Figure - PMC

Skip to main content

An official website of the United States government

Here's how you know

Here's how you know

Official websites use .gov
A .gov website belongs to an official government organization in the United States.

Secure .gov websites use HTTPS
A lock ( ) or https:// means you've safely connected to the .gov website. Share sensitive information only on official, secure websites.

View full-text article in PMC

. 2023 Jan 18;220(4):e20220440. doi: 10.1084/jem.20220440

Search in PMC
Search in PubMed
View in NLM Catalog
Add to search

© 2023 Li et al.

This article is distributed under the terms of an Attribution–Noncommercial–Share Alike–No Mirror Sites license for the first six months after the publication date (see http://www.rupress.org/terms/). After six months it is available under a Creative Commons License (Attribution–Noncommercial–Share Alike 4.0 International license, as described at https://creativecommons.org/licenses/by-nc-sa/4.0/).

PMC Copyright notice

Figure 4. — scATAC-seq data reveals increased ILC3 plasticity in BCL6-deficient mice. The total intestinal ILC were obtained from the SI and colon LPL of Vav1^creBcl6^fl/fl or Bcl6^fl/fl littermates (combination of three mice for each strain) by FACS sorting (gated on Lin⁻CD90⁺CD45⁺ live cells), and used for scATAC-seq analysis. UMAP visualizations for both Vav1^creBcl6^fl/fl and Bcl6^fl/fl samples are visually identical, so all UMAP figures shown are representative data of one sample unless specifically indicated. Raw data of scATAC-seq are available through GSE221341 on GEO DataSets. (A) UMAP visualization of clustering pattern of the ILCs post deletion of ILC2 form cells from original scATAC-seq data pool (Fig. S5 A). Proportional changes of each cluster of Vav1^creBcl6^fl/fl versus Bcl6^fl/fl littermate samples were labeled by blue-red colors with scales shown below. (B) Heatmap of marker genes (determined by gene score matrix) of each cluster (vertically labeled) of the total ILC2-depleted ILC in A. Selected ILC lineage specific genes (Gury-BenAri et al., 2016) with high gene scores in the 10 clusters were horizontally labeled on top (see also Table S5). (C) Frequencies of three subgroups from the total ILC2-depleted ILCs in A between Bcl6^fl/fl and Vav1^creBcl6^fl/fl samples. Each subgroup is consisted of specified clusters (labeled by different colors) indicated by chromatin level characterization from B and Fig. S5 D. Arrow indicated direction of cell number changes. (D) Trajectory analysis for Bcl6^fl/fl source clusters from A. See also Fig. S5 E for trajectory analysis result for Vav1^creBcl6^fl/fl sample. (E) Representative UMAP visualization of broad rename of cells from A. (F) GSVA of differential genesets generated by comparing chromatin accessibility of genes from TS vs. those from classic ILC3 for Vav1^creBcl6^fl/fl and Bcl6^fl/fl samples, respectively. The overlapped genes between the two genesets were excluded from analysis (see also Table S5). (G) Volcano plot for Vav1^creBcl6^fl/fl source TS vs. classic ILC3 differential geneset generated in F. Selective regulated peaks (labeled by nearest gene) were Vav1^creBcl6^fl/fl-specific representatives matching literature ILC1 marker genes (right red, up-regulated) or CCR6⁺ ILC3 marker genes (left blue, down-regulated). See also Table S2 for literature marker genes and Table S6 for detailed information of selected peaks and nearby genes. (H) Transcription factor motif enrichment scores of Vav1^creBcl6^fl/fl TS vs. those of Bcl6^fl/fl TS. The motifs shown here are selected by enrichment score of mlog10Padj >0.1. Value of score is labeled by blue-red color scale.