Question: Where to download In-vitro RNA-seq published experiments?
0
gravatar for daniel.soronellas
5.9 years ago by
Spain
daniel.soronellas330 wrote:

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!

 

rna-seq • 1.8k views
ADD COMMENTlink modified 5.9 years ago by Jelena Aleksic910 • written 5.9 years ago by daniel.soronellas330
6
gravatar for Devon Ryan
5.9 years ago by
Devon Ryan96k
Freiburg, Germany
Devon Ryan96k wrote:

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.
 

ADD COMMENTlink written 5.9 years ago by Devon Ryan96k
2
gravatar for Nicolas Rosewick
5.9 years ago by
Belgium, Brussels
Nicolas Rosewick9.0k wrote:

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

ADD COMMENTlink written 5.9 years ago by Nicolas Rosewick9.0k
2
gravatar for Manvendra Singh
5.9 years ago by
Manvendra Singh2.1k
Berlin, Germany
Manvendra Singh2.1k wrote:

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

 

ADD COMMENTlink written 5.9 years ago by Manvendra Singh2.1k
0
gravatar for Jelena Aleksic
5.9 years ago by
Cambridge, UK
Jelena Aleksic910 wrote:

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

ADD COMMENTlink written 5.9 years ago by Jelena Aleksic910
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