This information is over 2 years old. Information was current at time of publication.{"id":3321,"date":"2019-09-11T10:50:34","date_gmt":"2019-09-11T15:50:34","guid":{"rendered":"http:\/\/info.hsls.pitt.edu\/molbio\/?p=3321"},"modified":"2019-10-04T09:18:57","modified_gmt":"2019-10-04T14:18:57","slug":"10-2-wksp-bulk-rna-seq","status":"publish","type":"post","link":"https:\/\/info.hsls.pitt.edu\/molbio\/2019\/09\/11\/10-2-wksp-bulk-rna-seq\/","title":{"rendered":"10\/2 wksp: Bulk RNA-Seq"},"content":{"rendered":"<ul>\n<li><strong><span style=\"color: #a0ab4f\">WHAT:<\/span> <\/strong>Bulk RNA-Seq<\/li>\n<li><strong><span style=\"color: #a0ab4f\">WHEN:<\/span> <\/strong>October 2nd, 10am-12pm &amp; 1-3pm<\/li>\n<li><strong><span style=\"color: #a0ab4f\">WHERE:<\/span> <\/strong>Scaife Hall, Falk Library, Classroom 2<\/li>\n<li><strong><span style=\"color: #a0ab4f\">WHO:<\/span> <\/strong>Ansuman Chattopahyay &amp; Sri Chaparala<\/li>\n<li><strong><span style=\"color: #a0ab4f\">HOW:<\/span> <\/strong>Register <a href=\"https:\/\/www.hsls.pitt.edu\/instruction\/bulk-rna-seq\/3745\">here<\/a><\/li>\n<\/ul>\n<p><!--more--><br \/>\n<strong><span style=\"color: #a0ab4f\">Workshop Objective:<\/span><\/strong><\/p>\n<p>This is a 4-hour workshop on the techniques, platforms, and methods used in analyzing bulk RNA-Seq data. The morning session (<strong>10am &#8211; 12pm<\/strong>) starts with a presentation from the <a href=\"https:\/\/www.genetics.pitt.edu\/\">Genomics Research Core<\/a> on best practices in sample handling, followed by an overview of the basic steps involved in bulk RNA-Seq data analysis. The afternoon session (<strong>1pm &#8211; 3pm<\/strong>) focuses on hands-on practice using HSLS-licensed CLC Genomics Workbench software.<\/p>\n<p>Participants will learn how to<\/p>\n<ul>\n<li>access the <a href=\"https:\/\/crc.pitt.edu\/clcbioserver\">CLCbio Genomics Server<\/a> hosted on the <a href=\"https:\/\/crc.pitt.edu\/htc\">HTC Cluster<\/a> by <a href=\"https:\/\/crc.pitt.edu\/\">Pitt CRC<\/a><\/li>\n<li>mport RNA-seq FASTQ reads from a GEO dataset<\/li>\n<li>assess quality of RNA-seq data<\/li>\n<li>align reads to a reference genome<\/li>\n<li>estimate known gene and transcript expression<\/li>\n<li>perform differential expression analysis<\/li>\n<li>discover novel isoforms<\/li>\n<\/ul>\n<p><strong><span style=\"color: #a0ab4f\">Target Audience:<\/span><\/strong><\/p>\n<p>Experimental biologists seeking to analyze bulk RNA-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: #a0ab4f\">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<\/ul>\n<p><strong><span style=\"color: #a0ab4f\">Workshop Guide:<\/span><\/strong><\/p>\n<ul>\n<li><a href=\"https:\/\/hsls.libguides.com\/MolBioWorkshops\/BulkRNAseqCLC\">https:\/\/hsls.libguides.com\/MolBioWorkshops\/BulkRNAseqCLC<\/a><\/li>\n<\/ul>\n<p><strong><span style=\"color: #a0ab4f\">Suggested Reading:<\/span><\/strong><\/p>\n<ul>\n<li><a href=\"https:\/\/genomebiology.biomedcentral.com\/articles\/10.1186\/s13059-016-0881-8\">Conesa, A., Madrigal, P., Tarazona, S., Gomez-Cabrero, D., Cervera, A., McPherson, A., \u2026 Mortazavi, A. (2016). A survey of best practices for RNA-seq data analysis.\u00a0<em>Genome Biology<\/em>,\u00a0<em>17<\/em>(1), 13. doi:10.1186\/s13059-016-0881-8<\/a><\/li>\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.\u00a0<em>Cell<\/em>,\u00a0<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: #a0ab4f\">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 Fall 2019 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: #a0ab4f\">WHAT:<\/span> <\/strong>Bulk RNA-Seq<\/li>\n<li><strong><span style=\"color: #a0ab4f\">WHEN:<\/span> <\/strong>October 2nd, 10am-12pm &amp; 1-3pm<\/li>\n<li><strong><span style=\"color: #a0ab4f\">WHERE:<\/span> <\/strong>Scaife Hall, Falk Library, Classroom 2<\/li>\n<li><strong><span style=\"color: #a0ab4f\">WHO:<\/span> <\/strong>Ansuman Chattopahyay &amp; Sri Chaparala<\/li>\n<li><strong><span style=\"color: #a0ab4f\">HOW:<\/span> <\/strong>Register <a href=\"https:\/\/www.hsls.pitt.edu\/instruction\/bulk-rna-seq\/3745\">here<\/a><\/li>\n<\/ul>\n<p><a class=\"read-more\" alt= \"10\/2 wksp: Bulk RNA-Seq\" href=\"https:\/\/info.hsls.pitt.edu\/molbio\/2019\/09\/11\/10-2-wksp-bulk-rna-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-3321","post","type-post","status-publish","format-standard","hentry","category-uncategorized"],"_links":{"self":[{"href":"https:\/\/info.hsls.pitt.edu\/molbio\/wp-json\/wp\/v2\/posts\/3321","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=3321"}],"version-history":[{"count":3,"href":"https:\/\/info.hsls.pitt.edu\/molbio\/wp-json\/wp\/v2\/posts\/3321\/revisions"}],"predecessor-version":[{"id":3324,"href":"https:\/\/info.hsls.pitt.edu\/molbio\/wp-json\/wp\/v2\/posts\/3321\/revisions\/3324"}],"wp:attachment":[{"href":"https:\/\/info.hsls.pitt.edu\/molbio\/wp-json\/wp\/v2\/media?parent=3321"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/info.hsls.pitt.edu\/molbio\/wp-json\/wp\/v2\/categories?post=3321"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/info.hsls.pitt.edu\/molbio\/wp-json\/wp\/v2\/tags?post=3321"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}