Extended Data Fig. 5: RNA-seq analyses of T cells from various tissues.
From: The subfornical organ is a nucleus for gut-derived T cells that regulate behaviour
a, UMAP generated from single-cell RNA-seq of T cells (FACS: CD45 intravenous label−, CD11b−, CD19−, B220− and RNA: Cd3e > 1) sorted from brain, meninges, gonadal white fat, colon lamina propria, mLN and blood of 5 pooled 10-week-old C57BL/6 mice. Comparison of gene expression across all tissue T cells representing various T cell differentiation states. b, Schematic of bulk RNA-seq experimental setup. c, PCA analysis of the CD4 T cells from brain, fat and meninges. (n = 8 per biological replicate represented as a dot in the PCA). DEGs (cut-off FDR < 0.05) from comparing brain/white fat and brain/meningeal CD4 T cells were used for QIAGEN IPA. Volcano plots represent DEGs (cut-off FDR < 0.05) from comparing brain/white fat, brain/meninges and white fat/meninges. d, PCA analysis of the CD4 T cells from brain, iLN and lung. (n = 8 per biological replicate represented as a dot in the PCA) The circles in the PCA plot represent the 95% confidence interval. Volcano plot representing DEGs (cut-off FDR < 0.05) from bulk RNA-seq analysis of brain/LN and brain/lung CD4 T cells. e, DEGs (cut-off FDR < 0.05) from comparing brain/white fat, brain/meningeal and white fat/meningeal CD4 T cells were used for QIAGEN IPA. Images in b were created in BioRender.
