Download Gene Expression Data from UCSC

Question

[landscape95]

Hello everyone, I wonder is there any way to download the GTEx Gene gene expression data set with Chia-PET, human, hg19, tissue MCF7, target ESR1 of chr21:5020000-46700000 from UCSC (http://promoter.bx.psu.edu/hi-c/chiapet.php ). I have attempted and searched for it but I am just able to download a single gene at a time and cannot find a way to download the whole Breast Cancer data set including all genes in the area of interest.

Your help is very appreciated. Thank you!

http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&lastVirtModeType=default&lastVirtModeExtraState=&virtModeType=default&virtMode=0&nonVirtPosition=&position=chr21%3A5020000-46700000&hgsid=679051661_9284aiy4AEzyCFWPwClfwzeO0pRu

Answer 1

[jared.andrews07]

So you just want MCF7 gene expression data? You can find that many places, but here it is in the EBI Expression Atlas with the experiment done by Genentech. Or do you want GTEx data for breast tissue? You can download a table that contains RNA-seq counts for all GTEx tissues here after logging in - can use a Google account.

Answer 2

[jeff]

Or you could try searching Repositive, which pulls in datasets from many different genomic archives.

A search for 'MCF7' for example provides the following result: https://discover.repositive.io/datasets/search?query=MCF7

Just register (its free!) to filter the results on Assay type.

Good luck in your search.

Jeff