| Antibodies |
|
|
|
| anti-human CD3 purified (HIT3a) |
BD Biosciences |
Cat #555336; RRID: AB_395742 |
| anti-human CD28 (purified (CD28.2) |
BD Biosciences |
Cat #555725; RRID: AB_396068 |
| anti-human CD62L BV 421 (DREG-56) |
Biolegend |
Cat #302616; RRID: AB_493043 |
| anti-human CD4 PerCP Cy5.5 (A16A1) |
Biolegend |
Cat #357413; RRID: AB_2565666 |
| anti-human CD8 APC eFluor780 (RPA-T8) |
Thermo Fisher |
Cat #47-0088-42; RRID: AB_1272046 |
| anti-human CD25 Alexa 488 (BC960 |
Biolegend |
Cat #302616; RRID: AB_493043 |
| anti-human Granzyme B BV421 (GB11) |
BD Biosciences |
Cat #563389; RRID: AB_2738175 |
| anti-human pFoxO1 (S256) |
Cell Signaling Technologies |
Cat #9461 |
| anti-human FoxO1 (C29H4) |
Cell Signaling Technologies |
Cat #2880; RRID:AB_2106495 |
| anti-human NFIL3 (D5K80) |
Cell Signaling Technologies |
Cat #14312; RRID:AB_2798446 |
| anti-human BATF3 |
LS Bio |
Cat #LS-C413396-100 |
| anti-human Myc (D84C12) |
Cell Signaling Technologies |
Cat #5605; RRID:AB_1903938 |
| ant-human pMyc S62 (EPR17924) |
ABCAM |
Cat #ab185656 |
| anti-human GLUT1 PE(EPR3915) |
ABCAM |
Cat #ab209449 |
| anti-human TCF1 (C46C7) |
Cell Signaling Technologies |
Cat #2206; RRID:AB_2199300 |
| anti-mouse CD3 (2C11) |
BioXCell |
Cat #BE0001-1; RRID: AB_1107634 |
| anti-mouse CD4 BV605 (RM4-5) |
Biolegend |
Cat #100548; RRID: AB_2563054 |
| anti-mouse CD8 APC eFluor780 (53-6.7) |
Thermo Fisher |
Cat #47-0081-82; RRID: AB_1272185 |
| anti-mouse CD8 PE (53-6.7) |
Thermo Fisher |
Cat #12-0081-83; RRID: AB_465530 |
| anti-mouse CD11a FITC (M17/4) |
Thermo Fisher |
Cat #11-0111-85; RRID: AB_464931 |
| anti-mouse CD25 PE-Cy7 (PC61) |
Thermo Fisher |
Cat #25-0251-82; RRID: AB_469608 |
| anti-mouse CD27 FITC (LG.3A10) |
Thermo Fisher |
Cat #11-0271-85; RRID: AB_465002 |
| anti-mouse CD28 purified (37.51) |
BioXCell |
Cat #BE0015-1; RRID: AB_1107624 |
| anti-mouse CD28 APC (37.51) |
Thermo Fisher |
Cat #17-0281-82; RRID: AB_469374 |
| anti-mouse CD44 AF700 (IM7) |
Thermo Fisher |
Cat #56-0441-82; RRID: AB_494011 |
| anti-mouse CD44 FITC (IM7) |
Thermo Fisher |
Cat#11-0441-82; RRID: AB_465045 |
| anti-mouse CD45.1 BV605 (A20) |
Biolegend |
Cat #110738; RRID: AB_2562565 |
| anti-mouse CD45.2 PerCP(104) |
Biolegend |
Cat #109825; RRID: AB_893351 |
| anti-mouse CD62L PerCPCy5.5 (MEL-14) |
Thermo Fisher |
Cat #45-0621-82; RRID: AB_996667 |
| anti-mouse CD62L Alexa Fluor488 (MEL-14) |
Biolegend |
Cat #104420; RRID: AB_493376 |
| anti-mouse CD62L APC (MEL-14) |
Thermo Fisher |
Cat #17-0621-83; RRID: AB_469411 |
| anti-mouse CD62L eFluor 450 (MEL-14) |
Thermo Fisher |
Cat#48-0621-82; RRID: AB_1963590 |
| anti-mouse CD69 PE-Cy7 (H1.2F3) |
Biolegend |
Cat #104512; RRID: AB_493564 |
| anti-mouse CD71 PE (C2F2) |
BD Biosciences |
Cat #552367; RRID: AB_394744 |
| anti-mouse CD98 PE-Cy7 (RL388) |
Biolegend |
Cat #128214; RRID: AB_2750547 |
| anti-mouse CD127 eFluor 450 (A7R34) |
Thermo Fisher |
Cat #48-1271-82; RRID: AB_2016698 |
| anti-mouse CD137 PE (1AH2) |
Biolegend |
Cat # 106106; RRID: AB_2287565 |
| anti-mouse CD178 PE (MFL3) |
Biolegend |
Cat #106606; RRID: AB_313279 |
| anti-mouse CD215 PerCPeFluor 710 (DNT15Ra) |
Thermo Fisher |
Cat #46-7149-82; RRID: AB_11150247 |
| anti-mouse CD244 PE-Cy7 (244F4) |
Thermo Fisher |
Cat #25-2441-82; RRID: AB_2573432 |
| anti-mouse IFN-γ eFluor 450 (XMG1.2) |
Thermo Fisher |
Cat #48-7311-82; RRID: AB_1834366 |
| anti-mouse TNF-α PE-Cy7 (MO6-XT22BD) |
BD Biosciences |
Cat #557644; RRID: AB_396761 |
| anti-mouse IL-2 APC (JES6-5H4) |
Thermo Fisher |
Cat #17-7021-81; RRID: AB_469489 |
| anti-mouse IL-2 purified (S4B6) |
BioXCell |
Cat #BE0043-1; RRID: AB_1107705 |
| anti-mouse Eomes PerCP-eFluor710 (Dan11mag) |
Thermo Fisher |
Cat #46-4875-82; RRID:AB_10597455 |
| anti-mouse KLRG1 PE-Cy7 (2F1) |
Thermo Fisher |
Cat #25-5893-82; RRID: AB_1518768 |
| anti-mouse TCR Vα2 APC (B20.1) |
Thermo Fisher |
Cat #17-5812-82; RRID: AB_1659733 |
| anti-mouse TCR Vβ5 PE (MR9-4) |
BD Biosciences |
Cat #553190; RRID: AB_394698 |
| anti-mouse pSTAT5(Y694) PE (47/Stat5) |
BD Biosciences |
Cat #612567; RRID: AB_399858 |
| anti-mouse/human pS6(S240/244) Alexa 647(D68F8) |
Cell Signaling Technologies |
Cat #5044; RRID:AB_10829359 |
| anti-mouse/human pS6(S235/236) Alexa 488 (D57.2.2E) |
Cell Signaling Technologies |
Cat #4803; RRID:AB_916158 |
| Armenian hamster Ig control |
Biolegend |
Cat #400902 |
| Rat anti-mouse IgG2a control |
Thermo Fisher |
Cat #04-6200; RRID:AB_2532944 |
| anti-human pFoxO1 (T24) / FoxO3a (T32) |
Cell Signaling Technologies |
Cat #9464; RRID:AB_329842 |
| anti-human FoxO (C29H4) |
Cell Signaling Technologies |
Cat #2880; RRID:AB_2106495 |
| anti-human Hif1α (D1S7W) |
Cell Signaling Technologies |
Cat #36169; RRID:AB_2799095 |
| anti-human LAL |
Thermo Fisher |
Cat #PA5-27346; RRID: AB_2544822 |
| anti-human Tip47 |
Thermo Fisher |
Cat #PA1-46161; RRID:AB_2139115 |
| anti-human pAKT (S473) (D9E) |
Cell Signaling Technologies |
Cat #4060S; RRID:AB_231504 |
| anti-mouse AKT (C67E7) |
Cell Signaling Technologies |
Cat #4691S; RRID:AB_915783 |
| anti-human p110δ (D1Q7R) |
Cell Signaling Technologies |
Cat #34050; RRID:AB_2799043 |
| pZAP-70 antibody (Tyr319)/Syk (Tyr352) (65E4) |
Cell Signaling Technologies |
Cat #2717T; RRID:AB_2218658 |
| ZAP70 antibody (99F2) |
Cell Signaling Technologies |
Cat #2705S RRID:AB_2273231 |
| pERK antibody (Thr202/Tyr204) (D13.14.4E) |
Cell Signaling Technologies |
Cat #4370S; RRID:AB_2315112 |
| ERK antibody (137F5) |
Cell Signaling Technologies |
Cat #4695S; RRID:AB_390779 |
| anti-rabbit 488 |
Thermo Fisher |
Cat #A32731; RRID: AB_2633280 |
| anti-rabbit 647 |
Thermo Fisher |
Cat #A21245; RRID: AB_2535813 |
| anti-rabbit HRP |
Thermo Fisher |
Cat #31460; RRID: AB_228341 |
| anti-mouse HRP |
Thermo Fisher |
Cat #G-21040; RRID: AB_2536527 |
|
| Bacterial and virus strains |
|
|
|
| DH5a competent cells |
Thermo Fisher |
Cat #18265017 |
| Lymphocytic choriomeningitis virus Armstrong strain |
Provided by McGavern Lab, NINDS, NIH |
N/A |
| Influenza strain X31 |
Provided by M. Eichelberger, FDA McGuire Lab, NHGRI, NIH |
N/A |
| Influenza strain PR8 |
Provided by McGuire Lab, NHGRI, NIH |
N/A |
| Influenza strain X31-OVA |
Provided by McGuire Lab, NHGRI, NIH |
N/A |
| Influenza strain PR8-OVA |
Provided by McGuire Lab, NHGRI, NIH |
N/A |
|
| Biological samples |
|
|
|
| Blood Healthy Donor |
NIH Blood Bank |
N/A |
| Peripheral blood from patients with APDS |
Provided by H. Su and G. Uzel, NIAID |
N/A |
|
| Chemicals, peptides, and recombinant proteins |
|
|
|
| H-2Db LCMV NP396–404 (FQPQNGQFI) tetramer |
NIH Tetramer Facility |
N/A |
| H-2Db LCMV GP33–41 (KAVYNFATM) tetramer |
NIH Tetramer Facility |
N/A |
| H-2Db Influenza NP366–374 (ASNENMETM) tetramer |
NIH Tetramer Facility |
N/A |
| H-2Db Influenza PA224–233 (SSLENFRAYV) tetramer |
NIH Tetramer Facility |
N/A |
| OVA257–264 (SIINFEKL) |
AnaSpec |
Cat #AS-60193-1 |
| OVA T4 (SIITFEKL) |
AnaSpec |
Cat #AS-64403 |
| Influenza PA224–233
|
AnaSpec |
Cat #AS-61636 |
| Influenza NP366–374
|
AnaSpec |
Cat #AS-60624 |
| LCMV NP396–404 (FQPQNGQFI) |
AnaSpec |
Cat #AS-61700 |
| recombinant human IL-2 |
NIH AIDs Reagent Program |
Cat #136 |
| recombinant mouse IL-15 |
NCI Repository |
N/A |
| LIVE/DEAD™ Fixable Aqua 530 |
Thermo Fisher |
Cat #L34966
|
| LIVE/DEAD™ Fixable Near-IR |
Thermo Fisher |
Cat #L34976
|
| Annexin V APC |
Biolegend |
Cat #640920 |
| Annexin V binding buffer |
Biolegend |
Cat #422201 |
| CAL-101 |
Santa Cruz Biotechnology |
Cat #364453 |
| CAL-101, GS1101 |
Selleckchem |
Cat #S2226 |
| zVAD FMK |
R&D Systems |
Cat #FK001 |
| Akt inhibitor |
Calbiochem |
Cat #1240-17-1MG |
| Necrostatin-1 |
Cayman Chemical |
Cat #11658 |
| Liberase DL |
Millipore |
Cat #5401160001 |
| Oligomycin |
Sigma |
CAS # 1404-19-9 |
| Fluoro-carbonyl cyanide phenylhydrazone (FCCP) |
Sigma |
CAS # 370-86-5 |
| Antimycin A |
Sigma |
CAS # 1397-94-0 |
| Rotenone |
Sigma |
CAS # 83-79-4 |
| Lymphocyte Separation Medium |
MP Bio |
Cat # 50494X |
| Golgi Stop |
BD Biosciences |
Cat # 554724 |
| CellTrace Violet |
Thermo Fisher |
Cat #C34557
|
| cOmplete, Mini Protease Inhibitor Cocktail |
Sigma |
Cat #11836153001 |
| Sodium orthovanadate |
Sigma |
Cat # S6508-10G |
| Polybrene |
Sigma |
Cat #TR-1003-G |
| TRIzol™ Reagent |
Thermo Fisher |
Cat #15596026 |
| PowerUP™ SYBR™ Green Master Mix |
Thermo Fisher |
Cat# A25742 |
| SuperScriptTM IV First-Strand Synthesis |
Thermo Fisher |
Cat# 18091050 |
|
| Critical commercial assays |
|
|
|
| Fixation/Permeabilization Solution Kit |
BD Biosciences |
Cat #554717 |
| Foxp3 / Transcription Factor Staining Buffer Set |
Thermo Fisher |
Cat #00-5523-00 |
| PhiPhiLux-G1D2 kit |
OncoImmunin Inc |
Cat # A304R1G-5 |
| Naive CD8+ T cell isolation kit |
Miltenyibiotec |
Cat #130-096-543 |
| T cell enrichment columnns |
R&D Sytems |
Cat #MTCC-525 |
| PureLink Viral RNA/DNA Mini Kit |
Thermo Fisher |
Cat #12280050 |
| RNeasy Plus Mini Kit |
QIAGEN |
Cat #74136 |
| L-Lactate Assay kit |
Cayman Chemical |
Cat #700510 |
| Seahorse XFp Cell Mito Stress Test Kit |
Agilent |
Cat #103010-100 |
| Seahorse XF Glycolysis Stress Test Kit |
Agilent |
Cat #103020-100 |
|
| Deposited data |
|
|
|
| Bulk raw and processed RNA-Seq data |
GEO |
GEO: GSE155799
|
| Bulk raw and processed ATAQ-Seq data |
GEO |
GEO: GSE155799
|
|
| Experimental models: Cell lines |
|
|
|
| 293T |
ATCC |
CRL-11268 |
|
| Experimental models: Organisms/strains |
|
|
|
| C57BL/6 |
The Jackson Laboratory |
Stock# 000664 |
| C57BL/6-Tg(TcraTcrb)1100Mjb/J (OT-1) |
The Jackson Laboratory |
Stock# 003831 |
| B6.Cg-Tg(Prdm1-EYFP)1Mnz/J (Blimp-YFP) |
The Jackson Laboratory |
Stock# 008828 |
| B6.SJL-Ptprca Pepcb/BoyJ (CD45.1) |
The Jackson Laboratory |
Stock# 002014 |
|
Pi3kcd
E1020K/WT
|
Preite et al., 2018
|
N/A |
|
| Oligonucleotides |
|
|
|
| PR8-NS F 5′ TTC ACC ATT GCC TTC TCT TC 3′ |
IDT |
N/A |
| PR8-NS R 5′ CCC ATT CTC ATT ACT GCT TC 3′ |
IDT |
N/A |
| PR8-NP F 5′ CAG CCT AAT CAG ACC AAA TG 3′ |
IDT |
N/A |
| PR8-NP R 5′ TAC CTG CTT CTC AGT TCA AG 3′ |
IDT |
N/A |
| Beta-actin F 5′ GGC TGT ATT CCC CTC CAT CG 3′ |
IDT |
N/A |
| Beta-actin R 5′ CCA GTT GGT AAC AAT GCC ATG T 3′ |
IDT |
N/A |
|
| Recombinant DNA |
|
|
|
| Migr Foxo1 |
Provided by Crotty lab La Jolla Institute for Immunology |
N/A |
| Migr Foxo1AAA
|
Provided by Crotty lab La Jolla Institute for Immunology |
N/A |
|
| Software and algorithms |
|
|
|
| FlowJo v9.9.6 |
BD Bioscience |
https://www.flowjo.com
|
| Graphpad Prism version 7 |
GraphPad |
https://www.graphpad.com
|
| GSEA software |
Subramanian et al., 2005
|
https://www.gsea-msigdb.org/gsea/index.jsp
|
| Adobe Illustrator 2019 |
Adobe |
https://www.adobe.com
|
| MACS 1.4.2 |
Zhang et al., 2008
|
http://gensoft.pasteur.fr/docs/macs/1.4.2
|
| FastUniq |
Xu et al., 2012
|
https://sourceforge.net/projects/fastuniq/files/
|
| Homer v4.10 |
Heinz et al., 2010
|
http://homer.ucsd.edu/homer/
|
| Python 3.3.2 |
Python software foundation |
https://www.python.org
|
| R 3.4.0 |
R development core team |
https://www.r-project.org
|
| RStudio 1.0.143 |
RStudio Team |
https://www.rstudio.com
|
| IvG 2.3.42 |
The Broad Institute |
http://software.broadinstitute.org/software/igv/igv2.3
|
| CASAVA 1.8.2 |
Illumina |
http://bioweb.pasteur.fr/packages/pack@casava@1.8.2/
|
| TopHat 2.1.0 |
Anders et al., 2013
|
https://ccb.jhu.edu/software/tophat/index.shtml
|
| Cufflinks 2.2.1 |
Anders et al., 2013
|
http://cole-trapnell-lab.github.io/cufflinks/
|
| ClusterProfiler |
Yu et al., 2012
|
https://guangchuangyu.github.io/software/clusterProfiler/
|
| Partek Genomics Suite 6.6 |
Partek |
https://www.partek.com/partek-genomics-suite/
|
| Bowtie 0.12.8 |
Langmead et al., 2009
|
http://bowtie-bio.sourceforge.net/index.shtml
|
|
| Other |
|
|
|
| Seahorse Analyzer |
Aligent |
N/A |
| LSRII Analzyer |
BD Biosciences |
N/A |
| Fortessa Analyzer |
BD Biosciences |
N/A |
| Aria Cell Sorter |
BD Biosciences |
N/A |
| Novex WedgeWell 10%, Tris-Glycine |
Thermo Fisher |
Cat #XP00100BOX |
| Novex WedgeWell12% Tris glycine gels |
Thermo Fisher |
Cat #XP00120BOX |
| Trans-Blot Turbo Mini 0.2 μm Nitrocellulose |
BIO-RAD |
Cat #1704158 |
