|Number of samples:||7|
|Release date:||Oct 5 2010|
|Last update date:||Jul 20 2018|
|Genes:||AICDA, SUPT5H, SCARA3|
|Dataset link||Genome wide localization of Activation induced cytidine deaminase (AID), Spt5, and RNA Polymerase II (PolII) in mouse|
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.