This information is over 2 years old. Information was current at time of publication.{"id":3285,"date":"2019-08-28T14:35:32","date_gmt":"2019-08-28T19:35:32","guid":{"rendered":"http:\/\/info.hsls.pitt.edu\/molbio\/?p=3285"},"modified":"2019-09-06T10:04:35","modified_gmt":"2019-09-06T15:04:35","slug":"9-4-wksp-single-cell-rna-seq","status":"publish","type":"post","link":"https:\/\/info.hsls.pitt.edu\/molbio\/2019\/08\/28\/9-4-wksp-single-cell-rna-seq\/","title":{"rendered":"9\/4 wksp: Single Cell RNA-Seq"},"content":{"rendered":"<ul>\n<li><strong><span style=\"color: #4e364e\">WHAT:<\/span> <\/strong>Single Cell RNA-Seq<\/li>\n<li><strong><span style=\"color: #4e364e\">WHEN:<\/span> <\/strong>September 4th, 10am-12pm &amp; 1-3pm<\/li>\n<li><strong><span style=\"color: #4e364e\">WHERE:<\/span> <\/strong>Scaife Hall, Falk Library, Classroom 2<\/li>\n<li><strong><span style=\"color: #4e364e\">WHO:<\/span> <\/strong>Ansuman Chattopahyay &amp; Sri Chaparala<\/li>\n<li><strong><span style=\"color: #4e364e\">HOW:<\/span> <\/strong>Register <a href=\"https:\/\/www.hsls.pitt.edu\/instruction\/single-cell-rna-seq\/3721\">here<\/a><\/li>\n<\/ul>\n<p><!--more--><\/p>\n<p><strong><span style=\"color: #4e364e\">Workshop Objective:<\/span><\/strong><\/p>\n<p>This is a 4-hour workshop on the techniques, platforms, and methods used in analyzing single cell RNA-Seq data (scRNA-Seq). The morning session (<strong>10am &#8211; 12pm<\/strong>) starts with a presentation from the Genomics Research Core on best practices in sample handling, followed by an overview of the basic steps involved in scRNA-Seq data analysis. The afternoon session (<strong>1pm &#8211; 3pm<\/strong>) focuses on hands-on practice using HSLS-licensed Partek Flow software.<\/p>\n<p>Participants will learn how to:<\/p>\n<ul>\n<li>import the FASTQ files from scRNA-Seq experiments<\/li>\n<li>perform quality checks (QC) and trim tags<\/li>\n<li>align the reads to a reference genome<\/li>\n<li>perform deduplication of UMIs and Filter cell barcodes<\/li>\n<li>perform quantification and generate a single cell count matrix<\/li>\n<li>perform single cell QC and generate t-SNE plots<\/li>\n<li>classify cell types<\/li>\n<li>compare gene expression between cell types<\/li>\n<li>perform trajectory analyses<\/li>\n<\/ul>\n<p><strong><span style=\"color: #4e364e\">Target Audience:<\/span><\/strong><\/p>\n<p>Experimental biologists seeking to analyze scRNA-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: #4e364e\">Workshop Requirements:<\/span><\/strong><\/p>\n<p><a href=\"http:\/\/hsls.libguides.com\/molbio\/partekflow\">Register for Partek Flow<\/a><\/p>\n<p><strong><span style=\"color: #4e364e\">Workshop Guide:<\/span><\/strong><\/p>\n<p><a href=\"https:\/\/hsls.libguides.com\/MolBioWorkshops\/scRNAseq\">https:\/\/hsls.libguides.com\/MolBioWorkshops\/scRNAseq<\/a><\/p>\n<p><strong><span style=\"color: #4e364e\">Suggested Reading:<\/span><\/strong><\/p>\n<p><a href=\"https:\/\/www.embopress.org\/lookup\/doi\/10.15252\/msb.20188746\">Luecken, M. D., &amp; Theis, F. J. (2019). Current best practices in single-cell RNA-seq analysis: a tutorial. Molecular Systems Biology, 15(6), e8746. doi:10.15252\/msb.20188746<\/a><\/p>\n<p><strong><span style=\"color: #4e364e\">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: #4e364e\">WHAT:<\/span> <\/strong>Single Cell RNA-Seq<\/li>\n<li><strong><span style=\"color: #4e364e\">WHEN:<\/span> <\/strong>September 4th, 10am-12pm &amp; 1-3pm<\/li>\n<li><strong><span style=\"color: #4e364e\">WHERE:<\/span> <\/strong>Scaife Hall, Falk Library, Classroom 2<\/li>\n<li><strong><span style=\"color: #4e364e\">WHO:<\/span> <\/strong>Ansuman Chattopahyay &amp; Sri Chaparala<\/li>\n<li><strong><span style=\"color: #4e364e\">HOW:<\/span> <\/strong>Register <a href=\"https:\/\/www.hsls.pitt.edu\/instruction\/single-cell-rna-seq\/3721\">here<\/a><\/li>\n<\/ul>\n<p><a class=\"read-more\" alt= \"9\/4 wksp: Single Cell RNA-Seq\" href=\"https:\/\/info.hsls.pitt.edu\/molbio\/2019\/08\/28\/9-4-wksp-single-cell-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-3285","post","type-post","status-publish","format-standard","hentry","category-uncategorized"],"_links":{"self":[{"href":"https:\/\/info.hsls.pitt.edu\/molbio\/wp-json\/wp\/v2\/posts\/3285","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=3285"}],"version-history":[{"count":7,"href":"https:\/\/info.hsls.pitt.edu\/molbio\/wp-json\/wp\/v2\/posts\/3285\/revisions"}],"predecessor-version":[{"id":3295,"href":"https:\/\/info.hsls.pitt.edu\/molbio\/wp-json\/wp\/v2\/posts\/3285\/revisions\/3295"}],"wp:attachment":[{"href":"https:\/\/info.hsls.pitt.edu\/molbio\/wp-json\/wp\/v2\/media?parent=3285"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/info.hsls.pitt.edu\/molbio\/wp-json\/wp\/v2\/categories?post=3285"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/info.hsls.pitt.edu\/molbio\/wp-json\/wp\/v2\/tags?post=3285"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}