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/dcComp.html src/hg/makeDb/trackDb/zebrafish/danRer11/dcComp.html new file mode 100644 index 00000000000..835f07c808f --- /dev/null +++ src/hg/makeDb/trackDb/zebrafish/danRer11/dcComp.html @@ -0,0 +1,169 @@ +<h2>Description</h2> + +<p> +This track holds the DANIO-CODE annotation of candidate regulatory elements, at five +developmental stages: Dome, 75% epiboly, 5-9 somites, Prim-5 and Long-pec. Four +related annotations are shown for each stage. +</p> + +<p> +<b>ChromHMM</b> is a segmentation of the whole genome into ten chromatin states. The +segmentation is learned from the combination of histone modifications present at each +position, and each state was then given a name by hand, using the Roadmap Epigenomics +annotation as a reference: active transcription start sites, their flanking regions, +active and primed enhancers, poised elements, Polycomb-repressed regions and a +quiescent state with no detectable mark. +</p> + +<p> +<b>PADREs</b> are predicted ATAC-supported developmental regulatory elements: the +subset of the segmentation that also lies in a region of open chromatin, which is the +consortium's set of candidate regulatory elements. Across all stages there are more +than 140,000 of them. <b>cPADREs</b> are the consensus set of 83,553 elements that are +called at every stage, so they can be compared position by position across +development. <b>DOPEs</b> are dynamic orphan predicted elements: regions that are open +at a given stage but carry no histone mark at all. +</p> + +<p> +This track is part of the <a href="hgTrackUi?g=danioCode">DANIO-CODE</a> collection. +</p> + +<h2>Display Conventions and Configuration</h2> + +<p> +Each combination of annotation type and developmental stage is a separate track. On the +configuration page they are laid out as a grid, with the annotation type across and the +stage down. Only the ChromHMM tracks are checked when the grid is first opened. +</p> + +<p> +The ChromHMM and PADRE tracks are colored by chromatin state: +</p> + +<table class="stdTbl"> + <tr><th style="background-color:#A6CEE3;width:2em"> </th> + <td>1_TssA1 — active transcription start site</td></tr> + <tr><th style="background-color:#1F78B4;width:2em"> </th> + <td>2_TssA2 — active transcription start site, second class</td></tr> + <tr><th style="background-color:#33A02C;width:2em"> </th> + <td>3_TssFlank1 — region flanking a transcription start site</td></tr> + <tr><th style="background-color:#B2DF8A;width:2em"> </th> + <td>4_TssFlank2 — region flanking a transcription start site, second class</td></tr> + <tr><th style="background-color:#E31A1C;width:2em"> </th> + <td>5_EnhA1 — active enhancer</td></tr> + <tr><th style="background-color:#FB9A99;width:2em"> </th> + <td>6_EnhFlank — region flanking an enhancer</td></tr> + <tr><th style="background-color:#FF7F00;width:2em"> </th> + <td>7_EnhWk1 — primed enhancer</td></tr> + <tr><th style="background-color:#6A3D9A;width:2em"> </th> + <td>8_Pois — poised element</td></tr> + <tr><th style="background-color:#CAB2D6;width:2em"> </th> + <td>9_ReprPC — Polycomb-repressed region</td></tr> + <tr><th style="background-color:#A1A2A3;width:2em"> </th> + <td>10_Quies — quiescent, no mark detected</td></tr> +</table> + +<p> +The DOPE tracks carry no state and are drawn in black. +</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 different protocols can be compared with each other. 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>, and +samples were assigned to developmental stages using ZFIN and ENCODE nomenclature. See +Baranasic <em>et al</em>. 2022 for details. +</p> + +<p> +The genome was segmented with ChromHMM using the histone modification data in the +<a href="hgTrackUi?g=dcChIPseqComposite">DC ChIP-seq</a> track, and the ten resulting +states were named by comparison with the Roadmap Epigenomics annotation. Segments that +overlap an ATAC-seq peak were kept as PADREs. The PADREs were then classified further +by embedding their accessibility and histone signal with UMAP, which separates +promoters from enhancers and brings out subclasses that follow the timing of their +activity. Elements without any chromatin mark were split into those open at all stages +and those open only at some; the second group is shown here as DOPEs, and both groups +are shown pooled in the <a href="hgTrackUi?g=dcCopes_and_dopes">DC COPEs DOPEs</a> +track. +</p> + +<p> +Element counts per stage, for PADREs: 85,750 at Dome, 93,394 at 75% epiboly, 123,324 +at 5-9 somites, 122,462 at Prim-5 and 148,870 at Long-pec. For DOPEs: 4,896, 5,862, +7,384, 7,699 and 6,468 for the same stages. The consensus cPADRE set has 83,553 +elements at every stage. +</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> 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> +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>, track=<i>dcComp</i>. +</p> + +<p> +For automated download and analysis, the annotations are stored in bigBed files that +can be downloaded from +<a href="http://hgdownload.soe.ucsc.edu/gbdb/danRer11/danioCode/" target="_blank">our +download server</a>. Files are named after the stage and the annotation type, for example <tt>Prim5_PADREs.bb</tt>, <tt>Prim5_ChromHMM.bb</tt>, <tt>Prim5_cPADRE.bb</tt> and <tt>Prim5_DOPEs.bb</tt>. The stage names in the file names are Dome, Epi75, Hpf12, Prim5 and LongPec. Individual regions or the whole genome annotation can be +obtained using our tool <tt>bigBedToBed</tt>, which can be compiled from the source code +or downloaded as a precompiled binary 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 tool can also be used to obtain features within a given range, for example +</p> +<pre>bigBedToBed http://hgdownload.soe.ucsc.edu/gbdb/danRer11/danioCode/Prim5_PADREs.bb \ + -chrom=chr1 -start=20000000 -end=20100000 stdout</pre> + +<p> +The original data files, and the sample and protocol metadata behind them, are +available from the DANIO-CODE data coordination center at +<a href="https://danio-code.zfin.org" target="_blank">danio-code.zfin.org</a> and from +the consortium's track hub at +<a href="https://trackhub2.genereg.net/DANIO-CODE/DANIO-CODE.hub.txt" target="_blank"> +trackhub2.genereg.net/DANIO-CODE</a>. +</p> + +<h2>Credits</h2> + +<p> +Thanks to the DANIO-CODE consortium for collecting, reprocessing and publishing these +data, and to the laboratories that produced the original datasets. +</p> + +<h2>References</h2> + +<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://doi.org/10.1038/s41588-022-01089-w" 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> +