f5c96c14557e69252db6935d20ea55bdd250e519 max Fri Sep 4 17:12:57 2026 -0700 DANIO-CODE as native danRer11 tracks, alpha only. Converts the DANIO-CODE consortium's public track hub for danRer11 into a native trackDb: 897 stanzas under one superTrack, with 11 containers for RNA-seq, CAGE-seq, ChIP-seq, 3P-seq, Hi-C, regulatory elements, cell types, COPEs/DOPEs, validated enhancers, conservation and consensus promoters. The 879 data files, 69 GB, are mirrored under /gbdb/danRer11/danioCode and are byte-identical to the consortium's copies. Four cell-type subtracks are left out because their files 404 on the consortium's server. refs #38265 diff --git src/hg/makeDb/trackDb/zebrafish/danRer11/danioCode.html src/hg/makeDb/trackDb/zebrafish/danRer11/danioCode.html new file mode 100644 index 00000000000..392c5f716a6 --- /dev/null +++ src/hg/makeDb/trackDb/zebrafish/danRer11/danioCode.html @@ -0,0 +1,157 @@ +<h2>Description</h2> + +<p> +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. +</p> + +<p> +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. +</p> + +<p> +The collection contains the following tracks. Each has its own description page with +the details of that data type: +</p> + +<ul> + <li><a href="hgTrackUi?g=dcRNAseqComposite">DC RNA-seq</a> — + strand-specific and unstranded read coverage for 361 RNA-seq samples across 31 + developmental stages.</li> + <li><a href="hgTrackUi?g=dcCAGEseqComposite">DC CAGE-seq</a> — CAGE + signal and tag clusters, which mark the positions where transcription starts.</li> + <li><a href="hgTrackUi?g=dcChIPseqComposite">DC ChIP-seq</a> — signal + and called peaks for seven histone modifications, RNA polymerase II and nine + transcription factors.</li> + <li><a href="hgTrackUi?g=dc3PseqComposite">DC 3P-seq</a> — signal and + tag clusters marking the 3' ends of transcripts.</li> + <li><a href="hgTrackUi?g=dcHiC_Composite">DC Hi-C</a> — insulation index + and directionality index computed from Hi-C contact maps, used to locate the + boundaries of topologically associating domains.</li> + <li><a href="hgTrackUi?g=dcComp">DC Elements</a> — per-stage regulatory + element annotation at five stages: ChromHMM chromatin states, PADREs, the + consensus subset cPADREs, and DOPEs.</li> + <li><a href="hgTrackUi?g=dcComp_cell_type">DC Cell Types</a> — + regulatory elements assigned to a cell type using single-cell ATAC-seq.</li> + <li><a href="hgTrackUi?g=dcCopes_and_dopes">DC COPEs DOPEs</a> — open + chromatin regions that carry no histone mark at any stage, split by whether they + stay open throughout development or only at some stages.</li> + <li><a href="hgTrackUi?g=dcEvalidation">DC Enhancers</a> — a curated set + of zebrafish enhancers tested in transgenic reporter assays.</li> + <li><a href="hgTrackUi?g=dcComparativeGenomics">DC Conservation</a> — + phastCons conservation across four cyprinid fishes, the conserved non-coding + elements from it, and predicted CRISPR/Cas9 target sites, from the Shawn Burgess + laboratory at NHGRI.</li> + <li><a href="hgTrackUi?g=dcConsensus_promoters">DC Promoters</a> — + consensus promoters called from the CAGE data.</li> +</ul> + +<h2>Display Conventions and Configuration</h2> + +<p> +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. +</p> + +<h2>Methods</h2> + +<p> +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 +<a href="https://gitlab.com/danio-code" target="_blank">gitlab.com/danio-code</a>. +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 <em>et al</em>. 2022, and the data +coordination center is at +<a href="https://danio-code.zfin.org" target="_blank">danio-code.zfin.org</a>. The +methods that apply to one data type are described on that track's own description page. +</p> + +<p> +At UCSC, the tracks were converted from the consortium's public track hub at +<a href="https://trackhub2.genereg.net/DANIO-CODE/DANIO-CODE.hub.txt" target="_blank"> +trackhub2.genereg.net/DANIO-CODE</a> into native tracks with the script +<a href="https://github.com/ucscGenomeBrowser/kent/tree/master/src/hg/makeDb/scripts/danioCode" +target="_blank">danioCodeHubToRa.py</a>, and the data files were copied from the same +server. The data themselves were not modified. The steps are documented in +<a href="https://github.com/ucscGenomeBrowser/kent/blob/master/src/hg/makeDb/doc/danRer11/danioCode.txt" +target="_blank">our makeDoc</a>. +</p> + +<h2>Data Access</h2> + +<p> +This is a collection of tracks; open the description page of an individual track above +for the file names it uses and for examples. +</p> + +<p> +The data can be explored interactively in table format with the +<a href="../cgi-bin/hgTables">Table Browser</a> or the +<a href="../cgi-bin/hgIntegrator">Data Integrator</a> and exported from there to +spreadsheet or tab-separated tables. From scripts, the data can be accessed through our +<a href="https://api.genome.ucsc.edu">API</a>. +</p> + +<p> +For automated download and analysis, the annotations are stored in bigWig and bigBed +files that can be downloaded from +<a href="http://hgdownload.soe.ucsc.edu/gbdb/danRer11/danioCode/" target="_blank">our +download server</a>. Individual regions or the whole genome annotation can be obtained +using our tools <tt>bigWigToBedGraph</tt> and <tt>bigBedToBed</tt>, 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 +<a href="http://hgdownload.soe.ucsc.edu/downloads.html#utilities_downloads">here</a>. +The tools can also be used to obtain features within a given range, for example +</p> +<pre>bigBedToBed http://hgdownload.soe.ucsc.edu/gbdb/danRer11/danioCode/consens.canonical.danRer11.bigBed \ + -chrom=chr1 -start=20000000 -end=20100000 stdout</pre> + +<p> +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 <a href="https://danio-code.zfin.org" target="_blank">danio-code.zfin.org</a>. +</p> + +<h2>Credits</h2> + +<p> +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. +</p> + +<h2>References</h2> +Failed to fetch complete links from NCBI after 10 tries. Try again later or just use the PubMed paper link. + +<p> +Baranasic D, Hörtenhuber M, Balwierz PJ, Zehnder T, Mukarram AK, Nepal C, Várnai C, Hadzhiev Y, +Jimenez-Gonzalez A, Li N <em>et al</em>. +<a href="https://www.ncbi.nlm.nih.gov/pubmed/35789323" target="_blank"> +Multiomic atlas with functional stratification and developmental dynamics of zebrafish cis- +regulatory elements</a>. +<em>Nat Genet</em>. 2022 Jul;54(7):1037-1050. +PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/35789323" target="_blank">35789323</a>; PMC: <a +href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9279159/" target="_blank">PMC9279159</a> +</p> +