Additional file 3 of A low-input high resolution sequential chromatin immunoprecipitation method captures genome-wide dynamics of bivalent chromatin

Additional file 3: Table S1. library statistics, list of all bivalent peaks and list of peaks called in each replicate for total H3K4me3, total H3K27me3, bivalent K4-K27 and K27-K4 reChIP datasets generated in this study (E14 rep1 and rep2), independently generated (GSE135841) and Dppa2/4 WT (clones 57 and 58) and double knockout (clones 43 and 53) samples. In the list of all bivalent peaks (tab 2), peaks are classified as high-confidence (hc), K4-biased (k4b), K27-biased (K27b), or low confidence (lc) using either in-line total ChIPs (column E) or independent total ChIPs (column F). Table S2. motif analysis of bivalent peaks using monaLisa along with associated statistics. Table S3. list of bivalent genes classified as high confidence, K4-biased, K27-biased and low confidence along with log2 CPM/bp enrichment scores for independent total H3K4me3 and H3K27me3, IgG-IgG, in-line total H3K4me3 and H3K27me3 ChIP and K4-K27 and K27-K4 bivalent reChIP datasets. Table S4. Gene ontology enrichment of different bivalent gene classifications (first column) together with associated statistics and list of associated genes. Table S5. list of EDGER differentially enriched peaks for bivalent K4-K27 (tab1) and K27-K4 (tab2) reChIP between Dppa2/4 WT and DKO clones. Consensus differentially enriched peak list is shown in tab 3 along with HOMER classification of peak, enrichment statistics and (for promoters) whether they were previously classified as differentially enriched.