{"id":2720,"date":"2019-02-22T12:47:41","date_gmt":"2019-02-22T03:47:41","guid":{"rendered":"http:\/\/163.180.4.222\/lab\/?p=2720"},"modified":"2019-02-22T12:47:41","modified_gmt":"2019-02-22T03:47:41","slug":"the-single-cell-transcriptional-landscape-of-mammalian-organogenesis","status":"publish","type":"post","link":"https:\/\/biochemistry.khu.ac.kr\/lab\/?p=2720","title":{"rendered":"The single-cell transcriptional landscape of mammalian organogenesis"},"content":{"rendered":"<p>&nbsp;<\/p>\n<p>&nbsp;<\/p>\n<h5 class=\"js-section-title section-title strong position-relative tighten-line-height background-gray-light pt20 pb6 pl0 pr20 standard-space-below small-space-above mq640-pt10 mq640-pb10 mq640-pl20 mq640-mt0 mq640-ml-20 mq640-mr-20 extend-left\">Abstract<\/h5>\n<p>&nbsp;<\/p>\n<div id=\"Abs1-content\" class=\"pl20 mq875-pl0 js-collapsible-section\">\n<p>Mammalian organogenesis is a remarkable process. Within a short timeframe, the cells of the three germ layers transform into an embryo that includes most of the major internal and external organs. Here we investigate the transcriptional dynamics of mouse organogenesis at single-cell resolution. Using single-cell combinatorial indexing, we profiled the transcriptomes of around 2 million cells derived from 61 embryos staged between 9.5 and 13.5 days of gestation, in a single experiment. The resulting \u2018mouse organogenesis cell atlas\u2019 (MOCA) provides a global view of developmental processes during this critical window. We\u00a0use Monocle 3 to identify hundreds of cell types and 56 trajectories, many of which are detected only because of the depth of cellular coverage, and collectively define thousands of corresponding marker genes. We explore the dynamics of gene expression within cell types and trajectories over time, including focused analyses of the apical ectodermal ridge, limb mesenchyme and skeletal muscle.<\/p>\n<\/div>\n<p>&nbsp;<\/p>\n<p>&nbsp;<\/p>\n<p>(\uc6d0\ubb38: <a href=\"https:\/\/www.nature.com\/articles\/s41586-019-0969-x?utm_source=feedburner&amp;utm_medium=feed&amp;utm_campaign=Feed%3A+nature%2Frss%2Fcurrent+%28Nature+-+Issue%29\">\uc5ec\uae30<\/a>\ub97c \ud074\ub9ad\ud558\uc138\uc694~)<\/p>\n<p>&nbsp;<\/p>\n<p>&nbsp;<\/p>\n","protected":false},"excerpt":{"rendered":"<p>&nbsp; &nbsp; Abstract &nbsp; Mammalian organogenesis is a remarkable process. Within a short timeframe, the cells of the three germ layers transform into an embryo<a href=\"https:\/\/biochemistry.khu.ac.kr\/lab\/?p=2720\" class=\"more-link\">(more&#8230;)<\/a><\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"_monsterinsights_skip_tracking":false,"_monsterinsights_sitenote_active":false,"_monsterinsights_sitenote_note":"","_monsterinsights_sitenote_category":0,"jetpack_post_was_ever_published":false,"_jetpack_newsletter_access":"","_jetpack_dont_email_post_to_subs":false,"_jetpack_newsletter_tier_id":0,"_jetpack_memberships_contains_paywalled_content":false,"_jetpack_memberships_contains_paid_content":false,"footnotes":"","jetpack_publicize_message":"","jetpack_publicize_feature_enabled":true,"jetpack_social_post_already_shared":true,"jetpack_social_options":{"image_generator_settings":{"template":"highway","default_image_id":0,"font":"","enabled":false},"version":2}},"categories":[33,29,30],"tags":[],"class_list":["post-2720","post","type-post","status-publish","format-standard","hentry","category-do-biology","category-lets-do-science","category-recent-science-news"],"aioseo_notices":[],"jetpack_publicize_connections":[],"jetpack_featured_media_url":"","jetpack-related-posts":[{"id":2718,"url":"https:\/\/biochemistry.khu.ac.kr\/lab\/?p=2718","url_meta":{"origin":2720,"position":0},"title":"A single-cell molecular map of mouse gastrulation and early organogenesis","author":"biochemistry","date":"February 22, 2019","format":false,"excerpt":"\u00a0 \u00a0 Abstract \u00a0 Across the animal kingdom, gastrulation represents a key developmental event during which embryonic pluripotent cells diversify into lineage-specific precursors that will generate the adult organism. Here we report the transcriptional profiles of 116,312 single cells from mouse embryos collected at nine sequential time points ranging from\u2026","rel":"","context":"In &quot;Let's Do Biology!&quot;","block_context":{"text":"Let's Do Biology!","link":"https:\/\/biochemistry.khu.ac.kr\/lab\/?cat=33"},"img":{"alt_text":"","src":"","width":0,"height":0},"classes":[]},{"id":4849,"url":"https:\/\/biochemistry.khu.ac.kr\/lab\/?p=4849","url_meta":{"origin":2720,"position":1},"title":"Modeling the early development of a primate embryo","author":"biochemistry","date":"November 15, 2019","format":false,"excerpt":"\u00a0 \u00a0 Because mammalian embryos develop inside the uterus after implantation, they are practically inaccessible for direct observation and experimental analysis of the developmental process. To visualize and study the development of post-implantation embryos, it is necessary to develop a technology that maintains the viability and growth of embryos ex\u2026","rel":"","context":"In &quot;Let's Do Biology!&quot;","block_context":{"text":"Let's Do Biology!","link":"https:\/\/biochemistry.khu.ac.kr\/lab\/?cat=33"},"img":{"alt_text":"","src":"","width":0,"height":0},"classes":[]},{"id":1363,"url":"https:\/\/biochemistry.khu.ac.kr\/lab\/?p=1363","url_meta":{"origin":2720,"position":2},"title":"CRISPR \u2018barcodes\u2019 map mammalian development in exquisite detail","author":"biochemistry","date":"August 14, 2018","format":false,"excerpt":"\u00a0 \u00a0 (\uc6d0\ubb38) \u00a0 \u00a0 Genome-editing technique enables researchers to trace lineage of cells in developing mice. \u00a0 \u00a0 Researchers have used gene-editing to track the cell-by-cell development of a mouse embryo.\u00a0Credit: Agnieszka Jedrusik and Magdalena Zernicka-Goetz, Gurdon Institute.\u00a0CC0 \u00a0 \u00a0 For the first time, scientists have wielded CRISPR to\u2026","rel":"","context":"In &quot;Let's Do Biology!&quot;","block_context":{"text":"Let's Do Biology!","link":"https:\/\/biochemistry.khu.ac.kr\/lab\/?cat=33"},"img":{"alt_text":"","src":"","width":0,"height":0},"classes":[]},{"id":2016,"url":"https:\/\/biochemistry.khu.ac.kr\/lab\/?p=2016","url_meta":{"origin":2720,"position":3},"title":"How to lose your inheritance","author":"biochemistry","date":"October 5, 2018","format":false,"excerpt":"\u00a0 \u00a0 \ubc30\uc544\uc904\uae30\uc138\ud3ec\uc758 \ubd84\ud654 \uacfc\uc815\uc5d0\uc11c\uc758 \uc804\uc0ac\uc778\uc790\uc758 \uc911\uc694\uc131\uc5d0 \uad00\ud55c \ub0b4\uc6a9\uc785\ub2c8\ub2e4. (\uc6d0\ubb38: \uc5ec\uae30\ub97c \ud074\ub9ad\ud558\uc138\uc694~) \u00a0 In developing embryos, molecular and physical differences divide the cells that will form eggs or sperm and those that will form the body. The mouse protein OTX2 directs this decision by blocking reproductive-cell fate. \u00a0 \u00a0 In\u2026","rel":"","context":"In &quot;Let's Do Biology!&quot;","block_context":{"text":"Let's Do Biology!","link":"https:\/\/biochemistry.khu.ac.kr\/lab\/?cat=33"},"img":{"alt_text":"","src":"","width":0,"height":0},"classes":[]},{"id":1316,"url":"https:\/\/biochemistry.khu.ac.kr\/lab\/?p=1316","url_meta":{"origin":2720,"position":4},"title":"Technique to measure the expression dynamics of each gene in a single cell","author":"biochemistry","date":"August 9, 2018","format":false,"excerpt":"\u00a0 \u00a0 (\uc6d0\ubb38) \u00a0 \u00a0 A method has been developed to infer whether the expression of each gene in a single cell is increasing or decreasing, and at what rate, using RNA-sequencing data. This tool has many potential applications. \u00a0 \u00a0 To understand and control complex systems, we must be\u2026","rel":"","context":"In &quot;Let's Do Biology!&quot;","block_context":{"text":"Let's Do Biology!","link":"https:\/\/biochemistry.khu.ac.kr\/lab\/?cat=33"},"img":{"alt_text":"","src":"","width":0,"height":0},"classes":[]},{"id":1121,"url":"https:\/\/biochemistry.khu.ac.kr\/lab\/?p=1121","url_meta":{"origin":2720,"position":5},"title":"Double trouble at the beginning of life","author":"biochemistry","date":"July 17, 2018","format":false,"excerpt":"\u00a0 \u00a0 (\uc6d0\ubb38: \uc5ec\uae30\ub97c \ud074\ub9ad\ud558\uc138\uc694~) \u00a0 Science\u00a0\u00a013 Jul 2018: Vol. 361, Issue 6398, pp. 128-129 DOI: 10.1126\/science.aau3216 \u00a0 \u00a0 Every human life begins with the fertilization of an egg (1). Once the egg and the sperm have fused, the parental chromosomes need to be united. To this end, the egg\u2026","rel":"","context":"In &quot;Let's Do Biology!&quot;","block_context":{"text":"Let's Do Biology!","link":"https:\/\/biochemistry.khu.ac.kr\/lab\/?cat=33"},"img":{"alt_text":"","src":"","width":0,"height":0},"classes":[]}],"jetpack_sharing_enabled":false,"jetpack_shortlink":"https:\/\/wp.me\/p9Xo1j-HS","_links":{"self":[{"href":"https:\/\/biochemistry.khu.ac.kr\/lab\/index.php?rest_route=\/wp\/v2\/posts\/2720","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/biochemistry.khu.ac.kr\/lab\/index.php?rest_route=\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/biochemistry.khu.ac.kr\/lab\/index.php?rest_route=\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/biochemistry.khu.ac.kr\/lab\/index.php?rest_route=\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/biochemistry.khu.ac.kr\/lab\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=2720"}],"version-history":[{"count":1,"href":"https:\/\/biochemistry.khu.ac.kr\/lab\/index.php?rest_route=\/wp\/v2\/posts\/2720\/revisions"}],"predecessor-version":[{"id":2721,"href":"https:\/\/biochemistry.khu.ac.kr\/lab\/index.php?rest_route=\/wp\/v2\/posts\/2720\/revisions\/2721"}],"wp:attachment":[{"href":"https:\/\/biochemistry.khu.ac.kr\/lab\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=2720"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/biochemistry.khu.ac.kr\/lab\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=2720"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/biochemistry.khu.ac.kr\/lab\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=2720"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}