Question: TCGA RNA-seq data, a simple question.
1
gravatar for Calvin
3.3 years ago by
Calvin60
Australia
Calvin60 wrote:

Hi all,

Just a simple question, how was RNA-seq data prepared in TCGA database? for example, are they made from rRNA depleted RNA or polyA enriched RNA or non-polyA enriched RNA?

Cheers

rna-seq • 2.7k views
ADD COMMENTlink modified 3.2 years ago by Adamc640 • written 3.3 years ago by Calvin60
3
gravatar for Adamc
3.2 years ago by
Adamc640
United States
Adamc640 wrote:

Not all TCGA samples were sequenced in the same place, so it may vary depending on what type of tumor you're looking at. Check the papers that have been published from the TCGA.

For example for Glioblastoma, "Nonstrand specific RNA sequencing performed at the Broad Institute uses a large-scale, automated variant of the Illumina Tru Seq™ RNA Sample Preparation protocol. This method uses oligo dT beads to select mRNA from total RNA." from "The Somatic Genomic Landscape of Glioblastoma" Cell, 2013

You may also be able to get protocol information from the Data Portal (https://gdc-portal.nci.nih.gov/) but I'm not so familiar with this new portal (they migrated everything to there from the old one last year) and haven't had time to poke around it, so I'm not sure how hard it is to find. If there hasn't been an "official" TCGA paper published on the cancer type you're interested in, you should be able to find out which center did the sequencing, and send them an email. For simple questions like "what was the mRNA enrichment method for your TCGA RNA-Seq?" they should respond pretty quickly.

ADD COMMENTlink written 3.2 years ago by Adamc640

Thank you so much for your answer.

ADD REPLYlink modified 3.2 years ago • written 3.2 years ago by Calvin60
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