{"id":152,"date":"2021-12-06T14:39:06","date_gmt":"2021-12-06T14:39:06","guid":{"rendered":"https:\/\/dataportal.hgdc.genouest.org\/?page_id=152"},"modified":"2022-06-29T11:37:42","modified_gmt":"2022-06-29T11:37:42","slug":"pipelines-tools","status":"publish","type":"page","link":"https:\/\/dataportal.hgdc.genouest.org\/?page_id=152","title":{"rendered":"Tools, pipelines &#038; protocols"},"content":{"rendered":"\t\t<div data-elementor-type=\"wp-page\" data-elementor-id=\"152\" class=\"elementor elementor-152\" data-elementor-settings=\"[]\">\n\t\t\t\t\t\t\t<div class=\"elementor-section-wrap\">\n\t\t\t\t\t\t\t<section class=\"elementor-section elementor-top-section elementor-element elementor-element-2ecd858d elementor-section-content-middle elementor-section-boxed elementor-section-height-default elementor-section-height-default\" data-id=\"2ecd858d\" data-element_type=\"section\" data-settings=\"{&quot;background_background&quot;:&quot;classic&quot;}\">\n\t\t\t\t\t\t<div class=\"elementor-container elementor-column-gap-no\">\n\t\t\t\t\t<div class=\"aux-parallax-section elementor-column elementor-col-50 elementor-top-column elementor-element elementor-element-5a8c890\" data-id=\"5a8c890\" data-element_type=\"column\">\n\t\t\t<div class=\"elementor-widget-wrap elementor-element-populated\">\n\t\t\t\t\t\t\t\t<div class=\"elementor-element elementor-element-9849991 elementor-widget elementor-widget-text-editor\" data-id=\"9849991\" data-element_type=\"widget\" data-widget_type=\"text-editor.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t<p>BIOIMAGERY<\/p>\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-411d3dd0 elementor-widget elementor-widget-heading\" data-id=\"411d3dd0\" data-element_type=\"widget\" data-widget_type=\"heading.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t<h3 class=\"elementor-heading-title elementor-size-default\">Keen Eye AI<br>Plateform<\/h3>\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-7cbcfe3e elementor-widget elementor-widget-text-editor\" data-id=\"7cbcfe3e\" data-element_type=\"widget\" data-widget_type=\"text-editor.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t<p>The Keen Eye Platform is a web-based plateform which can be used to visualize different types of bioimagery (TMA, whole slide, H&amp;E, IHC, multiplex, fluorescent, bright-field, 2D, 3D and more). It is used by the HUGODECA consortium to store and visualize in a fluid manner 2D and 3D image stacks, all as well as ISS cell maps with up to 10 million annotations on one image.<\/p>\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<section class=\"elementor-section elementor-inner-section elementor-element elementor-element-d57c82f elementor-section-boxed elementor-section-height-default elementor-section-height-default\" data-id=\"d57c82f\" data-element_type=\"section\">\n\t\t\t\t\t\t<div class=\"elementor-container elementor-column-gap-no\">\n\t\t\t\t\t<div class=\"aux-parallax-section elementor-column elementor-col-50 elementor-inner-column elementor-element elementor-element-5373c8a\" data-id=\"5373c8a\" data-element_type=\"column\">\n\t\t\t<div class=\"elementor-widget-wrap elementor-element-populated\">\n\t\t\t\t\t\t\t\t<div class=\"elementor-element elementor-element-611bdbb elementor-widget elementor-widget-aux_button\" data-id=\"611bdbb\" data-element_type=\"widget\" data-settings=\"{&quot;_animation&quot;:&quot;none&quot;}\" data-widget_type=\"aux_button.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t<button   class=\"aux-button aux-large aux-brick-red aux-none aux-uppercase\" ><span class=\"aux-overlay\"><\/span><span class=\"aux-text\">KEEN EYE PLATEFORM<\/span><\/button>\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t<\/div>\n\t\t\t\t<div class=\"aux-parallax-section elementor-column elementor-col-50 elementor-inner-column elementor-element elementor-element-eedb4ad\" data-id=\"eedb4ad\" data-element_type=\"column\">\n\t\t\t<div class=\"elementor-widget-wrap elementor-element-populated\">\n\t\t\t\t\t\t\t\t<div class=\"elementor-element elementor-element-283b619 elementor-widget elementor-widget-aux_button\" data-id=\"283b619\" data-element_type=\"widget\" data-widget_type=\"aux_button.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t<a  href=\"https:\/\/www.keeneye.ai\/our-platform\" target=\"_self\"   class=\"aux-button aux-large aux-brick-red aux-none aux-uppercase\" ><span class=\"aux-overlay\"><\/span><span class=\"aux-text\">LEARN MORE<\/span><\/a>\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t<\/div>\n\t\t\t\t\t\t\t<\/div>\n\t\t<\/section>\n\t\t\t\t<div class=\"elementor-element elementor-element-e701c52 elementor-widget elementor-widget-text-editor\" data-id=\"e701c52\" data-element_type=\"widget\" data-widget_type=\"text-editor.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t<h6>Authentication required<\/h6>\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t<\/div>\n\t\t\t\t<div class=\"aux-parallax-section elementor-column elementor-col-50 elementor-top-column elementor-element elementor-element-5f467cc4\" data-id=\"5f467cc4\" data-element_type=\"column\">\n\t\t\t<div class=\"elementor-widget-wrap elementor-element-populated\">\n\t\t\t\t\t\t\t\t<div class=\"elementor-element elementor-element-2c3b42f elementor-widget elementor-widget-image\" data-id=\"2c3b42f\" data-element_type=\"widget\" data-widget_type=\"image.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t<img decoding=\"async\" src=\"https:\/\/dataportal.hgdc.genouest.org\/wp-content\/uploads\/elementor\/thumbs\/KeenEye_Platform-po0xonvb5b9joaz1fz3ax56aqzzy5uu55t7t3zu7eo.png\" title=\"KeenEye_Platform\" alt=\"KeenEye_Platform\" \/>\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t<\/div>\n\t\t\t\t\t\t\t<\/div>\n\t\t<\/section>\n\t\t\t\t<section class=\"elementor-section elementor-top-section elementor-element elementor-element-5a52b376 elementor-section-content-middle elementor-section-boxed elementor-section-height-default elementor-section-height-default\" data-id=\"5a52b376\" data-element_type=\"section\" data-settings=\"{&quot;background_background&quot;:&quot;classic&quot;}\">\n\t\t\t\t\t\t<div class=\"elementor-container elementor-column-gap-no\">\n\t\t\t\t\t<div class=\"aux-parallax-section elementor-column elementor-col-50 elementor-top-column elementor-element elementor-element-7eade5c0\" data-id=\"7eade5c0\" data-element_type=\"column\">\n\t\t\t<div class=\"elementor-widget-wrap elementor-element-populated\">\n\t\t\t\t\t\t\t\t<div class=\"elementor-element elementor-element-d41b7ef elementor-widget elementor-widget-image\" data-id=\"d41b7ef\" data-element_type=\"widget\" data-widget_type=\"image.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t<img loading=\"lazy\" decoding=\"async\" width=\"487\" height=\"362\" src=\"https:\/\/dataportal.hgdc.genouest.org\/wp-content\/uploads\/2022\/05\/visualizer.png\" class=\"attachment-medium_large size-medium_large\" alt=\"\" \/>\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t<\/div>\n\t\t\t\t<div class=\"aux-parallax-section elementor-column elementor-col-50 elementor-top-column elementor-element elementor-element-73b5f2be\" data-id=\"73b5f2be\" data-element_type=\"column\">\n\t\t\t<div class=\"elementor-widget-wrap elementor-element-populated\">\n\t\t\t\t\t\t\t\t<div class=\"elementor-element elementor-element-a95c45a elementor-widget elementor-widget-text-editor\" data-id=\"a95c45a\" data-element_type=\"widget\" data-widget_type=\"text-editor.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t<p>GENE EXPRESSION<\/p>\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-d2f540a elementor-widget elementor-widget-heading\" data-id=\"d2f540a\" data-element_type=\"widget\" data-widget_type=\"heading.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t<h3 class=\"elementor-heading-title elementor-size-default\">genoViewer<\/h3>\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-8fb91dd elementor-widget elementor-widget-text-editor\" data-id=\"8fb91dd\" data-element_type=\"widget\" data-widget_type=\"text-editor.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t<p>The genoViewer can be used to explore and analyze&nbsp; single-cell or spatial transcriptomics datasets. It enables you to view the repartition of cells according to multiple criteria and to compare gene expression in human developmental cells.<\/p>\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<section class=\"elementor-section elementor-inner-section elementor-element elementor-element-cf58890 elementor-section-boxed elementor-section-height-default elementor-section-height-default\" data-id=\"cf58890\" data-element_type=\"section\">\n\t\t\t\t\t\t<div class=\"elementor-container elementor-column-gap-default\">\n\t\t\t\t\t<div class=\"aux-parallax-section elementor-column elementor-col-50 elementor-inner-column elementor-element elementor-element-c08ebcc\" data-id=\"c08ebcc\" data-element_type=\"column\">\n\t\t\t<div class=\"elementor-widget-wrap elementor-element-populated\">\n\t\t\t\t\t\t\t\t<div class=\"elementor-element elementor-element-ddc83cf elementor-widget elementor-widget-aux_button\" data-id=\"ddc83cf\" data-element_type=\"widget\" data-widget_type=\"aux_button.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t<a  href=\"https:\/\/hudeca-viewer.genouest.org\/\" target=\"_self\"   class=\"aux-button aux-large aux-brick-red aux-none aux-uppercase\" ><span class=\"aux-overlay\"><\/span><span class=\"aux-text\">BROWSE DATASETS<\/span><\/a>\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t<\/div>\n\t\t\t\t<div class=\"aux-parallax-section elementor-column elementor-col-50 elementor-inner-column elementor-element elementor-element-80a17b1\" data-id=\"80a17b1\" data-element_type=\"column\">\n\t\t\t<div class=\"elementor-widget-wrap elementor-element-populated\">\n\t\t\t\t\t\t\t\t<div class=\"elementor-element elementor-element-249c5e6 elementor-widget elementor-widget-aux_button\" data-id=\"249c5e6\" data-element_type=\"widget\" data-widget_type=\"aux_button.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t<a  href=\"https:\/\/github.com\/umr1085-irset\" target=\"_self\"   class=\"aux-button aux-large aux-brick-red aux-none aux-uppercase\" ><span class=\"aux-overlay\"><\/span><span class=\"aux-text\">SOURCE CODE<\/span><\/a>\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t<\/div>\n\t\t\t\t\t\t\t<\/div>\n\t\t<\/section>\n\t\t\t\t\t<\/div>\n\t\t<\/div>\n\t\t\t\t\t\t\t<\/div>\n\t\t<\/section>\n\t\t\t\t<section class=\"elementor-section elementor-top-section elementor-element elementor-element-f4500f0 elementor-section-content-middle elementor-section-boxed elementor-section-height-default elementor-section-height-default\" data-id=\"f4500f0\" data-element_type=\"section\" data-settings=\"{&quot;background_background&quot;:&quot;classic&quot;}\">\n\t\t\t\t\t\t<div class=\"elementor-container elementor-column-gap-no\">\n\t\t\t\t\t<div class=\"aux-parallax-section elementor-column elementor-col-50 elementor-top-column elementor-element elementor-element-c12e936\" data-id=\"c12e936\" data-element_type=\"column\">\n\t\t\t<div class=\"elementor-widget-wrap elementor-element-populated\">\n\t\t\t\t\t\t\t\t<div class=\"elementor-element elementor-element-7754168 elementor-widget elementor-widget-text-editor\" data-id=\"7754168\" data-element_type=\"widget\" data-widget_type=\"text-editor.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t<p>OMICS DATA &amp; BIOIMAGERY<\/p>\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-cfc962f elementor-widget elementor-widget-heading\" data-id=\"cfc962f\" data-element_type=\"widget\" data-widget_type=\"heading.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t<h3 class=\"elementor-heading-title elementor-size-default\">Scripts<br>&amp; Pipelines<\/h3>\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-f7de2a9 elementor-widget elementor-widget-text-editor\" data-id=\"f7de2a9\" data-element_type=\"widget\" data-widget_type=\"text-editor.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t<p>developped by the HuGoDeCA consortium<\/p>\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t<\/div>\n\t\t\t\t<div class=\"aux-parallax-section elementor-column elementor-col-50 elementor-top-column elementor-element elementor-element-51407f7\" data-id=\"51407f7\" data-element_type=\"column\">\n\t\t\t<div class=\"elementor-widget-wrap elementor-element-populated\">\n\t\t\t\t\t\t\t\t<div class=\"elementor-element elementor-element-b5c2895 elementor-widget elementor-widget-text-editor\" data-id=\"b5c2895\" data-element_type=\"widget\" data-widget_type=\"text-editor.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t<h2><a style=\"color: black;\" href=\"https:\/\/github.com\/umr1085-irset\/scrnaseq_standard_pipes\" target=\"_blank\" rel=\"noopener\"><span style=\"font-size: 16.0016px;\">Standard preprocessing and processing of scRNAseq data (UMR1085 INSERM)<\/span><\/a><\/h2>\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-004072b elementor-widget-divider--view-line elementor-widget elementor-widget-divider\" data-id=\"004072b\" data-element_type=\"widget\" data-widget_type=\"divider.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t<div class=\"elementor-divider\">\n\t\t\t<span class=\"elementor-divider-separator\">\n\t\t\t\t\t\t<\/span>\n\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-371d338 elementor-widget elementor-widget-text-editor\" data-id=\"371d338\" data-element_type=\"widget\" data-widget_type=\"text-editor.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t<h2><a style=\"color: black;\" href=\"https:\/\/github.com\/Moldia\"><span style=\"font-size: 16.0016px;\">Molecular diagnosis &#8211; Scripts &amp; pipelines for ISS data (Mats Nilsson research group)<\/span><\/a><\/h2>\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-1baa6be elementor-widget-divider--view-line elementor-widget elementor-widget-divider\" data-id=\"1baa6be\" data-element_type=\"widget\" data-widget_type=\"divider.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t<div class=\"elementor-divider\">\n\t\t\t<span class=\"elementor-divider-separator\">\n\t\t\t\t\t\t<\/span>\n\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t<\/div>\n\t\t\t\t\t\t\t<\/div>\n\t\t<\/section>\n\t\t\t\t<section class=\"elementor-section elementor-top-section elementor-element elementor-element-23125a9 elementor-section-content-middle elementor-section-boxed elementor-section-height-default elementor-section-height-default\" data-id=\"23125a9\" data-element_type=\"section\" data-settings=\"{&quot;background_background&quot;:&quot;classic&quot;}\">\n\t\t\t\t\t\t<div class=\"elementor-container elementor-column-gap-no\">\n\t\t\t\t\t<div class=\"aux-parallax-section elementor-column elementor-col-50 elementor-top-column elementor-element elementor-element-4f52016\" data-id=\"4f52016\" data-element_type=\"column\">\n\t\t\t<div class=\"elementor-widget-wrap elementor-element-populated\">\n\t\t\t\t\t\t\t\t<div class=\"elementor-element elementor-element-54d57d6 elementor-widget elementor-widget-heading\" data-id=\"54d57d6\" data-element_type=\"widget\" data-widget_type=\"heading.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t<h3 class=\"elementor-heading-title elementor-size-default\">Protocols<\/h3>\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-0c4681e elementor-widget elementor-widget-text-editor\" data-id=\"0c4681e\" data-element_type=\"widget\" data-widget_type=\"text-editor.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t<p>applied to prepare the samples<\/p>\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t<\/div>\n\t\t\t\t<div class=\"aux-parallax-section elementor-column elementor-col-50 elementor-top-column elementor-element elementor-element-07313eb\" data-id=\"07313eb\" data-element_type=\"column\">\n\t\t\t<div class=\"elementor-widget-wrap elementor-element-populated\">\n\t\t\t\t\t\t\t\t<div class=\"elementor-element elementor-element-138873d elementor-widget elementor-widget-toggle\" data-id=\"138873d\" data-element_type=\"widget\" data-widget_type=\"toggle.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t<div class=\"elementor-toggle\" role=\"tablist\">\n\t\t\t\t\t\t\t<div class=\"elementor-toggle-item\">\n\t\t\t\t\t<div id=\"elementor-tab-title-2041\" class=\"elementor-tab-title\" data-tab=\"1\" role=\"tab\" aria-controls=\"elementor-tab-content-2041\" aria-expanded=\"false\">\n\t\t\t\t\t\t\t\t\t\t\t\t<span class=\"elementor-toggle-icon elementor-toggle-icon-left\" aria-hidden=\"true\">\n\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t<span class=\"elementor-toggle-icon-closed\"><i class=\"fas fa-caret-right\"><\/i><\/span>\n\t\t\t\t\t\t\t\t<span class=\"elementor-toggle-icon-opened\"><i class=\"elementor-toggle-icon-opened fas fa-caret-up\"><\/i><\/span>\n\t\t\t\t\t\t\t\t\t\t\t\t\t<\/span>\n\t\t\t\t\t\t\t\t\t\t\t\t<a href=\"\" class=\"elementor-toggle-title\">A simple method of 3D analysis of Immunolabeled Axonal Tracts in a Transparent Nervous System<\/a>\n\t\t\t\t\t<\/div>\n\n\t\t\t\t\t<div id=\"elementor-tab-content-2041\" class=\"elementor-tab-content elementor-clearfix\" data-tab=\"1\" role=\"tabpanel\" aria-labelledby=\"elementor-tab-title-2041\">Clearing techniques have been developed to transparentize mouse brains, thereby preserving 3D structure, but their complexity has limited their use. Here, we show that immunolabeling of axonal tracts followed by optical clearing with solvents (3DISCO) and light-sheet microscopy reveals brain connectivity in mouse embryos and postnatal brains. We show that the Robo3 receptor is selectively expressed by medial habenula axons forming the fasciculus retroflexus (FR) and analyzed the development of this commissural tract in mutants of the Slit\/Robo and DCC\/Netrin pathways. Netrin-1 and DCC are required to attract FR axons to the midline, but the two mutants exhibit specific and heterogeneous axon guidance defects. Moreover, floor-plate-specific deletion of Slit ligands with a conditional Slit2 allele perturbs not only midline crossing by FR axons but also their anteroposterior distribution. In conclusion, this method represents a unique and powerful imaging tool to study axonal connectivity in mutant mice.\n<br \/>\n<span style=\"font-size: 12px;\">Morgane Belle, David Godefroy, Chlo\u00e9 Dominici, C\u00e9line Heitz-Marchaland, Pavol Zelina, Farida Hellal, Frank Bradke, Alain Ch\u00e9dotal<\/span>\n<br \/>\nDOI : <a href=\"https:\/\/doi.org\/10.1016\/j.celrep.2014.10.037\">https:\/\/doi.org\/10.1016\/j.celrep.2014.10.037<\/a>\n\nLICENCE : CC BY 3.0<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t\t\t\t<div class=\"elementor-toggle-item\">\n\t\t\t\t\t<div id=\"elementor-tab-title-2042\" class=\"elementor-tab-title\" data-tab=\"2\" role=\"tab\" aria-controls=\"elementor-tab-content-2042\" aria-expanded=\"false\">\n\t\t\t\t\t\t\t\t\t\t\t\t<span class=\"elementor-toggle-icon elementor-toggle-icon-left\" aria-hidden=\"true\">\n\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t<span class=\"elementor-toggle-icon-closed\"><i class=\"fas fa-caret-right\"><\/i><\/span>\n\t\t\t\t\t\t\t\t<span class=\"elementor-toggle-icon-opened\"><i class=\"elementor-toggle-icon-opened fas fa-caret-up\"><\/i><\/span>\n\t\t\t\t\t\t\t\t\t\t\t\t\t<\/span>\n\t\t\t\t\t\t\t\t\t\t\t\t<a href=\"\" class=\"elementor-toggle-title\">Human embryonic gonad dissociation with Trypsin-EDTA<\/a>\n\t\t\t\t\t<\/div>\n\n\t\t\t\t\t<div id=\"elementor-tab-content-2042\" class=\"elementor-tab-content elementor-clearfix\" data-tab=\"2\" role=\"tabpanel\" aria-labelledby=\"elementor-tab-title-2042\"><!--StartFragment-->Protocol for enrichment of fetal gonadal cells<!--EndFragment-->\n<br \/>\n<span style=\"font-size: 12px;\">Regina Hoo,\u00a0Roser Vento-Tormo,\u00a0Carmen Sancho<\/span>\n<br \/>\nDOI : <a href=\"http:\/\/dx.doi.org\/10.17504\/protocols.io.66fhhbn\">dx.doi.org\/10.17504\/protocols.io.66fhhbn<\/a>\n\nLICENCE : CC BY 4.0<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t\t\t\t<div class=\"elementor-toggle-item\">\n\t\t\t\t\t<div id=\"elementor-tab-title-2043\" class=\"elementor-tab-title\" data-tab=\"3\" role=\"tab\" aria-controls=\"elementor-tab-content-2043\" aria-expanded=\"false\">\n\t\t\t\t\t\t\t\t\t\t\t\t<span class=\"elementor-toggle-icon elementor-toggle-icon-left\" aria-hidden=\"true\">\n\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t<span class=\"elementor-toggle-icon-closed\"><i class=\"fas fa-caret-right\"><\/i><\/span>\n\t\t\t\t\t\t\t\t<span class=\"elementor-toggle-icon-opened\"><i class=\"elementor-toggle-icon-opened fas fa-caret-up\"><\/i><\/span>\n\t\t\t\t\t\t\t\t\t\t\t\t\t<\/span>\n\t\t\t\t\t\t\t\t\t\t\t\t<a href=\"\" class=\"elementor-toggle-title\">Purification of HMW DNA from Fungi for long read sequencing<\/a>\n\t\t\t\t\t<\/div>\n\n\t\t\t\t\t<div id=\"elementor-tab-content-2043\" class=\"elementor-tab-content elementor-clearfix\" data-tab=\"3\" role=\"tabpanel\" aria-labelledby=\"elementor-tab-title-2043\"><div class=\" _protocols-io-draft-unstyled\" data-block=\"true\" data-editor=\"desc-draft-abstract\" data-offset-key=\"bo7pg-0-0\">\n<div class=\"public-DraftStyleDefault-block public-DraftStyleDefault-ltr\" data-offset-key=\"bo7pg-0-0\"><span data-offset-key=\"bo7pg-0-0\">Current long read sequencing, e. g. PacBio and Nanopore, requires high molecular weight (HMW) and highly pure DNA. Many fungal and plant species have high content of polysaccharides and other contaminants that are co-precipitated with DNA during ethanol precipitation. This protocol aims to purify HMW DNA from the DNA solution obtained using <a href=\"http:\/\/dx.doi.org\/10.17504\/protocols.io.ewtbfen\">Benjamin Schwessinger&#8217;s protocol<\/a>. T<\/span><span style=\"font-size: 16.0016px;\" data-offset-key=\"4ahh1-0-0\">he protocol was tested fuccessfully in wheat leaf rust, barley leaf rust, wheat stem rust and myrtle rust.\u00a0<\/span><span style=\"font-size: 16.0016px;\">Critcal step to seperate HMW DNA from low molecular weight DNA and other contaminants during ethanol precipitation is to allow cotton-fiber-like HMW DNA to sediment by gravity, while other small molecule DNA and contaminants remain in the supernatant.<\/span><\/div>\n<\/div>\n<span style=\"font-size: 12px;\">Chongmei Dong<\/span>\n<br \/>\nDOI : <a href=\"http:\/\/dx.doi.org\/10.17504\/protocols.io.hbvb2n6\">dx.doi.org\/10.17504\/protocols.io.66fhhbn<\/a>\n\nLICENCE : CC BY 4.0<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t<\/div>\n\t\t\t\t\t\t\t<\/div>\n\t\t<\/section>\n\t\t\t\t\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t","protected":false},"excerpt":{"rendered":"<p>BIOIMAGERY Keen Eye AIPlateform The Keen Eye Platform is a web-based plateform which can be used to visualize different types of bioimagery (TMA, whole slide, H&amp;E, IHC, multiplex, fluorescent, bright-field, 2D, 3D and more). It is used by the HUGODECA consortium to store and visualize in a fluid manner 2D and 3D image stacks, all [&hellip;]<\/p>\n","protected":false},"author":1,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"elementor_header_footer","meta":{"footnotes":""},"class_list":["post-152","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/dataportal.hgdc.genouest.org\/index.php?rest_route=\/wp\/v2\/pages\/152","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/dataportal.hgdc.genouest.org\/index.php?rest_route=\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/dataportal.hgdc.genouest.org\/index.php?rest_route=\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/dataportal.hgdc.genouest.org\/index.php?rest_route=\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/dataportal.hgdc.genouest.org\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=152"}],"version-history":[{"count":207,"href":"https:\/\/dataportal.hgdc.genouest.org\/index.php?rest_route=\/wp\/v2\/pages\/152\/revisions"}],"predecessor-version":[{"id":717,"href":"https:\/\/dataportal.hgdc.genouest.org\/index.php?rest_route=\/wp\/v2\/pages\/152\/revisions\/717"}],"wp:attachment":[{"href":"https:\/\/dataportal.hgdc.genouest.org\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=152"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}