Publicly Available Rna-Seq Data For Study Splicing Change In Human Brain

Question

[michealsmith]

Hi, I'm highly suspicious about there could be alternative splicing for one gene enriched in neuronal tissues I'm now quite interested in. Before getting into any benchwork, my idea is to first look at if any publicly available data can give any indication of splicing bioinformatically.

My questions:

1. By looking at browsers (say UCSC, or epigenome roadmap), which options I may use so that I'm able to directly find the possible splicing pattern across the region of interest? I only find some EST (expressed sequence tag) but they are not that informative.
2. I don't know where I can any RNA-seq data for human brain or any neuronal tissues? I can map the data myself to have a sense if there's alternative splicing or not.

thx!

[ancient_learner]

search GEO database with appropriate keywords :)

Answer 1

[Mikael Huss]

The easiest way is to use IGV and activate the BodyMap tracks (accessible from a menu) for brain. That will give you a view of the alignments and predicted transcripts.

Here are links to some human brain RNA-seq data sets that I collected in the past. There are surely more now.

• http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE13652
• ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR030
• http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE12946
• http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE30352
• http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE16368
• http://hugheslab.ccbr.utoronto.ca/supplementary-data/hm_transcriptome/
• http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE19166

Answer 2

[Denise CS]

It's easy to view the Illumina BodyMap data for brain on the Ensembl browser too.

Gene models, intron-spanning reads and BAM files are all available there and the BAM files can be downloaded via our FTP.

More details on this data and the Ensembl RNASeq pipeline can be found on our help pages, blog and youtube channel (RNASeq in the genebuild and Browsing RNASeq in Ensembl).

Answer 3

[EagleEye]

This might be useful:Human-bodymap 2.0 RNA-seq data (Includes human brain tissue samples)

http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-513/