Additional file 2 of Universal NicE-seq for high-resolution accessible chromatin profiling for formaldehyde-fixed and FFPE tissues

Additional file 2: Supplementary Table 1: HCT116 UniNicE-Seq matrix for library with different amounts of enzyme. Note 25 and 50 U NicE-seq labeling reactions were incubated at 37 °C at 800 RPM. Supplementary Table 2: Quality control metrics of UniNicE-seq libraries applied to two human cell lines K562 and MCF7 in comparison to libraries made on and off beads with either with 5mdCTP or dCTP in the dNTP mix. We examined percentage of mitochondrial reads (“%mito”), number of total peaks and promoter peaks (+/- 500 bp of TSS) and enrichment of signal at TSSs (“FRiP (TSS peaks)”). Two technical replicates were conducted for each sample. All the values were calculated from a subsample of 11 million de-duplicated alignment pairs. Supplementary Table 3. Quality control metrics of UniNicE-seq libraries applied to mouse kidney tissues. 25 K fixed cells were compared with 25 K, 10 K, 1 K, 0.5 K and 0.25 K unfixed cells. Supplementary Table 4. a. Quality control metrics of UniNicE-seq libraries applied to human adult lung tissues. b. Quality control metrics of UniNicE-seq libraries applied to different human adult and fetal tissues.* *Here the replicates are merged together and downsized to 50 M aligned pairs for the downstream analysis. Supplementary Table 5. Quality control metrics of UniNicE-seq libraries applied to human FFPE liver tissue sections. Supplemental Table 6. External ChIP-seq data sets of various human and mouse tissue and cell types in this work.