Question: RPKM values in normal cells
0
gravatar for akantusz
3.2 years ago by
akantusz0
Hungary
akantusz0 wrote:

Hello,

I would like to compare gene expression level data from COSMIC to expression level data of normal cells.

I've found the TCGA level 3 data (RPKM and normalized count values in case of RNASeq and RNASeqV2 platforms), from which COSMIC data derive, but where could I find RPKM scores for normal cells?

Thanks.

rna-seq tcga cosmic • 1.5k views
ADD COMMENTlink modified 3.2 years ago by ashah9030 • written 3.2 years ago by akantusz0
1
gravatar for Giovanni M Dall'Olio
3.2 years ago by
London, UK
Giovanni M Dall'Olio26k wrote:

There are many resources. The most recent are the Protein Atlas (http://www.proteinatlas.org/ ), providing data from 122 samples and 32 tissues (plus data for cell lines), and the GTEx portal (http://www.gtexportal.org/home/), with data from ~3,000 samples in 30 tissues.

ADD COMMENTlink written 3.2 years ago by Giovanni M Dall'Olio26k
0
gravatar for ashah90
3.2 years ago by
ashah9030
Canada
ashah9030 wrote:

The TCGA data portal has matched normal cell data as well. If you look at the data matrix (https://tcga-data.nci.nih.gov/tcga/dataAccessMatrix.htm) on the very right there is an option for "Normal-matched". Furthermore, if you don't like the data matrix you can always download the data in bulk using Broad's GDAC Firehose (http://gdac.broadinstitute.org/) and using the TCGA patient barcodes to determine whether the cell is a normal cell. You can determine that using this wiki (https://wiki.nci.nih.gov/display/TCGA/TCGA+barcode) and looking at the "Sample" field. If I remember correctly, a "01" or "11" in the sample fields means it is a normal cell.

ADD COMMENTlink written 3.2 years ago by ashah9030
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