650b51533a44058e6e9129448dc33eb947105a43 max Sun Sep 6 06:55:18 2026 -0700 DANIO-CODE: remove leftover getTrackReferences error message from the References section of 10 track description pages. refs #38265 diff --git src/hg/makeDb/trackDb/zebrafish/danRer11/danioCode.html src/hg/makeDb/trackDb/zebrafish/danRer11/danioCode.html index 392c5f716a6..5ead4c98ca3 100644 --- src/hg/makeDb/trackDb/zebrafish/danRer11/danioCode.html +++ src/hg/makeDb/trackDb/zebrafish/danRer11/danioCode.html @@ -1,157 +1,156 @@ <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>