{"id":3707,"date":"2015-04-14T11:55:11","date_gmt":"2015-04-14T09:55:11","guid":{"rendered":"http:\/\/news.embl.de\/?p=3707"},"modified":"2024-11-29T16:54:08","modified_gmt":"2024-11-29T15:54:08","slug":"1504-brain-atlas","status":"publish","type":"post","link":"https:\/\/www.embl.org\/news\/science\/1504-brain-atlas\/","title":{"rendered":"Towards an expression atlas for an entire brain"},"content":{"rendered":"\n<p><a href=\"http:\/\/www.ebi.ac.uk\/research\/marioni\">John Marioni<\/a> of EMBL-EBI and <a href=\"http:\/\/www.embl.de\/research\/units\/dev_biology\/arendt\/\">Detlev Arendt<\/a> of EMBL Heidelberg set out to augment an atlas of gene expression in the brain of a marine worm,&nbsp;<em>Platynereis dumerilii,<\/em>&nbsp;using single-cell RNA sequencing (RNAseq). The original atlas, constructed by the Arendt group, represents the expression patterns of around 170 genes in the worm brain at a specific point in development, all linked to their location.<\/p>\n\n\n\n<p>Organisms and tissues are not just a random mash of different types of cells \u2013 they are organised in a manner that facilitates specific functions. To understand how they work, it is important to establish both their genetic profiles and their precise spatial organisation.<\/p>\n\n\n\n<p>Marioni explains: \u201cSingle-cell sequencing generates expression profiles on a large scale, but these profiles are dissociated from the cells\u2019 spatial location. That has been incredibly useful for discovering new cell types, but to understand how gene expression varies within cell types in living things, we do need to link each cell\u2019s full expression profile with its specific location. That will allow us to explore, for a particular gene, how its expression profile changes across a tissue \u2013 and that will tell us a lot about how cell types function, how they interact with one another and how they evolved.\u201d<\/p>\n\n\n\n<blockquote class=\"vf-blockquote\"><p>To understand how gene expression varies within cell types in living things, we do need to link each cell\u2019s full expression profile with its specific location.<\/p><\/blockquote>\n\n\n\n<p>In 2010, Detlev\u2019s group published a meticulous 3D map of gene expression patterns in a relatively small number of genes. To augment the resource with thousands of genes expression profiles, the team back-mapped single-cell genomics data to the original atlas.<\/p>\n\n\n\n<p>\u201cIn our in situ hybridisation experiments, we knew exactly where the cells were coming from. We were able to determine their expression patterns computationally, but on a fairly modest scale,\u201d says Arendt. \u201cTo grasp what is going on throughout the tissue, we needed to be working on a much larger scale, and single-cell RNAseq offered that possibility. But with typical single-cell RNAseq experiments, you don\u2019t have that detailed knowledge of where the cells are coming from.\u201d<\/p>\n\n\n\n<p>\u201cWe had data on the expression patterns of thousands of genes, but to find out where those cells are located spatially we had to compare their profiles to those in the Atlas for every cell we ran,\u201d adds Marioni. \u201cThat told us which location in the reference atlas each cell most closely matched.\u201d<\/p>\n\n\n\n<p>The method allowed the researchers to match quantitative and spatial data, increasing by several orders of magnitude the number of markers that indicate specific cell types within a tissue. As a result, a wider pattern can start to emerge.<\/p>\n\n\n\n<p>\u201cMy group focuses on this particular species to understand how the brain has evolved, but you could apply our method to any system that has a good reference gene expression database,\u201d says Arendt.<\/p>\n\n\n\n<blockquote class=\"vf-blockquote\"><p>You could apply our method to any system that has a good reference gene expression database.<\/p><\/blockquote>\n\n\n\n<p>\u201cFrom the technical point of view, the simplicity and robustness of the method is very appealing \u2013 we achieved very high precision with a relatively low number of reference genes,\u201d says Kaia Achim, a fellow in&nbsp;<a title=\"EIPOD programme\" href=\"http:\/\/www.embl.de\/training\/postdocs\/08-eipod\/index.html\" target=\"_blank\" rel=\"noopener noreferrer\">EMBL&#8217;s Interdisciplinary Postdocs (EIPOD) programme<\/a>. \u201cPotentially, our method could be used to investigate how and in which aspects gene expression patterns are stereotypical across different individuals and even species.\u201d<\/p>\n\n\n\n<p>\u201cThis will make a big difference in the resources available to smaller research communities that study evolution at a very fundamental level,\u201d says Marioni. \u201cThe technology will help people gain much deeper insights into what\u2019s going on in these non-model systems, and tell us a lot about how animals have evolved and what is mutable in nature. And that is pretty exciting.\u201d<\/p>\n\n\n\n<p><em>This post was originally published on <a href=\"https:\/\/www.ebi.ac.uk\/about\/news\/press-releases\/towards-expression-atlas-entire-brain\" target=\"_blank\" rel=\"canonical nofollow noopener noreferrer\" data-href=\"https:\/\/www.ebi.ac.uk\/about\/news\/press-releases\/towards-expression-atlas-entire-brain\">EMBL-EBI News.<\/a><\/em><\/p>\n","protected":false},"excerpt":{"rendered":"<p>New single-cell genomics techniques bring \u2018omics to evolution and development research.<\/p>\n","protected":false},"author":13,"featured_media":3709,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"_acf_changed":false,"footnotes":""},"categories":[2,17591],"tags":[417,31,183,42,408,184,57],"embl_taxonomy":[],"class_list":["post-3707","post","type-post","status-publish","format-standard","has-post-thumbnail","hentry","category-science","category-science-technology","tag-arendt","tag-evolution","tag-gene-expression","tag-genomics","tag-marioni","tag-model-organism","tag-postdoc"],"acf":{"article_intro":"<p>Researchers who study how genes are expressed across a given tissue can now examine thousands of genes at once at cellular resolution, thanks to new methods developed at EMBL and published in <em>Nature Biotechnology<\/em>. The new techniques can be applied to a broad range of organisms, and expand the resources available for evolution-and-development research.<\/p>\n","related_links":false,"article_sources":[{"source_description":"<p>Achim K\u00a0<em>et al.\u00a0Nature Biotechnology,<\/em> 13 April 2015\u00a0DOI: 10.1038\/nbt.3209<\/p>\n","source_link_url":"http:\/\/dx.doi.org\/10.1038\/nbt.3209"}],"vf_locked":false,"featured":false,"color":"#007B53"},"embl_taxonomy_terms":[],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v26.2 - https:\/\/yoast.com\/wordpress\/plugins\/seo\/ -->\n<title>Towards an expression atlas for an entire brain | EMBL<\/title>\n<meta name=\"description\" content=\"New single-cell genomics techniques bring \u2018omics to evolution and development research.\" \/>\n<meta name=\"robots\" content=\"index, follow, max-snippet:-1, max-image-preview:large, max-video-preview:-1\" \/>\n<link rel=\"canonical\" href=\"https:\/\/www.embl.org\/news\/science\/1504-brain-atlas\/\" \/>\n<meta property=\"og:locale\" content=\"en_US\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Towards an expression atlas for an entire brain | EMBL\" \/>\n<meta property=\"og:description\" content=\"New single-cell genomics techniques bring \u2018omics to evolution and development research.\" \/>\n<meta property=\"og:url\" content=\"https:\/\/www.embl.org\/news\/science\/1504-brain-atlas\/\" \/>\n<meta property=\"og:site_name\" content=\"EMBL\" \/>\n<meta property=\"article:publisher\" content=\"https:\/\/www.facebook.com\/embl.org\/\" \/>\n<meta property=\"article:author\" content=\"www.facebook.com\/EMBLEBI\" \/>\n<meta property=\"article:published_time\" content=\"2015-04-14T09:55:11+00:00\" \/>\n<meta property=\"article:modified_time\" content=\"2024-11-29T15:54:08+00:00\" \/>\n<meta property=\"og:image\" content=\"https:\/\/www.embl.org\/news\/wp-content\/uploads\/2015\/04\/CELLS_3um_2015_EMBL-e1429782584129.jpg\" \/>\n\t<meta property=\"og:image:width\" content=\"620\" \/>\n\t<meta property=\"og:image:height\" content=\"424\" \/>\n\t<meta property=\"og:image:type\" content=\"image\/jpeg\" \/>\n<meta name=\"author\" content=\"Mary Todd Bergman\" \/>\n<meta name=\"twitter:card\" content=\"summary_large_image\" \/>\n<meta name=\"twitter:creator\" content=\"@EMBLEBI\" \/>\n<meta name=\"twitter:site\" content=\"@embl\" \/>\n<meta name=\"twitter:label1\" content=\"Written by\" \/>\n\t<meta name=\"twitter:data1\" content=\"Mary Todd Bergman\" \/>\n\t<meta name=\"twitter:label2\" content=\"Est. reading time\" \/>\n\t<meta name=\"twitter:data2\" content=\"3 minutes\" \/>\n<script type=\"application\/ld+json\" class=\"yoast-schema-graph\">{\"@context\":\"https:\/\/schema.org\",\"@graph\":[{\"@type\":\"NewsArticle\",\"@id\":\"https:\/\/www.embl.org\/news\/science\/1504-brain-atlas\/#article\",\"isPartOf\":{\"@id\":\"https:\/\/www.embl.org\/news\/science\/1504-brain-atlas\/\"},\"author\":{\"name\":\"Mary Todd Bergman\",\"@id\":\"https:\/\/www.embl.org\/news\/#\/schema\/person\/052a43af2beb3860bffa67c0f0474875\"},\"headline\":\"Towards an expression atlas for an entire brain\",\"datePublished\":\"2015-04-14T09:55:11+00:00\",\"dateModified\":\"2024-11-29T15:54:08+00:00\",\"mainEntityOfPage\":{\"@id\":\"https:\/\/www.embl.org\/news\/science\/1504-brain-atlas\/\"},\"wordCount\":637,\"publisher\":{\"@id\":\"https:\/\/www.embl.org\/news\/#organization\"},\"image\":{\"@id\":\"https:\/\/www.embl.org\/news\/science\/1504-brain-atlas\/#primaryimage\"},\"thumbnailUrl\":\"https:\/\/www.embl.org\/news\/wp-content\/uploads\/2015\/04\/CELLS_3um_2015_EMBL-e1429782584129.jpg\",\"keywords\":[\"arendt\",\"evolution\",\"gene expression\",\"genomics\",\"marioni\",\"model organism\",\"postdoc\"],\"articleSection\":[\"Science\",\"Science &amp; 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