Is There A "Gold Standard Rnaseq Data" To Compare With Various Rnaseq Tools For Differential Expression Analysis

Question

[Rm]

Especially I am looking for well tested RNASeq data set to compare differential expression at gene and transcript level

[David Westergaard]

I haven't really worked that much with RNASeq, but have you tried to read some of the technical papers, e.g. Cufflinks?

[Rm]

yes I did, I am interested in a dataset where it is reconfirmed by other means say qPCR etc...

Answer 1

[Malachi Griffith]

The following manuscript describes ~200 differential exon expression estimates from RNA-seq data that were valided by qPCR. Another ~200 alternative splicing structures were validated by RT-PCR, gel electrophoresis, and Sanger sequencing. The RNA-seq data is a bit old now (2x42-mer Illumina GAII data). The samples consist of biological triplicates of a drug sensitive and resistant cell line (derived from the sensitive line). In addition to RNA-seq and qPCR, Affy Exon Arrays were also used to profile these samples.

Alternative expression analysis by RNA sequencing. Nature Methods. 2010 Oct;7(10):843-847.

• ALEXA-seq website
• Pubmed abstract
• Full text of manuscript
• PDF of manuscript
• Supplementary Materials
• Validation Results Package
• RNA-seq data in GEO

[jobinv]

Just one correction: the PubMed abstract seems to be at http://www.ncbi.nlm.nih.gov/pubmed/20835245, getting a 404 error when clicking on the link posted above, http://www.ncbi.nlm.nih.gov/20835245

[Steve Lianoglou]

Just edited the post to fix the link ... thanks!

[Rm]

@Malachi Griffith thanks; will follow up them... I will wait for few more days to "accept" your answer

[Malachi Griffith]

Your welcome. If you come across a more recent dataset with validation data associated I would be keen to hear about it.

[Steve Lianoglou]

The SEQC dataset is "out there" ... somewhere ... eventually, perhaps. I'm actually not sure what the state of that dataset is (accessibility wise), but there have been many publications that reference it as the "MAQC-III" for some time, and at least one manuscript that uses the data directly here. Perhaps the FDA contacts listed in the first link are the best to get the data from?

[Rm]

@Steve: +1 for SEQC: Can you post it as answer