{"id":12,"date":"2019-10-07T16:05:28","date_gmt":"2019-10-07T16:05:28","guid":{"rendered":"https:\/\/fs-s-wpmu-03.facsci.ualberta.ca\/ephybase\/?page_id=12"},"modified":"2026-03-23T00:16:44","modified_gmt":"2026-03-23T00:16:44","slug":"resources","status":"publish","type":"page","link":"https:\/\/spaces.facsci.ualberta.ca\/ephybase\/resources\/","title":{"rendered":"Resources"},"content":{"rendered":"\t\t<div data-elementor-type=\"wp-page\" data-elementor-id=\"12\" class=\"elementor elementor-12\">\n\t\t\t\t\t\t<section class=\"elementor-section elementor-top-section elementor-element elementor-element-701b379d elementor-section-boxed elementor-section-height-default elementor-section-height-default\" data-id=\"701b379d\" data-element_type=\"section\" data-e-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=\"elementor-column elementor-col-100 elementor-top-column elementor-element elementor-element-6aab3223\" data-id=\"6aab3223\" data-element_type=\"column\" data-e-type=\"column\">\n\t\t\t<div class=\"elementor-widget-wrap elementor-element-populated\">\n\t\t\t\t\t\t<div class=\"elementor-element elementor-element-5e2f0510 elementor-widget elementor-widget-text-editor\" data-id=\"5e2f0510\" data-element_type=\"widget\" data-e-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\t\t<p><em>F<\/em>Resources<\/p><h2>Genome assembly, gene models and sequences<\/h2><ul><li><a href=\"https:\/\/bitbucket.org\/EphydatiaGenome\/ephydatiagenome\/downloads\/Emu_genome_v1.fa.gz\">Genome assembly (gzipped .fa)<\/a><br \/><em>Assembly of <span style=\"text-decoration: underline\">Ephydatia muelleri<\/span> genome<\/em><\/li><li><a href=\"https:\/\/bitbucket.org\/EphydatiaGenome\/ephydatiagenome\/downloads\/Emu_genome_v1.gff.gz\">Gene models (gff)<\/a><br \/><em>Gene models in gff format, giving co-ordinates and content<br \/><\/em><\/li><li>Gene sequences (<a href=\"https:\/\/bitbucket.org\/EphydatiaGenome\/ephydatiagenome\/downloads\/Emu_v1_prots.fasta.gz\">aa<\/a>, <a href=\"https:\/\/bitbucket.org\/EphydatiaGenome\/ephydatiagenome\/downloads\/Emu_genome_v1.codingseq.gz\">cds<\/a>, <a href=\"https:\/\/bitbucket.org\/EphydatiaGenome\/ephydatiagenome\/downloads\/Emu_genome_v1.mrna.gz\">mRNA<\/a>, <a href=\"https:\/\/bitbucket.org\/EphydatiaGenome\/ephydatiagenome\/downloads\/Emu_genome_v1.cdsexons.gz\">exons<\/a>)<br \/><em>Assorted sequence files representing genome contents<br \/><\/em><\/li><li><a href=\"https:\/\/bitbucket.org\/EphydatiaGenome\/ephydatiagenome\/downloads\/Emu_genome_v1.masked.gz\">Masked version of genome<\/a> (hard masked)<br \/><em>Repetitive sequence within genome masked as &#8216;N&#8217;<br \/><\/em><\/li><li><a href=\"http:\/\/ephydatia.biology.ualberta.ca\/jbrowse\/\" target=\"_blank\" rel=\"noopener\">jBROWSE website<\/a><br \/><em>Browsable version of the <\/em>E. muelleri<em> genome<\/em><\/li><li><a href=\"http:\/\/ephydatia.biology.ualberta.ca\/viroblast-p\/viroblast.php\" target=\"_blank\" rel=\"noopener\">BLAST server<\/a><br \/><em>Blastable version of the <\/em>E. muelleri<em> genome and protein set<\/em><\/li><li>RNAseq data: Differential gene expression: <a href=\"https:\/\/bitbucket.org\/EphydatiaGenome\/ephydatiagenome\/downloads\/Stage5VSStage3VSStage2VSStage1_Transcript_differential_expression.xlsx\">Transcript<\/a> and <a href=\"https:\/\/bitbucket.org\/EphydatiaGenome\/ephydatiagenome\/downloads\/Stage5VSStage3VSStage2VSStage1_Gene_differential_expression.xlsx\">Gene\u00a0<\/a><\/li><li><a href=\"https:\/\/borealisdata.ca\/dataset.xhtml?persistentId=doi:10.5683\/SP3\/UKHX6R\" target=\"_blank\" rel=\"noopener\">Raw RNAseq reads<\/a>\u00a0(associated with the above Transcript\/Gene data from Kenny et al 2020)<\/li><\/ul><h2>Paper and supplementary files<\/h2><ul><li>Genome paper: <a href=\"https:\/\/www.nature.com\/articles\/s41467-020-17397-w?utm_campaign=MultipleJournals_USG_ECOEVO&amp;utm_source=Nature_community&amp;utm_medium=Community_sites&amp;utm_content=BenJoh-Nature-MultipleJournals-Evolutionary_Biology-Global\">Nature Communications<\/a><br \/><em>Main text of paper describing the genome of<\/em> E. muelleri<\/li><li><a href=\"https:\/\/bitbucket.org\/EphydatiaGenome\/ephydatiagenome\/downloads\/Supplementary_Information_Notes_1-11.pdf\">Supplementary Information Fil<\/a><a href=\"https:\/\/bitbucket.org\/EphydatiaGenome\/ephydatiagenome\/downloads\/Supplementary_Information_Notes_1-11.pdf\">e<\/a> (contains Supplementary Notes 1-11)<\/li><li><a href=\"https:\/\/bitbucket.org\/EphydatiaGenome\/ephydatiagenome\/downloads\/Supplementary_Data_1.zip\">Supplementary Data 1<\/a>: <i>Flavobacterium<\/i> sp. sequence, predicted proteins and cds sequences\u00a0<\/li><li><a href=\"https:\/\/bitbucket.org\/EphydatiaGenome\/ephydatiagenome\/downloads\/Supplementary_Data_2.zip\">Supplementary Data 2<\/a>: BLAST\/functional annotation results, <em>Ephydatia muelleri<\/em> gene annotations<\/li><li><a href=\"https:\/\/bitbucket.org\/EphydatiaGenome\/ephydatiagenome\/downloads\/Supplementary_Data_3.zip\">Supplementary Data 3<\/a>: Comparative genome statistics and scripts used in generating figures\u00a0<\/li><li><a href=\"https:\/\/bitbucket.org\/EphydatiaGenome\/ephydatiagenome\/downloads\/Supplementary_Data_4.zip\">Supplementary Data 4<\/a>: Synteny analysis, additional plots and data<\/li><li><a href=\"https:\/\/bitbucket.org\/EphydatiaGenome\/ephydatiagenome\/downloads\/Supplementary_Data_5.zip\">Supplementary Data 5<\/a>: Full lists of genes, gain\/loss analyses<\/li><li><a href=\"https:\/\/bitbucket.org\/EphydatiaGenome\/ephydatiagenome\/downloads\/Supplementary_Data_6.zip\">Supplementary Data 6<\/a>: Full results and orthogroups, positive selection analyses <a href=\"https:\/\/bitbucket.org\/EphydatiaGenome\/ephydatiagenome\/downloads\/Supplementary_Data_6_extended.zip\">(and more<\/a>)<\/li><li><a href=\"https:\/\/bitbucket.org\/EphydatiaGenome\/ephydatiagenome\/downloads\/Supplementary_Data_7.zip\">Supplementary Data 7<\/a>: Clustering analyses, lists of genes in each cluster (<a href=\"https:\/\/bitbucket.org\/EphydatiaGenome\/ephydatiagenome\/downloads\/Supplementary_Data_7_extended.zip\">and with original fasta here<\/a>)<\/li><li><a href=\"https:\/\/bitbucket.org\/EphydatiaGenome\/ephydatiagenome\/downloads\/Supplementary_Data_8.zip\">Supplementary Data 8<\/a>: SNARE data, full gene sequences and annotation<\/li><li><a href=\"https:\/\/bitbucket.org\/EphydatiaGenome\/ephydatiagenome\/downloads\/Supplementary_Data_9.zip\">Supplementary Data 9<\/a>: Amplicon sequencing data, raw and intermediate results<\/li><li>High quality versions of all figures are available <a href=\"https:\/\/bitbucket.org\/EphydatiaGenome\/ephydatiagenome\/downloads\/HighQualityFigures.zip\">here<\/a><\/li><li>In case of issues with the above links, a mirror of the data is available <a href=\"https:\/\/doi.org\/10.6084\/m9.figshare.11847195\" target=\"_blank\" rel=\"noopener\">here<\/a><\/li><\/ul><h2>Additional resources<\/h2><ul><li><a href=\"https:\/\/communities.springernature.com\/posts\/chromosomal-level-genome-provides-an-encyclopedia-of-animal-evolution-and-adaptation-to-freshwater\">\u00a0Behind the paper<\/a> &#8211; a blog describing how this research unfolded<\/li><li><a href=\"https:\/\/youtu.be\/lcY9043eG9M\">&#8216;Sneezing&#8217; <em>Ephydatia muelleri<\/em><\/a><br \/><em>Inflation-contraction responses in response to stimuli<br \/><\/em><\/li><li>Useful papers: a community resource<br \/>A <a href=\"https:\/\/link.springer.com\/article\/10.1186\/s13227-025-00237-7\">Morphological Cell Atlas<\/a> of Ephydatia muelleri &#8211; Provides many images showing the morphology of the sponge and describing their function. This paper also includes single cell RNAseq data for choanocytes, archaeocytes and cystencytes. That data is available <a href=\"https:\/\/zenodo.org\/records\/10998268\">here<\/a>.<\/li><li><a href=\"https:\/\/link.springer.com\/article\/10.1007\/s13199-023-00934-8\">Algal symbiosis paper<\/a> from April Horton&#8217;s lab\u00a0<\/li><li><a href=\"https:\/\/leyslab.weebly.com\/publications.html\">A variety of papers<\/a> from the Leys lab<em><a href=\"https:\/\/leyslab.weebly.com\/publication-list.html\" target=\"_blank\" rel=\"noopener\"> <br \/><\/a>And <a href=\"https:\/\/leyslab.weebly.com\/uploads\/5\/4\/9\/4\/54947267\/freshwater_sponge_references.pdf\" target=\"_blank\" rel=\"noopener\">freshwater sponges<\/a> in particular<\/em><\/li><li><a href=\"https:\/\/leyslab.weebly.com\/data-available.html\" target=\"_blank\" rel=\"noopener\">Other sponge data &amp; videos<\/a><ul><li><a href=\"https:\/\/leyslab.weebly.com\/data-available.html\">Other Sponge transcriptomes<\/a><\/li><li><em><a href=\"https:\/\/doi.org\/10.7939\/r3-7jk2-ph04\">Ephydatia muelleri<\/a>\u00a0<\/em>Algal symbiosis transcriptomes<\/li><\/ul><\/li><\/ul><h2>Mirror download site<\/h2><div><ul><li>\u00a0In case of issues with the above links, a mirror of the data is available <a href=\"https:\/\/doi.org\/10.6084\/m9.figshare.11847195\" target=\"_blank\" rel=\"noopener\">here<\/a>nts\u00a0<\/li><\/ul><\/div>\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<\/div>\n\t\t<\/section>\n\t\t\t\t<\/div>\n\t\t","protected":false},"excerpt":{"rendered":"<p>FResources Genome assembly, gene models and sequences Genome assembly (gzipped .fa)Assembly of Ephydatia muelleri genome Gene models (gff)Gene models in gff format, giving co-ordinates and content Gene sequences (aa, cds, mRNA, exons)Assorted sequence files representing genome contents Masked version of genome (hard masked)Repetitive sequence within genome masked as &#8216;N&#8217; jBROWSE websiteBrowsable version of the E&#8230;.<\/p>\n","protected":false},"author":1,"featured_media":0,"parent":0,"menu_order":2,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-12","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/spaces.facsci.ualberta.ca\/ephybase\/wp-json\/wp\/v2\/pages\/12","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/spaces.facsci.ualberta.ca\/ephybase\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/spaces.facsci.ualberta.ca\/ephybase\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/spaces.facsci.ualberta.ca\/ephybase\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/spaces.facsci.ualberta.ca\/ephybase\/wp-json\/wp\/v2\/comments?post=12"}],"version-history":[{"count":57,"href":"https:\/\/spaces.facsci.ualberta.ca\/ephybase\/wp-json\/wp\/v2\/pages\/12\/revisions"}],"predecessor-version":[{"id":362,"href":"https:\/\/spaces.facsci.ualberta.ca\/ephybase\/wp-json\/wp\/v2\/pages\/12\/revisions\/362"}],"wp:attachment":[{"href":"https:\/\/spaces.facsci.ualberta.ca\/ephybase\/wp-json\/wp\/v2\/media?parent=12"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}