Where To Find Libraries/Read Files Of All Rnas Found In A Cell

Question

[Click downvote]

I'm looking for a read file containing all RNAs (and possibly other junk) found in certain cells of humans and mice. (Preferably from the "entorhinal cortex", but other alternatives are "hippocampus" or "whole brain".)

Where can I even begin looking for such a thing? I tried arrayexpress, but found nothing relevant.

What are some relevant search terms?

[Medhat]

check this linc noncoding RNA annotation

Answer 1

[k.nirmalraman]

Are you seeking for transcriptome database of human and mouse genome? What will be the intended purpose of such data?? This is one of the transcriptome repository. You can basically use the transcriptome indexes to get such information. However, I am not sure if region or cell-type specific transcriptome database exists specifically. These can be obtained though from specific studies/publications (keep an eye on the methods used to get such data) and for brain, this could be a good start.

Some clarity in question can help you get more specific answers.

[Click downvote]

Thanks, will look into those. Transcriptome is my new word for the day.

[Click downvote]

I am looking for the transcriptome of a certain brain cell type ("entorhinal cortex" or to be less specific "hippocampus") in mice and humans. Preferably in fasta or fastq format, but anything goes.

One problem with most databases is that they only seem to contain the transcriptome under certain disease/stress/drug states.

[k.nirmalraman]

As far as I have understood, the spatio-temporal transcriptomics studies of brain regions are handful and one of the pioneering studies where transcriptomics of different regions were analysed can be found in two papers by Heintz group: paper1 and paper2. However these studies are based on microarrays... If you find your requirement answered here in this paper, the best is to extract genes that are very significantly expressed in a particular cell type from the publicly available data of these papers and( for which you may have to analyse the data to answer ur questions) and extract the gene sequences from mouse genome or other sources such as UCSC. This can be one way to get there :)

Also, one might most certainly get is the transcriptome for an organism but nothing specifically as transcriptome for a cell type or region. What usually happens is relative preferential expression of genes and that is exactly what some studies try to find out to understand the functionality in each cell type. So may be you have to rethink the approach of "transcriptome of certain brain cell type".

Answer 2

[Sebastian Boegel]

Did you already try the short read archive (SRA) from NCBI (http://www.ncbi.nlm.nih.gov/sra)? This is a huge collection of primary sequencing data. You might find something there.