ReMap 2018 v1.2

An integrative ChIP-seq analysis of regulatory regions

22rv1

Name : 22Rv-1 cell - BTO:0002999
Description : Human prostate carcinoma cell line; derived from a human prostate carcinoma xenograft (CWR22R) that was serially propagated in nude mice after castration-induced regression and relapse of the parental, androgen-dependent CWR22 xenograft.


To address ChIP-seq variability in term of quality, we used four different metrics based on ENCODE ChIP-seq guidelines to retain high quality datasets for downstream analyses. First we used the normalized strand cross-correlation coefficient (NSC) which is a normalized ratio between the fragment-length cross-correlation peak and the background cross-correlation, and the relative strand cross-correlation coefficient (RSC), a ratio between the fragment-length peak and the read-length peak to exclude low quality datasets. We also used the fraction of reads in peaks (FRiP) and the number of peaks identified in each dataset to filter datasets.

Datasets retained for this tissue / cell line

Datasets excluded for this tissue / cell line


To address ChIP-seq variability in term of quality, we used four different metrics based on ENCODE ChIP-seq guidelines to retain high quality datasets for downstream analyses. First we used the normalized strand cross-correlation coefficient (NSC) which is a normalized ratio between the fragment-length cross-correlation peak and the background cross-correlation, and the relative strand cross-correlation coefficient (RSC), a ratio between the fragment-length peak and the read-length peak to exclude low quality datasets. We also used the fraction of reads in peaks (FRiP) and the number of peaks identified in each dataset to filter datasets.

Datasets retained for this tissue / cell line