Which repository is more appropriate to submit for cancer cell line (bulk) RNA-seq data ?

Question

[arta]

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 ?

[mbk0asis]

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

Answer 1

[ATpoint]

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.

[Kevin Blighe]

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

[ATpoint]

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.

[arta]

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

[WouterDeCoster]

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

Answer 2

[Arup Ghosh]

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.