ReMap 2018 v1.2

An integrative ChIP-seq analysis of regulatory regions

sknmc

Name : SK-N-MC cell - BTO:0002914
Description : Human neuroblastoma cell line; established from the supraorbital metastasis of a neuroblastoma of a 14-year-old girl in 1971; although described in the original paper as neuroblastoma, SK-N-MC is now widely regarded as having originated from the morphologically similar Askin's tumor related to Ewing's sarcoma.


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