76eabae1c28bb07c02af6a12fa9222c348b039d9 max Sun Sep 6 07:02:29 2026 -0700 DANIO-CODE: open each subtrack description with the sentence saying that the track is part of the DANIO-CODE container, linking to its hgTrackUi page, instead of burying it in a paragraph at the end of the description. refs #38265 diff --git src/hg/makeDb/trackDb/zebrafish/danRer11/dc3PseqComposite.html src/hg/makeDb/trackDb/zebrafish/danRer11/dc3PseqComposite.html index 6b04f889b4c..a8e988012d6 100644 --- src/hg/makeDb/trackDb/zebrafish/danRer11/dc3PseqComposite.html +++ src/hg/makeDb/trackDb/zebrafish/danRer11/dc3PseqComposite.html @@ -1,116 +1,113 @@ <h2>Description</h2> <p> +This track is part of the <a href="hgTrackUi?g=danioCode">DANIO-CODE</a> track collection. Most messenger RNAs end in a poly(A) tail, and the position where that tail is added determines the length of the 3' untranslated region. That region carries the binding sites for microRNAs and RNA-binding proteins, so a transcript that uses a different poly(A) site can be regulated quite differently. 3P-seq (poly(A)-position profiling by sequencing) sequences the junction between the transcript and its poly(A) tail, which places the 3' end of the transcript directly. </p> <p> This track shows 3P-seq data for 15 zebrafish samples covering 7 developmental stages, from the 1-cell stage to the adult. Both the raw signal and the tag clusters called from it are shown. During the first hours of development, when the embryo still lives on maternally deposited RNA, poly(A) tails are actively lengthened and shortened, so these data change substantially from stage to stage. </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>Regions</b> shows the tag clusters as blocks. Nothing is displayed until samples are selected on the configuration page, where they can be filtered by developmental stage and by sample. </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 3P-seq samples come from the Bartel laboratory and were originally deposited under GSE32880 and GSE37453. </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>dc3PseqComposite</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 DANIO-CODE data accession, for example <tt>DCD007934DT_tagCluster.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/DCD007934DT_tagCluster.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> <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>