Transcriptomics

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RNA-seq of wild type Arabidopsis seedlings to compare cross-replicate variability and false discovery rate in differential gene expression tools


ABSTRACT: RNA-Seq data from 17 wild-type biological replicates of Arabidopsis thaliana used to explore read count measurements across replicates along with the False Discovery Rate of Differential Gene Expression tools. Although A. thaliana has a relatively small genome, its transcriptome is similar in scale and complexity to that of model mammal species and its genome is extensively annotated and the conclusions presented here provide useful guidance for work in other complex eukaryotes. The findings show that the negative binomial and log-normal distributions are both good choices as models for the cross-replicate variability of RNA-seq read counts. 6 of 9 DGE tools controlled their identification of false positives well even with only 3 replicates. Our results reinforce the conclusions reached by Schurch et. al. (2015 RNA) in yeast.

INSTRUMENT(S): ERCC Spike-in Kit (Ambion) & Illumina TruSeq Stranded Total RNA with Ribo-Zero Plant kit, Illumina HiSeq 2000, RNeasy Plant Mini Kit & TURBOTM DNase (Ambion)

ORGANISM(S): Arabidopsis thaliana  

SUBMITTER: Geoff J Barton  Gordon G Simpson  Cline Duc  Nick Schurch  Marek Gierliski  Katarzyna Mackinnon  Kimon Froussios               

PROVIDER: E-MTAB-5446 | ArrayExpress | 2019-02-08

SECONDARY ACCESSION(S): ERP021226

REPOSITORIES: ArrayExpress, ENA

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