acf20930c5cdfa1e352826a702ad8f36344178c4 markd Thu Sep 24 21:16:13 2026 -0700 Fixes from an independent review of the TSS tracks. refs #35528 The Data Access sections told users to pass the composite name to the API, which returns HTTP 400. The API serves one bigWig at a time, so both pages now name a single strand of one cell line, verified to return 200. encode4ProCap.html claimed the kent tree held the manifest of which ENCODE files went into each track, and it did not. Commit that manifest as proCapNetEncodeFiles.tsv and name it on the page. It matters because proCapNetEncodeMeta resolves each experiment's default analysis at run time, so re-running it after an ENCODE reprocessing can pick different files. Cite Shah et al. for the ENCODE 4 nascent transcriptome survey the six PRO-cap experiments come from. Sagar Shah was credited by name with no reference. The hg38 makedoc called the 164268582 dropped bases "the N regions", but gap on the primary chromosomes is 150610728. The extra 13.7 Mb is sequence flanking each gap, dropped because most of its 2114 bp window was unresolved. diff --git src/hg/makeDb/trackDb/human/encode4ProCap.html src/hg/makeDb/trackDb/human/encode4ProCap.html index 4456dffb38e..41a57dc0988 100644 --- src/hg/makeDb/trackDb/human/encode4ProCap.html +++ src/hg/makeDb/trackDb/human/encode4ProCap.html @@ -1,165 +1,184 @@ <h2>Description</h2> <p> Transcription begins when RNA polymerase II starts making an RNA at a transcription start site. A promoter or an enhancer does not use a single start site: polymerase initiates across a spread of nearby bases, on both strands, and which bases are used is set largely by the local DNA sequence. PRO-cap is a nascent RNA run-on assay that captures the 5' end of each new transcript, so each read reports the exact base and strand of one initiation event. Unlike RNA-seq or CAGE, PRO-cap sees unstable RNAs as well as stable ones, which makes initiation at enhancers visible. </p> <p> This track shows PRO-cap signal from six ENCODE 4 experiments, one per cell line, on GRCh38/hg38 only. The predictions a deep learning model makes from sequence alone, trained on this same data, are in the ProCapNet track, available on GRCh38/hg38 and T2T-CHM13/hs1. </p> <h2>Display Conventions and Configuration</h2> <p> Cell lines are listed in the table on this page, one row each. Use the Sample class facet to narrow the list, and the Experiment column to open the experiment on the ENCODE portal. </p> <p> Each track is an overlay of the two strands: plus strand reads are drawn upward and minus strand reads downward. The y axis is the number of initiation events measured at that base, summed over the experiment's replicates, so tracks with deeper sequencing reach higher values. Tracks are colored by cell line: </p> <ul> <li><span style="display:inline-block; background-color:#0072B2; width:18px; height:12px; vertical-align:middle;"></span> <b>A673</b> Ewing sarcoma</li> <li><span style="display:inline-block; background-color:#D55E00; width:18px; height:12px; vertical-align:middle;"></span> <b>Caco-2</b> colorectal adenocarcinoma</li> <li><span style="display:inline-block; background-color:#009E73; width:18px; height:12px; vertical-align:middle;"></span> <b>Calu3</b> lung adenocarcinoma</li> <li><span style="display:inline-block; background-color:#CC79A7; width:18px; height:12px; vertical-align:middle;"></span> <b>HUVEC</b> umbilical vein endothelial cells</li> <li><span style="display:inline-block; background-color:#E69F00; width:18px; height:12px; vertical-align:middle;"></span> <b>K562</b> chronic myelogenous leukemia</li> <li><span style="display:inline-block; background-color:#56B4E9; width:18px; height:12px; vertical-align:middle;"></span> <b>MCF10A</b> non-tumorigenic breast epithelium</li> </ul> <h2>Methods</h2> <p> PRO-cap, in the CoPRO form described by Tome <em>et al</em>., permeabilizes cells and runs a nuclear run-on reaction with biotinylated NTPs, which RNA polymerase incorporates into the nascent transcripts it is actively making. Biotinylated RNAs are captured on streptavidin beads, selected for a 5' cap so that only transcripts still carrying their original start are kept, then reverse transcribed and paired-end sequenced. The 5' end of the second read marks the base at which transcription started, and the read's strand gives the strand of initiation. The six experiments here were produced by the Yu and Lis labs at Cornell University and processed through the ENCODE PRO-cap pipeline, which maps reads, removes PCR duplicates using unique molecular identifiers, and writes -single-base plus and minus strand signal for the uniquely mapping reads. +single-base plus and minus strand signal for the uniquely mapping reads. These +experiments are part of the ENCODE 4 nascent transcriptome survey described in +Shah <em>et al</em>. </p> <p> The signal files were downloaded from the <a href="https://www.encodeproject.org" target="_blank">ENCODE portal</a>, taking for each experiment only the plus and minus strand signal of unique reads files belonging to that experiment's default analysis, which drops files superseded by a later reprocessing. The experiments are ENCSR046BCI, ENCSR100LIJ, ENCSR935RNW, ENCSR098LLB, ENCSR261KBX and ENCSR799DGV for A673, Caco-2, Calu3, HUVEC, K562 and MCF10A respectively, and are linked from the Experiment column of the table on this page. ENCODE releases PRO-cap signal per replicate and, for MCF10A, per sequencing run, and publishes no pooled file, so the files were summed at UCSC to give one track per cell line per strand: two files for A673, Caco-2, Calu3 and K562, one for HUVEC, which has a single released replicate, and four for MCF10A. This is the same merge the ProCapNet models were trained on. Minus strand signal is negative as released by ENCODE and is kept that way. Total signal is conserved exactly by the summing. The steps are recorded in the <a href="https://github.com/ucscGenomeBrowser/kent/blob/master/src/hg/makeDb/doc/hg38/transcriptionStart.txt" target="_blank">makeDoc</a> and the scripts are in <a href="https://github.com/ucscGenomeBrowser/kent/tree/master/src/hg/makeDb/outside/proCapNet" -target="_blank">the kent source tree</a>, including the manifest recording exactly -which ENCODE files went into each track. +target="_blank">the kent source tree</a>, including +<tt>proCapNetEncodeFiles.tsv</tt>, which records exactly which ENCODE file +accessions went into each track. </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-sep tables. From scripts, the data can be accessed through our -<a href="https://api.genome.ucsc.edu" target="_blank">API</a>, track=<i>encode4ProCap</i>. +<a href="https://api.genome.ucsc.edu" target="_blank">API</a>. The API returns one +bigWig at a time, so name a single strand of one cell line rather than the +container, for example track=<i>encode4ProCap_K562_procap_pos</i>. </p> <p> The Files column of the table on this page links each cell line's bigWigs directly, so a single file can be fetched without working out its path. </p> <p> For automated download and analysis, the genome annotation is stored in bigWig files that can be downloaded from <a href="http://hgdownload.soe.ucsc.edu/gbdb/hg38/encode4ProCap/" target="_blank">our download server</a>. The files are named for the cell line, the ENCODE experiment accession and the strand, for example <tt>K562.ENCSR261KBX.pos.bw</tt> and <tt>K562.ENCSR261KBX.neg.bw</tt>. 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" target="_blank">here</a>. The tool can also be used to obtain features within a given range, e.g. <tt>bigWigToBedGraph http://hgdownload.soe.ucsc.edu/gbdb/hg38/encode4ProCap/K562.ENCSR261KBX.pos.bw -chrom=chr21 -start=0 -end=100000000 stdout</tt> </p> <p> The unmerged per-replicate files can be downloaded from the <a href="https://www.encodeproject.org" target="_blank">ENCODE portal</a> under the experiment accessions listed above. </p> <h2>Credits</h2> <p> PRO-cap data was generated as part of ENCODE by Sagar Shah and the Yu and Lis labs at Cornell University. Thanks to the ENCODE Consortium and the ENCODE production laboratories for making the data available. </p> <h2>References</h2> +<p> +Shah SR, Chen Y, Leung AK, Navarro PVC, Paramo MI, Gupta J, Gurumurthy A, Fite RF, Weimer AK, +Cochran K <em>et al</em>. +<a href="https://www.ncbi.nlm.nih.gov/pubmed/41040139" target="_blank"> +The nascent transcriptome delineates the regulatory landscape in human health and disease</a>. +<em>bioRxiv</em>. 2026 Jun 9;. +DOI: <a href="https://doi.org/10.1101/2025.09.24.676871" +target="_blank">10.1101/2025.09.24.676871</a>; PMID: <a +href="https://www.ncbi.nlm.nih.gov/pubmed/41040139" target="_blank">41040139</a>; PMC: <a +href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12485982/" target="_blank">PMC12485982</a> +</p> + + + <p> Tome JM, Tippens ND, Lis JT. <a href="https://www.ncbi.nlm.nih.gov/pubmed/30349116" target="_blank"> Single-molecule nascent RNA sequencing identifies regulatory domain architecture at promoters and enhancers</a>. <em>Nat Genet</em>. 2018 Nov;50(11):1533-1541. DOI: <a href="https://doi.org/10.1038/s41588-018-0234-5" target="_blank">10.1038/s41588-018-0234-5</a>; PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/30349116" target="_blank">30349116</a>; PMC: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6422046/" target="_blank">PMC6422046</a> </p> <p> Kwak H, Fuda NJ, Core LJ, Lis JT. <a href="https://www.ncbi.nlm.nih.gov/pubmed/23430654" target="_blank"> Precise maps of RNA polymerase reveal how promoters direct initiation and pausing</a>. <em>Science</em>. 2013 Feb 22;339(6122):950-3. DOI: <a href="https://doi.org/10.1126/science.1229386" target="_blank">10.1126/science.1229386</a>; PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/23430654" target="_blank">23430654</a>; PMC: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3974810/" target="_blank">PMC3974810</a> </p> <p> Luo Y, Hitz BC, Gabdank I, Hilton JA, Kagda MS, Lam B, Myers Z, Sud P, Jou J, Lin K <em>et al</em>. <a href="https://www.ncbi.nlm.nih.gov/pubmed/31713622" target="_blank"> New developments on the Encyclopedia of DNA Elements (ENCODE) data portal</a>. <em>Nucleic Acids Res</em>. 2020 Jan 8;48(D1):D882-D889. DOI: <a href="https://doi.org/10.1093/nar/gkz1062" target="_blank">10.1093/nar/gkz1062</a>; PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/31713622" target="_blank">31713622</a>; PMC: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7061942/" target="_blank">PMC7061942</a> </p>