RNA-seq of LN ILCs. (A) Sorting strategy for ILC RNA-seq. ILCs were sorted from pooled pLNs of Rorc^GFP reporter mice by surface markers as ILC1 (Lin⁻CD127⁺RORγt^GFP−NKp46⁺KLRG1⁻), ILC2 (Lin⁻CD127⁺RORγt^GFP−NKp46⁻KLRG1⁺), ILC3 (Lin⁻CD127⁺RORγt^GFP+CCR6⁻), LTi cells (Lin⁻CD127⁺RORγt^GFP+CCR6⁺). SSC, side scatter. (B) Purity reanalysis of sorted ILCs. (C) Multidimensional scaling (MDS) of rlog-transformed expression counts in ILCs. Sample relationship similarity is shown in 3D plot including sample group color code (ILC1 = blue, ILC2 = red, ILC3 = cyan, LTi = dark magenta). (D) Correlation analyses visualize the relation between methylation status of marker regions (methylation difference, x axis) and associated gene expression (log2 fold-change, y axis). Analysis of ILC1 vs. ILC3, ILC1 vs. LTi, or ILC3 vs. LTi revealed R = −0.71 (P = 0.003), R = −0.84 (P < 0.001), or R = −0.49 (P = 0.047), respectively. Plots show the comparison between ILC1 (blue dots), ILC3 (cyan dots), or LTi (magenta dots) including the linear regression line.