New Zebrafish Data Hub for UCSC Browser

To all zebrafish researchers:

I am writing to let everyone know of a new data resource for zebrafish genomics we have made available on the UCSC genome browser (we will eventually have this data available for the Ensembl browser too). This data comes from deep sequencing of a fish line we have recently described in Genetics called NHGRI-1 (http://www.genetics.org/content/early/2014/07/10/genetics.114.166769.full.pdf+html). If you use these fish, nearly all variations from the reference genome have been documented and can be easily visualized by connecting to our data hub via this page: http://genome.ucsc.edu/cgi-bin/hgHubConnect?hubSearchTerms=&hgHub_do_search=on

If you connect to the "zebrafishgenomics" hub you will be able to see all regions of the NHGRI-1 fish's genome that perfectly matches the reference sequence. This will simplify primer, morpholino, TALEN, or CRISPR/Cas design since you won't have to resequence these regions.

Even if you are not using NHGRI-1, the tracks document many of the common variants in the Tubingen or AB backgrounds, allowing you to more confidently make design choices. We have also put in tracks showing all our retroviral integrations and all predicted CRISPR/Cas9 targets in the genome (with the number of predicted off-targets listed).

We hope this data will be of use to everyone in the community.

Shawn Burgess