ReMap 2018 v1.2

An integrative ChIP-seq analysis of regulatory regions

hspc

Name : hematopoietic stem cell - BTO:0000725
Description : A blood cell progenitor or mother cell representing a slightly later stage than the blast cell; it has the capacity for both replication and differentiation, and has pluripotentiality, giving rise to precursors of various different blood cell lines, such as the proerythrocyte and myeloblast, which cannot self-replicate and must differentiate into more mature daughter cells.


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