A dataset containing small RNA-seq experiments over different tissues of human.

Question

[moinfar.amirali]

Hi Is there any dataset containing small RNA-seq experiments over different tissues of human?

Answer 1

[BioinfGuru]

Yes of course. There are loads. One easy example is the sequence read archive (SRA).

1) Go to SRA

2) Search term: "Homo sapiens"[orgn:__txid9606]

3) Filters: Public, RNA, and either exome or genome

4) Click the link to "Send results to Run Selector"

5) Play around with the facets (filter) menu to find what is suitable for you. "tissue" is at the bottom of the facet list.

Another is to go to the ENCODE data search tool

Other options: Repositive.io, CistromeDB, Allen Brain Atlas, BGEE expression database, Human Cell Atlas

I'm sure there are probably many more.

[moinfar.amirali]

I meant "small RNA"-seq. By the way, ENCODE data search tool which you suggested helped me. Thanks.

Answer 2

[igor]

GTEx: https://www.gtexportal.org/home/

The Genotype-Tissue Expression (GTEx) project aims to provide to the scientific community a resource with which to study human gene expression and regulation and its relationship to genetic variation. This project will collect and analyze multiple human tissues from donors who are also densely genotyped, to assess genetic variation within their genomes. By analyzing global RNA expression within individual tissues and treating the expression levels of genes as quantitative traits, variations in gene expression that are highly correlated with genetic variation can be identified as expression quantitative trait loci, or eQTLs.