The utility of shallow RNA-Seq for documenting differential gene expression in genes with high and low levels of expression

PloS One
Joel AtallahBrian R Johnson

Abstract

The sequencing depth necessary for documenting differential gene expression using RNA-Seq has been little explored outside of model systems. In particular, the depth required to analyze large-scale patterns of differential transcription factor expression is not known. The goal of the present study is to explore the effectiveness of shallow (relatively low read depth) RNA-Seq. We focus on two tissues in the honey bee: the sting gland and the digestive tract. The sting gland is an experimentally well-understood tissue that we use to benchmark the utility of this approach. We use the digestive tract to test the results obtained with the sting gland, and to conduct RNA-Seq between tissue types. Using a list of experimentally verified genes conferring tissue-specific functions in the sting gland, we show that relatively little read depth is necessary to identify them. We argue that this result should be broadly applicable, since genes important for tissue-specific functions often have robust expression patterns, and because we obtained similar results in our analysis of the digestive tract. Furthermore, we demonstrate that the differential expression of transcription factors, which are transcribed at low levels compared to other gen...Continue Reading

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Methods Mentioned

BETA
RNA-Seq
dissection
HT-Seq
RNAseq
dissections
PCR

Software Mentioned

BLAST
Blast2GO
R
Tophat
NOISeq
RNA
fastx
Bio
Seq
HT

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