ReMap 2018 v1.2

An integrative ChIP-seq analysis of regulatory regions

kidney

Name : kidney - BTO:0000671
Description : 1: One of a pair of vertebrate organs situated in the body cavity near the spinal column that excrete waste products of metabolism, in humans are bean-shaped organs about 4 1/2 inches (11 1/2 centimeters) long lying behind the peritoneum in a mass of fatty tissue, and consist chiefly of nephrons by which urine is secreted, collected, and discharged into a main cavity whence it is conveyed by the ureter to the bladder. 2: Any of various excretory organs of invertebrate animals.


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