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 |