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Fig. 2 | Clinical Epigenetics

Fig. 2

From: Universal NicE-seq for high-resolution accessible chromatin profiling for formaldehyde-fixed and FFPE tissues

Fig. 2

UniNicE-seq optimization and validation. a Reaction conditions and library making method comparison. Venn diagram showing the overlap of peaks in various reaction conditions and library making method. b Distribution of fold change (FC) values (derived from MACS2) of the accessible chromatin peaks detected by on bead 5mC, on bead C, off bead 5mC, and off bead C methods. Accessible chromatin peaks detected by on bead 5mC (red) showed higher FC values on average than other methods. c Pearson correlation of accessible chromatin peak read densities between UniNicE-seq, ATAC-seq, and DNase-seq of HCT116 cells. d Distribution of HCT116 UniNicE-seq (On Bead 5mC) peaks in different genomic regions at sequencing depth from 5 to 100 M alignment pairs. e Numbers of HCT116 UniNicE-seq accessible chromatin peaks that overlap and not overlap with the reference human DNase I hypersensitivity sites at sequencing depth from 5 to 100 M alignment pairs. f Fraction of reads in peaks that map to TSSs (+/−500 bp of TSS) and distal elements (> 500 bp from TSS) from libraries generated using the on-bead UniNicE-seq methods on three human cell lines (HCT116, K562, MCF7). g Representative IGV screenshot of the normalized read density of the UniNicE-seq libraries of the three human cell lines, HCT116, K562, and MCF7, from experimental replicates

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