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/dcHiC_Composite.html src/hg/makeDb/trackDb/zebrafish/danRer11/dcHiC_Composite.html new file mode 100644 index 00000000000..70c4558f6c2 --- /dev/null +++ src/hg/makeDb/trackDb/zebrafish/danRer11/dcHiC_Composite.html @@ -0,0 +1,126 @@ +<h2>Description</h2> + +<p> +A chromosome is not a straight line in the nucleus. It is folded so that some parts +touch each other far more often than others, and the regions of preferential contact +are called topologically associating domains. Domain boundaries matter for gene +regulation, because an enhancer usually acts on genes inside its own domain and rarely +across a boundary. Hi-C measures which parts of the genome are in contact by +crosslinking, cutting and religating chromatin, then sequencing the resulting pairs. +</p> + +<p> +This track does not show the contact matrix itself but two summary scores computed +from it along the genome. The <b>insulation index</b> is low where few contacts cross a +position, so its local minima mark domain boundaries. The <b>directionality index</b> +measures whether the contacts at a position point mostly upstream or mostly downstream, +and it flips sign at a boundary. Both are shown for 4 samples at 4 developmental stages +(256-cell, Dome, 75% epiboly and Prim-5) and at three window sizes, 50 kb, 500 kb and +1 Mb. +</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 sample, index type and window size is a separate auto-scaled graph. +Positive values are drawn in red and negative values in blue. The window size sets the +scale at which the index is computed, so the 50 kb tracks respond to local boundaries +and the 1 Mb tracks to large-scale compartments. +</p> + +<p> +Nothing is displayed until tracks are selected on the configuration page, where they +can be filtered by developmental stage, window size, index type and 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 Hi-C data were processed by the group that produced them, and the insulation and +directionality indices were computed from the resulting contact matrices at 50 kb, +500 kb and 1 Mb windows. The samples come from the de Wit laboratory and were +originally deposited under GSE105015. +</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>dcHiC_Composite</i>. +</p> + +<p> +For automated download and analysis, the annotations are stored in bigWig 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 sample, the window size and the index type, for example <tt>DCD003008SQ_DCD017502DT_50000_di.bigWig</tt> for the directionality index at 50 kb and <tt>..._ii.bigWig</tt> for the insulation index. Individual regions or the whole genome annotation can be +obtained using our tool <tt>bigWigToBedGraph</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>bigWigToBedGraph http://hgdownload.soe.ucsc.edu/gbdb/danRer11/danioCode/DCD003008SQ_DCD017502DT_50000_di.bigWig \ + -chrom=chr1 -start=20000000 -end=21000000 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> +