What databases are available for RNA-seq datasets?

[apr]

Currently, I'm looking into the Gene Expression Omnibus. Are there any other good websites that curate RNA-seq data (or perhaps provide links to where RNA-seq data can be found)? A bit of background: I'm looking for any publicly available RNA-seq data sets containing at least 10 individuals with some form of cancer (ideally breast cancer).

[sikidiri]

Hi,
ENCODE has publicly available RNA-seq datasets from different cell lines.
I hope this is helpful.

[GenoMax]

You can check the TCGA data portal for cancer sample data.

https://tcga-data.nci.nih.gov/tcga/

There are access tiers so you may need to look through those: https://tcga-data.nci.nih.gov/tcga/tcgaAccessTiers.jsp

[Richard Finney]

TCGA sequence data is censored. There is no public primary or metastatic tumor data for U.S. studies. There are cell lines. But, are cell lines cancer? Patients should be allowed to release their genomes (both tumor and normal) for public inspection. Hopefully future studies will accommodate them and there will be great benefits from making the data public.

[chadn737]

Try the SRA

Thats where GEO submits the raw data anyways.

[GenoMax]

As Richard Finney pointed out @apr is looking for data from "individuals". That is probably going to be hard to come by.

[alexdobin]

ENCODE data

ENCODE RNA-seq data from human cell lines can be found here:

http://genome-preview.ucsc.edu/cgi-bin/hgFileUi?db=hg19&g=wgEncodeCshlLongRnaSeq

For raw .fastq Read1/Read2 files select fastqRd1/2 in the "View" column.

[chadn737]

I went to the SRA and typed in Cancer. Then on the side I selected RNA as the source. On the second page there are a whole bunch of RNA-seq studies from individual patients. Here are some examples:

http://www.ncbi.nlm.nih.gov/sra/SRX134888

http://www.ncbi.nlm.nih.gov/sra/SRX134887

http://www.ncbi.nlm.nih.gov/sra/SRX134886

http://www.ncbi.nlm.nih.gov/sra/SRX134885

http://www.ncbi.nlm.nih.gov/sra/SRX134884

http://www.ncbi.nlm.nih.gov/sra/SRX134883

There six right there, lot more available.

[Richard Finney]

"Asian Gastric Cancer" : http://trace.ncbi.nlm.nih.gov/Traces...tudy=SRP012016

Great! I knew that Asian samples where showing up in GEO with Affy SNP6 data.
Good to see Solid RNA-seq data is now showing up in SRA.

(I wish NCBI SRA would turn off their "freeze the machine" ajax/javascript nonsense)

[apr]

Thanks for all the great suggestions. So far, I've mostly been looking into TCGA (https://tcga-data.nci.nih.gov/tcga/findArchives.htm). I downloaded the BRCA RNASeqV2 dataset (https://tcga-data.nci.nih.gov/tcga/s...rchiveId=10418). Does anyone know how to determine if each of the sample ID's came from distinct individuals? If that's the case, then there would be ~800-900 individuals in this data set - which seems to be unlikely given the size of other data sets. I wish there was a way to tell which samples came from distinct individuals.

The ENCODE database also looks very promising. Here is a tool that I've been using to find RNASeq data: http://genome.crg.es/~jlagarde/encode_RNA_dashboard/

[Richard Finney]

Note that TCGA BRCA (breast cancer) data from UNC is just the idf/sdrf MAGE-TAB files.
It's just a description of the data processing.
See here : http://tab2mage.sourceforge.net/docs/magetab_docs.html form mage info.

The RNA-Seq "Asian Gastric Cancer" samples can be downloaded here:
ftp://ftp-trace.ncbi.nlm.nih.gov/sra...012/SRP012016/

Use "wget -r" to get the whole thing.

The whole separting out the SRA study/sample/experiment/run thing is frustrating, but do-able. (The scars heal eventually.)

[GenoMax]

Original data files for TCGA are available from CGHub: https://cghub.ucsc.edu/

You will have to apply to get access: https://cghub.ucsc.edu/get_access.html

All the samples should be unique. Breast cancer was one of the major types included so there are many samples.

Additional information here: http://www.ncbi.nlm.nih.gov/projects...hs000178.v5.p5

[Dario1984]

Here's a dataset with 79 samples of RNA-seq for breast cancer patient samples.

https://www.ebi.ac.uk/ega/studies/EGAS00001000132

[Richard Finney]

NB: The EMBL-EBI data is controlled access:
From https://www.ebi.ac.uk/ega/datasets/EGAD00001000113
Who controls access to this dataset
For each dataset that requires access control, there is a corresponding Data Access Committee (DAC) who determine access permissions. Data access is not the responsibility of the EGA. If you need to request access to this data set, please contact: Department of Molecular Oncology, BC Cancer Research Centre, Data Access Committee

[apr]

Wow, the ebi dataset looks really promising. And it has a nice Nature journal article to accompany it too (http://www.nature.com/nature/journal...ture10933.html). Very cool.