KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| αCD4 (Clone: GK1.5) APC | Biolegend | Cat# 100412 |
| αCxcr4 | Abcam | Cat# ab124824 |
| αCathepsin E | R&D Systems | Cat# BAF1130 |
| αCxcr4 Biotin | BD Biosciences | Cat# 551968 |
| αStat4 (C-20) | Santa Cruz | Cat# sc-486X |
| αStreptavidin PE | BD Biosciences | Cat# BDB554061 |
| αH3K27Ac | Abcam | Cat# ab4729 |
| αCD3 (Clone: 145-2C11) | BD Biosciences | Cat# 553057 |
| αCD28 (Clone: 37.51) | BD Biosciences | Cat# 553294 |
| αIL-4 (11B11) | Biolegend | Cat# 504115 |
| PD-1 FITC (Clone: J43) | eBioscience | Cat# 11-9985-85 |
| Bcl-6 PerCP-Cy5.5 (Clone: K112-91) | BD Bioscience | Cat# 562198 |
| FOXP3 PE-Cy7 (Clone: FJK-16s) | eBioscience | Cat# 25-5773-82 |
| CXCR4 PE (Clone: 2B11) | BD Bioscience | Cat# 551966 |
| CXCR5 Brilliant Violet 421 (Clone: 2G8) | BD Biosciences | Cat# 562889 |
| CD3 APC-eFlour780 (Clone: 17A2) | eBioscience | Cat# 47-0032-82 |
| CD4 Qdot - 605 (Clone: RM4-5) | Invitrogen | Cat# Q10092 |
| CD8a V500 (Clone: 53-6.7) | BD Biosciences | Cat# 560776 |
| Bacterial and Virus Strains | ||
| Influenza Virus A/PR8/34 | generated in house | N/A |
| Biological Samples | ||
| N/A | ||
| Chemicals, Peptides, and Recombinant Proteins | ||
| 7-AAD | Calbiochem | Cat# 129935 |
| rmIL-12 | R&D systems | Cat# 419ML-010 |
| rhIL-2 | NCI repository | N/A |
| IMDM | Life Technologies | Cat# 12440-053 |
| FBS | Life Technologies | Cat# 26140-079 |
| Penicillin/Streptomycin | Life Technologies | Cat# 15140122 |
| 2-mercaptoethanol | Sigma | Cat# M3148 |
| iQSybr Green Mix | Biorad | Cat# 1708882 |
| Rnase, Dnase-free, High Concentration | Sigma-Aldrich | Cat# 11579681001 |
| Proteinase K | Clontech | Cat#9034 |
| Buffer NTB | Clontech | Cat# 740595.150 |
| GoTaq DNA Polymerase | Promega | Cat# M3005 |
| Critical Commercial Assays | ||
| MagCellect Mouse CD4+ T Cell Isolation Kit | R&D systems | Cat# MAGM202 |
| MagCellect Mouse CD8+ T Cell Isolation Kit | R&D systems | Cat# MAGM203 |
| Gentra Puregene Cell Kit | Qiagen | Cat# 158767 |
| Nucleospin RNA kit | Clontech | Cat# 740955.50 |
| PrimeScript first strand synthesis | Clontech | Cat# 6110A |
| TOPO TA Expression Kit | Invitrogen | Cat# K4800-01 |
| Nucleospin Gel and PCR Clean-Up Kit | Clontech | Cat# 740609.50 |
| Quant-iT dsDNA Assay kit, high sensitivity | Invitrogen | Cat# Q33120 |
| Deposited Data | ||
| RNA-seq | NCBI Gene Expression Omnibus | GSE129575 |
| ChIP-seq | NCBI Gene Expression Omnibus | GSE129576 |
| SuperSeries | NCBI Gene Expression Omnibus | GSE129577 |
| Experimental Models: Cell Lines | ||
| N/A | ||
| Experimental Models: Organisms/Strains | ||
| C57BL/6J | Jackson Laboratory; Bred at UAB facility with IACUC approval | Cat# 000664 |
| B6.SJL-PtprcaPepb/BoyJ | Jackson Laboratory; Bred at UAB facility with IACUC approval | Cat# 002014 |
| SJL/J | Jackson Laborarory | Cat# 000686 |
| C57BL/6NCrl | Charles River | Cat# 027 |
| B6.SJL-PtprcaPepcb/BoyCrCrl | Charles River | Cat# 564 |
| B6.SJL-Ptprca/BoyAiTac | Taconic Biosciences | Cat# 4007 |
| Germ-free B6.SJL-PtprcaPepcb/Boy | UAB Gnotobiotic Core | NA |
| F1: C57BL/6J x B6.SJL-PtprcaPepcb/BoyJ | Jackson Laboratory; Bred at UAB facility with IACUC approval | Cat# 000664, Cat# 002014 |
| B6.129S6-Tbx21tm1Glm/J | Jackson Laboratory; Bred at UAB facility with IACUC approval | Cat# 004648 |
| B6.129P2-Tcrbtm1Mom Tcrdtm1Mom/J | Jackson Laboratory | Cat# 002122 |
| Oligonucleotides | ||
| Atrnl1 Forward | Eurofins | CTACCGAGAGGATCTTCAGG |
| Atrnl1 Reverse | Eurofins | GACACAAGTTCCTTGACGTG |
| Ctse Forward | Eurofins | GAGCCTGACAGGAATCATTGG |
| Ctse Reverse | Eurofins | CAGACCCAGAATCCCATCAAAC |
| Ctse-(LTR) Forward | Eurofins | GTTTCCACACAGAGCTCAGC |
| Ctse-(LTR) Reverse | Eurofins | CAGACCTCTCGTTGTACTGC |
| Glul Forward | Eurofins | CATTCCAGGGAACTGGAATG |
| Glul Reverse | Eurofins | GAATGTGGTACTGGTGCCTC |
| Mfsd13a Forward | Eurofins | GCTCCTCTTTGGCATGGTTG |
| Mfsd13a Reverse | Eurofins | GATTGCTGAAAAAGGTCGTG |
| Additional oligonucleotide sequences can be found in Table S4 | ||
| Recombinant DNA | ||
| N/A | ||
| Software and Algorithms | ||
| GraphPad Online | GraphPad Software; http://www.graphpad.com/quickcalcs/ | N/A |
| FlowJo | FlowJo, LLC | v. 10 |
| TrimGalore! | https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/ | v. 0.4.4 |
| SAMtools | Li H et al., 2009 | v. 1.6.0 |
| BEDtools | Quinlan AR et al., 2010 | v. 2.26.0 |
| Bowtie2 | Langmead et al., 2009 | v 2.2.9 |
| Picard | http://broadinstitute.github.io/picard | v. 2.18.26 |
| MACS2 | Zhang et al., 2008 | v. 2.1.1 |
| deepTools | https://github.com/fidelram/deepTools | v. 3.1.3 |
| EnrichedHeatmap | https://github.com/jokergoo/EnrichedHeatmap | v. 1.12.0 |
| GREAT analysis | McLean et al., 2010 | v. 3.0.0 |
| STAR aligner | Dobin A et al., 2013 | v. 2.5.4b |
| Rsubread | Liao Y et al., 2014 | v. 1.32.2 |
| DESeq2 | https://github.com/mikelove/DESeq2 | v. 1.22.2 |
| Circlize | https://github.com/jokergoo/circlize | v. 0.4.5 |
| ComplexHeatmap | https://github.com/jokergoo/ComplexHeatmap | v. 1.20.0 |
| Other | ||