I am looking for a tool to easily analyze the expression of different genes during the differentiation of mouse or human pluripotent stem cells to different derivatives, something similar to ChIP-atlas but for RNA-seq.
I know there are repositories with RAW RNA-seq data such as GEO or SRA, which sometimes include the tables with analyzed data. However, in many cases this needs some processing, and sometimes you only get the fastq files.
I wonder if there is some database that feeds from GEO/SRA, where I could look for classified experiments, such as "Neural differentiation of human pluripotent stem cells", and where I could easily plot de expression of a GOI in the different conditions/timepoints.
Thanks a lot!
Hi Fernando, thanks for your answer. I recently found this, where they re processed GEO data
http://www.ilincs.org/apps/grein/
Cheers
Here are some of them:
- The Gene Expression Omnibus (GEO) database
- The Sequence Read Archive (SRA) database
- The Human Induced Pluripotent Stem Cell Initiative (HipSci) project
- The Human Pluripotent Stem Cell Registry (hPSCreg) database
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