Supplementary MaterialsDocument S1. Source Data, Related to Figures 3 and S3 Physique?3A (sort layout and post-sort QC); Figures 3B and 3D (TCR sequences); Physique?3C (inverse Simpson Index); Figures 3EC3G (TCR sequences); Physique?S3B (Seurat data output); Physique?S3C (Rpkm table and Deseq2). mmc4.xlsx (8.3M) GUID:?98604599-B145-4C00-BD1B-D1D9BEC990CF Table S4. Source Data, Related to Figures 4 and S4 Physique?4A (RNA velocity coordinates and vectors); Physique?4B (flow-cytometry data and statistics); Physique?4C (circulation cytometry data and statistics); Physique?4D (flow-cytometry data and statistics); Physique?4E (flow-cytometry data and statistics); Physique?4F (flow-cytometry data and statistics). mmc5.xlsx (759K) GUID:?E7F3ACD2-7358-4FAD-BAE4-BFA9FBA59720 Table S5. Source Data, Related to Figures 5 and S5 Physique?5A (data used to generate heatmap); Physique?5E (quantity of regions open); Physique?5F (raw data and p values); Physique?5G (distance from motif spreadsheet); Physique?5H (flow-cytometry data and statistics). mmc6.xlsx (21M) GUID:?ACD12A2A-0A6E-48DD-9237-3D08A16BB147 Table S6. Source Data, Related to Figures 6 and S6 Physique?6A (Dataset collection, p value (log), description of dataset, cell type utilized for chromatin IP, antibody utilized for chromatin IP, data source identifier, comparison name, direction, quantity of regions in public dataset, and quantity of overlapping regions (opening BML-284 (Wnt agonist 1) chromatin regions BML-284 (Wnt agonist 1) in progenitors with target public region set); Physique?6B (distance from motif spreadsheet); Physique?6C (percentage of overlapping regions); Physique?6E (flow-cytometry data and statistics); Physique?S6B (flow-cytometry data and statistics); Physique?S6C (flow-cytometry data and statistics); Physique?S6H (flow-cytometry data and statistics). mmc7.xlsx (172K) GUID:?143ED5D8-D4F4-47C0-9DB8-A46AB1537CF0 Table S7. Source Data, Related to Figures 7 and S7 Physique?7A (flow-cytometry data and statistics); Physique?7B (flow-cytometry data and statistics); Physique?7C (flow-cytometry data and statistics); Physique?7D (flow-cytometry data and statistics); Physique?7E (flow-cytometry data and statistics); Physique?7F (raw data for PCA); Physique?7G (data for heatmap); Physique?7H (fold change versus p value dataset); Physique?7I (de novo motif analysis data); Physique?7J (distance from motif spreadsheet); Physique?7K (peak opening table); Physique?7M (peak opening table); Physique?S7A (gene expression data for heatmap); Physique?S7B (gene expression and flow-cytometry data for heatmap); Physique?S7D (gene expression and circulation cytometry data for heatmap). mmc8.xlsx (64M) GUID:?BBDFFE42-30C7-4FA3-B7B4-00A247505EEF Document S2. Article plus Supplemental Information mmc9.pdf (16M) GUID:?D025789A-DF82-4001-8A8E-FFCFED365E2F Data Availability StatementThe accession figures for the RNA-Seq, scRNA-Seq, scTCR-Seq, and ATAC-seq data reported in this paper are: Gene Expression Omnibus (GEO) “type”:”entrez-geo”,”attrs”:”text”:”GSE130884″,”term_id”:”130884″GSE130884. Summary Specialized regulatory T (Treg) cells accumulate and?perform homeostatic and regenerative functions in nonlymphoid tissues. Whether common precursors for nonlymphoid-tissue Treg cells exist and how they Rabbit Polyclonal to STK17B differentiate remain elusive. Using transcription factor nuclear factor, interleukin 3 regulated (transcription factor (TF) motifs recognized in the core tisTregST2-signature (n?= 3C4). (F) Normalized ATAC-seq transmission from different cell types at core ATAC-seq peaks transporting a bZIP or GATA binding motif, respectively (n?= 3C4). (G) ATAC-seq data for the and loci with all cell types BML-284 (Wnt agonist 1) shown in (B). All datasets group-normalized to maximum peak height indicated in brackets. (H) Unsupervised hierarchical clustering of 1 1,345 ATAC peaks from pairwise comparisons of tisTregST2 populations from VAT, lung, skin, and colon (n?= 3C4). (I) Pathway enrichment of genes near differential peaks for tisTregST2 from different tissues (database: WikiPathways 2016). (J) ATAC-seq data for the and loci as in (G) (n?= 3C4). Data representative of impartial experiments or cell sorts. See also Figure? S1 and Table S1. motif discovery recognized DNA consensus binding motifs of several transcription factor families including bZIP (made up of AP-1 factors), ETS, nuclear factor B (NF-B), NRL and GATA in the core tisTregST2 cell-specific ATAC-seq peaks (Physique?1E). The expected strong ATAC-seq signals in tisTregST2 populations at respective transcription factor consensus motifs are displayed exemplarily for bZIP and GATA motifs (Physique?1F). Using gene expression data from RNA sequencing (RNA-seq) BML-284 (Wnt agonist 1) of tisTregST2 populations, as a GATA family member and Batf (as a bZIP family member were identified as being specifically upregulated in tisTregST2 cells and therefore likely contributing to the core tisTregST2 gene-regulatory program (Figures S1B and S1C). Further examples of this core program with tisTregST2-specific peaks include the and loci (Figures 1G and S1D). After specifying the shared core tisTregST2 chromatin convenience signature, we used the ATAC-seq data to identify tisTregST2 chromatin regions that are specific for each individual tissue (Physique?1H)..