Where to download In-vitro RNA-seq published experiments?

Question

[daniel.soronellas]

Dear all,

I have a newbie question, basically where I can find published experiments of in-vitro polyA+ strand-specific RNA-seq samples from mainly cancer cell lines? FASTQ raw is fine enough to go on.

Thanks for your help!

Answer 1

[Devon Ryan]

Aside from SRA, there's also GEO and ENA. Note that ENA and SRA will generally have the same datasets, but ENA has the advantage of providing fastq files rather than the annoying SRA format.

Answer 2

[Nicolas Rosewick]

You can start with SRA: http://www.ncbi.nlm.nih.gov/sra?term=(cell%20line)%20AND%20%22strategy%20rna%20seq%22%5BProperties%5D

Answer 3

[Manvendra Singh]

Encode might also work for you. They have K562, GM12878, HepG2 cell lines, you can download polyA, cytosolic, nuclear etc etc fastq files e.g.

http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=hub_4607_uniformRNA&hubUrl=http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/hub.txt

Answer 4

[Jelena Aleksic]

The Cancer Genome Atlas has a large selection of data from tumours: http://cancergenome.nih.gov/