Dataset features

Specifications


Application: ChIP-seq analysis
Number of samples: 7
Release date: Oct 5 2010
Last update date: Jul 20 2018
Access: Public
Chemicals: Cytidine
Genes: AICDA, SUPT5H, SCARA3
Dataset link Genome wide localization of Activation induced cytidine deaminase (AID), Spt5, and RNA Polymerase II (PolII) in mouse

Experimental Protocol


PolII, AID, and Spt5 were immunoprecipitated from in vitro activated B cells. For Spt5 and AID, two different antibodies were used in separate, biological replicates. Notes: Peaks of enrichment relative to a random background model were identified with SICER 1.03 (Zhang et al., 2009). For AID, the parameters used were window size = 100, gap size = 100, e = 0.000001, redundancy = 1, fragment size = 127 (AID+/+, ab1), 115 (AID-/-, ab1), and 125 (AID+/+, ab2). Fragment size estimates were calculated from the data based on a shifting algorithm that attempts to minimize a Shannon entropy measure. Read counts were adjusted for library size and are given as reads per million non-redundant aligned reads (RPM). Densities were then filtered to only display windows falling onto enriched regions as identified by SICER. AID-/- densities were additionally scaled by a factor of 0.592 to correct for an overestimation of background levels at 104 genes that displayed higher read densities in AID-/- cells than AID+/+ cells. Corrected values were used to calculate RPKM values in Table S1 of Yamane et al. (PMID 21113164) and for display in browser tracks. Please note a typo in Fig. 1a of Yamane et al. (PMID 21113164) where the Y axes of AID+/+ and AID-/- samples should read 0.15-1.2, instead of 0-1.2.

Repositories


GEO

GSE24178

ArrayExpress

E-GEOD-24178

ENA

SRP003605

BioProject

PRJNA130101

Download