Real-time Polymerase Chain Reaction:Article Title: Neurotrophic Activity and Its Modulation by Zinc Ion of a Dimeric Peptide Mimicking the Brain-Derived Neurotrophic Factor N-Terminal Region
Article Snippet: The RNA concentration and purity were checked at the Nanodrop instrument (Thermofisher). cDNA synthesis was performed with 1 μg of RNA using i-Script cDNA synthesis kit (BioRad). .. Real-time PCR reactions consisted of 10 μL of SsoAdvancedTM Universal SYBR® Green Supermix - Bio-Rad, 0.5 μL of both 10 μM forward and reverse primers, 5 μL of cDNA (50 ng), and 4 μL of H2O. ..
Article Title: CdGAP is a talin-binding protein and a target of TGF-β signaling that promotes HER2-positive breast cancer growth and metastasis.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER jetPRIME Polyplus Cat# 114-07 Protein G SepharoseTM 4 Fast Flow Affinity Chromatography media Thermo Fisher Scientific Cat# 17-0618-01 ClarityTM western ECL substrate Bor-Rad Cat# 1705061 SsoAdvancedTM Universal SYBR green Supermix Bio-Rad Cat#1725271 Fibronectin Sigma-Aldrich Cat# F1141 CorningTM MatrigelTM membrane matrix Thermo Fisher Scientific Cat# CB-40234A CorningTM MatrigelTM GFR membrane matrix Thermo Fisher Scientific Cat# CB-40230 FORMALDEHYDE, (formalin) reagent Grade Bioshop Cat# FOR201 Type 1 collagen BD Bioscience Cat# 354246 Critical commercial assays Mycoplasma PCR Detection kit ZmTech Scientific Cat# M209001 Dual-Luciferase reporter assay system Promega Cat# E1910 Qiagen RNeasy kit Qiagen Cat# 74104 RNase-free DNase set Qiagen Cat# 79254 RhoA G-LISA activation assay (luminescence) Cytoskeleton Cat# BK121 Rac1 G-LISA activation assay (luminescence) Cytoskeleton Cat# BK126 MTT Cell proliferation assay kit Abcam Cat# ab211091 Pierce BCA protein assay kit Thermo Fisher Scientific Cat# 23225 Deposited data RNA-sequencing raw data This paper GSE167457 Proteomics raw data This paper PXD043376 Experimental models: Cell lines Human breast cancer cell line: HCC1954 American type culture collection (ATCC) RRID: CVCL_1259 Human breast cancer cell line: SK-BR-3 American type culture collection (ATCC) RRID: CVCL_0033 Human breast cancer cell line: MDA-MB-361 American type culture collection (ATCC) RRID: CVCL_0620 Mouse: NIC+ explant cells Goyette et al.40 N/A Experimental models: Organisms/strains Mouse: Mammary Tumor Virus (MMTV)-NeuNDL2-5-Internal Ribosome Entry Site- Cre (NIC) FVB/NJ Ursini-Siegel et al.37 N/A Athymic Nude mouse Charles River Strain Code:490 Mouse: MMTV-Cre Wagner et al.36 N/A Mouse: CdGAPfl/fl Caron et al.35 N/A Oligonucleotides Smad4 specific silencer select validated siRNA Ambion Cat# 4390824 Mouse CdGAP primers for qPCR Qiagen Cat# QT00155162 Human CdGAP primers for qPCR Qiagen Cat# QT00076671 mouse E-cadherin primers for qPCR Qiagen Cat# QT00121163 All the other oligonucleotides, gRNAs, and shRNAs can be found in the Table S3 This paper Table S3 Recombinant DNA pSpCas9(BB)-2A-Puro (PX459) Ding et al.69 Addgene Cat#48139 mCherry-talin-18 a gift from Michael Davidson Addgene Cat#55137 EGFP-talin1 head Simonson et al.70 Addgene Cat# 32856 EGFP-talin1 rod Simonson et al.70 Addgene Cat# 32855 pGL3-basic CdGAP ( 896 to +601) This paper N/A MSCV luciferase PGK-hygro a gift from Scott lowe Addgene Cat# 18782 (Continued on next page) Cell Reports 42, 112936, August 29, 2023 21 .. REAGENT or RESOURCE SOURCE IDENTIFIER pCL-Eco Naviaux et al.71 Addgene Cat# 12371 pCMV5 Smad2-HA Hata et al.72 Addgene Cat# 14930 pRK5F Smad3 Zhang et al.73 Addgene Cat# 12625 pGL3-basic (CAGA)12-luc Kang 74 N/A pGL3-basic vector Promega Cat# E1751 pRK5-myc vector He et al.32 N/A pRK5-myc-CdGAP He et al.32 N/A pRK5-myc-CdGAP PRD He et al.32 N/A pRK5-myc-CdGAP 1-515 He et al.32 N/A GFP-CdGAP He et al.32 N/A Software and algorithms Imagescope software version 2.0.0 Leica Biosystems Inc. RRID: SCR_014311 ImageJ, version 1.8.0/1.53a N/A RRID: SCR_003070 Image Lab software 6.0.1 Bio-Rad RRID: SCR_014210 GraphPad Prism 8 GraphPad RRID: SCR_002798 GenPipes ‘‘RNAseq’’ pipeline Bourgey et al.75 https://github.com/c3g/GenPipes STAR aligner Dobin et al.76 https://github.com/alexdobin/STAR GATK DePristo et al.77 https://gatk.broadinstitute.org/hc/en-us Picard N/A https://broadinstitute.github.io/picard/ HT-seq Anders et al.78 https://github.com/htseq/htseq DESeq2 (v1.30.1) Lovet et al.79 N/A Msigdbr (v7.2.1) N/A https://igordot.github.io/msigdbr/ ClusterProfiler (v3.18.1) Yu et al.80 N/A MKmisc (v1.6) N/A https://github.com/stamats/MKmisc Singscore (v1.12.0) Foroutan et al.81 N/A
SYBR Green Assay:Article Title: Neurotrophic Activity and Its Modulation by Zinc Ion of a Dimeric Peptide Mimicking the Brain-Derived Neurotrophic Factor N-Terminal Region
Article Snippet: The RNA concentration and purity were checked at the Nanodrop instrument (Thermofisher). cDNA synthesis was performed with 1 μg of RNA using i-Script cDNA synthesis kit (BioRad). .. Real-time PCR reactions consisted of 10 μL of SsoAdvancedTM Universal SYBR® Green Supermix - Bio-Rad, 0.5 μL of both 10 μM forward and reverse primers, 5 μL of cDNA (50 ng), and 4 μL of H2O. ..
Article Title: Proton pump inhibitors modulate esophageal epithelial barrier function and crosstalk with eosinophils
Article Snippet: Nuclei counting was performed using the Color Deconvolution 2 and Cell Counter ImageJ plugins. .. RNA was isolated, and cDNA was synthesized from 1 μg of RNA using iScriptTM Reverse Transcription Supermix for RT‐qPCR (Bio‐Rad). qRT‐PCR was performed using 25 ng cDNA with SsoAdvancedTM Universal SYBR® Green Supermix (Bio‐Rad) and primers for CAPN14 (Bio‐Rad assay ID: qHsaCID0017001) and GAPDH (qHsaCED0038674). .. Cell lysates (15 μg protein) were resolved on 12% polyacrylamide gels, transferred to 0.2 μm PVDF, blocked, and incubated overnight at 4°C with primary antibodies (Mouse anti‐STAT6, 1:1000, sc‐374,021, Santa Cruz; Rabbit anti‐pSTAT6, 1:1000, SAB4300038, Sigma‐Aldrich; Mouse anti‐Dsg1, 1:1000, sc‐137,164, Santa Cruz; Mouse anti‐ICAM‐1, 1:500, MA5407, Invitrogen).
Article Title: IL-22 promotes mucin-type O-glycosylation and MATH1 + cell-mediated amelioration of intestinal inflammation.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit anti-Human Lysozyme FITC Dako Cat#: F037201; RRID: AB_578661 Goat anti-rabbit IgG AF488 Jackson ImmunoResearch Labs Cat#:111-545-144; RRID: AB 2338052 Mouse anti-GFP Cell Signaling Technology Cat#: 2955; RRID: AB 1196614 Goat anti-mouse IgG AF488 Jackson ImmunoResearch Labs Cat#:115-546-003; RRID: AB 2338859 UEA-I Dylight 649 Vector Laboratories Cat#: DL-1068 Mouse/Human anti-Tn Dr. Richard D Cummings, Harvard Medical School N/A Mouse anti-GFP antibody (biotin) GeneTex Cat#: GTX26658; RRID: AB 371422 Mouse anti-IL22Ra1-PE R&D FAB42941P; RRID: AB 1964624 Mouse anti-CD45-APC-eFluor 780 Invitrogen 47-0451-82; RRID: AB 1548781 Mouse anti-EpCAM-eFluor-450 Invitrogen 48-5791-82; RRID: AB 10717090 Rabbit anti-mouse CLCA1 Abcam Ab180851; RRID: AB 2722611 Recombinant Anti-STAT3 (Phospho Y705) Abcam ab76315; RRID: AB 1658549 Adenovirus hexon protein antibody (3G0) Santa Cruz Sc-80671; RRID: AB 1118724 Mouse PE/Cy7 anti-cKit Biolegend Cat#135111; RRID: AB 2131136 PerCP-Cy5.5 anti-mouse CD44 Invitrogen 45-0441-80; RRID: AB 925747 Live/Dead fixable Aqua dead cell stain kit Invitrogen L34957 IC fixation Buffer Invitrogen 00-8222-49 Horseradish Peroxidase labeled Goat anti-human/mouse IgM Southern Biotech Cat#: 1020-05; RRID: AB 2794201 Chemicals, peptides, and recombinant proteins VECTASHIELD HardSetTM Antifade mounting medium with DAPI Vector Laboratories Cat#: H-1500 Mouse HRP/DAB ABC detection IHC kit Abcam Cat#: ab64264 SsoAdvancedTM Universal Probes Supermix Bio-Rad Cat#: 1725281 SsoAdvancedTM Universal SYBR Green Supermix Bio-Rad Cat#: 1725271 Simple ChIP Enzymatic Chromatin IP kit Cell Signaling Technology Cat#: 9003S iScriptTM Reverse Transcription Supermix Bio-Rad Cat#: 1708840 High-Capacity cDNA Reverse Transcription Kit Thermo Fisher Cat#: 4368814 Roche Diagnostics LIGHTCYCLER 480 SYBR GREEN Roche Cat#: 04887352001 EDTA Invitrogen Cat#: AM9260G DSS MP Biomedicals Cat#: 160110 Alcian blue Alfa Aesar Cat#: J60122 Tamoxifen Sigma-Aldrich Cat#: T5648 DMSO ThermoFisher Cat#: BP231 DMEM/F12 Gibco Cat#: 12634-010 PBS Corning Cat#: 21040CV Fetal bovine serum Gibco Cat#: SH30071.03HI Nuclear Fast Red Electron Microscopy Sciences Cat#: 26078-05 Hematoxylin VWR Cat#: 95057-844 Eosin VWR Cat#: 95057-848 Matrigel Matrix Corning Cat#: 356231 (Continued on next page) Cell Reports 43, 114206, May 28, 2024 15 .. REAGENT or RESOURCE SOURCE IDENTIFIER 100x penicillin-streptomycin-glutamine Gibco Cat#: 10378016 Penicillin-Streptomycin solution, 100X Corning Cat#: 30-002-CI L-Glutamine Corning Cat#: 25-005-CI N2 Gibco Cat#: 17502048 B27 Gibco Cat#: 17504044 Mouse EGF Peprotech Cat#: 315-09 N-acetylcysteine Sigma-Aldrich Cat#: A9165 Gastrin-Leu15 Sigma-Aldrich Cat#: G9145 A83-01 Tocris Bioscience Cat#: 2939 Y-27632 Sigma-Aldrich Cat#: Y05030 Cell Recovery Medium Corning Cat#: 354253 2-mercaptoethanol Sigma-Aldrich Cat#: M6250 Triton X-100 Sigma-Aldrich Cat#: T8787 Tween 20 VWR Cat#: 0777 CHIR99021 Tocris Bioscience Cat#: 4423 Primocin InvivoGen Cat#:ant-pm-2 RLT buffer Qiagen RNeasy Micro kit Cat#:74004 Ad-B3galt5 Vector Biolabs N/A Ad-Y5 Vector Biolabs N/A RU-486 (Mifepristone) Sigma-Aldrich Cat#: M8046 TRIzol Invitrogen Cat#: 15596018 Qiagen RNeasy kit Qiagen Cat#: 74004 8M Lithium Chloride Sigma-Aldrich Cat#: L7026 Glycogen solution VWR Cat#: N632 Sodium Acetate Sigma-Aldrich Cat#: 127-09-3 IHC Tek Epitope retrieval solution IHC Tek Cat#: IW-1100 Tris base Sigma-Aldrich Cat#: 77-86-1 Bovine Serum Albumin Sigma-Aldrich Cat#: 9048-46-8 3,30-Diaminobenzidine Abcam Cat#: ab64264 Mouse rIL-22.Fc Evive Biotech Cat#: F-652 Mouse rIL-22 Biolegend Cat#: 576204 Human rIL-22 R & D systems Cat#: 782-IL DAPT Sigma-Aldrich Cat#: D5942 S3I-201 Sigma-Aldrich Cat#: 501919-59-1 L-WRN conditioned medium ATCC Cat#: CRL-3276 Advanced DMEM/F12 ThermoFisher Cat#: 12634028 NAC MP Biomedicals Cat#: 194603 FBS R&D Systems Cat#: S11150 Y-27632 MedChemExpress Cat#: HY-10583 B27 formulation ThermoFisher 17504-044 (50X) Gastrin AnaSpec Cat#: AS-64149 Primocin InvivoGen Cat#: ant-pm-2 A 83-01 Millipore-Sigma Cat#: SML078 SB 202190 LC Laboratories Cat#: S-1700 PGE2 Cayman Chemical Cat#: 14010 Nicotinamide Millipore-Sigma Cat#: N0636 Collagenase Worthington Cat#: LS004189 HEPES Corning Cat#: 25-060-CI GlutaMAX ThermoFisher Cat#: 25050061 (Continued on next page) 16 Cell Reports 43, 114206, May 28, 2024
Article Title: Integrated multiomics reveals starvation-driven keratin degradation and persistence in Fervidobacterium islandicum AW-1
Article Snippet: .. 492 493 STAR METHODS 494 KEY RESOURCES TABLE 495 REAGENT or RESOURCE SOURCE IDENTIFIER Chemicals, peptides, and recombinant proteins Jo urn al Pr -pr oo f 25 SYTO9 Invitrogen, MA, USA Cat# S34854 Propidium iodide Invitrogen, MA, USA Cat# P1304MP CPM (7- diethylamino-3-(4’maleimidylphenyl)4-methylcoumarin) Invitrogen, MA, USA Cat# D346 iScript cDNA Synthesis Kit Bio-Rad, CA, USA Cat# 1708890 2× SsoAdvancedTM Universal SYBR Green Supermix Bio-Rad, CA, USA Cat# 1725271 Thiamphenicol Sigma- Aldrich, MO, USA Cat# T0261 Critical commercial assays RNeasy Mini Kit QIAGEN, Hilden, Germany Cat# 74104 TruSeq RNA Sample Prep Kit v2 Illumina, CA, USA Cat# RS-122 Jo urn al Pr e-p roo f 26 TruSeq DNA Nano Prep Kit Illumina, CA, USA Cat# 20015964 c-di-GMP ELISA kit EIAab Science, Wuhan, China Cat# E0152Ge Deposited data RNA-seq data This study SRR33382689–SRR33382697 and SRX219354-SRX219357 Proteomics data This study PXD027063 Metabolomics data This study MSV000099151 Experimental models: Organisms/strains F. islandicum AW1 Yonsei University Korean Culture Collections of Microorganisms (KCCM) 80008 Oligonucleotides See Table S4 for oligonucleotides used in this study. ..
Article Title: CdGAP is a talin-binding protein and a target of TGF-β signaling that promotes HER2-positive breast cancer growth and metastasis.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER jetPRIME Polyplus Cat# 114-07 Protein G SepharoseTM 4 Fast Flow Affinity Chromatography media Thermo Fisher Scientific Cat# 17-0618-01 ClarityTM western ECL substrate Bor-Rad Cat# 1705061 SsoAdvancedTM Universal SYBR green Supermix Bio-Rad Cat#1725271 Fibronectin Sigma-Aldrich Cat# F1141 CorningTM MatrigelTM membrane matrix Thermo Fisher Scientific Cat# CB-40234A CorningTM MatrigelTM GFR membrane matrix Thermo Fisher Scientific Cat# CB-40230 FORMALDEHYDE, (formalin) reagent Grade Bioshop Cat# FOR201 Type 1 collagen BD Bioscience Cat# 354246 Critical commercial assays Mycoplasma PCR Detection kit ZmTech Scientific Cat# M209001 Dual-Luciferase reporter assay system Promega Cat# E1910 Qiagen RNeasy kit Qiagen Cat# 74104 RNase-free DNase set Qiagen Cat# 79254 RhoA G-LISA activation assay (luminescence) Cytoskeleton Cat# BK121 Rac1 G-LISA activation assay (luminescence) Cytoskeleton Cat# BK126 MTT Cell proliferation assay kit Abcam Cat# ab211091 Pierce BCA protein assay kit Thermo Fisher Scientific Cat# 23225 Deposited data RNA-sequencing raw data This paper GSE167457 Proteomics raw data This paper PXD043376 Experimental models: Cell lines Human breast cancer cell line: HCC1954 American type culture collection (ATCC) RRID: CVCL_1259 Human breast cancer cell line: SK-BR-3 American type culture collection (ATCC) RRID: CVCL_0033 Human breast cancer cell line: MDA-MB-361 American type culture collection (ATCC) RRID: CVCL_0620 Mouse: NIC+ explant cells Goyette et al.40 N/A Experimental models: Organisms/strains Mouse: Mammary Tumor Virus (MMTV)-NeuNDL2-5-Internal Ribosome Entry Site- Cre (NIC) FVB/NJ Ursini-Siegel et al.37 N/A Athymic Nude mouse Charles River Strain Code:490 Mouse: MMTV-Cre Wagner et al.36 N/A Mouse: CdGAPfl/fl Caron et al.35 N/A Oligonucleotides Smad4 specific silencer select validated siRNA Ambion Cat# 4390824 Mouse CdGAP primers for qPCR Qiagen Cat# QT00155162 Human CdGAP primers for qPCR Qiagen Cat# QT00076671 mouse E-cadherin primers for qPCR Qiagen Cat# QT00121163 All the other oligonucleotides, gRNAs, and shRNAs can be found in the Table S3 This paper Table S3 Recombinant DNA pSpCas9(BB)-2A-Puro (PX459) Ding et al.69 Addgene Cat#48139 mCherry-talin-18 a gift from Michael Davidson Addgene Cat#55137 EGFP-talin1 head Simonson et al.70 Addgene Cat# 32856 EGFP-talin1 rod Simonson et al.70 Addgene Cat# 32855 pGL3-basic CdGAP ( 896 to +601) This paper N/A MSCV luciferase PGK-hygro a gift from Scott lowe Addgene Cat# 18782 (Continued on next page) Cell Reports 42, 112936, August 29, 2023 21 .. REAGENT or RESOURCE SOURCE IDENTIFIER pCL-Eco Naviaux et al.71 Addgene Cat# 12371 pCMV5 Smad2-HA Hata et al.72 Addgene Cat# 14930 pRK5F Smad3 Zhang et al.73 Addgene Cat# 12625 pGL3-basic (CAGA)12-luc Kang 74 N/A pGL3-basic vector Promega Cat# E1751 pRK5-myc vector He et al.32 N/A pRK5-myc-CdGAP He et al.32 N/A pRK5-myc-CdGAP PRD He et al.32 N/A pRK5-myc-CdGAP 1-515 He et al.32 N/A GFP-CdGAP He et al.32 N/A Software and algorithms Imagescope software version 2.0.0 Leica Biosystems Inc. RRID: SCR_014311 ImageJ, version 1.8.0/1.53a N/A RRID: SCR_003070 Image Lab software 6.0.1 Bio-Rad RRID: SCR_014210 GraphPad Prism 8 GraphPad RRID: SCR_002798 GenPipes ‘‘RNAseq’’ pipeline Bourgey et al.75 https://github.com/c3g/GenPipes STAR aligner Dobin et al.76 https://github.com/alexdobin/STAR GATK DePristo et al.77 https://gatk.broadinstitute.org/hc/en-us Picard N/A https://broadinstitute.github.io/picard/ HT-seq Anders et al.78 https://github.com/htseq/htseq DESeq2 (v1.30.1) Lovet et al.79 N/A Msigdbr (v7.2.1) N/A https://igordot.github.io/msigdbr/ ClusterProfiler (v3.18.1) Yu et al.80 N/A MKmisc (v1.6) N/A https://github.com/stamats/MKmisc Singscore (v1.12.0) Foroutan et al.81 N/A
Isolation:Article Title: Proton pump inhibitors modulate esophageal epithelial barrier function and crosstalk with eosinophils
Article Snippet: Nuclei counting was performed using the Color Deconvolution 2 and Cell Counter ImageJ plugins. .. RNA was isolated, and cDNA was synthesized from 1 μg of RNA using iScriptTM Reverse Transcription Supermix for RT‐qPCR (Bio‐Rad). qRT‐PCR was performed using 25 ng cDNA with SsoAdvancedTM Universal SYBR® Green Supermix (Bio‐Rad) and primers for CAPN14 (Bio‐Rad assay ID: qHsaCID0017001) and GAPDH (qHsaCED0038674). .. Cell lysates (15 μg protein) were resolved on 12% polyacrylamide gels, transferred to 0.2 μm PVDF, blocked, and incubated overnight at 4°C with primary antibodies (Mouse anti‐STAT6, 1:1000, sc‐374,021, Santa Cruz; Rabbit anti‐pSTAT6, 1:1000, SAB4300038, Sigma‐Aldrich; Mouse anti‐Dsg1, 1:1000, sc‐137,164, Santa Cruz; Mouse anti‐ICAM‐1, 1:500, MA5407, Invitrogen).
Synthesized:Article Title: Proton pump inhibitors modulate esophageal epithelial barrier function and crosstalk with eosinophils
Article Snippet: Nuclei counting was performed using the Color Deconvolution 2 and Cell Counter ImageJ plugins. .. RNA was isolated, and cDNA was synthesized from 1 μg of RNA using iScriptTM Reverse Transcription Supermix for RT‐qPCR (Bio‐Rad). qRT‐PCR was performed using 25 ng cDNA with SsoAdvancedTM Universal SYBR® Green Supermix (Bio‐Rad) and primers for CAPN14 (Bio‐Rad assay ID: qHsaCID0017001) and GAPDH (qHsaCED0038674). .. Cell lysates (15 μg protein) were resolved on 12% polyacrylamide gels, transferred to 0.2 μm PVDF, blocked, and incubated overnight at 4°C with primary antibodies (Mouse anti‐STAT6, 1:1000, sc‐374,021, Santa Cruz; Rabbit anti‐pSTAT6, 1:1000, SAB4300038, Sigma‐Aldrich; Mouse anti‐Dsg1, 1:1000, sc‐137,164, Santa Cruz; Mouse anti‐ICAM‐1, 1:500, MA5407, Invitrogen).
Reverse Transcription:Article Title: Proton pump inhibitors modulate esophageal epithelial barrier function and crosstalk with eosinophils
Article Snippet: Nuclei counting was performed using the Color Deconvolution 2 and Cell Counter ImageJ plugins. .. RNA was isolated, and cDNA was synthesized from 1 μg of RNA using iScriptTM Reverse Transcription Supermix for RT‐qPCR (Bio‐Rad). qRT‐PCR was performed using 25 ng cDNA with SsoAdvancedTM Universal SYBR® Green Supermix (Bio‐Rad) and primers for CAPN14 (Bio‐Rad assay ID: qHsaCID0017001) and GAPDH (qHsaCED0038674). .. Cell lysates (15 μg protein) were resolved on 12% polyacrylamide gels, transferred to 0.2 μm PVDF, blocked, and incubated overnight at 4°C with primary antibodies (Mouse anti‐STAT6, 1:1000, sc‐374,021, Santa Cruz; Rabbit anti‐pSTAT6, 1:1000, SAB4300038, Sigma‐Aldrich; Mouse anti‐Dsg1, 1:1000, sc‐137,164, Santa Cruz; Mouse anti‐ICAM‐1, 1:500, MA5407, Invitrogen).
Article Title: IL-22 promotes mucin-type O-glycosylation and MATH1 + cell-mediated amelioration of intestinal inflammation.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit anti-Human Lysozyme FITC Dako Cat#: F037201; RRID: AB_578661 Goat anti-rabbit IgG AF488 Jackson ImmunoResearch Labs Cat#:111-545-144; RRID: AB 2338052 Mouse anti-GFP Cell Signaling Technology Cat#: 2955; RRID: AB 1196614 Goat anti-mouse IgG AF488 Jackson ImmunoResearch Labs Cat#:115-546-003; RRID: AB 2338859 UEA-I Dylight 649 Vector Laboratories Cat#: DL-1068 Mouse/Human anti-Tn Dr. Richard D Cummings, Harvard Medical School N/A Mouse anti-GFP antibody (biotin) GeneTex Cat#: GTX26658; RRID: AB 371422 Mouse anti-IL22Ra1-PE R&D FAB42941P; RRID: AB 1964624 Mouse anti-CD45-APC-eFluor 780 Invitrogen 47-0451-82; RRID: AB 1548781 Mouse anti-EpCAM-eFluor-450 Invitrogen 48-5791-82; RRID: AB 10717090 Rabbit anti-mouse CLCA1 Abcam Ab180851; RRID: AB 2722611 Recombinant Anti-STAT3 (Phospho Y705) Abcam ab76315; RRID: AB 1658549 Adenovirus hexon protein antibody (3G0) Santa Cruz Sc-80671; RRID: AB 1118724 Mouse PE/Cy7 anti-cKit Biolegend Cat#135111; RRID: AB 2131136 PerCP-Cy5.5 anti-mouse CD44 Invitrogen 45-0441-80; RRID: AB 925747 Live/Dead fixable Aqua dead cell stain kit Invitrogen L34957 IC fixation Buffer Invitrogen 00-8222-49 Horseradish Peroxidase labeled Goat anti-human/mouse IgM Southern Biotech Cat#: 1020-05; RRID: AB 2794201 Chemicals, peptides, and recombinant proteins VECTASHIELD HardSetTM Antifade mounting medium with DAPI Vector Laboratories Cat#: H-1500 Mouse HRP/DAB ABC detection IHC kit Abcam Cat#: ab64264 SsoAdvancedTM Universal Probes Supermix Bio-Rad Cat#: 1725281 SsoAdvancedTM Universal SYBR Green Supermix Bio-Rad Cat#: 1725271 Simple ChIP Enzymatic Chromatin IP kit Cell Signaling Technology Cat#: 9003S iScriptTM Reverse Transcription Supermix Bio-Rad Cat#: 1708840 High-Capacity cDNA Reverse Transcription Kit Thermo Fisher Cat#: 4368814 Roche Diagnostics LIGHTCYCLER 480 SYBR GREEN Roche Cat#: 04887352001 EDTA Invitrogen Cat#: AM9260G DSS MP Biomedicals Cat#: 160110 Alcian blue Alfa Aesar Cat#: J60122 Tamoxifen Sigma-Aldrich Cat#: T5648 DMSO ThermoFisher Cat#: BP231 DMEM/F12 Gibco Cat#: 12634-010 PBS Corning Cat#: 21040CV Fetal bovine serum Gibco Cat#: SH30071.03HI Nuclear Fast Red Electron Microscopy Sciences Cat#: 26078-05 Hematoxylin VWR Cat#: 95057-844 Eosin VWR Cat#: 95057-848 Matrigel Matrix Corning Cat#: 356231 (Continued on next page) Cell Reports 43, 114206, May 28, 2024 15 .. REAGENT or RESOURCE SOURCE IDENTIFIER 100x penicillin-streptomycin-glutamine Gibco Cat#: 10378016 Penicillin-Streptomycin solution, 100X Corning Cat#: 30-002-CI L-Glutamine Corning Cat#: 25-005-CI N2 Gibco Cat#: 17502048 B27 Gibco Cat#: 17504044 Mouse EGF Peprotech Cat#: 315-09 N-acetylcysteine Sigma-Aldrich Cat#: A9165 Gastrin-Leu15 Sigma-Aldrich Cat#: G9145 A83-01 Tocris Bioscience Cat#: 2939 Y-27632 Sigma-Aldrich Cat#: Y05030 Cell Recovery Medium Corning Cat#: 354253 2-mercaptoethanol Sigma-Aldrich Cat#: M6250 Triton X-100 Sigma-Aldrich Cat#: T8787 Tween 20 VWR Cat#: 0777 CHIR99021 Tocris Bioscience Cat#: 4423 Primocin InvivoGen Cat#:ant-pm-2 RLT buffer Qiagen RNeasy Micro kit Cat#:74004 Ad-B3galt5 Vector Biolabs N/A Ad-Y5 Vector Biolabs N/A RU-486 (Mifepristone) Sigma-Aldrich Cat#: M8046 TRIzol Invitrogen Cat#: 15596018 Qiagen RNeasy kit Qiagen Cat#: 74004 8M Lithium Chloride Sigma-Aldrich Cat#: L7026 Glycogen solution VWR Cat#: N632 Sodium Acetate Sigma-Aldrich Cat#: 127-09-3 IHC Tek Epitope retrieval solution IHC Tek Cat#: IW-1100 Tris base Sigma-Aldrich Cat#: 77-86-1 Bovine Serum Albumin Sigma-Aldrich Cat#: 9048-46-8 3,30-Diaminobenzidine Abcam Cat#: ab64264 Mouse rIL-22.Fc Evive Biotech Cat#: F-652 Mouse rIL-22 Biolegend Cat#: 576204 Human rIL-22 R & D systems Cat#: 782-IL DAPT Sigma-Aldrich Cat#: D5942 S3I-201 Sigma-Aldrich Cat#: 501919-59-1 L-WRN conditioned medium ATCC Cat#: CRL-3276 Advanced DMEM/F12 ThermoFisher Cat#: 12634028 NAC MP Biomedicals Cat#: 194603 FBS R&D Systems Cat#: S11150 Y-27632 MedChemExpress Cat#: HY-10583 B27 formulation ThermoFisher 17504-044 (50X) Gastrin AnaSpec Cat#: AS-64149 Primocin InvivoGen Cat#: ant-pm-2 A 83-01 Millipore-Sigma Cat#: SML078 SB 202190 LC Laboratories Cat#: S-1700 PGE2 Cayman Chemical Cat#: 14010 Nicotinamide Millipore-Sigma Cat#: N0636 Collagenase Worthington Cat#: LS004189 HEPES Corning Cat#: 25-060-CI GlutaMAX ThermoFisher Cat#: 25050061 (Continued on next page) 16 Cell Reports 43, 114206, May 28, 2024
Recombinant:Article Title: IL-22 promotes mucin-type O-glycosylation and MATH1 + cell-mediated amelioration of intestinal inflammation.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit anti-Human Lysozyme FITC Dako Cat#: F037201; RRID: AB_578661 Goat anti-rabbit IgG AF488 Jackson ImmunoResearch Labs Cat#:111-545-144; RRID: AB 2338052 Mouse anti-GFP Cell Signaling Technology Cat#: 2955; RRID: AB 1196614 Goat anti-mouse IgG AF488 Jackson ImmunoResearch Labs Cat#:115-546-003; RRID: AB 2338859 UEA-I Dylight 649 Vector Laboratories Cat#: DL-1068 Mouse/Human anti-Tn Dr. Richard D Cummings, Harvard Medical School N/A Mouse anti-GFP antibody (biotin) GeneTex Cat#: GTX26658; RRID: AB 371422 Mouse anti-IL22Ra1-PE R&D FAB42941P; RRID: AB 1964624 Mouse anti-CD45-APC-eFluor 780 Invitrogen 47-0451-82; RRID: AB 1548781 Mouse anti-EpCAM-eFluor-450 Invitrogen 48-5791-82; RRID: AB 10717090 Rabbit anti-mouse CLCA1 Abcam Ab180851; RRID: AB 2722611 Recombinant Anti-STAT3 (Phospho Y705) Abcam ab76315; RRID: AB 1658549 Adenovirus hexon protein antibody (3G0) Santa Cruz Sc-80671; RRID: AB 1118724 Mouse PE/Cy7 anti-cKit Biolegend Cat#135111; RRID: AB 2131136 PerCP-Cy5.5 anti-mouse CD44 Invitrogen 45-0441-80; RRID: AB 925747 Live/Dead fixable Aqua dead cell stain kit Invitrogen L34957 IC fixation Buffer Invitrogen 00-8222-49 Horseradish Peroxidase labeled Goat anti-human/mouse IgM Southern Biotech Cat#: 1020-05; RRID: AB 2794201 Chemicals, peptides, and recombinant proteins VECTASHIELD HardSetTM Antifade mounting medium with DAPI Vector Laboratories Cat#: H-1500 Mouse HRP/DAB ABC detection IHC kit Abcam Cat#: ab64264 SsoAdvancedTM Universal Probes Supermix Bio-Rad Cat#: 1725281 SsoAdvancedTM Universal SYBR Green Supermix Bio-Rad Cat#: 1725271 Simple ChIP Enzymatic Chromatin IP kit Cell Signaling Technology Cat#: 9003S iScriptTM Reverse Transcription Supermix Bio-Rad Cat#: 1708840 High-Capacity cDNA Reverse Transcription Kit Thermo Fisher Cat#: 4368814 Roche Diagnostics LIGHTCYCLER 480 SYBR GREEN Roche Cat#: 04887352001 EDTA Invitrogen Cat#: AM9260G DSS MP Biomedicals Cat#: 160110 Alcian blue Alfa Aesar Cat#: J60122 Tamoxifen Sigma-Aldrich Cat#: T5648 DMSO ThermoFisher Cat#: BP231 DMEM/F12 Gibco Cat#: 12634-010 PBS Corning Cat#: 21040CV Fetal bovine serum Gibco Cat#: SH30071.03HI Nuclear Fast Red Electron Microscopy Sciences Cat#: 26078-05 Hematoxylin VWR Cat#: 95057-844 Eosin VWR Cat#: 95057-848 Matrigel Matrix Corning Cat#: 356231 (Continued on next page) Cell Reports 43, 114206, May 28, 2024 15 .. REAGENT or RESOURCE SOURCE IDENTIFIER 100x penicillin-streptomycin-glutamine Gibco Cat#: 10378016 Penicillin-Streptomycin solution, 100X Corning Cat#: 30-002-CI L-Glutamine Corning Cat#: 25-005-CI N2 Gibco Cat#: 17502048 B27 Gibco Cat#: 17504044 Mouse EGF Peprotech Cat#: 315-09 N-acetylcysteine Sigma-Aldrich Cat#: A9165 Gastrin-Leu15 Sigma-Aldrich Cat#: G9145 A83-01 Tocris Bioscience Cat#: 2939 Y-27632 Sigma-Aldrich Cat#: Y05030 Cell Recovery Medium Corning Cat#: 354253 2-mercaptoethanol Sigma-Aldrich Cat#: M6250 Triton X-100 Sigma-Aldrich Cat#: T8787 Tween 20 VWR Cat#: 0777 CHIR99021 Tocris Bioscience Cat#: 4423 Primocin InvivoGen Cat#:ant-pm-2 RLT buffer Qiagen RNeasy Micro kit Cat#:74004 Ad-B3galt5 Vector Biolabs N/A Ad-Y5 Vector Biolabs N/A RU-486 (Mifepristone) Sigma-Aldrich Cat#: M8046 TRIzol Invitrogen Cat#: 15596018 Qiagen RNeasy kit Qiagen Cat#: 74004 8M Lithium Chloride Sigma-Aldrich Cat#: L7026 Glycogen solution VWR Cat#: N632 Sodium Acetate Sigma-Aldrich Cat#: 127-09-3 IHC Tek Epitope retrieval solution IHC Tek Cat#: IW-1100 Tris base Sigma-Aldrich Cat#: 77-86-1 Bovine Serum Albumin Sigma-Aldrich Cat#: 9048-46-8 3,30-Diaminobenzidine Abcam Cat#: ab64264 Mouse rIL-22.Fc Evive Biotech Cat#: F-652 Mouse rIL-22 Biolegend Cat#: 576204 Human rIL-22 R & D systems Cat#: 782-IL DAPT Sigma-Aldrich Cat#: D5942 S3I-201 Sigma-Aldrich Cat#: 501919-59-1 L-WRN conditioned medium ATCC Cat#: CRL-3276 Advanced DMEM/F12 ThermoFisher Cat#: 12634028 NAC MP Biomedicals Cat#: 194603 FBS R&D Systems Cat#: S11150 Y-27632 MedChemExpress Cat#: HY-10583 B27 formulation ThermoFisher 17504-044 (50X) Gastrin AnaSpec Cat#: AS-64149 Primocin InvivoGen Cat#: ant-pm-2 A 83-01 Millipore-Sigma Cat#: SML078 SB 202190 LC Laboratories Cat#: S-1700 PGE2 Cayman Chemical Cat#: 14010 Nicotinamide Millipore-Sigma Cat#: N0636 Collagenase Worthington Cat#: LS004189 HEPES Corning Cat#: 25-060-CI GlutaMAX ThermoFisher Cat#: 25050061 (Continued on next page) 16 Cell Reports 43, 114206, May 28, 2024
Article Title: Integrated multiomics reveals starvation-driven keratin degradation and persistence in Fervidobacterium islandicum AW-1
Article Snippet: .. 492 493 STAR METHODS 494 KEY RESOURCES TABLE 495 REAGENT or RESOURCE SOURCE IDENTIFIER Chemicals, peptides, and recombinant proteins Jo urn al Pr -pr oo f 25 SYTO9 Invitrogen, MA, USA Cat# S34854 Propidium iodide Invitrogen, MA, USA Cat# P1304MP CPM (7- diethylamino-3-(4’maleimidylphenyl)4-methylcoumarin) Invitrogen, MA, USA Cat# D346 iScript cDNA Synthesis Kit Bio-Rad, CA, USA Cat# 1708890 2× SsoAdvancedTM Universal SYBR Green Supermix Bio-Rad, CA, USA Cat# 1725271 Thiamphenicol Sigma- Aldrich, MO, USA Cat# T0261 Critical commercial assays RNeasy Mini Kit QIAGEN, Hilden, Germany Cat# 74104 TruSeq RNA Sample Prep Kit v2 Illumina, CA, USA Cat# RS-122 Jo urn al Pr e-p roo f 26 TruSeq DNA Nano Prep Kit Illumina, CA, USA Cat# 20015964 c-di-GMP ELISA kit EIAab Science, Wuhan, China Cat# E0152Ge Deposited data RNA-seq data This study SRR33382689–SRR33382697 and SRX219354-SRX219357 Proteomics data This study PXD027063 Metabolomics data This study MSV000099151 Experimental models: Organisms/strains F. islandicum AW1 Yonsei University Korean Culture Collections of Microorganisms (KCCM) 80008 Oligonucleotides See Table S4 for oligonucleotides used in this study. ..
Article Title: CdGAP is a talin-binding protein and a target of TGF-β signaling that promotes HER2-positive breast cancer growth and metastasis.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER jetPRIME Polyplus Cat# 114-07 Protein G SepharoseTM 4 Fast Flow Affinity Chromatography media Thermo Fisher Scientific Cat# 17-0618-01 ClarityTM western ECL substrate Bor-Rad Cat# 1705061 SsoAdvancedTM Universal SYBR green Supermix Bio-Rad Cat#1725271 Fibronectin Sigma-Aldrich Cat# F1141 CorningTM MatrigelTM membrane matrix Thermo Fisher Scientific Cat# CB-40234A CorningTM MatrigelTM GFR membrane matrix Thermo Fisher Scientific Cat# CB-40230 FORMALDEHYDE, (formalin) reagent Grade Bioshop Cat# FOR201 Type 1 collagen BD Bioscience Cat# 354246 Critical commercial assays Mycoplasma PCR Detection kit ZmTech Scientific Cat# M209001 Dual-Luciferase reporter assay system Promega Cat# E1910 Qiagen RNeasy kit Qiagen Cat# 74104 RNase-free DNase set Qiagen Cat# 79254 RhoA G-LISA activation assay (luminescence) Cytoskeleton Cat# BK121 Rac1 G-LISA activation assay (luminescence) Cytoskeleton Cat# BK126 MTT Cell proliferation assay kit Abcam Cat# ab211091 Pierce BCA protein assay kit Thermo Fisher Scientific Cat# 23225 Deposited data RNA-sequencing raw data This paper GSE167457 Proteomics raw data This paper PXD043376 Experimental models: Cell lines Human breast cancer cell line: HCC1954 American type culture collection (ATCC) RRID: CVCL_1259 Human breast cancer cell line: SK-BR-3 American type culture collection (ATCC) RRID: CVCL_0033 Human breast cancer cell line: MDA-MB-361 American type culture collection (ATCC) RRID: CVCL_0620 Mouse: NIC+ explant cells Goyette et al.40 N/A Experimental models: Organisms/strains Mouse: Mammary Tumor Virus (MMTV)-NeuNDL2-5-Internal Ribosome Entry Site- Cre (NIC) FVB/NJ Ursini-Siegel et al.37 N/A Athymic Nude mouse Charles River Strain Code:490 Mouse: MMTV-Cre Wagner et al.36 N/A Mouse: CdGAPfl/fl Caron et al.35 N/A Oligonucleotides Smad4 specific silencer select validated siRNA Ambion Cat# 4390824 Mouse CdGAP primers for qPCR Qiagen Cat# QT00155162 Human CdGAP primers for qPCR Qiagen Cat# QT00076671 mouse E-cadherin primers for qPCR Qiagen Cat# QT00121163 All the other oligonucleotides, gRNAs, and shRNAs can be found in the Table S3 This paper Table S3 Recombinant DNA pSpCas9(BB)-2A-Puro (PX459) Ding et al.69 Addgene Cat#48139 mCherry-talin-18 a gift from Michael Davidson Addgene Cat#55137 EGFP-talin1 head Simonson et al.70 Addgene Cat# 32856 EGFP-talin1 rod Simonson et al.70 Addgene Cat# 32855 pGL3-basic CdGAP ( 896 to +601) This paper N/A MSCV luciferase PGK-hygro a gift from Scott lowe Addgene Cat# 18782 (Continued on next page) Cell Reports 42, 112936, August 29, 2023 21 .. REAGENT or RESOURCE SOURCE IDENTIFIER pCL-Eco Naviaux et al.71 Addgene Cat# 12371 pCMV5 Smad2-HA Hata et al.72 Addgene Cat# 14930 pRK5F Smad3 Zhang et al.73 Addgene Cat# 12625 pGL3-basic (CAGA)12-luc Kang 74 N/A pGL3-basic vector Promega Cat# E1751 pRK5-myc vector He et al.32 N/A pRK5-myc-CdGAP He et al.32 N/A pRK5-myc-CdGAP PRD He et al.32 N/A pRK5-myc-CdGAP 1-515 He et al.32 N/A GFP-CdGAP He et al.32 N/A Software and algorithms Imagescope software version 2.0.0 Leica Biosystems Inc. RRID: SCR_014311 ImageJ, version 1.8.0/1.53a N/A RRID: SCR_003070 Image Lab software 6.0.1 Bio-Rad RRID: SCR_014210 GraphPad Prism 8 GraphPad RRID: SCR_002798 GenPipes ‘‘RNAseq’’ pipeline Bourgey et al.75 https://github.com/c3g/GenPipes STAR aligner Dobin et al.76 https://github.com/alexdobin/STAR GATK DePristo et al.77 https://gatk.broadinstitute.org/hc/en-us Picard N/A https://broadinstitute.github.io/picard/ HT-seq Anders et al.78 https://github.com/htseq/htseq DESeq2 (v1.30.1) Lovet et al.79 N/A Msigdbr (v7.2.1) N/A https://igordot.github.io/msigdbr/ ClusterProfiler (v3.18.1) Yu et al.80 N/A MKmisc (v1.6) N/A https://github.com/stamats/MKmisc Singscore (v1.12.0) Foroutan et al.81 N/A
Staining:Article Title: IL-22 promotes mucin-type O-glycosylation and MATH1 + cell-mediated amelioration of intestinal inflammation.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit anti-Human Lysozyme FITC Dako Cat#: F037201; RRID: AB_578661 Goat anti-rabbit IgG AF488 Jackson ImmunoResearch Labs Cat#:111-545-144; RRID: AB 2338052 Mouse anti-GFP Cell Signaling Technology Cat#: 2955; RRID: AB 1196614 Goat anti-mouse IgG AF488 Jackson ImmunoResearch Labs Cat#:115-546-003; RRID: AB 2338859 UEA-I Dylight 649 Vector Laboratories Cat#: DL-1068 Mouse/Human anti-Tn Dr. Richard D Cummings, Harvard Medical School N/A Mouse anti-GFP antibody (biotin) GeneTex Cat#: GTX26658; RRID: AB 371422 Mouse anti-IL22Ra1-PE R&D FAB42941P; RRID: AB 1964624 Mouse anti-CD45-APC-eFluor 780 Invitrogen 47-0451-82; RRID: AB 1548781 Mouse anti-EpCAM-eFluor-450 Invitrogen 48-5791-82; RRID: AB 10717090 Rabbit anti-mouse CLCA1 Abcam Ab180851; RRID: AB 2722611 Recombinant Anti-STAT3 (Phospho Y705) Abcam ab76315; RRID: AB 1658549 Adenovirus hexon protein antibody (3G0) Santa Cruz Sc-80671; RRID: AB 1118724 Mouse PE/Cy7 anti-cKit Biolegend Cat#135111; RRID: AB 2131136 PerCP-Cy5.5 anti-mouse CD44 Invitrogen 45-0441-80; RRID: AB 925747 Live/Dead fixable Aqua dead cell stain kit Invitrogen L34957 IC fixation Buffer Invitrogen 00-8222-49 Horseradish Peroxidase labeled Goat anti-human/mouse IgM Southern Biotech Cat#: 1020-05; RRID: AB 2794201 Chemicals, peptides, and recombinant proteins VECTASHIELD HardSetTM Antifade mounting medium with DAPI Vector Laboratories Cat#: H-1500 Mouse HRP/DAB ABC detection IHC kit Abcam Cat#: ab64264 SsoAdvancedTM Universal Probes Supermix Bio-Rad Cat#: 1725281 SsoAdvancedTM Universal SYBR Green Supermix Bio-Rad Cat#: 1725271 Simple ChIP Enzymatic Chromatin IP kit Cell Signaling Technology Cat#: 9003S iScriptTM Reverse Transcription Supermix Bio-Rad Cat#: 1708840 High-Capacity cDNA Reverse Transcription Kit Thermo Fisher Cat#: 4368814 Roche Diagnostics LIGHTCYCLER 480 SYBR GREEN Roche Cat#: 04887352001 EDTA Invitrogen Cat#: AM9260G DSS MP Biomedicals Cat#: 160110 Alcian blue Alfa Aesar Cat#: J60122 Tamoxifen Sigma-Aldrich Cat#: T5648 DMSO ThermoFisher Cat#: BP231 DMEM/F12 Gibco Cat#: 12634-010 PBS Corning Cat#: 21040CV Fetal bovine serum Gibco Cat#: SH30071.03HI Nuclear Fast Red Electron Microscopy Sciences Cat#: 26078-05 Hematoxylin VWR Cat#: 95057-844 Eosin VWR Cat#: 95057-848 Matrigel Matrix Corning Cat#: 356231 (Continued on next page) Cell Reports 43, 114206, May 28, 2024 15 .. REAGENT or RESOURCE SOURCE IDENTIFIER 100x penicillin-streptomycin-glutamine Gibco Cat#: 10378016 Penicillin-Streptomycin solution, 100X Corning Cat#: 30-002-CI L-Glutamine Corning Cat#: 25-005-CI N2 Gibco Cat#: 17502048 B27 Gibco Cat#: 17504044 Mouse EGF Peprotech Cat#: 315-09 N-acetylcysteine Sigma-Aldrich Cat#: A9165 Gastrin-Leu15 Sigma-Aldrich Cat#: G9145 A83-01 Tocris Bioscience Cat#: 2939 Y-27632 Sigma-Aldrich Cat#: Y05030 Cell Recovery Medium Corning Cat#: 354253 2-mercaptoethanol Sigma-Aldrich Cat#: M6250 Triton X-100 Sigma-Aldrich Cat#: T8787 Tween 20 VWR Cat#: 0777 CHIR99021 Tocris Bioscience Cat#: 4423 Primocin InvivoGen Cat#:ant-pm-2 RLT buffer Qiagen RNeasy Micro kit Cat#:74004 Ad-B3galt5 Vector Biolabs N/A Ad-Y5 Vector Biolabs N/A RU-486 (Mifepristone) Sigma-Aldrich Cat#: M8046 TRIzol Invitrogen Cat#: 15596018 Qiagen RNeasy kit Qiagen Cat#: 74004 8M Lithium Chloride Sigma-Aldrich Cat#: L7026 Glycogen solution VWR Cat#: N632 Sodium Acetate Sigma-Aldrich Cat#: 127-09-3 IHC Tek Epitope retrieval solution IHC Tek Cat#: IW-1100 Tris base Sigma-Aldrich Cat#: 77-86-1 Bovine Serum Albumin Sigma-Aldrich Cat#: 9048-46-8 3,30-Diaminobenzidine Abcam Cat#: ab64264 Mouse rIL-22.Fc Evive Biotech Cat#: F-652 Mouse rIL-22 Biolegend Cat#: 576204 Human rIL-22 R & D systems Cat#: 782-IL DAPT Sigma-Aldrich Cat#: D5942 S3I-201 Sigma-Aldrich Cat#: 501919-59-1 L-WRN conditioned medium ATCC Cat#: CRL-3276 Advanced DMEM/F12 ThermoFisher Cat#: 12634028 NAC MP Biomedicals Cat#: 194603 FBS R&D Systems Cat#: S11150 Y-27632 MedChemExpress Cat#: HY-10583 B27 formulation ThermoFisher 17504-044 (50X) Gastrin AnaSpec Cat#: AS-64149 Primocin InvivoGen Cat#: ant-pm-2 A 83-01 Millipore-Sigma Cat#: SML078 SB 202190 LC Laboratories Cat#: S-1700 PGE2 Cayman Chemical Cat#: 14010 Nicotinamide Millipore-Sigma Cat#: N0636 Collagenase Worthington Cat#: LS004189 HEPES Corning Cat#: 25-060-CI GlutaMAX ThermoFisher Cat#: 25050061 (Continued on next page) 16 Cell Reports 43, 114206, May 28, 2024
Labeling:Article Title: IL-22 promotes mucin-type O-glycosylation and MATH1 + cell-mediated amelioration of intestinal inflammation.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit anti-Human Lysozyme FITC Dako Cat#: F037201; RRID: AB_578661 Goat anti-rabbit IgG AF488 Jackson ImmunoResearch Labs Cat#:111-545-144; RRID: AB 2338052 Mouse anti-GFP Cell Signaling Technology Cat#: 2955; RRID: AB 1196614 Goat anti-mouse IgG AF488 Jackson ImmunoResearch Labs Cat#:115-546-003; RRID: AB 2338859 UEA-I Dylight 649 Vector Laboratories Cat#: DL-1068 Mouse/Human anti-Tn Dr. Richard D Cummings, Harvard Medical School N/A Mouse anti-GFP antibody (biotin) GeneTex Cat#: GTX26658; RRID: AB 371422 Mouse anti-IL22Ra1-PE R&D FAB42941P; RRID: AB 1964624 Mouse anti-CD45-APC-eFluor 780 Invitrogen 47-0451-82; RRID: AB 1548781 Mouse anti-EpCAM-eFluor-450 Invitrogen 48-5791-82; RRID: AB 10717090 Rabbit anti-mouse CLCA1 Abcam Ab180851; RRID: AB 2722611 Recombinant Anti-STAT3 (Phospho Y705) Abcam ab76315; RRID: AB 1658549 Adenovirus hexon protein antibody (3G0) Santa Cruz Sc-80671; RRID: AB 1118724 Mouse PE/Cy7 anti-cKit Biolegend Cat#135111; RRID: AB 2131136 PerCP-Cy5.5 anti-mouse CD44 Invitrogen 45-0441-80; RRID: AB 925747 Live/Dead fixable Aqua dead cell stain kit Invitrogen L34957 IC fixation Buffer Invitrogen 00-8222-49 Horseradish Peroxidase labeled Goat anti-human/mouse IgM Southern Biotech Cat#: 1020-05; RRID: AB 2794201 Chemicals, peptides, and recombinant proteins VECTASHIELD HardSetTM Antifade mounting medium with DAPI Vector Laboratories Cat#: H-1500 Mouse HRP/DAB ABC detection IHC kit Abcam Cat#: ab64264 SsoAdvancedTM Universal Probes Supermix Bio-Rad Cat#: 1725281 SsoAdvancedTM Universal SYBR Green Supermix Bio-Rad Cat#: 1725271 Simple ChIP Enzymatic Chromatin IP kit Cell Signaling Technology Cat#: 9003S iScriptTM Reverse Transcription Supermix Bio-Rad Cat#: 1708840 High-Capacity cDNA Reverse Transcription Kit Thermo Fisher Cat#: 4368814 Roche Diagnostics LIGHTCYCLER 480 SYBR GREEN Roche Cat#: 04887352001 EDTA Invitrogen Cat#: AM9260G DSS MP Biomedicals Cat#: 160110 Alcian blue Alfa Aesar Cat#: J60122 Tamoxifen Sigma-Aldrich Cat#: T5648 DMSO ThermoFisher Cat#: BP231 DMEM/F12 Gibco Cat#: 12634-010 PBS Corning Cat#: 21040CV Fetal bovine serum Gibco Cat#: SH30071.03HI Nuclear Fast Red Electron Microscopy Sciences Cat#: 26078-05 Hematoxylin VWR Cat#: 95057-844 Eosin VWR Cat#: 95057-848 Matrigel Matrix Corning Cat#: 356231 (Continued on next page) Cell Reports 43, 114206, May 28, 2024 15 .. REAGENT or RESOURCE SOURCE IDENTIFIER 100x penicillin-streptomycin-glutamine Gibco Cat#: 10378016 Penicillin-Streptomycin solution, 100X Corning Cat#: 30-002-CI L-Glutamine Corning Cat#: 25-005-CI N2 Gibco Cat#: 17502048 B27 Gibco Cat#: 17504044 Mouse EGF Peprotech Cat#: 315-09 N-acetylcysteine Sigma-Aldrich Cat#: A9165 Gastrin-Leu15 Sigma-Aldrich Cat#: G9145 A83-01 Tocris Bioscience Cat#: 2939 Y-27632 Sigma-Aldrich Cat#: Y05030 Cell Recovery Medium Corning Cat#: 354253 2-mercaptoethanol Sigma-Aldrich Cat#: M6250 Triton X-100 Sigma-Aldrich Cat#: T8787 Tween 20 VWR Cat#: 0777 CHIR99021 Tocris Bioscience Cat#: 4423 Primocin InvivoGen Cat#:ant-pm-2 RLT buffer Qiagen RNeasy Micro kit Cat#:74004 Ad-B3galt5 Vector Biolabs N/A Ad-Y5 Vector Biolabs N/A RU-486 (Mifepristone) Sigma-Aldrich Cat#: M8046 TRIzol Invitrogen Cat#: 15596018 Qiagen RNeasy kit Qiagen Cat#: 74004 8M Lithium Chloride Sigma-Aldrich Cat#: L7026 Glycogen solution VWR Cat#: N632 Sodium Acetate Sigma-Aldrich Cat#: 127-09-3 IHC Tek Epitope retrieval solution IHC Tek Cat#: IW-1100 Tris base Sigma-Aldrich Cat#: 77-86-1 Bovine Serum Albumin Sigma-Aldrich Cat#: 9048-46-8 3,30-Diaminobenzidine Abcam Cat#: ab64264 Mouse rIL-22.Fc Evive Biotech Cat#: F-652 Mouse rIL-22 Biolegend Cat#: 576204 Human rIL-22 R & D systems Cat#: 782-IL DAPT Sigma-Aldrich Cat#: D5942 S3I-201 Sigma-Aldrich Cat#: 501919-59-1 L-WRN conditioned medium ATCC Cat#: CRL-3276 Advanced DMEM/F12 ThermoFisher Cat#: 12634028 NAC MP Biomedicals Cat#: 194603 FBS R&D Systems Cat#: S11150 Y-27632 MedChemExpress Cat#: HY-10583 B27 formulation ThermoFisher 17504-044 (50X) Gastrin AnaSpec Cat#: AS-64149 Primocin InvivoGen Cat#: ant-pm-2 A 83-01 Millipore-Sigma Cat#: SML078 SB 202190 LC Laboratories Cat#: S-1700 PGE2 Cayman Chemical Cat#: 14010 Nicotinamide Millipore-Sigma Cat#: N0636 Collagenase Worthington Cat#: LS004189 HEPES Corning Cat#: 25-060-CI GlutaMAX ThermoFisher Cat#: 25050061 (Continued on next page) 16 Cell Reports 43, 114206, May 28, 2024
Immunohistochemistry:Article Title: IL-22 promotes mucin-type O-glycosylation and MATH1 + cell-mediated amelioration of intestinal inflammation.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit anti-Human Lysozyme FITC Dako Cat#: F037201; RRID: AB_578661 Goat anti-rabbit IgG AF488 Jackson ImmunoResearch Labs Cat#:111-545-144; RRID: AB 2338052 Mouse anti-GFP Cell Signaling Technology Cat#: 2955; RRID: AB 1196614 Goat anti-mouse IgG AF488 Jackson ImmunoResearch Labs Cat#:115-546-003; RRID: AB 2338859 UEA-I Dylight 649 Vector Laboratories Cat#: DL-1068 Mouse/Human anti-Tn Dr. Richard D Cummings, Harvard Medical School N/A Mouse anti-GFP antibody (biotin) GeneTex Cat#: GTX26658; RRID: AB 371422 Mouse anti-IL22Ra1-PE R&D FAB42941P; RRID: AB 1964624 Mouse anti-CD45-APC-eFluor 780 Invitrogen 47-0451-82; RRID: AB 1548781 Mouse anti-EpCAM-eFluor-450 Invitrogen 48-5791-82; RRID: AB 10717090 Rabbit anti-mouse CLCA1 Abcam Ab180851; RRID: AB 2722611 Recombinant Anti-STAT3 (Phospho Y705) Abcam ab76315; RRID: AB 1658549 Adenovirus hexon protein antibody (3G0) Santa Cruz Sc-80671; RRID: AB 1118724 Mouse PE/Cy7 anti-cKit Biolegend Cat#135111; RRID: AB 2131136 PerCP-Cy5.5 anti-mouse CD44 Invitrogen 45-0441-80; RRID: AB 925747 Live/Dead fixable Aqua dead cell stain kit Invitrogen L34957 IC fixation Buffer Invitrogen 00-8222-49 Horseradish Peroxidase labeled Goat anti-human/mouse IgM Southern Biotech Cat#: 1020-05; RRID: AB 2794201 Chemicals, peptides, and recombinant proteins VECTASHIELD HardSetTM Antifade mounting medium with DAPI Vector Laboratories Cat#: H-1500 Mouse HRP/DAB ABC detection IHC kit Abcam Cat#: ab64264 SsoAdvancedTM Universal Probes Supermix Bio-Rad Cat#: 1725281 SsoAdvancedTM Universal SYBR Green Supermix Bio-Rad Cat#: 1725271 Simple ChIP Enzymatic Chromatin IP kit Cell Signaling Technology Cat#: 9003S iScriptTM Reverse Transcription Supermix Bio-Rad Cat#: 1708840 High-Capacity cDNA Reverse Transcription Kit Thermo Fisher Cat#: 4368814 Roche Diagnostics LIGHTCYCLER 480 SYBR GREEN Roche Cat#: 04887352001 EDTA Invitrogen Cat#: AM9260G DSS MP Biomedicals Cat#: 160110 Alcian blue Alfa Aesar Cat#: J60122 Tamoxifen Sigma-Aldrich Cat#: T5648 DMSO ThermoFisher Cat#: BP231 DMEM/F12 Gibco Cat#: 12634-010 PBS Corning Cat#: 21040CV Fetal bovine serum Gibco Cat#: SH30071.03HI Nuclear Fast Red Electron Microscopy Sciences Cat#: 26078-05 Hematoxylin VWR Cat#: 95057-844 Eosin VWR Cat#: 95057-848 Matrigel Matrix Corning Cat#: 356231 (Continued on next page) Cell Reports 43, 114206, May 28, 2024 15 .. REAGENT or RESOURCE SOURCE IDENTIFIER 100x penicillin-streptomycin-glutamine Gibco Cat#: 10378016 Penicillin-Streptomycin solution, 100X Corning Cat#: 30-002-CI L-Glutamine Corning Cat#: 25-005-CI N2 Gibco Cat#: 17502048 B27 Gibco Cat#: 17504044 Mouse EGF Peprotech Cat#: 315-09 N-acetylcysteine Sigma-Aldrich Cat#: A9165 Gastrin-Leu15 Sigma-Aldrich Cat#: G9145 A83-01 Tocris Bioscience Cat#: 2939 Y-27632 Sigma-Aldrich Cat#: Y05030 Cell Recovery Medium Corning Cat#: 354253 2-mercaptoethanol Sigma-Aldrich Cat#: M6250 Triton X-100 Sigma-Aldrich Cat#: T8787 Tween 20 VWR Cat#: 0777 CHIR99021 Tocris Bioscience Cat#: 4423 Primocin InvivoGen Cat#:ant-pm-2 RLT buffer Qiagen RNeasy Micro kit Cat#:74004 Ad-B3galt5 Vector Biolabs N/A Ad-Y5 Vector Biolabs N/A RU-486 (Mifepristone) Sigma-Aldrich Cat#: M8046 TRIzol Invitrogen Cat#: 15596018 Qiagen RNeasy kit Qiagen Cat#: 74004 8M Lithium Chloride Sigma-Aldrich Cat#: L7026 Glycogen solution VWR Cat#: N632 Sodium Acetate Sigma-Aldrich Cat#: 127-09-3 IHC Tek Epitope retrieval solution IHC Tek Cat#: IW-1100 Tris base Sigma-Aldrich Cat#: 77-86-1 Bovine Serum Albumin Sigma-Aldrich Cat#: 9048-46-8 3,30-Diaminobenzidine Abcam Cat#: ab64264 Mouse rIL-22.Fc Evive Biotech Cat#: F-652 Mouse rIL-22 Biolegend Cat#: 576204 Human rIL-22 R & D systems Cat#: 782-IL DAPT Sigma-Aldrich Cat#: D5942 S3I-201 Sigma-Aldrich Cat#: 501919-59-1 L-WRN conditioned medium ATCC Cat#: CRL-3276 Advanced DMEM/F12 ThermoFisher Cat#: 12634028 NAC MP Biomedicals Cat#: 194603 FBS R&D Systems Cat#: S11150 Y-27632 MedChemExpress Cat#: HY-10583 B27 formulation ThermoFisher 17504-044 (50X) Gastrin AnaSpec Cat#: AS-64149 Primocin InvivoGen Cat#: ant-pm-2 A 83-01 Millipore-Sigma Cat#: SML078 SB 202190 LC Laboratories Cat#: S-1700 PGE2 Cayman Chemical Cat#: 14010 Nicotinamide Millipore-Sigma Cat#: N0636 Collagenase Worthington Cat#: LS004189 HEPES Corning Cat#: 25-060-CI GlutaMAX ThermoFisher Cat#: 25050061 (Continued on next page) 16 Cell Reports 43, 114206, May 28, 2024
Chromatin Immunoprecipitation:Article Title: IL-22 promotes mucin-type O-glycosylation and MATH1 + cell-mediated amelioration of intestinal inflammation.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit anti-Human Lysozyme FITC Dako Cat#: F037201; RRID: AB_578661 Goat anti-rabbit IgG AF488 Jackson ImmunoResearch Labs Cat#:111-545-144; RRID: AB 2338052 Mouse anti-GFP Cell Signaling Technology Cat#: 2955; RRID: AB 1196614 Goat anti-mouse IgG AF488 Jackson ImmunoResearch Labs Cat#:115-546-003; RRID: AB 2338859 UEA-I Dylight 649 Vector Laboratories Cat#: DL-1068 Mouse/Human anti-Tn Dr. Richard D Cummings, Harvard Medical School N/A Mouse anti-GFP antibody (biotin) GeneTex Cat#: GTX26658; RRID: AB 371422 Mouse anti-IL22Ra1-PE R&D FAB42941P; RRID: AB 1964624 Mouse anti-CD45-APC-eFluor 780 Invitrogen 47-0451-82; RRID: AB 1548781 Mouse anti-EpCAM-eFluor-450 Invitrogen 48-5791-82; RRID: AB 10717090 Rabbit anti-mouse CLCA1 Abcam Ab180851; RRID: AB 2722611 Recombinant Anti-STAT3 (Phospho Y705) Abcam ab76315; RRID: AB 1658549 Adenovirus hexon protein antibody (3G0) Santa Cruz Sc-80671; RRID: AB 1118724 Mouse PE/Cy7 anti-cKit Biolegend Cat#135111; RRID: AB 2131136 PerCP-Cy5.5 anti-mouse CD44 Invitrogen 45-0441-80; RRID: AB 925747 Live/Dead fixable Aqua dead cell stain kit Invitrogen L34957 IC fixation Buffer Invitrogen 00-8222-49 Horseradish Peroxidase labeled Goat anti-human/mouse IgM Southern Biotech Cat#: 1020-05; RRID: AB 2794201 Chemicals, peptides, and recombinant proteins VECTASHIELD HardSetTM Antifade mounting medium with DAPI Vector Laboratories Cat#: H-1500 Mouse HRP/DAB ABC detection IHC kit Abcam Cat#: ab64264 SsoAdvancedTM Universal Probes Supermix Bio-Rad Cat#: 1725281 SsoAdvancedTM Universal SYBR Green Supermix Bio-Rad Cat#: 1725271 Simple ChIP Enzymatic Chromatin IP kit Cell Signaling Technology Cat#: 9003S iScriptTM Reverse Transcription Supermix Bio-Rad Cat#: 1708840 High-Capacity cDNA Reverse Transcription Kit Thermo Fisher Cat#: 4368814 Roche Diagnostics LIGHTCYCLER 480 SYBR GREEN Roche Cat#: 04887352001 EDTA Invitrogen Cat#: AM9260G DSS MP Biomedicals Cat#: 160110 Alcian blue Alfa Aesar Cat#: J60122 Tamoxifen Sigma-Aldrich Cat#: T5648 DMSO ThermoFisher Cat#: BP231 DMEM/F12 Gibco Cat#: 12634-010 PBS Corning Cat#: 21040CV Fetal bovine serum Gibco Cat#: SH30071.03HI Nuclear Fast Red Electron Microscopy Sciences Cat#: 26078-05 Hematoxylin VWR Cat#: 95057-844 Eosin VWR Cat#: 95057-848 Matrigel Matrix Corning Cat#: 356231 (Continued on next page) Cell Reports 43, 114206, May 28, 2024 15 .. REAGENT or RESOURCE SOURCE IDENTIFIER 100x penicillin-streptomycin-glutamine Gibco Cat#: 10378016 Penicillin-Streptomycin solution, 100X Corning Cat#: 30-002-CI L-Glutamine Corning Cat#: 25-005-CI N2 Gibco Cat#: 17502048 B27 Gibco Cat#: 17504044 Mouse EGF Peprotech Cat#: 315-09 N-acetylcysteine Sigma-Aldrich Cat#: A9165 Gastrin-Leu15 Sigma-Aldrich Cat#: G9145 A83-01 Tocris Bioscience Cat#: 2939 Y-27632 Sigma-Aldrich Cat#: Y05030 Cell Recovery Medium Corning Cat#: 354253 2-mercaptoethanol Sigma-Aldrich Cat#: M6250 Triton X-100 Sigma-Aldrich Cat#: T8787 Tween 20 VWR Cat#: 0777 CHIR99021 Tocris Bioscience Cat#: 4423 Primocin InvivoGen Cat#:ant-pm-2 RLT buffer Qiagen RNeasy Micro kit Cat#:74004 Ad-B3galt5 Vector Biolabs N/A Ad-Y5 Vector Biolabs N/A RU-486 (Mifepristone) Sigma-Aldrich Cat#: M8046 TRIzol Invitrogen Cat#: 15596018 Qiagen RNeasy kit Qiagen Cat#: 74004 8M Lithium Chloride Sigma-Aldrich Cat#: L7026 Glycogen solution VWR Cat#: N632 Sodium Acetate Sigma-Aldrich Cat#: 127-09-3 IHC Tek Epitope retrieval solution IHC Tek Cat#: IW-1100 Tris base Sigma-Aldrich Cat#: 77-86-1 Bovine Serum Albumin Sigma-Aldrich Cat#: 9048-46-8 3,30-Diaminobenzidine Abcam Cat#: ab64264 Mouse rIL-22.Fc Evive Biotech Cat#: F-652 Mouse rIL-22 Biolegend Cat#: 576204 Human rIL-22 R & D systems Cat#: 782-IL DAPT Sigma-Aldrich Cat#: D5942 S3I-201 Sigma-Aldrich Cat#: 501919-59-1 L-WRN conditioned medium ATCC Cat#: CRL-3276 Advanced DMEM/F12 ThermoFisher Cat#: 12634028 NAC MP Biomedicals Cat#: 194603 FBS R&D Systems Cat#: S11150 Y-27632 MedChemExpress Cat#: HY-10583 B27 formulation ThermoFisher 17504-044 (50X) Gastrin AnaSpec Cat#: AS-64149 Primocin InvivoGen Cat#: ant-pm-2 A 83-01 Millipore-Sigma Cat#: SML078 SB 202190 LC Laboratories Cat#: S-1700 PGE2 Cayman Chemical Cat#: 14010 Nicotinamide Millipore-Sigma Cat#: N0636 Collagenase Worthington Cat#: LS004189 HEPES Corning Cat#: 25-060-CI GlutaMAX ThermoFisher Cat#: 25050061 (Continued on next page) 16 Cell Reports 43, 114206, May 28, 2024
Electron Microscopy:Article Title: IL-22 promotes mucin-type O-glycosylation and MATH1 + cell-mediated amelioration of intestinal inflammation.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit anti-Human Lysozyme FITC Dako Cat#: F037201; RRID: AB_578661 Goat anti-rabbit IgG AF488 Jackson ImmunoResearch Labs Cat#:111-545-144; RRID: AB 2338052 Mouse anti-GFP Cell Signaling Technology Cat#: 2955; RRID: AB 1196614 Goat anti-mouse IgG AF488 Jackson ImmunoResearch Labs Cat#:115-546-003; RRID: AB 2338859 UEA-I Dylight 649 Vector Laboratories Cat#: DL-1068 Mouse/Human anti-Tn Dr. Richard D Cummings, Harvard Medical School N/A Mouse anti-GFP antibody (biotin) GeneTex Cat#: GTX26658; RRID: AB 371422 Mouse anti-IL22Ra1-PE R&D FAB42941P; RRID: AB 1964624 Mouse anti-CD45-APC-eFluor 780 Invitrogen 47-0451-82; RRID: AB 1548781 Mouse anti-EpCAM-eFluor-450 Invitrogen 48-5791-82; RRID: AB 10717090 Rabbit anti-mouse CLCA1 Abcam Ab180851; RRID: AB 2722611 Recombinant Anti-STAT3 (Phospho Y705) Abcam ab76315; RRID: AB 1658549 Adenovirus hexon protein antibody (3G0) Santa Cruz Sc-80671; RRID: AB 1118724 Mouse PE/Cy7 anti-cKit Biolegend Cat#135111; RRID: AB 2131136 PerCP-Cy5.5 anti-mouse CD44 Invitrogen 45-0441-80; RRID: AB 925747 Live/Dead fixable Aqua dead cell stain kit Invitrogen L34957 IC fixation Buffer Invitrogen 00-8222-49 Horseradish Peroxidase labeled Goat anti-human/mouse IgM Southern Biotech Cat#: 1020-05; RRID: AB 2794201 Chemicals, peptides, and recombinant proteins VECTASHIELD HardSetTM Antifade mounting medium with DAPI Vector Laboratories Cat#: H-1500 Mouse HRP/DAB ABC detection IHC kit Abcam Cat#: ab64264 SsoAdvancedTM Universal Probes Supermix Bio-Rad Cat#: 1725281 SsoAdvancedTM Universal SYBR Green Supermix Bio-Rad Cat#: 1725271 Simple ChIP Enzymatic Chromatin IP kit Cell Signaling Technology Cat#: 9003S iScriptTM Reverse Transcription Supermix Bio-Rad Cat#: 1708840 High-Capacity cDNA Reverse Transcription Kit Thermo Fisher Cat#: 4368814 Roche Diagnostics LIGHTCYCLER 480 SYBR GREEN Roche Cat#: 04887352001 EDTA Invitrogen Cat#: AM9260G DSS MP Biomedicals Cat#: 160110 Alcian blue Alfa Aesar Cat#: J60122 Tamoxifen Sigma-Aldrich Cat#: T5648 DMSO ThermoFisher Cat#: BP231 DMEM/F12 Gibco Cat#: 12634-010 PBS Corning Cat#: 21040CV Fetal bovine serum Gibco Cat#: SH30071.03HI Nuclear Fast Red Electron Microscopy Sciences Cat#: 26078-05 Hematoxylin VWR Cat#: 95057-844 Eosin VWR Cat#: 95057-848 Matrigel Matrix Corning Cat#: 356231 (Continued on next page) Cell Reports 43, 114206, May 28, 2024 15 .. REAGENT or RESOURCE SOURCE IDENTIFIER 100x penicillin-streptomycin-glutamine Gibco Cat#: 10378016 Penicillin-Streptomycin solution, 100X Corning Cat#: 30-002-CI L-Glutamine Corning Cat#: 25-005-CI N2 Gibco Cat#: 17502048 B27 Gibco Cat#: 17504044 Mouse EGF Peprotech Cat#: 315-09 N-acetylcysteine Sigma-Aldrich Cat#: A9165 Gastrin-Leu15 Sigma-Aldrich Cat#: G9145 A83-01 Tocris Bioscience Cat#: 2939 Y-27632 Sigma-Aldrich Cat#: Y05030 Cell Recovery Medium Corning Cat#: 354253 2-mercaptoethanol Sigma-Aldrich Cat#: M6250 Triton X-100 Sigma-Aldrich Cat#: T8787 Tween 20 VWR Cat#: 0777 CHIR99021 Tocris Bioscience Cat#: 4423 Primocin InvivoGen Cat#:ant-pm-2 RLT buffer Qiagen RNeasy Micro kit Cat#:74004 Ad-B3galt5 Vector Biolabs N/A Ad-Y5 Vector Biolabs N/A RU-486 (Mifepristone) Sigma-Aldrich Cat#: M8046 TRIzol Invitrogen Cat#: 15596018 Qiagen RNeasy kit Qiagen Cat#: 74004 8M Lithium Chloride Sigma-Aldrich Cat#: L7026 Glycogen solution VWR Cat#: N632 Sodium Acetate Sigma-Aldrich Cat#: 127-09-3 IHC Tek Epitope retrieval solution IHC Tek Cat#: IW-1100 Tris base Sigma-Aldrich Cat#: 77-86-1 Bovine Serum Albumin Sigma-Aldrich Cat#: 9048-46-8 3,30-Diaminobenzidine Abcam Cat#: ab64264 Mouse rIL-22.Fc Evive Biotech Cat#: F-652 Mouse rIL-22 Biolegend Cat#: 576204 Human rIL-22 R & D systems Cat#: 782-IL DAPT Sigma-Aldrich Cat#: D5942 S3I-201 Sigma-Aldrich Cat#: 501919-59-1 L-WRN conditioned medium ATCC Cat#: CRL-3276 Advanced DMEM/F12 ThermoFisher Cat#: 12634028 NAC MP Biomedicals Cat#: 194603 FBS R&D Systems Cat#: S11150 Y-27632 MedChemExpress Cat#: HY-10583 B27 formulation ThermoFisher 17504-044 (50X) Gastrin AnaSpec Cat#: AS-64149 Primocin InvivoGen Cat#: ant-pm-2 A 83-01 Millipore-Sigma Cat#: SML078 SB 202190 LC Laboratories Cat#: S-1700 PGE2 Cayman Chemical Cat#: 14010 Nicotinamide Millipore-Sigma Cat#: N0636 Collagenase Worthington Cat#: LS004189 HEPES Corning Cat#: 25-060-CI GlutaMAX ThermoFisher Cat#: 25050061 (Continued on next page) 16 Cell Reports 43, 114206, May 28, 2024
other:
cDNA Synthesis:Article Title: Integrated multiomics reveals starvation-driven keratin degradation and persistence in Fervidobacterium islandicum AW-1
Article Snippet: .. 492 493 STAR METHODS 494 KEY RESOURCES TABLE 495 REAGENT or RESOURCE SOURCE IDENTIFIER Chemicals, peptides, and recombinant proteins Jo urn al Pr -pr oo f 25 SYTO9 Invitrogen, MA, USA Cat# S34854 Propidium iodide Invitrogen, MA, USA Cat# P1304MP CPM (7- diethylamino-3-(4’maleimidylphenyl)4-methylcoumarin) Invitrogen, MA, USA Cat# D346 iScript cDNA Synthesis Kit Bio-Rad, CA, USA Cat# 1708890 2× SsoAdvancedTM Universal SYBR Green Supermix Bio-Rad, CA, USA Cat# 1725271 Thiamphenicol Sigma- Aldrich, MO, USA Cat# T0261 Critical commercial assays RNeasy Mini Kit QIAGEN, Hilden, Germany Cat# 74104 TruSeq RNA Sample Prep Kit v2 Illumina, CA, USA Cat# RS-122 Jo urn al Pr e-p roo f 26 TruSeq DNA Nano Prep Kit Illumina, CA, USA Cat# 20015964 c-di-GMP ELISA kit EIAab Science, Wuhan, China Cat# E0152Ge Deposited data RNA-seq data This study SRR33382689–SRR33382697 and SRX219354-SRX219357 Proteomics data This study PXD027063 Metabolomics data This study MSV000099151 Experimental models: Organisms/strains F. islandicum AW1 Yonsei University Korean Culture Collections of Microorganisms (KCCM) 80008 Oligonucleotides See Table S4 for oligonucleotides used in this study. ..
Sample Prep:Article Title: Integrated multiomics reveals starvation-driven keratin degradation and persistence in Fervidobacterium islandicum AW-1
Article Snippet: .. 492 493 STAR METHODS 494 KEY RESOURCES TABLE 495 REAGENT or RESOURCE SOURCE IDENTIFIER Chemicals, peptides, and recombinant proteins Jo urn al Pr -pr oo f 25 SYTO9 Invitrogen, MA, USA Cat# S34854 Propidium iodide Invitrogen, MA, USA Cat# P1304MP CPM (7- diethylamino-3-(4’maleimidylphenyl)4-methylcoumarin) Invitrogen, MA, USA Cat# D346 iScript cDNA Synthesis Kit Bio-Rad, CA, USA Cat# 1708890 2× SsoAdvancedTM Universal SYBR Green Supermix Bio-Rad, CA, USA Cat# 1725271 Thiamphenicol Sigma- Aldrich, MO, USA Cat# T0261 Critical commercial assays RNeasy Mini Kit QIAGEN, Hilden, Germany Cat# 74104 TruSeq RNA Sample Prep Kit v2 Illumina, CA, USA Cat# RS-122 Jo urn al Pr e-p roo f 26 TruSeq DNA Nano Prep Kit Illumina, CA, USA Cat# 20015964 c-di-GMP ELISA kit EIAab Science, Wuhan, China Cat# E0152Ge Deposited data RNA-seq data This study SRR33382689–SRR33382697 and SRX219354-SRX219357 Proteomics data This study PXD027063 Metabolomics data This study MSV000099151 Experimental models: Organisms/strains F. islandicum AW1 Yonsei University Korean Culture Collections of Microorganisms (KCCM) 80008 Oligonucleotides See Table S4 for oligonucleotides used in this study. ..
Enzyme-linked Immunosorbent Assay:Article Title: Integrated multiomics reveals starvation-driven keratin degradation and persistence in Fervidobacterium islandicum AW-1
Article Snippet: .. 492 493 STAR METHODS 494 KEY RESOURCES TABLE 495 REAGENT or RESOURCE SOURCE IDENTIFIER Chemicals, peptides, and recombinant proteins Jo urn al Pr -pr oo f 25 SYTO9 Invitrogen, MA, USA Cat# S34854 Propidium iodide Invitrogen, MA, USA Cat# P1304MP CPM (7- diethylamino-3-(4’maleimidylphenyl)4-methylcoumarin) Invitrogen, MA, USA Cat# D346 iScript cDNA Synthesis Kit Bio-Rad, CA, USA Cat# 1708890 2× SsoAdvancedTM Universal SYBR Green Supermix Bio-Rad, CA, USA Cat# 1725271 Thiamphenicol Sigma- Aldrich, MO, USA Cat# T0261 Critical commercial assays RNeasy Mini Kit QIAGEN, Hilden, Germany Cat# 74104 TruSeq RNA Sample Prep Kit v2 Illumina, CA, USA Cat# RS-122 Jo urn al Pr e-p roo f 26 TruSeq DNA Nano Prep Kit Illumina, CA, USA Cat# 20015964 c-di-GMP ELISA kit EIAab Science, Wuhan, China Cat# E0152Ge Deposited data RNA-seq data This study SRR33382689–SRR33382697 and SRX219354-SRX219357 Proteomics data This study PXD027063 Metabolomics data This study MSV000099151 Experimental models: Organisms/strains F. islandicum AW1 Yonsei University Korean Culture Collections of Microorganisms (KCCM) 80008 Oligonucleotides See Table S4 for oligonucleotides used in this study. ..
RNA Sequencing:Article Title: Integrated multiomics reveals starvation-driven keratin degradation and persistence in Fervidobacterium islandicum AW-1
Article Snippet: .. 492 493 STAR METHODS 494 KEY RESOURCES TABLE 495 REAGENT or RESOURCE SOURCE IDENTIFIER Chemicals, peptides, and recombinant proteins Jo urn al Pr -pr oo f 25 SYTO9 Invitrogen, MA, USA Cat# S34854 Propidium iodide Invitrogen, MA, USA Cat# P1304MP CPM (7- diethylamino-3-(4’maleimidylphenyl)4-methylcoumarin) Invitrogen, MA, USA Cat# D346 iScript cDNA Synthesis Kit Bio-Rad, CA, USA Cat# 1708890 2× SsoAdvancedTM Universal SYBR Green Supermix Bio-Rad, CA, USA Cat# 1725271 Thiamphenicol Sigma- Aldrich, MO, USA Cat# T0261 Critical commercial assays RNeasy Mini Kit QIAGEN, Hilden, Germany Cat# 74104 TruSeq RNA Sample Prep Kit v2 Illumina, CA, USA Cat# RS-122 Jo urn al Pr e-p roo f 26 TruSeq DNA Nano Prep Kit Illumina, CA, USA Cat# 20015964 c-di-GMP ELISA kit EIAab Science, Wuhan, China Cat# E0152Ge Deposited data RNA-seq data This study SRR33382689–SRR33382697 and SRX219354-SRX219357 Proteomics data This study PXD027063 Metabolomics data This study MSV000099151 Experimental models: Organisms/strains F. islandicum AW1 Yonsei University Korean Culture Collections of Microorganisms (KCCM) 80008 Oligonucleotides See Table S4 for oligonucleotides used in this study. ..
Affinity Chromatography:Article Title: CdGAP is a talin-binding protein and a target of TGF-β signaling that promotes HER2-positive breast cancer growth and metastasis.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER jetPRIME Polyplus Cat# 114-07 Protein G SepharoseTM 4 Fast Flow Affinity Chromatography media Thermo Fisher Scientific Cat# 17-0618-01 ClarityTM western ECL substrate Bor-Rad Cat# 1705061 SsoAdvancedTM Universal SYBR green Supermix Bio-Rad Cat#1725271 Fibronectin Sigma-Aldrich Cat# F1141 CorningTM MatrigelTM membrane matrix Thermo Fisher Scientific Cat# CB-40234A CorningTM MatrigelTM GFR membrane matrix Thermo Fisher Scientific Cat# CB-40230 FORMALDEHYDE, (formalin) reagent Grade Bioshop Cat# FOR201 Type 1 collagen BD Bioscience Cat# 354246 Critical commercial assays Mycoplasma PCR Detection kit ZmTech Scientific Cat# M209001 Dual-Luciferase reporter assay system Promega Cat# E1910 Qiagen RNeasy kit Qiagen Cat# 74104 RNase-free DNase set Qiagen Cat# 79254 RhoA G-LISA activation assay (luminescence) Cytoskeleton Cat# BK121 Rac1 G-LISA activation assay (luminescence) Cytoskeleton Cat# BK126 MTT Cell proliferation assay kit Abcam Cat# ab211091 Pierce BCA protein assay kit Thermo Fisher Scientific Cat# 23225 Deposited data RNA-sequencing raw data This paper GSE167457 Proteomics raw data This paper PXD043376 Experimental models: Cell lines Human breast cancer cell line: HCC1954 American type culture collection (ATCC) RRID: CVCL_1259 Human breast cancer cell line: SK-BR-3 American type culture collection (ATCC) RRID: CVCL_0033 Human breast cancer cell line: MDA-MB-361 American type culture collection (ATCC) RRID: CVCL_0620 Mouse: NIC+ explant cells Goyette et al.40 N/A Experimental models: Organisms/strains Mouse: Mammary Tumor Virus (MMTV)-NeuNDL2-5-Internal Ribosome Entry Site- Cre (NIC) FVB/NJ Ursini-Siegel et al.37 N/A Athymic Nude mouse Charles River Strain Code:490 Mouse: MMTV-Cre Wagner et al.36 N/A Mouse: CdGAPfl/fl Caron et al.35 N/A Oligonucleotides Smad4 specific silencer select validated siRNA Ambion Cat# 4390824 Mouse CdGAP primers for qPCR Qiagen Cat# QT00155162 Human CdGAP primers for qPCR Qiagen Cat# QT00076671 mouse E-cadherin primers for qPCR Qiagen Cat# QT00121163 All the other oligonucleotides, gRNAs, and shRNAs can be found in the Table S3 This paper Table S3 Recombinant DNA pSpCas9(BB)-2A-Puro (PX459) Ding et al.69 Addgene Cat#48139 mCherry-talin-18 a gift from Michael Davidson Addgene Cat#55137 EGFP-talin1 head Simonson et al.70 Addgene Cat# 32856 EGFP-talin1 rod Simonson et al.70 Addgene Cat# 32855 pGL3-basic CdGAP ( 896 to +601) This paper N/A MSCV luciferase PGK-hygro a gift from Scott lowe Addgene Cat# 18782 (Continued on next page) Cell Reports 42, 112936, August 29, 2023 21 .. REAGENT or RESOURCE SOURCE IDENTIFIER pCL-Eco Naviaux et al.71 Addgene Cat# 12371 pCMV5 Smad2-HA Hata et al.72 Addgene Cat# 14930 pRK5F Smad3 Zhang et al.73 Addgene Cat# 12625 pGL3-basic (CAGA)12-luc Kang 74 N/A pGL3-basic vector Promega Cat# E1751 pRK5-myc vector He et al.32 N/A pRK5-myc-CdGAP He et al.32 N/A pRK5-myc-CdGAP PRD He et al.32 N/A pRK5-myc-CdGAP 1-515 He et al.32 N/A GFP-CdGAP He et al.32 N/A Software and algorithms Imagescope software version 2.0.0 Leica Biosystems Inc. RRID: SCR_014311 ImageJ, version 1.8.0/1.53a N/A RRID: SCR_003070 Image Lab software 6.0.1 Bio-Rad RRID: SCR_014210 GraphPad Prism 8 GraphPad RRID: SCR_002798 GenPipes ‘‘RNAseq’’ pipeline Bourgey et al.75 https://github.com/c3g/GenPipes STAR aligner Dobin et al.76 https://github.com/alexdobin/STAR GATK DePristo et al.77 https://gatk.broadinstitute.org/hc/en-us Picard N/A https://broadinstitute.github.io/picard/ HT-seq Anders et al.78 https://github.com/htseq/htseq DESeq2 (v1.30.1) Lovet et al.79 N/A Msigdbr (v7.2.1) N/A https://igordot.github.io/msigdbr/ ClusterProfiler (v3.18.1) Yu et al.80 N/A MKmisc (v1.6) N/A https://github.com/stamats/MKmisc Singscore (v1.12.0) Foroutan et al.81 N/A
Western Blot:Article Title: CdGAP is a talin-binding protein and a target of TGF-β signaling that promotes HER2-positive breast cancer growth and metastasis.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER jetPRIME Polyplus Cat# 114-07 Protein G SepharoseTM 4 Fast Flow Affinity Chromatography media Thermo Fisher Scientific Cat# 17-0618-01 ClarityTM western ECL substrate Bor-Rad Cat# 1705061 SsoAdvancedTM Universal SYBR green Supermix Bio-Rad Cat#1725271 Fibronectin Sigma-Aldrich Cat# F1141 CorningTM MatrigelTM membrane matrix Thermo Fisher Scientific Cat# CB-40234A CorningTM MatrigelTM GFR membrane matrix Thermo Fisher Scientific Cat# CB-40230 FORMALDEHYDE, (formalin) reagent Grade Bioshop Cat# FOR201 Type 1 collagen BD Bioscience Cat# 354246 Critical commercial assays Mycoplasma PCR Detection kit ZmTech Scientific Cat# M209001 Dual-Luciferase reporter assay system Promega Cat# E1910 Qiagen RNeasy kit Qiagen Cat# 74104 RNase-free DNase set Qiagen Cat# 79254 RhoA G-LISA activation assay (luminescence) Cytoskeleton Cat# BK121 Rac1 G-LISA activation assay (luminescence) Cytoskeleton Cat# BK126 MTT Cell proliferation assay kit Abcam Cat# ab211091 Pierce BCA protein assay kit Thermo Fisher Scientific Cat# 23225 Deposited data RNA-sequencing raw data This paper GSE167457 Proteomics raw data This paper PXD043376 Experimental models: Cell lines Human breast cancer cell line: HCC1954 American type culture collection (ATCC) RRID: CVCL_1259 Human breast cancer cell line: SK-BR-3 American type culture collection (ATCC) RRID: CVCL_0033 Human breast cancer cell line: MDA-MB-361 American type culture collection (ATCC) RRID: CVCL_0620 Mouse: NIC+ explant cells Goyette et al.40 N/A Experimental models: Organisms/strains Mouse: Mammary Tumor Virus (MMTV)-NeuNDL2-5-Internal Ribosome Entry Site- Cre (NIC) FVB/NJ Ursini-Siegel et al.37 N/A Athymic Nude mouse Charles River Strain Code:490 Mouse: MMTV-Cre Wagner et al.36 N/A Mouse: CdGAPfl/fl Caron et al.35 N/A Oligonucleotides Smad4 specific silencer select validated siRNA Ambion Cat# 4390824 Mouse CdGAP primers for qPCR Qiagen Cat# QT00155162 Human CdGAP primers for qPCR Qiagen Cat# QT00076671 mouse E-cadherin primers for qPCR Qiagen Cat# QT00121163 All the other oligonucleotides, gRNAs, and shRNAs can be found in the Table S3 This paper Table S3 Recombinant DNA pSpCas9(BB)-2A-Puro (PX459) Ding et al.69 Addgene Cat#48139 mCherry-talin-18 a gift from Michael Davidson Addgene Cat#55137 EGFP-talin1 head Simonson et al.70 Addgene Cat# 32856 EGFP-talin1 rod Simonson et al.70 Addgene Cat# 32855 pGL3-basic CdGAP ( 896 to +601) This paper N/A MSCV luciferase PGK-hygro a gift from Scott lowe Addgene Cat# 18782 (Continued on next page) Cell Reports 42, 112936, August 29, 2023 21 .. REAGENT or RESOURCE SOURCE IDENTIFIER pCL-Eco Naviaux et al.71 Addgene Cat# 12371 pCMV5 Smad2-HA Hata et al.72 Addgene Cat# 14930 pRK5F Smad3 Zhang et al.73 Addgene Cat# 12625 pGL3-basic (CAGA)12-luc Kang 74 N/A pGL3-basic vector Promega Cat# E1751 pRK5-myc vector He et al.32 N/A pRK5-myc-CdGAP He et al.32 N/A pRK5-myc-CdGAP PRD He et al.32 N/A pRK5-myc-CdGAP 1-515 He et al.32 N/A GFP-CdGAP He et al.32 N/A Software and algorithms Imagescope software version 2.0.0 Leica Biosystems Inc. RRID: SCR_014311 ImageJ, version 1.8.0/1.53a N/A RRID: SCR_003070 Image Lab software 6.0.1 Bio-Rad RRID: SCR_014210 GraphPad Prism 8 GraphPad RRID: SCR_002798 GenPipes ‘‘RNAseq’’ pipeline Bourgey et al.75 https://github.com/c3g/GenPipes STAR aligner Dobin et al.76 https://github.com/alexdobin/STAR GATK DePristo et al.77 https://gatk.broadinstitute.org/hc/en-us Picard N/A https://broadinstitute.github.io/picard/ HT-seq Anders et al.78 https://github.com/htseq/htseq DESeq2 (v1.30.1) Lovet et al.79 N/A Msigdbr (v7.2.1) N/A https://igordot.github.io/msigdbr/ ClusterProfiler (v3.18.1) Yu et al.80 N/A MKmisc (v1.6) N/A https://github.com/stamats/MKmisc Singscore (v1.12.0) Foroutan et al.81 N/A
Membrane:Article Title: CdGAP is a talin-binding protein and a target of TGF-β signaling that promotes HER2-positive breast cancer growth and metastasis.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER jetPRIME Polyplus Cat# 114-07 Protein G SepharoseTM 4 Fast Flow Affinity Chromatography media Thermo Fisher Scientific Cat# 17-0618-01 ClarityTM western ECL substrate Bor-Rad Cat# 1705061 SsoAdvancedTM Universal SYBR green Supermix Bio-Rad Cat#1725271 Fibronectin Sigma-Aldrich Cat# F1141 CorningTM MatrigelTM membrane matrix Thermo Fisher Scientific Cat# CB-40234A CorningTM MatrigelTM GFR membrane matrix Thermo Fisher Scientific Cat# CB-40230 FORMALDEHYDE, (formalin) reagent Grade Bioshop Cat# FOR201 Type 1 collagen BD Bioscience Cat# 354246 Critical commercial assays Mycoplasma PCR Detection kit ZmTech Scientific Cat# M209001 Dual-Luciferase reporter assay system Promega Cat# E1910 Qiagen RNeasy kit Qiagen Cat# 74104 RNase-free DNase set Qiagen Cat# 79254 RhoA G-LISA activation assay (luminescence) Cytoskeleton Cat# BK121 Rac1 G-LISA activation assay (luminescence) Cytoskeleton Cat# BK126 MTT Cell proliferation assay kit Abcam Cat# ab211091 Pierce BCA protein assay kit Thermo Fisher Scientific Cat# 23225 Deposited data RNA-sequencing raw data This paper GSE167457 Proteomics raw data This paper PXD043376 Experimental models: Cell lines Human breast cancer cell line: HCC1954 American type culture collection (ATCC) RRID: CVCL_1259 Human breast cancer cell line: SK-BR-3 American type culture collection (ATCC) RRID: CVCL_0033 Human breast cancer cell line: MDA-MB-361 American type culture collection (ATCC) RRID: CVCL_0620 Mouse: NIC+ explant cells Goyette et al.40 N/A Experimental models: Organisms/strains Mouse: Mammary Tumor Virus (MMTV)-NeuNDL2-5-Internal Ribosome Entry Site- Cre (NIC) FVB/NJ Ursini-Siegel et al.37 N/A Athymic Nude mouse Charles River Strain Code:490 Mouse: MMTV-Cre Wagner et al.36 N/A Mouse: CdGAPfl/fl Caron et al.35 N/A Oligonucleotides Smad4 specific silencer select validated siRNA Ambion Cat# 4390824 Mouse CdGAP primers for qPCR Qiagen Cat# QT00155162 Human CdGAP primers for qPCR Qiagen Cat# QT00076671 mouse E-cadherin primers for qPCR Qiagen Cat# QT00121163 All the other oligonucleotides, gRNAs, and shRNAs can be found in the Table S3 This paper Table S3 Recombinant DNA pSpCas9(BB)-2A-Puro (PX459) Ding et al.69 Addgene Cat#48139 mCherry-talin-18 a gift from Michael Davidson Addgene Cat#55137 EGFP-talin1 head Simonson et al.70 Addgene Cat# 32856 EGFP-talin1 rod Simonson et al.70 Addgene Cat# 32855 pGL3-basic CdGAP ( 896 to +601) This paper N/A MSCV luciferase PGK-hygro a gift from Scott lowe Addgene Cat# 18782 (Continued on next page) Cell Reports 42, 112936, August 29, 2023 21 .. REAGENT or RESOURCE SOURCE IDENTIFIER pCL-Eco Naviaux et al.71 Addgene Cat# 12371 pCMV5 Smad2-HA Hata et al.72 Addgene Cat# 14930 pRK5F Smad3 Zhang et al.73 Addgene Cat# 12625 pGL3-basic (CAGA)12-luc Kang 74 N/A pGL3-basic vector Promega Cat# E1751 pRK5-myc vector He et al.32 N/A pRK5-myc-CdGAP He et al.32 N/A pRK5-myc-CdGAP PRD He et al.32 N/A pRK5-myc-CdGAP 1-515 He et al.32 N/A GFP-CdGAP He et al.32 N/A Software and algorithms Imagescope software version 2.0.0 Leica Biosystems Inc. RRID: SCR_014311 ImageJ, version 1.8.0/1.53a N/A RRID: SCR_003070 Image Lab software 6.0.1 Bio-Rad RRID: SCR_014210 GraphPad Prism 8 GraphPad RRID: SCR_002798 GenPipes ‘‘RNAseq’’ pipeline Bourgey et al.75 https://github.com/c3g/GenPipes STAR aligner Dobin et al.76 https://github.com/alexdobin/STAR GATK DePristo et al.77 https://gatk.broadinstitute.org/hc/en-us Picard N/A https://broadinstitute.github.io/picard/ HT-seq Anders et al.78 https://github.com/htseq/htseq DESeq2 (v1.30.1) Lovet et al.79 N/A Msigdbr (v7.2.1) N/A https://igordot.github.io/msigdbr/ ClusterProfiler (v3.18.1) Yu et al.80 N/A MKmisc (v1.6) N/A https://github.com/stamats/MKmisc Singscore (v1.12.0) Foroutan et al.81 N/A
Polymerase Chain Reaction:Article Title: CdGAP is a talin-binding protein and a target of TGF-β signaling that promotes HER2-positive breast cancer growth and metastasis.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER jetPRIME Polyplus Cat# 114-07 Protein G SepharoseTM 4 Fast Flow Affinity Chromatography media Thermo Fisher Scientific Cat# 17-0618-01 ClarityTM western ECL substrate Bor-Rad Cat# 1705061 SsoAdvancedTM Universal SYBR green Supermix Bio-Rad Cat#1725271 Fibronectin Sigma-Aldrich Cat# F1141 CorningTM MatrigelTM membrane matrix Thermo Fisher Scientific Cat# CB-40234A CorningTM MatrigelTM GFR membrane matrix Thermo Fisher Scientific Cat# CB-40230 FORMALDEHYDE, (formalin) reagent Grade Bioshop Cat# FOR201 Type 1 collagen BD Bioscience Cat# 354246 Critical commercial assays Mycoplasma PCR Detection kit ZmTech Scientific Cat# M209001 Dual-Luciferase reporter assay system Promega Cat# E1910 Qiagen RNeasy kit Qiagen Cat# 74104 RNase-free DNase set Qiagen Cat# 79254 RhoA G-LISA activation assay (luminescence) Cytoskeleton Cat# BK121 Rac1 G-LISA activation assay (luminescence) Cytoskeleton Cat# BK126 MTT Cell proliferation assay kit Abcam Cat# ab211091 Pierce BCA protein assay kit Thermo Fisher Scientific Cat# 23225 Deposited data RNA-sequencing raw data This paper GSE167457 Proteomics raw data This paper PXD043376 Experimental models: Cell lines Human breast cancer cell line: HCC1954 American type culture collection (ATCC) RRID: CVCL_1259 Human breast cancer cell line: SK-BR-3 American type culture collection (ATCC) RRID: CVCL_0033 Human breast cancer cell line: MDA-MB-361 American type culture collection (ATCC) RRID: CVCL_0620 Mouse: NIC+ explant cells Goyette et al.40 N/A Experimental models: Organisms/strains Mouse: Mammary Tumor Virus (MMTV)-NeuNDL2-5-Internal Ribosome Entry Site- Cre (NIC) FVB/NJ Ursini-Siegel et al.37 N/A Athymic Nude mouse Charles River Strain Code:490 Mouse: MMTV-Cre Wagner et al.36 N/A Mouse: CdGAPfl/fl Caron et al.35 N/A Oligonucleotides Smad4 specific silencer select validated siRNA Ambion Cat# 4390824 Mouse CdGAP primers for qPCR Qiagen Cat# QT00155162 Human CdGAP primers for qPCR Qiagen Cat# QT00076671 mouse E-cadherin primers for qPCR Qiagen Cat# QT00121163 All the other oligonucleotides, gRNAs, and shRNAs can be found in the Table S3 This paper Table S3 Recombinant DNA pSpCas9(BB)-2A-Puro (PX459) Ding et al.69 Addgene Cat#48139 mCherry-talin-18 a gift from Michael Davidson Addgene Cat#55137 EGFP-talin1 head Simonson et al.70 Addgene Cat# 32856 EGFP-talin1 rod Simonson et al.70 Addgene Cat# 32855 pGL3-basic CdGAP ( 896 to +601) This paper N/A MSCV luciferase PGK-hygro a gift from Scott lowe Addgene Cat# 18782 (Continued on next page) Cell Reports 42, 112936, August 29, 2023 21 .. REAGENT or RESOURCE SOURCE IDENTIFIER pCL-Eco Naviaux et al.71 Addgene Cat# 12371 pCMV5 Smad2-HA Hata et al.72 Addgene Cat# 14930 pRK5F Smad3 Zhang et al.73 Addgene Cat# 12625 pGL3-basic (CAGA)12-luc Kang 74 N/A pGL3-basic vector Promega Cat# E1751 pRK5-myc vector He et al.32 N/A pRK5-myc-CdGAP He et al.32 N/A pRK5-myc-CdGAP PRD He et al.32 N/A pRK5-myc-CdGAP 1-515 He et al.32 N/A GFP-CdGAP He et al.32 N/A Software and algorithms Imagescope software version 2.0.0 Leica Biosystems Inc. RRID: SCR_014311 ImageJ, version 1.8.0/1.53a N/A RRID: SCR_003070 Image Lab software 6.0.1 Bio-Rad RRID: SCR_014210 GraphPad Prism 8 GraphPad RRID: SCR_002798 GenPipes ‘‘RNAseq’’ pipeline Bourgey et al.75 https://github.com/c3g/GenPipes STAR aligner Dobin et al.76 https://github.com/alexdobin/STAR GATK DePristo et al.77 https://gatk.broadinstitute.org/hc/en-us Picard N/A https://broadinstitute.github.io/picard/ HT-seq Anders et al.78 https://github.com/htseq/htseq DESeq2 (v1.30.1) Lovet et al.79 N/A Msigdbr (v7.2.1) N/A https://igordot.github.io/msigdbr/ ClusterProfiler (v3.18.1) Yu et al.80 N/A MKmisc (v1.6) N/A https://github.com/stamats/MKmisc Singscore (v1.12.0) Foroutan et al.81 N/A
Reporter Assay:Article Title: CdGAP is a talin-binding protein and a target of TGF-β signaling that promotes HER2-positive breast cancer growth and metastasis.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER jetPRIME Polyplus Cat# 114-07 Protein G SepharoseTM 4 Fast Flow Affinity Chromatography media Thermo Fisher Scientific Cat# 17-0618-01 ClarityTM western ECL substrate Bor-Rad Cat# 1705061 SsoAdvancedTM Universal SYBR green Supermix Bio-Rad Cat#1725271 Fibronectin Sigma-Aldrich Cat# F1141 CorningTM MatrigelTM membrane matrix Thermo Fisher Scientific Cat# CB-40234A CorningTM MatrigelTM GFR membrane matrix Thermo Fisher Scientific Cat# CB-40230 FORMALDEHYDE, (formalin) reagent Grade Bioshop Cat# FOR201 Type 1 collagen BD Bioscience Cat# 354246 Critical commercial assays Mycoplasma PCR Detection kit ZmTech Scientific Cat# M209001 Dual-Luciferase reporter assay system Promega Cat# E1910 Qiagen RNeasy kit Qiagen Cat# 74104 RNase-free DNase set Qiagen Cat# 79254 RhoA G-LISA activation assay (luminescence) Cytoskeleton Cat# BK121 Rac1 G-LISA activation assay (luminescence) Cytoskeleton Cat# BK126 MTT Cell proliferation assay kit Abcam Cat# ab211091 Pierce BCA protein assay kit Thermo Fisher Scientific Cat# 23225 Deposited data RNA-sequencing raw data This paper GSE167457 Proteomics raw data This paper PXD043376 Experimental models: Cell lines Human breast cancer cell line: HCC1954 American type culture collection (ATCC) RRID: CVCL_1259 Human breast cancer cell line: SK-BR-3 American type culture collection (ATCC) RRID: CVCL_0033 Human breast cancer cell line: MDA-MB-361 American type culture collection (ATCC) RRID: CVCL_0620 Mouse: NIC+ explant cells Goyette et al.40 N/A Experimental models: Organisms/strains Mouse: Mammary Tumor Virus (MMTV)-NeuNDL2-5-Internal Ribosome Entry Site- Cre (NIC) FVB/NJ Ursini-Siegel et al.37 N/A Athymic Nude mouse Charles River Strain Code:490 Mouse: MMTV-Cre Wagner et al.36 N/A Mouse: CdGAPfl/fl Caron et al.35 N/A Oligonucleotides Smad4 specific silencer select validated siRNA Ambion Cat# 4390824 Mouse CdGAP primers for qPCR Qiagen Cat# QT00155162 Human CdGAP primers for qPCR Qiagen Cat# QT00076671 mouse E-cadherin primers for qPCR Qiagen Cat# QT00121163 All the other oligonucleotides, gRNAs, and shRNAs can be found in the Table S3 This paper Table S3 Recombinant DNA pSpCas9(BB)-2A-Puro (PX459) Ding et al.69 Addgene Cat#48139 mCherry-talin-18 a gift from Michael Davidson Addgene Cat#55137 EGFP-talin1 head Simonson et al.70 Addgene Cat# 32856 EGFP-talin1 rod Simonson et al.70 Addgene Cat# 32855 pGL3-basic CdGAP ( 896 to +601) This paper N/A MSCV luciferase PGK-hygro a gift from Scott lowe Addgene Cat# 18782 (Continued on next page) Cell Reports 42, 112936, August 29, 2023 21 .. REAGENT or RESOURCE SOURCE IDENTIFIER pCL-Eco Naviaux et al.71 Addgene Cat# 12371 pCMV5 Smad2-HA Hata et al.72 Addgene Cat# 14930 pRK5F Smad3 Zhang et al.73 Addgene Cat# 12625 pGL3-basic (CAGA)12-luc Kang 74 N/A pGL3-basic vector Promega Cat# E1751 pRK5-myc vector He et al.32 N/A pRK5-myc-CdGAP He et al.32 N/A pRK5-myc-CdGAP PRD He et al.32 N/A pRK5-myc-CdGAP 1-515 He et al.32 N/A GFP-CdGAP He et al.32 N/A Software and algorithms Imagescope software version 2.0.0 Leica Biosystems Inc. RRID: SCR_014311 ImageJ, version 1.8.0/1.53a N/A RRID: SCR_003070 Image Lab software 6.0.1 Bio-Rad RRID: SCR_014210 GraphPad Prism 8 GraphPad RRID: SCR_002798 GenPipes ‘‘RNAseq’’ pipeline Bourgey et al.75 https://github.com/c3g/GenPipes STAR aligner Dobin et al.76 https://github.com/alexdobin/STAR GATK DePristo et al.77 https://gatk.broadinstitute.org/hc/en-us Picard N/A https://broadinstitute.github.io/picard/ HT-seq Anders et al.78 https://github.com/htseq/htseq DESeq2 (v1.30.1) Lovet et al.79 N/A Msigdbr (v7.2.1) N/A https://igordot.github.io/msigdbr/ ClusterProfiler (v3.18.1) Yu et al.80 N/A MKmisc (v1.6) N/A https://github.com/stamats/MKmisc Singscore (v1.12.0) Foroutan et al.81 N/A
Activation Assay:Article Title: CdGAP is a talin-binding protein and a target of TGF-β signaling that promotes HER2-positive breast cancer growth and metastasis.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER jetPRIME Polyplus Cat# 114-07 Protein G SepharoseTM 4 Fast Flow Affinity Chromatography media Thermo Fisher Scientific Cat# 17-0618-01 ClarityTM western ECL substrate Bor-Rad Cat# 1705061 SsoAdvancedTM Universal SYBR green Supermix Bio-Rad Cat#1725271 Fibronectin Sigma-Aldrich Cat# F1141 CorningTM MatrigelTM membrane matrix Thermo Fisher Scientific Cat# CB-40234A CorningTM MatrigelTM GFR membrane matrix Thermo Fisher Scientific Cat# CB-40230 FORMALDEHYDE, (formalin) reagent Grade Bioshop Cat# FOR201 Type 1 collagen BD Bioscience Cat# 354246 Critical commercial assays Mycoplasma PCR Detection kit ZmTech Scientific Cat# M209001 Dual-Luciferase reporter assay system Promega Cat# E1910 Qiagen RNeasy kit Qiagen Cat# 74104 RNase-free DNase set Qiagen Cat# 79254 RhoA G-LISA activation assay (luminescence) Cytoskeleton Cat# BK121 Rac1 G-LISA activation assay (luminescence) Cytoskeleton Cat# BK126 MTT Cell proliferation assay kit Abcam Cat# ab211091 Pierce BCA protein assay kit Thermo Fisher Scientific Cat# 23225 Deposited data RNA-sequencing raw data This paper GSE167457 Proteomics raw data This paper PXD043376 Experimental models: Cell lines Human breast cancer cell line: HCC1954 American type culture collection (ATCC) RRID: CVCL_1259 Human breast cancer cell line: SK-BR-3 American type culture collection (ATCC) RRID: CVCL_0033 Human breast cancer cell line: MDA-MB-361 American type culture collection (ATCC) RRID: CVCL_0620 Mouse: NIC+ explant cells Goyette et al.40 N/A Experimental models: Organisms/strains Mouse: Mammary Tumor Virus (MMTV)-NeuNDL2-5-Internal Ribosome Entry Site- Cre (NIC) FVB/NJ Ursini-Siegel et al.37 N/A Athymic Nude mouse Charles River Strain Code:490 Mouse: MMTV-Cre Wagner et al.36 N/A Mouse: CdGAPfl/fl Caron et al.35 N/A Oligonucleotides Smad4 specific silencer select validated siRNA Ambion Cat# 4390824 Mouse CdGAP primers for qPCR Qiagen Cat# QT00155162 Human CdGAP primers for qPCR Qiagen Cat# QT00076671 mouse E-cadherin primers for qPCR Qiagen Cat# QT00121163 All the other oligonucleotides, gRNAs, and shRNAs can be found in the Table S3 This paper Table S3 Recombinant DNA pSpCas9(BB)-2A-Puro (PX459) Ding et al.69 Addgene Cat#48139 mCherry-talin-18 a gift from Michael Davidson Addgene Cat#55137 EGFP-talin1 head Simonson et al.70 Addgene Cat# 32856 EGFP-talin1 rod Simonson et al.70 Addgene Cat# 32855 pGL3-basic CdGAP ( 896 to +601) This paper N/A MSCV luciferase PGK-hygro a gift from Scott lowe Addgene Cat# 18782 (Continued on next page) Cell Reports 42, 112936, August 29, 2023 21 .. REAGENT or RESOURCE SOURCE IDENTIFIER pCL-Eco Naviaux et al.71 Addgene Cat# 12371 pCMV5 Smad2-HA Hata et al.72 Addgene Cat# 14930 pRK5F Smad3 Zhang et al.73 Addgene Cat# 12625 pGL3-basic (CAGA)12-luc Kang 74 N/A pGL3-basic vector Promega Cat# E1751 pRK5-myc vector He et al.32 N/A pRK5-myc-CdGAP He et al.32 N/A pRK5-myc-CdGAP PRD He et al.32 N/A pRK5-myc-CdGAP 1-515 He et al.32 N/A GFP-CdGAP He et al.32 N/A Software and algorithms Imagescope software version 2.0.0 Leica Biosystems Inc. RRID: SCR_014311 ImageJ, version 1.8.0/1.53a N/A RRID: SCR_003070 Image Lab software 6.0.1 Bio-Rad RRID: SCR_014210 GraphPad Prism 8 GraphPad RRID: SCR_002798 GenPipes ‘‘RNAseq’’ pipeline Bourgey et al.75 https://github.com/c3g/GenPipes STAR aligner Dobin et al.76 https://github.com/alexdobin/STAR GATK DePristo et al.77 https://gatk.broadinstitute.org/hc/en-us Picard N/A https://broadinstitute.github.io/picard/ HT-seq Anders et al.78 https://github.com/htseq/htseq DESeq2 (v1.30.1) Lovet et al.79 N/A Msigdbr (v7.2.1) N/A https://igordot.github.io/msigdbr/ ClusterProfiler (v3.18.1) Yu et al.80 N/A MKmisc (v1.6) N/A https://github.com/stamats/MKmisc Singscore (v1.12.0) Foroutan et al.81 N/A
MTT Assay:Article Title: CdGAP is a talin-binding protein and a target of TGF-β signaling that promotes HER2-positive breast cancer growth and metastasis.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER jetPRIME Polyplus Cat# 114-07 Protein G SepharoseTM 4 Fast Flow Affinity Chromatography media Thermo Fisher Scientific Cat# 17-0618-01 ClarityTM western ECL substrate Bor-Rad Cat# 1705061 SsoAdvancedTM Universal SYBR green Supermix Bio-Rad Cat#1725271 Fibronectin Sigma-Aldrich Cat# F1141 CorningTM MatrigelTM membrane matrix Thermo Fisher Scientific Cat# CB-40234A CorningTM MatrigelTM GFR membrane matrix Thermo Fisher Scientific Cat# CB-40230 FORMALDEHYDE, (formalin) reagent Grade Bioshop Cat# FOR201 Type 1 collagen BD Bioscience Cat# 354246 Critical commercial assays Mycoplasma PCR Detection kit ZmTech Scientific Cat# M209001 Dual-Luciferase reporter assay system Promega Cat# E1910 Qiagen RNeasy kit Qiagen Cat# 74104 RNase-free DNase set Qiagen Cat# 79254 RhoA G-LISA activation assay (luminescence) Cytoskeleton Cat# BK121 Rac1 G-LISA activation assay (luminescence) Cytoskeleton Cat# BK126 MTT Cell proliferation assay kit Abcam Cat# ab211091 Pierce BCA protein assay kit Thermo Fisher Scientific Cat# 23225 Deposited data RNA-sequencing raw data This paper GSE167457 Proteomics raw data This paper PXD043376 Experimental models: Cell lines Human breast cancer cell line: HCC1954 American type culture collection (ATCC) RRID: CVCL_1259 Human breast cancer cell line: SK-BR-3 American type culture collection (ATCC) RRID: CVCL_0033 Human breast cancer cell line: MDA-MB-361 American type culture collection (ATCC) RRID: CVCL_0620 Mouse: NIC+ explant cells Goyette et al.40 N/A Experimental models: Organisms/strains Mouse: Mammary Tumor Virus (MMTV)-NeuNDL2-5-Internal Ribosome Entry Site- Cre (NIC) FVB/NJ Ursini-Siegel et al.37 N/A Athymic Nude mouse Charles River Strain Code:490 Mouse: MMTV-Cre Wagner et al.36 N/A Mouse: CdGAPfl/fl Caron et al.35 N/A Oligonucleotides Smad4 specific silencer select validated siRNA Ambion Cat# 4390824 Mouse CdGAP primers for qPCR Qiagen Cat# QT00155162 Human CdGAP primers for qPCR Qiagen Cat# QT00076671 mouse E-cadherin primers for qPCR Qiagen Cat# QT00121163 All the other oligonucleotides, gRNAs, and shRNAs can be found in the Table S3 This paper Table S3 Recombinant DNA pSpCas9(BB)-2A-Puro (PX459) Ding et al.69 Addgene Cat#48139 mCherry-talin-18 a gift from Michael Davidson Addgene Cat#55137 EGFP-talin1 head Simonson et al.70 Addgene Cat# 32856 EGFP-talin1 rod Simonson et al.70 Addgene Cat# 32855 pGL3-basic CdGAP ( 896 to +601) This paper N/A MSCV luciferase PGK-hygro a gift from Scott lowe Addgene Cat# 18782 (Continued on next page) Cell Reports 42, 112936, August 29, 2023 21 .. REAGENT or RESOURCE SOURCE IDENTIFIER pCL-Eco Naviaux et al.71 Addgene Cat# 12371 pCMV5 Smad2-HA Hata et al.72 Addgene Cat# 14930 pRK5F Smad3 Zhang et al.73 Addgene Cat# 12625 pGL3-basic (CAGA)12-luc Kang 74 N/A pGL3-basic vector Promega Cat# E1751 pRK5-myc vector He et al.32 N/A pRK5-myc-CdGAP He et al.32 N/A pRK5-myc-CdGAP PRD He et al.32 N/A pRK5-myc-CdGAP 1-515 He et al.32 N/A GFP-CdGAP He et al.32 N/A Software and algorithms Imagescope software version 2.0.0 Leica Biosystems Inc. RRID: SCR_014311 ImageJ, version 1.8.0/1.53a N/A RRID: SCR_003070 Image Lab software 6.0.1 Bio-Rad RRID: SCR_014210 GraphPad Prism 8 GraphPad RRID: SCR_002798 GenPipes ‘‘RNAseq’’ pipeline Bourgey et al.75 https://github.com/c3g/GenPipes STAR aligner Dobin et al.76 https://github.com/alexdobin/STAR GATK DePristo et al.77 https://gatk.broadinstitute.org/hc/en-us Picard N/A https://broadinstitute.github.io/picard/ HT-seq Anders et al.78 https://github.com/htseq/htseq DESeq2 (v1.30.1) Lovet et al.79 N/A Msigdbr (v7.2.1) N/A https://igordot.github.io/msigdbr/ ClusterProfiler (v3.18.1) Yu et al.80 N/A MKmisc (v1.6) N/A https://github.com/stamats/MKmisc Singscore (v1.12.0) Foroutan et al.81 N/A
Proliferation Assay:Article Title: CdGAP is a talin-binding protein and a target of TGF-β signaling that promotes HER2-positive breast cancer growth and metastasis.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER jetPRIME Polyplus Cat# 114-07 Protein G SepharoseTM 4 Fast Flow Affinity Chromatography media Thermo Fisher Scientific Cat# 17-0618-01 ClarityTM western ECL substrate Bor-Rad Cat# 1705061 SsoAdvancedTM Universal SYBR green Supermix Bio-Rad Cat#1725271 Fibronectin Sigma-Aldrich Cat# F1141 CorningTM MatrigelTM membrane matrix Thermo Fisher Scientific Cat# CB-40234A CorningTM MatrigelTM GFR membrane matrix Thermo Fisher Scientific Cat# CB-40230 FORMALDEHYDE, (formalin) reagent Grade Bioshop Cat# FOR201 Type 1 collagen BD Bioscience Cat# 354246 Critical commercial assays Mycoplasma PCR Detection kit ZmTech Scientific Cat# M209001 Dual-Luciferase reporter assay system Promega Cat# E1910 Qiagen RNeasy kit Qiagen Cat# 74104 RNase-free DNase set Qiagen Cat# 79254 RhoA G-LISA activation assay (luminescence) Cytoskeleton Cat# BK121 Rac1 G-LISA activation assay (luminescence) Cytoskeleton Cat# BK126 MTT Cell proliferation assay kit Abcam Cat# ab211091 Pierce BCA protein assay kit Thermo Fisher Scientific Cat# 23225 Deposited data RNA-sequencing raw data This paper GSE167457 Proteomics raw data This paper PXD043376 Experimental models: Cell lines Human breast cancer cell line: HCC1954 American type culture collection (ATCC) RRID: CVCL_1259 Human breast cancer cell line: SK-BR-3 American type culture collection (ATCC) RRID: CVCL_0033 Human breast cancer cell line: MDA-MB-361 American type culture collection (ATCC) RRID: CVCL_0620 Mouse: NIC+ explant cells Goyette et al.40 N/A Experimental models: Organisms/strains Mouse: Mammary Tumor Virus (MMTV)-NeuNDL2-5-Internal Ribosome Entry Site- Cre (NIC) FVB/NJ Ursini-Siegel et al.37 N/A Athymic Nude mouse Charles River Strain Code:490 Mouse: MMTV-Cre Wagner et al.36 N/A Mouse: CdGAPfl/fl Caron et al.35 N/A Oligonucleotides Smad4 specific silencer select validated siRNA Ambion Cat# 4390824 Mouse CdGAP primers for qPCR Qiagen Cat# QT00155162 Human CdGAP primers for qPCR Qiagen Cat# QT00076671 mouse E-cadherin primers for qPCR Qiagen Cat# QT00121163 All the other oligonucleotides, gRNAs, and shRNAs can be found in the Table S3 This paper Table S3 Recombinant DNA pSpCas9(BB)-2A-Puro (PX459) Ding et al.69 Addgene Cat#48139 mCherry-talin-18 a gift from Michael Davidson Addgene Cat#55137 EGFP-talin1 head Simonson et al.70 Addgene Cat# 32856 EGFP-talin1 rod Simonson et al.70 Addgene Cat# 32855 pGL3-basic CdGAP ( 896 to +601) This paper N/A MSCV luciferase PGK-hygro a gift from Scott lowe Addgene Cat# 18782 (Continued on next page) Cell Reports 42, 112936, August 29, 2023 21 .. REAGENT or RESOURCE SOURCE IDENTIFIER pCL-Eco Naviaux et al.71 Addgene Cat# 12371 pCMV5 Smad2-HA Hata et al.72 Addgene Cat# 14930 pRK5F Smad3 Zhang et al.73 Addgene Cat# 12625 pGL3-basic (CAGA)12-luc Kang 74 N/A pGL3-basic vector Promega Cat# E1751 pRK5-myc vector He et al.32 N/A pRK5-myc-CdGAP He et al.32 N/A pRK5-myc-CdGAP PRD He et al.32 N/A pRK5-myc-CdGAP 1-515 He et al.32 N/A GFP-CdGAP He et al.32 N/A Software and algorithms Imagescope software version 2.0.0 Leica Biosystems Inc. RRID: SCR_014311 ImageJ, version 1.8.0/1.53a N/A RRID: SCR_003070 Image Lab software 6.0.1 Bio-Rad RRID: SCR_014210 GraphPad Prism 8 GraphPad RRID: SCR_002798 GenPipes ‘‘RNAseq’’ pipeline Bourgey et al.75 https://github.com/c3g/GenPipes STAR aligner Dobin et al.76 https://github.com/alexdobin/STAR GATK DePristo et al.77 https://gatk.broadinstitute.org/hc/en-us Picard N/A https://broadinstitute.github.io/picard/ HT-seq Anders et al.78 https://github.com/htseq/htseq DESeq2 (v1.30.1) Lovet et al.79 N/A Msigdbr (v7.2.1) N/A https://igordot.github.io/msigdbr/ ClusterProfiler (v3.18.1) Yu et al.80 N/A MKmisc (v1.6) N/A https://github.com/stamats/MKmisc Singscore (v1.12.0) Foroutan et al.81 N/A
Bicinchoninic Acid Protein Assay:Article Title: CdGAP is a talin-binding protein and a target of TGF-β signaling that promotes HER2-positive breast cancer growth and metastasis.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER jetPRIME Polyplus Cat# 114-07 Protein G SepharoseTM 4 Fast Flow Affinity Chromatography media Thermo Fisher Scientific Cat# 17-0618-01 ClarityTM western ECL substrate Bor-Rad Cat# 1705061 SsoAdvancedTM Universal SYBR green Supermix Bio-Rad Cat#1725271 Fibronectin Sigma-Aldrich Cat# F1141 CorningTM MatrigelTM membrane matrix Thermo Fisher Scientific Cat# CB-40234A CorningTM MatrigelTM GFR membrane matrix Thermo Fisher Scientific Cat# CB-40230 FORMALDEHYDE, (formalin) reagent Grade Bioshop Cat# FOR201 Type 1 collagen BD Bioscience Cat# 354246 Critical commercial assays Mycoplasma PCR Detection kit ZmTech Scientific Cat# M209001 Dual-Luciferase reporter assay system Promega Cat# E1910 Qiagen RNeasy kit Qiagen Cat# 74104 RNase-free DNase set Qiagen Cat# 79254 RhoA G-LISA activation assay (luminescence) Cytoskeleton Cat# BK121 Rac1 G-LISA activation assay (luminescence) Cytoskeleton Cat# BK126 MTT Cell proliferation assay kit Abcam Cat# ab211091 Pierce BCA protein assay kit Thermo Fisher Scientific Cat# 23225 Deposited data RNA-sequencing raw data This paper GSE167457 Proteomics raw data This paper PXD043376 Experimental models: Cell lines Human breast cancer cell line: HCC1954 American type culture collection (ATCC) RRID: CVCL_1259 Human breast cancer cell line: SK-BR-3 American type culture collection (ATCC) RRID: CVCL_0033 Human breast cancer cell line: MDA-MB-361 American type culture collection (ATCC) RRID: CVCL_0620 Mouse: NIC+ explant cells Goyette et al.40 N/A Experimental models: Organisms/strains Mouse: Mammary Tumor Virus (MMTV)-NeuNDL2-5-Internal Ribosome Entry Site- Cre (NIC) FVB/NJ Ursini-Siegel et al.37 N/A Athymic Nude mouse Charles River Strain Code:490 Mouse: MMTV-Cre Wagner et al.36 N/A Mouse: CdGAPfl/fl Caron et al.35 N/A Oligonucleotides Smad4 specific silencer select validated siRNA Ambion Cat# 4390824 Mouse CdGAP primers for qPCR Qiagen Cat# QT00155162 Human CdGAP primers for qPCR Qiagen Cat# QT00076671 mouse E-cadherin primers for qPCR Qiagen Cat# QT00121163 All the other oligonucleotides, gRNAs, and shRNAs can be found in the Table S3 This paper Table S3 Recombinant DNA pSpCas9(BB)-2A-Puro (PX459) Ding et al.69 Addgene Cat#48139 mCherry-talin-18 a gift from Michael Davidson Addgene Cat#55137 EGFP-talin1 head Simonson et al.70 Addgene Cat# 32856 EGFP-talin1 rod Simonson et al.70 Addgene Cat# 32855 pGL3-basic CdGAP ( 896 to +601) This paper N/A MSCV luciferase PGK-hygro a gift from Scott lowe Addgene Cat# 18782 (Continued on next page) Cell Reports 42, 112936, August 29, 2023 21 .. REAGENT or RESOURCE SOURCE IDENTIFIER pCL-Eco Naviaux et al.71 Addgene Cat# 12371 pCMV5 Smad2-HA Hata et al.72 Addgene Cat# 14930 pRK5F Smad3 Zhang et al.73 Addgene Cat# 12625 pGL3-basic (CAGA)12-luc Kang 74 N/A pGL3-basic vector Promega Cat# E1751 pRK5-myc vector He et al.32 N/A pRK5-myc-CdGAP He et al.32 N/A pRK5-myc-CdGAP PRD He et al.32 N/A pRK5-myc-CdGAP 1-515 He et al.32 N/A GFP-CdGAP He et al.32 N/A Software and algorithms Imagescope software version 2.0.0 Leica Biosystems Inc. RRID: SCR_014311 ImageJ, version 1.8.0/1.53a N/A RRID: SCR_003070 Image Lab software 6.0.1 Bio-Rad RRID: SCR_014210 GraphPad Prism 8 GraphPad RRID: SCR_002798 GenPipes ‘‘RNAseq’’ pipeline Bourgey et al.75 https://github.com/c3g/GenPipes STAR aligner Dobin et al.76 https://github.com/alexdobin/STAR GATK DePristo et al.77 https://gatk.broadinstitute.org/hc/en-us Picard N/A https://broadinstitute.github.io/picard/ HT-seq Anders et al.78 https://github.com/htseq/htseq DESeq2 (v1.30.1) Lovet et al.79 N/A Msigdbr (v7.2.1) N/A https://igordot.github.io/msigdbr/ ClusterProfiler (v3.18.1) Yu et al.80 N/A MKmisc (v1.6) N/A https://github.com/stamats/MKmisc Singscore (v1.12.0) Foroutan et al.81 N/A
RNA sequencing:Article Title: CdGAP is a talin-binding protein and a target of TGF-β signaling that promotes HER2-positive breast cancer growth and metastasis.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER jetPRIME Polyplus Cat# 114-07 Protein G SepharoseTM 4 Fast Flow Affinity Chromatography media Thermo Fisher Scientific Cat# 17-0618-01 ClarityTM western ECL substrate Bor-Rad Cat# 1705061 SsoAdvancedTM Universal SYBR green Supermix Bio-Rad Cat#1725271 Fibronectin Sigma-Aldrich Cat# F1141 CorningTM MatrigelTM membrane matrix Thermo Fisher Scientific Cat# CB-40234A CorningTM MatrigelTM GFR membrane matrix Thermo Fisher Scientific Cat# CB-40230 FORMALDEHYDE, (formalin) reagent Grade Bioshop Cat# FOR201 Type 1 collagen BD Bioscience Cat# 354246 Critical commercial assays Mycoplasma PCR Detection kit ZmTech Scientific Cat# M209001 Dual-Luciferase reporter assay system Promega Cat# E1910 Qiagen RNeasy kit Qiagen Cat# 74104 RNase-free DNase set Qiagen Cat# 79254 RhoA G-LISA activation assay (luminescence) Cytoskeleton Cat# BK121 Rac1 G-LISA activation assay (luminescence) Cytoskeleton Cat# BK126 MTT Cell proliferation assay kit Abcam Cat# ab211091 Pierce BCA protein assay kit Thermo Fisher Scientific Cat# 23225 Deposited data RNA-sequencing raw data This paper GSE167457 Proteomics raw data This paper PXD043376 Experimental models: Cell lines Human breast cancer cell line: HCC1954 American type culture collection (ATCC) RRID: CVCL_1259 Human breast cancer cell line: SK-BR-3 American type culture collection (ATCC) RRID: CVCL_0033 Human breast cancer cell line: MDA-MB-361 American type culture collection (ATCC) RRID: CVCL_0620 Mouse: NIC+ explant cells Goyette et al.40 N/A Experimental models: Organisms/strains Mouse: Mammary Tumor Virus (MMTV)-NeuNDL2-5-Internal Ribosome Entry Site- Cre (NIC) FVB/NJ Ursini-Siegel et al.37 N/A Athymic Nude mouse Charles River Strain Code:490 Mouse: MMTV-Cre Wagner et al.36 N/A Mouse: CdGAPfl/fl Caron et al.35 N/A Oligonucleotides Smad4 specific silencer select validated siRNA Ambion Cat# 4390824 Mouse CdGAP primers for qPCR Qiagen Cat# QT00155162 Human CdGAP primers for qPCR Qiagen Cat# QT00076671 mouse E-cadherin primers for qPCR Qiagen Cat# QT00121163 All the other oligonucleotides, gRNAs, and shRNAs can be found in the Table S3 This paper Table S3 Recombinant DNA pSpCas9(BB)-2A-Puro (PX459) Ding et al.69 Addgene Cat#48139 mCherry-talin-18 a gift from Michael Davidson Addgene Cat#55137 EGFP-talin1 head Simonson et al.70 Addgene Cat# 32856 EGFP-talin1 rod Simonson et al.70 Addgene Cat# 32855 pGL3-basic CdGAP ( 896 to +601) This paper N/A MSCV luciferase PGK-hygro a gift from Scott lowe Addgene Cat# 18782 (Continued on next page) Cell Reports 42, 112936, August 29, 2023 21 .. REAGENT or RESOURCE SOURCE IDENTIFIER pCL-Eco Naviaux et al.71 Addgene Cat# 12371 pCMV5 Smad2-HA Hata et al.72 Addgene Cat# 14930 pRK5F Smad3 Zhang et al.73 Addgene Cat# 12625 pGL3-basic (CAGA)12-luc Kang 74 N/A pGL3-basic vector Promega Cat# E1751 pRK5-myc vector He et al.32 N/A pRK5-myc-CdGAP He et al.32 N/A pRK5-myc-CdGAP PRD He et al.32 N/A pRK5-myc-CdGAP 1-515 He et al.32 N/A GFP-CdGAP He et al.32 N/A Software and algorithms Imagescope software version 2.0.0 Leica Biosystems Inc. RRID: SCR_014311 ImageJ, version 1.8.0/1.53a N/A RRID: SCR_003070 Image Lab software 6.0.1 Bio-Rad RRID: SCR_014210 GraphPad Prism 8 GraphPad RRID: SCR_002798 GenPipes ‘‘RNAseq’’ pipeline Bourgey et al.75 https://github.com/c3g/GenPipes STAR aligner Dobin et al.76 https://github.com/alexdobin/STAR GATK DePristo et al.77 https://gatk.broadinstitute.org/hc/en-us Picard N/A https://broadinstitute.github.io/picard/ HT-seq Anders et al.78 https://github.com/htseq/htseq DESeq2 (v1.30.1) Lovet et al.79 N/A Msigdbr (v7.2.1) N/A https://igordot.github.io/msigdbr/ ClusterProfiler (v3.18.1) Yu et al.80 N/A MKmisc (v1.6) N/A https://github.com/stamats/MKmisc Singscore (v1.12.0) Foroutan et al.81 N/A
Multiple Displacement Amplification:Article Title: CdGAP is a talin-binding protein and a target of TGF-β signaling that promotes HER2-positive breast cancer growth and metastasis.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER jetPRIME Polyplus Cat# 114-07 Protein G SepharoseTM 4 Fast Flow Affinity Chromatography media Thermo Fisher Scientific Cat# 17-0618-01 ClarityTM western ECL substrate Bor-Rad Cat# 1705061 SsoAdvancedTM Universal SYBR green Supermix Bio-Rad Cat#1725271 Fibronectin Sigma-Aldrich Cat# F1141 CorningTM MatrigelTM membrane matrix Thermo Fisher Scientific Cat# CB-40234A CorningTM MatrigelTM GFR membrane matrix Thermo Fisher Scientific Cat# CB-40230 FORMALDEHYDE, (formalin) reagent Grade Bioshop Cat# FOR201 Type 1 collagen BD Bioscience Cat# 354246 Critical commercial assays Mycoplasma PCR Detection kit ZmTech Scientific Cat# M209001 Dual-Luciferase reporter assay system Promega Cat# E1910 Qiagen RNeasy kit Qiagen Cat# 74104 RNase-free DNase set Qiagen Cat# 79254 RhoA G-LISA activation assay (luminescence) Cytoskeleton Cat# BK121 Rac1 G-LISA activation assay (luminescence) Cytoskeleton Cat# BK126 MTT Cell proliferation assay kit Abcam Cat# ab211091 Pierce BCA protein assay kit Thermo Fisher Scientific Cat# 23225 Deposited data RNA-sequencing raw data This paper GSE167457 Proteomics raw data This paper PXD043376 Experimental models: Cell lines Human breast cancer cell line: HCC1954 American type culture collection (ATCC) RRID: CVCL_1259 Human breast cancer cell line: SK-BR-3 American type culture collection (ATCC) RRID: CVCL_0033 Human breast cancer cell line: MDA-MB-361 American type culture collection (ATCC) RRID: CVCL_0620 Mouse: NIC+ explant cells Goyette et al.40 N/A Experimental models: Organisms/strains Mouse: Mammary Tumor Virus (MMTV)-NeuNDL2-5-Internal Ribosome Entry Site- Cre (NIC) FVB/NJ Ursini-Siegel et al.37 N/A Athymic Nude mouse Charles River Strain Code:490 Mouse: MMTV-Cre Wagner et al.36 N/A Mouse: CdGAPfl/fl Caron et al.35 N/A Oligonucleotides Smad4 specific silencer select validated siRNA Ambion Cat# 4390824 Mouse CdGAP primers for qPCR Qiagen Cat# QT00155162 Human CdGAP primers for qPCR Qiagen Cat# QT00076671 mouse E-cadherin primers for qPCR Qiagen Cat# QT00121163 All the other oligonucleotides, gRNAs, and shRNAs can be found in the Table S3 This paper Table S3 Recombinant DNA pSpCas9(BB)-2A-Puro (PX459) Ding et al.69 Addgene Cat#48139 mCherry-talin-18 a gift from Michael Davidson Addgene Cat#55137 EGFP-talin1 head Simonson et al.70 Addgene Cat# 32856 EGFP-talin1 rod Simonson et al.70 Addgene Cat# 32855 pGL3-basic CdGAP ( 896 to +601) This paper N/A MSCV luciferase PGK-hygro a gift from Scott lowe Addgene Cat# 18782 (Continued on next page) Cell Reports 42, 112936, August 29, 2023 21 .. REAGENT or RESOURCE SOURCE IDENTIFIER pCL-Eco Naviaux et al.71 Addgene Cat# 12371 pCMV5 Smad2-HA Hata et al.72 Addgene Cat# 14930 pRK5F Smad3 Zhang et al.73 Addgene Cat# 12625 pGL3-basic (CAGA)12-luc Kang 74 N/A pGL3-basic vector Promega Cat# E1751 pRK5-myc vector He et al.32 N/A pRK5-myc-CdGAP He et al.32 N/A pRK5-myc-CdGAP PRD He et al.32 N/A pRK5-myc-CdGAP 1-515 He et al.32 N/A GFP-CdGAP He et al.32 N/A Software and algorithms Imagescope software version 2.0.0 Leica Biosystems Inc. RRID: SCR_014311 ImageJ, version 1.8.0/1.53a N/A RRID: SCR_003070 Image Lab software 6.0.1 Bio-Rad RRID: SCR_014210 GraphPad Prism 8 GraphPad RRID: SCR_002798 GenPipes ‘‘RNAseq’’ pipeline Bourgey et al.75 https://github.com/c3g/GenPipes STAR aligner Dobin et al.76 https://github.com/alexdobin/STAR GATK DePristo et al.77 https://gatk.broadinstitute.org/hc/en-us Picard N/A https://broadinstitute.github.io/picard/ HT-seq Anders et al.78 https://github.com/htseq/htseq DESeq2 (v1.30.1) Lovet et al.79 N/A Msigdbr (v7.2.1) N/A https://igordot.github.io/msigdbr/ ClusterProfiler (v3.18.1) Yu et al.80 N/A MKmisc (v1.6) N/A https://github.com/stamats/MKmisc Singscore (v1.12.0) Foroutan et al.81 N/A
Virus:Article Title: CdGAP is a talin-binding protein and a target of TGF-β signaling that promotes HER2-positive breast cancer growth and metastasis.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER jetPRIME Polyplus Cat# 114-07 Protein G SepharoseTM 4 Fast Flow Affinity Chromatography media Thermo Fisher Scientific Cat# 17-0618-01 ClarityTM western ECL substrate Bor-Rad Cat# 1705061 SsoAdvancedTM Universal SYBR green Supermix Bio-Rad Cat#1725271 Fibronectin Sigma-Aldrich Cat# F1141 CorningTM MatrigelTM membrane matrix Thermo Fisher Scientific Cat# CB-40234A CorningTM MatrigelTM GFR membrane matrix Thermo Fisher Scientific Cat# CB-40230 FORMALDEHYDE, (formalin) reagent Grade Bioshop Cat# FOR201 Type 1 collagen BD Bioscience Cat# 354246 Critical commercial assays Mycoplasma PCR Detection kit ZmTech Scientific Cat# M209001 Dual-Luciferase reporter assay system Promega Cat# E1910 Qiagen RNeasy kit Qiagen Cat# 74104 RNase-free DNase set Qiagen Cat# 79254 RhoA G-LISA activation assay (luminescence) Cytoskeleton Cat# BK121 Rac1 G-LISA activation assay (luminescence) Cytoskeleton Cat# BK126 MTT Cell proliferation assay kit Abcam Cat# ab211091 Pierce BCA protein assay kit Thermo Fisher Scientific Cat# 23225 Deposited data RNA-sequencing raw data This paper GSE167457 Proteomics raw data This paper PXD043376 Experimental models: Cell lines Human breast cancer cell line: HCC1954 American type culture collection (ATCC) RRID: CVCL_1259 Human breast cancer cell line: SK-BR-3 American type culture collection (ATCC) RRID: CVCL_0033 Human breast cancer cell line: MDA-MB-361 American type culture collection (ATCC) RRID: CVCL_0620 Mouse: NIC+ explant cells Goyette et al.40 N/A Experimental models: Organisms/strains Mouse: Mammary Tumor Virus (MMTV)-NeuNDL2-5-Internal Ribosome Entry Site- Cre (NIC) FVB/NJ Ursini-Siegel et al.37 N/A Athymic Nude mouse Charles River Strain Code:490 Mouse: MMTV-Cre Wagner et al.36 N/A Mouse: CdGAPfl/fl Caron et al.35 N/A Oligonucleotides Smad4 specific silencer select validated siRNA Ambion Cat# 4390824 Mouse CdGAP primers for qPCR Qiagen Cat# QT00155162 Human CdGAP primers for qPCR Qiagen Cat# QT00076671 mouse E-cadherin primers for qPCR Qiagen Cat# QT00121163 All the other oligonucleotides, gRNAs, and shRNAs can be found in the Table S3 This paper Table S3 Recombinant DNA pSpCas9(BB)-2A-Puro (PX459) Ding et al.69 Addgene Cat#48139 mCherry-talin-18 a gift from Michael Davidson Addgene Cat#55137 EGFP-talin1 head Simonson et al.70 Addgene Cat# 32856 EGFP-talin1 rod Simonson et al.70 Addgene Cat# 32855 pGL3-basic CdGAP ( 896 to +601) This paper N/A MSCV luciferase PGK-hygro a gift from Scott lowe Addgene Cat# 18782 (Continued on next page) Cell Reports 42, 112936, August 29, 2023 21 .. REAGENT or RESOURCE SOURCE IDENTIFIER pCL-Eco Naviaux et al.71 Addgene Cat# 12371 pCMV5 Smad2-HA Hata et al.72 Addgene Cat# 14930 pRK5F Smad3 Zhang et al.73 Addgene Cat# 12625 pGL3-basic (CAGA)12-luc Kang 74 N/A pGL3-basic vector Promega Cat# E1751 pRK5-myc vector He et al.32 N/A pRK5-myc-CdGAP He et al.32 N/A pRK5-myc-CdGAP PRD He et al.32 N/A pRK5-myc-CdGAP 1-515 He et al.32 N/A GFP-CdGAP He et al.32 N/A Software and algorithms Imagescope software version 2.0.0 Leica Biosystems Inc. RRID: SCR_014311 ImageJ, version 1.8.0/1.53a N/A RRID: SCR_003070 Image Lab software 6.0.1 Bio-Rad RRID: SCR_014210 GraphPad Prism 8 GraphPad RRID: SCR_002798 GenPipes ‘‘RNAseq’’ pipeline Bourgey et al.75 https://github.com/c3g/GenPipes STAR aligner Dobin et al.76 https://github.com/alexdobin/STAR GATK DePristo et al.77 https://gatk.broadinstitute.org/hc/en-us Picard N/A https://broadinstitute.github.io/picard/ HT-seq Anders et al.78 https://github.com/htseq/htseq DESeq2 (v1.30.1) Lovet et al.79 N/A Msigdbr (v7.2.1) N/A https://igordot.github.io/msigdbr/ ClusterProfiler (v3.18.1) Yu et al.80 N/A MKmisc (v1.6) N/A https://github.com/stamats/MKmisc Singscore (v1.12.0) Foroutan et al.81 N/A
Luciferase:Article Title: CdGAP is a talin-binding protein and a target of TGF-β signaling that promotes HER2-positive breast cancer growth and metastasis.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER jetPRIME Polyplus Cat# 114-07 Protein G SepharoseTM 4 Fast Flow Affinity Chromatography media Thermo Fisher Scientific Cat# 17-0618-01 ClarityTM western ECL substrate Bor-Rad Cat# 1705061 SsoAdvancedTM Universal SYBR green Supermix Bio-Rad Cat#1725271 Fibronectin Sigma-Aldrich Cat# F1141 CorningTM MatrigelTM membrane matrix Thermo Fisher Scientific Cat# CB-40234A CorningTM MatrigelTM GFR membrane matrix Thermo Fisher Scientific Cat# CB-40230 FORMALDEHYDE, (formalin) reagent Grade Bioshop Cat# FOR201 Type 1 collagen BD Bioscience Cat# 354246 Critical commercial assays Mycoplasma PCR Detection kit ZmTech Scientific Cat# M209001 Dual-Luciferase reporter assay system Promega Cat# E1910 Qiagen RNeasy kit Qiagen Cat# 74104 RNase-free DNase set Qiagen Cat# 79254 RhoA G-LISA activation assay (luminescence) Cytoskeleton Cat# BK121 Rac1 G-LISA activation assay (luminescence) Cytoskeleton Cat# BK126 MTT Cell proliferation assay kit Abcam Cat# ab211091 Pierce BCA protein assay kit Thermo Fisher Scientific Cat# 23225 Deposited data RNA-sequencing raw data This paper GSE167457 Proteomics raw data This paper PXD043376 Experimental models: Cell lines Human breast cancer cell line: HCC1954 American type culture collection (ATCC) RRID: CVCL_1259 Human breast cancer cell line: SK-BR-3 American type culture collection (ATCC) RRID: CVCL_0033 Human breast cancer cell line: MDA-MB-361 American type culture collection (ATCC) RRID: CVCL_0620 Mouse: NIC+ explant cells Goyette et al.40 N/A Experimental models: Organisms/strains Mouse: Mammary Tumor Virus (MMTV)-NeuNDL2-5-Internal Ribosome Entry Site- Cre (NIC) FVB/NJ Ursini-Siegel et al.37 N/A Athymic Nude mouse Charles River Strain Code:490 Mouse: MMTV-Cre Wagner et al.36 N/A Mouse: CdGAPfl/fl Caron et al.35 N/A Oligonucleotides Smad4 specific silencer select validated siRNA Ambion Cat# 4390824 Mouse CdGAP primers for qPCR Qiagen Cat# QT00155162 Human CdGAP primers for qPCR Qiagen Cat# QT00076671 mouse E-cadherin primers for qPCR Qiagen Cat# QT00121163 All the other oligonucleotides, gRNAs, and shRNAs can be found in the Table S3 This paper Table S3 Recombinant DNA pSpCas9(BB)-2A-Puro (PX459) Ding et al.69 Addgene Cat#48139 mCherry-talin-18 a gift from Michael Davidson Addgene Cat#55137 EGFP-talin1 head Simonson et al.70 Addgene Cat# 32856 EGFP-talin1 rod Simonson et al.70 Addgene Cat# 32855 pGL3-basic CdGAP ( 896 to +601) This paper N/A MSCV luciferase PGK-hygro a gift from Scott lowe Addgene Cat# 18782 (Continued on next page) Cell Reports 42, 112936, August 29, 2023 21 .. REAGENT or RESOURCE SOURCE IDENTIFIER pCL-Eco Naviaux et al.71 Addgene Cat# 12371 pCMV5 Smad2-HA Hata et al.72 Addgene Cat# 14930 pRK5F Smad3 Zhang et al.73 Addgene Cat# 12625 pGL3-basic (CAGA)12-luc Kang 74 N/A pGL3-basic vector Promega Cat# E1751 pRK5-myc vector He et al.32 N/A pRK5-myc-CdGAP He et al.32 N/A pRK5-myc-CdGAP PRD He et al.32 N/A pRK5-myc-CdGAP 1-515 He et al.32 N/A GFP-CdGAP He et al.32 N/A Software and algorithms Imagescope software version 2.0.0 Leica Biosystems Inc. RRID: SCR_014311 ImageJ, version 1.8.0/1.53a N/A RRID: SCR_003070 Image Lab software 6.0.1 Bio-Rad RRID: SCR_014210 GraphPad Prism 8 GraphPad RRID: SCR_002798 GenPipes ‘‘RNAseq’’ pipeline Bourgey et al.75 https://github.com/c3g/GenPipes STAR aligner Dobin et al.76 https://github.com/alexdobin/STAR GATK DePristo et al.77 https://gatk.broadinstitute.org/hc/en-us Picard N/A https://broadinstitute.github.io/picard/ HT-seq Anders et al.78 https://github.com/htseq/htseq DESeq2 (v1.30.1) Lovet et al.79 N/A Msigdbr (v7.2.1) N/A https://igordot.github.io/msigdbr/ ClusterProfiler (v3.18.1) Yu et al.80 N/A MKmisc (v1.6) N/A https://github.com/stamats/MKmisc Singscore (v1.12.0) Foroutan et al.81 N/A
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