Transcriptomics,Genomics

Dataset Information

94

RNA-Seq: assessment of transcript level analysis tools [array]


ABSTRACT: This study uses spiked-in transcript in order to compare various bioinformatics approaches and tools to assemble, quantify abundance and detect differentially expressed transcripts using RNA-Seq data. Mouse total RNA seq was extracted from embryonic stem cells (ES) before (designated as day 0) and four days after the addition of retinoic acid. 48 spikes were made in vitro from plasmid constructs and added to the total RNA in different concentrations (each mix has a set of different spike concentrations, see paper's method). We found that detection of differential expression at the gene level is acceptable, yet on the transcript-isofom level all tools tested were lacking accuracy and precision. This set of microarrays was performed for the purpose of selecting unexpressed loci, to which spikes can be added Overall design: Microarray of mouse embryonic bodies in response to Retinoic acid. Microarrays were performed before Retinoic addition, and after 3 and 4 days.

INSTRUMENT(S): [MoGene-1_0-st] Affymetrix Mouse Gene 1.0 ST Array [transcript (gene) version]

SUBMITTER: Gilgi Friedlander 

PROVIDER: GSE75138 | GEO | 2016-04-26

SECONDARY ACCESSION(S): PRJNA302627

REPOSITORIES: GEO

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Publications

Using Synthetic Mouse Spike-In Transcripts to Evaluate RNA-Seq Analysis Tools.

Leshkowitz Dena D   Feldmesser Ester E   Friedlander Gilgi G   Jona Ghil G   Ainbinder Elena E   Parmet Yisrael Y   Horn-Saban Shirley S  

PloS one 20160421 4


One of the key applications of next-generation sequencing (NGS) technologies is RNA-Seq for transcriptome genome-wide analysis. Although multiple studies have evaluated and benchmarked RNA-Seq tools dedicated to gene level analysis, few studies have assessed their effectiveness on the transcript-isoform level. Alternative splicing is a naturally occurring phenomenon in eukaryotes, significantly increasing the biodiversity of proteins that can be encoded by the genome. The aim of this study was t  ...[more]

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