How can I download data from Ensembl Zv9 for a specific developmental stage.

Question

[evobio]

SCENARIO example:

1. Go to Ensembl Zv9 (http://mar2015.archive.ensembl.org/Danio_rerio/Info/Index).
2. Search for gene "ghra".
3. Go to the "Location" tab.
4. Click on "Configure this page" on the menu on the left.
5. Click on "RNASeq models", under "Genes and transcripts".
6. Select all the rows on the "Exons" column.
7. Save and close (check mark on the upper left).

Now we can see the developmental stages at which the transcripts related to that gene are expressed, according to RNA-seq data.

QUESTION:

Is it possible to download the list of all transcripts and genes that are expressed at a specific developmental stage in zebrafish? If yes, how? I'm new in bioinformatics. I have tried BioMart, but it doesn't have the option for RNASeq per developmental stage.

[Joseph Pearson]

I also wasn't able to find the appropriate track in BioMart (or biomaRt), but that doesn't mean it's not there. I did find this reference:

http://genome.cshlp.org/content/22/10/2067.long

Which describes connections to the otherfeatures database with Perl. I think the answer is in there, but you would need to learn at least a little Perl to get the syntax right. Good luck!