Antibodies
|
BUV737 CD8a |
BD |
Cat#612759; RRID: AB_2870090 |
BV421 CD8a |
BioLegend |
Cat#100738; RRID: AB_11204079 |
BV605 CD44 |
BD |
Cat#563058; RRID: AB_2737979 |
BUV395 Thy1.1 |
BD |
Cat#563804; RRID: AB_2632398 |
BUV496 Thy1.2 |
BD |
Cat#741046; RRID: AB_2870661 |
PE CD127 |
BioLegend |
Cat#135010; RRID: AB_1937251 |
PE-Cy7 KLRG1 |
Invitrogen |
Cat#25-5893-82; RRID: AB_1518768 |
PerCP-Cy5.5 CX3CR1 |
BioLegend |
Cat#149010; RRID: AB_2564494 |
BUV395 CXCR3 |
BD |
Cat#745689; RRID AB_2743174 |
BV711 CD49a |
BD |
Cat#564863: RRID: AB_2738987 |
BUV737 CD69 |
BD |
Cat#564684; RRID: AB_2738891 |
BUV395 CD103 |
BD |
Cat#740238; RRID: AB_2739985 |
BV480 Va2 |
BD |
Cat#746615; RRID: AB_2743895 |
R718 TCRb |
BD |
Cat#567299 |
PE Tbet |
BioLegend |
Cat#644810; RRID: AB_2200542 |
PE-Cy7 Eomes |
Invitrogen |
Cat#25-4875-82; RRID: AB_2573454 |
AF647 Tcf1 |
Cell Signaling Technology |
Cat#6709S |
ARID1A |
Abcam |
Cat#ab182561 |
BV421 IFNg |
BioLegend |
Cat#505830; RRID: AB_2563105 |
PE-Cy7 TNF |
BioLegend |
Cat#506324; RRID: AB_2256076 |
APC CCL3 |
R&D Systems |
Cat#IC450A |
PE IL-2 |
BioLegend |
Cat#503808; RRID: AB_315302 |
PE-Cy7 Granzyme B |
Biolegend |
Cat#372214; RRID: AB_2728381 |
PE Granzyme A |
ThermoFisher Scientific |
Cat#17-5831-82; RRID: AB_2573228 |
eBioscience™ Fixable Viability Dye eFluor™ 780 |
ThermoFisher Scientific |
Cat#65-0865-14 |
CellTrace Violet |
ThermoFisher Scientific |
Cat#C34557
|
DAPI |
BD |
Cat#564907 |
H3K27ac |
Abcam |
Cat#4729 |
H3K27me3 |
Cell Signaling Technology |
Cat#9733S |
ARID1A |
Cell Signaling Technology |
Cat#12354S |
BATF |
Brookwood Biomed |
Cat#4003 |
Tbet |
Cell Signaling Technology |
Cat#97135S |
ETS1 |
Cell Signaling Technology |
Cat#14069 |
Purified NA/LE Hamster anti-Mouse CD3e |
BD |
Cat#567114 |
Purified Hamster anti-Mouse CD28 |
BD |
Cat#553295; RRID: AB_394764 |
|
|
|
Bacterial and virus strains
|
LCMV Armstrong |
Kaech and Ahmed, 2001 |
NA |
Listeria monocytogenes GP33-41 |
Ananda Goldrath |
NA |
|
|
|
Chemicals, peptides, and recombinant proteins
|
GP33-41 peptide |
GenScript |
Cat#RP20091 |
Recombinant Murine IL-12p70 |
R&D Systems |
Cat#419-ML-010 |
Recombinant Murine IL-2 |
PEPROTECH |
Cat# 212-12 |
Recombinant Murine IL-18 |
R&D Systems |
Cat#9139-IL-010 |
ACBI1 |
opnMe |
NA |
BRM014 |
MedChemExpress |
Cat#HY-119374 |
Brefeldin A |
BioLegend |
Cat#420601 |
ACK Lysing Buffer |
VWR |
Cat#10128-804 |
eBioscience Foxp3/Transcription factor staining buffer set |
ThermoFisher Scientific |
Cat#00-5523-00 |
eBioscience 10X Permeabilization buffer |
ThermoFisher Scientific |
Cat#00-8333-56 |
Cytofix/Cytoperm |
BD |
Cat#554714 |
RPMI 1640 Medium |
GIBCO |
Cat#21875034 |
Fetal bovine serum |
Sigma-Aldrich |
Cat#F0804 |
L-Glutamine |
GIBCO |
Cat#25030081 |
2-Mercaptoethanol |
GIBCO |
Cat#21985023 |
Penicillin-streptomycin |
Invitrogen |
Cat#15140148 |
Collegenase D |
Sigma-Aldrich |
Cat#11088882001 |
DnaseI |
Sigma-Aldrich |
Cat#DN25-5G |
HBSS |
GIBCO |
Cat#14025092 |
Dithioerythritol |
EMD Millipore |
Cat#233152 |
1M HEPES |
ThermoFisher Scientific |
Cat#15630080 |
Alt-R S.p. Cas9 Nuclease V3 |
IDT |
Cat#1081059 |
pA/G-MNase |
Epicypher |
Cat#14-1048 |
|
|
|
Critical commercial assays
|
P3 Primary Cell 4D X Kit S |
Lonza |
V4XP-3032 |
|
|
|
Deposited data
|
Raw and analyzed data |
This paper |
GEO: GSE228381
|
Experimental models: Organisms/strains
|
Mouse: granzyme-B-Cre |
The Jackson Laboratory |
JAX: 003734 |
Mouse: C57BL/6J |
The Jackson Laboratory |
JAX: 000664 |
Mouse: Tg(TcrLCMV)327Sdz (P14) |
Pircher et al., 1989 |
MGI: 2665105 |
Mouse: Arid1atm1.1Mag |
Chandler et al., 2015 |
MGI: 5708705 |
Mouse: Tbx21 KO |
Szabo et al., 2002 |
JAX: 004648 |
|
|
|
Oligonucleotides
|
Recombinant DNA
|
MIGR1-Tbet |
Joshi et al., 2007 |
NA |
|
|
|
Software and algorithms
|
STAR |
Dobin et al, 2013 |
https://github.com/alexdobin/STAR
|
bwa-mem2 |
Vasimuddin et al., 2019 |
https://github.com/bwa-mem2/bwa-mem2
|
Homer |
Heinz et al., 2010 |
http://homer.ucsd.edu/homer/
|
DESeq2 |
Love et al., 2014 |
https://bioconductor.org/packages/release/bioc/html/DESeq2.html
|
ggplot2 |
|
https://cran.r-proiect.org/web/packages/ggplot2/index.html
|
deepTools |
Ramírez et al., 2016 |
https://github.com/deeptools/deepTools/
|
fgsea |
|
https://github.com/ctlab/fgsea
|