Question: looking for databases to download whole RNA RNA-seq data
0
gravatar for jack
4.0 years ago by
jack760
Germany
jack760 wrote:

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 ? 

ADD COMMENTlink modified 4.0 years ago by Jautis270 • written 4.0 years ago by jack760
1

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

ADD REPLYlink written 4.0 years ago by Devon Ryan90k

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.

ADD REPLYlink written 4.0 years ago by jack760

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

ADD REPLYlink written 4.0 years ago by h.mon26k
0
gravatar for Jautis
4.0 years ago by
Jautis270
United States
Jautis270 wrote:

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

ADD COMMENTlink written 4.0 years ago by Jautis270

non coding RNA!

ADD REPLYlink written 4.0 years ago by jack760

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. 

ADD REPLYlink written 4.0 years ago by Jautis270

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

ADD REPLYlink written 4.0 years ago by jack760

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

ADD REPLYlink written 4.0 years ago by jack760
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