No RNA-seq data in Metastatic Prostate Cancer (SU2C/PCF Dream Team, Cell 2015)

[Alberto Indacochea Cusirramos]

Hello,

I was working with this dataset 

Metastatic Prostate Cancer (SU2C/PCF Dream Team, Cell 2015)

When I read the publication I understood they had RNA-seq data but in cBio portal is not avaiable.

"Transcriptome libraries were prepared using 200–1,000 ng of total RNA. PolyA+ RNA isolation, cDNA synthesis, end-repair, A-base addition, and ligation of the Illumina indexed adapters were performed according to the TruSeq RNA protocol (Illumina). Libraries were size selected for 250–300 bp cDNA fragments on a 3% Nusieve 3:1 (Lonza) gel, recovered using QIAEX II reagents (QIAGEN), and PCR amplified using Phusion DNA polymerase (New England Biolabs). Total transcriptome libraries were prepared as above, omitting the poly A selection step and captured using Agilent SureSelect Human All Exon V4 reagents and protocols. Library quality was measured on an Agilent 2100 Bioanalyzer for product size and concentration. Paired-end libraries were sequenced with the Illumina HiSeq 2500, (23100 nucleotide read length) with sequence coverage to 50 M paired reads and 100 M total reads. Paired-end transcriptome sequencing reads were aligned to the human reference genome (GRCh37/hg19) using a RNA-seq spliced read mapper Tophat2 (Kim and Salzberg, 2011) (Tophat 2.0.4), with ‘‘–fusion-search’’ option turned on to detect potential gene fusion transcripts. Potential false-positive fusion candidates were filtered out using ‘‘Tophat-Post-Fusion’’ module. Further, the fusion candidates were manually examined for annotation and ligation artifacts. Gene expression, as fragments per kilobase of exon per million fragments mapped (FPKM; normalized measure of gene expression), was calculated using Cufflinks"

Are you going to add this new data in the new update or before?

Regards

Alberto

[Ritika Kundra]

Hi Alberto,

We do have the RNA expression data but we removed it as we are working on fixing some inconsistent gene names present in the file. We will be including the RNA dataset back soon. Apologies for the inconvenience.

Thanks,

Ritika

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