af96452e1c6ccf783697cead2630de1ca4e91635 markd Sat Sep 26 06:42:20 2026 -0700 Put the primary citation first again on the TSS track pages. refs #35528 Alphabetical order buried the paper each track is actually built on: Cochran et al. for ProCapNet, behind Avsec, and Shah et al. for the ENCODE 4 PRO-cap experiments, behind Kwak and Luo. Lead with the primary paper and leave the rest in the order they stood. Reordering only. The years and DOIs added in 38ccb38771e are unchanged. diff --git src/hg/makeDb/trackDb/human/encode4ProCap.html src/hg/makeDb/trackDb/human/encode4ProCap.html index 317caa8407c..1ab67b3c140 100644 --- src/hg/makeDb/trackDb/human/encode4ProCap.html +++ src/hg/makeDb/trackDb/human/encode4ProCap.html @@ -120,58 +120,58 @@ 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> -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> - <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>