{"id":73,"date":"2023-04-25T13:48:28","date_gmt":"2023-04-25T20:48:28","guid":{"rendered":"https:\/\/labs.wsu.edu\/duttke\/?page_id=73"},"modified":"2025-12-05T09:01:16","modified_gmt":"2025-12-05T17:01:16","slug":"protocols","status":"publish","type":"page","link":"https:\/\/labs.wsu.edu\/duttke\/protocols\/","title":{"rendered":"Protocols"},"content":{"rendered":"\n<h2 class=\"wp-block-heading\">csRNA-seq<\/h2>\n\n\n\n<p>This method captures active transcription, and thus all currently made RNAs including unstable RNAs from total RNA. Please see our paper for more detail.<\/p>\n\n\n\n<p>A csRNA-seq tutorial is available on the <a href=\"http:\/\/homer.ucsd.edu\/homer\/ngs\/csRNAseq\/\">HOMER <\/a> or check out our <a rel=\"noreferrer noopener\" href=\"https:\/\/genome.cshlp.org\/content\/early\/2019\/10\/24\/gr.253492.119.full.pdf+html\">\u200ecsRNA-seq paper <\/a><\/p>\n\n\n\n<p>To download our <a href=\"https:\/\/s3.wp.wsu.edu\/uploads\/sites\/3142\/2024\/03\/csrna_protocol.pdf\" data-type=\"URL\">latest capped small (cs)RNA-seq protocol<\/a> <\/p>\n\n\n\n<p>To download our <a href=\"https:\/\/s3.wp.wsu.edu\/uploads\/sites\/3142\/2024\/03\/csrna_sampling.pdf\"> Guidelines for collecting csRNA-seq samples<\/a><\/p>\n\n\n\n<p>To download our <a href=\"https:\/\/s3.wp.wsu.edu\/uploads\/sites\/3142\/2024\/03\/csrna_reagents.pdf\">the csRNA-seq reagent list<\/a><\/p>\n\n\n\n<p>A video  detailing an older version of our csRNA-seq protocol can be found on YouTube<br>! Note, we no longer do the bead cleanup after the frist round of CIP as quickCIP is now thermostable!<\/p>\n\n\n\n<figure class=\"wp-block-embed is-type-video is-provider-youtube wp-block-embed-youtube wp-embed-aspect-16-9 wp-has-aspect-ratio\"><div class=\"wp-block-embed__wrapper\">\n<div class='embed-youtube' style='text-align:center; display: block;'><iframe class='youtube-player' type='text\/html' width='640' height='390' src='https:\/\/www.youtube.com\/embed\/tFSEX7W4EEM?version=3&#038;rel=1&#038;fs=1&#038;autohide=2&#038;showsearch=0&#038;showinfo=1&#038;iv_load_policy=1&#038;wmode=transparent' frameborder='0' allowfullscreen='true'><\/iframe><\/div>\n<\/div><\/figure>\n\n\n\n<p>All protocols are provided as PDFs. If you need an accessible version of any document, please contact sascha.duttke@wsu.edu &#8211; we&#8217;re happy to help where we can :-).<\/p>\n\n\n\n<p><\/p>\n\n\n\n<p>Want more?<br>Here an intro video from our csRNA-seq course<\/p>\n\n\n\n<p><br><\/p>\n\n\n\n<figure class=\"wp-block-embed is-type-video is-provider-youtube wp-block-embed-youtube wp-embed-aspect-16-9 wp-has-aspect-ratio\"><div class=\"wp-block-embed__wrapper\">\n<div class='embed-youtube' style='text-align:center; display: block;'><iframe class='youtube-player' type='text\/html' width='640' height='390' src='https:\/\/www.youtube.com\/embed\/7CsVBDKExT0?version=3&#038;rel=1&#038;fs=1&#038;autohide=2&#038;showsearch=0&#038;showinfo=1&#038;iv_load_policy=1&#038;wmode=transparent' frameborder='0' allowfullscreen='true'><\/iframe><\/div>\n<\/div><\/figure>\n\n\n\n<p>And another one discussing csRNA-seq analysis<\/p>\n\n\n\n<figure class=\"wp-block-embed is-type-video is-provider-youtube wp-block-embed-youtube wp-embed-aspect-16-9 wp-has-aspect-ratio\"><div class=\"wp-block-embed__wrapper\">\n<div class='embed-youtube' style='text-align:center; display: block;'><iframe class='youtube-player' type='text\/html' width='640' height='390' src='https:\/\/www.youtube.com\/embed\/5r0sVXuNisM?version=3&#038;rel=1&#038;fs=1&#038;autohide=2&#038;showsearch=0&#038;showinfo=1&#038;iv_load_policy=1&#038;wmode=transparent' frameborder='0' allowfullscreen='true'><\/iframe><\/div>\n<\/div><\/figure>\n","protected":false},"excerpt":{"rendered":"<p>csRNA-seq This method captures active transcription, and thus all currently made RNAs including unstable RNAs from total RNA. Please see our paper for more detail. A csRNA-seq tutorial is available on the HOMER or check out our \u200ecsRNA-seq paper To download our latest capped small (cs)RNA-seq protocol To download our Guidelines for collecting csRNA-seq samples [&hellip;]<\/p>\n","protected":false},"author":1351,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":[],"categories":[],"tags":[],"wsuwp_university_location":[],"wsuwp_university_org":[],"_links":{"self":[{"href":"https:\/\/labs.wsu.edu\/duttke\/wp-json\/wp\/v2\/pages\/73"}],"collection":[{"href":"https:\/\/labs.wsu.edu\/duttke\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/labs.wsu.edu\/duttke\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/labs.wsu.edu\/duttke\/wp-json\/wp\/v2\/users\/1351"}],"replies":[{"embeddable":true,"href":"https:\/\/labs.wsu.edu\/duttke\/wp-json\/wp\/v2\/comments?post=73"}],"version-history":[{"count":16,"href":"https:\/\/labs.wsu.edu\/duttke\/wp-json\/wp\/v2\/pages\/73\/revisions"}],"predecessor-version":[{"id":477,"href":"https:\/\/labs.wsu.edu\/duttke\/wp-json\/wp\/v2\/pages\/73\/revisions\/477"}],"wp:attachment":[{"href":"https:\/\/labs.wsu.edu\/duttke\/wp-json\/wp\/v2\/media?parent=73"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/labs.wsu.edu\/duttke\/wp-json\/wp\/v2\/categories?post=73"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/labs.wsu.edu\/duttke\/wp-json\/wp\/v2\/tags?post=73"},{"taxonomy":"wsuwp_university_location","embeddable":true,"href":"https:\/\/labs.wsu.edu\/duttke\/wp-json\/wp\/v2\/wsuwp_university_location?post=73"},{"taxonomy":"wsuwp_university_org","embeddable":true,"href":"https:\/\/labs.wsu.edu\/duttke\/wp-json\/wp\/v2\/wsuwp_university_org?post=73"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}