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/dcChIPseqComposite.html src/hg/makeDb/trackDb/zebrafish/danRer11/dcChIPseqComposite.html index 05e36139374..d549afff4ff 100644 --- src/hg/makeDb/trackDb/zebrafish/danRer11/dcChIPseqComposite.html +++ src/hg/makeDb/trackDb/zebrafish/danRer11/dcChIPseqComposite.html @@ -1,130 +1,129 @@ <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>