ReMap 2018 v1.2

An integrative ChIP-seq analysis of regulatory regions

ccrfcem

Name : CCRF-CEM cell - BTO:0000736
Description : Peripheral blood, T lymphoblast, acute lymphoblastic leukemia cell line. CCRF-CEM is a T lymphoblastoid cell line derived by G.E. Foley, et al. Cells were obtained in November, 1964 from peripheral blood buffy coat of a 4-year-old Caucasian female with acute lymphoblastic leukemia.


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


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