RPKM values in normal cells
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6.1 years ago
akantusz • 0

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.

COSMIC TCGA RNA-Seq • 2.4k views
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6.1 years ago

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.

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6.1 years ago
ashah90 ▴ 30

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.

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