{"id":2225,"date":"2013-11-21T11:44:41","date_gmt":"2013-11-21T16:44:41","guid":{"rendered":"https:\/\/www.bumc.bu.edu\/gsi\/?page_id=2225"},"modified":"2018-01-08T15:50:16","modified_gmt":"2018-01-08T20:50:16","slug":"mrna-seq-library-preparation","status":"publish","type":"page","link":"https:\/\/www.bumc.bu.edu\/gsi\/initiatives\/2019workshop\/mrna-seq-library-preparation\/","title":{"rendered":"2015 RNA-seq data generation and analysis hands-on workshops"},"content":{"rendered":"<p style=\"text-align: justify;\">This hands-on workshop is designed to offer BU researchers the opportunity to generate mRNA-seq differential expression data that can be used as preliminary data for extramural grant applications. \u00a0The workshop will be compose of two parts: data generation and data analysis. \u00a0For the\u00a0first part of the workshop (wet lab), investigators will\u00a0supply their own experimental and control RNA samples and will be trained in sample preparation methods to generate directional RNA-seq libraries. \u00a0These libraries will then be high throughput (deep) sequenced using the Illumina HiSeq platform. \u00a0In the second part of the workshop, participants will learn\u00a0how to analyze the\u00a0resulting NGS sequencing data using computational and bioinformatics tools to obtain differential gene expression data.<\/p>\n<p style=\"text-align: justify;\">This GSI-sponsored no cost workshop is free and open to all researchers at BU. \u00a0Because there is a 24 participant limit, we may request additional information in order to select participants. \u00a0The deadline for application is <span style=\"color: #ff0000;\">April 7, 2015<\/span>.<\/p>\n<p style=\"text-align: center;\"><strong>Please register <a title=\"RNA-seq Hands-On Workshop Registration: Deadline April 7th\" href=\"https:\/\/www.bumc.bu.edu\/gsi\/rna-seq-hands-on-workshop-registration-deadline-december-9th\/\">here<\/a><\/strong><\/p>\n<p style=\"text-align: center;\"><strong>For more details please email <a href=\"mailto:gsi@bu.edu\">gsi@bu.edu<\/a><\/strong><\/p>\n<hr align=\"center\" size=\"2\" width=\"100%\" \/>\n<h4 style=\"text-align: center;\">Part 1: RNA-seq Library Preparation<\/h4>\n<p style=\"text-align: center;\"><strong>Dates: May\u00a06-7, 2015<\/strong><\/p>\n<p style=\"text-align: center;\"><strong>Place: BUMC Medical School Instructional Building, L401<\/strong><\/p>\n<p style=\"text-align: center;\"><strong>Time: 9 a.m.-5 p.m. daily<\/strong><\/p>\n<p style=\"text-align: center;\"><strong>Goal: Generate high throughput sequencing libraries from participant-provided total RNA samples<\/strong><\/p>\n<ul>\n<li>A two day hands-on wet lab workshop, taught by experts from NEB and BU.<\/li>\n<li>Participants will prepare directional mRNA-seq libraries using <a href=\"https:\/\/www.neb.com\/products\/e7420-nebnext-ultra-directional-rna-library-prep-kit-for-illumina\" target=\"_blank\">NEBNext Ultra Directional RNA Library Prep Kits\u00a0for Illumina<\/a>\u00a0and their own experimental and control samples (one of each).<\/li>\n<li><span>We will utilize the <a href=\"https:\/\/www.neb.com\/products\/e6310-nebnext-rrna-depletion-kit-human-mouse-rat\" target=\"_blank\">NEBNext rRNA Depletion Kit\u00a0(Human\/Mouse\/Rat)<\/a>, so libraries can only be prepared using RNA from these three species.<\/span><\/li>\n<li>Libraries will be sequenced on the Illumina HiSeq platform using a multiplexing strategy. \u00a0Single end 50bp reads will be generated with a target of 20-25 million reads\/sample.<\/li>\n<\/ul>\n<p><strong>Participant Responsibilities:<br \/>\n<\/strong><\/p>\n<ul>\n<li>Provide one experimental and one control high-quality total RNA sample (500-1000ng) to the BUMC Microarray Core Facility by the close of business on <span style=\"color: #ff0000;\">April\u00a027, 2015<\/span>. \u00a0Each RNA sample will be quantitated and assessed for quality using an Agilent Bioanalyzer.<\/li>\n<li>You will be asked to bring some basic lab supplies to the workshop (e.g., pipettes, pipet tips, an ice bucket, etc.).<\/li>\n<\/ul>\n<ul><\/ul>\n<p style=\"text-align: center;\"><strong><span style=\"font-size: 1.17em;\">Generously Sponsored by <a href=\"https:\/\/www.neb.com\/products\/e7420-nebnext-ultra-directional-rna-library-prep-kit-for-illumina\">New England Biolabs<\/a><br \/>\n<\/span>Costs for high throughput sequencing underwritten by the GSI<\/strong><\/p>\n<hr align=\"center\" size=\"2\" width=\"100%\" \/>\n<h4 style=\"text-align: center;\">Part 2: Computational Analysis of High Throughput RNA-seq Data<\/h4>\n<p style=\"text-align: center;\"><strong>Date:\u00a0TBA<\/strong><\/p>\n<p style=\"text-align: center;\"><strong>Place:\u00a0TBA<\/strong><\/p>\n<p style=\"text-align: center;\"><strong>Time:\u00a0TBA<\/strong><\/p>\n<p style=\"text-align: center;\"><strong>Goal:\u00a0<\/strong><span><strong>Learn how to implement a computational analysis pipeline to move your sequencing data from raw reads to differential gene expression results.<\/strong><\/span><\/p>\n<p style=\"text-align: center;\"><span style=\"font-size: 13px; font-weight: normal;\"><span>Participants will learn how to process and initially analyze the generated data using the GSI-sponsored Globus Genomics Galaxy Platform (<\/span><span><a href=\"https:\/\/www.bumc.bu.edu\/gsi\/initiatives\/globus-genomics\/\">https:\/\/www.bumc.bu.edu\/gsi\/initiatives\/globus-genomics\/<\/a><\/span><span>) to obtain differential gene expression data.<\/span><\/span><\/p>\n<p style=\"text-align: center;\"><strong>Developed in collaboration with <a href=\"https:\/\/www.globus.org\/genomics\/\" target=\"_blank\">Globus Genomics<\/a><\/strong><\/p>\n<p>&nbsp;<\/p>\n<div><strong><strong><br \/>\n<\/strong><\/strong><\/div>\n<h4 style=\"text-align: center;\"><\/h4>\n<p>&nbsp;<\/p>\n<ul><\/ul>\n<p>&nbsp;<\/p>\n<h3 style=\"text-align: center;\"><\/h3>\n<p>&nbsp;<\/p>\n<p>&nbsp;<\/p>\n<p>&nbsp;<\/p>\n<p><!--EndFragment--><\/p>\n","protected":false},"excerpt":{"rendered":"<p>This hands-on workshop is designed to offer BU researchers the opportunity to generate mRNA-seq differential expression data that can be used as preliminary data for extramural grant applications. \u00a0The workshop will be compose of two parts: data generation and data analysis. \u00a0For the\u00a0first part of the workshop (wet lab), investigators will\u00a0supply their own experimental and [&hellip;]<\/p>\n","protected":false},"author":1326,"featured_media":0,"parent":2244,"menu_order":1,"comment_status":"closed","ping_status":"closed","template":"","meta":[],"_links":{"self":[{"href":"https:\/\/www.bumc.bu.edu\/gsi\/wp-json\/wp\/v2\/pages\/2225"}],"collection":[{"href":"https:\/\/www.bumc.bu.edu\/gsi\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/www.bumc.bu.edu\/gsi\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/www.bumc.bu.edu\/gsi\/wp-json\/wp\/v2\/users\/1326"}],"replies":[{"embeddable":true,"href":"https:\/\/www.bumc.bu.edu\/gsi\/wp-json\/wp\/v2\/comments?post=2225"}],"version-history":[{"count":50,"href":"https:\/\/www.bumc.bu.edu\/gsi\/wp-json\/wp\/v2\/pages\/2225\/revisions"}],"predecessor-version":[{"id":3314,"href":"https:\/\/www.bumc.bu.edu\/gsi\/wp-json\/wp\/v2\/pages\/2225\/revisions\/3314"}],"up":[{"embeddable":true,"href":"https:\/\/www.bumc.bu.edu\/gsi\/wp-json\/wp\/v2\/pages\/2244"}],"wp:attachment":[{"href":"https:\/\/www.bumc.bu.edu\/gsi\/wp-json\/wp\/v2\/media?parent=2225"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}