|
| Antibodies |
|
| Rabbit polyclonal anti-p21 |
Santa Cruz |
Cat#sc-397; RRID:AB_632126 |
| Rabbit polyclonal anti-Histone H3 (tri methyl K9) |
abcam |
Cat#ab8898; RRID:AB_306848 |
| Rabbit monoclonal anti-E-cadherin |
Cell Signaling Technology |
Cat#3195; RRID:AB_2291471 |
| Rabbit polyclonal anti-TGF-β Receptor II |
Cell Signaling Technology |
Cat#79424; RRID:AB_2799933 |
| Rabbit polyclonal anti-β-Tubulin |
Cell Signaling Technology |
Cat#2146; RRID:AB_2210545 |
| Rabbit polyclonal anti-GAPDH |
Sigma-Aldrich |
Cat#SAB2108266 |
| Goat anti-rabbit IgG (H+L) Secondary Antibody, HRP |
BioRad |
Cat#170-6515; RRID:AB_11125142 |
| Goat anti-mouse IgG (H+L) Secondary Antibody, HRP |
BioRad |
Cat#1706516; RRID:AB_2921252 |
| Anti-rabbit IgG, HRP-linked Antibody |
Cell Signaling Technology |
Cat#7074; RRID:AB_2099233 |
| Rabbit monoclonal anti-tubulin |
NOVUS |
Cat#NB100-690; RRID:AB_521686 |
| Rabbit monoclonal anti-p21 |
abcam |
Cat#ab188224; RRID:AB_2734729 |
| Rat monoclonal anti-granzyme B |
ThermoFischer |
Cat#14-8822-80; RRID:AB_468529 |
| Rat monoclonal anti-CD45 |
Invitrogen |
Cat#MCD4501; RRID:AB_10371770 |
| Rat monoclonal anti-Ly-6G |
StemCell Technologies Inc |
Cat#60031 PB.1 |
| Rat monoclonal anti-Ly6C |
Life Technologies |
Cat#17-5932-82; RRID:AB_1724153 |
| Rat monoclonal anti-CD11b |
Life Technologies |
Cat#53-0112-82; RRID:AB_469901 |
| Rat monoclonal anti-F4/80 |
Life Technologies |
Cat#17-4801-80; RRID:AB_2784647 |
| Rat monoclonal anti-B220 |
Life Technologies |
Cat#17-0452-82; RRID:AB_469395 |
| Armenian hamster monoclonal anti-CD3 |
Life Technologies |
Cat#11-0031-82; RRID:AB_464882 |
| Rat monoclonal anti-CD8 |
BioLegend |
Cat#100712; RRID:AB_312751 |
| Rat monoclonal anti-CD4 |
Life Technologies |
Cat#48-0041-82; RRID:AB_10718983 |
| Mouse monoclonal anti-NK1.1 |
BioLegend |
Cat#108706; RRID:AB_313393 |
| Phospho-S6 Ribosomal Protein (Ser240/244) Antibody |
Cell Signaling Technology |
Cat#2215; RRID:AB_331682 |
| Phospho-S6 Ribosomal Protein (Ser235/236) Antibody |
Cell Signaling Technology |
Cat#4858; RRID:AB_916156 |
| Phospho-4E-BP1 (Thr37/46) (236B4) Rabbit mAb |
Cell Signaling Technology |
Cat#2855; RRID:AB_560835 |
| Phospho-Akt (Ser473) |
Cell Signaling Technology |
Cat#4051; RRID:AB_331158 |
| Phospho-Smad3 (Ser423/425) (C25A9) Rabbit mAb |
Cell Signaling Technology |
Cat#9520; RRID:AB_2193207 |
| Smad3 Antibody |
Cell Signaling Technology |
Cat#9513; RRID:AB_2286450 |
|
| Bacterial and virus strains |
|
| One Shot™ Stbl3™ Chemically Competent E. coli
|
Invitrogen |
C737303 |
|
| Biological samples |
|
| Immunotherapy Clinical Cohort Collection |
Patients treated with anti-PD(L)1 therapy either as single agent or in combination with other therapies between 2013 and 2019 at Massachusetts General Hospital |
Umbrella sequencing protocol Massachusetts General Hospital #13-416 |
|
| Chemicals, peptides, and recombinant proteins |
|
| Recombinant Human TGF-beta 1 |
R&D |
240-B |
| SB431542 |
Sigma Aldrich |
S4317 |
|
| Critical commercial assays |
|
| Cellular Senescence Detection Kit-SPiDER-βGal |
Dojindo, Kumamoto, Japan |
SG03 |
| Senescence Cells Histochemical Staining Kit |
Sigma Aldrich |
CS0030 |
| RNeasy Mini kit |
Qiagen |
74106 |
| Quantikine ELISA Human/Mouse/Rat/Porcine/Canine TGFβ1 |
R&D Systems |
DB100C |
| SMARTer Ultra Ultra-Low-input RNA kit, version 4 |
Clontech Laboratory |
012516 |
| Nextera XT DNA Library Preparation Kit |
Illumina |
FC-131-1024 |
| ERCC RNA Spike-In Mix |
ThermoFisher Scientific |
4456740 |
| KAPA SYBR® FAST Universal qPCR Kit |
Kapa Biosystems |
N/A |
| X-tremeGENE HP DNA transfection reagent |
Roche Applied Science |
6366236001 |
| Power SYBR Green PCR Master Mix |
Applied Biosystem |
4367659 |
| CellTiter-Glo® Cell Viability Assay |
Promega |
G9243 |
| SuperScript™ III First-Strand Synthesis SuperMix for qRT-PCR |
Invitrogen |
11752-050 |
| HiSpeed Plasmid Midi Kit (25) |
Qiagen |
12643 |
| Pierce BCA Protein Assay kit |
Thermo Scientific |
23227 |
|
| Deposited data |
|
| RNA-seq data |
This paper |
GEO: GSE223037
|
|
| Experimental models: Cell lines |
|
| A549 |
ATCC |
CCL-185 |
| HepG2 |
ATCC |
HB-8065 |
| TE4 |
ATCC |
HB-207 |
| Patient derived lung cancer associated fibroblasts |
Dr. Cyril Benes, Massachusetts General Hospital, MA 02129 |
Hu et al.44
|
| LLC-1 |
ATCC |
CRL-1642 |
|
| Experimental models: Organisms/strains |
|
| Mice (C57/BL6) |
Charles River Laboratories |
CCM21211956 |
|
| Oligonucleotides |
|
| Primers used for Real-time PCR reactions |
See Table S3
|
N/A |
|
| Software and algorithms |
|
| FlowJo software |
FlowJo |
FlowJo-Win64-10. |
| Halo software |
Indica Labs |
https://indicalab.com/halo/
|
| R software |
R core team, R foundation |
https://www.r-project.org/
|
| Illustrator software (26.5) |
Adobe |
https://www.adobe.com/products/illustrator.html
|
| Photoshop software (22.3.0) |
Adobe |
https://www.adobe.com/products/photoshop.html
|
| Fiji software |
ImageJ |
https://imagej.net/software/fiji
|
| TrimGalore |
https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/
|
0.43 |
| TopHat |
https://ccb.jhu.edu/software/tophat/index.shtml
|
2.1.1 |
| HTSeq |
See Ref.63. |
0.6.1 |
| GraphPad Prism 9.2.0 software |
GraphPad Software |
https://www.graphpad.com/scientific-software/prism/
|
| Bio Render |
Bio Render software |
CI24XNA2XR |
