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 ?
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.
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.