{"id":8823,"date":"2025-05-05T09:28:13","date_gmt":"2025-05-05T00:28:13","guid":{"rendered":"http:\/\/dna.brc.riken.jp\/en\/?page_id=8823"},"modified":"2025-05-05T09:28:49","modified_gmt":"2025-05-05T00:28:49","slug":"cephyac01en","status":"publish","type":"page","link":"http:\/\/dna.brc.riken.jp\/en\/bacyacen\/cephyac01en","title":{"rendered":"CEPH Mega YAC clone"},"content":{"rendered":"<p><!-- js calling begin --><code><script type=\"text\/javascript\" src=\"\/en\/wp-content\/uploads\/js\/functions_list.js\"><\/script><\/code><!-- js calling end --><\/p>\n<h2>Information<\/h2>\n<ul>\n<li>Clone : 35,712 clone<\/li>\n<li>Vector : pYAC4 (EcoRI site)<\/li>\n<li>Host strain : Saccharomyces cerevisiae AB1380.<\/li>\n<li>Insert size : 560 kb (#613 to #731), 918 kb (#732 to #984).<\/li>\n<li>DNA source : XY EBV human cell line.<\/li>\n<li>Strage condition : AHC agar-stab.<\/li>\n<li>References :\n<ul>\n<li>Chumakov, I. et al. Continuum of overlapping clones spanning the entire human chromosome 21q. Nature 359(6394): 380-387 (1992). doi: 10.1038\/359380a0. PMID: 1406950.<\/li>\n<li>Cohen, D. et al. A first-generation physical map of the human genome. Nature 366 (6456): 698-701 (1993). doi: 10.1038\/366698a0. PMID: 8259213.<\/li>\n<li>&#8220;The Genome Directory&#8221;, supplement to Nature 28 September 1995, vol. 377 issue no. 6547S.<\/li>\n<li>Miller, P.L. et al. Internet-based support for bioscience research: a collaborative genome center for human chromosome 12. J. Am. Med. Inform. Assoc. 2 (6): 351-364 (1995). doi: 10.1136\/jamia.1995.96157828. PMID: 8581551.<\/li>\n<li>Wang, S.Y. et al. A high-resolution physical map of human chromosome 21p using yeast artificial chromosomes. Genome Res. 9 (11): 1059-1073 (1999). doi: 10.1101\/gr.9.11.1059. PMID: 10568746.<\/li>\n<li>Peterson, E.T. An integrated physical map for the short arm of human chromosome 5. Genome Res. 9 (12): 1250-1267 (1999). doi: 10.1101\/gr.9.12.1250. PMID: 10613848.<\/li>\n<\/ul>\n<\/li>\n<li>Link\n<ul>\n<li><a href=\"http:\/\/www.cephb.fr\/\" target=\"_blank\">CEPH<\/a><\/li>\n<li><a href=\"https:\/\/genome.ucsc.edu\/index.html\">UCSC Genome Browser<\/a><\/li>\n<\/ul>\n<\/li>\n<li>Please visit <a href=\"https:\/\/brc.riken.jp\/dna\/RDB04215\">Informaion site <img decoding=\"async\" alt=\"\" src=\"https:\/\/dnaconda.riken.jp\/images\/datasheet097.gif\" width=\"30\" \/><\/a> for articles published by using this materials, references and tips.<\/li>\n<\/ul>\n<div align=\"right\">\n<\/div>\n<hr \/>\n<h2>Search for CEPH Mega YAC clone<\/h2>\n<p class=\"text02e\">Following process is maybe not best but how we find the particular YAC clone containing locus of interest by STS marker information.<br \/>\nBecause end sequences of the YAC clone have not analyzed, the YAC clones are not mapped on a genome browser.<br \/>\nWe show a case for human IGL locus (Gene ID: 3535, 22q11.2) as an example.<\/p>\n<ol>\n<li>set up your ftp client\n<ul>\n<li>ftp site information\n<ul>\n<li>ftp server: ftp.broadinstitute.org<\/li>\n<li>user to access: anonymous<\/li>\n<li>directory: \/pub\/human_STS_releases\/july97\/<\/li>\n<\/ul>\n<\/li>\n<\/ul>\n<\/li>\n<li>download &#8220;07-97.YAC2STS.txt&#8221; data file to your computer. This file contains YAC clone ID with corresponding STS hits.\n<div align=\"center\"><img decoding=\"async\" src=\"https:\/\/dnaconda.riken.jp\/images\/cephyac01.png\" \/>\n<\/div>\n<\/li>\n<hr \/>\n<li>STS are positioned to the human genome available at the &#8220;UCSC Genome Browser&#8221;.<br \/>\nVisit UCSC genome browser web site.<\/li>\n<li>Chose lates version of Human Assembly ex. &#8220;Human GRCh38\/hg38&#8221;.\n<div align=\"center\"><img decoding=\"async\" src=\"https:\/\/dnaconda.riken.jp\/images\/cephyac02.png\" \/>\n<\/div>\n<\/li>\n<hr \/>\n<li>Set region of chromosome and then click &#8220;go&#8221;.<\/li>\n<li>Set options as indicated below and click &#8220;refresh&#8221;.<\/li>\n<li>STS markers will show up on top panel.\n<div align=\"center\"><img decoding=\"async\" src=\"https:\/\/dnaconda.riken.jp\/images\/cephyac03.png\" \/>\n<\/div>\n<\/li>\n<hr \/>\n<li>Click STS name. Click the right button of your mouse to &#8220;Open details page in new window&#8230;&#8221;.<\/li>\n<li>STS maker info will show up.<\/li>\n<li>Please find &#8220;STS Marker, Start, End and Other names&#8221;.<\/li>\n<li>Copy these items to a table of Excel file.\n<div align=\"center\"><img decoding=\"async\" src=\"https:\/\/dnaconda.riken.jp\/images\/cephyac04.png\" \/>\n<\/div>\n<\/li>\n<hr \/>\n<li>Find the STS marker and corresponding YAC in the &#8220;07-97.YAC2STS.txt&#8221;.<br \/>\nI hope you or your colleague can handle MS-DOS command. The following text is an example of a batch file.<\/p>\n<ul>\n<ul class=\"text02\">set target=&#8221;07-97.YAC2STS.txt&#8221;<\/ul>\n<\/ul>\n<ul class=\"text02\">\n<ul class=\"text02\">echo &#8220;RH48655&#8221; &gt;result.txt<\/ul>\n<\/ul>\n<ul class=\"text02\">\n<ul class=\"text02\">find \/I &#8220;RH48655&#8221; %target% &gt;&gt;result.txt<\/ul>\n<\/ul>\n<ul class=\"text02\">\n<ul class=\"text02\">echo &#8220;STSG30889&#8221; &gt;&gt;result.txt<\/ul>\n<\/ul>\n<ul class=\"text02\">\n<ul class=\"text02\">find \/I &#8220;STSG30889&#8221; %target% &gt;&gt;result.txt<\/ul>\n<\/ul>\n<ul class=\"text02\">\n<ul class=\"text02\">echo &#8220;WI-362&#8221; &gt;&gt;result.txt<\/ul>\n<\/ul>\n<ul class=\"text02\">\n<ul class=\"text02\">find \/I &#8220;WI-362&#8221; %target% &gt;&gt;result.txt<\/ul>\n<\/ul>\n<ul class=\"text02\">\n<ul class=\"text02\">echo &#8220;D22S636&#8221; &gt;&gt;result.txt<\/ul>\n<\/ul>\n<ul class=\"text02\">\n<ul class=\"text02\">find \/I &#8220;D22S636&#8221; %target% &gt;&gt;result.txt<\/ul>\n<\/ul>\n<ul class=\"text02\">\n<ul class=\"text02\">echo &#8220;AC22-362&#8221; &gt;&gt;result.txt<\/ul>\n<\/ul>\n<ul class=\"text02\">\n<ul class=\"text02\">find \/I &#8220;AC22-362&#8221; %target% &gt;&gt;result.txt<\/ul>\n<\/ul>\n<ul class=\"text02\">\n<ul class=\"text02\">echo &#8220;PH838&#8221; &gt;&gt;result.txt<\/ul>\n<\/ul>\n<ul class=\"text02\">\n<ul class=\"text02\">find \/I &#8220;PH838&#8221; %target% &gt;&gt;result.txt<\/ul>\n<\/ul>\n<ul class=\"text02\">\n<ul class=\"text02\">:<\/ul>\n<\/ul>\n<\/li>\n<li>Put YAC ID to the Excel.<\/li>\n<li>The clone you find now maybe include false-positive. So please find the clone which hit multiple STS of locus. With this way, you may find the clone usable for your research at last.\n<div align=\"center\"><img decoding=\"async\" src=\"https:\/\/dnaconda.riken.jp\/images\/cephyac05.png\" \/>\n<\/div>\n<\/li>\n<\/ol>\n<hr \/>\n<p style=\"text-align: left;\">2025.05.05 (T.M. GRP0063e)<\/p>\n","protected":false},"excerpt":{"rendered":"<p>Information Clone : 35,712 clone Vector : pYAC4 (EcoRI site) Host strain : Saccharomyces cerevisiae AB1380. Insert size : 560 kb (#613 to #731), 918 kb (#732 to #984). DNA source : XY EBV human cell line. Strage condition : AHC agar-stab. References : Chumakov, I. et al. Continuum of overlapping clones spanning the entire human chromosome 21q. Nature 359(6394): 380-387 (1992). doi: 10.1038\/359380a0. PMID: 1406950. Cohen, D. et al. A first-generation physical map of the human genome. Nature 366 (6456): 698-701 (1993). doi: 10.1038\/366698a0. PMID: 8259213. &#8220;The Genome Directory&#8221;, supplement to Nature 28 September 1995, vol. 377 issue no. 6547S. Miller, P.L. et al. Internet-based support for bioscience research: a collaborative genome center for human chromosome 12. J. Am. Med. Inform. Assoc. 2 (6): 351-364 (1995). doi: 10.1136\/jamia.1995.96157828. PMID: 8581551. Wang, S.Y. et al. A high-resolution physical map of human chromosome 21p using yeast artificial chromosomes. Genome Res. 9 (11): 1059-1073 (1999). doi: 10.1101\/gr.9.11.1059. PMID: 10568746. Peterson, E.T. An integrated physical map for the short arm of human chromosome 5. Genome Res. 9 (12): 1250-1267 (1999). doi: 10.1101\/gr.9.12.1250. PMID: 10613848. Link CEPH UCSC Genome Browser Please visit Informaion site for articles published by using this materials, references and tips. [&hellip;]<\/p>\n","protected":false},"author":13,"featured_media":0,"parent":8803,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"_seopress_titles_title":"","_seopress_titles_desc":"","_seopress_robots_index":"","_seopress_robots_follow":"","_seopress_robots_imageindex":"","_seopress_robots_snippet":"","_seopress_robots_primary_cat":"","_seopress_robots_breadcrumbs":"","_seopress_robots_freeze_modified_date":"","_seopress_robots_custom_modified_date":"","_seopress_robots_canonical":"","_seopress_social_fb_title":"","_seopress_social_fb_desc":"","_seopress_social_fb_img":"","_seopress_social_fb_img_attachment_id":0,"_seopress_social_fb_img_width":0,"_seopress_social_fb_img_height":0,"_seopress_social_twitter_title":"","_seopress_social_twitter_desc":"","_seopress_social_twitter_img":"","_seopress_social_twitter_img_attachment_id":0,"_seopress_social_twitter_img_width":0,"_seopress_social_twitter_img_height":0,"_seopress_redirections_value":"","_seopress_redirections_enabled":"","_seopress_redirections_enabled_regex":"","_seopress_redirections_logged_status":"both","_seopress_redirections_param":"","_seopress_redirections_type":301,"_seopress_analysis_target_kw":"","footnotes":"","_wp_rev_ctl_limit":""},"class_list":["post-8823","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"http:\/\/dna.brc.riken.jp\/en\/wp-json\/wp\/v2\/pages\/8823","targetHints":{"allow":["GET"]}}],"collection":[{"href":"http:\/\/dna.brc.riken.jp\/en\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"http:\/\/dna.brc.riken.jp\/en\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"http:\/\/dna.brc.riken.jp\/en\/wp-json\/wp\/v2\/users\/13"}],"replies":[{"embeddable":true,"href":"http:\/\/dna.brc.riken.jp\/en\/wp-json\/wp\/v2\/comments?post=8823"}],"version-history":[{"count":2,"href":"http:\/\/dna.brc.riken.jp\/en\/wp-json\/wp\/v2\/pages\/8823\/revisions"}],"predecessor-version":[{"id":8827,"href":"http:\/\/dna.brc.riken.jp\/en\/wp-json\/wp\/v2\/pages\/8823\/revisions\/8827"}],"up":[{"embeddable":true,"href":"http:\/\/dna.brc.riken.jp\/en\/wp-json\/wp\/v2\/pages\/8803"}],"wp:attachment":[{"href":"http:\/\/dna.brc.riken.jp\/en\/wp-json\/wp\/v2\/media?parent=8823"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}