This information is over 2 years old. Information was current at time of publication.{"id":4085,"date":"2021-02-28T11:33:38","date_gmt":"2021-02-28T16:33:38","guid":{"rendered":"http:\/\/info.hsls.pitt.edu\/molbio\/?p=4085"},"modified":"2021-03-08T11:09:21","modified_gmt":"2021-03-08T16:09:21","slug":"3-3-wksp-scrna-seq","status":"publish","type":"post","link":"https:\/\/info.hsls.pitt.edu\/molbio\/2021\/02\/28\/3-3-wksp-scrna-seq\/","title":{"rendered":"3\/3 wksp: scRNA-Seq"},"content":{"rendered":"<ul>\n<li><strong><span style=\"color: #3c12fb\">WHAT:<\/span> <\/strong>Single Cell RNA-Seq<\/li>\n<li><strong><span style=\"color: #3c12fb\">WHEN:<\/span> <\/strong>March 3rd, 10am-12pm &amp; 1-4pm<\/li>\n<li><strong><span style=\"color: #3c12fb\">WHERE:<\/span> <\/strong>Online; instructions upon registration<\/li>\n<li><strong><span style=\"color: #3c12fb\">WHO:<\/span> <\/strong>Ansuman Chattopadhyay &amp; Sri Chaparala<\/li>\n<li><strong><span style=\"color: #3c12fb\">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--><br \/>\nThis is a 5 hour workshop on the techniques, platforms, and methods used in analyzing single cell RNA-Seq data (scRNA-Seq). The morning session (<strong>10 am &#8211; 12 pm<\/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 scRNA-Seq data analysis. The afternoon session (<strong>1 pm &#8211; 4 pm<\/strong>) focuses on software demonstration using HSLS-licensed <a href=\"http:\/\/hsls.libguides.com\/molbio\/partekflow\">Partek Flow<\/a> software.<\/p>\n<p>One week after this class we will host a follow up session (1 pm to 3 pm) to review the hands-on exercise questions distributed during the workshop. Registration is not required for the hands-on follow up session. To attend, use the same Zoom link you received upon registration for the original workshop. <\/p>\n<p>Participants will learn how to<\/p>\n<ul>\n<li>import FASTQ files from scRNA-Seq experiments using GEO<\/li>\n<li>perform quality checks (QC) on single cell data<\/li>\n<li>filter and normalize of data<\/li>\n<li>generate PCA and t-SNE plots to visualize data<\/li>\n<li>identify cell populations, biomarkers, and differential gene expression<\/li>\n<li>perform trajectory analyses<\/li>\n<\/ul>\n<p><strong><span style=\"color: #3c12fb\">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 the command line interface is required.<\/p>\n<p><strong><span style=\"color: #3c12fb\">Workshop Guide:<\/span><\/strong><\/p>\n<ul>\n<li><a href=\"https:\/\/hsls.libguides.com\/MBISworkshops\/scRNAseq\">https:\/\/hsls.libguides.com\/MBISworkshops\/scRNAseq<\/a><\/li>\n<\/ul>\n<p><strong><span style=\"color: #3c12fb\">Suggested Reading:<\/span><\/strong><\/p>\n<ul>\n<li><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. <em>Molecular Systems Biology<\/em>, <em>15<\/em>(6), e8746. doi:10.15252\/msb.20188746<\/a><\/li>\n<\/ul>\n<p><strong><span style=\"color: #3c12fb\">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 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\/@nci?utm_source=unsplash&amp;utm_medium=referral&amp;utm_content=creditCopyText\">National Cancer Institute<\/a> on <a href=\"https:\/\/unsplash.com\/s\/photos\/cell-biology\">Unsplash<\/a>)<\/p>\n","protected":false},"excerpt":{"rendered":"<ul>\n<li><strong><span style=\"color: #3c12fb\">WHAT:<\/span> <\/strong>Single Cell RNA-Seq<\/li>\n<li><strong><span style=\"color: #3c12fb\">WHEN:<\/span> <\/strong>March 3rd, 10am-12pm &amp; 1-4pm<\/li>\n<li><strong><span style=\"color: #3c12fb\">WHERE:<\/span> <\/strong>Online; instructions upon registration<\/li>\n<li><strong><span style=\"color: #3c12fb\">WHO:<\/span> <\/strong>Ansuman Chattopadhyay &amp; Sri Chaparala<\/li>\n<li><strong><span style=\"color: #3c12fb\">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= \"3\/3 wksp: scRNA-Seq\" href=\"https:\/\/info.hsls.pitt.edu\/molbio\/2021\/02\/28\/3-3-wksp-scrna-seq\/\">Read more&hellip;<\/a><\/p>\n","protected":false},"author":31,"featured_media":3680,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"footnotes":"","_links_to":"","_links_to_target":""},"categories":[1],"tags":[],"class_list":["post-4085","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\/4085","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=4085"}],"version-history":[{"count":2,"href":"https:\/\/info.hsls.pitt.edu\/molbio\/wp-json\/wp\/v2\/posts\/4085\/revisions"}],"predecessor-version":[{"id":4087,"href":"https:\/\/info.hsls.pitt.edu\/molbio\/wp-json\/wp\/v2\/posts\/4085\/revisions\/4087"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/info.hsls.pitt.edu\/molbio\/wp-json\/wp\/v2\/media\/3680"}],"wp:attachment":[{"href":"https:\/\/info.hsls.pitt.edu\/molbio\/wp-json\/wp\/v2\/media?parent=4085"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/info.hsls.pitt.edu\/molbio\/wp-json\/wp\/v2\/categories?post=4085"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/info.hsls.pitt.edu\/molbio\/wp-json\/wp\/v2\/tags?post=4085"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}