Comprehensive database for RNA-seq transcriptome sequencing ?

Question

[jack]

Hi,

I'm looking for a comprehensive database to download data of RNA-seq transcriptome sequencing of drosophila.

Would someone recommend some?

Answer 1

[Cytosine]

Already tried SRA?

Should be more than enough RNA-Seq data of drosophila for you over there.

Answer 2

[Obi Griffith]

You could try an advanced search of GEO specifically for GEO Datasets where 'Organism'='Drosophila' and the 'DataSet Type'='Expression profiling by high-throughput sequencing'. There were 188 studies that qualify at time of posting.

Caveats:

• Not all GEO datasets will necessarily have links to SRA with raw data. In some cases you will get just processed expression values (e.g., FPKMs, etc).
• The many platforms that fall under 'Expression profiling by high throughput sequencing' should generally be for expression estimation of RNA and will therefore be variants of what is commonly called RNA-seq. However, some may be more specialized, incorrectly categorized, or represent datasets with mixed data types. For example, they might involve sample/library preparations designed to assay just small non-coding RNAs, or other special cases.