TCGS gene expression data

Question

[aj123]

Hello,

1. I'm trying to get RNA-Seq data for a particular cancer type from TCGA specific to a certain cell line. I'm not sure how to do this.
2. Also looking for a good website where I can get a list of genes pertaining to a specific disease. Have tried various NIH and Weizmann Institute sites but am looking for something more comprehensive. Thanks!

Answer 1

[5utr]

Hi,

1. If you are interested in gene expression data for specific cell lines and not human samples you should look at this experiment 'RNA-seq of 675 commonly used human cancer cell lines'. You can download the data from arrayexpress: https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-2706/

   Another resource it's the Cell line encyclopedia, but it's microarray data and not RNA-seq: http://www.broadinstitute.org/ccle/home

2. You can use OMIM, if you search for a disease you'll get the genes associated. You can also register and download the entire database: http://omim.org/

Answer 2

[Lemire]

To get raw sequencing data from TCGA, your lab needs to apply and get approved access from dbGaP (http://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000178.v9.p8). If you have access already, I can guide you.

You can still get some interpreted data by going to https://tcga-data.nci.nih.gov/tcga/dataAccessMatrix.htm

Select the disease you are interested in and data type (RNAseq if available), then Apply.

Then, you can then select the samples that you want. You might want to read about the barcode system: https://wiki.nci.nih.gov/display/TCGA/TCGA+barcode

Then click Build Archive, which will bring you to the Data Download page. Enter your email and wait for the download link.

Mathieu