This information is over 2 years old. Information was current at time of publication.{"id":4199,"date":"2021-06-07T16:14:31","date_gmt":"2021-06-07T21:14:31","guid":{"rendered":"https:\/\/info.hsls.pitt.edu\/molbio\/?p=4199"},"modified":"2021-06-10T08:22:58","modified_gmt":"2021-06-10T13:22:58","slug":"6-9-wksp-bulk-rna-seq","status":"publish","type":"post","link":"https:\/\/info.hsls.pitt.edu\/molbio\/2021\/06\/07\/6-9-wksp-bulk-rna-seq\/","title":{"rendered":"6\/9 wksp: Bulk RNA-Seq"},"content":{"rendered":"<ul>\n<li><strong><span style=\"color: #cb4d1d\">WHAT:<\/span> <\/strong>Bulk RNA-Seq<\/li>\n<li><strong><span style=\"color: #cb4d1d\">WHEN:<\/span> <\/strong>June 9th, 1-4pm<\/li>\n<li><strong><span style=\"color: #cb4d1d\">WHERE:<\/span> <\/strong>Online; instructions upon registration<\/li>\n<li><strong><span style=\"color: #cb4d1d\">WHO:<\/span> <\/strong>Ansuman Chattopadhyay &amp; Sri Chaparala<\/li>\n<li><strong><span style=\"color: #cb4d1d\">HOW:<\/span> <\/strong>Register <a href=\"https:\/\/www.hsls.pitt.edu\/instruction\/bulk-rna-seq-data-analysis-using-clc-genomics-workbench\/5909\">here<\/a><\/li>\n<\/ul>\n<p><!--more--><\/p>\n<p>This is <strong>a flipped class <\/strong>covering bulk RNA-Seq data analysis using CLC Genomics Workbench software. Upon registration, you will receive links to workshop materials (<strong>PowerPoint slides<\/strong>, <strong>lecture videos<\/strong>, and <strong>practice exercises<\/strong>) that you can view on your schedule. During the class, you will learn how to solve the exercise problems.<\/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>import RNA-Seq FASTQ reads from a GEO dataset<\/li>\n<li>assess the 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>visualize data by generating PCA and heatmaps<\/li>\n<\/ul>\n<p><strong><span style=\"color: #cb4d1d\">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 the command line interface is required.<\/p>\n<p><strong><span style=\"color: #cb4d1d\">Workshop Guide:<\/span><\/strong><\/p>\n<ul>\n<li><a href=\"https:\/\/hsls.libguides.com\/MBISworkshops\/bulkRNAseq\">https:\/\/hsls.libguides.com\/MBISworkshops\/bulkRNAseq<\/a><\/li>\n<\/ul>\n<p><a href=\"http:\/\/files.hsls.pitt.edu\/files\/molbio\/MolbioWorkshops.pdf\">HSLS Summer 2021 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<p>(Photo by <a href=\"https:\/\/unsplash.com\/@mike_swigunski?utm_source=unsplash&amp;utm_medium=referral&amp;utm_content=creditCopyText\">Mike Swigunski<\/a> on <a href=\"https:\/\/unsplash.com\/s\/photos\/sumo?utm_source=unsplash&amp;utm_medium=referral&amp;utm_content=creditCopyText\">Unsplash<\/a>)<\/p>\n","protected":false},"excerpt":{"rendered":"<ul>\n<li><strong><span style=\"color: #cb4d1d\">WHAT:<\/span> <\/strong>Bulk RNA-Seq<\/li>\n<li><strong><span style=\"color: #cb4d1d\">WHEN:<\/span> <\/strong>June 9th, 1-4pm<\/li>\n<li><strong><span style=\"color: #cb4d1d\">WHERE:<\/span> <\/strong>Online; instructions upon registration<\/li>\n<li><strong><span style=\"color: #cb4d1d\">WHO:<\/span> <\/strong>Ansuman Chattopadhyay &amp; Sri Chaparala<\/li>\n<li><strong><span style=\"color: #cb4d1d\">HOW:<\/span> <\/strong>Register <a href=\"https:\/\/www.hsls.pitt.edu\/instruction\/bulk-rna-seq-data-analysis-using-clc-genomics-workbench\/5909\">here<\/a><\/li>\n<\/ul>\n<p><a class=\"read-more\" alt= \"6\/9 wksp: Bulk RNA-Seq\" href=\"https:\/\/info.hsls.pitt.edu\/molbio\/2021\/06\/07\/6-9-wksp-bulk-rna-seq\/\">Read more&hellip;<\/a><\/p>\n","protected":false},"author":31,"featured_media":3735,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"footnotes":"","_links_to":"","_links_to_target":""},"categories":[1],"tags":[],"class_list":["post-4199","post","type-post","status-publish","format-standard","has-post-thumbnail","hentry","category-uncategorized"],"_links":{"self":[{"href":"https:\/\/info.hsls.pitt.edu\/molbio\/wp-json\/wp\/v2\/posts\/4199","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=4199"}],"version-history":[{"count":1,"href":"https:\/\/info.hsls.pitt.edu\/molbio\/wp-json\/wp\/v2\/posts\/4199\/revisions"}],"predecessor-version":[{"id":4200,"href":"https:\/\/info.hsls.pitt.edu\/molbio\/wp-json\/wp\/v2\/posts\/4199\/revisions\/4200"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/info.hsls.pitt.edu\/molbio\/wp-json\/wp\/v2\/media\/3735"}],"wp:attachment":[{"href":"https:\/\/info.hsls.pitt.edu\/molbio\/wp-json\/wp\/v2\/media?parent=4199"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/info.hsls.pitt.edu\/molbio\/wp-json\/wp\/v2\/categories?post=4199"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/info.hsls.pitt.edu\/molbio\/wp-json\/wp\/v2\/tags?post=4199"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}