DANIO-CODE is an international consortium that annotates the non-coding part of the zebrafish genome, in the same spirit as ENCODE for the human genome. Rather than cataloguing genes, it maps the sequences that control when and where genes are used: promoters, enhancers, chromatin states and the contacts between them. What sets the zebrafish effort apart is that it is centered on development, so the annotation is built stage by stage, from the fertilized egg through gastrulation and organogenesis to the adult fish.
The consortium collected and reprocessed 1,802 zebrafish functional genomics datasets from a single pipeline per data type, so that samples from different laboratories can be compared with each other, and used them to annotate more than 140,000 candidate cis-regulatory elements across development. This collection shows those data on danRer11: RNA-seq coverage, CAGE-seq transcription start sites, ChIP-seq signal and peaks, 3P-seq polyadenylation sites, Hi-C chromosome folding, and the regulatory element annotations derived from them.
The collection contains the following tracks. Each has its own description page with the details of that data type:
Each of the tracks above is a container that groups many individual data files. Click a track name to open its configuration page, where samples can be selected by developmental stage, by sequencing sample, by ChIP-seq target and, for RNA-seq, by strand. Nothing is turned on by default; pick the samples you need, since turning on all of them at once will make the display very slow.
The DANIO-CODE consortium assembled 1,802 zebrafish developmental genomics datasets, 1,438 of them already published and 366 generated by consortium members, and reprocessed all of them from the raw sequencing reads so that samples from different laboratories and protocols can be compared. ChIP-seq and ATAC-seq were run through the ENCODE pipelines, CAGE-seq through the FANTOM pipeline, and Hi-C and 4C-seq through the pipelines of the groups that produced them; the pipelines are published at gitlab.com/danio-code. Samples were assigned to developmental stages using ZFIN and ENCODE nomenclature. Regulatory elements were predicted by segmenting the genome with ChromHMM using the histone modification data, then keeping the segments supported by an ATAC-seq peak; the resulting PADREs were classified further with a UMAP embedding of their accessibility and histone signal. Details are in Baranasic et al. 2022, and the data coordination center is at danio-code.zfin.org. The methods that apply to one data type are described on that track's own description page.
At UCSC, the tracks were converted from the consortium's public track hub at trackhub2.genereg.net/DANIO-CODE into native tracks with the script danioCodeHubToRa.py, and the data files were copied from the same server. The data themselves were not modified. The steps are documented in our makeDoc.
This is a collection of tracks; open the description page of an individual track above for the file names it uses and for examples.
The data can be explored interactively in table format with the Table Browser or the Data Integrator and exported from there to spreadsheet or tab-separated tables. From scripts, the data can be accessed through our API.
For automated download and analysis, the annotations are stored in bigWig and bigBed files that can be downloaded from our download server. Individual regions or the whole genome annotation can be obtained using our tools bigWigToBedGraph and bigBedToBed, which can be compiled from the source code or downloaded as precompiled binaries for your system. Instructions for downloading source code and binaries can be found here. The tools can also be used to obtain features within a given range, for example
bigBedToBed http://hgdownload.soe.ucsc.edu/gbdb/danRer11/danioCode/consens.canonical.danRer11.bigBed \
-chrom=chr1 -start=20000000 -end=20100000 stdout
The same files, together with the raw data, the sample and protocol metadata and the consortium's own analyses, can be downloaded from the DANIO-CODE data coordination center at danio-code.zfin.org.
Thanks to the DANIO-CODE consortium for producing, reprocessing and publishing these data, and to the Shawn Burgess laboratory at NHGRI for the conservation and CRISPR target tracks.
Baranasic D, Hörtenhuber M, Balwierz PJ, Zehnder T, Mukarram AK, Nepal C, Várnai C, Hadzhiev Y, Jimenez-Gonzalez A, Li N et al. Multiomic atlas with functional stratification and developmental dynamics of zebrafish cis- regulatory elements. Nat Genet. 2022 Jul;54(7):1037-1050. PMID: 35789323; PMC: PMC9279159