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/dcChIPseqComposite.html src/hg/makeDb/trackDb/zebrafish/danRer11/dcChIPseqComposite.html new file mode 100644 index 00000000000..05e36139374 --- /dev/null +++ src/hg/makeDb/trackDb/zebrafish/danRer11/dcChIPseqComposite.html @@ -0,0 +1,130 @@ +<h2>Description</h2> + +<p> +ChIP-seq finds the places in the genome where a particular protein sits. Chromatin is +crosslinked, sheared and pulled down with an antibody against the protein of interest, +and the DNA that comes with it is sequenced. For histone modifications the result is a +map of the chemical marks on the histones that DNA is wrapped around, and different +marks tend to sit at different kinds of element: H3K4me3 at active promoters, H3K4me1 +and H3K27ac at enhancers, H3K27me3 at genes that are silenced by Polycomb, and +H3K36me3 across the bodies of transcribed genes. For a transcription factor the result +is a map of its binding sites. +</p> + +<p> +This track shows ChIP-seq data for 104 zebrafish samples across 17 developmental +stages and 18 targets: the histone marks H3K4me3, H3K4me1, H3K27ac, H3K27me3, +H3K36me3, H3K14ac and the histone variant H2AFV; RNA polymerase II with two antibodies +(4H8 and 8WG16); and the transcription factors Pou5f3, Nanog, Sox10, Zic3, CTCF, Cdx4, +Sall4, Mxtx2 and Gata1. These are the data the consortium used to segment the genome +into chromatin states, which are shown in the +<a href="hgTrackUi?g=dcComp">DC Elements</a> track. +</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> +The track has two views that can be configured separately. <b>Signal</b> shows one +auto-scaled coverage graph per sample. <b>Peaks</b> shows the enriched regions called +from that signal, as blocks. +</p> + +<p> +Nothing is displayed until samples are selected on the configuration page, where they +can be filtered by ChIP-seq target, developmental stage and sample. There are more than +200 individual tracks, so select only the targets and stages you need. +</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> +ChIP-seq libraries were mapped and peak-called with the ENCODE ChIP-seq pipeline. The +samples come from 10 laboratories, among them the Schier, Cairns, Bartel, Zon, +Horsfield, Driever, Skarmeta, Shkumatava, Mathavan and Mueller laboratories, and were +originally deposited under accessions including GSE32483, GSE41458, GSE44269, +GSE48254, GSE75356, GSE84602 and GSE95033. The accession of each sample is shown in +its track description line. +</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>dcChIPseqComposite</i>. +</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>. Files are named after the target and the DANIO-CODE sample accession, for example <tt>CTCF_DCD002910SQ_signal.bigWig</tt> and <tt>CTCF_DCD002910SQ_peak.bigBed</tt>. 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/CTCF_DCD002910SQ_peak.bigBed \ + -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> +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> +