KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Mouse monoclonal anti-ACTIN | Millipore | Cat. MAB1501; RRID:AB_2223041 |
| Rabbit polyclonal anti-AMPKα | Cell Signaling | Cat. #2532S; RRID:AB_330331 |
| Rabbit polyclonal anti-p-AMPKα (T172) | Cell Signaling | Cat. #2535S; RRID:AB_331250 |
| Rabbit polyclonal anti-FKBP5 | Cell Signaling | Cat. #12210S; RRID:AB_2797846 |
| Rabbit polyclonal anti-FOXO4 | Cell Signaling | Cat. #9472S; RRID:AB_10831833 |
| Rabbit polyclonal anti-FOXO4 | Abcam | Cat. AB63254; RRID:AB_1140571 |
| Rabbit monoclonal anti-mTOR | Cell Signaling | Cat. #2983S; RRID:AB_2105622 |
| Rabbit polyclonal anti-p-mTOR (S2448) | Cell Signaling | Cat. #2971S; RRID:AB_330970 |
| Rabbit polyclonal anti-P70S6K | Cell Signaling | Cat. #9202S; RRID:AB_331676 |
| Rabbit polyclonal anti-p-P70S6K (T389) | Cell Signaling | Cat. #9205S; RRID:AB_330944 |
| Mouse monoclonal anti-S6 | Cell Signaling | Cat. #2317S; RRID:AB_2238583 |
| Rabbit monoclonal anti-pS6 (S240/244) | Cell Signaling | Cat. #5364S; RRID:AB_10694233 |
| Rabbit monoclonal anti-STAT1 | Cell Signaling | Cat. #14994S; RRID:AB_2737027 |
| Rabbit monoclonal anti-p-STAT1 (Y701) | Cell Signaling | Cat. #9167S; RRID:AB_561284 |
| Rabbit monoclonal anti-STAT3 | Cell Signaling | Cat. #12640S; RRID:AB_2629499 |
| Rabbit monoclonal anti-p-STAT3 (Y705) | Cell Signaling | Cat. #9145S; RRID:AB_2491009 |
| Rabbit monoclonal anti-STAT6 | Cell Signaling | Cat. #5397S; RRID:AB_11220421 |
| Rabbit polyclonal anti-p-STAT6 (Y641) | Cell Signaling | Cat. #9361S; RRID:AB_331595 |
| Rabbit monoclonal anti-TBX21 | Cell Signaling | Cat. #13232; RRID:AB_2616022 |
| Mouse monoclonal anti-GATA3 | Cell Signaling | Cat. #5852; RRID:AB_10835690 |
| Rat monoclonal anti-RORC | ThermoFisher Scientific | Cat. #14-6988-82; RRID: AB_1834475 |
| Mouse monoclonal anti-human CD3 | Biolegend | Cat. #317326; RRID:AB_11150592 |
| Mouse monoclonal anti-human CD28 | Biolegend | Cat. #302934; RRID:AB_11148949 |
| Mouse monoclonal anti-IFNγ | eBioscience | Cat. #16731885; RRID:AB_469251 |
| Mouse monoclonal anti-IL-4 | eBioscience | Cat. #16704885; RRID:AB_469211 |
| Hamster anti-mouse CD3 | Biolegend | Cat. #100340; RRID:AB_11149115 |
| Hamster anti-mouse CD28 | Biolegend | Cat. #102116; RRID:AB_11147170 |
| IRDye800CW Goat anti-rabbit IgG | Li-Cor Bioscience | Cat. #926–32211, RRID:AB_621843 |
| IRDye680RD Donkey anti-mouse IgG | Li-Cor Bioscience | Cat. #926–68072, RRID: AB_10954628 |
| IRDye680RD Goat anti-rabbit IgG | Li-Cor Bioscience | Cat. #926–68071, RRID: AB_10956166 |
| Bacterial and Virus Strains | ||
| One Shot TOP10 E. coli | ThermoFisher Scientific | Cat. C404003 |
| pLenti-c-Myc-DDK | Origene Technologies | Cat. PS1000064 |
| pLenti-c-Myc-DDK-FOXO4 | Origene Technologies | Cat. RC213185L1 |
| pLenti-c-mGFP | Origene Technologies | Cat. PS100071 |
| pLenti-c-mGFP-FOXO4 | Origene Technologies | Cat. RC213185L2 |
| pLVX-IRES-GFP | This paper | N/A |
| pLVX-FKBP5-IRES-GFP | This paper | N/A |
| Biological Samples | ||
| Human serum | From subject cohort - ClinicalTrials.gov ID-NCT02719899 | N/A |
| Chemicals, Peptides, and Recombinant Proteins | ||
| PMA | Sigma Aldrich | Cat. P8139 |
| Ionomycin | Sigma Aldrich | Cat. I0634 |
| Cell Stimulation Cocktail plus Protein Transport Inhibitors | eBioscience | Cat. 00-4975-03 |
| Brefeldin A | Biolegend | Cat. 420601 |
| DEAE-Dextran | Sigma Aldrich | Cat. D9885 |
| Human IL-2 Recombinant protein | Peprotech | Cat. 200–02B |
| Human IL-4 Recombinant protein | Peprotech | Cat. 200–04B |
| Human IL-6 Recombinant protein | Peprotech | Cat. 200–06B |
| Human IL-12 Recombinant protein | Peprotech | Cat. 200–12B |
| Human IL-23 Recombinant protein | Peprotech | Cat. 200–23B |
| Human TGF-β1 Recombinant protein | Peprotech | Cat. 100–21B |
| Human IL-1ββRecombinant protein | Peprotech | Cat. 200–01B |
| Critical Commercial Assays | ||
| Lyoplate Stain 175 See Suppl. Table 1 for Flow Cytometry Panel |
BD | Mat. 624215, Lot. 5260872 |
| Compensation Plate Stain 177 | BD | Mat. 624217, Lot. 5260875 |
| CyQuant Cell Proliferation Assay | Invitrogen | Cat. C7026 |
| Human IFNγβDuoset ELISA Kit | R&D Systems | Cat. DY285B |
| Human IL-4 Duoset ELISA Kit | R&D Systems | Cat. DY204 |
| Human IL-5 Duoset ELISA Kit | R&D Systems | Cat. DY205 |
| Human IL-13 Duoset ELISA Kit | R&D Systems | Cat. DY213 |
| Human IL-17 Duoset ELISA Kit | R&D Systems | Cat. DY317 |
| Human IL-22 Duoset ELISA Kit | R&D Systems | Cat. DY782 |
| Mouse IFNγβDuoset ELISA Kit | R&D Systems | Cat. DY485 |
| Mouse IL-4 Duoset ELISA Kit | R&D Systems | Cat. DY404 |
| Mouse IL-17 Duoset ELISA Kit | R&D Systems | Cat. DY421 |
| Deposited Data | ||
| Raw and analyzed data | This paper | GEO database: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE165149 Codes: https://github.com/NHLBI-BCB/PTNA |
| Human reference genome NCBI build 37, GRCh37 | Genome Reference Consortium | http://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/human/ |
| Experimental Models: Cell Lines | ||
| HEK293T | Dr. Toren Finkel’s Lab | N/A |
| Experimental Models: Organisms/Strains | ||
| Human Healthy Volunteer | NIH Clinical Center Blood Bank (NCT00001846) and ClinicalTrials.gov ID-NCT01143454 | N/A |
| Oligonucleotides | ||
| Human TBX21 | Integrated DNA Technologies | F: CGTGACTGCCTACCAGAAT R: ATCTCCCCCAAGGAATTGAC |
| Human GATA3 | Integrated DNA Technologies | F: GAACCGGCCCCTCATTAAG R: ATTTTTCGGTTTCTGGTCTGGAT |
| Human RORC | Integrated DNA Technologies | F: GCATGTCCCGAGATGCTGTC R: CTGGGAGCCCCAAGGTGTAG |
| Human EF1a | Integrated DNA Technologies | F: GTTGATATGGTTCCTGGCAAGC R: GCCAGCTCCAGCAGCCTTC |
| QuantiTech Primer Assays | Qiagen | N/A |
| Accell Non-targeting Control | Dharmacon | Cat. D-001910-01-20 |
| SMARTpool: Accell FOXO4 | Dharmacon | Cat. E-003016-00-0010 |
| SMARTpool: Accell FKBP5 | Dharmacon | Cat. E-004224-00-0010 |
| Recombinant DNA | ||
| psPAX2 | Addgene | Cat. 12260 |
| pMD2.G | Origene Technologies | Cat. 12259 |
| pCMV6-Entry-c-Myc-DDK | Origene Technologies | Cat. PS100001 |
| pCMV6-Entry-c-Myc-DDK-FOXO4 | Origene Technologies | Cat. RC213185 |
| pCMV3-C-Flag | Sino Biological Inc. | Cat. CV012 |
| pCMV3-C-FKBP5-Flag | Sino Biological Inc. | Cat. HG11487-CF |
| Software and Algorithms | ||
| GraphPad PRIZM7 | NIH | N/A |
| Image Studio | Li-Cor Biosciences | N/A |
| FlowJo 9.9.6 | FlowJo | N/A |
| FastQC | http://www.bioinformatics.babraham.ac.uk/projects/fastqc | N/A |
| HISAT2 | https://daehwankimlab.github.io/hisat2/ | NA |
| Trimmomatic | https://github.com/timflutre/trimmomatic | |
| Stringtie | https://github.com/gpertea/stringtie | NA |
| Ballgown | http://bioconductor.org/packages/release/bioc/html/ballgown.html | NA |
| WGCNA | https://cran.r-project.org/web/packages/WGCNA/index.html | NA |
| ClusterProfiler | https://bioconductor.org/packages/release/bioc/html/clusterProfiler.html | N/A |
| R and R Studio | http://www.r-project.org/ | N/A |
| Cytoscape 3.7.2 | http://cytoscape.org/ | N/A |
| GeneNet tool box | http://avigailtaylor.github.io/gntat14 | N/A |
| Find Individual Motif Occurrences | http://meme-suite.org/doc/fimo.html | N/A |
| PLS-DA | https://bioconductor.org/packages/mixOmics/ | |
| Other | ||
| Lymphocyte Separation Medium | MP Biomedicals | Cat. 0850494 |
| Human CD4+ T Cell Isolation Kit | Miltenyi Biotec | Cat. 130-096-533 |
| Mouse CD4+ T Cell Isolation Kit | Miltenyi Biotec | Cat. 130-104-454 |
| miRNeasy Micro Kit | Qiagen | Cat. 217084 |
| TruSeq Stranded Total RNA HT Kit | Illumina | Cat. 20020595 |
| Human T cell Nucleofector kit | Lonza | Cat. VVPA-1002 |
| Accell siRNA Delivery Media | Dharmacon | Cat. B-005000–100 |
| Polyjet In Vitro DNA Transfection Reagent | Signagen Laboratories | Cat. SL100688 |
| NucleoSpin RNA Kit | Macherey-Nagel | Cat. 740955 |
| First-strand Synthesis SuperMix | Invitrogen | Cat. 11752250 |
| FastStart Essential DNA Green Master Mix | Roche Life Science | Cat. 06924204001 |
| ImmunoCult Human CD3/CD28 T Cell Activator | Stemcell | Cat. 10971 |
| Trans-Blot Turbo Nitrocellulose Transfer Packs | Bio-Rad | Cat. 1704158 |
| Live/Dead Fixable Yellow Dead Cell Stain Kit | Invitrogen | Cat. L34968 |