Extended Data Fig. 5: Genomic landscape of naive CD8+ T cells undergoing intrahepatic priming.
From: Dynamics and genomic landscape of CD8+ T cells undergoing hepatic priming
a, Box plots showing expression levels (log2(RPKM)) in the indicated experimental condition of genes belonging to the categories described in Fig. 2a. Box plots are as in Fig. 3f. Naive (n = 2), WT + rLCMV-core (n = 3), MUP-core (day1 and 3, n = 2; day 7, n = 3). b, Box plots showing ATAC-seq signal intensity (log2(CPM)) in the indicated experimental condition of peaks belonging to the categories described in Fig. 2c. Box plots are as in Fig. 3f. Naive (n = 2), WT + rLCMV-core (day 1 and 7, n = 2; day 3, n = 3), MUP-core (day 1 and 3, n = 2; day 7, n = 3). P values in a and b were determined by two-sided Mann–Whitney U-test. c, Bar plot showing the number of inducible ATAC-seq peaks (logFCCPM > 2.5, FDR < 0.001 versus Cor93 TN) in the indicated conditions. ATAC-seq peaks with higher intensity signal in Cor93 T cells from WT + rLCMV-core (logFCCPM > 1.5, FDR < 0.1) or from MUP-core mice (logFCCPM < −1.5, FDR < 0.1) are shown in blue and red, respectively. Differences in peak signal intensities were evaluated fitting a negative binomial generalized linear model on the dataset and then performing a quasi-likelihood F-test. The Benjamini–Hochberg procedure was applied to correct for multiple tests. Naive (n = 2), WT + rLCMV-core (day 1 and 7, n = 2; day 3, n = 3), MUP-core (day 1 and 3, n = 2; day 7, n = 3).
