other:
Article Title: Modular pooled discovery of synthetic knockin sequences to program durable cell therapies.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Pierce 16% Formaldehyde (w/v), Methanol-free Thermo Fisher Scientific Cat#28906 Poly-L-glutamic acid Alamanda Polymers Cat#26247-79-0 Poly-L-ornithine solution MilliporeSigma Cat#P4957-50ML Dynabeads Protein A for Immunoprecipitation Invitrogen Cat#10002D Recombinant Human IL-15 GMP Protein, CF 25ug R&D Systems Cat#247-GMP-025 Recombinant Human IL-2 GMP Protein, CF R&D Systems Cat#202-GMP-01M Recombinant Human IL-7 GMP Protein, CF 25ug R&D Systems Cat#BT-007-GMP025 RetroNectin Recombinant Human Fibronectin Fragment Takara Bio Cat#T100B RNAse A, Dnase and protease-free (10mg/mL) Thermo Fisher Scientific Cat#EN0531 Sera-Mag magnetic speedbeads Thermo Fisher Scientific Cat#09-981-123 SPRIselect Beckman Coulter Cat#B23318 tracrRNA Dharmacon Cat#U-002005-1000 TRI Reagent MilliporeSigma Cat#93289-25ML TRIzol Reagent Thermo Fisher Scientific Cat#15596018 X-Vivo 15 Lonza Cat#BE02-060Q Critical commercial assays CellTrace Violet Cell Proliferation Kit, for flow cytometry Thermo Fisher Scientific Cat#C34557 Chromium Single Cell 5’ Reagent Kit, v1 chemistry 10x Genomics Cat#PN-1000166 EasySep Human T Cell Isolation Kit Stemcell Cat#100-0695 EasySep Human TCR Alpha/Beta Depletion Kit Stemcell Cat#17847 eBioscience Foxp3 / Transcription Factor Staining Buffer Set Thermo Fisher Scientific Cat#00-5523-00 FIX & PERM Cell Fixation & Cell Permeabilization Kit Thermo Fisher Scientific Cat#GAS004 LEGENDplex Human CD8/NK Panel (13-plex) with Filter Plate Biolegend Cat#740267 MiniSeq High Output Reagent Kit (150-cycles) Illumina Cat#FC-420-1002 Nextera Chromium i7 Sample Indices N Set A 10x Genomics Cat#PN-3000262 Nextera XT DNA Library Preparation Kit Illumina Cat#FC-131-1096 NextSeq 500/550 High Output Kit v2.5 (75 Cycles) Illumina Cat#20024906 NextSeq 500/550 Mid Output Kit v2.5 (150 Cycles) Illumina Cat#20024904 Ovation RNA-Seq System V2 Tecan Cat#7102-32 Ovation Ultralow V2 DNA-Seq Library Preparation Kit Tecan Cat#0344NB-A01 P3 Primary Cell 96-well Nucleofector Kit (960 RCT) Lonza Cat#V4SP-3960 Phusion High-Fidelity PCR Master Mix with HF Buffer New England Biolabs Cat#M0531L Qubit 1X dsDNA HS Assay Kit Fisher Scientific Cat#Q33231 Deposited data Bulk RNA-seq, combined ATAC-, ChIPand RNA-seq and ModPoKI-Seq datasets This paper GEO: GSE232824 DICE dataset N/A https://dice-database.org/ Bulk RNA-seq Carnevale et al.23 GEO: GSE204862 Experimental models: Cell lines
Article Title: CD8 + T cells promote HIV latency by remodeling CD4 + T cell metabolism to enhance their survival, quiescence, and stemness.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Experimental models: Cell lines ACH-2 cell line HIV reagent program RRID:CVCL_0138 Oligonucleotides HCD3 OUT5 Primer for intHIV on Table S5 Integrated DNA Technologies N/A HCD3 OUT3 Primer for intHIV on Table S5 Integrated DNA Technologies N/A ULF1 Primer for intHIV on Table S5 Integrated DNA Technologies N/A ALU1 Primer for intHIV on Table S5 Integrated DNA Technologies N/A ALU2 Primer for intHIV on Table S5 Integrated DNA Technologies N/A HCD3 IN5 Primer for intHIV on Table S5 Integrated DNA Technologies N/A HCD3 IN3 Primer for intHIV on Table S5 Integrated DNA Technologies N/A LambdaT Primer for intHIV on Table S5 Integrated DNA Technologies N/A UR2 Primer for intHIV on Table S5 Integrated DNA Technologies N/A panCD3_P (HEX) on Table S5 Integrated DNA Technologies N/A UHIV-Taqman (FAM) on Table S5 Integrated DNA Technologies N/A crRNA ß2M-1 position 44715430 on Table S5 Integrated DNA Technologies N/A crRNA ß2M-2 position 44715511 on Table S5 Integrated DNA Technologies N/A Software and algorithms FlowJo v10 BD Bioscience https://www.bdbiosciences.com/en-us/ products/software/flowjo-v10-software Prism 9.0.2 GraphPad Software LLC https://www.graphpad.com/scientific- software/prism/ R version 4.1.2 (2021-11-01) - "Bird Hippie" The R foundation for Statistical Computing https://cran.r-project.org/bin/windows/ base/old/4.1.2/ RStudio 2021.09.0+351 "Ghost Orchid" Release R Studio https://dailies.rstudio.com/version/2021.
Western Blot:Article Title: Canagliflozin impairs T cell effector function via metabolic suppression in autoimmunity.
Article Snippet: Eur. analytical reagent VWR 20624.262 PD-98,059 Merck 513000 PhosphoSafe Extraction Buffer Merck 71296 Pierce Formic Acid, LC-MS Grade ThermoFisher 85178 Pierce Trypsin Protease, MS Grade ThermoFisher 90057 Piericidin A Enzo Life Sciences ALX380235M002 PMA Merck 79346 Puromycin Merck P7255 R162 Merck 5.38098 Rapamycin Merck 553210 Rotenone Merck R8875 Sodium dodecyl sulfate Merck L4509 TGF-b PeproTech Cat#100-21 TMB Substrate Reagent Set BD Biosciences Cat#555214 Triethylammonium bicarbonate buffer Merck T7408 Water, HiPerSolv CHROMANORM for LC-MS, suitable for UPLC/UHPLC instruments VWR 83645.290 (Continued on next page) e2 Cell Metabolism 35, 1132–1146.e1–e9, July 11, 2023 .. REAGENT or RESOURCE SOURCE IDENTIFIER Critical commercial assays Acclaim PepMap 100 Å, 100 mm i.d. x 2cm NanoViper (2pk) - 164564 ThermoFisher 11312263 Acclaim PepMap C18 2um 75um x 500mm NVFS 1200bar - 164942 ThermoFisher 15567530 Acclaim PepMap RSLC C18, 2 mm, 100 Å, 75 mm i.d. x 15 cm - 164534 ThermoFisher 11342013 Amersham ECL Select Western Blotting detection reagent Cytiva RPN2235 CD4+ Effector Memory T cell isolation kit, human Miltenyi 130-094-125 CD4+ T cell isolation kit, human Miltenyi 130-096-533 CD8+ T cell isolation kit, human Miltenyi 130-096-495 CellTrace Violet Cell Proliferation Kit, for flow cytometry ThermoFisher C34557 DC Protein Assay II Bio-Rad 5000112 DRAQ7 Biostatus DR71000 ES791 - EASY-Spray 50cm x 20um Dual ThermoFisher 15176864 ES800\A - EASY-Spray 15 cm x 75 mm ThermoFisher 12886016 / 15988997 Human Granzyme B DuoSet ELISA R&D Systems DY2906 Human IFNg DuoSet ELISA R&D Systems DY285B Human IL-2 DuoSet ELISA R&D Systems DY202 Human IL-4 DuoSet ELISA R&D Systems DY204 Human IL-10 DuoSet ELISA R&D Systems DY217B Human IL-17 DuoSet ELISA R&D Systems DY317 Human IL-21 DuoSet ELISA R&D Systems DY8879 Human TNFa DuoSet ELISA R&D Systems DY210 Immunocult T cell activator StemCell Technologies Cat#10971 Inside Stain Kit Miltenyi 130-090-477 L-Lactate Assay Kit I Eton Bioscience Cat#120001200P Micro BCA Protein Assay Kit ThermoFisher 23235 MitoSOX Red ThermoFisher M36008 MitoTracker Green FM ThermoFisher M7514 Naı̈ve CD4+ T cell isolation kit, human Miltenyi 130-094-131 nCounter Autoimmune Profiling Panel Nanostring XT-CSO-HAIP1-12 nCounter Metabolic Pathways Panel Nanostring XT-CSO-HMP1-12 PepSwift Monolithic Capillary LC Columns - 164584 ThermoFisher 11382263 Pierce Quantitative Fluorometric Peptide Assay ThermoFisher 23290 Restore PLUS Western Blot Stripping buffer ThermoFisher 21063 RNeasy Mini Kit columns Qiagen Cat#74014 SimplyBlue SafeStain ThermoFisher LC6060 TMRE-Mitochondrial Membrane Potential Assay Kit abcam Ab113852 Trifluoroacetic Acid, Optima LC/MS Grade, Fisher Chemical Fisher Scientific 10266617 Trypsin Sequencing Grade, modified Merck 11418025001 Deposited data Raw data for Nanostring nCounter Autoimmune Profiling Panel NCBI Gene Expression Omnibus (GEO) GSE228911; https://www.ncbi.nlm.nih.gov/ geo/query/acc.cgi?acc=GSE228911 Raw data for Nanostring nCounter Metabolic Pathways Panel NCBI Gene Expression Omnibus (GEO) GSE228911; https://www.ncbi.nlm.nih.gov/ geo/query/acc.cgi?acc=GSE228911 (Continued on next page) Cell Metabolism 35, 1132–1146.e1–e9, July 11, 2023 e3 .. REAGENT or RESOURCE SOURCE IDENTIFIER Raw data for Proteomics analysis EMBL-EBI Proteomics Identification Database (PRIDE) Identifier: PXD041523 Experimental models: Cell lines Human: PBMCs from healthy controls (primary) N/A N/A Human: PBMCs from rheumatoid arthritis patients (primary) N/A N/A Human: PBMCs from systemic lupus erythematosus patients (primary) N/A N/A Human: SFMCs from rheumatoid arthritis patients (primary) N/A N/A Software and algorithms ChemStation E.02.02.1431 Agilent https://www.agilent.com/en/product/software- informatics/analytical-software-suite/ chromatography-data-systems/openlabchemstation FlowJo 10.8.0 Tree Star www.flowjo.com GraphPad Prism 9 GraphPad Software, Inc. www.graphpad.com ImageJ ImageJ www.imagej.nih.gov/ij/ Morpheus Broad Institute https://software.broadinstitute.org/morpheus NovoExpress 1.4.1 Agilent https://www.agilent.com/en/product/research- flow-cytometry/flow-cytometry-software/ novocyte-novoexpress-software-1320805 nSolver 4.0 Nanostring www.nanostring.com/ncounterpro Seahorse Wave Software 2.6 Agilent https://www.agilent.com/en/product/cell- analysis/real-time-cell-metabolic-analysis/ xf-software/seahorse-wave-desktopsoftware-740897 TraceFinder 4.1 ThermoFisher https://www.thermofisher.com/uk/en/home/ industrial/mass-spectrometry/liquidchromatography-mass-spectrometry-lc-ms/ lc-ms-software/lc-ms-data-acquisitionsoftware/tracefinder-software.html Other HBSS, no calcium, no magnesium, no phenol red Gibco 14175053 Human plasma-like medium Gibco A4899101 RPMI 1640 Medium, GlutaMAX Supplement Gibco 61870036 RPMI 1640 Medium, no glucose Gibco 11879020 RPMI 1640 Medium, no glutamine Gibco 31870025 Seahorse XF RPMI medium, pH 7.4 Agilent 103576-100 S-Trap mini columns (100 - 300 mg) Protifi CO2-mini-80 SeQuant ZIC-pHILIC, 5 micron, 150x4.6 mm Merck 1.50461.0001
Cell Isolation:Article Title: Canagliflozin impairs T cell effector function via metabolic suppression in autoimmunity.
Article Snippet: Eur. analytical reagent VWR 20624.262 PD-98,059 Merck 513000 PhosphoSafe Extraction Buffer Merck 71296 Pierce Formic Acid, LC-MS Grade ThermoFisher 85178 Pierce Trypsin Protease, MS Grade ThermoFisher 90057 Piericidin A Enzo Life Sciences ALX380235M002 PMA Merck 79346 Puromycin Merck P7255 R162 Merck 5.38098 Rapamycin Merck 553210 Rotenone Merck R8875 Sodium dodecyl sulfate Merck L4509 TGF-b PeproTech Cat#100-21 TMB Substrate Reagent Set BD Biosciences Cat#555214 Triethylammonium bicarbonate buffer Merck T7408 Water, HiPerSolv CHROMANORM for LC-MS, suitable for UPLC/UHPLC instruments VWR 83645.290 (Continued on next page) e2 Cell Metabolism 35, 1132–1146.e1–e9, July 11, 2023 .. REAGENT or RESOURCE SOURCE IDENTIFIER Critical commercial assays Acclaim PepMap 100 Å, 100 mm i.d. x 2cm NanoViper (2pk) - 164564 ThermoFisher 11312263 Acclaim PepMap C18 2um 75um x 500mm NVFS 1200bar - 164942 ThermoFisher 15567530 Acclaim PepMap RSLC C18, 2 mm, 100 Å, 75 mm i.d. x 15 cm - 164534 ThermoFisher 11342013 Amersham ECL Select Western Blotting detection reagent Cytiva RPN2235 CD4+ Effector Memory T cell isolation kit, human Miltenyi 130-094-125 CD4+ T cell isolation kit, human Miltenyi 130-096-533 CD8+ T cell isolation kit, human Miltenyi 130-096-495 CellTrace Violet Cell Proliferation Kit, for flow cytometry ThermoFisher C34557 DC Protein Assay II Bio-Rad 5000112 DRAQ7 Biostatus DR71000 ES791 - EASY-Spray 50cm x 20um Dual ThermoFisher 15176864 ES800\A - EASY-Spray 15 cm x 75 mm ThermoFisher 12886016 / 15988997 Human Granzyme B DuoSet ELISA R&D Systems DY2906 Human IFNg DuoSet ELISA R&D Systems DY285B Human IL-2 DuoSet ELISA R&D Systems DY202 Human IL-4 DuoSet ELISA R&D Systems DY204 Human IL-10 DuoSet ELISA R&D Systems DY217B Human IL-17 DuoSet ELISA R&D Systems DY317 Human IL-21 DuoSet ELISA R&D Systems DY8879 Human TNFa DuoSet ELISA R&D Systems DY210 Immunocult T cell activator StemCell Technologies Cat#10971 Inside Stain Kit Miltenyi 130-090-477 L-Lactate Assay Kit I Eton Bioscience Cat#120001200P Micro BCA Protein Assay Kit ThermoFisher 23235 MitoSOX Red ThermoFisher M36008 MitoTracker Green FM ThermoFisher M7514 Naı̈ve CD4+ T cell isolation kit, human Miltenyi 130-094-131 nCounter Autoimmune Profiling Panel Nanostring XT-CSO-HAIP1-12 nCounter Metabolic Pathways Panel Nanostring XT-CSO-HMP1-12 PepSwift Monolithic Capillary LC Columns - 164584 ThermoFisher 11382263 Pierce Quantitative Fluorometric Peptide Assay ThermoFisher 23290 Restore PLUS Western Blot Stripping buffer ThermoFisher 21063 RNeasy Mini Kit columns Qiagen Cat#74014 SimplyBlue SafeStain ThermoFisher LC6060 TMRE-Mitochondrial Membrane Potential Assay Kit abcam Ab113852 Trifluoroacetic Acid, Optima LC/MS Grade, Fisher Chemical Fisher Scientific 10266617 Trypsin Sequencing Grade, modified Merck 11418025001 Deposited data Raw data for Nanostring nCounter Autoimmune Profiling Panel NCBI Gene Expression Omnibus (GEO) GSE228911; https://www.ncbi.nlm.nih.gov/ geo/query/acc.cgi?acc=GSE228911 Raw data for Nanostring nCounter Metabolic Pathways Panel NCBI Gene Expression Omnibus (GEO) GSE228911; https://www.ncbi.nlm.nih.gov/ geo/query/acc.cgi?acc=GSE228911 (Continued on next page) Cell Metabolism 35, 1132–1146.e1–e9, July 11, 2023 e3 .. REAGENT or RESOURCE SOURCE IDENTIFIER Raw data for Proteomics analysis EMBL-EBI Proteomics Identification Database (PRIDE) Identifier: PXD041523 Experimental models: Cell lines Human: PBMCs from healthy controls (primary) N/A N/A Human: PBMCs from rheumatoid arthritis patients (primary) N/A N/A Human: PBMCs from systemic lupus erythematosus patients (primary) N/A N/A Human: SFMCs from rheumatoid arthritis patients (primary) N/A N/A Software and algorithms ChemStation E.02.02.1431 Agilent https://www.agilent.com/en/product/software- informatics/analytical-software-suite/ chromatography-data-systems/openlabchemstation FlowJo 10.8.0 Tree Star www.flowjo.com GraphPad Prism 9 GraphPad Software, Inc. www.graphpad.com ImageJ ImageJ www.imagej.nih.gov/ij/ Morpheus Broad Institute https://software.broadinstitute.org/morpheus NovoExpress 1.4.1 Agilent https://www.agilent.com/en/product/research- flow-cytometry/flow-cytometry-software/ novocyte-novoexpress-software-1320805 nSolver 4.0 Nanostring www.nanostring.com/ncounterpro Seahorse Wave Software 2.6 Agilent https://www.agilent.com/en/product/cell- analysis/real-time-cell-metabolic-analysis/ xf-software/seahorse-wave-desktopsoftware-740897 TraceFinder 4.1 ThermoFisher https://www.thermofisher.com/uk/en/home/ industrial/mass-spectrometry/liquidchromatography-mass-spectrometry-lc-ms/ lc-ms-software/lc-ms-data-acquisitionsoftware/tracefinder-software.html Other HBSS, no calcium, no magnesium, no phenol red Gibco 14175053 Human plasma-like medium Gibco A4899101 RPMI 1640 Medium, GlutaMAX Supplement Gibco 61870036 RPMI 1640 Medium, no glucose Gibco 11879020 RPMI 1640 Medium, no glutamine Gibco 31870025 Seahorse XF RPMI medium, pH 7.4 Agilent 103576-100 S-Trap mini columns (100 - 300 mg) Protifi CO2-mini-80 SeQuant ZIC-pHILIC, 5 micron, 150x4.6 mm Merck 1.50461.0001
Flow Cytometry:Article Title: Canagliflozin impairs T cell effector function via metabolic suppression in autoimmunity.
Article Snippet: Eur. analytical reagent VWR 20624.262 PD-98,059 Merck 513000 PhosphoSafe Extraction Buffer Merck 71296 Pierce Formic Acid, LC-MS Grade ThermoFisher 85178 Pierce Trypsin Protease, MS Grade ThermoFisher 90057 Piericidin A Enzo Life Sciences ALX380235M002 PMA Merck 79346 Puromycin Merck P7255 R162 Merck 5.38098 Rapamycin Merck 553210 Rotenone Merck R8875 Sodium dodecyl sulfate Merck L4509 TGF-b PeproTech Cat#100-21 TMB Substrate Reagent Set BD Biosciences Cat#555214 Triethylammonium bicarbonate buffer Merck T7408 Water, HiPerSolv CHROMANORM for LC-MS, suitable for UPLC/UHPLC instruments VWR 83645.290 (Continued on next page) e2 Cell Metabolism 35, 1132–1146.e1–e9, July 11, 2023 .. REAGENT or RESOURCE SOURCE IDENTIFIER Critical commercial assays Acclaim PepMap 100 Å, 100 mm i.d. x 2cm NanoViper (2pk) - 164564 ThermoFisher 11312263 Acclaim PepMap C18 2um 75um x 500mm NVFS 1200bar - 164942 ThermoFisher 15567530 Acclaim PepMap RSLC C18, 2 mm, 100 Å, 75 mm i.d. x 15 cm - 164534 ThermoFisher 11342013 Amersham ECL Select Western Blotting detection reagent Cytiva RPN2235 CD4+ Effector Memory T cell isolation kit, human Miltenyi 130-094-125 CD4+ T cell isolation kit, human Miltenyi 130-096-533 CD8+ T cell isolation kit, human Miltenyi 130-096-495 CellTrace Violet Cell Proliferation Kit, for flow cytometry ThermoFisher C34557 DC Protein Assay II Bio-Rad 5000112 DRAQ7 Biostatus DR71000 ES791 - EASY-Spray 50cm x 20um Dual ThermoFisher 15176864 ES800\A - EASY-Spray 15 cm x 75 mm ThermoFisher 12886016 / 15988997 Human Granzyme B DuoSet ELISA R&D Systems DY2906 Human IFNg DuoSet ELISA R&D Systems DY285B Human IL-2 DuoSet ELISA R&D Systems DY202 Human IL-4 DuoSet ELISA R&D Systems DY204 Human IL-10 DuoSet ELISA R&D Systems DY217B Human IL-17 DuoSet ELISA R&D Systems DY317 Human IL-21 DuoSet ELISA R&D Systems DY8879 Human TNFa DuoSet ELISA R&D Systems DY210 Immunocult T cell activator StemCell Technologies Cat#10971 Inside Stain Kit Miltenyi 130-090-477 L-Lactate Assay Kit I Eton Bioscience Cat#120001200P Micro BCA Protein Assay Kit ThermoFisher 23235 MitoSOX Red ThermoFisher M36008 MitoTracker Green FM ThermoFisher M7514 Naı̈ve CD4+ T cell isolation kit, human Miltenyi 130-094-131 nCounter Autoimmune Profiling Panel Nanostring XT-CSO-HAIP1-12 nCounter Metabolic Pathways Panel Nanostring XT-CSO-HMP1-12 PepSwift Monolithic Capillary LC Columns - 164584 ThermoFisher 11382263 Pierce Quantitative Fluorometric Peptide Assay ThermoFisher 23290 Restore PLUS Western Blot Stripping buffer ThermoFisher 21063 RNeasy Mini Kit columns Qiagen Cat#74014 SimplyBlue SafeStain ThermoFisher LC6060 TMRE-Mitochondrial Membrane Potential Assay Kit abcam Ab113852 Trifluoroacetic Acid, Optima LC/MS Grade, Fisher Chemical Fisher Scientific 10266617 Trypsin Sequencing Grade, modified Merck 11418025001 Deposited data Raw data for Nanostring nCounter Autoimmune Profiling Panel NCBI Gene Expression Omnibus (GEO) GSE228911; https://www.ncbi.nlm.nih.gov/ geo/query/acc.cgi?acc=GSE228911 Raw data for Nanostring nCounter Metabolic Pathways Panel NCBI Gene Expression Omnibus (GEO) GSE228911; https://www.ncbi.nlm.nih.gov/ geo/query/acc.cgi?acc=GSE228911 (Continued on next page) Cell Metabolism 35, 1132–1146.e1–e9, July 11, 2023 e3 .. REAGENT or RESOURCE SOURCE IDENTIFIER Raw data for Proteomics analysis EMBL-EBI Proteomics Identification Database (PRIDE) Identifier: PXD041523 Experimental models: Cell lines Human: PBMCs from healthy controls (primary) N/A N/A Human: PBMCs from rheumatoid arthritis patients (primary) N/A N/A Human: PBMCs from systemic lupus erythematosus patients (primary) N/A N/A Human: SFMCs from rheumatoid arthritis patients (primary) N/A N/A Software and algorithms ChemStation E.02.02.1431 Agilent https://www.agilent.com/en/product/software- informatics/analytical-software-suite/ chromatography-data-systems/openlabchemstation FlowJo 10.8.0 Tree Star www.flowjo.com GraphPad Prism 9 GraphPad Software, Inc. www.graphpad.com ImageJ ImageJ www.imagej.nih.gov/ij/ Morpheus Broad Institute https://software.broadinstitute.org/morpheus NovoExpress 1.4.1 Agilent https://www.agilent.com/en/product/research- flow-cytometry/flow-cytometry-software/ novocyte-novoexpress-software-1320805 nSolver 4.0 Nanostring www.nanostring.com/ncounterpro Seahorse Wave Software 2.6 Agilent https://www.agilent.com/en/product/cell- analysis/real-time-cell-metabolic-analysis/ xf-software/seahorse-wave-desktopsoftware-740897 TraceFinder 4.1 ThermoFisher https://www.thermofisher.com/uk/en/home/ industrial/mass-spectrometry/liquidchromatography-mass-spectrometry-lc-ms/ lc-ms-software/lc-ms-data-acquisitionsoftware/tracefinder-software.html Other HBSS, no calcium, no magnesium, no phenol red Gibco 14175053 Human plasma-like medium Gibco A4899101 RPMI 1640 Medium, GlutaMAX Supplement Gibco 61870036 RPMI 1640 Medium, no glucose Gibco 11879020 RPMI 1640 Medium, no glutamine Gibco 31870025 Seahorse XF RPMI medium, pH 7.4 Agilent 103576-100 S-Trap mini columns (100 - 300 mg) Protifi CO2-mini-80 SeQuant ZIC-pHILIC, 5 micron, 150x4.6 mm Merck 1.50461.0001
Article Title: Targeting stromal cell sialylation reverses T cell-mediated immunosuppression in the tumor microenvironment.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Mouse anti-human CD105 BioLegend RRID:AB_755960 Cat: 323208 Rabbit anti-human CD3 Roche RRID:AB_2335978 Cat: 790-4341 Mouse anti-human CD4 BioLegend RRID:AB_314082 or RRID:AB_314086 Cat: 300514 or 300518 Mouse anti-human CD44 BioLegend RRID:AB_2716000 Cat: 338815 Mouse anti-human CD45 BioLegend RRID:AB_2566370 Cat: 368510 Mouse anti-human CD73 BioLegend RRID:AB_2561809 or RRID:AB_2298698 Cat: 344016 or 344004 Mouse anti-human CD8 BioLegend RRID:AB_1953244 or RRID:AB_2564624 Cat: 344706 or 344732 Mouse anti-human CD8 Agilent Technologies RRID:AB_2075537 Cat: M710301-2 Mouse anti-human CD90 BioLegend RRID:AB_893431 Cat: 328114 Mouse anti-human CD326 (EpCAM) BioLegend RRID:AB_756082 Cat: 324208 Mouse anti-human HLA-DR BioLegend RRID:AB_493588 Cat: 307616 Mouse anti-human CD279 (PD-1) BioLegend RRID:AB_2562256 Cat: 329932 Mouse anti-human CD140a (PDGFR-a) BioLegend RRID:AB_2565596 Cat: 323507 Mouse anti-human CD140b (PDGFR-b) BioLegend RRID:AB_2162787 Cat:323608 Rat anti-human Podoplanin BioLegend RRID:AB_2750289 Cat: 337029 Anti-human CD328 (Siglec-7) Miltenyi Biotec RRID:AB_2657535 Cat: 130-101-016 Anti-human CD329 (Siglec-9) Miltenyi Biotec RRID:AB_2657547 Cat: 130-107-607 Rat anti-mouse CD73 BioLegend RRID:AB_11218786 Cat: 127210 Rat anti-mouse CD105 BioLegend RRID:AB_2277914 Cat: 120414 Rat anti-mouse CD90.2 (Thy1.2) BioLegend RRID:AB_313179 Cat: 105308 Rat anti-mouse CD25 BioLegend RRID:AB_312847 Cat: 101904 Armenian hamster anti-mouse CD3 BioLegend RRID:AB_312671 Cat: 100306 Rat anti-mouse CD4 BioLegend RRID:AB_312707 Cat: 100422 Rat anti-mouse CD8 BioLegend RRID:AB_2562100 Cat: 100748 (Continued on next page) 20 Cell Reports 42, 112475, May 30, 2023 .. REAGENT or RESOURCE SOURCE IDENTIFIER Rat anti-mouse Siglec-E BioLegend RRID:AB_2566169 Cat: 677104 Mouse anti-mouse/human Granzyme B BioLegend RRID:AB_2687032 Cat: 372208 Biological samples Colorectal cancer patient-derived tumor sections Galway University Hospital N/A Chemicals, peptides, and recombinant proteins 3FaxNeu5Ac Bio-Techne Cat: 5760/10 APC AffiniPure F(ab’)2 Fragment Goat Anti-Human IgG, Fcg Fragment Specific (min X Bov,Ms,Rb Sr Prot) Jackson ImmunoResearch Cat: 109-096-170 ChromPure Human IgG, Fc fragment Jackson ImmunoResearch Cat: 009-000-008 E-610-1A sialidase Palleon Pharmaceuticals N/A Human FGF-basic PeproTech Cat: 100-18B Biotinylated Sambucus Nigra Lectin (SNA-I, EBL) Vector Laboratories Cat: B-1305-2 Biotinylated Maackia Amurensis Lectin II (MAL-II) Vector Laboratories Cat: B-1265-1 Biotinylated Wheat Germ Agglutinin (WGA) Vector Laboratories Cat: B-1025-5 Biotinylated Galanthus Nivalis Lectin (GNA) Vector Laboratories Cat: B-1245-2 Biotinylated Concanavalin A (Con A) Vector Laboratories Cat: B-1005-5 Recombinant Human Siglec-7/CD328 Fc Chimera Protein Bio-Techne Cat: 1138-SL-050 Recombinant Human Siglec-9/CD329 Fc Chimera Protein Bio-Techne Cat: 1139-SL-050 Recombinant Mouse Siglec-E Fc Chimera Protein Bio-Techne Cat: 5806-SL-050 FITC Streptavidin BioLegend Cat: 405201 PE Streptavidin BioLegend Cat: 405204 APC Streptavidin BioLegend Cat: 405207 Critical commercial assays CellTrace Violet Cell Proliferation Kit, for flow cytometry ThermoFisher Scientific Cat: C34557 DynabeadsTM Human T-Activator CD3/CD28 for T Cell Expansion and Activation ThermoFisher Scientific Cat: 11131D DynabeadsTM Mouse T-Activator CD3/CD28 for T-Cell Expansion and Activation ThermoFisher Scientific Cat: 11452D SYTOX Blue Dead Cell Stain ThermoFisher Scientific Cat: S34857 SYTOX AADvanced Dead Cell Stain Kit ThermoFisher Scientific Cat: S10349 Tumor Dissociation Kit, human Miltenyi Biotec Cat: 130-095-929 Tumor Dissociation Kit, mouse Miltenyi Biotec Cat: 130-096-730 Deposited data Raw and analyzed data This paper GEO: GSE229054 Experimental models: Cell lines CT26 American Type Culture Collection (ATCC) RRID:CVCL_7256 Cat: CRL-2638 HCT116 American Type Culture Collection (ATCC) Cat:CCL-247 HT29 American Type Culture Collection (ATCC) RRID:CVCL_0320 Cat: HTB-38 Experimental models: Organisms/strains Balb/c Envigo Laboratories Balb/cAnNCrl C57BL6 Envigo Laboratories C57BL/6N C57BL/KaLwRij Lab of Prof. Karin Vanderkerken N/A (Continued on next page) Cell Reports 42, 112475, May 30, 2023 21 .. REAGENT or RESOURCE SOURCE IDENTIFIER Software and algorithms BioRender Biorender.com RRID:SCR_018361 FlowJo Version 10 Tree Star Inc. RRID:SCR_008520 GraphPad Prisim Version 9 GraphPad RRID:SCR_002798 Partek Genomics Suite Partek.com RRID:SCR_011860 QuPath Qupath.github.io RRID:SCR_018257
Article Title: Combined TLR2/TLR4 activation equip non-mucosal dendritic cells to prime Th1 cells with gut tropism
Article Snippet: iScience Article ll OPEN ACCESS Combined TLR2/TLR4 activation equip nonmucosal dendritic cells to prime Th1 cells with gut tropism Sara Zúquete, Mariana Ferreira, Inês L.S.. Delgado, ..., Luı́s Graça, Alexandre Leitão, Afonso P. Basto alexandre@fmv.ulisboa.pt (A.L.) abasto@fmv.ulisboa.pt (A.P.B.). Highlights Combined TLR2/TLR4 activation induces ALDH activity in non-mucosal DCs CD4+ T cells primed by TLR2/TLR4 activated DCs co-express IFN-g and a4b7/CCR9 CD4+ T cells thus primed show an enhanced in vivo tropism to the gut Subcutaneous immunization with TLR2/ TLR4 agonists primes gutassociated Th1 cells Zúquete et al., iScience 27, 111232 December 20, 2024a 2024 The Author(s).
Article Title: Prolonged T-cell activation and long COVID symptoms independently associate with severe COVID-19 at 3 months
Article Snippet: Commercial assay or kit , Pan T Cell Isolation Kit, human , Miltenyi Biotec , Cat# 130-096-535 , . .. Commercial assay or kit , CellTrace Violet Cell Proliferation Kit, for flow cytometry , Thermo Fisher Scientific , Cat# C34557 , . .. Commercial assay or kit , eBioscience Foxp3/Transcription factor fixation/permeabilisation buffer , Invitrogen , Cat# 00-5523-00 , .
DC Protein Assay:Article Title: Canagliflozin impairs T cell effector function via metabolic suppression in autoimmunity.
Article Snippet: Eur. analytical reagent VWR 20624.262 PD-98,059 Merck 513000 PhosphoSafe Extraction Buffer Merck 71296 Pierce Formic Acid, LC-MS Grade ThermoFisher 85178 Pierce Trypsin Protease, MS Grade ThermoFisher 90057 Piericidin A Enzo Life Sciences ALX380235M002 PMA Merck 79346 Puromycin Merck P7255 R162 Merck 5.38098 Rapamycin Merck 553210 Rotenone Merck R8875 Sodium dodecyl sulfate Merck L4509 TGF-b PeproTech Cat#100-21 TMB Substrate Reagent Set BD Biosciences Cat#555214 Triethylammonium bicarbonate buffer Merck T7408 Water, HiPerSolv CHROMANORM for LC-MS, suitable for UPLC/UHPLC instruments VWR 83645.290 (Continued on next page) e2 Cell Metabolism 35, 1132–1146.e1–e9, July 11, 2023 .. REAGENT or RESOURCE SOURCE IDENTIFIER Critical commercial assays Acclaim PepMap 100 Å, 100 mm i.d. x 2cm NanoViper (2pk) - 164564 ThermoFisher 11312263 Acclaim PepMap C18 2um 75um x 500mm NVFS 1200bar - 164942 ThermoFisher 15567530 Acclaim PepMap RSLC C18, 2 mm, 100 Å, 75 mm i.d. x 15 cm - 164534 ThermoFisher 11342013 Amersham ECL Select Western Blotting detection reagent Cytiva RPN2235 CD4+ Effector Memory T cell isolation kit, human Miltenyi 130-094-125 CD4+ T cell isolation kit, human Miltenyi 130-096-533 CD8+ T cell isolation kit, human Miltenyi 130-096-495 CellTrace Violet Cell Proliferation Kit, for flow cytometry ThermoFisher C34557 DC Protein Assay II Bio-Rad 5000112 DRAQ7 Biostatus DR71000 ES791 - EASY-Spray 50cm x 20um Dual ThermoFisher 15176864 ES800\A - EASY-Spray 15 cm x 75 mm ThermoFisher 12886016 / 15988997 Human Granzyme B DuoSet ELISA R&D Systems DY2906 Human IFNg DuoSet ELISA R&D Systems DY285B Human IL-2 DuoSet ELISA R&D Systems DY202 Human IL-4 DuoSet ELISA R&D Systems DY204 Human IL-10 DuoSet ELISA R&D Systems DY217B Human IL-17 DuoSet ELISA R&D Systems DY317 Human IL-21 DuoSet ELISA R&D Systems DY8879 Human TNFa DuoSet ELISA R&D Systems DY210 Immunocult T cell activator StemCell Technologies Cat#10971 Inside Stain Kit Miltenyi 130-090-477 L-Lactate Assay Kit I Eton Bioscience Cat#120001200P Micro BCA Protein Assay Kit ThermoFisher 23235 MitoSOX Red ThermoFisher M36008 MitoTracker Green FM ThermoFisher M7514 Naı̈ve CD4+ T cell isolation kit, human Miltenyi 130-094-131 nCounter Autoimmune Profiling Panel Nanostring XT-CSO-HAIP1-12 nCounter Metabolic Pathways Panel Nanostring XT-CSO-HMP1-12 PepSwift Monolithic Capillary LC Columns - 164584 ThermoFisher 11382263 Pierce Quantitative Fluorometric Peptide Assay ThermoFisher 23290 Restore PLUS Western Blot Stripping buffer ThermoFisher 21063 RNeasy Mini Kit columns Qiagen Cat#74014 SimplyBlue SafeStain ThermoFisher LC6060 TMRE-Mitochondrial Membrane Potential Assay Kit abcam Ab113852 Trifluoroacetic Acid, Optima LC/MS Grade, Fisher Chemical Fisher Scientific 10266617 Trypsin Sequencing Grade, modified Merck 11418025001 Deposited data Raw data for Nanostring nCounter Autoimmune Profiling Panel NCBI Gene Expression Omnibus (GEO) GSE228911; https://www.ncbi.nlm.nih.gov/ geo/query/acc.cgi?acc=GSE228911 Raw data for Nanostring nCounter Metabolic Pathways Panel NCBI Gene Expression Omnibus (GEO) GSE228911; https://www.ncbi.nlm.nih.gov/ geo/query/acc.cgi?acc=GSE228911 (Continued on next page) Cell Metabolism 35, 1132–1146.e1–e9, July 11, 2023 e3 .. REAGENT or RESOURCE SOURCE IDENTIFIER Raw data for Proteomics analysis EMBL-EBI Proteomics Identification Database (PRIDE) Identifier: PXD041523 Experimental models: Cell lines Human: PBMCs from healthy controls (primary) N/A N/A Human: PBMCs from rheumatoid arthritis patients (primary) N/A N/A Human: PBMCs from systemic lupus erythematosus patients (primary) N/A N/A Human: SFMCs from rheumatoid arthritis patients (primary) N/A N/A Software and algorithms ChemStation E.02.02.1431 Agilent https://www.agilent.com/en/product/software- informatics/analytical-software-suite/ chromatography-data-systems/openlabchemstation FlowJo 10.8.0 Tree Star www.flowjo.com GraphPad Prism 9 GraphPad Software, Inc. www.graphpad.com ImageJ ImageJ www.imagej.nih.gov/ij/ Morpheus Broad Institute https://software.broadinstitute.org/morpheus NovoExpress 1.4.1 Agilent https://www.agilent.com/en/product/research- flow-cytometry/flow-cytometry-software/ novocyte-novoexpress-software-1320805 nSolver 4.0 Nanostring www.nanostring.com/ncounterpro Seahorse Wave Software 2.6 Agilent https://www.agilent.com/en/product/cell- analysis/real-time-cell-metabolic-analysis/ xf-software/seahorse-wave-desktopsoftware-740897 TraceFinder 4.1 ThermoFisher https://www.thermofisher.com/uk/en/home/ industrial/mass-spectrometry/liquidchromatography-mass-spectrometry-lc-ms/ lc-ms-software/lc-ms-data-acquisitionsoftware/tracefinder-software.html Other HBSS, no calcium, no magnesium, no phenol red Gibco 14175053 Human plasma-like medium Gibco A4899101 RPMI 1640 Medium, GlutaMAX Supplement Gibco 61870036 RPMI 1640 Medium, no glucose Gibco 11879020 RPMI 1640 Medium, no glutamine Gibco 31870025 Seahorse XF RPMI medium, pH 7.4 Agilent 103576-100 S-Trap mini columns (100 - 300 mg) Protifi CO2-mini-80 SeQuant ZIC-pHILIC, 5 micron, 150x4.6 mm Merck 1.50461.0001
Enzyme-linked Immunosorbent Assay:Article Title: Canagliflozin impairs T cell effector function via metabolic suppression in autoimmunity.
Article Snippet: Eur. analytical reagent VWR 20624.262 PD-98,059 Merck 513000 PhosphoSafe Extraction Buffer Merck 71296 Pierce Formic Acid, LC-MS Grade ThermoFisher 85178 Pierce Trypsin Protease, MS Grade ThermoFisher 90057 Piericidin A Enzo Life Sciences ALX380235M002 PMA Merck 79346 Puromycin Merck P7255 R162 Merck 5.38098 Rapamycin Merck 553210 Rotenone Merck R8875 Sodium dodecyl sulfate Merck L4509 TGF-b PeproTech Cat#100-21 TMB Substrate Reagent Set BD Biosciences Cat#555214 Triethylammonium bicarbonate buffer Merck T7408 Water, HiPerSolv CHROMANORM for LC-MS, suitable for UPLC/UHPLC instruments VWR 83645.290 (Continued on next page) e2 Cell Metabolism 35, 1132–1146.e1–e9, July 11, 2023 .. REAGENT or RESOURCE SOURCE IDENTIFIER Critical commercial assays Acclaim PepMap 100 Å, 100 mm i.d. x 2cm NanoViper (2pk) - 164564 ThermoFisher 11312263 Acclaim PepMap C18 2um 75um x 500mm NVFS 1200bar - 164942 ThermoFisher 15567530 Acclaim PepMap RSLC C18, 2 mm, 100 Å, 75 mm i.d. x 15 cm - 164534 ThermoFisher 11342013 Amersham ECL Select Western Blotting detection reagent Cytiva RPN2235 CD4+ Effector Memory T cell isolation kit, human Miltenyi 130-094-125 CD4+ T cell isolation kit, human Miltenyi 130-096-533 CD8+ T cell isolation kit, human Miltenyi 130-096-495 CellTrace Violet Cell Proliferation Kit, for flow cytometry ThermoFisher C34557 DC Protein Assay II Bio-Rad 5000112 DRAQ7 Biostatus DR71000 ES791 - EASY-Spray 50cm x 20um Dual ThermoFisher 15176864 ES800\A - EASY-Spray 15 cm x 75 mm ThermoFisher 12886016 / 15988997 Human Granzyme B DuoSet ELISA R&D Systems DY2906 Human IFNg DuoSet ELISA R&D Systems DY285B Human IL-2 DuoSet ELISA R&D Systems DY202 Human IL-4 DuoSet ELISA R&D Systems DY204 Human IL-10 DuoSet ELISA R&D Systems DY217B Human IL-17 DuoSet ELISA R&D Systems DY317 Human IL-21 DuoSet ELISA R&D Systems DY8879 Human TNFa DuoSet ELISA R&D Systems DY210 Immunocult T cell activator StemCell Technologies Cat#10971 Inside Stain Kit Miltenyi 130-090-477 L-Lactate Assay Kit I Eton Bioscience Cat#120001200P Micro BCA Protein Assay Kit ThermoFisher 23235 MitoSOX Red ThermoFisher M36008 MitoTracker Green FM ThermoFisher M7514 Naı̈ve CD4+ T cell isolation kit, human Miltenyi 130-094-131 nCounter Autoimmune Profiling Panel Nanostring XT-CSO-HAIP1-12 nCounter Metabolic Pathways Panel Nanostring XT-CSO-HMP1-12 PepSwift Monolithic Capillary LC Columns - 164584 ThermoFisher 11382263 Pierce Quantitative Fluorometric Peptide Assay ThermoFisher 23290 Restore PLUS Western Blot Stripping buffer ThermoFisher 21063 RNeasy Mini Kit columns Qiagen Cat#74014 SimplyBlue SafeStain ThermoFisher LC6060 TMRE-Mitochondrial Membrane Potential Assay Kit abcam Ab113852 Trifluoroacetic Acid, Optima LC/MS Grade, Fisher Chemical Fisher Scientific 10266617 Trypsin Sequencing Grade, modified Merck 11418025001 Deposited data Raw data for Nanostring nCounter Autoimmune Profiling Panel NCBI Gene Expression Omnibus (GEO) GSE228911; https://www.ncbi.nlm.nih.gov/ geo/query/acc.cgi?acc=GSE228911 Raw data for Nanostring nCounter Metabolic Pathways Panel NCBI Gene Expression Omnibus (GEO) GSE228911; https://www.ncbi.nlm.nih.gov/ geo/query/acc.cgi?acc=GSE228911 (Continued on next page) Cell Metabolism 35, 1132–1146.e1–e9, July 11, 2023 e3 .. REAGENT or RESOURCE SOURCE IDENTIFIER Raw data for Proteomics analysis EMBL-EBI Proteomics Identification Database (PRIDE) Identifier: PXD041523 Experimental models: Cell lines Human: PBMCs from healthy controls (primary) N/A N/A Human: PBMCs from rheumatoid arthritis patients (primary) N/A N/A Human: PBMCs from systemic lupus erythematosus patients (primary) N/A N/A Human: SFMCs from rheumatoid arthritis patients (primary) N/A N/A Software and algorithms ChemStation E.02.02.1431 Agilent https://www.agilent.com/en/product/software- informatics/analytical-software-suite/ chromatography-data-systems/openlabchemstation FlowJo 10.8.0 Tree Star www.flowjo.com GraphPad Prism 9 GraphPad Software, Inc. www.graphpad.com ImageJ ImageJ www.imagej.nih.gov/ij/ Morpheus Broad Institute https://software.broadinstitute.org/morpheus NovoExpress 1.4.1 Agilent https://www.agilent.com/en/product/research- flow-cytometry/flow-cytometry-software/ novocyte-novoexpress-software-1320805 nSolver 4.0 Nanostring www.nanostring.com/ncounterpro Seahorse Wave Software 2.6 Agilent https://www.agilent.com/en/product/cell- analysis/real-time-cell-metabolic-analysis/ xf-software/seahorse-wave-desktopsoftware-740897 TraceFinder 4.1 ThermoFisher https://www.thermofisher.com/uk/en/home/ industrial/mass-spectrometry/liquidchromatography-mass-spectrometry-lc-ms/ lc-ms-software/lc-ms-data-acquisitionsoftware/tracefinder-software.html Other HBSS, no calcium, no magnesium, no phenol red Gibco 14175053 Human plasma-like medium Gibco A4899101 RPMI 1640 Medium, GlutaMAX Supplement Gibco 61870036 RPMI 1640 Medium, no glucose Gibco 11879020 RPMI 1640 Medium, no glutamine Gibco 31870025 Seahorse XF RPMI medium, pH 7.4 Agilent 103576-100 S-Trap mini columns (100 - 300 mg) Protifi CO2-mini-80 SeQuant ZIC-pHILIC, 5 micron, 150x4.6 mm Merck 1.50461.0001
Staining:Article Title: Canagliflozin impairs T cell effector function via metabolic suppression in autoimmunity.
Article Snippet: Eur. analytical reagent VWR 20624.262 PD-98,059 Merck 513000 PhosphoSafe Extraction Buffer Merck 71296 Pierce Formic Acid, LC-MS Grade ThermoFisher 85178 Pierce Trypsin Protease, MS Grade ThermoFisher 90057 Piericidin A Enzo Life Sciences ALX380235M002 PMA Merck 79346 Puromycin Merck P7255 R162 Merck 5.38098 Rapamycin Merck 553210 Rotenone Merck R8875 Sodium dodecyl sulfate Merck L4509 TGF-b PeproTech Cat#100-21 TMB Substrate Reagent Set BD Biosciences Cat#555214 Triethylammonium bicarbonate buffer Merck T7408 Water, HiPerSolv CHROMANORM for LC-MS, suitable for UPLC/UHPLC instruments VWR 83645.290 (Continued on next page) e2 Cell Metabolism 35, 1132–1146.e1–e9, July 11, 2023 .. REAGENT or RESOURCE SOURCE IDENTIFIER Critical commercial assays Acclaim PepMap 100 Å, 100 mm i.d. x 2cm NanoViper (2pk) - 164564 ThermoFisher 11312263 Acclaim PepMap C18 2um 75um x 500mm NVFS 1200bar - 164942 ThermoFisher 15567530 Acclaim PepMap RSLC C18, 2 mm, 100 Å, 75 mm i.d. x 15 cm - 164534 ThermoFisher 11342013 Amersham ECL Select Western Blotting detection reagent Cytiva RPN2235 CD4+ Effector Memory T cell isolation kit, human Miltenyi 130-094-125 CD4+ T cell isolation kit, human Miltenyi 130-096-533 CD8+ T cell isolation kit, human Miltenyi 130-096-495 CellTrace Violet Cell Proliferation Kit, for flow cytometry ThermoFisher C34557 DC Protein Assay II Bio-Rad 5000112 DRAQ7 Biostatus DR71000 ES791 - EASY-Spray 50cm x 20um Dual ThermoFisher 15176864 ES800\A - EASY-Spray 15 cm x 75 mm ThermoFisher 12886016 / 15988997 Human Granzyme B DuoSet ELISA R&D Systems DY2906 Human IFNg DuoSet ELISA R&D Systems DY285B Human IL-2 DuoSet ELISA R&D Systems DY202 Human IL-4 DuoSet ELISA R&D Systems DY204 Human IL-10 DuoSet ELISA R&D Systems DY217B Human IL-17 DuoSet ELISA R&D Systems DY317 Human IL-21 DuoSet ELISA R&D Systems DY8879 Human TNFa DuoSet ELISA R&D Systems DY210 Immunocult T cell activator StemCell Technologies Cat#10971 Inside Stain Kit Miltenyi 130-090-477 L-Lactate Assay Kit I Eton Bioscience Cat#120001200P Micro BCA Protein Assay Kit ThermoFisher 23235 MitoSOX Red ThermoFisher M36008 MitoTracker Green FM ThermoFisher M7514 Naı̈ve CD4+ T cell isolation kit, human Miltenyi 130-094-131 nCounter Autoimmune Profiling Panel Nanostring XT-CSO-HAIP1-12 nCounter Metabolic Pathways Panel Nanostring XT-CSO-HMP1-12 PepSwift Monolithic Capillary LC Columns - 164584 ThermoFisher 11382263 Pierce Quantitative Fluorometric Peptide Assay ThermoFisher 23290 Restore PLUS Western Blot Stripping buffer ThermoFisher 21063 RNeasy Mini Kit columns Qiagen Cat#74014 SimplyBlue SafeStain ThermoFisher LC6060 TMRE-Mitochondrial Membrane Potential Assay Kit abcam Ab113852 Trifluoroacetic Acid, Optima LC/MS Grade, Fisher Chemical Fisher Scientific 10266617 Trypsin Sequencing Grade, modified Merck 11418025001 Deposited data Raw data for Nanostring nCounter Autoimmune Profiling Panel NCBI Gene Expression Omnibus (GEO) GSE228911; https://www.ncbi.nlm.nih.gov/ geo/query/acc.cgi?acc=GSE228911 Raw data for Nanostring nCounter Metabolic Pathways Panel NCBI Gene Expression Omnibus (GEO) GSE228911; https://www.ncbi.nlm.nih.gov/ geo/query/acc.cgi?acc=GSE228911 (Continued on next page) Cell Metabolism 35, 1132–1146.e1–e9, July 11, 2023 e3 .. REAGENT or RESOURCE SOURCE IDENTIFIER Raw data for Proteomics analysis EMBL-EBI Proteomics Identification Database (PRIDE) Identifier: PXD041523 Experimental models: Cell lines Human: PBMCs from healthy controls (primary) N/A N/A Human: PBMCs from rheumatoid arthritis patients (primary) N/A N/A Human: PBMCs from systemic lupus erythematosus patients (primary) N/A N/A Human: SFMCs from rheumatoid arthritis patients (primary) N/A N/A Software and algorithms ChemStation E.02.02.1431 Agilent https://www.agilent.com/en/product/software- informatics/analytical-software-suite/ chromatography-data-systems/openlabchemstation FlowJo 10.8.0 Tree Star www.flowjo.com GraphPad Prism 9 GraphPad Software, Inc. www.graphpad.com ImageJ ImageJ www.imagej.nih.gov/ij/ Morpheus Broad Institute https://software.broadinstitute.org/morpheus NovoExpress 1.4.1 Agilent https://www.agilent.com/en/product/research- flow-cytometry/flow-cytometry-software/ novocyte-novoexpress-software-1320805 nSolver 4.0 Nanostring www.nanostring.com/ncounterpro Seahorse Wave Software 2.6 Agilent https://www.agilent.com/en/product/cell- analysis/real-time-cell-metabolic-analysis/ xf-software/seahorse-wave-desktopsoftware-740897 TraceFinder 4.1 ThermoFisher https://www.thermofisher.com/uk/en/home/ industrial/mass-spectrometry/liquidchromatography-mass-spectrometry-lc-ms/ lc-ms-software/lc-ms-data-acquisitionsoftware/tracefinder-software.html Other HBSS, no calcium, no magnesium, no phenol red Gibco 14175053 Human plasma-like medium Gibco A4899101 RPMI 1640 Medium, GlutaMAX Supplement Gibco 61870036 RPMI 1640 Medium, no glucose Gibco 11879020 RPMI 1640 Medium, no glutamine Gibco 31870025 Seahorse XF RPMI medium, pH 7.4 Agilent 103576-100 S-Trap mini columns (100 - 300 mg) Protifi CO2-mini-80 SeQuant ZIC-pHILIC, 5 micron, 150x4.6 mm Merck 1.50461.0001
Article Title: Targeting stromal cell sialylation reverses T cell-mediated immunosuppression in the tumor microenvironment.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Mouse anti-human CD105 BioLegend RRID:AB_755960 Cat: 323208 Rabbit anti-human CD3 Roche RRID:AB_2335978 Cat: 790-4341 Mouse anti-human CD4 BioLegend RRID:AB_314082 or RRID:AB_314086 Cat: 300514 or 300518 Mouse anti-human CD44 BioLegend RRID:AB_2716000 Cat: 338815 Mouse anti-human CD45 BioLegend RRID:AB_2566370 Cat: 368510 Mouse anti-human CD73 BioLegend RRID:AB_2561809 or RRID:AB_2298698 Cat: 344016 or 344004 Mouse anti-human CD8 BioLegend RRID:AB_1953244 or RRID:AB_2564624 Cat: 344706 or 344732 Mouse anti-human CD8 Agilent Technologies RRID:AB_2075537 Cat: M710301-2 Mouse anti-human CD90 BioLegend RRID:AB_893431 Cat: 328114 Mouse anti-human CD326 (EpCAM) BioLegend RRID:AB_756082 Cat: 324208 Mouse anti-human HLA-DR BioLegend RRID:AB_493588 Cat: 307616 Mouse anti-human CD279 (PD-1) BioLegend RRID:AB_2562256 Cat: 329932 Mouse anti-human CD140a (PDGFR-a) BioLegend RRID:AB_2565596 Cat: 323507 Mouse anti-human CD140b (PDGFR-b) BioLegend RRID:AB_2162787 Cat:323608 Rat anti-human Podoplanin BioLegend RRID:AB_2750289 Cat: 337029 Anti-human CD328 (Siglec-7) Miltenyi Biotec RRID:AB_2657535 Cat: 130-101-016 Anti-human CD329 (Siglec-9) Miltenyi Biotec RRID:AB_2657547 Cat: 130-107-607 Rat anti-mouse CD73 BioLegend RRID:AB_11218786 Cat: 127210 Rat anti-mouse CD105 BioLegend RRID:AB_2277914 Cat: 120414 Rat anti-mouse CD90.2 (Thy1.2) BioLegend RRID:AB_313179 Cat: 105308 Rat anti-mouse CD25 BioLegend RRID:AB_312847 Cat: 101904 Armenian hamster anti-mouse CD3 BioLegend RRID:AB_312671 Cat: 100306 Rat anti-mouse CD4 BioLegend RRID:AB_312707 Cat: 100422 Rat anti-mouse CD8 BioLegend RRID:AB_2562100 Cat: 100748 (Continued on next page) 20 Cell Reports 42, 112475, May 30, 2023 .. REAGENT or RESOURCE SOURCE IDENTIFIER Rat anti-mouse Siglec-E BioLegend RRID:AB_2566169 Cat: 677104 Mouse anti-mouse/human Granzyme B BioLegend RRID:AB_2687032 Cat: 372208 Biological samples Colorectal cancer patient-derived tumor sections Galway University Hospital N/A Chemicals, peptides, and recombinant proteins 3FaxNeu5Ac Bio-Techne Cat: 5760/10 APC AffiniPure F(ab’)2 Fragment Goat Anti-Human IgG, Fcg Fragment Specific (min X Bov,Ms,Rb Sr Prot) Jackson ImmunoResearch Cat: 109-096-170 ChromPure Human IgG, Fc fragment Jackson ImmunoResearch Cat: 009-000-008 E-610-1A sialidase Palleon Pharmaceuticals N/A Human FGF-basic PeproTech Cat: 100-18B Biotinylated Sambucus Nigra Lectin (SNA-I, EBL) Vector Laboratories Cat: B-1305-2 Biotinylated Maackia Amurensis Lectin II (MAL-II) Vector Laboratories Cat: B-1265-1 Biotinylated Wheat Germ Agglutinin (WGA) Vector Laboratories Cat: B-1025-5 Biotinylated Galanthus Nivalis Lectin (GNA) Vector Laboratories Cat: B-1245-2 Biotinylated Concanavalin A (Con A) Vector Laboratories Cat: B-1005-5 Recombinant Human Siglec-7/CD328 Fc Chimera Protein Bio-Techne Cat: 1138-SL-050 Recombinant Human Siglec-9/CD329 Fc Chimera Protein Bio-Techne Cat: 1139-SL-050 Recombinant Mouse Siglec-E Fc Chimera Protein Bio-Techne Cat: 5806-SL-050 FITC Streptavidin BioLegend Cat: 405201 PE Streptavidin BioLegend Cat: 405204 APC Streptavidin BioLegend Cat: 405207 Critical commercial assays CellTrace Violet Cell Proliferation Kit, for flow cytometry ThermoFisher Scientific Cat: C34557 DynabeadsTM Human T-Activator CD3/CD28 for T Cell Expansion and Activation ThermoFisher Scientific Cat: 11131D DynabeadsTM Mouse T-Activator CD3/CD28 for T-Cell Expansion and Activation ThermoFisher Scientific Cat: 11452D SYTOX Blue Dead Cell Stain ThermoFisher Scientific Cat: S34857 SYTOX AADvanced Dead Cell Stain Kit ThermoFisher Scientific Cat: S10349 Tumor Dissociation Kit, human Miltenyi Biotec Cat: 130-095-929 Tumor Dissociation Kit, mouse Miltenyi Biotec Cat: 130-096-730 Deposited data Raw and analyzed data This paper GEO: GSE229054 Experimental models: Cell lines CT26 American Type Culture Collection (ATCC) RRID:CVCL_7256 Cat: CRL-2638 HCT116 American Type Culture Collection (ATCC) Cat:CCL-247 HT29 American Type Culture Collection (ATCC) RRID:CVCL_0320 Cat: HTB-38 Experimental models: Organisms/strains Balb/c Envigo Laboratories Balb/cAnNCrl C57BL6 Envigo Laboratories C57BL/6N C57BL/KaLwRij Lab of Prof. Karin Vanderkerken N/A (Continued on next page) Cell Reports 42, 112475, May 30, 2023 21 .. REAGENT or RESOURCE SOURCE IDENTIFIER Software and algorithms BioRender Biorender.com RRID:SCR_018361 FlowJo Version 10 Tree Star Inc. RRID:SCR_008520 GraphPad Prisim Version 9 GraphPad RRID:SCR_002798 Partek Genomics Suite Partek.com RRID:SCR_011860 QuPath Qupath.github.io RRID:SCR_018257
Article Title: Combined TLR2/TLR4 activation equip non-mucosal dendritic cells to prime Th1 cells with gut tropism
Article Snippet: iScience Article ll OPEN ACCESS Combined TLR2/TLR4 activation equip nonmucosal dendritic cells to prime Th1 cells with gut tropism Sara Zúquete, Mariana Ferreira, Inês L.S.. Delgado, ..., Luı́s Graça, Alexandre Leitão, Afonso P. Basto alexandre@fmv.ulisboa.pt (A.L.) abasto@fmv.ulisboa.pt (A.P.B.). Highlights Combined TLR2/TLR4 activation induces ALDH activity in non-mucosal DCs CD4+ T cells primed by TLR2/TLR4 activated DCs co-express IFN-g and a4b7/CCR9 CD4+ T cells thus primed show an enhanced in vivo tropism to the gut Subcutaneous immunization with TLR2/ TLR4 agonists primes gutassociated Th1 cells Zúquete et al., iScience 27, 111232 December 20, 2024a 2024 The Author(s).
Bicinchoninic Acid Protein Assay:Article Title: Canagliflozin impairs T cell effector function via metabolic suppression in autoimmunity.
Article Snippet: Eur. analytical reagent VWR 20624.262 PD-98,059 Merck 513000 PhosphoSafe Extraction Buffer Merck 71296 Pierce Formic Acid, LC-MS Grade ThermoFisher 85178 Pierce Trypsin Protease, MS Grade ThermoFisher 90057 Piericidin A Enzo Life Sciences ALX380235M002 PMA Merck 79346 Puromycin Merck P7255 R162 Merck 5.38098 Rapamycin Merck 553210 Rotenone Merck R8875 Sodium dodecyl sulfate Merck L4509 TGF-b PeproTech Cat#100-21 TMB Substrate Reagent Set BD Biosciences Cat#555214 Triethylammonium bicarbonate buffer Merck T7408 Water, HiPerSolv CHROMANORM for LC-MS, suitable for UPLC/UHPLC instruments VWR 83645.290 (Continued on next page) e2 Cell Metabolism 35, 1132–1146.e1–e9, July 11, 2023 .. REAGENT or RESOURCE SOURCE IDENTIFIER Critical commercial assays Acclaim PepMap 100 Å, 100 mm i.d. x 2cm NanoViper (2pk) - 164564 ThermoFisher 11312263 Acclaim PepMap C18 2um 75um x 500mm NVFS 1200bar - 164942 ThermoFisher 15567530 Acclaim PepMap RSLC C18, 2 mm, 100 Å, 75 mm i.d. x 15 cm - 164534 ThermoFisher 11342013 Amersham ECL Select Western Blotting detection reagent Cytiva RPN2235 CD4+ Effector Memory T cell isolation kit, human Miltenyi 130-094-125 CD4+ T cell isolation kit, human Miltenyi 130-096-533 CD8+ T cell isolation kit, human Miltenyi 130-096-495 CellTrace Violet Cell Proliferation Kit, for flow cytometry ThermoFisher C34557 DC Protein Assay II Bio-Rad 5000112 DRAQ7 Biostatus DR71000 ES791 - EASY-Spray 50cm x 20um Dual ThermoFisher 15176864 ES800\A - EASY-Spray 15 cm x 75 mm ThermoFisher 12886016 / 15988997 Human Granzyme B DuoSet ELISA R&D Systems DY2906 Human IFNg DuoSet ELISA R&D Systems DY285B Human IL-2 DuoSet ELISA R&D Systems DY202 Human IL-4 DuoSet ELISA R&D Systems DY204 Human IL-10 DuoSet ELISA R&D Systems DY217B Human IL-17 DuoSet ELISA R&D Systems DY317 Human IL-21 DuoSet ELISA R&D Systems DY8879 Human TNFa DuoSet ELISA R&D Systems DY210 Immunocult T cell activator StemCell Technologies Cat#10971 Inside Stain Kit Miltenyi 130-090-477 L-Lactate Assay Kit I Eton Bioscience Cat#120001200P Micro BCA Protein Assay Kit ThermoFisher 23235 MitoSOX Red ThermoFisher M36008 MitoTracker Green FM ThermoFisher M7514 Naı̈ve CD4+ T cell isolation kit, human Miltenyi 130-094-131 nCounter Autoimmune Profiling Panel Nanostring XT-CSO-HAIP1-12 nCounter Metabolic Pathways Panel Nanostring XT-CSO-HMP1-12 PepSwift Monolithic Capillary LC Columns - 164584 ThermoFisher 11382263 Pierce Quantitative Fluorometric Peptide Assay ThermoFisher 23290 Restore PLUS Western Blot Stripping buffer ThermoFisher 21063 RNeasy Mini Kit columns Qiagen Cat#74014 SimplyBlue SafeStain ThermoFisher LC6060 TMRE-Mitochondrial Membrane Potential Assay Kit abcam Ab113852 Trifluoroacetic Acid, Optima LC/MS Grade, Fisher Chemical Fisher Scientific 10266617 Trypsin Sequencing Grade, modified Merck 11418025001 Deposited data Raw data for Nanostring nCounter Autoimmune Profiling Panel NCBI Gene Expression Omnibus (GEO) GSE228911; https://www.ncbi.nlm.nih.gov/ geo/query/acc.cgi?acc=GSE228911 Raw data for Nanostring nCounter Metabolic Pathways Panel NCBI Gene Expression Omnibus (GEO) GSE228911; https://www.ncbi.nlm.nih.gov/ geo/query/acc.cgi?acc=GSE228911 (Continued on next page) Cell Metabolism 35, 1132–1146.e1–e9, July 11, 2023 e3 .. REAGENT or RESOURCE SOURCE IDENTIFIER Raw data for Proteomics analysis EMBL-EBI Proteomics Identification Database (PRIDE) Identifier: PXD041523 Experimental models: Cell lines Human: PBMCs from healthy controls (primary) N/A N/A Human: PBMCs from rheumatoid arthritis patients (primary) N/A N/A Human: PBMCs from systemic lupus erythematosus patients (primary) N/A N/A Human: SFMCs from rheumatoid arthritis patients (primary) N/A N/A Software and algorithms ChemStation E.02.02.1431 Agilent https://www.agilent.com/en/product/software- informatics/analytical-software-suite/ chromatography-data-systems/openlabchemstation FlowJo 10.8.0 Tree Star www.flowjo.com GraphPad Prism 9 GraphPad Software, Inc. www.graphpad.com ImageJ ImageJ www.imagej.nih.gov/ij/ Morpheus Broad Institute https://software.broadinstitute.org/morpheus NovoExpress 1.4.1 Agilent https://www.agilent.com/en/product/research- flow-cytometry/flow-cytometry-software/ novocyte-novoexpress-software-1320805 nSolver 4.0 Nanostring www.nanostring.com/ncounterpro Seahorse Wave Software 2.6 Agilent https://www.agilent.com/en/product/cell- analysis/real-time-cell-metabolic-analysis/ xf-software/seahorse-wave-desktopsoftware-740897 TraceFinder 4.1 ThermoFisher https://www.thermofisher.com/uk/en/home/ industrial/mass-spectrometry/liquidchromatography-mass-spectrometry-lc-ms/ lc-ms-software/lc-ms-data-acquisitionsoftware/tracefinder-software.html Other HBSS, no calcium, no magnesium, no phenol red Gibco 14175053 Human plasma-like medium Gibco A4899101 RPMI 1640 Medium, GlutaMAX Supplement Gibco 61870036 RPMI 1640 Medium, no glucose Gibco 11879020 RPMI 1640 Medium, no glutamine Gibco 31870025 Seahorse XF RPMI medium, pH 7.4 Agilent 103576-100 S-Trap mini columns (100 - 300 mg) Protifi CO2-mini-80 SeQuant ZIC-pHILIC, 5 micron, 150x4.6 mm Merck 1.50461.0001
Stripping:Article Title: Canagliflozin impairs T cell effector function via metabolic suppression in autoimmunity.
Article Snippet: Eur. analytical reagent VWR 20624.262 PD-98,059 Merck 513000 PhosphoSafe Extraction Buffer Merck 71296 Pierce Formic Acid, LC-MS Grade ThermoFisher 85178 Pierce Trypsin Protease, MS Grade ThermoFisher 90057 Piericidin A Enzo Life Sciences ALX380235M002 PMA Merck 79346 Puromycin Merck P7255 R162 Merck 5.38098 Rapamycin Merck 553210 Rotenone Merck R8875 Sodium dodecyl sulfate Merck L4509 TGF-b PeproTech Cat#100-21 TMB Substrate Reagent Set BD Biosciences Cat#555214 Triethylammonium bicarbonate buffer Merck T7408 Water, HiPerSolv CHROMANORM for LC-MS, suitable for UPLC/UHPLC instruments VWR 83645.290 (Continued on next page) e2 Cell Metabolism 35, 1132–1146.e1–e9, July 11, 2023 .. REAGENT or RESOURCE SOURCE IDENTIFIER Critical commercial assays Acclaim PepMap 100 Å, 100 mm i.d. x 2cm NanoViper (2pk) - 164564 ThermoFisher 11312263 Acclaim PepMap C18 2um 75um x 500mm NVFS 1200bar - 164942 ThermoFisher 15567530 Acclaim PepMap RSLC C18, 2 mm, 100 Å, 75 mm i.d. x 15 cm - 164534 ThermoFisher 11342013 Amersham ECL Select Western Blotting detection reagent Cytiva RPN2235 CD4+ Effector Memory T cell isolation kit, human Miltenyi 130-094-125 CD4+ T cell isolation kit, human Miltenyi 130-096-533 CD8+ T cell isolation kit, human Miltenyi 130-096-495 CellTrace Violet Cell Proliferation Kit, for flow cytometry ThermoFisher C34557 DC Protein Assay II Bio-Rad 5000112 DRAQ7 Biostatus DR71000 ES791 - EASY-Spray 50cm x 20um Dual ThermoFisher 15176864 ES800\A - EASY-Spray 15 cm x 75 mm ThermoFisher 12886016 / 15988997 Human Granzyme B DuoSet ELISA R&D Systems DY2906 Human IFNg DuoSet ELISA R&D Systems DY285B Human IL-2 DuoSet ELISA R&D Systems DY202 Human IL-4 DuoSet ELISA R&D Systems DY204 Human IL-10 DuoSet ELISA R&D Systems DY217B Human IL-17 DuoSet ELISA R&D Systems DY317 Human IL-21 DuoSet ELISA R&D Systems DY8879 Human TNFa DuoSet ELISA R&D Systems DY210 Immunocult T cell activator StemCell Technologies Cat#10971 Inside Stain Kit Miltenyi 130-090-477 L-Lactate Assay Kit I Eton Bioscience Cat#120001200P Micro BCA Protein Assay Kit ThermoFisher 23235 MitoSOX Red ThermoFisher M36008 MitoTracker Green FM ThermoFisher M7514 Naı̈ve CD4+ T cell isolation kit, human Miltenyi 130-094-131 nCounter Autoimmune Profiling Panel Nanostring XT-CSO-HAIP1-12 nCounter Metabolic Pathways Panel Nanostring XT-CSO-HMP1-12 PepSwift Monolithic Capillary LC Columns - 164584 ThermoFisher 11382263 Pierce Quantitative Fluorometric Peptide Assay ThermoFisher 23290 Restore PLUS Western Blot Stripping buffer ThermoFisher 21063 RNeasy Mini Kit columns Qiagen Cat#74014 SimplyBlue SafeStain ThermoFisher LC6060 TMRE-Mitochondrial Membrane Potential Assay Kit abcam Ab113852 Trifluoroacetic Acid, Optima LC/MS Grade, Fisher Chemical Fisher Scientific 10266617 Trypsin Sequencing Grade, modified Merck 11418025001 Deposited data Raw data for Nanostring nCounter Autoimmune Profiling Panel NCBI Gene Expression Omnibus (GEO) GSE228911; https://www.ncbi.nlm.nih.gov/ geo/query/acc.cgi?acc=GSE228911 Raw data for Nanostring nCounter Metabolic Pathways Panel NCBI Gene Expression Omnibus (GEO) GSE228911; https://www.ncbi.nlm.nih.gov/ geo/query/acc.cgi?acc=GSE228911 (Continued on next page) Cell Metabolism 35, 1132–1146.e1–e9, July 11, 2023 e3 .. REAGENT or RESOURCE SOURCE IDENTIFIER Raw data for Proteomics analysis EMBL-EBI Proteomics Identification Database (PRIDE) Identifier: PXD041523 Experimental models: Cell lines Human: PBMCs from healthy controls (primary) N/A N/A Human: PBMCs from rheumatoid arthritis patients (primary) N/A N/A Human: PBMCs from systemic lupus erythematosus patients (primary) N/A N/A Human: SFMCs from rheumatoid arthritis patients (primary) N/A N/A Software and algorithms ChemStation E.02.02.1431 Agilent https://www.agilent.com/en/product/software- informatics/analytical-software-suite/ chromatography-data-systems/openlabchemstation FlowJo 10.8.0 Tree Star www.flowjo.com GraphPad Prism 9 GraphPad Software, Inc. www.graphpad.com ImageJ ImageJ www.imagej.nih.gov/ij/ Morpheus Broad Institute https://software.broadinstitute.org/morpheus NovoExpress 1.4.1 Agilent https://www.agilent.com/en/product/research- flow-cytometry/flow-cytometry-software/ novocyte-novoexpress-software-1320805 nSolver 4.0 Nanostring www.nanostring.com/ncounterpro Seahorse Wave Software 2.6 Agilent https://www.agilent.com/en/product/cell- analysis/real-time-cell-metabolic-analysis/ xf-software/seahorse-wave-desktopsoftware-740897 TraceFinder 4.1 ThermoFisher https://www.thermofisher.com/uk/en/home/ industrial/mass-spectrometry/liquidchromatography-mass-spectrometry-lc-ms/ lc-ms-software/lc-ms-data-acquisitionsoftware/tracefinder-software.html Other HBSS, no calcium, no magnesium, no phenol red Gibco 14175053 Human plasma-like medium Gibco A4899101 RPMI 1640 Medium, GlutaMAX Supplement Gibco 61870036 RPMI 1640 Medium, no glucose Gibco 11879020 RPMI 1640 Medium, no glutamine Gibco 31870025 Seahorse XF RPMI medium, pH 7.4 Agilent 103576-100 S-Trap mini columns (100 - 300 mg) Protifi CO2-mini-80 SeQuant ZIC-pHILIC, 5 micron, 150x4.6 mm Merck 1.50461.0001
Membrane:Article Title: Canagliflozin impairs T cell effector function via metabolic suppression in autoimmunity.
Article Snippet: Eur. analytical reagent VWR 20624.262 PD-98,059 Merck 513000 PhosphoSafe Extraction Buffer Merck 71296 Pierce Formic Acid, LC-MS Grade ThermoFisher 85178 Pierce Trypsin Protease, MS Grade ThermoFisher 90057 Piericidin A Enzo Life Sciences ALX380235M002 PMA Merck 79346 Puromycin Merck P7255 R162 Merck 5.38098 Rapamycin Merck 553210 Rotenone Merck R8875 Sodium dodecyl sulfate Merck L4509 TGF-b PeproTech Cat#100-21 TMB Substrate Reagent Set BD Biosciences Cat#555214 Triethylammonium bicarbonate buffer Merck T7408 Water, HiPerSolv CHROMANORM for LC-MS, suitable for UPLC/UHPLC instruments VWR 83645.290 (Continued on next page) e2 Cell Metabolism 35, 1132–1146.e1–e9, July 11, 2023 .. REAGENT or RESOURCE SOURCE IDENTIFIER Critical commercial assays Acclaim PepMap 100 Å, 100 mm i.d. x 2cm NanoViper (2pk) - 164564 ThermoFisher 11312263 Acclaim PepMap C18 2um 75um x 500mm NVFS 1200bar - 164942 ThermoFisher 15567530 Acclaim PepMap RSLC C18, 2 mm, 100 Å, 75 mm i.d. x 15 cm - 164534 ThermoFisher 11342013 Amersham ECL Select Western Blotting detection reagent Cytiva RPN2235 CD4+ Effector Memory T cell isolation kit, human Miltenyi 130-094-125 CD4+ T cell isolation kit, human Miltenyi 130-096-533 CD8+ T cell isolation kit, human Miltenyi 130-096-495 CellTrace Violet Cell Proliferation Kit, for flow cytometry ThermoFisher C34557 DC Protein Assay II Bio-Rad 5000112 DRAQ7 Biostatus DR71000 ES791 - EASY-Spray 50cm x 20um Dual ThermoFisher 15176864 ES800\A - EASY-Spray 15 cm x 75 mm ThermoFisher 12886016 / 15988997 Human Granzyme B DuoSet ELISA R&D Systems DY2906 Human IFNg DuoSet ELISA R&D Systems DY285B Human IL-2 DuoSet ELISA R&D Systems DY202 Human IL-4 DuoSet ELISA R&D Systems DY204 Human IL-10 DuoSet ELISA R&D Systems DY217B Human IL-17 DuoSet ELISA R&D Systems DY317 Human IL-21 DuoSet ELISA R&D Systems DY8879 Human TNFa DuoSet ELISA R&D Systems DY210 Immunocult T cell activator StemCell Technologies Cat#10971 Inside Stain Kit Miltenyi 130-090-477 L-Lactate Assay Kit I Eton Bioscience Cat#120001200P Micro BCA Protein Assay Kit ThermoFisher 23235 MitoSOX Red ThermoFisher M36008 MitoTracker Green FM ThermoFisher M7514 Naı̈ve CD4+ T cell isolation kit, human Miltenyi 130-094-131 nCounter Autoimmune Profiling Panel Nanostring XT-CSO-HAIP1-12 nCounter Metabolic Pathways Panel Nanostring XT-CSO-HMP1-12 PepSwift Monolithic Capillary LC Columns - 164584 ThermoFisher 11382263 Pierce Quantitative Fluorometric Peptide Assay ThermoFisher 23290 Restore PLUS Western Blot Stripping buffer ThermoFisher 21063 RNeasy Mini Kit columns Qiagen Cat#74014 SimplyBlue SafeStain ThermoFisher LC6060 TMRE-Mitochondrial Membrane Potential Assay Kit abcam Ab113852 Trifluoroacetic Acid, Optima LC/MS Grade, Fisher Chemical Fisher Scientific 10266617 Trypsin Sequencing Grade, modified Merck 11418025001 Deposited data Raw data for Nanostring nCounter Autoimmune Profiling Panel NCBI Gene Expression Omnibus (GEO) GSE228911; https://www.ncbi.nlm.nih.gov/ geo/query/acc.cgi?acc=GSE228911 Raw data for Nanostring nCounter Metabolic Pathways Panel NCBI Gene Expression Omnibus (GEO) GSE228911; https://www.ncbi.nlm.nih.gov/ geo/query/acc.cgi?acc=GSE228911 (Continued on next page) Cell Metabolism 35, 1132–1146.e1–e9, July 11, 2023 e3 .. REAGENT or RESOURCE SOURCE IDENTIFIER Raw data for Proteomics analysis EMBL-EBI Proteomics Identification Database (PRIDE) Identifier: PXD041523 Experimental models: Cell lines Human: PBMCs from healthy controls (primary) N/A N/A Human: PBMCs from rheumatoid arthritis patients (primary) N/A N/A Human: PBMCs from systemic lupus erythematosus patients (primary) N/A N/A Human: SFMCs from rheumatoid arthritis patients (primary) N/A N/A Software and algorithms ChemStation E.02.02.1431 Agilent https://www.agilent.com/en/product/software- informatics/analytical-software-suite/ chromatography-data-systems/openlabchemstation FlowJo 10.8.0 Tree Star www.flowjo.com GraphPad Prism 9 GraphPad Software, Inc. www.graphpad.com ImageJ ImageJ www.imagej.nih.gov/ij/ Morpheus Broad Institute https://software.broadinstitute.org/morpheus NovoExpress 1.4.1 Agilent https://www.agilent.com/en/product/research- flow-cytometry/flow-cytometry-software/ novocyte-novoexpress-software-1320805 nSolver 4.0 Nanostring www.nanostring.com/ncounterpro Seahorse Wave Software 2.6 Agilent https://www.agilent.com/en/product/cell- analysis/real-time-cell-metabolic-analysis/ xf-software/seahorse-wave-desktopsoftware-740897 TraceFinder 4.1 ThermoFisher https://www.thermofisher.com/uk/en/home/ industrial/mass-spectrometry/liquidchromatography-mass-spectrometry-lc-ms/ lc-ms-software/lc-ms-data-acquisitionsoftware/tracefinder-software.html Other HBSS, no calcium, no magnesium, no phenol red Gibco 14175053 Human plasma-like medium Gibco A4899101 RPMI 1640 Medium, GlutaMAX Supplement Gibco 61870036 RPMI 1640 Medium, no glucose Gibco 11879020 RPMI 1640 Medium, no glutamine Gibco 31870025 Seahorse XF RPMI medium, pH 7.4 Agilent 103576-100 S-Trap mini columns (100 - 300 mg) Protifi CO2-mini-80 SeQuant ZIC-pHILIC, 5 micron, 150x4.6 mm Merck 1.50461.0001
Sequencing:Article Title: Canagliflozin impairs T cell effector function via metabolic suppression in autoimmunity.
Article Snippet: Eur. analytical reagent VWR 20624.262 PD-98,059 Merck 513000 PhosphoSafe Extraction Buffer Merck 71296 Pierce Formic Acid, LC-MS Grade ThermoFisher 85178 Pierce Trypsin Protease, MS Grade ThermoFisher 90057 Piericidin A Enzo Life Sciences ALX380235M002 PMA Merck 79346 Puromycin Merck P7255 R162 Merck 5.38098 Rapamycin Merck 553210 Rotenone Merck R8875 Sodium dodecyl sulfate Merck L4509 TGF-b PeproTech Cat#100-21 TMB Substrate Reagent Set BD Biosciences Cat#555214 Triethylammonium bicarbonate buffer Merck T7408 Water, HiPerSolv CHROMANORM for LC-MS, suitable for UPLC/UHPLC instruments VWR 83645.290 (Continued on next page) e2 Cell Metabolism 35, 1132–1146.e1–e9, July 11, 2023 .. REAGENT or RESOURCE SOURCE IDENTIFIER Critical commercial assays Acclaim PepMap 100 Å, 100 mm i.d. x 2cm NanoViper (2pk) - 164564 ThermoFisher 11312263 Acclaim PepMap C18 2um 75um x 500mm NVFS 1200bar - 164942 ThermoFisher 15567530 Acclaim PepMap RSLC C18, 2 mm, 100 Å, 75 mm i.d. x 15 cm - 164534 ThermoFisher 11342013 Amersham ECL Select Western Blotting detection reagent Cytiva RPN2235 CD4+ Effector Memory T cell isolation kit, human Miltenyi 130-094-125 CD4+ T cell isolation kit, human Miltenyi 130-096-533 CD8+ T cell isolation kit, human Miltenyi 130-096-495 CellTrace Violet Cell Proliferation Kit, for flow cytometry ThermoFisher C34557 DC Protein Assay II Bio-Rad 5000112 DRAQ7 Biostatus DR71000 ES791 - EASY-Spray 50cm x 20um Dual ThermoFisher 15176864 ES800\A - EASY-Spray 15 cm x 75 mm ThermoFisher 12886016 / 15988997 Human Granzyme B DuoSet ELISA R&D Systems DY2906 Human IFNg DuoSet ELISA R&D Systems DY285B Human IL-2 DuoSet ELISA R&D Systems DY202 Human IL-4 DuoSet ELISA R&D Systems DY204 Human IL-10 DuoSet ELISA R&D Systems DY217B Human IL-17 DuoSet ELISA R&D Systems DY317 Human IL-21 DuoSet ELISA R&D Systems DY8879 Human TNFa DuoSet ELISA R&D Systems DY210 Immunocult T cell activator StemCell Technologies Cat#10971 Inside Stain Kit Miltenyi 130-090-477 L-Lactate Assay Kit I Eton Bioscience Cat#120001200P Micro BCA Protein Assay Kit ThermoFisher 23235 MitoSOX Red ThermoFisher M36008 MitoTracker Green FM ThermoFisher M7514 Naı̈ve CD4+ T cell isolation kit, human Miltenyi 130-094-131 nCounter Autoimmune Profiling Panel Nanostring XT-CSO-HAIP1-12 nCounter Metabolic Pathways Panel Nanostring XT-CSO-HMP1-12 PepSwift Monolithic Capillary LC Columns - 164584 ThermoFisher 11382263 Pierce Quantitative Fluorometric Peptide Assay ThermoFisher 23290 Restore PLUS Western Blot Stripping buffer ThermoFisher 21063 RNeasy Mini Kit columns Qiagen Cat#74014 SimplyBlue SafeStain ThermoFisher LC6060 TMRE-Mitochondrial Membrane Potential Assay Kit abcam Ab113852 Trifluoroacetic Acid, Optima LC/MS Grade, Fisher Chemical Fisher Scientific 10266617 Trypsin Sequencing Grade, modified Merck 11418025001 Deposited data Raw data for Nanostring nCounter Autoimmune Profiling Panel NCBI Gene Expression Omnibus (GEO) GSE228911; https://www.ncbi.nlm.nih.gov/ geo/query/acc.cgi?acc=GSE228911 Raw data for Nanostring nCounter Metabolic Pathways Panel NCBI Gene Expression Omnibus (GEO) GSE228911; https://www.ncbi.nlm.nih.gov/ geo/query/acc.cgi?acc=GSE228911 (Continued on next page) Cell Metabolism 35, 1132–1146.e1–e9, July 11, 2023 e3 .. REAGENT or RESOURCE SOURCE IDENTIFIER Raw data for Proteomics analysis EMBL-EBI Proteomics Identification Database (PRIDE) Identifier: PXD041523 Experimental models: Cell lines Human: PBMCs from healthy controls (primary) N/A N/A Human: PBMCs from rheumatoid arthritis patients (primary) N/A N/A Human: PBMCs from systemic lupus erythematosus patients (primary) N/A N/A Human: SFMCs from rheumatoid arthritis patients (primary) N/A N/A Software and algorithms ChemStation E.02.02.1431 Agilent https://www.agilent.com/en/product/software- informatics/analytical-software-suite/ chromatography-data-systems/openlabchemstation FlowJo 10.8.0 Tree Star www.flowjo.com GraphPad Prism 9 GraphPad Software, Inc. www.graphpad.com ImageJ ImageJ www.imagej.nih.gov/ij/ Morpheus Broad Institute https://software.broadinstitute.org/morpheus NovoExpress 1.4.1 Agilent https://www.agilent.com/en/product/research- flow-cytometry/flow-cytometry-software/ novocyte-novoexpress-software-1320805 nSolver 4.0 Nanostring www.nanostring.com/ncounterpro Seahorse Wave Software 2.6 Agilent https://www.agilent.com/en/product/cell- analysis/real-time-cell-metabolic-analysis/ xf-software/seahorse-wave-desktopsoftware-740897 TraceFinder 4.1 ThermoFisher https://www.thermofisher.com/uk/en/home/ industrial/mass-spectrometry/liquidchromatography-mass-spectrometry-lc-ms/ lc-ms-software/lc-ms-data-acquisitionsoftware/tracefinder-software.html Other HBSS, no calcium, no magnesium, no phenol red Gibco 14175053 Human plasma-like medium Gibco A4899101 RPMI 1640 Medium, GlutaMAX Supplement Gibco 61870036 RPMI 1640 Medium, no glucose Gibco 11879020 RPMI 1640 Medium, no glutamine Gibco 31870025 Seahorse XF RPMI medium, pH 7.4 Agilent 103576-100 S-Trap mini columns (100 - 300 mg) Protifi CO2-mini-80 SeQuant ZIC-pHILIC, 5 micron, 150x4.6 mm Merck 1.50461.0001
Modification:Article Title: Canagliflozin impairs T cell effector function via metabolic suppression in autoimmunity.
Article Snippet: Eur. analytical reagent VWR 20624.262 PD-98,059 Merck 513000 PhosphoSafe Extraction Buffer Merck 71296 Pierce Formic Acid, LC-MS Grade ThermoFisher 85178 Pierce Trypsin Protease, MS Grade ThermoFisher 90057 Piericidin A Enzo Life Sciences ALX380235M002 PMA Merck 79346 Puromycin Merck P7255 R162 Merck 5.38098 Rapamycin Merck 553210 Rotenone Merck R8875 Sodium dodecyl sulfate Merck L4509 TGF-b PeproTech Cat#100-21 TMB Substrate Reagent Set BD Biosciences Cat#555214 Triethylammonium bicarbonate buffer Merck T7408 Water, HiPerSolv CHROMANORM for LC-MS, suitable for UPLC/UHPLC instruments VWR 83645.290 (Continued on next page) e2 Cell Metabolism 35, 1132–1146.e1–e9, July 11, 2023 .. REAGENT or RESOURCE SOURCE IDENTIFIER Critical commercial assays Acclaim PepMap 100 Å, 100 mm i.d. x 2cm NanoViper (2pk) - 164564 ThermoFisher 11312263 Acclaim PepMap C18 2um 75um x 500mm NVFS 1200bar - 164942 ThermoFisher 15567530 Acclaim PepMap RSLC C18, 2 mm, 100 Å, 75 mm i.d. x 15 cm - 164534 ThermoFisher 11342013 Amersham ECL Select Western Blotting detection reagent Cytiva RPN2235 CD4+ Effector Memory T cell isolation kit, human Miltenyi 130-094-125 CD4+ T cell isolation kit, human Miltenyi 130-096-533 CD8+ T cell isolation kit, human Miltenyi 130-096-495 CellTrace Violet Cell Proliferation Kit, for flow cytometry ThermoFisher C34557 DC Protein Assay II Bio-Rad 5000112 DRAQ7 Biostatus DR71000 ES791 - EASY-Spray 50cm x 20um Dual ThermoFisher 15176864 ES800\A - EASY-Spray 15 cm x 75 mm ThermoFisher 12886016 / 15988997 Human Granzyme B DuoSet ELISA R&D Systems DY2906 Human IFNg DuoSet ELISA R&D Systems DY285B Human IL-2 DuoSet ELISA R&D Systems DY202 Human IL-4 DuoSet ELISA R&D Systems DY204 Human IL-10 DuoSet ELISA R&D Systems DY217B Human IL-17 DuoSet ELISA R&D Systems DY317 Human IL-21 DuoSet ELISA R&D Systems DY8879 Human TNFa DuoSet ELISA R&D Systems DY210 Immunocult T cell activator StemCell Technologies Cat#10971 Inside Stain Kit Miltenyi 130-090-477 L-Lactate Assay Kit I Eton Bioscience Cat#120001200P Micro BCA Protein Assay Kit ThermoFisher 23235 MitoSOX Red ThermoFisher M36008 MitoTracker Green FM ThermoFisher M7514 Naı̈ve CD4+ T cell isolation kit, human Miltenyi 130-094-131 nCounter Autoimmune Profiling Panel Nanostring XT-CSO-HAIP1-12 nCounter Metabolic Pathways Panel Nanostring XT-CSO-HMP1-12 PepSwift Monolithic Capillary LC Columns - 164584 ThermoFisher 11382263 Pierce Quantitative Fluorometric Peptide Assay ThermoFisher 23290 Restore PLUS Western Blot Stripping buffer ThermoFisher 21063 RNeasy Mini Kit columns Qiagen Cat#74014 SimplyBlue SafeStain ThermoFisher LC6060 TMRE-Mitochondrial Membrane Potential Assay Kit abcam Ab113852 Trifluoroacetic Acid, Optima LC/MS Grade, Fisher Chemical Fisher Scientific 10266617 Trypsin Sequencing Grade, modified Merck 11418025001 Deposited data Raw data for Nanostring nCounter Autoimmune Profiling Panel NCBI Gene Expression Omnibus (GEO) GSE228911; https://www.ncbi.nlm.nih.gov/ geo/query/acc.cgi?acc=GSE228911 Raw data for Nanostring nCounter Metabolic Pathways Panel NCBI Gene Expression Omnibus (GEO) GSE228911; https://www.ncbi.nlm.nih.gov/ geo/query/acc.cgi?acc=GSE228911 (Continued on next page) Cell Metabolism 35, 1132–1146.e1–e9, July 11, 2023 e3 .. REAGENT or RESOURCE SOURCE IDENTIFIER Raw data for Proteomics analysis EMBL-EBI Proteomics Identification Database (PRIDE) Identifier: PXD041523 Experimental models: Cell lines Human: PBMCs from healthy controls (primary) N/A N/A Human: PBMCs from rheumatoid arthritis patients (primary) N/A N/A Human: PBMCs from systemic lupus erythematosus patients (primary) N/A N/A Human: SFMCs from rheumatoid arthritis patients (primary) N/A N/A Software and algorithms ChemStation E.02.02.1431 Agilent https://www.agilent.com/en/product/software- informatics/analytical-software-suite/ chromatography-data-systems/openlabchemstation FlowJo 10.8.0 Tree Star www.flowjo.com GraphPad Prism 9 GraphPad Software, Inc. www.graphpad.com ImageJ ImageJ www.imagej.nih.gov/ij/ Morpheus Broad Institute https://software.broadinstitute.org/morpheus NovoExpress 1.4.1 Agilent https://www.agilent.com/en/product/research- flow-cytometry/flow-cytometry-software/ novocyte-novoexpress-software-1320805 nSolver 4.0 Nanostring www.nanostring.com/ncounterpro Seahorse Wave Software 2.6 Agilent https://www.agilent.com/en/product/cell- analysis/real-time-cell-metabolic-analysis/ xf-software/seahorse-wave-desktopsoftware-740897 TraceFinder 4.1 ThermoFisher https://www.thermofisher.com/uk/en/home/ industrial/mass-spectrometry/liquidchromatography-mass-spectrometry-lc-ms/ lc-ms-software/lc-ms-data-acquisitionsoftware/tracefinder-software.html Other HBSS, no calcium, no magnesium, no phenol red Gibco 14175053 Human plasma-like medium Gibco A4899101 RPMI 1640 Medium, GlutaMAX Supplement Gibco 61870036 RPMI 1640 Medium, no glucose Gibco 11879020 RPMI 1640 Medium, no glutamine Gibco 31870025 Seahorse XF RPMI medium, pH 7.4 Agilent 103576-100 S-Trap mini columns (100 - 300 mg) Protifi CO2-mini-80 SeQuant ZIC-pHILIC, 5 micron, 150x4.6 mm Merck 1.50461.0001
Gene Expression:Article Title: Canagliflozin impairs T cell effector function via metabolic suppression in autoimmunity.
Article Snippet: Eur. analytical reagent VWR 20624.262 PD-98,059 Merck 513000 PhosphoSafe Extraction Buffer Merck 71296 Pierce Formic Acid, LC-MS Grade ThermoFisher 85178 Pierce Trypsin Protease, MS Grade ThermoFisher 90057 Piericidin A Enzo Life Sciences ALX380235M002 PMA Merck 79346 Puromycin Merck P7255 R162 Merck 5.38098 Rapamycin Merck 553210 Rotenone Merck R8875 Sodium dodecyl sulfate Merck L4509 TGF-b PeproTech Cat#100-21 TMB Substrate Reagent Set BD Biosciences Cat#555214 Triethylammonium bicarbonate buffer Merck T7408 Water, HiPerSolv CHROMANORM for LC-MS, suitable for UPLC/UHPLC instruments VWR 83645.290 (Continued on next page) e2 Cell Metabolism 35, 1132–1146.e1–e9, July 11, 2023 .. REAGENT or RESOURCE SOURCE IDENTIFIER Critical commercial assays Acclaim PepMap 100 Å, 100 mm i.d. x 2cm NanoViper (2pk) - 164564 ThermoFisher 11312263 Acclaim PepMap C18 2um 75um x 500mm NVFS 1200bar - 164942 ThermoFisher 15567530 Acclaim PepMap RSLC C18, 2 mm, 100 Å, 75 mm i.d. x 15 cm - 164534 ThermoFisher 11342013 Amersham ECL Select Western Blotting detection reagent Cytiva RPN2235 CD4+ Effector Memory T cell isolation kit, human Miltenyi 130-094-125 CD4+ T cell isolation kit, human Miltenyi 130-096-533 CD8+ T cell isolation kit, human Miltenyi 130-096-495 CellTrace Violet Cell Proliferation Kit, for flow cytometry ThermoFisher C34557 DC Protein Assay II Bio-Rad 5000112 DRAQ7 Biostatus DR71000 ES791 - EASY-Spray 50cm x 20um Dual ThermoFisher 15176864 ES800\A - EASY-Spray 15 cm x 75 mm ThermoFisher 12886016 / 15988997 Human Granzyme B DuoSet ELISA R&D Systems DY2906 Human IFNg DuoSet ELISA R&D Systems DY285B Human IL-2 DuoSet ELISA R&D Systems DY202 Human IL-4 DuoSet ELISA R&D Systems DY204 Human IL-10 DuoSet ELISA R&D Systems DY217B Human IL-17 DuoSet ELISA R&D Systems DY317 Human IL-21 DuoSet ELISA R&D Systems DY8879 Human TNFa DuoSet ELISA R&D Systems DY210 Immunocult T cell activator StemCell Technologies Cat#10971 Inside Stain Kit Miltenyi 130-090-477 L-Lactate Assay Kit I Eton Bioscience Cat#120001200P Micro BCA Protein Assay Kit ThermoFisher 23235 MitoSOX Red ThermoFisher M36008 MitoTracker Green FM ThermoFisher M7514 Naı̈ve CD4+ T cell isolation kit, human Miltenyi 130-094-131 nCounter Autoimmune Profiling Panel Nanostring XT-CSO-HAIP1-12 nCounter Metabolic Pathways Panel Nanostring XT-CSO-HMP1-12 PepSwift Monolithic Capillary LC Columns - 164584 ThermoFisher 11382263 Pierce Quantitative Fluorometric Peptide Assay ThermoFisher 23290 Restore PLUS Western Blot Stripping buffer ThermoFisher 21063 RNeasy Mini Kit columns Qiagen Cat#74014 SimplyBlue SafeStain ThermoFisher LC6060 TMRE-Mitochondrial Membrane Potential Assay Kit abcam Ab113852 Trifluoroacetic Acid, Optima LC/MS Grade, Fisher Chemical Fisher Scientific 10266617 Trypsin Sequencing Grade, modified Merck 11418025001 Deposited data Raw data for Nanostring nCounter Autoimmune Profiling Panel NCBI Gene Expression Omnibus (GEO) GSE228911; https://www.ncbi.nlm.nih.gov/ geo/query/acc.cgi?acc=GSE228911 Raw data for Nanostring nCounter Metabolic Pathways Panel NCBI Gene Expression Omnibus (GEO) GSE228911; https://www.ncbi.nlm.nih.gov/ geo/query/acc.cgi?acc=GSE228911 (Continued on next page) Cell Metabolism 35, 1132–1146.e1–e9, July 11, 2023 e3 .. REAGENT or RESOURCE SOURCE IDENTIFIER Raw data for Proteomics analysis EMBL-EBI Proteomics Identification Database (PRIDE) Identifier: PXD041523 Experimental models: Cell lines Human: PBMCs from healthy controls (primary) N/A N/A Human: PBMCs from rheumatoid arthritis patients (primary) N/A N/A Human: PBMCs from systemic lupus erythematosus patients (primary) N/A N/A Human: SFMCs from rheumatoid arthritis patients (primary) N/A N/A Software and algorithms ChemStation E.02.02.1431 Agilent https://www.agilent.com/en/product/software- informatics/analytical-software-suite/ chromatography-data-systems/openlabchemstation FlowJo 10.8.0 Tree Star www.flowjo.com GraphPad Prism 9 GraphPad Software, Inc. www.graphpad.com ImageJ ImageJ www.imagej.nih.gov/ij/ Morpheus Broad Institute https://software.broadinstitute.org/morpheus NovoExpress 1.4.1 Agilent https://www.agilent.com/en/product/research- flow-cytometry/flow-cytometry-software/ novocyte-novoexpress-software-1320805 nSolver 4.0 Nanostring www.nanostring.com/ncounterpro Seahorse Wave Software 2.6 Agilent https://www.agilent.com/en/product/cell- analysis/real-time-cell-metabolic-analysis/ xf-software/seahorse-wave-desktopsoftware-740897 TraceFinder 4.1 ThermoFisher https://www.thermofisher.com/uk/en/home/ industrial/mass-spectrometry/liquidchromatography-mass-spectrometry-lc-ms/ lc-ms-software/lc-ms-data-acquisitionsoftware/tracefinder-software.html Other HBSS, no calcium, no magnesium, no phenol red Gibco 14175053 Human plasma-like medium Gibco A4899101 RPMI 1640 Medium, GlutaMAX Supplement Gibco 61870036 RPMI 1640 Medium, no glucose Gibco 11879020 RPMI 1640 Medium, no glutamine Gibco 31870025 Seahorse XF RPMI medium, pH 7.4 Agilent 103576-100 S-Trap mini columns (100 - 300 mg) Protifi CO2-mini-80 SeQuant ZIC-pHILIC, 5 micron, 150x4.6 mm Merck 1.50461.0001
Recombinant:Article Title: Targeting stromal cell sialylation reverses T cell-mediated immunosuppression in the tumor microenvironment.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Mouse anti-human CD105 BioLegend RRID:AB_755960 Cat: 323208 Rabbit anti-human CD3 Roche RRID:AB_2335978 Cat: 790-4341 Mouse anti-human CD4 BioLegend RRID:AB_314082 or RRID:AB_314086 Cat: 300514 or 300518 Mouse anti-human CD44 BioLegend RRID:AB_2716000 Cat: 338815 Mouse anti-human CD45 BioLegend RRID:AB_2566370 Cat: 368510 Mouse anti-human CD73 BioLegend RRID:AB_2561809 or RRID:AB_2298698 Cat: 344016 or 344004 Mouse anti-human CD8 BioLegend RRID:AB_1953244 or RRID:AB_2564624 Cat: 344706 or 344732 Mouse anti-human CD8 Agilent Technologies RRID:AB_2075537 Cat: M710301-2 Mouse anti-human CD90 BioLegend RRID:AB_893431 Cat: 328114 Mouse anti-human CD326 (EpCAM) BioLegend RRID:AB_756082 Cat: 324208 Mouse anti-human HLA-DR BioLegend RRID:AB_493588 Cat: 307616 Mouse anti-human CD279 (PD-1) BioLegend RRID:AB_2562256 Cat: 329932 Mouse anti-human CD140a (PDGFR-a) BioLegend RRID:AB_2565596 Cat: 323507 Mouse anti-human CD140b (PDGFR-b) BioLegend RRID:AB_2162787 Cat:323608 Rat anti-human Podoplanin BioLegend RRID:AB_2750289 Cat: 337029 Anti-human CD328 (Siglec-7) Miltenyi Biotec RRID:AB_2657535 Cat: 130-101-016 Anti-human CD329 (Siglec-9) Miltenyi Biotec RRID:AB_2657547 Cat: 130-107-607 Rat anti-mouse CD73 BioLegend RRID:AB_11218786 Cat: 127210 Rat anti-mouse CD105 BioLegend RRID:AB_2277914 Cat: 120414 Rat anti-mouse CD90.2 (Thy1.2) BioLegend RRID:AB_313179 Cat: 105308 Rat anti-mouse CD25 BioLegend RRID:AB_312847 Cat: 101904 Armenian hamster anti-mouse CD3 BioLegend RRID:AB_312671 Cat: 100306 Rat anti-mouse CD4 BioLegend RRID:AB_312707 Cat: 100422 Rat anti-mouse CD8 BioLegend RRID:AB_2562100 Cat: 100748 (Continued on next page) 20 Cell Reports 42, 112475, May 30, 2023 .. REAGENT or RESOURCE SOURCE IDENTIFIER Rat anti-mouse Siglec-E BioLegend RRID:AB_2566169 Cat: 677104 Mouse anti-mouse/human Granzyme B BioLegend RRID:AB_2687032 Cat: 372208 Biological samples Colorectal cancer patient-derived tumor sections Galway University Hospital N/A Chemicals, peptides, and recombinant proteins 3FaxNeu5Ac Bio-Techne Cat: 5760/10 APC AffiniPure F(ab’)2 Fragment Goat Anti-Human IgG, Fcg Fragment Specific (min X Bov,Ms,Rb Sr Prot) Jackson ImmunoResearch Cat: 109-096-170 ChromPure Human IgG, Fc fragment Jackson ImmunoResearch Cat: 009-000-008 E-610-1A sialidase Palleon Pharmaceuticals N/A Human FGF-basic PeproTech Cat: 100-18B Biotinylated Sambucus Nigra Lectin (SNA-I, EBL) Vector Laboratories Cat: B-1305-2 Biotinylated Maackia Amurensis Lectin II (MAL-II) Vector Laboratories Cat: B-1265-1 Biotinylated Wheat Germ Agglutinin (WGA) Vector Laboratories Cat: B-1025-5 Biotinylated Galanthus Nivalis Lectin (GNA) Vector Laboratories Cat: B-1245-2 Biotinylated Concanavalin A (Con A) Vector Laboratories Cat: B-1005-5 Recombinant Human Siglec-7/CD328 Fc Chimera Protein Bio-Techne Cat: 1138-SL-050 Recombinant Human Siglec-9/CD329 Fc Chimera Protein Bio-Techne Cat: 1139-SL-050 Recombinant Mouse Siglec-E Fc Chimera Protein Bio-Techne Cat: 5806-SL-050 FITC Streptavidin BioLegend Cat: 405201 PE Streptavidin BioLegend Cat: 405204 APC Streptavidin BioLegend Cat: 405207 Critical commercial assays CellTrace Violet Cell Proliferation Kit, for flow cytometry ThermoFisher Scientific Cat: C34557 DynabeadsTM Human T-Activator CD3/CD28 for T Cell Expansion and Activation ThermoFisher Scientific Cat: 11131D DynabeadsTM Mouse T-Activator CD3/CD28 for T-Cell Expansion and Activation ThermoFisher Scientific Cat: 11452D SYTOX Blue Dead Cell Stain ThermoFisher Scientific Cat: S34857 SYTOX AADvanced Dead Cell Stain Kit ThermoFisher Scientific Cat: S10349 Tumor Dissociation Kit, human Miltenyi Biotec Cat: 130-095-929 Tumor Dissociation Kit, mouse Miltenyi Biotec Cat: 130-096-730 Deposited data Raw and analyzed data This paper GEO: GSE229054 Experimental models: Cell lines CT26 American Type Culture Collection (ATCC) RRID:CVCL_7256 Cat: CRL-2638 HCT116 American Type Culture Collection (ATCC) Cat:CCL-247 HT29 American Type Culture Collection (ATCC) RRID:CVCL_0320 Cat: HTB-38 Experimental models: Organisms/strains Balb/c Envigo Laboratories Balb/cAnNCrl C57BL6 Envigo Laboratories C57BL/6N C57BL/KaLwRij Lab of Prof. Karin Vanderkerken N/A (Continued on next page) Cell Reports 42, 112475, May 30, 2023 21 .. REAGENT or RESOURCE SOURCE IDENTIFIER Software and algorithms BioRender Biorender.com RRID:SCR_018361 FlowJo Version 10 Tree Star Inc. RRID:SCR_008520 GraphPad Prisim Version 9 GraphPad RRID:SCR_002798 Partek Genomics Suite Partek.com RRID:SCR_011860 QuPath Qupath.github.io RRID:SCR_018257
Whole Genome Amplification:Article Title: Targeting stromal cell sialylation reverses T cell-mediated immunosuppression in the tumor microenvironment.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Mouse anti-human CD105 BioLegend RRID:AB_755960 Cat: 323208 Rabbit anti-human CD3 Roche RRID:AB_2335978 Cat: 790-4341 Mouse anti-human CD4 BioLegend RRID:AB_314082 or RRID:AB_314086 Cat: 300514 or 300518 Mouse anti-human CD44 BioLegend RRID:AB_2716000 Cat: 338815 Mouse anti-human CD45 BioLegend RRID:AB_2566370 Cat: 368510 Mouse anti-human CD73 BioLegend RRID:AB_2561809 or RRID:AB_2298698 Cat: 344016 or 344004 Mouse anti-human CD8 BioLegend RRID:AB_1953244 or RRID:AB_2564624 Cat: 344706 or 344732 Mouse anti-human CD8 Agilent Technologies RRID:AB_2075537 Cat: M710301-2 Mouse anti-human CD90 BioLegend RRID:AB_893431 Cat: 328114 Mouse anti-human CD326 (EpCAM) BioLegend RRID:AB_756082 Cat: 324208 Mouse anti-human HLA-DR BioLegend RRID:AB_493588 Cat: 307616 Mouse anti-human CD279 (PD-1) BioLegend RRID:AB_2562256 Cat: 329932 Mouse anti-human CD140a (PDGFR-a) BioLegend RRID:AB_2565596 Cat: 323507 Mouse anti-human CD140b (PDGFR-b) BioLegend RRID:AB_2162787 Cat:323608 Rat anti-human Podoplanin BioLegend RRID:AB_2750289 Cat: 337029 Anti-human CD328 (Siglec-7) Miltenyi Biotec RRID:AB_2657535 Cat: 130-101-016 Anti-human CD329 (Siglec-9) Miltenyi Biotec RRID:AB_2657547 Cat: 130-107-607 Rat anti-mouse CD73 BioLegend RRID:AB_11218786 Cat: 127210 Rat anti-mouse CD105 BioLegend RRID:AB_2277914 Cat: 120414 Rat anti-mouse CD90.2 (Thy1.2) BioLegend RRID:AB_313179 Cat: 105308 Rat anti-mouse CD25 BioLegend RRID:AB_312847 Cat: 101904 Armenian hamster anti-mouse CD3 BioLegend RRID:AB_312671 Cat: 100306 Rat anti-mouse CD4 BioLegend RRID:AB_312707 Cat: 100422 Rat anti-mouse CD8 BioLegend RRID:AB_2562100 Cat: 100748 (Continued on next page) 20 Cell Reports 42, 112475, May 30, 2023 .. REAGENT or RESOURCE SOURCE IDENTIFIER Rat anti-mouse Siglec-E BioLegend RRID:AB_2566169 Cat: 677104 Mouse anti-mouse/human Granzyme B BioLegend RRID:AB_2687032 Cat: 372208 Biological samples Colorectal cancer patient-derived tumor sections Galway University Hospital N/A Chemicals, peptides, and recombinant proteins 3FaxNeu5Ac Bio-Techne Cat: 5760/10 APC AffiniPure F(ab’)2 Fragment Goat Anti-Human IgG, Fcg Fragment Specific (min X Bov,Ms,Rb Sr Prot) Jackson ImmunoResearch Cat: 109-096-170 ChromPure Human IgG, Fc fragment Jackson ImmunoResearch Cat: 009-000-008 E-610-1A sialidase Palleon Pharmaceuticals N/A Human FGF-basic PeproTech Cat: 100-18B Biotinylated Sambucus Nigra Lectin (SNA-I, EBL) Vector Laboratories Cat: B-1305-2 Biotinylated Maackia Amurensis Lectin II (MAL-II) Vector Laboratories Cat: B-1265-1 Biotinylated Wheat Germ Agglutinin (WGA) Vector Laboratories Cat: B-1025-5 Biotinylated Galanthus Nivalis Lectin (GNA) Vector Laboratories Cat: B-1245-2 Biotinylated Concanavalin A (Con A) Vector Laboratories Cat: B-1005-5 Recombinant Human Siglec-7/CD328 Fc Chimera Protein Bio-Techne Cat: 1138-SL-050 Recombinant Human Siglec-9/CD329 Fc Chimera Protein Bio-Techne Cat: 1139-SL-050 Recombinant Mouse Siglec-E Fc Chimera Protein Bio-Techne Cat: 5806-SL-050 FITC Streptavidin BioLegend Cat: 405201 PE Streptavidin BioLegend Cat: 405204 APC Streptavidin BioLegend Cat: 405207 Critical commercial assays CellTrace Violet Cell Proliferation Kit, for flow cytometry ThermoFisher Scientific Cat: C34557 DynabeadsTM Human T-Activator CD3/CD28 for T Cell Expansion and Activation ThermoFisher Scientific Cat: 11131D DynabeadsTM Mouse T-Activator CD3/CD28 for T-Cell Expansion and Activation ThermoFisher Scientific Cat: 11452D SYTOX Blue Dead Cell Stain ThermoFisher Scientific Cat: S34857 SYTOX AADvanced Dead Cell Stain Kit ThermoFisher Scientific Cat: S10349 Tumor Dissociation Kit, human Miltenyi Biotec Cat: 130-095-929 Tumor Dissociation Kit, mouse Miltenyi Biotec Cat: 130-096-730 Deposited data Raw and analyzed data This paper GEO: GSE229054 Experimental models: Cell lines CT26 American Type Culture Collection (ATCC) RRID:CVCL_7256 Cat: CRL-2638 HCT116 American Type Culture Collection (ATCC) Cat:CCL-247 HT29 American Type Culture Collection (ATCC) RRID:CVCL_0320 Cat: HTB-38 Experimental models: Organisms/strains Balb/c Envigo Laboratories Balb/cAnNCrl C57BL6 Envigo Laboratories C57BL/6N C57BL/KaLwRij Lab of Prof. Karin Vanderkerken N/A (Continued on next page) Cell Reports 42, 112475, May 30, 2023 21 .. REAGENT or RESOURCE SOURCE IDENTIFIER Software and algorithms BioRender Biorender.com RRID:SCR_018361 FlowJo Version 10 Tree Star Inc. RRID:SCR_008520 GraphPad Prisim Version 9 GraphPad RRID:SCR_002798 Partek Genomics Suite Partek.com RRID:SCR_011860 QuPath Qupath.github.io RRID:SCR_018257
Activation Assay:Article Title: Targeting stromal cell sialylation reverses T cell-mediated immunosuppression in the tumor microenvironment.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Mouse anti-human CD105 BioLegend RRID:AB_755960 Cat: 323208 Rabbit anti-human CD3 Roche RRID:AB_2335978 Cat: 790-4341 Mouse anti-human CD4 BioLegend RRID:AB_314082 or RRID:AB_314086 Cat: 300514 or 300518 Mouse anti-human CD44 BioLegend RRID:AB_2716000 Cat: 338815 Mouse anti-human CD45 BioLegend RRID:AB_2566370 Cat: 368510 Mouse anti-human CD73 BioLegend RRID:AB_2561809 or RRID:AB_2298698 Cat: 344016 or 344004 Mouse anti-human CD8 BioLegend RRID:AB_1953244 or RRID:AB_2564624 Cat: 344706 or 344732 Mouse anti-human CD8 Agilent Technologies RRID:AB_2075537 Cat: M710301-2 Mouse anti-human CD90 BioLegend RRID:AB_893431 Cat: 328114 Mouse anti-human CD326 (EpCAM) BioLegend RRID:AB_756082 Cat: 324208 Mouse anti-human HLA-DR BioLegend RRID:AB_493588 Cat: 307616 Mouse anti-human CD279 (PD-1) BioLegend RRID:AB_2562256 Cat: 329932 Mouse anti-human CD140a (PDGFR-a) BioLegend RRID:AB_2565596 Cat: 323507 Mouse anti-human CD140b (PDGFR-b) BioLegend RRID:AB_2162787 Cat:323608 Rat anti-human Podoplanin BioLegend RRID:AB_2750289 Cat: 337029 Anti-human CD328 (Siglec-7) Miltenyi Biotec RRID:AB_2657535 Cat: 130-101-016 Anti-human CD329 (Siglec-9) Miltenyi Biotec RRID:AB_2657547 Cat: 130-107-607 Rat anti-mouse CD73 BioLegend RRID:AB_11218786 Cat: 127210 Rat anti-mouse CD105 BioLegend RRID:AB_2277914 Cat: 120414 Rat anti-mouse CD90.2 (Thy1.2) BioLegend RRID:AB_313179 Cat: 105308 Rat anti-mouse CD25 BioLegend RRID:AB_312847 Cat: 101904 Armenian hamster anti-mouse CD3 BioLegend RRID:AB_312671 Cat: 100306 Rat anti-mouse CD4 BioLegend RRID:AB_312707 Cat: 100422 Rat anti-mouse CD8 BioLegend RRID:AB_2562100 Cat: 100748 (Continued on next page) 20 Cell Reports 42, 112475, May 30, 2023 .. REAGENT or RESOURCE SOURCE IDENTIFIER Rat anti-mouse Siglec-E BioLegend RRID:AB_2566169 Cat: 677104 Mouse anti-mouse/human Granzyme B BioLegend RRID:AB_2687032 Cat: 372208 Biological samples Colorectal cancer patient-derived tumor sections Galway University Hospital N/A Chemicals, peptides, and recombinant proteins 3FaxNeu5Ac Bio-Techne Cat: 5760/10 APC AffiniPure F(ab’)2 Fragment Goat Anti-Human IgG, Fcg Fragment Specific (min X Bov,Ms,Rb Sr Prot) Jackson ImmunoResearch Cat: 109-096-170 ChromPure Human IgG, Fc fragment Jackson ImmunoResearch Cat: 009-000-008 E-610-1A sialidase Palleon Pharmaceuticals N/A Human FGF-basic PeproTech Cat: 100-18B Biotinylated Sambucus Nigra Lectin (SNA-I, EBL) Vector Laboratories Cat: B-1305-2 Biotinylated Maackia Amurensis Lectin II (MAL-II) Vector Laboratories Cat: B-1265-1 Biotinylated Wheat Germ Agglutinin (WGA) Vector Laboratories Cat: B-1025-5 Biotinylated Galanthus Nivalis Lectin (GNA) Vector Laboratories Cat: B-1245-2 Biotinylated Concanavalin A (Con A) Vector Laboratories Cat: B-1005-5 Recombinant Human Siglec-7/CD328 Fc Chimera Protein Bio-Techne Cat: 1138-SL-050 Recombinant Human Siglec-9/CD329 Fc Chimera Protein Bio-Techne Cat: 1139-SL-050 Recombinant Mouse Siglec-E Fc Chimera Protein Bio-Techne Cat: 5806-SL-050 FITC Streptavidin BioLegend Cat: 405201 PE Streptavidin BioLegend Cat: 405204 APC Streptavidin BioLegend Cat: 405207 Critical commercial assays CellTrace Violet Cell Proliferation Kit, for flow cytometry ThermoFisher Scientific Cat: C34557 DynabeadsTM Human T-Activator CD3/CD28 for T Cell Expansion and Activation ThermoFisher Scientific Cat: 11131D DynabeadsTM Mouse T-Activator CD3/CD28 for T-Cell Expansion and Activation ThermoFisher Scientific Cat: 11452D SYTOX Blue Dead Cell Stain ThermoFisher Scientific Cat: S34857 SYTOX AADvanced Dead Cell Stain Kit ThermoFisher Scientific Cat: S10349 Tumor Dissociation Kit, human Miltenyi Biotec Cat: 130-095-929 Tumor Dissociation Kit, mouse Miltenyi Biotec Cat: 130-096-730 Deposited data Raw and analyzed data This paper GEO: GSE229054 Experimental models: Cell lines CT26 American Type Culture Collection (ATCC) RRID:CVCL_7256 Cat: CRL-2638 HCT116 American Type Culture Collection (ATCC) Cat:CCL-247 HT29 American Type Culture Collection (ATCC) RRID:CVCL_0320 Cat: HTB-38 Experimental models: Organisms/strains Balb/c Envigo Laboratories Balb/cAnNCrl C57BL6 Envigo Laboratories C57BL/6N C57BL/KaLwRij Lab of Prof. Karin Vanderkerken N/A (Continued on next page) Cell Reports 42, 112475, May 30, 2023 21 .. REAGENT or RESOURCE SOURCE IDENTIFIER Software and algorithms BioRender Biorender.com RRID:SCR_018361 FlowJo Version 10 Tree Star Inc. RRID:SCR_008520 GraphPad Prisim Version 9 GraphPad RRID:SCR_002798 Partek Genomics Suite Partek.com RRID:SCR_011860 QuPath Qupath.github.io RRID:SCR_018257
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