{"id":797,"date":"2018-06-21T12:32:19","date_gmt":"2018-06-21T19:32:19","guid":{"rendered":"https:\/\/sci.sdsu.edu\/kalyuzhlab\/?page_id=797"},"modified":"2018-12-10T22:58:15","modified_gmt":"2018-12-11T06:58:15","slug":"omics-datasets","status":"publish","type":"page","link":"https:\/\/sci.sdsu.edu\/kalyuzhlab\/omics-datasets\/","title":{"rendered":"Omics datasets"},"content":{"rendered":"<p>[et_pb_section bb_built=&#8221;1&#8243;][et_pb_row][et_pb_column type=&#8221;4_4&#8243;][et_pb_text _builder_version=&#8221;3.4.1&#8243;]<\/p>\n<h3><span style=\"color: #000000;\">Genome overview of <em>Methylomicrobium alcaliphilum<\/em> 20Z:<\/span><\/h3>\n<ul>\n<li><span style=\"color: #000000;\">Gram: &#8211;<\/span><\/li>\n<li><span style=\"color: #000000;\">Taxonomy: Bacteria &gt; Proteobacteria &gt; Gammaproteobacteria &gt; Methylococcales &gt; Methylococcaceae &gt; Methylomicrobium &gt; Methylomicrobium alcaliphilum<\/span><\/li>\n<li><span style=\"color: #000000;\">Assembly information: <a href=\"https:\/\/www.genoscope.cns.fr\/agc\/microscope\/genomic\/overview.php?&amp;wwwpkgdb=4ecfe6387ed0d0a4bbc03e224279cf75\" target=\"_blank\" rel=\"noopener\">MAGE_000000532.1<\/a><\/span><\/li>\n<li><span style=\"color: #000000;\">Total number of CDS ( without artefacts ) = 4117<\/span><\/li>\n<li><span style=\"color: #000000;\">Total genome length = 4796711 bases<\/span><\/li>\n<\/ul>\n<p>[\/et_pb_text][\/et_pb_column][\/et_pb_row][et_pb_row][et_pb_column type=&#8221;4_4&#8243;][et_pb_text _builder_version=&#8221;3.4.1&#8243;]<\/p>\n<h3 style=\"text-align: left;\"><span style=\"color: #000000;\">Transcriptomics data<\/span><\/h3>\n<p><span style=\"color: #000000;\">Transcriptomic analysis of cells from cultures of the <em>M.\u00a0alcaliphilum<\/em> 20ZR grown on methanol or methane accounting for the presence of Ca (-Cu\\+Cu) or La (-Cu\\+Cu) was conducted according to the protocol (<a href=\"https:\/\/doi.org\/10.3389\/fmicb.2018.02735\" target=\"_blank\" rel=\"noopener\">Akberdin et al., 2018<\/a>)<\/span><\/p>\n<p>[embeddoc url=&#8221;https:\/\/sci.sdsu.edu\/kalyuzhlab\/wp-content\/uploads\/2018\/06\/Transcriptomics_all_vs_all_last.xlsx&#8221; download=&#8221;all&#8221; viewer=&#8221;microsoft&#8221;]<\/p>\n<p>[\/et_pb_text][\/et_pb_column][\/et_pb_row][et_pb_row _builder_version=&#8221;3.4.1&#8243;][et_pb_column type=&#8221;4_4&#8243;][et_pb_text _builder_version=&#8221;3.4.1&#8243;]<\/p>\n<h3><span style=\"color: #000000;\">Proteomics data<\/span><\/h3>\n<p><span style=\"color: #000000;\">Proteomic analysis of cells from cultures of the <em>M.\u00a0alcaliphilum<\/em> 20ZR grown on methanol or methane accounting for the presence of Ca (-Cu\\+Cu) or La (-Cu\\+Cu) and a set of starvation experiments were conducted according to the protocol (<a href=\"https:\/\/doi.org\/10.3389\/fmicb.2018.02735\" target=\"_blank\" rel=\"noopener\">Akberdin et al., 2018<\/a>)<\/span><\/p>\n<p>[embeddoc url=&#8221;https:\/\/sci.sdsu.edu\/kalyuzhlab\/wp-content\/uploads\/2018\/06\/Ca_La_Cu-noCu_20Z_set.xlsx&#8221; download=&#8221;all&#8221; viewer=&#8221;microsoft&#8221;]<\/p>\n<p>&nbsp;<\/p>\n<p>[embeddoc url=&#8221;https:\/\/sci.sdsu.edu\/kalyuzhlab\/wp-content\/uploads\/2018\/06\/Starvation-exp_20Z_set.xlsx&#8221; download=&#8221;all&#8221; viewer=&#8221;microsoft&#8221;]<\/p>\n<p>[\/et_pb_text][\/et_pb_column][\/et_pb_row][et_pb_row][et_pb_column type=&#8221;4_4&#8243;][et_pb_text _builder_version=&#8221;3.4.1&#8243;]<\/p>\n<h3 style=\"text-align: left;\"><span style=\"color: #000000;\">Metabolomics data<\/span><\/h3>\n<p style=\"text-align: left;\">Metabolomic analysis of cells and spent supernatant from cultures of the<em> M. alcaliphilum<\/em> 20ZR grown in different growth conditions was performed according to the published protocol (<a href=\"https:\/\/www.nature.com\/articles\/s41598-018-20574-z\" target=\"_blank\" rel=\"noopener\">Akberdin et al., 2018<\/a> and <a href=\"https:\/\/doi.org\/10.3389\/fmicb.2018.02735\" target=\"_blank\" rel=\"noopener\">Akberdin et al., 2018<\/a>).<\/p>\n<p>[embeddoc url=&#8221;https:\/\/sci.sdsu.edu\/kalyuzhlab\/wp-content\/uploads\/2018\/06\/Metabolomics-dataset-Cells-Exp-1.xlsx&#8221; download=&#8221;all&#8221; viewer=&#8221;microsoft&#8221;]<\/p>\n<p>&nbsp;<\/p>\n<p>&nbsp;<\/p>\n<p>[embeddoc url=&#8221;https:\/\/sci.sdsu.edu\/kalyuzhlab\/wp-content\/uploads\/2018\/06\/Metabolomics-dataset-Sup-Exp.xlsx&#8221; download=&#8221;all&#8221; viewer=&#8221;microsoft&#8221;]<\/p>\n<p>[\/et_pb_text][\/et_pb_column][\/et_pb_row][\/et_pb_section]<\/p>\n","protected":false},"excerpt":{"rendered":"<p><div class=\"et_pb_row et_pb_row_0 et_pb_row_empty\">\n\t\t\t\t\n\t\t\t\t\n\t\t\t\t\n\t\t\t\t\n\t\t\t\t\n\t\t\t<\/div> Genome overview of Methylomicrobium alcaliphilum 20Z: Gram: &#8211; Taxonomy: Bacteria &gt; Proteobacteria &gt; Gammaproteobacteria &gt; Methylococcales &gt; Methylococcaceae &gt; Methylomicrobium &gt; Methylomicrobium alcaliphilum Assembly information: MAGE_000000532.1 Total number of CDS ( without artefacts ) = 4117 Total genome length = 4796711 bases <div class=\"et_pb_row et_pb_row_1 et_pb_row_empty\">\n\t\t\t\t\n\t\t\t\t\n\t\t\t\t\n\t\t\t\t\n\t\t\t\t\n\t\t\t<\/div> Transcriptomics data Transcriptomic analysis of cells from cultures of the M.\u00a0alcaliphilum [&hellip;]<\/p>\n","protected":false},"author":3,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"_et_pb_use_builder":"on","_et_pb_old_content":"","_et_gb_content_width":"","footnotes":""},"class_list":["post-797","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/sci.sdsu.edu\/kalyuzhlab\/wp-json\/wp\/v2\/pages\/797","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/sci.sdsu.edu\/kalyuzhlab\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/sci.sdsu.edu\/kalyuzhlab\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/sci.sdsu.edu\/kalyuzhlab\/wp-json\/wp\/v2\/users\/3"}],"replies":[{"embeddable":true,"href":"https:\/\/sci.sdsu.edu\/kalyuzhlab\/wp-json\/wp\/v2\/comments?post=797"}],"version-history":[{"count":15,"href":"https:\/\/sci.sdsu.edu\/kalyuzhlab\/wp-json\/wp\/v2\/pages\/797\/revisions"}],"predecessor-version":[{"id":1080,"href":"https:\/\/sci.sdsu.edu\/kalyuzhlab\/wp-json\/wp\/v2\/pages\/797\/revisions\/1080"}],"wp:attachment":[{"href":"https:\/\/sci.sdsu.edu\/kalyuzhlab\/wp-json\/wp\/v2\/media?parent=797"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}