looking for databases to download whole RNA RNA-seq data

Question

[jack]

Hi all,

I'm looking for database where I can download total RNA RNA-seq data for substantial amount of samples.

Does anyone has idea?

[Devon Ryan]

Have you checked the normal sources (ENA, SRA and GEO)?

[jack]

I'm looking something like TCGA which I can download total RNA-seq data for hundreds samples of one tissue. but unfortunately I couldn't find it. TCGA mostly contain mRNA not total RNA.

[h.mon]

Total RNA extraction has huge amounts of ribosomal RNA, so it is uncommon people sequence total RNA.

Answer 1

[Jautis]

I would suggest finding recent RNAseq paper(s) that have the scale of data you're looking for and then identifying their digital archive. The encode project or work on Arabidopsis may be a place to start

[jack]

non coding RNA!

[Jautis]

You should be able to find that. They typically publish the raw data files, so all the reads should be in there as long as the noncoding RNAs are long enough to not be size selected out.

[jack]

The problem is that non coding RNAs are not polyadenlated. So they are washed out during library preparation