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. Author manuscript; available in PMC: 2024 Jun 21.
Published in final edited form as: Nat Methods. 2022 May 2;19(5):547–553. doi: 10.1038/s41592-022-01461-y

Fig. 2: Profiling of CD4 memory T cells using NEAT-seq reveals modes of regulation across the central dogma.

Fig. 2:

a) scATAC-seq UMAP of CD4 memory T cells with cell type classifications. Annotations with cell numbers in parentheses: Th1 (1562), Th2 (939), Th17 (1855), Treg (583), TCM = central memory (2512), Act. = recently activated cells (116), Uncom. = uncommitted memory cells (905). b) Top enriched motifs in peaks that are more accessible in each cluster. c) Plots on scATAC UMAP of TF chromVAR deviations (motif accessibility), accessibility surrounding the TF gene locus (gene accessibility), RNA levels, and protein levels as measured by ADTs for the indicated TFs. n = 8472 cells in each plot except for ADTs, where n = 3841 cells. d) Scatterplot of log2-transformed, normalized RNA vs ADT counts for GATA3 with cutoffs shown for high RNA, high protein, and low protein indicated. e) Differentially expressed genes between cells with high RNA and high protein vs high RNA and low protein for GATA3 based on a two-sided Wilcoxon rank sum test. Adjusted p-values indicate Benjamini-Hochberg corrected values. Points in red represent genes with adjusted p-value < 0.05 and log2 fold change > 0.5.