KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Rat monoclonal anti-A/E (clone M5/114.15.2), Pacific Blue, APC, BV605 | Biolegend | Cat# 107620 |
| Cat# 107614 | ||
| Cat# 107639 | ||
| Rat monoclonal anti-Ly51 (clone 6C3), PE, Alexa Fluor 647 | Biolegend | Cat# 108308 |
| Cat# 108312 | ||
| Rat monoclonal anti-CD45 (clone 30-F11), Pacific Blue, Alexa Fluor 647, BV605, PE-Cy7 | Biolegend | Cat# 103126 |
| Cat# 103124 | ||
| Cat# 103155 | ||
| Cat# 103114 | ||
| Rat monoclonal anti-EpCAM (clone G8.8), biotinylated, PE, APC, APC-Cy7 | Biolegend | Cat# 118204 |
| Cat# 118206 | ||
| Cat# 118214 | ||
| Cat# 118218 | ||
| Human monoclonal anti-IRF8, PE | Miltenyi | Cat# 130-122-971 |
| Rabbit monoclonal anti-FoxA2 (clone D56D6) | Cell Signaling | Cat# 8186T |
| Mouse monoclonal anti-Hnf4a (clone K9218; CUT&Tag) | Abcam | Cat# ab41898 |
| Rabbit monoclonal anti-Hnf4a (clone EPR16885; IF) | Abcam | Cat# ab181604 |
| Rabbit polyclonal anti-FoxJ1 | Novus | Cat# NBP1-87928 |
| Rat monoclonal anti-GP2 (clone 2F11-C3), Alexa Fluor 488 | MBL | Cat# D278-A48 |
| Rabbit polyclonal anti-Grhl1 | Novus | Cat# NBP1-81321 |
| Rabbit polyclonal anti-H3K27ac | Abcam | Cat# ab4729 |
| Rabbit polyclonal anti-Sox8 | Proteintech | Cat# 20627-1-AP |
| Rabbit polyclonal anti-GFP | Abcam | Cat# ab290 |
| Chicken polyclonal anti-GFP | Aves Labs | Cat# GFP-1010 |
| Rabbit monoclonal anti-Slug (clone C19G7) | Cell Signaling | Cat# 9585 |
| Rabbit polyclonal anti-Pou2f3 | Sigma-Aldrich | Cat# HPA019562 |
| Rabbit monoclonal anti-Villin (clone SP145) | Abcam | Cat# ab130751 |
| Rabbit monoclonal anti-Desmin (clone D93F5) | Cell Signaling | Cat# 5332 |
| Mouse monoclonal anti-Acetylated-Tubulin (clone 6–11B-1) | Sigma-Aldrich | Cat# T7451 |
| Donkey polyclonal anti-rat IgG, FITC, Cy3, Alexa Fluor 647 | Jackson ImmunoResearch | Cat# 712-095-153 |
| Cat# 712-166-153 | ||
| Cat# 712-606-153 | ||
| Donkey polyclonal anti-mouse IgG, Cy5 | Jackson ImmunoResearch | Cat #715-175-150 |
| Donkey polyclonal anti-rabbit IgG, FITC, Cy3, Alexa Fluor 647 | Jackson ImmunoResearch | Cat# 711-096-152 |
| Cat# 711-165-152 | ||
| Cat# 711-606-152 | ||
| Donkey polyclonal anti-chicken IgY, FITC | Jackson ImmunoResearch | Cat# 703-095-155 |
| Armenian hamster monoclonal anti-CD29 (clone HMB1-1), biotinylated | Biolegend | Cat# 102203 |
| Rat monoclonal anti-H-2 (clone AF6-88.5), biotinylated | Biolegend | Cat# 116504 |
| Guinea pig polyclonal anti-rabbit IgG | Rockland | Cat# 611-201-122 |
| Rabbit polyclonal anti-mouse IgG | Abcam | Cat# ab46540 |
| Rat monoclonal anti-microfold (clone NKM16-2-4), PE | Miltenyi | Cat#130-102-150 |
| Rat monoclonal anti-CD31 (clone 390), Alexa Fluor 647 | Biolegend | Cat# 102416 |
| Mouse monoclonal anti-CD45.1 (clone A20), PE-Cy7 | Biolegend | Cat# 3110730 |
| Mouse monoclonal anti-CD45.2 (clone 104), APC-Cy7 | Biolegend | Cat# 109824 |
| Rat monoclonal anti-CD3e (clone KT3.1.1), FITC | Biolegend | Cat# 155604 |
| Rat monoclonal anti-CD4 (clone RM4–5), PE-eFluor 610 | eBioscience | Cat# 61-0042-82 |
| Rat monoclonal anti-CD8a (clone 53–6.7), FITC | Biolegend | Cat# 100706 |
| Rat monoclonal anti-TCRb (clone H57-597), PE-Cy7 | Biolegend | Cat# 109222 |
| Rat monoclonal anti-CD25 (clone 3C7), APC-Cy7 | Biolegend | Cat# 101918 |
| Rat monoclonal anti-CD73 (clone TY/11.8), PE | Biolegend | Cat# 127206 |
| Rat monoclonal anti-Foxp3 (clone FJK-16s), APC, PE-Cy7 | eBioscience | Cat# 17-5773-82 |
| Cat# 25-5773-82 | ||
| Armenian hamster monoclonal anti-CD11c (clone N418), PE-eFluor 610 | eBioscience | Cat# 61-0114-82 |
| Rat monoclonal anti-CD11b (clone M1/70), PerCP-Cy5.5 | Biolegend | Cat# 101228 |
| Rat monoclonal anti-CD19 (clone 6D5), PE | Biolegend | Cat# 152408 |
| Rat monoclonal anti-CD45R/B220 (clone RA3-6B2), FITC, PerCP-Cy5.5 | Biolegend | Cat# 103206 |
| Cat# 103236 | ||
| Rat monoclonal anti-CD44 (clone IM7), APC-Cy7 | Biolegend | Cat# 103028 |
| Mouse monoclonal anti-APC (clone APC003) | Biolegend | Cat# 408004 |
| TotalSeq-A anti-biotin hashtags | Biolegend | N/A |
| TotalSeq-A anti-mouse hashtags | Biolegend | Cat# 155801 |
| Cat# 155803 | ||
| Cat# 155805 | ||
| Cat# 155807 | ||
| Cat# 155809 | ||
| Cat# 155811 | ||
| Cat# 155813 | ||
| Cat# 155815 | ||
| Cat# 155817 | ||
| Cat# 155819 | ||
| Cat# 155821 | ||
| Chemicals, peptides, and recombinant proteins | ||
| Collagenase, from Clostridium histolyticum | Sigma-Aldrich | Cat# C6885 |
| Collagenase/Dispase | Roche | Cat# 10269638001 |
| Deoxyribonuclease I, from bovine pancreas | Sigma-Aldrich | Cat# D4527 |
| LIVE/DEAD Fixable Yellow | Invitrogen | Cat# L34959 |
| Hoescht 33342 | Sigma-Aldrich | Cat# B2261 |
| ProLong Diamond Antifade Mountant | Invitrogen | Cat# P36965 |
| Digitonin | Sigma-Aldrich | Cat# D141 |
| Spermidine | Sigma-Aldrich | Cat# S2501 |
| Concavalin A beads | Bangs Labs | Cat# BP531 |
| TCL RNA lysis buffer | Qiagen | Cat# 1031576 |
| Liberase TM | Roche | Cat# 5401119001 |
| Elastase, from porcine pancreas | Worthington Biochem | Cat# LS002292 |
| Tamoxifen | Sigma-Aldrich | Cat# T5648 |
| TRIzol | Invitrogen | Cat# 15596026 |
| Complete Freund’s adjuvant | Sigma-Aldrich | Cat# F5881 |
| YFP81–95 peptide (HDFFKSAMPEGYVQE) | Genscript | N/A |
| Dasatinib | LC Laboratories | Cat# D-3307 |
| PE- and APC-labeled YFP81–95:Ab tetramers | NIH Tetramer Core | N/A |
| Critical commercial assays | ||
| Anti-CD45 microbeads | Miltenyi | Cat# 130-052-301 |
| Anti-PE microbeads | Miltenyi | Cat# 130-048-801 |
| MACS LS columns | Miltenyi | Cat# 130-042-401 |
| Intracellular fixation/permeabilization buffer | eBioscience | Cat# 88-8824-00 |
| Permeabilization buffer (10X) | eBioscience | Cat# 00-8333-56 |
| Chromium Single Cell ATAC | 10X Genomics | Cat# 1000176 |
| Chromium Single Cell Gene Expression 3’ v3 | 10X Genomics | Cat# 1000269 |
| NEBNext 2X Master Mix | NEB | Cat# M0541 |
| 123count eBeads | Invitrogen | Cat# 01-1234-42 |
| Deposited data | ||
| Raw and analyzed scATAC-seq | This paper | GEO: GSE194233 |
| Raw and analyzed scRNA-seq | This paper | GEO: GSE194252 |
| Raw and analyzed bulk RNA-seq | This paper | GEO: GSE194232 |
| Raw and analyzed CUT&Tag | This paper | GEO: GSE194231 |
| Histone mark ChIP-seq | (Handel et al., 2018; Sansom et al., 2014) | GEO: GSE114713, GEO: GSE53109 |
| Human fetal scRNA-seq | (Park et al., 2020) | E-MTAB-8581 |
| Aire−/− RNA-seq | (Bansal et al., 2021) | GEO: GSE180935 |
| Aire ChIP-seq | (Bansal et al., 2017) | GEO: GSE92597 |
| Aire lineage-tracing scRNA-seq | (Wells et al., 2020) | GEO: GSE137699 |
| Experimental models: Organisms/strains | ||
| Mouse: C57BL/6J | The Jackson Laboratory | JAX #000664 |
| Mouse: B6.Aire | Our colony | (Anderson et al., 2002) |
| Mouse: B6.SJL-Ptprca Pepcb/BoyJ | The Jackson Laboratory | JAX #002014 |
| Mouse: B6(Cg)-Foxn1tm3(cre)Nrm/J | The Jackson Laboratory | JAX #018448 |
| Mouse: Foxj1tm1.1(cre/ERT2/GFP)Htg/J (backcrossed to B6) | The Jackson Laboratory | JAX #027012 |
| Mouse: B6.FVB(129S4)-Tg(Ckmm-cre)5Khn/J | The Jackson Laboratory | JAX #000664 |
| Mouse: B6.129X1-Gt(ROSA)26Sortm1(EYFP)Cos/J | The Jackson Laboratory | JAX #006148 |
| Mouse: B6.Sox8 | Dr. Koji Hase | (O’Bryan et al., 2008) |
| Mouse: B6.Spib | Dr. Tsuneyasu Kaisho | (Sasaki et al., 2012) |
| Recombinant DNA | ||
| 3Xflag-pA-Tn5-Fl | Dr. Steve Henikoff | Addgene #124601 |
| Software and algorithms | ||
| Cell Ranger ATAC v1.1.0 | 10X Genomics | N/A |
| SnapTools v1.4.1 | (Fang et al., 2021) | https://github.com/r3fang/SnapTools |
| SnapATAC v1.0.0 | (Fang et al., 2021) | https://github.com/r3fang/SnapATAC |
| macs2 v2.1.1.2 | (Zhang et al., 2008) | https://pypi.org/project/MACS2/ |
| IGV v2.4.14 | (Robinson et al., 2011) | https://software.broadinstitute.org/software/igv/ |
| bedtools v2.26.0 | (Quinlan and Hall, 2010) | https://bedtools.readthedocs.io |
| HOMER v4.9 | (Heinz et al., 2010) | http://homer.ucsd.edu |
| chromVAR v1.4.1 | (Schep et al., 2017) | https://github.com/GreenleafLab/chromVAR |
| HINT-ATAC v0.13.1 | (Li et al., 2019) | https://www.regulatory-genomics.org |
| STAR v2.7.3a | (Dobin et al., 2013) | https://github.com/alexdobin/STAR |
| Subread v2.0.0 | (Liao et al., 2013) | http://subread.sourceforge.net/ |
| R v4.1.0 | R Core Team | https://www.r-project.org/ |
| DESeq2 v1.28.1 | (Love et al., 2014) | https://bioconductor.org/packages/release/bioc/html/DESeq2.html |
| edgeR v3.34.0 | (Robinson et al., 2010) | https://bioconductor.org/packages/release/bioc/html/edgeR.html |
| Cell Ranger v6.1.0 | 10X Genomics | N/A |
| CITE-seq-count v1.4.3 | doi:10.5281/zenodo.2590196 | https://hoohm.github.io/CITE-seq-Count/ |
| Seurat v4.0.2 | (Hao et al., 2021) | https://satijalab.org/seurat/ |
| kallisto-bustools v0.24.4 | (Melsted et al., 2021) | https://www.kallistobus.tools/ |
| scVelo v0.2.2 | (Bergen et al., 2020) | https://scvelo.readthedocs.io/ |
| Trimmomatic v0.36 | (Bolger et al., 2014) | http://www.usadellab.org/cms/?page=trimmomatic |
| bowtie2 v2.2.9 | (Langmead and Salzberg, 2012) | http://bowtie-bio.sourceforge.net/bowtie2/ |
| SAMtools v1.3.1 | (Li et al., 2009) | http://www.htslib.org/ |
| picard v2.8.0 | N/A | http://broadinstitute.github.io/picard |
| deeptools v3.0.2 | (Ramírez et al., 2016) | https://deeptools.readthedocs.io |
| SEACR v1.3 | (Meers et al., 2019) | https://github.com/FredHutch/SEACR |
| Nikon Elements v5.02 | Nikon | N/A |
| Vision 4D v3.4 | Arivis | N/A |
| Flowjo v10.7.1 | BD Biosciences | N/A |
| Prism v7.0 | GraphPad | N/A |
| ImageJ v1.52 | (Schindelin et al., 2012) | https://imagej.net/software/fiji/ |