SAMN02232076
External Id
University of Illinois at Urbana-Champaign
INSDC center name
2014-07-01T00:00:00Z
INSDC first public
2021-02-28T02:07:44.274Z
INSDC last update
SRS457671
INSDC secondary accession
live
INSDC status
Generic
NCBI submission model
Generic.1.0
NCBI submission package
SRS457671
SRA accession
fat body
http://purl.obolibrary.org/obo/UBERON_0003917
body site
apis
breed
2012-09
collection date
Genomic DNA extracted from pooled abdominal fat body samples (18 bees/group) were used to generate BS-Seq libraries using a previously published protocol (40). Data processing, mapping, and methylation assessments are described in ref. 40. Identical reads were collapsed into single reads. The methylation level was calculated as the ratio of methylated reads over all reads covering each CpG site, using the following threshold. There were 123,023 mCpG sites with at least 20% methylation and read coverage > 4 in either control or treated samples. A threshold of > 7% resulted in no mC signal from the mitochondrial genome; we increased it to 20%, which resulted in a FDR of ca. 0.05. Using a binomial error model (41, 7), the maximum likelihood estimation for the error rate is 0.014. The methylation level reported here is similar to what was reported in ref 7. dnmt3 KD caused an overall decrease in CpG methylation levels (an average of -0.045 per mCpG).
description
USA
geo loc name
Apis mellifera
http://purl.obolibrary.org/obo/NCBITaxon_7460
organism
General Sample for Apis mellifera ligustica
title