Fig. 3

UniNicE-seq of mouse T cells and kidney tissue. a Venn diagram demonstrating common accessible regions in mouse T cells with sample size from 25 K, 5 K, and 0.5 K cells. b Three-dimensional scatter plot of technical duplicate T cell samples from 25 K, 5 K, and 0.5 K cells. Average log₂ (normalized reads) in common accessible chromatin peaks between all samples are plotted. A correlation matrix of Pearson values of the common accessible chromatin peaks is shown on top. c Representative IGV screenshot of the normalized read density of the UniNicE-seq libraries of mouse kidney nuclei. A comparison between formaldehyde-fixed nuclei and non-fixed nuclei is shown. Non-fixed nuclei numbers were between 100 K to 0.25 K. d UniNicE-seq libraries of 25 K fixed and non-fixed mouse kidney cells were down-sized to 21.5 M properly aligned read pairs (after removing mitochondrial reads and PCR duplicates). MACS2 called 40716 narrow peaks from the fixed sample, and 27853 peaks from the non-fixed sample, among them, 15901 are common to both samples. The read density of the 2 libraries in the set of common peaks is highly correlated with a Pearson correlation efficiency of 0.99. e Heatmap showing normalized RPKM of 100 K fixed, 0.5 K nonfixed, and 0.25 K non-fixed mouse kidney nuclei at TSS, PolII, and random along with chromatin features including CTCF, H3K4me3, H3K27Ac, and random fragments