ReMap 2018 v1.2

An integrative ChIP-seq analysis of regulatory regions

islet

Name : pancreatic islet - BTO:0000991
Description : Irregular microscopic structures scattered throughout the pancreas and comprising its endocrine part (the endocrine pancreas). In humans, they are composed of at least four types of cells: the alpha cells, which secrete glucagon; the beta cells, which are the most abundant and secrete insulin; the delta cells, which secrete somatostatin; and the PP cells, which secrete pancreatic polypeptide. Degeneration of the beta cells, whose secretion (insulin) is important in carbohydrate metabolism, is the major cause of type I diabetes mellitus.


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