Chunk #59 — Online Methods — 1. Data matrix, primary analysis and processing, quality control — 1.2 ChIP-seq and DNase-seq uniform reprocessing for consolidated epigenomes — e. Quality Control
subsequently used to produce Release 9 data. ChIP-seq data for 6 histone modifications (H3K4me3, H3K27me3, H3K9ac, H3K9me3, H3K36me3, and H3K4me1) were independently generated for the H1 cell line by three REMCs (Broad, UCSD, UCSF-UBC). To quantify concordance, the reads from each experiment were mapped (Level 1 data), read density tracks (Level 2 data) were generated using the EDACC's primary data processing pipeline, and finally Pearson correlation coefficients were computed between each pair of experiments, as well as between experiments and H1 input acting as a control for background correlation between signals (Table S2). The methylome processing pipeline was characterized experimentally on four independent samples38-39. The same pipeline was used to process bisulfite-treated reads in Release 9 and the same read mappings were used for consolidated epigenomes.
