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Series GSE71802 Query DataSets for GSE71802
Status Public on Apr 26, 2016
Title RNA-Seq: assessment of transcript level analysis tools [seq]
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary 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.
 
Overall design Mouse total RNA was extracted from embryonic stem cells (ES) before (designated as day 0) and four days after the addition of retinoic acid (RA) (designated as day 4). Mouse spike-ins consisting of 48 different mouse RNA transcripts were generated in vitro from plasmid constructs and added to the total RNA. 23 of the spike-ins originate from 10 different locus regions, so that each locus is represented by at least two different transcripts. The remaining 25 spike-ins represent different loci.
 
Contributor(s) Leshkowitz D, Feldmesser E, Friedlander G, Jona G, Ainbinder E, Parmet Y, Horn-Saban S
Citation(s) 27100792
Submission date Aug 06, 2015
Last update date May 15, 2019
Contact name Gilgi Friedlander
Organization name Weizmann Institute of Science
Street address Hertzel st
City Rehovot
ZIP/Postal code 76100
Country Israel
 
Platforms (1)
GPL17021 Illumina HiSeq 2500 (Mus musculus)
Samples (16)
GSM1846074 C2
GSM1846075 D2
GSM1846076 E2
This SubSeries is part of SuperSeries:
GSE75139 RNA-Seq: assessment of transcript level analysis tools
Relations
BioProject PRJNA292105
SRA SRP062126

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE71802_stranded_rsem_isoforms_160216.TMM.fpkm.matrix.txt.gz 1.0 Mb (ftp)(http) TXT
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Raw data are available in SRA
Processed data are available on Series record

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