7d9184716dc20689e28ab957e9d7ed6ed9c28887 lrnassar Wed Sep 4 11:58:25 2019 -0700 Adding new assembly rheMac10 to credits.html #23771 diff --git src/hg/htdocs/goldenPath/credits.html src/hg/htdocs/goldenPath/credits.html index 9bd9375..a14b7f6 100755 --- src/hg/htdocs/goldenPath/credits.html +++ src/hg/htdocs/goldenPath/credits.html @@ -2644,54 +2644,71 @@ target="_blank">Genome sequence of the Brown Norway rat yields insights into mammalian evolution</a>. <em>Nature</em>. 2004 Apr 1;428(6982):493-521. PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/15057822" target="_blank">15057822</a></p> <p> See the Baylor <a href="https://www.hgsc.bcm.edu/bcm-hgsc-conditions-use" target="_blank">conditions of use</a> web page for restrictions on the use of these data.</p> <!-- Rhesus Credits --> <a name="rhesus_credits"></a> <h2>Rhesus genome</h2> <p> The UCSC Genome Browser displays multiple assemblies of the Rhesus macaque genome produced by different institutions: </p> <ul> <li> + <strong><a href="../../cgi-bin/hgGateway?db=rheMac10" target="_blank">rheMac10</a> Genome + Browser:</strong> Feb. 2019 draft assembly of the rhesus monkey, version Mmul_10, from the + <a href="https://www.genome.wustl.edu/" + target="_blank">Genome Institute at Washington University School of Medicine</a>. </li> + <li> <strong><a href="../../cgi-bin/hgGateway?db=rheMac8" target="_blank">rheMac8</a> Genome Browser:</strong> Nov. 2015 draft assembly of the rhesus monkey, version Mmul_8.0.1, from the <a href="https://www.hgsc.bcm.edu/non-human-primates/rhesus-monkey-genome-project" target="_blank">Baylor College of Medicine Human Genome Sequencing Center</a>. </li> <li> <strong><a href="../../cgi-bin/hgGateway?db=rheMac3" target="_blank">rheMac3</a> Genome Browser:</strong> Oct. 2010 draft assembly of the rhesus monkey, version CR_1.0 from <a href="http://www.genomics.cn/en/index" target=_blank>Beijing Genomics Institute-Shenzhen</a> (BGI), Shenzhen, China </li> <li> <strong><a href="../../cgi-bin/hgGateway?db=rheMac2" target="_blank">rheMac2</a> Genome Browser:</strong> Jan. 2006 draft assembly of the rhesus monkey, version Mmul_051212 from the Macaca mulatta Genome Sequencing Consortium (MMGSC) led by the <a href="https://www.hgsc.bcm.edu/rhesus-monkey-genome-project" target="_blank">Baylor College of Medicine Human Genome Sequencing Center (BCM-HGSC)</a>, in collaboration with the <a href="http://www.jcvi.org/cms/home/" target="_blank">J. Craig Venter Science Foundation Joint Technology Center</a> and <a href="http://genome.wustl.edu/genomes/detail/macaca-mulatta/" target="_blank">The Genome Institute at Washington University (WUSTL)</a> </li> <li> <strong>rheMac1 Genome Browser:</strong> Jan. 2005 draft assembly of the rhesus monkey, version Mmul_0.1 from MMGSC (see above) </li> </ul> <hr> <p> +The Genome Institute at Washington University School of Medicine assembly is provided with the +following acknowledgments:</p> +<p> +Macaca mulatta Sequence and Assembly Credits: Sequencing Funds - This work was supported by the +NHGRI grant No. 5U24HG00908103, HIGH QUALITY HUMAN AND NON-HUMAN PRIMATE GENOME ASSEMBLIES, at +the McDonnell Genome Institute, Washington University School of Medicine DNA source - Coriell +sample id: AG07107, MMU Genome Sequencing - The McDonnell Genome Institute, Washington +University School of Medicine. Sequence Assembly - The McDonnell Genome Institute, Washington +University School of Medicine. Sequence assembly curation - The McDonnell Genome Institute, +Washington University School of Medicine; The University of Washington, Seattle, WA.</p> +<hr> +<p> The BGI assembly is provided with the following acknowledgments: </p> <p> <strong>Funding:</strong> Southern China Center for Innovative Pharmaceuticals (SCCIP), the National Natural Science Foundation of China, the Shenzhen Municipal Government of China, the Major State Basic Research Development Program of China, the National Basic Research Program of China, and the National Science and Technology Major Project of Key Drug Innovation and Development </p> <p> <strong>Sequencing/Assembly:</strong> BGI, Shenzhen, China </p> <hr> <p> The MMGSC assembly is provided with the following acknowledgments: </p> <p> <strong>Funding: </strong> <a href="http://www.genome.gov/" target="_blank">National Human Genome Research Institute</a> (NHGRI), USA </p> @@ -2706,45 +2723,56 @@ <p> <strong>BAC resources: </strong> <a href="http://bacpac.chori.org/rhesus250.htm" target="_blank">Children's Hospital Oakland Research Institute</a> (CHORI), Oakland, CA, USA</p> <p> <strong>BAC-based fingerprint map: </strong> <a href="http://www.bcgsc.ca/" target=-blank>Genome Sciences Centre</a>, Vancouver, B.C. </p> <p> For more information on the MMGSC rhesus macaque genome project, see the BCM HGSC <a href="https://www.hgsc.bcm.edu/rhesus-monkey-genome-project" target="_blank">Rhesus Monkey Genome Project</a> web page. </p> <hr> <p> <strong>UCSC Rhesus Genome Browser/Annotations:</strong> </p> <ul> <li> + <a href="../../cgi-bin/hgGateway?db=rheMac10" target="_blank">rheMac10</a>: Hiram Clawson + and Lou Nassar</li> + <li> <a href="../../cgi-bin/hgGateway?db=rheMac8" target="_blank">rheMac8</a>: Hiram Clawson, Christopher Lee, and Cath Tyner </li> <li> <a href="../../cgi-bin/hgGateway?db=rheMac3" target="_blank">rheMac3</a>: Hiram Clawson, Chin Li, Brian Raney, Pauline Fujita, Luvina Guruvadoo, Steve Heitner, Brooke Rhead, Greg Roe, and Donna Karolchik </li> <li> <a href="../../cgi-bin/hgGateway?db=rheMac2" target="_blank">rheMac2</a>: Robert Baertsch, Kayla Smith, Ann Zweig, Robert Kuhn, and Donna Karolchik </li> <li> rheMac1 (archived): Robert Baertsch, Galt Barber, and Donna Karolchik </li> </ul> <a name="rhesus_use"></a> <h3>Data use</h3> <p> +The Macaca mulatta Mmul_9.0 and Mmul_10 assembly sequences are made available to the community +by the McDonnell Genome Institute, Washington University, St Louis, MO with the following +understanding: Users are free to analyze these data if the providers of this data are properly +cited, any whole genome analyses should follow guidelines outlined in the Toronto agreement +on the use of this assembly.</p> + +<hr> +<p> The initial sequencing and analysis of the rhesus macaque genome produced by the MMGSC was published in: Rhesus Macaque Genome Sequencing and Analysis Consortium. <a href="http://www.sciencemag.org/content/316/5822/222.long" target="_blank">Evolutionary and Biomedical Insights from the Rhesus Macaque Genome</a>. <em>Science</em>. 2007 Apr 13;316(5822):222-34. PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/17431167" target="_blank">17431167</a></p> <p> The initial sequencing and analysis of the rhesus macaque genome produced by BGI was published in: Yan G, Zhang G, Fang X, Zhang Y, Li C, Ling F, Cooper DN, Li Q, Li Y, van Gool AJ <em>et al</em> <a href="http://www.nature.com/nbt/journal/v29/n11/full/nbt.1992.html" target=_blank>Genome sequencing and comparison of two nonhuman primate animal models, the cynomolgus and Chinese rhesus macaques</a>. <em>Nat Biotechnol</em>. 2011 Oct 16;29(11):1019-23. PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/22002653" target="_blank">22002653</a></p> <p> The rhesus macaque sequence is made freely available for public use with the following