| Antibodies
|
|
| SOX4 |
Abcam |
ab86809 |
| SOX4 |
Diagenode |
CS-129-100 |
| ITGAV |
CST |
4711S |
| GAPDH |
CST |
8884 |
| pSMAD2 |
CST |
18338 |
| CD51 |
ThermoFisherScientific |
14051282 |
| ITGB6 |
ThermoFisherScientific |
PAS-47588 |
| CD45 |
BioLegend |
103112 |
| CD3 |
BioLegend |
100222 |
| CD4 |
BioLegend |
100552 |
| CD8 |
BioLegend |
100742 |
| PD1 |
BioLegend |
135225 |
| IFNγ |
BioLegend |
505836 |
| F4/80 |
BioLegend |
123132 |
| Gr1 |
Biolegend |
108407 |
| CD11b |
BioLegend |
101216 |
| CD11c |
BioLegend |
117328 |
| MHC-II |
BioLegend |
107606 |
| H-2Kb
|
BioLegend |
116518 |
| E-cadherin |
BioLegend |
147304 |
| HLA-ABC |
BioLegend |
311410 |
| HLA-A0201 |
BioLegend |
343306 |
| Mouse anti-PD1 |
inVivoMAb |
BioXcell RMPI-14 clone |
| Rat IgG2a isotype control |
inVivoMAb |
BioXcell 2A3 clone |
| CD8 depletion antibody |
inVivoMAb |
BioXcell, 2.43 clone |
| Alexa Fluor 594 |
Thermo |
#40957 |
| E-cadherin antibody |
CST |
CST3195S, Clone 24E10 |
| Alexa Fluor 488 |
Thermo |
#40953 |
| CD8 antibody |
Dako |
M7103, Clone C8/144B |
| Alexa Fluor 647 |
Thermo |
# B40958
|
| Vimentin antibody |
Dako |
0725, Clone V9 |
| αSMA antibody |
Abcam |
ab5694 |
| Anti-human PD-1 |
Bioxcell |
clone J116, BE0188 |
| IgG control |
Bioxcell |
clone MOPC-21 #BE0083 |
| anti-murine PD-1 |
Bioxcell |
clone RMP1-14 #BE0146 |
| anti-trinitrophenol rat IgG2a isotype control |
Bioxcell |
clone 2A3 #BE0089 |
| CD16/CD32 antibody |
PharMingen |
clone 2.4G2, BD |
| Chemicals, Peptides, and Recombinant Proteins |
|
| Human IL2 |
BioLegend |
589104 |
| Murine IL2 |
BioLegend |
575406 |
| Human IFNγ |
PeproTech |
#300-02 |
| Murine IFNγ |
Abcam |
#Ab9922 |
| collagenase type IV |
Sigma-Aldrich |
#C5138 |
| DNAse type IV |
Sigma-Aldrich |
#D5205 |
| Hyaluronidase Type V |
Sigma-Aldrich |
#H6254 |
| ACK lysis buffer |
Life Technologies |
#A1049201 |
| Percoll density gradient media |
Sigma-Aldrich |
#P1644 |
| puromycin |
Takara Bio |
631306 |
| GlutaMAX |
Life Technologies |
35050061 |
| Cas9 protein (20 μM) |
Macrolab |
CAS9-200 |
| Protease inhibitor cocktail |
Roche |
11836170001 |
| Halt Phosphatase Inhibitor Cocktail |
Thermo Scientific |
#78427 |
| HRP-catalyzed detection |
Perkin Elmer |
#NEL104001EA |
| Cell Culture Lysis Reagent |
Promega |
#E1531 |
| Passive Lysis Buffer |
Promega |
#E1941 |
| Reporter Lysis Buffer |
Promega |
#E3971 |
| Collagen I |
ThermoFisher |
#A1048301 |
| Fibronectin |
Corning |
356008 |
| protamine sulfate |
Sigma-Aldrich |
P3369 |
| Retronectin |
Takara Bio |
T100B |
| αCD3/αCD28 beads |
Life Technologies |
#11132D |
| CD8 Dynabeads |
StemCell |
#19053 |
| CD3/CD28 Dynabeads |
Life Technologies |
#11453D |
| RPMI 1640 media |
ThermoFisher |
#11875093 |
| Fix/Perm buffer |
eBioscience |
#00-5521-00 |
| Hyaluronidase Type V |
Sigma-Aldrich |
#H6254 |
| DNAse Type IV |
Sigma-Aldrich |
#D5205 |
| Collagenase Type IV |
Sigma-Aldrich |
#C5138 |
| Critical Commercial Assays |
|
| TSA Fluorescein kit |
Perkin-Elmer |
#NEL701001KT |
| TSA Biotin kit |
Perkin-Elmer |
#NEL700001KT |
| BOND Polymer Refine Detection kit |
Leica |
#DS9800 |
| BOND Polymer Refine Red Detection kit |
Leica |
#DS9390 |
| BOND Intense R Detection kit |
Leica |
#DS9263 |
| Cytofix kit |
BD Bioscience |
#554655 |
| Transcription Factor Staining kit |
eBioscience |
#00-5523-00 |
| cDNA synthesis kit |
Applied Biosystems, Carlsbad, CA |
4368813 |
| CD8 T cell isolation kit |
STEMCELL |
#19753 |
| MycoAlert mycoplasma detection kit |
Lonza |
#LT07-118 |
| Pierce BCA Protein Assay Kit |
ThermoFisher Pierce |
23225 |
| PrimeScript RT reagent kit |
Takara |
RR037B |
| SYBR Premix Ex Taq II |
Takara |
RR820B |
| RNeasy Plus Mini Kit |
Qiagen |
(# 74134 |
| TruSeq RNA Sample Prep Kit v2 |
Illumina |
RS-122-2001 |
| Luciferase Assay System® (Glo Lysis Buffer |
Promega |
#E2661 |
| LIVE/DEAD Fixable Dead Cell Stain Kit |
Molecular Probes |
L23105 |
| gentleMACS™ Dissociator |
Miltenyibiotech |
#130-093-235 |
| CFX96 Real-Time PCR System |
Bio-Rad |
1855196 |
| 7900HT Fast Real-Time PCR System |
Applied Biosystems, Carlsbad, CA |
4351405 |
| The BOND Polymer Refine Detection kit |
Leica Biosystems |
DS9800 |
| Aperio ScanScope CS System |
Aperio Technologies |
NA |
| Lonza 4D Nucleofector Core Unit |
Lonza |
#AAF-1002B |
| SF Cell Line 96-well NucleofectorTM Kit |
Lonza |
#V4SC-2096 |
| ChemiDoc MP Imaging System |
Bio-Rad |
#12003154 |
| FACSDiva Software version 8.0. |
BD |
330798 |
| LSR Fortessa X-20 cell analyzer |
BD |
658222R1 |
| Deposited Data |
|
| RNA Seq. raw reads and processed data |
this paper |
GEO: GSE144014 |
| ChIP Seq. raw reads and processed data |
this paper |
GEO: GSE144014 |
| Experimental Models: Cell Lines |
|
| 4T1 |
ATCC |
CRL-2539 |
| Py8119 |
ATCC |
CRL-3278 |
| BT549 |
ATCC |
HTB-122 |
| Hs578T |
ATCC |
HTB-126 |
| B16F10 |
ATCC |
CRL-6475 |
| HEK293T |
ATCC |
CRL-11268 |
| HepG2-Luc |
Signosis |
SL-0016-NP |
| Experimental Models: Organisms/Strains |
|
| Balb/c |
JAX |
#000651 |
| C57BI/6J |
JAX |
#000664 |
| B6.Cg-Thy1a/Cy Tg(TcraTcrb) 8Rest/J |
JAX |
#005023 |
| Oligonucleotides |
|
| Primers for RT-qPCR, see Table S3
|
NA |
NA |
| crRNA sequences, see Table S3
|
NA |
NA |
| Recombinant DNA |
|
| pINDUCER21-SOX4 |
Gift from George Daley |
Addgene plasmid # 51304 |
| pENTER-CMV-SOX4 |
Vigene Biosciences |
CH830603 |
| Software and Algorithms |
|
| Flowjo v10.5 |
Flowjo, L.L.C. |
RRID: SCR_008520 |
| Prism v8.0.1 |
Graphpad |
RRID: SCR_002798 |
| Fiji v2.0.0 |
ImageJ |
RRID: SCR_002285 |
| cBioportal v2.2.0 |
MSK Center for Mol Onc |
https://www.cbioportal.org/ |
| ssGSEA v2.0 |
Broad Institute |
http://software.broadinstitute.org/gsea/index.jsp |
| FACSDiva |
BD Biosciences |
RRID: SCR_001456 |
| MSIgDB (Molecular signature database) |
Broad Institute |
https://www.gsea-msigdb.org/gsea/msigdb |
| ImageScope software |
Aperio Technologies |
Aperio, V10.2.1.2315 |
| GraphPad Prism |
GraphPad |
https://www.graphpad.com/scientific-software/prism/ |
| Other |
| Optimum Growth shaker flasks |
Thompson Scientific |
507516355 |
| Multitron incubation shaker |
Infors HT |
IN3001 |
| Protein G Sepharose affinity columns |
GE Healthcare |
17061802 |
| Superose 6 HPLC column |
GE Biosciences |
29091596 |
| Amicon spin columns |
Millipore |
UFC900396 |
| 96 Well Black Polystyrene Microplates |
Corning |
#3603 |
| Collagen I coated 96 well plates |
ThermoFisher |
#A1142803 |
