KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Biotinylated Goat anti-mouse Areg polyclonal | R&D Systems | Cat# BAF989; RRID: AB_2060662 |
| Brilliant Violet 750 anti-mouse CD11b | BioLegend | Cat# 101267; RRID: AB_2810328, Clone: M1/70 |
| eFluor 450 anti-mouse CD11c | ThermoFisher | Cat# 48-0114-82; RRID: AB_1548654, Clone: N418 |
| PE-eFluor610 anti-mouse CD11c | ThermoFisher | Cat# 61-0114-82; RRID: AB_2574530, Clone: N418 |
| PE anti-mouse CD122 | BioLegend | Cat# 105906; RRID: AB_2125736, Clone: 5H4 |
| Brilliant Violet 421 anti-mouse CD127 | BioLegend | Cat# 135023; RRID: AB_10897948, Clone: A7R34 |
| Brilliant Violet 785 anti-mouse CD127 | BioLegend | Cat# 135037; RRID: AB_2565269, Clone: A7R34 |
| PE anti-mouse CD127 | TONBO biosciences | Cat# 50-1271-U100; RRID: AB_2621780, Clone: A7R34 |
| PE-Cy5 anti-mouse CD19 | BioLegend | Cat# 115510; RRID: AB_313645, Clone: 6D5 |
| eFluor 450 anti-mouse CD218 | ThermoFisher | Cat# 48-5183-82; RRID: AB_2574069, Clone: P3TUNIA |
| Brilliant Violet 605 anti-mouse CD24 | BioLegend | Cat# 101827; RRID: AB_2563464, Clone: M1/69 |
| eFluor 450 anti-mouse CD24 | ThermoFisher | Cat# 48-0242-82; RRID: AB_1311169, Clone: M1/69 |
| APC anti-mouse CD25 | ThermoFisher | Cat# 17-0251-82; RRID: AB_469366, Clone: PC61.5 |
| Brilliant UltraViolet 395 anti-mouse CD25 | BD Biosciences | Cat# 564022; RRID: AB_2722574, Clone: PC61.5 |
| PE anti-mouse CD25 | ThermoFisher | Cat# 12-0251-83; RRID: AB_465608, Clone: PC61.5 |
| PE-Cy5.5 anti-mouse CD25 | ThermoFisher | Cat# 35-0251-82; RRID: AB_11218898, Clone: PC61.5 |
| PE-Cy7 anti-mouse CD25 | ThermoFisher | Cat# 25-0251-82; RRID: AB_469608, Clone: PC61.5 |
| Brilliant Violet 421 anti-mouse CD304 | BioLegend | Cat# 145209; RRID: AB_2562358, Clone: 3E12 |
| PE-eFluor610 anti-mouse CD304 | ThermoFisher | Cat# 61-3041-82; RRID: AB_2574600, Clone: 3DS304M |
| Brilliant Violet 605 anti-mouse CD3ε | BioLegend | Cat# 100237; RRID: AB_2562039, Clone: 17A2 |
| Brilliant Violet 650 anti-mouse CD3ε | BioLegend | Cat# 100229; RRID: AB_11204249, Clone: 17A2 |
| PE-Cy7 anti-mouse CD3ε | TONBO biosciences | Cat# 60-0031-U100; RRID: AB_2621824, Clone: 145-2C11 |
| AlexaFluor 647 anti-mouse CD4 | BioLegend | Cat# 100530; RRID: AB_389325, Clone: RM4-5 |
| AlexaFluor 700 anti-mouse CD4 | BioLegend | Cat# 116022; RRID: AB_2715958, Clone: RM4-4 |
| Brilliant UltraViolet 496 anti-mouse CD4 | BD Biosciences | Cat# 564667; RRID: AB_2722549, Clone: GK1.5 |
| Brilliant Violet 510 anti-mouse CD4 | BioLegend | Cat# 100553; RRID: AB_2561388, Clone: RM4-5 |
| Brilliant Violet 605 anti-mouse CD4 | BioLegend | Cat# 100548; RRID: AB_2563054, Clone: RM4-5 |
| PerCP-Cy5.5 anti-mouse CD4 | BioLegend | Cat# 116012; RRID: AB_2563023, Clone: RM4-4 |
| Brilliant Violet 650 anti-mouse CD44 | BioLegend | Cat# 103049; RRID: AB_2562600, Clone: IM7 |
| Brilliant Violet 711 anti-mouse CD44 | BD Biosciences | Cat# 563971; RRID: AB_2738518, Clone: IM7 |
| AlexaFluor 700 anti-mouse CD45 | ThermoFisher | Cat# 56-0451-82; RRID: AB_891454, Clone: 30-F11 |
| Brilliant Violet 510 anti-mouse CD45 | BioLegend | Cat# 103137; RRID: AB_2561392, Clone: 30-F11 |
| Brilliant Violet 570 anti-mouse CD45 | BioLegend | Cat# 103136; RRID: AB_2562612, Clone: 30-F11 |
| Brilliant Violet 750 anti-mouse CD45 | BioLegend | Cat# 103157; RRID: AB_2734155, Clone: 30-F11 |
| Brilliant Violet 711 anti-mouse CD49a | BD Biosciences | Cat# 564863; RRID: AB_2738987, Clone: Ha31/8 |
| Brilliant Violet 711 anti-mouse CD5 | BioLegend | Cat# 100639; RRID: AB_2810322, Clone: 53-7.3 |
| Brilliant UltraViolet 737 anti-mouse CD62L | BD Biosciences | Cat# 565213; RRID: AB_2721774, Clone: MEL-14 |
| Brilliant Violet 510 anti-mouse CD62L | BioLegend | Cat# 104441; RRID: AB_2561537, Clone: MEL-14 |
| Brilliant Violet 570 anti-mouse CD62L | BioLegend | Cat# 104433; RRID: AB_10900262, Clone: MEL-14 |
| Brilliant Violet 605 anti-mouse CD62L | BioLegend | Cat# 104438; RRID: AB_2563058, Clone: MEL-14 |
| PE anti-mouse CD62L | ThermoFisher | Cat# 12-0621-83; RRID: AB_465722, Clone: MEL-14 |
| APC anti-mouse CD64 | BioLegend | Cat# 139306; RRID: AB_11219391, Clone: X54-5/7.1 |
| APC anti-mouse CD69 | ThermoFisher | Cat# 17-0691-82; RRID: AB_1210795, Clone: H1.2F3 |
| PE-Cy7 anti-mouse CD69 | ThermoFisher | Cat# 25-0691-82; RRID: AB_469637, Clone: H1.2F3 |
| Brilliant Violet 605 anti-mouse CD73 | BioLegend | Cat# 127215; RRID: AB_2561528, Clone: TY/11.8 |
| eFluor 450 anti-mouse CD73 | ThermoFisher | Cat# 48-0731-82; RRID: AB_1272196, Clone: TY/11.8 |
| PerCP-eFluor 710 anti-mouse CD73 | ThermoFisher | Cat# 46-0731-82; RRID: AB_10853356, Clone: TY/11.8 |
| AlexaFluor 532 anti-mouse CD8α | ThermoFisher | Cat# 58-0081-82; RRID: AB_11220469, Clone: 53-6.7 |
| AlexaFluor 700 anti-mouse CD8α | BD Biosciences | Cat# 557959; RRID: AB_396959, Clone: 53-6.7 |
| Brilliant Violet 510 anti-mouse CD8α | BioLegend | Cat# 100752; RRID: AB_2563057, Clone: 53-6.7 |
| Brilliant Violet 711 anti-mouse CD8α | BioLegend | Cat# 100759; RRID: AB_2563510, Clone: 53–6.7 |
| PE-Cy5 anti-mouse CD8α | ThermoFisher | Cat# 15-0081-83; RRID: AB_468707, Clone: 53–6.7 |
| AlexaFluor 700 anti-mouse CD8β.2 | BioLegend | Cat# 126618; RRID: AB_2563949, Clone: YTS156.7.7 |
| AlexaFluor 700 anti-mouse CD90.2 | BioLegend | Cat# 105320; RRID: AB_493725, Clone: 30-H12 |
| Brilliant Violet 786 anti-mouse CD90.2 | BD Biosciences | Cat# 564365; RRID: AB_2734760, Clone: 30-H12 |
| APC anti-mouse Egr2 | ThermoFisher | Cat# 17-6691-82; RRID: AB_11151502, Clone: erongr2 |
| PE anti-mouse Egr2 | ThermoFisher | Cat# 12-6691-82; RRID: AB_10717804, Clone: erongr2 |
| PE-Cy7 anti-mouse Eomes | ThermoFisher | Cat# 25-4875-82; RRID: AB_2573454, Clone: Dan11mag |
| FITC anti-mouse Foxp3 | ThermoFisher | Cat# 11-5773-82; RRID: AB_465243, Clone: FJK-16s |
| eFluor 660 anti-mouse Gata-3 | ThermoFisher | Cat# 50-9966-42; RRID: AB_10596663, Clone: TWAJ |
| efluor450 anti-mouse GITR | ThermoFisher | Cat# 48-5874-82; RRID: AB_1944394, Clone: DTA-1 |
| FITC anti-mouse GITR | ThermoFisher | Cat# 11-5874-82; RRID: AB_465286, Clone: DTA-1 |
| PerCP-Cy5.5 anti-mouse GM-CSF | BioLegend | Cat# 505410; RRID: AB_2562376, Clone: MP1-22E9 |
| AlexaFluor 532 anti-mouse Gr-1 | ThermoFisher | Cat# 58-5931-82; RRID: AB_11220477, Clone: RB6-8C5 |
| APC anti-mouse IFNγ | ThermoFisher | Cat# 17-7311-82; RRID: AB_469504, Clone: XMG1.2 |
| Brilliant UltraViolet 737 anti-mouse IFNγ | BD Biosciences | Cat# 564693; RRID: AB_2722494, Clone: XMG1.2 |
| PE anti-mouse IFNγ | TONBO biosciences | Cat# 50-7311-U100; RRID: AB_2621810, Clone: XMG1.2 |
| AlexaFluor 647 anti-mouse IgD | ThermoFisher | Cat# 51-5993-82; RRID: AB_837118, Clone: 11-26 |
| PE anti-mouse IL-13 | ThermoFisher | Cat# 12-7133-82; RRID: AB_763559, Clone: eBio13A |
| PE-Cy7 anti-mouse IL-13 | ThermoFisher | Cat# 25-7133-82; RRID: AB_2573530, Clone: ebio13A |
| Brilliant UltraViolet 395 anti-mouse IL-17 | BD Biosciences | Cat# 565246; RRID: AB_2722575, Clone: TC11-18H10 |
| eFluor 450 anti-mouse IL-17 | ThermoFisher | Cat# 48-7177-82; RRID: AB_11149503, Clone: eBio17B7 |
| AlexaFluor 700 anti-mouse IL-2 | BioLegend | Cat# 503818; RRID: AB_528931, Clone: JES6-5H4 |
| Brilliant Violet 510 anti-mouse IL-2 | BioLegend | Cat# 503833; RRID: AB_2562977, Clone: JES6-5H4 |
| PE anti-mouse IL-2 | ThermoFisher | Cat# 12-7021-82; RRID: AB_466150, Clone: JES6-5H4 |
| PerCP-eFluor 710 anti-mouse IL-22 | ThermoFisher | Cat# 46-7221-82; RRID: AB_10598646, Clone: 1H8PWSR |
| APC anti-mouse IL-4 | ThermoFisher | Cat# 17-7041-82; RRID: AB_469494, Clone: 11B11 |
| PE-Cy7 anti-mouse IL-4 | ThermoFisher | Cat# 25-7042-82; RRID: AB_469674, Clone: BVD6-24G2 |
| eFluor 450 anti-mouse Ki-67 | ThermoFisher | Cat# 48-5698-82; RRID: AB_11149124, Clone: SoIA15 |
| PE anti-mouse Ki-67 | ThermoFisher | Cat# 12-5698-82; RRID: AB_11150954, Clone: SolA15 |
| PE-eFluor610 anti-mouse Ki-67 | ThermoFisher | Cat# 61-5698-82; RRID: AB_2574620, Clone: SolA15 |
| PerCP-eFluor 710 anti-mouse Ki-67 | ThermoFisher | Cat# 46-5698-82; RRID: AB_11040981, Clone: SolA15 |
| Brilliant Violet 711 anti-mouse KLRG1 | BD Biosciences | Cat# 564014; RRID: AB_2738542, Clone: 2F1 |
| PE-eFluor610 anti-mouse KLRG1 | ThermoFisher | Cat# 61-5893-82; RRID: AB_2574630, Clone: 2F1 |
| APC anti-mouse Lag-3 | BioLegend | Cat# 125210; RRID: AB_10639727, Clone: C9B7W |
| Brilliant Violet 421 anti-mouse LAP | BioLegend | Cat# 141408; RRID: AB_2650898, Clone: TW7-16B4 |
| Brilliant Violet 711 anti-mouse Ly-6C | BioLegend | Cat# 128037; RRID: AB_2562630, Clone: HK1.4 |
| Brilliant Violet 480 anti-mouse MHCII | BD Biosciences | Cat# 566086; RRID: AB_2869739, Clone: M5/114.15.2 |
| APC-eFluor 780 anti-mouse NK1.1 | ThermoFisher | Cat# 47-5941-82; RRID: AB_2735070, Clone: PK136 |
| Brilliant Violet 510 anti-mouse NK1.1 | BioLegend | Cat# 108738; RRID: AB_2562217, Clone: PK136 |
| eFluor 450 anti-mouse NK1.1 | ThermoFisher | Cat# 48-5941-82; RRID: AB_2043877, Clone: PK136 |
| PE-Cy7 anti-mouse NK1.1 | ThermoFisher | Cat# 25-5941-82; RRID: AB_469665, Clone: PK136 |
| eFluor 660 anti-mouse NKp46 | ThermoFisher | Cat# 50-3351-82; RRID: AB_10598664, Clone: 29A1.4 |
| Brilliant Violet 785 anti-mouse PD1 | BioLegend | Cat# 135225; RRID: AB_2563680, Clone: 29F.1A12 |
| Brilliant Violet 421 anti-mouse RORγt | BD Horizon | Cat# 562894; RRID: AB_2687545, Clone: Q31-378 |
| Brilliant Violet 421 anti-mouse SiglecF | BD Biosciences | Cat# 562681; RRID: AB_2722581, Clone: E50-2440 |
| PE anti-mouse T-bet | ThermoFisher | Cat# 12-5825-82; RRID: AB_925761, Clone: 4B10 |
| APC anti-mouse TCRβ | ThermoFisher | Cat# 17-5961-82; RRID: AB_469481, Clone: H57-597 |
| APC-eFluor 780 anti-mouse TCRβ | ThermoFisher | Cat# 47-5961-82; RRID: AB_1272173, Clone: H57-597 |
| PE-eFluor610 anti-mouse TCRβ | ThermoFisher | Cat# 61-5961-82; RRID: AB_2574644, Clone: H57-597 |
| PerCP-Cy5.5 anti-mouse TCRβ | BioLegend | Cat# 109227; RRID: AB_1575176, Clone: H57-597 |
| Brilliant Violet 421 anti-mouse TCRγδ | BioLegend | Cat# 118119; RRID: AB_10896753, Clone: GL3 |
| PerCP-eFluor 710 anti-mouse TCRγδ | ThermoFisher | Cat# 46-5711-82; RRID: AB_2016707, Clone: GL3 |
| Brilliant Violet 605 anti-mouse TNFα | BioLegend | Cat# 506329; RRID: AB_11123912, Clone: MP6-XT22 |
| PE-Cy7 anti-mouse TCR Vβ5.1, 5.2 | BioLegend | Cat# 139508; RRID: AB_2566021, Clone: MR9-4 |
| PerCP-eFluor 710 anti-mouse TCR Vβ6 | ThermoFisher | Cat# 46-5795-82; RRID: AB_11150054, Clone: RR4-7 |
| AlexaFluor 647 anti-mouse TCR Vβ8.1, 8.2 | BioLegend | Cat# 118414; RRID: AB_1186096, Clone: KJ16-133.18 |
| redFluor™ 710 Anti-Mouse CD45.2 | TONBO biosciences | Cat# 80-0454-U100; RRID: AB_2621988, Clone: 104 |
| Rabbit anti-STAT5 monoclonal | Cell Signaling Technologies | Cat# 94205S; RRID: AB_2737403, Clone: D206Y |
| Rabbit anti-H3Kme1 polyclonal | Abcam | Cat# ab8895; RRID: AB_306847 |
| Hamster anti-mouse CD3ε monoclonal | BioXCell | Cat# BE0001-1; RRID: AB_1107634, Clone: 145-2C11 |
| Hamster anti-mouse CD28 monoclonal | BioXCell | Cat# BE0015-1; RRID: AB_1107624, Clone: 37.51 |
| Rat anti-mouse IL-2 monoclonal | BioXCell | Cat# BE0043; RRID: AB_1107702, Clone: JES6-1A12 |
| Rat anti-mouse IL-2 monoclonal | BioXCell | Cat# BE0043-1; RRID: AB_1107705, Clone: S4B6-1 |
| Chemicals, Peptides, and Recombinant Proteins | ||
| Recombinant human Interleukin-2 | NIH-NCI-FNLCRBRB | Cat# BULK Ro 23-6019 |
| DSG (disuccinimidyl glutarate) | ThermoFisher | Cat# 20593 |
| cOmplete™ Protease Inhibitor Cocktail | Millipore Sigma | Cat# 11697498001 |
| cOmplete™ EDTA-free Protease Inhibitor Cocktail | Millipore Sigma | Cat# 11836170001 |
| Collagenase A | Millipore Sigma | Cat# 11088793001 |
| Dnase I | Millipore Sigma | Cat# 10104159001 |
| Collagenase, Type IV | Worthington | Cat# LS004189 |
| Recombinant human TGF-β1 | R&D Systems | Cat# 240-B-002 |
| Recombinant human IL-2 | PeproTech | Cat# AF-200-02 |
| Recombinant mouse IL-4 | PeproTech | Cat# 214-14 |
| Recombinant mouse IL-6 | PeproTech | Cat# 216-16 |
| Diphtheria Toxin, Unnicked, from Corynebacterium diphtheriae | list labs | Cat# 150 |
| Tamoxifen | Millipore Sigma | Cat# T5648 |
| Proteinase K, recombinant, PCR grade | Millipore Sigma | Cat# 3115887001 |
| Uracil-DNA Glycosylase | New England Biolabs |
Cat# M0280 |
| Micrococcal Nuclease | New England Biolabs | Cat# M0247S |
| Rnasin® Ribonuclease Inhibitor, recombinant | Promega | Cat# 2511 |
| PBS57-loaded CD1d Tetramer (APCconjugated) | NIH Tetramer Core Facility |
https://tetramer.yerkes.emory.edu/ |
| Ghost Dye™ Violet 510 | Tonbo Bioscience | Cat# 13-0870-T500 |
| Ghost Dye™ Red 780 | Tonbo Bioscience | Cat# 13-0865-T500 |
| Zombie NIR™ Fixable Viability Kit | BioLegend | Cat# 423106 |
| CellTrace™ CFSE Cell Proliferation Kit | ThermoFisher | Cat# C34554 |
| TRIzol™ Reagent | ThermoFisher | Cat# 15596018 |
| Critical Commercial Assays | ||
| truChIP Chromatin Shearing Kit with Formaldehyde | Covaris | Cat# 520154 |
| Pierce Protein A/G Magnetic Beads | ThermoFisher | Cat# 88803 |
| Dynabeads™ Protein A for Immunoprecipitation | ThermoFisher | Cat # 10001D |
| GlycoBlue™ Coprecipitant | ThermoFisher | Cat# AM9516 |
| PowerUp™ SYBR™ Green Master Mix | ThermoFisher | Cat# A25741 |
| KAPA HyperPrep Kit | Roche | Cat# 7962347001 |
| AMPure XP PCR Purification | Beckman Coulter | Cat# A63881 |
| NEBNext® Library Quant Kit for Illumina® | New England Biolabs |
Cat# E7630S |
| Q5® Hot Start High-Fidelity 2X Master Mix | New England Biolabs |
Cat# M0494 |
| eBioscience™ Foxp3 / Transcription Factor Staining Buffer Set | ThermoFisher | Cat# 00-5523-00 |
| Cytofix/Cytoperm™ Fixation/Permeablization Kit |
BD Biosciences | Cat# 554714 |
| Dynabeads™ FlowComp™ Mouse CD8 Kit | ThermoFisher | Cat# 11462D |
| Dynabeads™ FlowComp™ Mouse CD4 Kit | ThermoFisher | Cat# 11461D |
| Dynabeads™ FlowComp™ Mouse Pan T (CD90.2) Kit | ThermoFisher | Cat# 11465D |
| SMARTScribe™ Reverse Transcriptase | TaKaRa | Cat# 639538 |
| SBA Clonotyping System-HRP | SouthernBiotech | Cat#5300-05 |
| SMARTer® PCR cDNA Synthesis Kit | TaKaRa | Cat# 634926 |
| Illumina Tagment DNA TDE1 Enzyme and Buffer Kit |
Illumina | Cat# 20034197 |
| MinElute Reaction Cleanup Kit | QIAGEN | Cat# 28204 |
| NEBNext® High-Fidelity 2X PCR Master Mix | New England Biolabs |
Cat# M0541L |
| EpiTect Bisulfite Kit | QIAGEN | Cat# 59104 |
| EpiTaq™ HS | Takara | Cat# R110B |
| NucleoSpin Gel and PCR Clean-up Kit | MACHEREYNAGEL | Cat# 740609.250 |
| TruSeq DNA PCR-Free LT Library Prep Kit | Illumina | Cat# 20015962 |
| Deposited Data | ||
| Cis-BP Database | (Weirauch et al., 2014) | http://cisbp.ccbr.utoronto.ca/ |
| C57BL/6 genome assembly (mm10) | (Mouse Genome Sequencing Consortium et al., 2002) | http://genome.ucsc.edu/ |
| C57BL/6 genome assembly (mm9) | (Mouse Genome Sequencing Consortium et al., 2002) | http://genome.ucsc.edu/ |
| UCSC Genome Browser | (Kent et al., 2002) | http://genome.ucsc.edu/ |
| ATAC-seq (Figure 1A) | This study | Accession: GSE164118 |
| ATAC-seq (Figure S1A) | This study | Accession: GSE164118 |
| STAT5 ChIP-seq | This study | Accession: GSE164118 |
| RNA-Seq | This study | Accession: GSE164118 |
| ATAC-seq (Figures 6, S6, and S7) | This study, (Hemmers et al., 2019) |
Accession: GSE164118 |
| TCR-seq | This study | Accession: GSE164118 |
| Experimental Models: Organisms/Strains | ||
| Mouse: Foxp3GFP: B6.129-Foxp3tm2Ayr/J | (Fontenot et al., 2005) |
RRID: IMSR_APB:3598 |
| Mouse: Foxp3DTR: B6.129(Cg)- Foxp3tm3(DTR/GFP)Ayr/J |
(Kim et al., 2007) | RRID: IMSR_JAX:016958 |
| Mouse: Aire−/−: B6.129S2-Airetm1.1Doi/J | (Anderson et al., 2002) | RRID: IMSR_JAX:004743 |
| Mouse: Ndor1UBC-creER: B6.Cg-Ndor1Tg(UBCcre/ERT2)1Ejb/1J | (Ruzankina et al., 2007) | RRID: IMSR_JAX:007001 |
| Mouse: TcrbΔTcrdΔ (B6.129P2Tcrbtm1MomTcrdtm1Mom/J) | (Mombaerts et al., 1992) | RRID: IMSR_JAX:002122 |
| Mouse: CD45.1: B6.SJL-PtprcaPepcb/BoyJ | (Shen et al., 1985) | RRID: IMSR_JAX:002014 |
| Mouse: CNS0FL | This study | N/A |
| Mouse: CNS0Δ | This study | N/A |
| Mouse: Il2−/− | This study | N/A |
| Oligonucleotides | ||
| Primers for STAT5 ChIP, see Table S4 | This study | N/A |
| Primers for Bisulfite sequencing, see Table S4 | This study | N/A |
| Primers for TCR sequencing, see Table S4 | This study | N/A |
| Primers for ATAC-sequencing libraries, see Table S4 | (Buenrostro et al., 2013) | N/A |
| Primers for H3K4me1 ChIP, see Table S4 | This study | N/A |
| All oligonucleotides | Integrated DNA Technologies | https://www.idtdna.com/ |
| Software and Algorithms | ||
| FIMO | (Grant et al., 2011) | http://meme-suite.org/doc/fimo.html |
| PHAST | (Pollard et al., 2010; Siepel et al., 2005) |
http://compgen.cshl.edu/phast/ |
| FlowJo (v10) | BD Biosciences | https://www.flowjo.com/solutions/flowjo |
| R | (R Core Team, 2020) | https://cran.r-project.org/ |
| MIGEC | (Shugay et al., 2014) | https://milaboratory.com/software/migec/ |
| VDJTools | (Shugay et al., 2015) | https://milaboratory.com/software/vdjtools/ |
| immunarch | (Nazarov et al., 2020) | https://immunarch.com/ |
| Trimmomatic | (Bolger et al., 2014) | http://www.usadellab.org/cms/?page=trimmomatic |
| STAR | (Dobin et al., 2013) | https://github.com/alexdobin/STAR |
| samtools | (Li et al., 2009) | http://www.htslib.org/ |
| Genrich | (Gaspar, 2020) | https://github.com/jsh58/Genrich |
| GenomicAlignments (R package) | (Lawrence et al., 2013) | https://doi.org/doi:10.18129/B9.bioc.GenomicAlignments |
| DESeq2 (R Package) | (Love et al., 2014) | https://doi.org/doi:10.18129/B9.bioc.DESeq2 |
| HOMER | (Heinz et al., 2010) | http://homer.ucsd.edu/homer/motif/ |
| bedtools | (Quinlan and Hall, 2010) | https://github.com/arq5x/bedtools2 |
| wigToBigWig | (Kent et al., 2010) | https://hgdownload.cse.ucsc.edu/admin/exe/ |
| BSMAP | (Xi and Li, 2009) | https://code.google.com/archive/p/bsmap/ |
| ggplot2 (R package) | (Wickham, 2009) | https://ggplot2.tidyverse.org/ |
| Prism v9 | GraphPad | https://www.graphpad.com/scientific-software/prism/ |
| Other | ||
| Instrument: M220 Focused-ultrasonicator | Covaris | Cat# 500295 |
| Instrument: CFX384 Touch Real-Time PCR Detection System | BIO-RAD | Cat# 1855485 |
| Instrument: QuantStudio™ 6 Flex RealTime PCR System | ThermoFisher | Cat# 4485691 |
| Instrument: Aurora | Cytek | https://cytekbio.com/pages/aurora |
| Instrument: LSR II | BD Biosciences | https://www.bdbiosciences.com/enus/instruments |
| Instrument: Aria II | BD Biosciences | https://www.bdbiosciences.com/enus/instruments |
| Instrument: Synergy HTX | BioTek | Cat# S1A |
| Instrument: Bioruptor® Twin | diagenode | Cat # UCD-400 |