This information is over 2 years old. Information was current at time of publication.{"id":3677,"date":"2020-06-05T14:20:36","date_gmt":"2020-06-05T19:20:36","guid":{"rendered":"http:\/\/info.hsls.pitt.edu\/molbio\/?p=3677"},"modified":"2020-06-19T09:06:29","modified_gmt":"2020-06-19T14:06:29","slug":"6-17-wksp-scrna-seq","status":"publish","type":"post","link":"https:\/\/info.hsls.pitt.edu\/molbio\/2020\/06\/05\/6-17-wksp-scrna-seq\/","title":{"rendered":"6\/17 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>June 17th, 10am-12pm &amp; 1-3:30pm<\/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 Chattopahyay &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 4\u00bd 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; 3:30 pm<\/strong>) focuses on software demonstration using HSLS-licensed <a href=\"http:\/\/hsls.libguides.com\/molbio\/partekflow\">Partek Flow<\/a> software.<\/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\">Hands-On Follow Up:<\/span><\/strong><\/p>\n<p>Every Wednesday after a workshop, a follow up session (<strong>1 pm &#8211; 3 pm<\/strong>) will review the hands-on exercise questions distributed during the workshop. We will not be addressing questions on data analysis for personal research projects\u2014researchers are encouraged to <a href=\"https:\/\/www.hsls.pitt.edu\/ask-a-molbio-specialist\">request a one-on-one consultation with MBIS<\/a> for this type of discussion. Registration is not required for the hands-on follow up session. To attend, use the same Zoom link you receive upon registration for this workshop.<\/p>\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 Requirements:<\/span><\/strong><\/p>\n<ul>\n<li><a href=\"http:\/\/hsls.libguides.com\/molbio\/partekflow\">Register for Partek Flow<\/a><\/li>\n<\/ul>\n<p><strong><span style=\"color: #3c12fb\">Workshop Guide:<\/span><\/strong><\/p>\n<ul>\n<li><a href=\"https:\/\/hsls.libguides.com\/MolBioWorkshops\/scRNAseq\">https:\/\/hsls.libguides.com\/MolBioWorkshops\/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.\u00a0<em>Molecular Systems Biology<\/em>,\u00a0<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 Summer 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<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>June 17th, 10am-12pm &amp; 1-3:30pm<\/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 Chattopahyay &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= \"6\/17 wksp: scRNA-Seq\" href=\"https:\/\/info.hsls.pitt.edu\/molbio\/2020\/06\/05\/6-17-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-3677","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\/3677","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=3677"}],"version-history":[{"count":3,"href":"https:\/\/info.hsls.pitt.edu\/molbio\/wp-json\/wp\/v2\/posts\/3677\/revisions"}],"predecessor-version":[{"id":3682,"href":"https:\/\/info.hsls.pitt.edu\/molbio\/wp-json\/wp\/v2\/posts\/3677\/revisions\/3682"}],"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=3677"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/info.hsls.pitt.edu\/molbio\/wp-json\/wp\/v2\/categories?post=3677"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/info.hsls.pitt.edu\/molbio\/wp-json\/wp\/v2\/tags?post=3677"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}