| Antibodies |
| T cell stimulation anti-CD3e |
Thermo Fisher Scientific |
16-0031-86 |
| T cell stimulation anti-CD28 |
Thermo Fisher Scientific |
16-0281-86 |
| WB: anti-ZAP-70 (cl. D1C10E) |
Cell Signaling Tech. |
3165T |
| WB: anti-GAPDH (cl. 14C10) |
Cell Signaling Tech. |
85925SF |
| WB: anti-Lamin B1 (cl. D9V6H) |
Cell Signaling Tech. |
13435S |
| WB: anti-NOTCH1 (cl. D1E11) |
Cell Signaling Tech. |
3608T |
| WB: anti-RARα |
Cell Signaling Tech. |
2554 |
| WB: anti-RARγ1 (cl. D3A4) |
Cell Signaling Tech. |
8965T |
| WB: anti-CRABP2 |
One World Lab |
11250 |
| WB: anti-RARa |
Assay Biotechnology Company |
R12-3424 |
| WB: anti-HSP90 (cl. AC16) |
Santa Cruz |
sc-101494 |
| WB: anti-Flag (cl. M2) |
Millipore Sigma |
A2220 |
| WB: anti-AKT |
Cell Signaling Tech. |
9272 |
| WB: anti-Phospho-AKT |
Cell Signaling Tech. |
9271T |
| WB: anti-Phospho- PLCγ1 |
Cell Signaling Tech. |
2821 |
| WB: anti-Phospho-ZAP-70 (cl. 65E4) |
Cell Signaling Tech. |
2717 |
| WB: anti-Phospho-ERK1/2 (cl. D13.14.4E) |
Cell Signaling Tech. |
4370 |
| Activation: H-2Kb-SIINFEKL tetramer |
In house |
N/A |
| IP: anti-RARα |
Santa Cruz |
sc-551 |
| Flow /Conf. Im.: anti-CD16-CD32 (cl. 2.4G2) |
In house |
N/A |
| Flow: anti-CD4-APC (cl. RM4-5) |
BD |
553051 |
| Flow: anti-TCRgd-FITC (cl. GL3) |
BD |
553177 |
| Flow: anti-CD45.1-FITC (cl. A20) |
BD |
553775 |
| Flow: anti-CD44-V450 (cl. IM7) |
BD |
560452 |
| Flow: anti-CD8a-PercpCy5.5 (cl. 53-6.7) |
BD |
551162 |
| Flow: anti- CD8a-PeCy7 (cl. 53-6.7) |
BD |
552877 |
| Flow: anti-IFNg-BV711 (cl. XMG1.2) |
Biolegend |
505835 |
| Flow: anti-Il-17-PeCy7 (cl. TC11-18H10.1) |
Biolegend |
506922 |
| Flow: anti-CD8a-AF700 (cl. 53-6.7) |
Biolegend |
100730 |
| Flow: anti-CD4-AF700 (cl. GK1.5) |
Biolegend |
100430 |
| Flow: anti-FOXP3-PercpCy5.5 (cl. FJK-16s) |
Thermo Fisher Scientific |
45-5773-82 |
| Flow: anti-CCR9-FITC (cl. eBioCW-1.2) |
Thermo Fisher Scientific |
11-1991-85 |
| Flow: anti-TCRb-APCeF780 (cl. H57-597) |
Thermo Fisher Scientific |
47-5961-82 |
| Flow: anti-CD45.2-APC (cl.104) |
Thermo Fisher Scientific |
17-0454-82 |
| Flow: anti-RORgt-Pe (cl. AFKJS-9) |
Thermo Fisher Scientific |
12-6988-80 |
| Flow: anti-CD45-eF450 (cl. 30-F11) |
Thermo Fisher Scientific |
48-0451-82 |
| Flow: anti-FOXP3-AF488 (cl. FJK-16s) |
Thermo Fisher Scientific |
53-5773-82 |
| Flow: anti-FOXP3-Pe (cl. FJK-16s) |
Thermo Fisher Scientific |
12-5773-82 |
| Flow: anti-CD25-APC (cl. PC61.5) |
Thermo Fisher Scientific |
17-0251-82 |
| Flow: anti-CD4-eF450 (cl. RM4-5) |
Thermo Fisher Scientific |
48-0042-82 |
| Flow: anti-c-MYC-FITC (cl. 9E10) |
Thermo Fisher Scientific |
13-2511 |
| Conf. Im.: anti- CD3ε-biotin (cl. 2C11) |
Biolegend |
100304 |
| Conf. Im.: Goat anti-mouse IgG-DyLight™ 488 |
Biolegend |
405310 |
| Conf. Im.: Rabbit anti-Goat IgG-Alexa Fluor 647 |
Life Technology |
A21446 |
| Conf. Im.: anti-ZAP70 (cl. M20) |
Santa Cruz |
sc-1526 |
| Conf. Im.: anti-RARa (c. Ralpha10) |
Thermo Fisher Scientific |
MA1810A |
| Bacterial and virus strains |
| Listeria monocytogenes expressing OVA (ActA− Lm-OVA) |
(64) |
Gift |
| Biological samples |
|
|
| N/A |
|
|
| Chemicals, peptides, and recombinant proteins |
| LIVE/DEAD™ Fixable Yellow Dead Cell Stain |
Thermo Fisher Scientific |
L34959 |
| EDTA |
Thermo Fisher Scientific |
15575020 |
| Collagenase D |
Millipore Sigma |
11088858001 |
| DNAse I |
Millipore Sigma |
10104159001 |
| Human recombinant TGF-β |
R&D System |
240-B-002 |
| Trans retinoic acid |
Millipore Sigma |
R2625 |
| RAR antagonist LE540 |
FUJIFILM Wako Pure Chemical Corporation |
Distributor 123-04521 Barcode No 4987481365261 |
| RARα-selective antagonist |
Enzo lifescience |
Ro 41-5253 |
| RARγ-selective antagonist MM 11253 |
Tocris bioscience |
3822 |
| MEK1/2 inhibitor U0126 |
Invivogen |
tlrl-u0126 |
| PI3K inhibitor LY294002 |
Invivogen |
tlrl-ly29 |
| γ-secretase inhibitor GSI |
Tocris bioscience |
2870 |
| Human recombinant IL-2 |
Peprotech |
200-02 |
| AKT Inhibitor VIII |
Cayman Chemical Company, Inc |
14870 |
| DMSO |
Millipore Sigma |
D2438-5X |
| TRIzol reagent |
Thermo Fisher Scientific |
15596026 |
| TGX FastCast Acrylamide Solutions for SDS-PAGE gel |
Biorad |
1610171 |
| PVDF membrane |
Santa Cruz |
sc-3723 |
| NaCl |
Millipore Sigma |
S9888 |
| Tris base |
Santa Cruz |
sc-362305 |
| Glycerol |
Milliopore Sigma |
G5516 |
| Triton X-100 |
Milliopore Sigma |
X100 |
| Protease and phosphatase inhibitor mixture |
Milliopore Sigma |
11697498001 |
| ECL solution |
Santa Cruz |
sc-2048 |
| Polybrene |
Milliopore Sigma |
TR-1003-G |
| Poly I:C (HMW) |
InvivoGen |
tlrl-pic |
| OVA257-264 peptide |
AnaSpec Inc. |
AS-62572 |
| Poly-L-lysine |
R&D System |
3438-100-01 |
| NH4Cl |
Milliopore Sigma |
A4514 |
| Saponin |
Millipore Sigma |
47036 |
| Fish gelatin |
Milliopore Sigma |
G7041 |
| ProLong™ Gold Antifade Mountant with DNA Stain DAPI |
Thermo Fisher Scientific |
P36935 |
| Dithiothreitol |
Milliopore Sigma |
D2438 |
| Percoll |
Cytiva |
17089109 |
| Freund’s adjuvant |
BD |
263910 |
| M Tuberculosis H37Ra Dessicated |
BD |
231141 |
| Pertussis toxin |
List Biological Laboratories Inc |
180 |
| Zinc formalin |
Anatech Lt |
175 |
| Pro-Par Clearant |
Anatech Ltd |
510 |
| Conf. Im.: Streptavidine-Cyanine3 |
Biolegend |
405215 |
| Critical commercial assays |
| MACS CD8α+ T cell isolation kit |
Miltenyi Biotec |
130-096-543 |
| MACS CD4+ T cell isolation kit |
Miltenyi Biotec |
130-104-453 |
| CD11c-Microbeads Ultrapure |
Miltenyi Biotec |
130-125-835 |
| SureSelectXT RNA Direct Library Preparation kit |
Agilent Technologies |
G7564A |
| Pierce™ NE-PER® Nuclear and Cytoplasmic Extraction Reagent Kit |
Thermo Fisher Scientific |
78833 |
| JetPrime transfection reagent |
Polyplus transfection |
101000027 |
| Tandem mass tags (TMT) 11-plex reagents |
Thermo Fisher Scientific |
A34808 |
| Cell Trace Violet |
Thermo Fisher Scientific |
C34557 |
| Deposited data |
| Raw and analyzed data |
This paper |
GEO: GSE112609
|
| Database of Immune Cell Expression, Expression quantitative trait loci (eQTLs) and Epigenomics (DICE) |
(66) |
https://dice-database.org
|
| UCSC mouse genome assembly (GRCm38/mm10) |
UCSC Genome Browser Group
|
https://genome.ucsc.edu/cgi-bin/hgGateway
|
| Experimental models: Cell lines |
| Platinum-E |
Cell Biolabs |
RV-101 |
| Jurkat, Clone E6-1 |
ATCC |
TIB-152 |
| MCC-T CD4 T cell hybridoma cells |
(31) |
Gift |
| Mutant ES cell (LoxP sites flanking Crabp2 exons) |
EUCOMM |
HEPD0679_8_F03 |
| Experimental models: Organisms/strains |
| Mouse: C57BL/6J |
Jackson Lab. |
000664 |
| Mouse: Crabp2−/−(10 generation backcrossed to B6 background) |
Fawcett et al., 1995 |
Gift |
| Mouse: RARE-Luciferase (DR5) |
(39) |
Gift |
| Mouse: RAR403 (DOMINANT NEGATIVE) |
(28) |
Gift |
| Mouse: CD4-Cre |
(58) |
Gift |
| Mouse: E8I-cre |
(59) |
Gift |
| Mouse: OT-I TCRM |
Jackson Lab. |
003831 |
| Mouse: Act-mOVA |
(60) |
Gift |
| Mouse: RARα1−/−
|
Jackson Lab. |
023845 |
| Mouse: Crabp2flox/flox Crabp2tm1e(EUCOMM)Hmgu
|
This paper |
N/A |
| Mouse: Distal LCK-Cre |
Jackson Lab. |
Jackson Lab. |
| Oligonucleotides |
| RT-RARa F1: CAGTCAGTGGTTACAGCACACCGTC |
IDT DNA |
N/A |
| RT-RARa F2: GGACTCCGCTTTGGAATGGCTC |
IDT DNA |
N/A |
| RT-RARa F3: GATGTCCAGGCCCAAGTAGAAGCCAG |
IDT DNA |
N/A |
| RT-RARa R1: GCTGCAATCTGCTGCTCATGCCTACAC |
IDT DNA |
N/A |
| RT-RARa R2: GGACTGACCTGCTGCAATCTGCTG |
IDT DNA |
N/A |
| RT-RARa R3: CTGGCTTCTACTTGGGCCTGGACATC |
IDT DNA |
N/A |
| RT-RARa R4: CAGGCTGTGAAAGACTCCTGCGGCT |
IDT DNA |
N/A |
| RT-RARa R5: CAGCATGTGTTATGCCAGGCTGTGAAAG |
IDT DNA |
N/A |
| RT-RARa R6: CCAACAGCATGTGTTATGCCAGGCTG |
IDT DNA |
N/A |
| RT-RARa R7: TTCACCTCACTTCCTTCTCGGGAG |
IDT DNA |
N/A |
| RT-RARa R9: CCCCATAGTGGTAGCCGGATGATTTG |
IDT DNA |
N/A |
| RT-RARa R15: TCAGTGGAAACCCAGCAGGAACAGGTG |
IDT DNA |
N/A |
| RT-Hprt F: GTCGTGATTAGCGATGATGAACC |
IDT DNA |
N/A |
| RT-Hprt R: ATGACATCTCGAGCAAGTCTTTCAG |
IDT DNA |
N/A |
| qRT-Crabp2 F: CCCAGAGCTTTTAGCATTTCC |
IDT DNA |
N/A |
| qRT-Crabp2 R: GAAGATCTAAAGAGAAAGCCACCT |
IDT DNA |
N/A |
| qRT-cMYC F: TTGAAGGCTGGATTTCCTTTGGGC |
IDT DNA |
N/A |
| qRT-cMYC R: TCGTCGCAGATGAAATAGGGCTGT |
IDT DNA |
N/A |
| qRT-GADPH F: CAGATGCCTGCTTCACCA |
IDT DNA |
N/A |
| qRT-GADPH R: ATGGCCTTCCGTGTTCCT |
IDT DNA |
N/A |
| qRT-bACTIN F: CCAGAAGGACTGTTATGTGGGA |
IDT DNA |
N/A |
| qRT-bACTIN R: GACTCCGTGTTCAATGGGATAC |
IDT DNA |
N/A |
| qRT-HPRT F: GTCGTGATTAGCGATGATGAACC |
IDT DNA |
N/A |
| qRT-HPRT R: ATGACATCTCGAGCAAGTCTTTCAG |
IDT DNA |
N/A |
| Recombinant DNA |
| Plasmid: MSCV-IRES-GFP |
Addgene |
20672 |
| Plasmid: MSCV-IRES-Puromycin |
Addgene |
68469 |
| Plasmid: CD3ζ-GFP |
Katz et al., 2016 |
Gift |
| Software and algorithms |
| FlowJo software v10.8.0 |
Becton Dickinson & Company |
https://www.flowjo.com/solutions/flowjo/downloads
|
| HISAT2 |
(67) |
https://github.com/DaehwanKimLab/hisat2
|
| Tools (written in C using htslib) for manipulating next-generation sequencing data |
Samtools |
https://github.com/samtools/samtools
|
| Integrative Genomics Viewer |
Broad Institute |
https://software.broadinstitute.org/software/igv/
|
| FACSDIVA |
Becton Dickinson & Company |
https://www.bdbiosciences.com/en-us/products/software/instrument-software/bd-facsdiva-software
|
| Spectrum Mill |
Agilent/Broad Institute |
https://proteomics.broadinstitute.org/millhome.htm
|
| ZEN software |
ZEISS |
https://www.zeiss.com/microscopy/en/products/software/zeiss-zen.html
|
| Prism 8.4.2 |
GraphPad |
https://www.graphpad.com/features
|
| Other |
| Penicillin, streptomycin |
Thermo Fisher Scientific |
15140122 |
| Puromycin |
Invivogen |
ant-pr-1 |
| Balsticidin |
Invivogen |
ant-bl-05 |
