{"id":21,"date":"2017-01-05T19:44:36","date_gmt":"2017-01-05T19:44:36","guid":{"rendered":"http:\/\/wordpress.uchospitals.edu\/basu-lab\/?page_id=21"},"modified":"2023-04-16T19:38:06","modified_gmt":"2023-04-16T19:38:06","slug":"drop-seq","status":"publish","type":"page","link":"https:\/\/medpress.bsd.uchicago.edu\/basu-lab\/drop-seq\/","title":{"rendered":"Drop-Seq: High Throughput Single Cell mRNA Sequencing"},"content":{"rendered":"<header>\u0393\u00c7\u00ffDrop-Seq\u0393\u00c7\u00d6 is a high-throughput technique to profile transcriptomes of tens of thousands of single mammalian cells using a combination of DNA barcoding and emulsion microfluidics. This is accomplished by encapsulating and lysing one cell along with a uniquely barcoded microbead per emulsion droplet with Poisson loading, that allows us to molecularly tag the RNA contents from each cell. Drop-Seq enables study of transcription profiles of an unprecedented number of cells at single-cell resolution.<\/header>\n<header><\/header>\n<header><\/header>\n<header><\/header>\n<header><img loading=\"lazy\" decoding=\"async\" class=\"size-medium wp-image-188 alignleft\" src=\"http:\/\/medpress.bsd.uchicago.edu\/basu-lab\/files\/2017\/03\/dropseq_40um-bead_125um-coflow-300x300.jpg\" alt=\"\" width=\"300\" height=\"300\" srcset=\"https:\/\/medpress.bsd.uchicago.edu\/basu-lab\/files\/2017\/03\/dropseq_40um-bead_125um-coflow-300x300.jpg 300w, https:\/\/medpress.bsd.uchicago.edu\/basu-lab\/files\/2017\/03\/dropseq_40um-bead_125um-coflow-150x150.jpg 150w, https:\/\/medpress.bsd.uchicago.edu\/basu-lab\/files\/2017\/03\/dropseq_40um-bead_125um-coflow-768x769.jpg 768w, https:\/\/medpress.bsd.uchicago.edu\/basu-lab\/files\/2017\/03\/dropseq_40um-bead_125um-coflow-100x100.jpg 100w, https:\/\/medpress.bsd.uchicago.edu\/basu-lab\/files\/2017\/03\/dropseq_40um-bead_125um-coflow.jpg 1014w\" sizes=\"auto, (max-width: 300px) 100vw, 300px\" \/><\/header>\n<header>To demonstrate Drop-Seq\u0393\u00c7\u00d6s power to categorize cell types in complex tissues, it was applied to mouse retina. ~45,000 single cells from the retina were analyzed to computationally assemble cell classification of the retina cells into 39 sub-types based on their transcription profiles.  This classification faithfully reproduced existing molecular, physiological, and anatomical knowledge, while predicting novel classifications which were validated since, using complementary experiments.The findings were published in Cell, <strong>161<\/strong>, 1202, (2015), <em>Highly Parallel Genome-Wide Expression Profiling of Individual Cells Using Nanoliter Droplets<\/em>, E.  Z. Macosko, A. Basu, et al. (<a href=\"http:\/\/scholar.harvard.edu\/files\/abasu\/files\/abasu_dropseq_0.pdf\">pdf<\/a>), along with a video abstract below:<\/header>\n<header><\/header>\n<header><\/header>\n<header><\/header>\n<div id=\"content-panels\" class=\"at-panel gpanel panel-display content clearfix\">\n<div class=\"region region-content-top\">\n<div class=\"region-inner clearfix\">\n<div id=\"block-os-pages-main-content\" class=\"block block-os-pages no-title\">\n<div class=\"block-inner clearfix\">\n<div class=\"block-content content\">\n<article id=\"node-313336\" class=\"node node-page article clearfix\">\n<div class=\"node-content\">\n<div class=\"field field-name-body field-type-text-with-summary field-label-hidden view-mode-full\">\n<div class=\"field-items\">\n<div class=\"field-item even\">\n<p><span title=\"Drop-seq: Droplet barcoding of single cells\"><iframe loading=\"lazy\" src=\"https:\/\/www.youtube.com\/embed\/vL7ptq2Dcf0?feature=oembed\" width=\"480\" height=\"270\" frameborder=\"0\" allowfullscreen=\"allowfullscreen\" data-mce-fragment=\"1\"><\/iframe><\/span><span style=\"color: #c00000;\"><br style=\"color: #c00000;\" \/><\/span><\/p>\n<p>Upon publication, Drop-Seq received considerable media coverage and was featured in the NIH Director\u0393\u00c7\u00d6s blog: <a href=\"http:\/\/directorsblog.nih.gov\/tag\/drop-seq\/\">http:\/\/directorsblog.nih.gov\/tag\/drop-seq\/<\/a><\/p>\n<p><a href=\"http:\/\/www.satijalab.org\/seurat.html\">Rahul Satija&#8217;s Seurat<\/a> package (written in R) is highly effective in analyzing 3-prime Digital Gene Expression (3&#8242; DGE) data obtained from Drop-Seq.<\/p>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/article>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n","protected":false},"excerpt":{"rendered":"<p>\u0393\u00c7\u00ffDrop-Seq\u0393\u00c7\u00d6 is a high-throughput technique to profile transcriptomes of tens of thousands of single mammalian cells using a combination of DNA barcoding and emulsion microfluidics. This is accomplished by encapsulating and lysing one cell along with a uniquely barcoded microbead per emulsion droplet with Poisson loading, that allows us to molecularly tag the RNA contents &hellip; <\/p>\n<p class=\"link-more\"><a href=\"https:\/\/medpress.bsd.uchicago.edu\/basu-lab\/drop-seq\/\" class=\"more-link\">Continue reading<span class=\"screen-reader-text\"> &#8220;Drop-Seq: High Throughput Single Cell mRNA Sequencing&#8221;<\/span><\/a><\/p>\n","protected":false},"author":233,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-21","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/medpress.bsd.uchicago.edu\/basu-lab\/wp-json\/wp\/v2\/pages\/21","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/medpress.bsd.uchicago.edu\/basu-lab\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/medpress.bsd.uchicago.edu\/basu-lab\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/medpress.bsd.uchicago.edu\/basu-lab\/wp-json\/wp\/v2\/users\/233"}],"replies":[{"embeddable":true,"href":"https:\/\/medpress.bsd.uchicago.edu\/basu-lab\/wp-json\/wp\/v2\/comments?post=21"}],"version-history":[{"count":8,"href":"https:\/\/medpress.bsd.uchicago.edu\/basu-lab\/wp-json\/wp\/v2\/pages\/21\/revisions"}],"predecessor-version":[{"id":300,"href":"https:\/\/medpress.bsd.uchicago.edu\/basu-lab\/wp-json\/wp\/v2\/pages\/21\/revisions\/300"}],"wp:attachment":[{"href":"https:\/\/medpress.bsd.uchicago.edu\/basu-lab\/wp-json\/wp\/v2\/media?parent=21"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}