Antibodies |
CD45 |
BioLegend |
103116 |
CD3 |
Fisher |
460032-80 |
CD4 |
BioLegend |
100438 |
CD8 |
BioLegend |
100712 |
NK1.1 |
BioLegend |
108708 |
CD19 |
Miltenyi |
130-105-171 |
CD44 |
BioLegend |
103025 |
CD62L |
BioLegend |
104417 |
TIM3 |
BioLegend |
119721 |
LAG3 |
BioLegend |
125219 |
CXCR3 |
BioLegend |
126531 |
CD8a |
Thermofisher |
46-0081-82 |
CD11C |
BioLegend |
117330 |
F4/80 |
Thermofisher |
17-4801-80 |
CD206 |
BioLegend |
141705 |
CD11b |
BioLegend |
101217 |
I-A/I-E |
BioLegend |
107622 |
Ly6G |
BioLegend |
127617 |
Ly-6C |
BioLegend |
128035 |
CD103 |
BD |
564322 |
PD-L1 |
BD |
740614 |
CD45 |
BD |
564279 |
CD69 |
Invitrogen |
11-0691-85 |
FOXP3 |
BioLegend |
126404 |
CD25 |
Invitrogen |
56-0251-80 |
MHC Class I |
Invitrogen |
25-5958-80 |
CD137 |
Invitrogen |
46-1371-80 |
CD134 |
BD |
740945 |
CD3e |
BD |
563024 |
CD8 |
BioLegend |
100712 |
CD11b |
BioLegend |
101267 |
CD8-depleting antibody (YTS 169.4) |
BioXcell (West Lebanon, NH) |
BPO 117 |
Anti-OX-40 (OX-86) |
BioXcell (West Lebanon, NH) |
BE0031 |
Anti-4-1BB (LOB12.3) |
BioXcell (West Lebanon, NH) |
BPO169 |
Purified anti-mouse CD183 (CXCR3) |
Biolegend |
126502 |
Anti-CD3e |
Biolegend |
100302 |
Anti-CD28 |
Biolegend |
102102 |
Anti-mouse CD16/32 |
Biolegend |
156604 |
RB1 |
Cell signaling |
9309S |
Phospho- RB (S807/S811) rabbit antibody |
Cell signaling |
8516S |
S6 Ribosomal protein rabbit antibody |
Cell signaling |
2217S |
Phospho-S6 (S235/236) Ribosomal protein rabbit antibody |
Cell signaling |
2211S |
Phospho-S6 (S240/244) ribosomal protein rabbit antibody |
Cell signaling |
5364T |
Phospho-p70 S6 (T389) kinase rabbit antibody |
Cell signaling |
9234T |
p70 S6 kinase rabbit antibody |
Cell signaling |
2708T |
p21 Waf1/Cip1 rabbit antibody |
Cell signaling |
2947S |
β-actin rabbit antibody |
Cell signaling |
4970S |
β-tubulin rabbit antibody |
Cell signaling |
2146S |
HSP90 rabbit antibody |
Cell signaling |
4874S |
Bacterial and Virus Strains |
NA |
|
|
Biological Samples |
|
|
NA |
|
|
Chemicals, Peptides, and Recombinant Proteins |
Dulbecco’s modified Eagle’s medium/F12 |
Gibco |
11330032 |
GlutaMAX |
Gibco |
35050061 |
Gibco™ Penicillin-Streptomycin |
Gibco |
15-140-122
|
Fetal Bovine Serum
|
Gibco |
16000036
|
Palbociclib |
Pfizer |
NA |
Palbociclib |
LC laboratories |
P-7766 |
Rapamycin |
Tocris |
1292 |
N-acetylcysteine |
Sigma |
A9165
|
benzylserine |
Sigma |
13900 |
Bay876 |
Sigma |
SML1774 |
BKM120 |
Sigma |
10296 |
Maraviroc |
Adooq |
A10556 |
CellTracker Green CMFDA Dye |
Invitrogen |
C2925 |
Murine recombinant CCL5 |
Peprotech |
25007 |
MitoTracker Green |
Invitrogen |
T7514 |
CellRox Deep Red |
Invitrogen |
C10422 |
LysoTracker Deep Red |
Invitrogen |
L12492 |
DAPI |
Invitrogen |
D1306 |
Hoechst 33342 |
Invitrogen |
H1399 |
JC-1 Mitochondrial Membrane Potential Dye |
Thermo Fisher |
3168 |
Fixable Viability Dye eFluor™ 780 |
Invitrogen |
65-0865-14 |
LIVE/DEAD™ Fixable Aqua Dead Cell Stain Kit |
Thermofisher |
L34957 |
Everolimus |
LC Laboratories |
E-4040 |
10X Tris/Glycine/SDS Buffer |
Biorad |
1610772 |
Tris Buffer Saline |
Fisher Bioreagents |
BP2471-1 |
Tween 20 |
Fisher Bioreagents |
BP 337-500 |
Trans Blot Turbo RTA transfer kit |
Biorad |
170-4270 |
Bovine serum Albumin |
Fisher Bioreagents |
BP9706-100 |
Protein assay dye reagent concentrate |
Biorad |
5000006 |
Critical Commercial Assays |
Reverse Phase Protein Array (RPPA) |
Core Facility at MD Anderson Cancer Center (Houston, TX) |
NA |
RNA-easy mini kit |
Qiagen |
74104 |
iScript cDNA synthesis kit |
BioRad |
1708890 |
Quantiline ELISA HumanCXCL10/IP-10 |
R&D system |
DIP100 |
Quantiline ELISA Human CCL5/RANTES |
R%D system |
DRN00B |
Tumor tissue dissociation kit |
Miltenyi Biotech |
130-096-730 |
FXP3/ Transcription Factor Staining Buffer Set |
Invitrogen |
00-5523-00 |
SYBR-green master mix |
BioRad |
1725270 |
Senescence β-Galactosidase Staining Kit |
Sigma |
CS0030 |
Deposited Data |
N/A |
|
|
Experimental Models: Cell Lines |
MCF7 Cell line |
American Type Culture Collection |
ATCC® HTB22™ |
Cal120 cell line |
Carlos L. Arteaga Vanderbilt-Ingram Cancer Center. |
NA |
MDA-MB-453 cell line |
Carlos L. Arteaga Vanderbilt-Ingram Cancer Center. |
NA |
MDA-MB-468 cell line |
Carlos L. Arteaga Vanderbilt-Ingram Cancer Center. |
NA |
HCC70 cell line |
Carlos L. Arteaga Vanderbilt-Ingram Cancer Center. |
NA |
BT20 cell line |
Carlos L. Arteaga Vanderbilt-Ingram Cancer Center. |
NA |
PYMT cell line |
Philip Owens (VA Eastern Colorado Health Care System, Denver, CO) |
NA |
PYMT-OVA cell line |
David DeNardo (Washington University St. Louis, St. Louis MO) |
NA |
Experimental Models: Organisms/Strains |
C57BL/6 mice |
The Jackson Laboratory |
000664 |
C57BL/6 mice |
Charles River/NCI |
Strain code :027 |
OT-1 mice |
Marc Boothby, Richard O’Neil (Vanderbilt University, Nashville, TN) |
NA |
OT-1 mice |
The Jackson Laboratory |
003831 |
FVB-PYMT transgenic mice |
Harold Moses (Vanderbilt University, Nashville, TN) |
NA |
Oligonucleotides |
Primer: h CXCL10 F GTGGCATTCAAGGAGTACCTC |
Sigma |
NA |
Primer: h CXCL10 R TGATGGCCTTCGATTCTGGATT |
Sigma |
NA |
Primer: h CXCL9 F CCAGTAGTGAGAAAGGGTCGC |
Sigma |
NA |
Primer: h CXCL9 R AGGGCTTGGGGCAAATTGTT |
Sigma |
NA |
Primer: m CXCL9 F GGAGTTCGAGGAACCCTA |
Sigma |
NA |
Primer: m CXCL9 R GGGATTTGTAGTAGTGGATCGTGC |
Sigma |
NA |
Primer: m CCL5 F GCTGCTTTGCCTACCTCTCC |
Sigma |
NA |
Primer: m CCL5 R TCGAGTGACAAACACGACTGC |
Sigma |
NA |
Primer: h CCL5 F CCAGCAGTCGTCTTTGTCAC |
Sigma |
NA |
Primer: h CCL5 R CTCTGGGTTGGCACACACTT |
Sigma |
NA |
Recombinant DNA |
NA |
|
|
Software and Algorithms |
ImageJ |
NIH Image |
https://imagej.nih.gov/ij/index.html
|
Graphpad’s Prism 7.03 software |
GraphPad |
https://www.graphpad.com/
|
R (version3.3.0.) |
Bioconductor |
https://www.bioconductor.org/packages/devel/bioc/vignettes/limma/inst/doc/usersguide.pdf
|
Timer version 2.0 |
Li et al, 2020
|
http://timer.cistrome.org/
|
Morpheus |
Broad Institute |
https://software.broadinstitute.org/morpheus/
|
cBioPortal for Cancer Genomics version 3.6.3 |
Cerami et al, 2012
|
https://www.cbioportal.org/
|
Other |
N/A |
|
|