+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 +
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