other:Article Title: A membrane arm of mitochondrial complex I sufficient to promote respirasome formation.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER HEK293T Laboratory of Haihua Gu (Wenzhou Medical University) RRID: CVCL_0063 Immortalized human B lymphocyte This Paper N/A Experimental models: Organisms/strains AB Danio rerio China Zebrafish Resource Center RRID:ZIRC_ZL1 Oligonucleotides siRNA: siCOX14 (50-GACAUUGGCUAUAAGA CCUUCUCUA-30) RiboBio N/A siRNA: siCOA1 (50-GUCAGCAGAUUCCUGU GUU-30) RiboBio N/A siRNA: siCOA3 (50-CGCAGUUGUUACGAGG UUA-30) RiboBio N/A siRNA: siSURF1 (50-CCUAUGUGGUCACUC CCUU-30) RiboBio N/A siRNA: siNC (50-GGCTCTAGAAAAGCCTA TGC-30) RiboBio N/A Sequencing Primer: TIMMDC1-F (50-AGAG CTGTCACCACAACGGT-30) This paper N/A Sequencing Primer: TIMMDC1-R (50-AGTG AGAGTACAACAGCCCC-30) This paper N/A Morpholino: MO-timmdc1 (50-GACACATCA CTGATACTCACACGTT-30) GeneTools N/A Morpholino: MO-control (50-CCTCTTACCT CAGTTACAATTTATA-30) GeneTools N/A RT-PCR Primer: timmdc1-F (50-CCTGACAC AGGATGGGACC-30) This paper N/A RT-PCR Primer: timmdc1-R (50-TCATCCCC ACTATGGCTGAA-30) This paper N/A qPCR primers, see in Table S3 This paper N/A Recombinant DNA pLVEXP01 Cyagen N/A pLVSHG01 Cyagen N/A pMD2.G Didier Trono Lab Addgene plasmid # 12259; http://addgene. org/12259; RRID: Addgene_12259 psPAX2 Didier Trono Lab Addgene plasmid # 12260; http://addgene. org/12260; RRID: Addgene_12260 pX330-U6-Chimeric_BB-CBh-hSpCas9 Cong et al., 2013 Addgene plasmid # 42230; http://addgene. org/42230; RRID: Addgene_42230 KLHL29FLAG in pLVEXP01 This paper N/A TIMMDC1 in pLVEXP01 This paper N/A TIMMDC1FLAG in pLVEXP01 This paper N/A TIMMDC1 c.596+2146A>G in pLVEXP01 This paper N/A TIMMDC1 c.847delG in pLVEXP01 This paper N/A KO and KD vectors, see in Table S3 This paper N/A Software and algorithms GraphPad Prism v8.0 GraphPad Software RRID: SCR_002798 ImageJ PMID 22930834 https://imagej.nih.gov/ij/; RRID: SCR_00307 MaxQuant Platform Tyanova et al., 2016 RRID: SCR_014485 R package R Core Team http://www.R-project.org/; RRID: SCR_001905 SPSS v21.0 IBM RRID: SCR_002865 e3 Cell Reports 35, 108963, April 13, 2021
Virus:Article Title: Shigella ubiquitin ligase IpaH7.8 targets gasdermin D for degradation to prevent pyroptosis and enable infection.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Mouse monoclonal anti Actin MP Biomedicals SKU: 0869100-CF, Clone C4 Rabbit polyclonal anti beta-tubulin Abcam Cat#: Ab6046, RRID:AB_2210370 Rabbit polyclonal anti IpaH9.8 EpiGentek Cat#: A55475 Mouse monoclonal anti Cul1 ThermoFisher Cat#: 32-2400, 2H4C9, RRID:AB_86218 Mouse monoclonal anti Myc Cell Signaling Cat#: 2276S, RRID:AB_331783 Mouse monoclonal anti FLAG M2Peroxidase Millipore Sigma SKU: A8592, RRID:AB_439702 Mouse monoclonal anti FLAG M2 Millipore Sigma SKU: F3165, RRID:AB_259529 Rat monoclonal anti GSDMD Aglietti et al., 2016 Clone 17G2G9, Genentech Mouse monoclonal anti Rho-1D4 University of British Colombia https://ubc.flintbox.com/ technologies/0f1ef64b-fa5d4a58-9003-3e01f6f672a6 Mouse monoclonal anti-Ubiquitin LifeSensors SKU: VU-0101, clone VU-1, RRID:AB_2716558 Human monoclonal anti K11-Ubiquitin Matsumoto et al., 2010 Genentech Human monoclonal anti K48-Ubiquitin Newton et al., 2008 Genentech Human monoclonal anti K63-Ubiquitin Newton et al., 2008 Genentech Rabbit monoclonal anti GSDMD Cell Signaling Technology Cat#: 97558S, E8G3F, RRID:AB_2864253 Rabbit monoclonal anti GSDMD(Asp275) Cell Signaling Technology Cat#: 36425S, E7H9G, RRID:AB_2799099 Mouse monoclonal caspase-4 Enzo Cat#: ADI-AAM-114 RRID:AB_10621609 Bacterial and virus strains Shigella flexneri M90T wild-type (WT) John Rohde, Dalhousie University N/A Shigella flexneri M90T wild-type (WT) GFP This study Genentech Shigella flexneri M90T DIpaH7.8 (WT) GFP This study Genentech Chemicals, peptides, and recombinant proteins Ultra-pure LPS E. coli 0111:B4 InvivoGen Cat#: 0111:B4 Egg phosphatidylcholine (Egg PC) Avanti Polar Lipids Cat#: 840051 Egg phosphatidylethanolamine (Egg PE) Avanti Polar Lipids Cat#: 840021 Egg Liss Rhod phosphatidylethanolamine Avanti Polar Lipids Cat#: 810146 Val-boroPro Millipore Sigma Cat#: 531465 Doxycycline Fisher scientific (Clontech) Cat#: NC042034 3X FLAG Peptide Millipore Sigma SKU: F4799 1D4 peptide (TETSQVAPA) Genscript Custom peptide MLN-7243 ChemieTek Cat#: CT-M7243 MLN-4924 (Pevonedistat) ChemieTek Cat#: CT-M4924 Bortezomib ChemieTek Cat#: CT-BZ001 Propidium iodide Millipore Sigma SKU: P4170 YOYO-1 Iodide ThermoFisher Cat#: Y3601 Nuclight Rapid Red Dye Essenbioscience Cat#: 4717 Congo Red Millipore Sigma SKU: C6277 Poly-L-lysine Millipore Sigma SKU: P4707 (Continued on next page) Cell Host & Microbe 29, 1–10.e1–e10, October 13, 2021 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Alt-R CRISPR-Cas9 IDT Cat#: 1081060 IpaH7.8 wild-type (recombinant) This study Genentech IpaH7.8 C357A (recombinant) This study Genentech Human GSDMD (recombinant) This study Genentech Mouse GSDMD (recombinant) This study Genentech Human E1 R&D systems Cat#: E-304-050 Human UBE2D3 R&D systems Cat#: E2-627-100 Human Ubiquitin R&D systems Cat#: U-100H-10M K11-linked tetra-Ub chains R&D systems Cat#: UC-45-025 K48-linked tetra-Ub chains R&D systems Cat#: UC-210B-025 K63-linked tetra-Ub chains R&D systems Cat#: UC-310B-025 Critical commercial assays CytoTox 96 Non-radioactive Cytotoxicity Assay Promega Cat#: G1780 Power SYBR Green Cells-to-CT Kit ThermoFisher Cat#: 4402955 Protein labeling kit RED-MALEIMIDE 2nd Generation NanoTemper SKU: MO-L014 Deposited data Shigella flexneri whole-genome sequencing This study SRA: PRJNA697993 Experimental models: Cell lines Ea.hy926 human endothelial cells Genentech gCell facility N/A Ea.hy926 GSDMD-/- CRISPR-KO cells This study N/A 293T human embryonic kidney cells Genentech gCell facility N/A HeLa human cervical epithelial cells Genentech gCell facility N/A Caco-2 human intestinal epithelial cells Genentech gCell facility N/A HeLa GSDMD-/- CRISPR-KO cells This study N/A ER-Hoxb8-immortalized murine myeloid progenitor cells Wang et al., 2006 Genentech Experimental models: Organisms/strains Nlrc4-/- mice (C57BL6/N) Mariathasan et al., 2004 Genentech Gsdmd-/- mice (C57BL6/N) Kayagaki et al., 2015 Genentech Nlrc4-/- Gsdmd-/- mice (C57BL6/N) This study Genentech Oligonucleotides Human GSDMD gRNA IDT TTCCACTTCTACGATGCCA GSDMD RT-qPCR forward primer IDT GTGTGTCAACCTGTCTATCAAGG GSDMD RT-qPCR reverse primer IDT CATGGCATCGTAGAAGTGGAAG ipaH7.8 RT-qPCR forward primer IDT CCCTGATCGTGGAGAACAATAA ipaH7.8 RT-qPCR reverse primer IDT CACGGACAGGCGATTGTTA GAPDH RT-qPCR forward primer IDT GTCTCCTCTGACTTCAACAGCG GAPDH RT-qPCR reverse primer IDT ACCACCCTGTTGCTGTAGCCAA Recombinant DNA pMIN-ducer (dox-inducible, lentiviral expression) Genscript, this study N/A pMIN-ducer Shigella effector library Genscript, Table S1, this study N/A pMIN-ducer FLAG-IpaH7.8 Genscript, this study N/A pMIN-ducer FLAG-IpaH7.8 C357A Genscript, this study N/A pCDNA3.1 (+) zeo (mammalian transient overexpression) Genscript, this study N/A pCDNA3.1 (+) zeo FLAG-IpaH7.8 Genscript, this study N/A pCDNA3.1 (+) zeo FLAG-IpaH7.8 C357A Genscript, this study N/A (Continued on next page) e2 Cell Host & Microbe 29, 1–10.e1–e10, October 13, 2021
Recombinant:Article Title: Shigella ubiquitin ligase IpaH7.8 targets gasdermin D for degradation to prevent pyroptosis and enable infection.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Mouse monoclonal anti Actin MP Biomedicals SKU: 0869100-CF, Clone C4 Rabbit polyclonal anti beta-tubulin Abcam Cat#: Ab6046, RRID:AB_2210370 Rabbit polyclonal anti IpaH9.8 EpiGentek Cat#: A55475 Mouse monoclonal anti Cul1 ThermoFisher Cat#: 32-2400, 2H4C9, RRID:AB_86218 Mouse monoclonal anti Myc Cell Signaling Cat#: 2276S, RRID:AB_331783 Mouse monoclonal anti FLAG M2Peroxidase Millipore Sigma SKU: A8592, RRID:AB_439702 Mouse monoclonal anti FLAG M2 Millipore Sigma SKU: F3165, RRID:AB_259529 Rat monoclonal anti GSDMD Aglietti et al., 2016 Clone 17G2G9, Genentech Mouse monoclonal anti Rho-1D4 University of British Colombia https://ubc.flintbox.com/ technologies/0f1ef64b-fa5d4a58-9003-3e01f6f672a6 Mouse monoclonal anti-Ubiquitin LifeSensors SKU: VU-0101, clone VU-1, RRID:AB_2716558 Human monoclonal anti K11-Ubiquitin Matsumoto et al., 2010 Genentech Human monoclonal anti K48-Ubiquitin Newton et al., 2008 Genentech Human monoclonal anti K63-Ubiquitin Newton et al., 2008 Genentech Rabbit monoclonal anti GSDMD Cell Signaling Technology Cat#: 97558S, E8G3F, RRID:AB_2864253 Rabbit monoclonal anti GSDMD(Asp275) Cell Signaling Technology Cat#: 36425S, E7H9G, RRID:AB_2799099 Mouse monoclonal caspase-4 Enzo Cat#: ADI-AAM-114 RRID:AB_10621609 Bacterial and virus strains Shigella flexneri M90T wild-type (WT) John Rohde, Dalhousie University N/A Shigella flexneri M90T wild-type (WT) GFP This study Genentech Shigella flexneri M90T DIpaH7.8 (WT) GFP This study Genentech Chemicals, peptides, and recombinant proteins Ultra-pure LPS E. coli 0111:B4 InvivoGen Cat#: 0111:B4 Egg phosphatidylcholine (Egg PC) Avanti Polar Lipids Cat#: 840051 Egg phosphatidylethanolamine (Egg PE) Avanti Polar Lipids Cat#: 840021 Egg Liss Rhod phosphatidylethanolamine Avanti Polar Lipids Cat#: 810146 Val-boroPro Millipore Sigma Cat#: 531465 Doxycycline Fisher scientific (Clontech) Cat#: NC042034 3X FLAG Peptide Millipore Sigma SKU: F4799 1D4 peptide (TETSQVAPA) Genscript Custom peptide MLN-7243 ChemieTek Cat#: CT-M7243 MLN-4924 (Pevonedistat) ChemieTek Cat#: CT-M4924 Bortezomib ChemieTek Cat#: CT-BZ001 Propidium iodide Millipore Sigma SKU: P4170 YOYO-1 Iodide ThermoFisher Cat#: Y3601 Nuclight Rapid Red Dye Essenbioscience Cat#: 4717 Congo Red Millipore Sigma SKU: C6277 Poly-L-lysine Millipore Sigma SKU: P4707 (Continued on next page) Cell Host & Microbe 29, 1–10.e1–e10, October 13, 2021 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Alt-R CRISPR-Cas9 IDT Cat#: 1081060 IpaH7.8 wild-type (recombinant) This study Genentech IpaH7.8 C357A (recombinant) This study Genentech Human GSDMD (recombinant) This study Genentech Mouse GSDMD (recombinant) This study Genentech Human E1 R&D systems Cat#: E-304-050 Human UBE2D3 R&D systems Cat#: E2-627-100 Human Ubiquitin R&D systems Cat#: U-100H-10M K11-linked tetra-Ub chains R&D systems Cat#: UC-45-025 K48-linked tetra-Ub chains R&D systems Cat#: UC-210B-025 K63-linked tetra-Ub chains R&D systems Cat#: UC-310B-025 Critical commercial assays CytoTox 96 Non-radioactive Cytotoxicity Assay Promega Cat#: G1780 Power SYBR Green Cells-to-CT Kit ThermoFisher Cat#: 4402955 Protein labeling kit RED-MALEIMIDE 2nd Generation NanoTemper SKU: MO-L014 Deposited data Shigella flexneri whole-genome sequencing This study SRA: PRJNA697993 Experimental models: Cell lines Ea.hy926 human endothelial cells Genentech gCell facility N/A Ea.hy926 GSDMD-/- CRISPR-KO cells This study N/A 293T human embryonic kidney cells Genentech gCell facility N/A HeLa human cervical epithelial cells Genentech gCell facility N/A Caco-2 human intestinal epithelial cells Genentech gCell facility N/A HeLa GSDMD-/- CRISPR-KO cells This study N/A ER-Hoxb8-immortalized murine myeloid progenitor cells Wang et al., 2006 Genentech Experimental models: Organisms/strains Nlrc4-/- mice (C57BL6/N) Mariathasan et al., 2004 Genentech Gsdmd-/- mice (C57BL6/N) Kayagaki et al., 2015 Genentech Nlrc4-/- Gsdmd-/- mice (C57BL6/N) This study Genentech Oligonucleotides Human GSDMD gRNA IDT TTCCACTTCTACGATGCCA GSDMD RT-qPCR forward primer IDT GTGTGTCAACCTGTCTATCAAGG GSDMD RT-qPCR reverse primer IDT CATGGCATCGTAGAAGTGGAAG ipaH7.8 RT-qPCR forward primer IDT CCCTGATCGTGGAGAACAATAA ipaH7.8 RT-qPCR reverse primer IDT CACGGACAGGCGATTGTTA GAPDH RT-qPCR forward primer IDT GTCTCCTCTGACTTCAACAGCG GAPDH RT-qPCR reverse primer IDT ACCACCCTGTTGCTGTAGCCAA Recombinant DNA pMIN-ducer (dox-inducible, lentiviral expression) Genscript, this study N/A pMIN-ducer Shigella effector library Genscript, Table S1, this study N/A pMIN-ducer FLAG-IpaH7.8 Genscript, this study N/A pMIN-ducer FLAG-IpaH7.8 C357A Genscript, this study N/A pCDNA3.1 (+) zeo (mammalian transient overexpression) Genscript, this study N/A pCDNA3.1 (+) zeo FLAG-IpaH7.8 Genscript, this study N/A pCDNA3.1 (+) zeo FLAG-IpaH7.8 C357A Genscript, this study N/A (Continued on next page) e2 Cell Host & Microbe 29, 1–10.e1–e10, October 13, 2021
RNA Sequencing:Article Title: Expression of Tim-3 drives phenotypic and functional changes in Treg cells in secondary lymphoid organs and the tumor microenvironment
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies mCD25 BD Biosciences, BioLegend, Tonbo Clone PC61 FoxP3 Invitrogen Clone FJK16S mCD44 BD Biosciences, BioLegend, Tonbo Clone IM7 mCD62L BioLegend, Tonbo Clone MEL-14 mICOS BioLegend Clone 398.4A Ki67 BD Biosciences Clone B56 mCTLA-4 BioLegend Clone UC10-4B9 mCD103 BD Biosciences Clone M290 mNrp-1 BD Biosciences Clone 3E12 mCD39 BioLegend Clone Duha 59 mCD73 BioLegend Clone TY/11.8 mTim-3 BioLegend Clone RMT 3-23 mTim-3 R&D Systems Clone FAB1529 Flag BioLegend Clone L5 mPD-1 BioLegend Clone RMP1-30 mIL-10 BioLegend Clone JES5-16E3 mCD90.2 BD Biosciences, BioLegend Clone 532.1 mCD45.2 BioLegend Clone 104 Helios BioLegend Clone 22F6 mKlrg-1 BioLegend Clone 2F1 mLy6g Tonbo Clone IA8 mGITR eBioscience Clone DTA-1 mCD4 BD Biosciences, BioLegend, Tonbo Clone RM-4-5 mTIGIT BioLegend Clone 1G9 mLAG-3 Invitrogen Clone C9B7W mGARP BioLegend Clone F011-5 phospho-S6 BioLegend Clone A17020B phospho-ERK BioLegend Clone 4B11B69 phospho-Akt BD Biosciences Clone M89-61 phospho-MTOR eBioscience Clone MRRBY phospho-STAT3 BD Biosciences Clone 4 CD16/CD32 (Fc Block) Tonbo Clone 2.4G2 mCD8a BD Biosciences, BioLegend, Tonbo Clone H35-17.2 mCD19 BD Biosciences, BioLegend, Tonbo Clone ID3 mCD11b eBioscience Clone M1/70 mCD3 (purified) BioLegend Clone 2C11 Chemicals, peptides, and recombinant proteins CellTrace Violet Invitrogen Cat#C34571 FoxP3 Staining Kit eBioscience Cat#00-5523-00 GhostDye-Violet510 Tonbo Biosciences Cat#13-0870-T500 RBC lysis buffer eBioscience Cat#00-4333-57 (Continued on next page) e1 Cell Reports 36, 109699, September 14, 2021 .. REAGENT or RESOURCE SOURCE IDENTIFIER Collagenase D Roche Cat#11088866001 DNase I, type IV Sigma-Aldrich Cat#D5025 Hyclone Fetal bovine serum Cytiva Cat#SH30071 Tamoxifen MP Biomedical Cat02156738-CF Deposited data RNA sequencing of Tim-3 Tg Treg and WT Treg Data obtained for this study GEO record GSE155825 single-cell RNA sequencing of HNC tumors Cillo et al. (2020) GEO record GSE139324 Experimental models: Cell lines MC38 tumor line Dario Vignali, Univ. of Pittsburgh RRID:CVCL_B288 B16-F10 tumor line Dario Vignali, Univ. of Pittsburgh RRID:CVCL_0159 Experimental models: Organisms/strains Mouse: FoxP3eGFP-Cre-ERT2: Foxp3tm9(EGFP/ cre/ERT2)Ayr The Jackson Laboratory Cat#016961 Mouse: Tim-3fl/fl: B6-Havcr2fl/fl Developed with the Pitt Department of Immunolgy Transgenic and Gene Targeting Core for this study N/A Mouse: FSF-Tim-3: B6-Rosa26flox-stop-floxFlag-Tim-3 Developed for the investigators by GenOway Avery et al. (2018) Mouse: C57BL/6J The Jackson Laboratory Cat#000664 Software and algorithms FlowJo BD Biosciences version 10 Prism GraphPad version 9 FastQC Babraham Bioinformatics version 0.11.7 Cutadapt https://cutadapt.readthedocs.io/en/stable/ version 1.18 HISAT2 http://daehwankimlab.github.io/hisat2/ main/ version 2.1.0 SAMtools http://www.htslib.org/ version 1.9 HTSeq https://htseq.readthedocs.io/en/master/ version 0.11.2 Bioconductor edgeR https://bioconductor.org/packages/ release/bioc/html/edgeR.html version 3.24.1 Enrichr https://maayanlab.cloud/Enrichr/ Kuleshov et al., 2016 Scanpy https://github.com/theislab/scanpy Wolf et al., 2018 Article ll OPEN ACCESS ..
Single Cell:Article Title: Expression of Tim-3 drives phenotypic and functional changes in Treg cells in secondary lymphoid organs and the tumor microenvironment
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies mCD25 BD Biosciences, BioLegend, Tonbo Clone PC61 FoxP3 Invitrogen Clone FJK16S mCD44 BD Biosciences, BioLegend, Tonbo Clone IM7 mCD62L BioLegend, Tonbo Clone MEL-14 mICOS BioLegend Clone 398.4A Ki67 BD Biosciences Clone B56 mCTLA-4 BioLegend Clone UC10-4B9 mCD103 BD Biosciences Clone M290 mNrp-1 BD Biosciences Clone 3E12 mCD39 BioLegend Clone Duha 59 mCD73 BioLegend Clone TY/11.8 mTim-3 BioLegend Clone RMT 3-23 mTim-3 R&D Systems Clone FAB1529 Flag BioLegend Clone L5 mPD-1 BioLegend Clone RMP1-30 mIL-10 BioLegend Clone JES5-16E3 mCD90.2 BD Biosciences, BioLegend Clone 532.1 mCD45.2 BioLegend Clone 104 Helios BioLegend Clone 22F6 mKlrg-1 BioLegend Clone 2F1 mLy6g Tonbo Clone IA8 mGITR eBioscience Clone DTA-1 mCD4 BD Biosciences, BioLegend, Tonbo Clone RM-4-5 mTIGIT BioLegend Clone 1G9 mLAG-3 Invitrogen Clone C9B7W mGARP BioLegend Clone F011-5 phospho-S6 BioLegend Clone A17020B phospho-ERK BioLegend Clone 4B11B69 phospho-Akt BD Biosciences Clone M89-61 phospho-MTOR eBioscience Clone MRRBY phospho-STAT3 BD Biosciences Clone 4 CD16/CD32 (Fc Block) Tonbo Clone 2.4G2 mCD8a BD Biosciences, BioLegend, Tonbo Clone H35-17.2 mCD19 BD Biosciences, BioLegend, Tonbo Clone ID3 mCD11b eBioscience Clone M1/70 mCD3 (purified) BioLegend Clone 2C11 Chemicals, peptides, and recombinant proteins CellTrace Violet Invitrogen Cat#C34571 FoxP3 Staining Kit eBioscience Cat#00-5523-00 GhostDye-Violet510 Tonbo Biosciences Cat#13-0870-T500 RBC lysis buffer eBioscience Cat#00-4333-57 (Continued on next page) e1 Cell Reports 36, 109699, September 14, 2021 .. REAGENT or RESOURCE SOURCE IDENTIFIER Collagenase D Roche Cat#11088866001 DNase I, type IV Sigma-Aldrich Cat#D5025 Hyclone Fetal bovine serum Cytiva Cat#SH30071 Tamoxifen MP Biomedical Cat02156738-CF Deposited data RNA sequencing of Tim-3 Tg Treg and WT Treg Data obtained for this study GEO record GSE155825 single-cell RNA sequencing of HNC tumors Cillo et al. (2020) GEO record GSE139324 Experimental models: Cell lines MC38 tumor line Dario Vignali, Univ. of Pittsburgh RRID:CVCL_B288 B16-F10 tumor line Dario Vignali, Univ. of Pittsburgh RRID:CVCL_0159 Experimental models: Organisms/strains Mouse: FoxP3eGFP-Cre-ERT2: Foxp3tm9(EGFP/ cre/ERT2)Ayr The Jackson Laboratory Cat#016961 Mouse: Tim-3fl/fl: B6-Havcr2fl/fl Developed with the Pitt Department of Immunolgy Transgenic and Gene Targeting Core for this study N/A Mouse: FSF-Tim-3: B6-Rosa26flox-stop-floxFlag-Tim-3 Developed for the investigators by GenOway Avery et al. (2018) Mouse: C57BL/6J The Jackson Laboratory Cat#000664 Software and algorithms FlowJo BD Biosciences version 10 Prism GraphPad version 9 FastQC Babraham Bioinformatics version 0.11.7 Cutadapt https://cutadapt.readthedocs.io/en/stable/ version 1.18 HISAT2 http://daehwankimlab.github.io/hisat2/ main/ version 2.1.0 SAMtools http://www.htslib.org/ version 1.9 HTSeq https://htseq.readthedocs.io/en/master/ version 0.11.2 Bioconductor edgeR https://bioconductor.org/packages/ release/bioc/html/edgeR.html version 3.24.1 Enrichr https://maayanlab.cloud/Enrichr/ Kuleshov et al., 2016 Scanpy https://github.com/theislab/scanpy Wolf et al., 2018 Article ll OPEN ACCESS ..
Transgenic Assay:Article Title: Expression of Tim-3 drives phenotypic and functional changes in Treg cells in secondary lymphoid organs and the tumor microenvironment
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies mCD25 BD Biosciences, BioLegend, Tonbo Clone PC61 FoxP3 Invitrogen Clone FJK16S mCD44 BD Biosciences, BioLegend, Tonbo Clone IM7 mCD62L BioLegend, Tonbo Clone MEL-14 mICOS BioLegend Clone 398.4A Ki67 BD Biosciences Clone B56 mCTLA-4 BioLegend Clone UC10-4B9 mCD103 BD Biosciences Clone M290 mNrp-1 BD Biosciences Clone 3E12 mCD39 BioLegend Clone Duha 59 mCD73 BioLegend Clone TY/11.8 mTim-3 BioLegend Clone RMT 3-23 mTim-3 R&D Systems Clone FAB1529 Flag BioLegend Clone L5 mPD-1 BioLegend Clone RMP1-30 mIL-10 BioLegend Clone JES5-16E3 mCD90.2 BD Biosciences, BioLegend Clone 532.1 mCD45.2 BioLegend Clone 104 Helios BioLegend Clone 22F6 mKlrg-1 BioLegend Clone 2F1 mLy6g Tonbo Clone IA8 mGITR eBioscience Clone DTA-1 mCD4 BD Biosciences, BioLegend, Tonbo Clone RM-4-5 mTIGIT BioLegend Clone 1G9 mLAG-3 Invitrogen Clone C9B7W mGARP BioLegend Clone F011-5 phospho-S6 BioLegend Clone A17020B phospho-ERK BioLegend Clone 4B11B69 phospho-Akt BD Biosciences Clone M89-61 phospho-MTOR eBioscience Clone MRRBY phospho-STAT3 BD Biosciences Clone 4 CD16/CD32 (Fc Block) Tonbo Clone 2.4G2 mCD8a BD Biosciences, BioLegend, Tonbo Clone H35-17.2 mCD19 BD Biosciences, BioLegend, Tonbo Clone ID3 mCD11b eBioscience Clone M1/70 mCD3 (purified) BioLegend Clone 2C11 Chemicals, peptides, and recombinant proteins CellTrace Violet Invitrogen Cat#C34571 FoxP3 Staining Kit eBioscience Cat#00-5523-00 GhostDye-Violet510 Tonbo Biosciences Cat#13-0870-T500 RBC lysis buffer eBioscience Cat#00-4333-57 (Continued on next page) e1 Cell Reports 36, 109699, September 14, 2021 .. REAGENT or RESOURCE SOURCE IDENTIFIER Collagenase D Roche Cat#11088866001 DNase I, type IV Sigma-Aldrich Cat#D5025 Hyclone Fetal bovine serum Cytiva Cat#SH30071 Tamoxifen MP Biomedical Cat02156738-CF Deposited data RNA sequencing of Tim-3 Tg Treg and WT Treg Data obtained for this study GEO record GSE155825 single-cell RNA sequencing of HNC tumors Cillo et al. (2020) GEO record GSE139324 Experimental models: Cell lines MC38 tumor line Dario Vignali, Univ. of Pittsburgh RRID:CVCL_B288 B16-F10 tumor line Dario Vignali, Univ. of Pittsburgh RRID:CVCL_0159 Experimental models: Organisms/strains Mouse: FoxP3eGFP-Cre-ERT2: Foxp3tm9(EGFP/ cre/ERT2)Ayr The Jackson Laboratory Cat#016961 Mouse: Tim-3fl/fl: B6-Havcr2fl/fl Developed with the Pitt Department of Immunolgy Transgenic and Gene Targeting Core for this study N/A Mouse: FSF-Tim-3: B6-Rosa26flox-stop-floxFlag-Tim-3 Developed for the investigators by GenOway Avery et al. (2018) Mouse: C57BL/6J The Jackson Laboratory Cat#000664 Software and algorithms FlowJo BD Biosciences version 10 Prism GraphPad version 9 FastQC Babraham Bioinformatics version 0.11.7 Cutadapt https://cutadapt.readthedocs.io/en/stable/ version 1.18 HISAT2 http://daehwankimlab.github.io/hisat2/ main/ version 2.1.0 SAMtools http://www.htslib.org/ version 1.9 HTSeq https://htseq.readthedocs.io/en/master/ version 0.11.2 Bioconductor edgeR https://bioconductor.org/packages/ release/bioc/html/edgeR.html version 3.24.1 Enrichr https://maayanlab.cloud/Enrichr/ Kuleshov et al., 2016 Scanpy https://github.com/theislab/scanpy Wolf et al., 2018 Article ll OPEN ACCESS ..
Software:Article Title: Expression of Tim-3 drives phenotypic and functional changes in Treg cells in secondary lymphoid organs and the tumor microenvironment
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies mCD25 BD Biosciences, BioLegend, Tonbo Clone PC61 FoxP3 Invitrogen Clone FJK16S mCD44 BD Biosciences, BioLegend, Tonbo Clone IM7 mCD62L BioLegend, Tonbo Clone MEL-14 mICOS BioLegend Clone 398.4A Ki67 BD Biosciences Clone B56 mCTLA-4 BioLegend Clone UC10-4B9 mCD103 BD Biosciences Clone M290 mNrp-1 BD Biosciences Clone 3E12 mCD39 BioLegend Clone Duha 59 mCD73 BioLegend Clone TY/11.8 mTim-3 BioLegend Clone RMT 3-23 mTim-3 R&D Systems Clone FAB1529 Flag BioLegend Clone L5 mPD-1 BioLegend Clone RMP1-30 mIL-10 BioLegend Clone JES5-16E3 mCD90.2 BD Biosciences, BioLegend Clone 532.1 mCD45.2 BioLegend Clone 104 Helios BioLegend Clone 22F6 mKlrg-1 BioLegend Clone 2F1 mLy6g Tonbo Clone IA8 mGITR eBioscience Clone DTA-1 mCD4 BD Biosciences, BioLegend, Tonbo Clone RM-4-5 mTIGIT BioLegend Clone 1G9 mLAG-3 Invitrogen Clone C9B7W mGARP BioLegend Clone F011-5 phospho-S6 BioLegend Clone A17020B phospho-ERK BioLegend Clone 4B11B69 phospho-Akt BD Biosciences Clone M89-61 phospho-MTOR eBioscience Clone MRRBY phospho-STAT3 BD Biosciences Clone 4 CD16/CD32 (Fc Block) Tonbo Clone 2.4G2 mCD8a BD Biosciences, BioLegend, Tonbo Clone H35-17.2 mCD19 BD Biosciences, BioLegend, Tonbo Clone ID3 mCD11b eBioscience Clone M1/70 mCD3 (purified) BioLegend Clone 2C11 Chemicals, peptides, and recombinant proteins CellTrace Violet Invitrogen Cat#C34571 FoxP3 Staining Kit eBioscience Cat#00-5523-00 GhostDye-Violet510 Tonbo Biosciences Cat#13-0870-T500 RBC lysis buffer eBioscience Cat#00-4333-57 (Continued on next page) e1 Cell Reports 36, 109699, September 14, 2021 .. REAGENT or RESOURCE SOURCE IDENTIFIER Collagenase D Roche Cat#11088866001 DNase I, type IV Sigma-Aldrich Cat#D5025 Hyclone Fetal bovine serum Cytiva Cat#SH30071 Tamoxifen MP Biomedical Cat02156738-CF Deposited data RNA sequencing of Tim-3 Tg Treg and WT Treg Data obtained for this study GEO record GSE155825 single-cell RNA sequencing of HNC tumors Cillo et al. (2020) GEO record GSE139324 Experimental models: Cell lines MC38 tumor line Dario Vignali, Univ. of Pittsburgh RRID:CVCL_B288 B16-F10 tumor line Dario Vignali, Univ. of Pittsburgh RRID:CVCL_0159 Experimental models: Organisms/strains Mouse: FoxP3eGFP-Cre-ERT2: Foxp3tm9(EGFP/ cre/ERT2)Ayr The Jackson Laboratory Cat#016961 Mouse: Tim-3fl/fl: B6-Havcr2fl/fl Developed with the Pitt Department of Immunolgy Transgenic and Gene Targeting Core for this study N/A Mouse: FSF-Tim-3: B6-Rosa26flox-stop-floxFlag-Tim-3 Developed for the investigators by GenOway Avery et al. (2018) Mouse: C57BL/6J The Jackson Laboratory Cat#000664 Software and algorithms FlowJo BD Biosciences version 10 Prism GraphPad version 9 FastQC Babraham Bioinformatics version 0.11.7 Cutadapt https://cutadapt.readthedocs.io/en/stable/ version 1.18 HISAT2 http://daehwankimlab.github.io/hisat2/ main/ version 2.1.0 SAMtools http://www.htslib.org/ version 1.9 HTSeq https://htseq.readthedocs.io/en/master/ version 0.11.2 Bioconductor edgeR https://bioconductor.org/packages/ release/bioc/html/edgeR.html version 3.24.1 Enrichr https://maayanlab.cloud/Enrichr/ Kuleshov et al., 2016 Scanpy https://github.com/theislab/scanpy Wolf et al., 2018 Article ll OPEN ACCESS ..
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