 2-Mercaptoethanol Sigma Cat# M3148 Non-Essential Amino Acids (MEM) Corning Cat#25025-Cl L-Glutamine Corning Cat#25-005-Cl HEPES Corning Cat#25-060-Cl Sodium Pyruvate Corning Cat#25-000-Cl Trizol ThermoFisher Cat# 15596018 RNaseA ThermoFisher Cat# EN0531 Critical Commercial Assays CD4+CD62L+ T Cell Isolation Kit, mouse Miltenyi Biotec Cat#130-106-643 QuikChange XL Site-Directed Mutagenesis Kit Agilent Technologies Cat# 200517 Nucleofector Kits for Mouse T Cells Lonza Cat#VPA-1006 Dual-Luciferase Reporter Assay System Promega Cat#E1910 NEBNext DNA Library Prep Master Mix Set for Illumina NEB Cat# E6040S NEBNext Ultra II DNA Library Prep Kit for Illumina NEB Cat#E7645S Nextera DNA Library Prep Kit (24 samples) Illumina Cat# FC-121-1030 Qubit dsDNA HS Assay Kit ThermoFisher Scientific Cat# Q32851 MinElute PCR Purification Kit QIAGEN Cat#28004 LS Columns Miltenyi Biotec Cat# 130-042-401 MS Columns Miltenyi Biotec Cat# 130-042-201 LIVE/DEAD Fixable Near-IR Dead Cell Stain Kit ThermoFisher Scientific Cat# L34976 Deposited Data ATAC-seq GEO database GSE: 123209 ChIP-seq GEO database GSE: 123209 Hi-C seq GEO database GSE: 123209 Experimental Models: Primary cells Mouse: primary T lymphocytes This paper N/A Experimental Models: Organisms/Strains Mouse: C57BL/6J The Jackson Laboratory Stock No: 000664 Mouse: Batf KO The Jackson Laboratory Stock No: 013758 Mouse: Irf4fl/fl The Jackson Laboratory Stock No: 009380 Mouse: Ets1fl/fl Zook et al., 2016 N/A Mouse: CD4-Cre The Jackson Laboratory Stock No: 022071 Recombinant DNA Mouse BAC DNA Il21 BACPAC Resources Center Cat#RP23-290D8 Mouse BAC DNA Il21 BACPAC Resources Center Cat#RP23-128L14 Mouse BAC DNA Gapdh BACPAC Resources Center Cat#RP23-410F11 MSCV-IRES-Thy1.1 Jabeen et al., 2013 N/A MSCV-IRES-Thy1.1 Batf Jabeen et al., 2013 N/A pCMV6-Ets1 Origene Cat#MR207015 MSCV-IRES-Thy1.1 Ets1 This paper N/A, generated in house pRL-TK Promega Cat#E2231 pGL3-Il2p This paper N/A, generated in house pGL3-Il2p 35 This paper N/A, generated in house pGL3-Il2p 47 This paper N/A, generated in house pGL3-Il2p 64 This paper N/A, generated in house (Continued on next page) e2 Cell Reports 29, 1203–1220.e1–e7, October 29, 2019
Transfection:Article Title: Periostin Promotes Colorectal Tumorigenesis through Integrin-FAK-Src Pathway-Mediated YAP/TAZ Activation.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Chemicals, Peptides, and Recombinant Proteins Lipofectamine RNAi-MAX Reagent Invitrogen Cat# 13778030 STAT3 inhibitor Stattic Selleck Chemicals Cat# S7024 Src inhibitor PP2 Selleck Chemicals Cat# S7008 Src inhibitor dasatinib Selleck Chemicals Cat# S1021 AKT inhibitor LY294002 Selleck Chemicals Cat# S1105 RGD peptide PEPTIDES Cat# PCI-3661-PI Recombinant Human Periostin/OSF-2 Protein R&D Systems Cat# 3548-F2-050 Recombinant Mouse Periostin/OSF-2 Protein R&D Systems Cat# 2955-F2-050 Recombinant Mouse IL-6 Protein R&D Systems Cat# 406-ML-025 Azoxymethane (AOM) Sigma-Aldrich Cat# A5486 Dextran sulfate sodium salt (DSS) MP Biomedicals Cat# 160110 Lipofectamine 3000 Transfection Reagent Invitrogen Cat# L3000001 FAK inhibitor PF573228 Selleck Chemicals Cat# S2013 Critical Commercial Assays Mouse IL-6 ELISA Kit R&D Systems Cat# DY406 Mouse TNFa ELISA Kit R&D Systems Cat# DY410 Mouse IL-1b ELISA Kit R&D Systems Cat# DY401 Experimental Models: Cell Lines Mouse: CMT93 ATCC CCL-223 Human: DLD1 ATCC CCL-221 Mouse: CMF (colon myofibroblast) This paper N/A Mouse: CAF (cancer-associated fibroblast) This paper N/A Experimental Models: Organisms/Strains Mouse: B6.129-Postntm1Jmol/J Jackson Laboratory JAX: 009067 Mouse: C57BL/6 Nanjing Biomedical Research Institute of Nanjing University N000013 Mouse: C57BL/6J-ApcMin/J Jackson Laboratory JAX: 002020 Oligonucleotides siRNA targeting sequence: siYAP 1# GCAUGAGCAGCUACAGCAUTT This paper N/A siRNA targeting sequence: siYAP 2# GCUGAUGAAUUCUGCCUCATT This paper N/A siRNA targeting sequence: siYAP 3# GAUCCCUGAUGAUGUACCATT This paper N/A siRNA targeting sequence: siTAZ 1# GGAUUAGGAUGCGUCAAGATT Calvo et al., 2013 N/A siRNA targeting sequence: siLATS1 1# GCAAGUCACUCUGCUAAUUTT This paper N/A siRNA targeting sequence: siLATS1 2# GGUGAAGUCUGUCUAGCATT This paper N/A siRNA targeting sequence: siLATS2 1# GCCACAACUUACUCUGGAATT This paper N/A siRNA targeting sequence: siLATS2 2# GCCUCAAUGCUGACUUGUATT This paper N/A siRNA targeting sequence: siTAZ 2# CGAGAUGGAUACAGGUGAATT Calvo et al., 2013 N/A See Table S1 for qRT-PCR primer sequences This paper N/A (Continued on next page) e2 Cell Reports 30, 793–806.e1–e6, January 21, 2020 .. REAGENT or RESOURCE SOURCE IDENTIFIER Recombinant DNA Plasmid: pCMV5-Flag-YAP wild-type Liu et al., 2018 N/A Plasmid: pCMV5-Flag-YAP 5SA Liu et al., 2018 N/A Software and Algorithms GraphPad Prism 5 GraphPad Software https://www.graphpad.com/ Bio-Rad CFX Manager 3.0 CFX Manager Software http://www.advanceduninstaller.com
Article Title: Transcription factor RORα enforces stability of the Th17 cell effector program by binding to a Rorc cis-regulatory element.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Flow Cytometry: anti-mouse IFNg (XM61.2) eFluor450 ThermoFisher Cat# 48-7311; RRID:AB_1834366 In vitro T cell differentiation: antihamster IgGs MP Biomedicals Catalog Cat# 55398 In vitro T cell differentiation: anti-mouse CD3ε (145-2C11) BioXCell Cat# BP0001-1 In vitro T cell differentiation: anti-mouse CD28 (37.51) BioXCell Cat# BE0015-1 In vitro T cell differentiation: anti-mouse IL-4 (11B11) BioXCell Cat# BP0045 In vitro T cell differentiation: anti-mouse IFNg (XMG1.2) BioXCell Cat# BP0055 RORa ChIP qPCR : polyclonal rabbit antimouse RORa This paper N/A Biological samples Fetal Bovine Serum Atlanta Biologicals Cat# S11195 Lot. .. A16003 Chemicals, peptides, and recombinant proteins EDTA, 0.5M, pH8.0 Ambion Cat# AM9260G TransIT -293 Transfection Reagent Mirus Cat# MIR2704 Collagenase D Roche Cat# 11088882001 Dispase Worthington Cat# LS02104 DNase I Sigma Cat# DN25 DTT Sigma Cat# D9779 Percoll GE Healthcare Life Sciences Cat# 45001747 Ficoll-Paque Premium GE Healthcare Life Sciences Cat# 17-5442-02 2-Mercaptoethanol (BME) ThermoFisher Cat# 21985023 Phorbol Myristate Acetate Sigma Cat# P1585 Ionomycin Sigma Cat# I0634 Recombinant Human IL-2 NIH AIDS Reagent Program Cat# 136 Recombinant Human TGFb Protein Peprotech Cat# 100-21-10ug Recombinant Mouse IL-6 Protein R&D systems Cat# 406-ML-200/CF Recombinant Mouse IL-23 Protein R&D systems Cat# 1887-ML Alt-R S.p. .. HiFi Cas9 Nuclease V3 Integrated DNA Technologies Lot #0000473804, 0000469029 Alt-R Cas9 Electroporation Enhancer Integrated DNA Technologies Lot #0000472336 Critical commercial assays LIVE/DEAD Fixable Blue Dead Cell Stain Kit ThermoFisher Cat# L34961 CountBright absolute counting beads ThermoFisher Cat# C36950 BD Cytofix/Cytoperm Plus Fixation/ Permeabilization Solution Kit BD Biosciences Cat# 554714 eBioscience Foxp3 / Transcription Factor Staining Buffer Set ThermoFisher Cat# 00-5523-00 LightCycler 480 SYBR Green I Master Roche Life Science Cat# 04707516001 SuperScript III First-Strand Synthesis System ThermoFisher Cat# 18080051 RNeasy Mini Kit QIAGEN Cat# 74104 RNeasy MinElute Cleanup Kit QIAGEN Cat# 74204 RNase-Free DNase Set QIAGEN Cat# 79254 TRIzol Reagent ThermoFisher Cat# 15596026 (Continued on next page) Immunity 55, 2027–2043.e1–e9, November 8, 2022 e2
Enzyme-linked Immunosorbent Assay:Article Title: Periostin Promotes Colorectal Tumorigenesis through Integrin-FAK-Src Pathway-Mediated YAP/TAZ Activation.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Chemicals, Peptides, and Recombinant Proteins Lipofectamine RNAi-MAX Reagent Invitrogen Cat# 13778030 STAT3 inhibitor Stattic Selleck Chemicals Cat# S7024 Src inhibitor PP2 Selleck Chemicals Cat# S7008 Src inhibitor dasatinib Selleck Chemicals Cat# S1021 AKT inhibitor LY294002 Selleck Chemicals Cat# S1105 RGD peptide PEPTIDES Cat# PCI-3661-PI Recombinant Human Periostin/OSF-2 Protein R&D Systems Cat# 3548-F2-050 Recombinant Mouse Periostin/OSF-2 Protein R&D Systems Cat# 2955-F2-050 Recombinant Mouse IL-6 Protein R&D Systems Cat# 406-ML-025 Azoxymethane (AOM) Sigma-Aldrich Cat# A5486 Dextran sulfate sodium salt (DSS) MP Biomedicals Cat# 160110 Lipofectamine 3000 Transfection Reagent Invitrogen Cat# L3000001 FAK inhibitor PF573228 Selleck Chemicals Cat# S2013 Critical Commercial Assays Mouse IL-6 ELISA Kit R&D Systems Cat# DY406 Mouse TNFa ELISA Kit R&D Systems Cat# DY410 Mouse IL-1b ELISA Kit R&D Systems Cat# DY401 Experimental Models: Cell Lines Mouse: CMT93 ATCC CCL-223 Human: DLD1 ATCC CCL-221 Mouse: CMF (colon myofibroblast) This paper N/A Mouse: CAF (cancer-associated fibroblast) This paper N/A Experimental Models: Organisms/Strains Mouse: B6.129-Postntm1Jmol/J Jackson Laboratory JAX: 009067 Mouse: C57BL/6 Nanjing Biomedical Research Institute of Nanjing University N000013 Mouse: C57BL/6J-ApcMin/J Jackson Laboratory JAX: 002020 Oligonucleotides siRNA targeting sequence: siYAP 1# GCAUGAGCAGCUACAGCAUTT This paper N/A siRNA targeting sequence: siYAP 2# GCUGAUGAAUUCUGCCUCATT This paper N/A siRNA targeting sequence: siYAP 3# GAUCCCUGAUGAUGUACCATT This paper N/A siRNA targeting sequence: siTAZ 1# GGAUUAGGAUGCGUCAAGATT Calvo et al., 2013 N/A siRNA targeting sequence: siLATS1 1# GCAAGUCACUCUGCUAAUUTT This paper N/A siRNA targeting sequence: siLATS1 2# GGUGAAGUCUGUCUAGCATT This paper N/A siRNA targeting sequence: siLATS2 1# GCCACAACUUACUCUGGAATT This paper N/A siRNA targeting sequence: siLATS2 2# GCCUCAAUGCUGACUUGUATT This paper N/A siRNA targeting sequence: siTAZ 2# CGAGAUGGAUACAGGUGAATT Calvo et al., 2013 N/A See Table S1 for qRT-PCR primer sequences This paper N/A (Continued on next page) e2 Cell Reports 30, 793–806.e1–e6, January 21, 2020 .. REAGENT or RESOURCE SOURCE IDENTIFIER Recombinant DNA Plasmid: pCMV5-Flag-YAP wild-type Liu et al., 2018 N/A Plasmid: pCMV5-Flag-YAP 5SA Liu et al., 2018 N/A Software and Algorithms GraphPad Prism 5 GraphPad Software https://www.graphpad.com/ Bio-Rad CFX Manager 3.0 CFX Manager Software http://www.advanceduninstaller.com
Sequencing:Article Title: Periostin Promotes Colorectal Tumorigenesis through Integrin-FAK-Src Pathway-Mediated YAP/TAZ Activation.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Chemicals, Peptides, and Recombinant Proteins Lipofectamine RNAi-MAX Reagent Invitrogen Cat# 13778030 STAT3 inhibitor Stattic Selleck Chemicals Cat# S7024 Src inhibitor PP2 Selleck Chemicals Cat# S7008 Src inhibitor dasatinib Selleck Chemicals Cat# S1021 AKT inhibitor LY294002 Selleck Chemicals Cat# S1105 RGD peptide PEPTIDES Cat# PCI-3661-PI Recombinant Human Periostin/OSF-2 Protein R&D Systems Cat# 3548-F2-050 Recombinant Mouse Periostin/OSF-2 Protein R&D Systems Cat# 2955-F2-050 Recombinant Mouse IL-6 Protein R&D Systems Cat# 406-ML-025 Azoxymethane (AOM) Sigma-Aldrich Cat# A5486 Dextran sulfate sodium salt (DSS) MP Biomedicals Cat# 160110 Lipofectamine 3000 Transfection Reagent Invitrogen Cat# L3000001 FAK inhibitor PF573228 Selleck Chemicals Cat# S2013 Critical Commercial Assays Mouse IL-6 ELISA Kit R&D Systems Cat# DY406 Mouse TNFa ELISA Kit R&D Systems Cat# DY410 Mouse IL-1b ELISA Kit R&D Systems Cat# DY401 Experimental Models: Cell Lines Mouse: CMT93 ATCC CCL-223 Human: DLD1 ATCC CCL-221 Mouse: CMF (colon myofibroblast) This paper N/A Mouse: CAF (cancer-associated fibroblast) This paper N/A Experimental Models: Organisms/Strains Mouse: B6.129-Postntm1Jmol/J Jackson Laboratory JAX: 009067 Mouse: C57BL/6 Nanjing Biomedical Research Institute of Nanjing University N000013 Mouse: C57BL/6J-ApcMin/J Jackson Laboratory JAX: 002020 Oligonucleotides siRNA targeting sequence: siYAP 1# GCAUGAGCAGCUACAGCAUTT This paper N/A siRNA targeting sequence: siYAP 2# GCUGAUGAAUUCUGCCUCATT This paper N/A siRNA targeting sequence: siYAP 3# GAUCCCUGAUGAUGUACCATT This paper N/A siRNA targeting sequence: siTAZ 1# GGAUUAGGAUGCGUCAAGATT Calvo et al., 2013 N/A siRNA targeting sequence: siLATS1 1# GCAAGUCACUCUGCUAAUUTT This paper N/A siRNA targeting sequence: siLATS1 2# GGUGAAGUCUGUCUAGCATT This paper N/A siRNA targeting sequence: siLATS2 1# GCCACAACUUACUCUGGAATT This paper N/A siRNA targeting sequence: siLATS2 2# GCCUCAAUGCUGACUUGUATT This paper N/A siRNA targeting sequence: siTAZ 2# CGAGAUGGAUACAGGUGAATT Calvo et al., 2013 N/A See Table S1 for qRT-PCR primer sequences This paper N/A (Continued on next page) e2 Cell Reports 30, 793–806.e1–e6, January 21, 2020 .. REAGENT or RESOURCE SOURCE IDENTIFIER Recombinant DNA Plasmid: pCMV5-Flag-YAP wild-type Liu et al., 2018 N/A Plasmid: pCMV5-Flag-YAP 5SA Liu et al., 2018 N/A Software and Algorithms GraphPad Prism 5 GraphPad Software https://www.graphpad.com/ Bio-Rad CFX Manager 3.0 CFX Manager Software http://www.advanceduninstaller.com
Quantitative RT-PCR:Article Title: Periostin Promotes Colorectal Tumorigenesis through Integrin-FAK-Src Pathway-Mediated YAP/TAZ Activation.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Chemicals, Peptides, and Recombinant Proteins Lipofectamine RNAi-MAX Reagent Invitrogen Cat# 13778030 STAT3 inhibitor Stattic Selleck Chemicals Cat# S7024 Src inhibitor PP2 Selleck Chemicals Cat# S7008 Src inhibitor dasatinib Selleck Chemicals Cat# S1021 AKT inhibitor LY294002 Selleck Chemicals Cat# S1105 RGD peptide PEPTIDES Cat# PCI-3661-PI Recombinant Human Periostin/OSF-2 Protein R&D Systems Cat# 3548-F2-050 Recombinant Mouse Periostin/OSF-2 Protein R&D Systems Cat# 2955-F2-050 Recombinant Mouse IL-6 Protein R&D Systems Cat# 406-ML-025 Azoxymethane (AOM) Sigma-Aldrich Cat# A5486 Dextran sulfate sodium salt (DSS) MP Biomedicals Cat# 160110 Lipofectamine 3000 Transfection Reagent Invitrogen Cat# L3000001 FAK inhibitor PF573228 Selleck Chemicals Cat# S2013 Critical Commercial Assays Mouse IL-6 ELISA Kit R&D Systems Cat# DY406 Mouse TNFa ELISA Kit R&D Systems Cat# DY410 Mouse IL-1b ELISA Kit R&D Systems Cat# DY401 Experimental Models: Cell Lines Mouse: CMT93 ATCC CCL-223 Human: DLD1 ATCC CCL-221 Mouse: CMF (colon myofibroblast) This paper N/A Mouse: CAF (cancer-associated fibroblast) This paper N/A Experimental Models: Organisms/Strains Mouse: B6.129-Postntm1Jmol/J Jackson Laboratory JAX: 009067 Mouse: C57BL/6 Nanjing Biomedical Research Institute of Nanjing University N000013 Mouse: C57BL/6J-ApcMin/J Jackson Laboratory JAX: 002020 Oligonucleotides siRNA targeting sequence: siYAP 1# GCAUGAGCAGCUACAGCAUTT This paper N/A siRNA targeting sequence: siYAP 2# GCUGAUGAAUUCUGCCUCATT This paper N/A siRNA targeting sequence: siYAP 3# GAUCCCUGAUGAUGUACCATT This paper N/A siRNA targeting sequence: siTAZ 1# GGAUUAGGAUGCGUCAAGATT Calvo et al., 2013 N/A siRNA targeting sequence: siLATS1 1# GCAAGUCACUCUGCUAAUUTT This paper N/A siRNA targeting sequence: siLATS1 2# GGUGAAGUCUGUCUAGCATT This paper N/A siRNA targeting sequence: siLATS2 1# GCCACAACUUACUCUGGAATT This paper N/A siRNA targeting sequence: siLATS2 2# GCCUCAAUGCUGACUUGUATT This paper N/A siRNA targeting sequence: siTAZ 2# CGAGAUGGAUACAGGUGAATT Calvo et al., 2013 N/A See Table S1 for qRT-PCR primer sequences This paper N/A (Continued on next page) e2 Cell Reports 30, 793–806.e1–e6, January 21, 2020 .. REAGENT or RESOURCE SOURCE IDENTIFIER Recombinant DNA Plasmid: pCMV5-Flag-YAP wild-type Liu et al., 2018 N/A Plasmid: pCMV5-Flag-YAP 5SA Liu et al., 2018 N/A Software and Algorithms GraphPad Prism 5 GraphPad Software https://www.graphpad.com/ Bio-Rad CFX Manager 3.0 CFX Manager Software http://www.advanceduninstaller.com
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