A question from my PI:
"We would like to search a RNA-seq database(s) using a sequence to determine what tissues, cells etc a particular transcript is expressed in. I looked on the NCBI and UCSC Genome Bioinformatics sites but unless I am mistaken, it doesn’t appear a search of this type is possible. Does anyone know of a searchable RNA-seq database based on experiment type, cell type, disease type, etc.?"
For tissue specificity, GTEX is probably the best option: http://www.gtexportal.org/home/
You can search by gene name, then click on Plot - Isoform.Then you can order the tissues by relative isoform levels and visualise the specificity.
The isoform annotation used is a slightly out of date Gencode GTF so you might have trouble finding some of the isoform in Ensembl, but all of them should still be in the database in the archive section.
I do not know what species you are interested in but I would think https://www.ebi.ac.uk/gxa/home is your best bet. It has multiple species as well cell types, treatments, etc. It also contains GTEx data, which as Jaroslav pointed out is a good source for baseline tissue expression.
https://www.ebi.ac.uk/gxa/home
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