Databases miRNA sequencing data

Question

[lenC_biotecLover]

Hello everyone, is there any database (except for TCGA) where I can download miRNAs cancer sequencing data? (raw counts related to normal tissue , tumoral tissue, circulating).

Thank you

[Ram]

You could explore cBioPortal datasets and exclude any TCGA dataset.

[lenC_biotecLover]

thank you, I'll try!

[ivivek_ngs]

Have you tried TCGABiolinks where one can download the miRNA expression data for specific cancers. Here is a link with some R code. This used to be one way but I have not tried it recently.

The other way I can think of is to search Gene Expression Omnibus using terms like microRNA AND Cancer to find the list of studies and their corresponding ID where you can find the datasets (raw datasets). From a quick check, I do see quite a lot of hits but mostly cancer cell line works. Good luck!

[lenC_biotecLover]

Thank you, I've heard about GTEx too but I don't know how to download data from it.

[ivivek_ngs]

A few things here. AFAIK GTEx does not have microRNA data and also it does not have cancer data. More on data summary and tissue information can be found here.

One can also use Recount2 to access and download GTEx data (although check the version release, as it might not be the latest).

There is also yarn BioC package that can help download GTEx data version 6.

But if it is miRNA for cancers, I hardly doubt the above resources will help.

[lenC_biotecLover]

Very helpful, thank you so much, really!!