Comprehensive database for RNA-seq transcriptome sequencing ?
2
0
Entering edit mode
8.5 years ago
jack ▴ 960

Hi,

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

Would someone recommend some?

sequencing RNA-Seq • 1.7k views
ADD COMMENT
1
Entering edit mode
8.5 years ago
Cytosine ▴ 460

Already tried SRA?

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

ADD COMMENT
1
Entering edit mode
8.5 years ago

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.
ADD COMMENT

Login before adding your answer.

Traffic: 1143 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6