PLX015275

GSE71802: RNA-Seq: assessment of transcript level analysis tools [seq]

• Organsim mouse
• Type RNASEQ
• Target gene
• Project ARCHS4

This study uses spiked-in transcript in order to compares 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. SOURCE: Gilgi Friedlander Weizmann Institute of Science