{"id":14,"date":"2016-04-05T21:59:11","date_gmt":"2016-04-05T21:59:11","guid":{"rendered":"http:\/\/projects.nib.si\/podefsig\/?page_id=14"},"modified":"2018-03-19T14:16:24","modified_gmt":"2018-03-19T13:16:24","slug":"datasets","status":"publish","type":"page","link":"https:\/\/projects.nib.si\/podefsig\/datasets\/","title":{"rendered":"Datasets"},"content":{"rendered":"<p><strong>Supplemental Online Files<\/strong> for the\u00a0manuscript\u00a0entitled &#8220;Salicylic acid perturbs sRNA-gibberellin regulatory network in immune response of potato to <em>Potato virus Y<\/em> infection&#8221; submitted to\u00a0Frontiers in Plant Science:<\/p>\n<ul>\n<li><strong><a href=\"http:\/\/projects.nib.si\/podefsig\/wp-content\/uploads\/sites\/14\/2017\/11\/Supplemental-Online-File-1.cys\" rel=\"\">Supplemental Online File 1<\/a>.\u00a0<\/strong><strong>sRNA regulatory network connecting endogenous miRNAs, phasiRNAs and their targets<\/strong>. For each predicted interaction, miRNA\/phasiRNA identifiers, the target transcript identifiers, short gene name, full descriptions and MapMan ontology annotations (GoMapMan; (Ram\u0161ak et al., 2014) are shown. Additionally, <em>PHAS<\/em> loci and their producing phasiRNAs are also included. Short names for potato genes were inferred from <em>Arabidopsis thaliana<\/em> orthologs where applicable, else the StNIB_v1 gene identifier was set (Ram\u0161ak et al., 2014). For each sRNA-target interaction, interaction properties were also included (see <strong>Dataset S6 and S7)<\/strong>. Additionally, for each sRNA the log<sub>2<\/sub>FC and p-values among different comparisons are given and the log<sub>2<\/sub>FC ratios of target transcripts between PVY<sup>NTN<\/sup> and mock inoculated D\u00e9sir\u00e9e or NahG-D\u00e9sir\u00e9e plants (from the study of Stare et al. 2015). \u2013 statistically not significant (FDR p &gt; 0.05); NA \u2013 not analyzed or not available; NR \u2013 not relevant.\u00a0 D \u2013 D\u00e9sir\u00e9e; NahG \u2013 NahG-D\u00e9sir\u00e9e; M \u2013 mock; P \u2013 PVY<sup>NTN<\/sup>.<\/li>\n<\/ul>\n<p>&nbsp;<\/p>\n<ul>\n<li><strong><a href=\"http:\/\/projects.nib.si\/podefsig\/wp-content\/uploads\/sites\/14\/2017\/11\/Supplemental-Online-File-2.cys\" rel=\"\">Supplemental Online File 2<\/a>. sRNA regulatory network connecting miRNAs, phasiRNAs, PVY-derived siRNAs (vsiRNAs) and their targets.<\/strong> For each predicted interaction, miRNA\/phasiRNA identifiers, the target transcript identifiers, short gene name, full descriptions and MapMan ontology annotations (GoMapMan; Ram\u0161ak et al., 2014) are shown. Additionally, <em>PHAS<\/em> loci and their producing phasiRNAs are also included. Short names for potato genes were inferred from <em>Arabidopsis thaliana<\/em> orthologs where applicable, else the StNIB_v1 gene identifier was set (Ram\u0161ak et al., 2014). For each sRNA-target interaction, interaction properties were also included (see<strong> Dataset S6, S7 and S9<\/strong>). Additionally, for each sRNA the log<sub>2<\/sub>FC and p-values among different comparisons are given and the log<sub>2<\/sub>FC ratios of target transcripts between PVY<sup>NTN<\/sup> and mock inoculated D\u00e9sir\u00e9e or NahG-D\u00e9sir\u00e9e plants (from the study of Stare et al. 2015). \u2013 statistically not significant (FDR p &gt; 0.05); NA \u2013 not analyzed or not available; NR \u2013 not relevant.\u00a0 D \u2013 D\u00e9sir\u00e9e; NahG \u2013 NahG-D\u00e9sir\u00e9e; M \u2013 mock; P \u2013 PVY<sup>NTN<\/sup>.<\/li>\n<\/ul>\n<p>&nbsp;<\/p>\n<p><strong>Links to public database entries associated with the project:<\/strong><\/p>\n<ul>\n<li>microarray gene expression dataset of\u00a0cv. D\u00e9sir\u00e9e response to PVY (GEO:<a href=\"https:\/\/www.ncbi.nlm.nih.gov\/geo\/query\/acc.cgi?acc=GSE58593\">GSE58593<\/a>)<\/li>\n<li>smallRNA-Seq and degradome-Seq\u00a0dataset of\u00a0cv. D\u00e9sir\u00e9e response to PVY (GEO: <a href=\"https:\/\/www.ncbi.nlm.nih.gov\/geo\/query\/acc.cgi?acc=GSE84967\">GSE84967<\/a>)<\/li>\n<li>smallRNA-Seq of potatoes infected with various viruses (SRA: <a href=\"https:\/\/trace.ncbi.nlm.nih.gov\/Traces\/sra\/?study=SRP083247\">SRP083247<\/a>)<\/li>\n<\/ul>\n","protected":false},"excerpt":{"rendered":"<p>Supplemental Online Files for the\u00a0manuscript\u00a0entitled &#8220;Salicylic acid perturbs sRNA-gibberellin regulatory network in immune response of potato to Potato virus Y infection&#8221; submitted to\u00a0Frontiers in Plant Science: Supplemental Online File 1.\u00a0sRNA regulatory network connecting endogenous miRNAs, phasiRNAs and their targets. For each predicted interaction, miRNA\/phasiRNA identifiers, the target transcript identifiers, short gene name, full descriptions and [&hellip;]<\/p>\n","protected":false},"author":3,"featured_media":0,"parent":0,"menu_order":2,"comment_status":"closed","ping_status":"closed","template":"page-fullwidth.php","meta":{"jetpack_post_was_ever_published":false,"footnotes":""},"class_list":["post-14","page","type-page","status-publish","hentry"],"jetpack_sharing_enabled":true,"jetpack_shortlink":"https:\/\/wp.me\/P7RkZK-e","jetpack-related-posts":[],"_links":{"self":[{"href":"https:\/\/projects.nib.si\/podefsig\/wp-json\/wp\/v2\/pages\/14","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/projects.nib.si\/podefsig\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/projects.nib.si\/podefsig\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/projects.nib.si\/podefsig\/wp-json\/wp\/v2\/users\/3"}],"replies":[{"embeddable":true,"href":"https:\/\/projects.nib.si\/podefsig\/wp-json\/wp\/v2\/comments?post=14"}],"version-history":[{"count":21,"href":"https:\/\/projects.nib.si\/podefsig\/wp-json\/wp\/v2\/pages\/14\/revisions"}],"predecessor-version":[{"id":265,"href":"https:\/\/projects.nib.si\/podefsig\/wp-json\/wp\/v2\/pages\/14\/revisions\/265"}],"wp:attachment":[{"href":"https:\/\/projects.nib.si\/podefsig\/wp-json\/wp\/v2\/media?parent=14"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}