| Antibodies |
| anti-CD3ε |
Bio X Cell |
BE0001-1 |
| anti-CD28 |
Bio X Cell |
BE0015-5 |
| anti-CD44-PE/Cy7 |
BioLegend |
103030 |
| anti-c-Myc |
CST |
5605 |
| anti-Sirt1 |
Abcam |
ab110304 |
| anti-eIF4A1 |
Abcam |
ab31217 |
| anti-phospho-eIF4G1S1108
|
CST |
2441 |
| anti-eIF4G1 |
CST |
2858 |
| anti-phospho-mTORS2481
|
CST |
2974 |
| anti-mTOR |
CST |
4517 |
| anti-CD11c |
BioLegend |
117301 |
| anti-tubulin |
Invitrogen |
MA1-80189 |
| anti-tubulin |
Invitrogen |
PA5-19489 |
| anti-tubulin |
Invitrogen |
13-8000 |
| anti-RPL26 |
Sigma-Aldrich |
PLA0299 |
| anti- CD8-PerCP5.5 |
eBioscience |
45-0081-82 |
| anti-CD45.1-PE |
eBioscience |
12-0453-82 |
| anti-CD45.2-FITC |
eBioscience |
11-0454-82 |
| anti-TCR-Va2-APC |
eBioscience |
17-5812-82 |
| anti-CD62L-BV605 |
Biolegend |
104437 |
| anti-RagC |
CST |
5466 |
| anti-eIF4G1 |
CST |
8701 |
| anti-Raptor |
CST |
2280 |
| anti-lamin B1 |
abcam |
ab16048 |
| anti-S6 |
CST |
2317 |
| anti-Mcl1 |
CST |
94296 |
|
|
|
| donkey anti-mouse AFplus488 |
Invitrogen |
A32766 |
| donkey anti-rabbit AFplus555 |
Invitrogen |
A32794 |
| donkey anti-rat AF647plus |
Jackson ImmunoResearch |
712-605-153 |
| goat anti-hamster AF488 |
Jackson ImmunoResearch |
127-545-160 |
| donkey anti-rat CF488 |
Biotium |
20027 |
| donkey anti-goat CF568 |
Biotium |
20106 |
| donkey anti-rabbit AF647 |
Jackson ImmunoResearch |
711-605-152 |
| donkey anti-rabbit AF488plus |
ThermoFisher |
A32790 |
| donkey anti-rat CF568 |
Biotium |
20092 |
|
|
|
|
|
|
| Bacterial and Virus Strains |
| influenza virus A/X-31-OVA (H3N2) |
kindly gifted by P. Thomas |
|
| influenza virus A/PR/8-OVA (H1N1) |
kindly gifted by P. Thomas |
|
|
|
|
| Biological Samples |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| Chemicals, Peptides, and Recombinant Proteins |
| SIINFEKL peptide |
AnaSpec Inc. |
AS-60193-1 |
| human ICAM |
Huppa et al., 2010
|
|
| PMA |
MedChemExpress |
HY-18739 |
| Ionomycin |
MedChemExpress |
HY-13434 |
| Silvestrol |
MedChemExpress |
HY-13251 |
| Hippuristanol |
gifted by J. Pelletier |
N/A |
| Torin 1 |
Selleckchem |
S2827 |
| Dynarrestin |
Sigma |
SML2332 |
| Ciliobrevin D |
Selleckchem |
S2827 |
| Puromycin |
Tocris |
4098 |
| PFA |
Electron Microscopy Science |
15710 |
| PhosSTOP |
Sigma-Aldrich |
04906837001 |
| cOmplete, Mini Protease Inhibitor Cocktail |
Roche |
11836153001 |
| RNAse A |
ThermoFisher |
EN0531 |
| GlycoBlue |
Invitrogen |
AM9515 |
| M-MLV Reverse Transcriptase |
ThermoFisher |
2805013 |
| acryloyl-X-SE |
ThermoFisher |
A20770 |
|
|
|
| Critical Commercial Assays |
| CD11c MicroBeads |
Miltenyi Biotec |
130-108-338 |
| Dynabeads Untouched Mouse CD8 Cell Kit |
Invitrogen |
11417D |
| CellTrace Violet (CTV) Cell Proliferation Kit |
Invitrogen |
C34557 |
| High Sensitivity D5000 Screen Tape |
Aligent Technologies |
5067-5588 |
| Prolong Glass Antifade Mountant |
Invitrogen |
P36980 |
| Dynabeads Co-Immunoprecipitation Kit |
Invitrogen |
14321D |
| Dynabeads M-270 Epoxy beads |
Invitrogen |
14301 |
| Concanavalin A-coated magnetic beads |
Bang Laboratories |
BP531 |
| NEB Monarch PCR&DNA Cleanup Kit |
NEB |
T1030S |
| NEBNext Ultra II DNA Library Prep Kit |
NEB |
E7645S |
| AMPure SPRI beads |
Beckman-Coulter |
B23318 |
| RNeasy Mini Kit |
Qiagen |
74104 |
| PreAmp Master Mix |
Fluidigm |
1005580 |
| RNAscope Probe-Mm-Myc |
ACD |
413451 |
| RNAscope Fluorescent Miltiplex Detection Kit |
ACD |
320851 |
|
|
|
| Deposited Data |
| Single Cell RNAseq data |
BioProject |
PRJNA641918 |
|
|
|
|
|
|
|
|
|
|
|
|
| Experimental Models: Cell Lines |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| Experimental Models: Organisms/Strains |
| BCM1+ mice |
kindly provided by T. Schumacher (Gerlach et al., 2013) |
N/A |
| GFP-c-Myc fusion knock-in mice |
kindly provided by B. Sleckman (Huang et al., 2008) |
N/A |
| OT-I Tg (C57BL/6-Tg (TcraTcrb)1100Mjb/J) |
Jackson Laboratory |
003831 |
|
|
|
| Oligonucleotides |
| BCM-amp_1st fwd |
this paper |
N/A |
| AAT GAT ACG GCG ACC ACC GAG ATC TAC ACT CTT TCC CTA CAC GAC GCT C |
|
|
| BCM-amp_1st rev |
this paper |
N/A |
| GCT GAA CTT GTG GCC GTT TA |
|
|
| BCM-amp_2nd fwd |
this paper |
N/A |
| AAT GAT ACG GCG ACC ACC GAG ATC T |
|
|
| BCM-amp_2nd rev |
this paper |
N/A |
| CGT CCA GCT CGA CCA GGA T |
|
|
| c-myc fwd |
this paper |
N/A |
| TTT GTC TAT TTG GGG ACA GTG TT |
|
|
| c-myc rev |
this paper |
N/A |
| CAT CGT CGT GGC TGT CTG |
|
|
| Dro-rpl32-fwd |
this paper |
N/A |
| ATG CTA AGC TGT CGC ACA AAT G |
|
|
| Dro-rpl32-fwd |
this paper |
N/A |
| GTT CGA TCC GTA ACC GAT GT |
|
|
|
|
|
| Recombinant DNA |
| pAG-MNase |
Addgene |
123461 |
|
|
|
|
|
|
| Software and Algorithms |
| CellRanger VDJ v3.0.2 |
10x Genomics |
|
| MUSCLE v3.8.31 |
Edgar, 2004
|
|
| Seurat v3.1.4 |
Stuart et al., 2019
|
|
| Uniform Manifold Approximation and Projection (UMAP) |
McInnes et al., 2018
|
|
| Density-Based Spatial Clustering of Applications with Noise (DBSCAN) |
Ester et al., 1996
|
|
| normalized spatial intensity correlation (NSInC) |
Lui et al. under revision |
|
| Trim Galore v0.5.0 |
Krueger et al., 2020
|
|
| Bowtie 2 v2.3.5.1 |
Langmead and Salzberg, 2012
|
|
| Picard Mark Duplicate v2.19.0 |
Broad Institute |
|
| SAMtools v1.9 |
Li et al., 2009
|
|
| MACS v2.1.2 |
Zhang et al., 2008
|
|
| BEDTools v2.27.1 |
Quinlan and Hall, 2010
|
|
| bedGraphToBigWing v377 |
Kent et al., 2010
|
|
| deepTools plot Heatmap v3.2.1 |
Ramirez et al., 2016
|
|
|
|
|
|
|
|
| Slidebook 6 |
Intelligent Imaging Innovations |
|
| Imaris 9.5 |
Oxford Instruments |
|
| FlowJo 10.1r7 |
FlowJo, LLC |
|
| GraphPad Prism 8.0 |
GraphPad Software |
|
|
|
|
| Other |
|
|
|
|
|
|
|
|
|
|
|
|
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|
