📈 Scaling CAGE analysis across tens of #DANIO-CODE samples with the @nf-co.re inspired CAGEflow pipeline —big data meets promoters. Catch Ira's poster D-515! 🦓🐠

🦓🐠 Building the first promoter atlas of adult zebrafish organs—expanding #DANIO-CODE. Visit Marta at poster C-514. #zebrafish #CAGE

Important !!!! #DANIO-CODE data coordination is back online!!!

Correction: trackhub2.genereg.net/DANIO-CODE/D...

I am glad to announce that the #DANIO-CODE Data Coordination Center is back online at a new home:
danio-code-dcc.genereg.net
Thank you all for your patience and sorry for any inconvenience!

Track hub for UCSC browser: trackhub2genereg.net/DANIO-CODE/D...

#IZFC2025 #zebrafish #DANIO-CODE data coordination centre is back online. Note changed address: danio-code-dcc.genereg.net

I am excited to see the method we used in DANIO-CODE now fully developed as #IPP — and successfully tested on heart enhancers between chicken 🐔 and mouse 🐭! 🧬 Thanks to @danielibrahim.bsky.social for leading this. Proud to be part of it! Exciting times for future comparative regulatory analyses 🚀

For the DANIO-CODE tracks, there are many more tracks than it looks like on the browser page. If you want to see all the data available for a specific data type, you need to click on the hyperlink for the data which brings you to a page that lists all the available tracks. Click on the ones you want

Note that all the CRISPR and conservation tracks in our hub are also included as options in the DANIO-CODE hub (red circle). The only ones not included are our tracks that document common snps and indels we have identified in TU and AB.

that likely represents a conserved enhancer. If you also project DANIO-CODE tracks for histone methylation, you can see regions (green H3K2ac) where ChIP-seq overlaps the conserved sequence helping confirm that the region is likely to be a functional part of the promoter/enhancer.

Once you get to the track hubs pick the "Public Hubs" tab and then search for "zebrafish" I have circled the two hubs I am talking about here, the DANIO-CODE hub and the ZebrafishGenomics Hub you can connect to them by clicking the "connect" button.

It has been a while since I advertised some of the tools we have released to help researchers analyze the zebrafish genome. So a brief Bluetorial on our zebrafish genomics UCSC public data hub and the bigger effort led by @ferencmueller.bsky.social to create a zebrafish ENCODE project (Danio-CODE):