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. 2024 Jan 26;5(2):101393. doi: 10.1016/j.xcrm.2024.101393
REAGENT or RESOURCE SOURCE IDENTIFIER
Antibodies

Mouse BD Fc block BD Biosciences Cat # 553142; RRID: AB_394656
PE anti-mouse PDL1 Biolegend Cat # 155404; RRID: AB_2728222
AF700 anti-mouse CD8 BD Biosciences Cat # 557959; RRID: AB_396959
APC anti-mouse CD45 BD Biosciences Cat # 559864; RRID: AB_398672
Human TruStain FcX Biolegend Cat # 422302; RRID: AB_2818986
PE anti-human PD-L1 Biolegend Cat # 329706; RRID: AB_940368
Pacific Blue anti-mouse CD40 BioLegend Cat # 124626; RRID: AB_2561476
BUV395 Rat Anti-Mouse H-2 Class I BD Biosciences Cat # 749705; RRID: AB_2873959
PE rat anti-mouse CD86 BD Biosciences Cat # 553692; RRID:AB_394994
APC rat anti-mouse CD209a BD Biosciences Cat # 564928; RRID:AB_2739011
BV421 anti-human CD4 Biolegend Cat # 317434; RRID: AB_2562134
BUV805 mouse anti-human CD8 BD Biosciences Cat # 612889; RRID: AB_2833078
FITC Ki-67 monoclonal antibody eBiosciences Cat # 11-5698-82; RRID: AB_11151330
BV786 mouse anti-human CD69 BD Biosciences Cat # 563834; RRID: AB_2738441
PE-Cy7 mouse anti-human IFN-γ BD Biosciences Cat # 557643; RRID: AB_396760
Annexin V- PE BD Biosciences Cat # 556421; RRID: AB_2869071
7-AAD BD Biosciences Cat # 559925; RRID: AB_2869266
p-ATM S1981 Cell Signaling Technology Cat #5883
p-ATR T1989 Cell Signaling Technology Cat #30632; RRID: AB_2798992
p-Chk1 S317 Cell Signaling Technology Cat #12302; RRID: AB_2893473
p-Chk2 T68 Cell Signaling Technology Cat #2197; RRID: AB_331479
GAPDH Cell Signaling Technology Cat #2118; RRID: AB_561053
Peroxidase AffiniPure goat anti-rabbit IgG (H + L) Jackson Immunoresearch Cat #111-035-144; RRID: AB_2307391

Biological samples

IMvigor130 mUC samples Genentech N/A
IMvigor130 PBMC collection for CITE-seq (n = 113) This study N/A

Chemicals, peptides, and recombinant proteins

Cisplatin Sigma Aldrich CAS#: 15663-27-1
Carboplatin Sigma Aldrich CAS#: 41575-94-4
KU-55933 (ATM Kinase Inhibitor) Selleckchem Cat#: S1092
VE-821(ATR inhibitor IV) Selleckchem Cat#: S8007
Halt protease and phosphatase inhibitor cocktail, EDTA-free Thermo Fisher Cat#: 78441

Critical commercial assays

10x Chromium Next GEM Chip G Kit 10X Genomics
Pan T cell Isolation Kit, human Miltenyi Biotec Cat# 130-096-535
Dynabeads Human T-Activator CD3/CD28 for T cell expansion and activation Thermo Fisher Cat# 11161D
CD14 MicroBeads, human Miltenyi Biotec Cat# 130-050-201
CellXVivo human monocyte-derived DC differentiation kit R&D Cat# CDK004
Cytiva Ficoll-Paque PLUS Media Fisher Scientific Cat# 45-001-749
Human IFNg ELISA kit BD Biosciences Cat.# 555142
Mouse CXCL10 ELISA kit Thermo Fisher Scientific Cat# BMS6018
Mouse HMGB1 ELISA kit Tecan Cat# 30164033
CellTrace Blue Cell Proliferation kit Thermo Fisher Scientific Cat# C34568
RNeasy kits Qiagen
FITC Annexin V Apoptosis Detection Kit with 7-AAD BD Biosciences Cat#: 556547
RIPA buffer Sigma
LIVE/DEAD Fixable Aqua Dead Cell Stain Kit Invitrogen L34957

Deposited data

Raw and analyzed bulk RNAseq (cell lines) This paper GEO: GSE235066
PBMC scRNA-seq raw counts and metadata This paper EGAS50000000104
IMvigor130 bulk RNAseq processed data (patient tumors) This paper EGAS50000000104

Experimental models: Cell lines

Human cell line: 5637 Genentech N/A
Human cell line: RT112 Genentech N/A
Mouse cell line: MC38 Genentech N/A
Mouse cell line: MC38-OVA Genentech N/A

Experimental models: Organisms/strains

C57BL/6
C57BL/6J.OT-I.Thy1.1

Software and algorithms

R statistical software, version 4.0.2 The R Foundation https://www.r-project.org/
GSNAP Wu et al., 201649; Wu et al., 201050
survminer package, version 0.4.8 CRAN Repository https://cran.r-project.org/web/packages/survminer/index.html
survival package, version 3.2–7 CRAN Repository https://cran.r-project.org/web/packages/survival/index.html
limma package, 3.44.3 Bioconductor https://bioconductor.org/packages/release/bioc/html/limma.html
fgsea package, 1.14.0 Bioconductor http://bioconductor.org/packages/fgsea
CellRanger, 3.1.0 10X Genomics http://10xgenomics.com/
Seurat, v3.2.2 Stuart et al., 201951 https://satijalab.org/seurat
Harmony, v1.0 Korsunsky et al., 201952 https://github.com/immunogenomics/harmony
FlowJo Becton Dickinson https://flowjo.com/
Graphpad Prism 7.0 software GraphPad Software, Inc. http://www.graphpad.com/scientificsoftware/prism/
GSVA Bioconductor https://bioconductor.org/packages/release/bioc/html/GSVA.html