Extended Data Fig. 2: Changes in compartment distribution in ILCs are accompanied by changes in expression patterns concordant with euchromatin/heterochromatin state.

a, Fraction of regions in the A or B compartments in common lymphoid progenitors (CLP), group 1 (splenic NK cells), group 2 (bone marrow ILC2s), and group 3 (MNK3) ILC. b, Proportion of regions in CLPs that flipped compartment status in at least one ILC group (brown) or that remained unchanged in all ILC groups (gray). Sidebar indicates the proportion of flipped regions that were in the A (red) or B (blue) compartment at the CLP stage. c, Examples of compartment state distribution in the vicinity of genes with known roles in ILC biology such as Id2, Tcf7, Nfil3, Gata3, Lifr and Tox. Regions in the A and B compartment correspond to positive (red) and negative (blue) values in the PC1 bar, respectively. Each square represents 25kb. d, Percentage of expressed genes among genes within compartments that underwent similar flipping from CLP. The Y-axis represents the different combinations of final compartment states in ILC for flipping regions originally in the status indicated on the left. Parenthetical numbers indicate the total number of genes overlapping the corresponding group of regions. Expressed genes correspond to genes with average RPKM > 1. RPKM: Reads per kilobase of transcripts per million mapped reads. Letter triplets represent the compartment status in group 1, group 2 and group 3 ILC, respectively. e, (left) Heatmap of the compartment status in ILCs of flipping regions that were in the B compartment in CLPs. Regions in the A and B compartment correspond to positive (red) and negative (blue) values in the PC1 bar. (right) Comparison of gene expression levels between group 1 (blue boxes), group 2 (green boxes) and group 3 (red boxes) ILCs of groups of genes undergoing similar compartment flipping from CLP. The Y-axis represents the different combinations of final compartment states in ILC. RPKM: Reads per kilobase of transcripts per million mapped reads. Letter triplets represent the compartment status in group 1, group 2 and group 3 ILC, respectively. Box shows dataset quartiles and whiskers the distribution range. Dots represent outliers as determined by the inter-quartile range. f, (left) Heatmap of the compartment status in ILCs of flipping regions that were in the A compartment in CLP. Regions in the A and B compartment correspond to positive (red) and negative (blue) values in the PC1 bar. (right) Comparison of gene expression levels between group 1 (blue boxes), group 2 (green boxes) and group 3 (red boxes) ILCs of groups of genes undergoing similar compartment flipping from CLP. The Y-axis represents the different combinations of final compartment states in ILC. RPKM: Reads per kilobase of transcripts per million mapped reads. Letter triplets represent the compartment status in group 1, group 2 and group 3 ILC, respectively. Box shows dataset quartiles and whiskers the distribution range. Dots represent outliers as determined by the inter-quartile range. g, Table with the p-values (Mann-Whitney U two-tailed test) for Fig. 1e,f of the pairwise comparison between ILC of expression levels of genes that underwent similar compartment flippings from the A or B compartment in CLP. Letter triplets represent the compartment status in group 1, group 2 and group 3 ILC, respectively.