52ebb985f6e3658f463e971b7acd4c3959d36f92 gperez2 Wed Apr 22 17:38:06 2026 -0700 Enlarged classification diagram (40% to 60%) on the cCRE registry and Core Collection description pages. Updated the shortLabels on all 90 Core Collection subtracks with biosample + age + assay labels. refs #37131 diff --git src/hg/makeDb/trackDb/mouse/mm10/cCREregistry.html src/hg/makeDb/trackDb/mouse/mm10/cCREregistry.html index 88defafdefa..d6c09ea03ca 100644 --- src/hg/makeDb/trackDb/mouse/mm10/cCREregistry.html +++ src/hg/makeDb/trackDb/mouse/mm10/cCREregistry.html @@ -67,31 +67,31 @@ Candidate cis-regulatory elements (cCREs) were first anchored on nucleosome-sized DNase hypersensitive sites (rDHSs) identified from DNase-seq data. These rDHSs were then annotated using ChIP-seq data for histone modifications (H3K4me3 and H3K27ac, marking promoters and enhancers, respectively) and CTCF, marking insulators. To supplement rDHS-anchored cCRE definitions, transcription factor ChIP-seq peaks were incorporated, enabling identification of cCREs even in regions of low chromatin accessibility. Although not used for anchoring, ATAC-seq data were used to assess chromatin accessibility in biosamples lacking DNase-seq. Because ATAC-seq was not standardized across all biosamples, the ATAC max-Z score is not included in the registry bigBed fields or mouseOver. Only the four core assays (DNase, H3K4me3, H3K27ac, and CTCF) are reported as max-Z scores. ATAC-seq signal tracks are available in the <a href="../cgi-bin/hgTrackUi?db=mm10&g=encode4Reg">ENCODE4 Regulation</a> track.</p> <p> The following diagram illustrates the biochemical signal patterns used to classify each cCRE type:</p> <p> -<img src="../images/encode4cCREs.png" alt="Graphic of cCRE classifications" width="40%"></p> +<img src="../images/encode4cCREs.png" alt="Graphic of cCRE classifications" width="60%"></p> <h2>Data Access</h2> <p> The ENCODE accession numbers of the constituent datasets at the <a target="_blank" href="https://encodeproject.org/">ENCODE Portal</a> are available from the cCRE details page.</p> <p> The data in this track can be interactively explored with the <a target="_blank" href="/cgi-bin/hgTables">Table Browser</a> or the <a target="_blank" href="/cgi-bin/hgIntegrator">Data Integrator</a>. The data can be accessed from scripts through our <a target="_blank" href="https://api.genome.ucsc.edu/">API</a>, the track name is "cCREregistry".</p> <p> For automated download and analysis, this annotation is stored in a bigBed file that can be downloaded from <a target="_blank" href="http://hgdownload.soe.ucsc.edu/gbdb/mm10/encode4/ccre/">our download server</a>.