Question: Which repository is more appropriate to submit for cancer cell line (bulk) RNA-seq data ?
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gravatar for arta
2.1 years ago by
arta580
Sweden
arta580 wrote:

I would like to submit our RNA-seq data (2 cell lines with triplicates) to repository to make it public. I know there are some options such as Sequence Read Archive (SRA) and European Nucleotide Archive. How do you submit your data, i mean how do you decide ? Is there any criteria ?

rna-seq • 770 views
ADD COMMENTlink modified 22 months ago by Biostar ♦♦ 20 • written 2.1 years ago by arta580
1

If I remember correctly, SRA and ENA mirror each other to sync the data. So I think it's a matter of personal preference.

ADD REPLYlink written 2.1 years ago by mbk0asis550
4
gravatar for ATpoint
2.1 years ago by
ATpoint36k
Germany
ATpoint36k wrote:

Did you publish your results in any journal or do you plan to do so? If so, then there might be a journal guideline that requires you to choose one repository over the other. If not, I would go for the ENA, because they offer data directly in fastq format, and not in this terrible NCBI SRA format.

ADD COMMENTlink written 2.1 years ago by ATpoint36k
1

Yes, SRA is very annoying. I have spent more than 1 week converting ~130 SRA files to FASTQ

ADD REPLYlink written 2.1 years ago by Kevin Blighe61k

Agreed! Still have nighmares from converting a cohort of 30 matched-normal WGS samples and 80 RNA-seqs from SRA to fq while our HPC cluster had massive I/O issues.

ADD REPLYlink written 2.1 years ago by ATpoint36k

We will publish it soon. So ENA makes more sense. Thanks.

ADD REPLYlink written 2.1 years ago by arta580
2

Note that you can already upload the data to ENA and put it under embargo until your paper is published.

ADD REPLYlink modified 2.1 years ago • written 2.1 years ago by WouterDeCoster44k
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gravatar for Arup Ghosh
2.1 years ago by
Arup Ghosh2.5k
India
Arup Ghosh2.5k wrote:

EBI Annotare has a very easy to use interface for RNA-seq and ChIP-seq data submission and they accept .fastq files. They offer file upload via both the web interface and FTP server. Uploaded files are processed automatically and you will get accession number to include in manuscript within 10 mins.

ADD COMMENTlink written 2.1 years ago by Arup Ghosh2.5k
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