This information is over 2 years old. Information was current at time of publication.{"id":3432,"date":"2020-01-27T09:53:19","date_gmt":"2020-01-27T14:53:19","guid":{"rendered":"http:\/\/info.hsls.pitt.edu\/molbio\/?p=3432"},"modified":"2020-01-29T12:14:43","modified_gmt":"2020-01-29T17:14:43","slug":"1-29-wksp-chip-seq","status":"publish","type":"post","link":"https:\/\/info.hsls.pitt.edu\/molbio\/2020\/01\/27\/1-29-wksp-chip-seq\/","title":{"rendered":"1\/29 wksp: ChIP-Seq"},"content":{"rendered":"<ul>\n<li><strong><span style=\"color: #0181a6\">WHAT:<\/span> <\/strong>ChIP-Seq<\/li>\n<li><strong><span style=\"color: #0181a6\">WHEN:<\/span> <\/strong>January 29th, 10am-12pm &amp; 1-3pm<\/li>\n<li><strong><span style=\"color: #0181a6\">WHERE:<\/span> <\/strong>Scaife Hall, Falk Library, Classroom 2<\/li>\n<li><strong><span style=\"color: #0181a6\">WHO:<\/span> <\/strong>Ansuman Chattopahyay &amp; Sri Chaparala<\/li>\n<li><strong><span style=\"color: #0181a6\">HOW:<\/span> <\/strong>Register <a href=\"https:\/\/www.hsls.pitt.edu\/instruction\/chip-seq\/4101\">here<\/a><\/li>\n<\/ul>\n<p><!--more--><br \/>\nThis is a 4-hour workshop. The morning session (<strong>10am &#8211; 12pm<\/strong>) provides a brief introduction to techniques, platforms, and methods used in chromatin profiling experiments, including Transcription Factor \/ Histone ChIP-Seq and ATAC-Seq. The afternoon session (<strong>1pm &#8211; 3pm<\/strong>) focuses on data analysis practice using HSLS-licensed CLC Genomics Workbench, Partek Flow, and TRANSFAC\/Match software.<\/p>\n<p>Participants will learn how to<\/p>\n<ul>\n<li>import NGS reads from a GEO dataset<\/li>\n<li>align ChIP-Seq reads to a reference genome<\/li>\n<li>identify and annotate peaks<\/li>\n<li>visualize and summarize the ChIP-Seq results <\/li>\n<li>search for known transcription factor binding motifs using TRANSFAC\/Match software <\/li>\n<\/ul>\n<p><strong><span style=\"color: #0181a6\">Target Audience:<\/span><\/strong><\/p>\n<p>Experimental biologists seeking to analyze ChIP-Seq data generated through experiments or retrieved from a repository such as GEO. The software covered in the workshop operates through a user-friendly, point-and-click graphical user Interface, so neither programming experience nor familiarity with command line interface is required..<\/p>\n<p><strong><span style=\"color: #0181a6\">Workshop Requirements:<\/span><\/strong><\/p>\n<ul>\n<li><a href=\"http:\/\/hsls.libguides.com\/molbio\/clcgenomics\">Register for CLC Genomics Workbench<\/a><\/li>\n<li><a href=\"http:\/\/hsls.libguides.com\/molbio\/partekflow\">Register for Partek Flow<\/a><\/li>\n<li><a href=\"http:\/\/hsls.libguides.com\/molbio\/transfac\">Register for TRANSFAC\/Match<\/a><\/li>\n<\/ul>\n<p><strong><span style=\"color: #0181a6\">Workshop Guide:<\/span><\/strong><\/p>\n<ul>\n<li><a href=\"https:\/\/hsls.libguides.com\/MolBioWorkshops\/ChIPseq\">https:\/\/hsls.libguides.com\/MolBioWorkshops\/ChIPseq<\/a><\/li>\n<\/ul>\n<p><strong><span style=\"color: #0181a6\">Suggested Reading:<\/span><\/strong><\/p>\n<ul>\n<li><a href=\"https:\/\/www.sciencedirect.com\/science\/article\/pii\/S0092867418307098?via%3Dihub\">Pulikkan, J. A., Hegde, M., Ahmad, H. M., Belaghzal, H., Illendula, A., Yu, J., \u2026 Castilla, L. H. (2018). CBF\u03b2-SMMHC Inhibition Triggers Apoptosis by Disrupting MYC Chromatin Dynamics in Acute Myeloid Leukemia. <em>Cell<\/em>, <em>174<\/em>(1), 172\u2013186.e21. doi:10.1016\/j.cell.2018.05.048<\/a><\/li>\n<\/ul>\n<p><strong><span style=\"color: #0181a6\">Attribution:<\/span><\/strong><\/p>\n<p>Please include the following statement in the acknowledgments section for all publications, posters, and presentations: <strong>Data analysis was performed using {name of software} software licensed through the Molecular Biology Information Service of the Health Sciences Library System, University of Pittsburgh.<\/strong><\/p>\n<p><a href=\"http:\/\/files.hsls.pitt.edu\/files\/molbio\/MolbioWorkshops.pdf\">HSLS Winter\/Spring 2020 MolBio Info Service Training Workshops schedule<\/a><\/p>\n<p><a href=\"https:\/\/www.hsls.pitt.edu\/ask-a-molbio-specialist\">Contact<\/a> the <a href=\"http:\/\/www.hsls.pitt.edu\/molbio\">HSLS Molecular Biology Information Service<\/a> with any questions.<\/p>\n","protected":false},"excerpt":{"rendered":"<ul>\n<li><strong><span style=\"color: #0181a6\">WHAT:<\/span> <\/strong>ChIP-Seq<\/li>\n<li><strong><span style=\"color: #0181a6\">WHEN:<\/span> <\/strong>January 29th, 10am-12pm &amp; 1-3pm<\/li>\n<li><strong><span style=\"color: #0181a6\">WHERE:<\/span> <\/strong>Scaife Hall, Falk Library, Classroom 2<\/li>\n<li><strong><span style=\"color: #0181a6\">WHO:<\/span> <\/strong>Ansuman Chattopahyay &amp; Sri Chaparala<\/li>\n<li><strong><span style=\"color: #0181a6\">HOW:<\/span> <\/strong>Register <a href=\"https:\/\/www.hsls.pitt.edu\/instruction\/chip-seq\/4101\">here<\/a><\/li>\n<\/ul>\n<p><a class=\"read-more\" alt= \"1\/29 wksp: ChIP-Seq\" href=\"https:\/\/info.hsls.pitt.edu\/molbio\/2020\/01\/27\/1-29-wksp-chip-seq\/\">Read more&hellip;<\/a><\/p>\n","protected":false},"author":31,"featured_media":0,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"footnotes":"","_links_to":"","_links_to_target":""},"categories":[1],"tags":[],"class_list":["post-3432","post","type-post","status-publish","format-standard","hentry","category-uncategorized"],"_links":{"self":[{"href":"https:\/\/info.hsls.pitt.edu\/molbio\/wp-json\/wp\/v2\/posts\/3432","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/info.hsls.pitt.edu\/molbio\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/info.hsls.pitt.edu\/molbio\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/info.hsls.pitt.edu\/molbio\/wp-json\/wp\/v2\/users\/31"}],"replies":[{"embeddable":true,"href":"https:\/\/info.hsls.pitt.edu\/molbio\/wp-json\/wp\/v2\/comments?post=3432"}],"version-history":[{"count":2,"href":"https:\/\/info.hsls.pitt.edu\/molbio\/wp-json\/wp\/v2\/posts\/3432\/revisions"}],"predecessor-version":[{"id":3434,"href":"https:\/\/info.hsls.pitt.edu\/molbio\/wp-json\/wp\/v2\/posts\/3432\/revisions\/3434"}],"wp:attachment":[{"href":"https:\/\/info.hsls.pitt.edu\/molbio\/wp-json\/wp\/v2\/media?parent=3432"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/info.hsls.pitt.edu\/molbio\/wp-json\/wp\/v2\/categories?post=3432"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/info.hsls.pitt.edu\/molbio\/wp-json\/wp\/v2\/tags?post=3432"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}