{"id":479,"date":"2023-11-13T09:48:22","date_gmt":"2023-11-13T17:48:22","guid":{"rendered":"https:\/\/dornsife.usc.edu\/caron\/?page_id=479"},"modified":"2023-11-13T09:56:01","modified_gmt":"2023-11-13T17:56:01","slug":"moore-protocols-sequence","status":"publish","type":"page","link":"https:\/\/dornsife.usc.edu\/caron\/moore-protocols-sequence\/","title":{"rendered":"Comparative Functional Analyses of Mixotrophy among Microbial Eukaryotes"},"content":{"rendered":"\n\n  \n    \n\n\n\n\n\n\n<div\n  class=\"cc--component-container cc--rich-text \"\n\n  \n  \n  \n  \n  \n  \n  >\n  <div class=\"c--component c--rich-text\"\n    \n      >\n\n    \n      \n<div class=\"f--field f--wysiwyg\">\n\n    \n  <h3>Protocols<\/h3>\n<p>Caron Lab protocols can be found at our protocols.io page:\u00a0<a href=\"https:\/\/www.protocols.io\/groups\/caron-lab-protistan-ecology\" target=\"_blank\" rel=\"noopener\">https:\/\/www.protocols.io\/groups\/caron-lab-protistan-ecology.\u00a0<\/a><\/p>\n<p>&nbsp;<\/p>\n<h3>Sequence Data<\/h3>\n<p>Koid, AE, A Jones, Z Liu, DA Caron, KB Heidelberg. 2014. Comparative transcriptome analysis of four prymnesiophytes.\u00a0<em>PLoS ONE<\/em>. 6: e97801\u00a0<a href=\"https:\/\/dornsife.usc.edu\/capone\/wp-content\/uploads\/sites\/214\/2023\/11\/2014_Koid_etal_PLoSONE_4Haptos.pdf\" target=\"_blank\" rel=\"noopener\">pdf<\/a><\/p>\n<ul>\n<li>The sequences for the four transcriptomes were deposited in\u00a0<a href=\"http:\/\/camera.calit2.net\/\" target=\"_blank\" rel=\"noopener\">CAMERA\u00a0<\/a>(Community Cyberinfrastructure for Advanced Microbial Ecology Research and Analysis) with the following accession numbers: CAM_ASM_000151 (<em>P. parvum<\/em>), CAM_ASM_000808 (<em>C. brevifilum<\/em>), CAM_ASM_000453 (<em>C. ericina<\/em>), CAM_ASM_000460 (<em>P. antarctica<\/em>).<\/li>\n<\/ul>\n<p>Liu, Z, AC Jones, V Campbell, KD Hambright, KB Heidelberg, DA Caron.\u00a0<strong>2015<\/strong>. Gene expression in the mixotrophic haptophyte,\u00a0<em>Prymnesium parvum<\/em>, responds to prey availability.\u00a0\u00a0<em>Front. Microbiol<\/em>. 6:319.\u00a0<a href=\"https:\/\/dornsife.usc.edu\/capone\/wp-content\/uploads\/sites\/214\/2023\/11\/2015_Liu_Frontiers_PrymPrey.pdf\" target=\"_blank\" rel=\"noopener\">pdf<\/a><\/p>\n<ul>\n<li>Sequence data deposited into the\u00a0<a href=\"http:\/\/www.ncbi.nlm.nih.gov\/sra\" target=\"_blank\" rel=\"noopener\">NCBI Sequence Read Archive<\/a>\u00a0under accession number SRA166613 and sample IDs MMETSP0006_2, MMETSP0815, and MMETSP0008_2, for axenic, bacterized and ciliate treatment, respectively.<\/li>\n<\/ul>\n<p>Lie, AAY, Z Liu, S Hu, AC Jones, DY Kim, PD Countway, LA Amaral-Zettler, RJ Gast, EB Sherr, BF Sherr, SC Cary and DA Caron.\u00a0\u00a02014.\u00a0\u00a0Investigating microbial eukaryote diversity: Insights from a comparison of pyrotag and full-length sequences of 18S rDNA from a global survey.\u00a0\u00a0<em>App. Env. Microbiol<\/em>.\u00a0\u00a080: 4363-4373\u00a0<a href=\"https:\/\/dornsife.usc.edu\/capone\/wp-content\/uploads\/sites\/214\/2023\/11\/2014_Lie_etal_AEM_FLTagSeqs.pdf\" target=\"_blank\" rel=\"noopener\">pdf<\/a><\/p>\n<ul>\n<li>The full-length 18S rRNA gene sequences were submitted to\u00a0<a href=\"http:\/\/www.ncbi.nlm.nih.gov\/genbank\/\" target=\"_blank\" rel=\"noopener\">GenBank\u00a0<\/a>under accession numbers KJ757035 to KJ759741, KJ760393 to KJ762454, and KJ762829 to KJ764638.<\/li>\n<\/ul>\n<p>Hu, S, Z Liu, AA Lie, PD Countway, DY Kim, AC Jones, RJ Gast, SC Cary, EB Sherr, BF Sherr, and DA Caron.\u00a0\u00a02015. Estimating protistan diversity using high-throughput sequencing.\u00a0<em>J. Eukayot. Microbiol<\/em>. 62:688-693. doi: 10.1111\/jeu.12217.\u00a0<a href=\"https:\/\/dornsife.usc.edu\/capone\/wp-content\/uploads\/sites\/214\/2023\/11\/2015_Hu_etal_JEM.pdf\" target=\"_blank\" rel=\"noopener\">pdf<\/a><\/p>\n<ul>\n<li>Sequences were submitted to\u00a0<a href=\"http:\/\/www.ncbi.nlm.nih.gov\/genbank\/\" target=\"_blank\" rel=\"noopener\">GenBank\u00a0<\/a>with accession numbers: KJ757035\u2013KJ764638.<\/li>\n<\/ul>\n<p>Liu, Z, AE Koid, R Terrado, V Campbell, DA Caron, KB Heidelberg. 2015. Changes in gene expression of\u00a0<em>Prymnesium parvum<\/em>\u00a0induced by nitrogen and phosphorus limitation.\u00a0<em>Front Microbiol<\/em>. 6:631. doi: 10.3389\/fmicb.2015.00631.\u00a0<a href=\"https:\/\/dornsife.usc.edu\/capone\/wp-content\/uploads\/sites\/214\/2023\/11\/2015_Liu_etal_Prym_NPlim.pdf\" target=\"_blank\" rel=\"noopener\">pdf<\/a><\/p>\n<ul>\n<li>Original sequence data were deposited in\u00a0<a href=\"http:\/\/www.ncbi.nlm.nih.gov\/sra\" target=\"_blank\" rel=\"noopener\">NCBI Sequence Read Archive<\/a>\u00a0under accession number SRA166613 and sample IDs MMETSP0006_2, MMETSP0007 and MMETSP0814, for axenic, P-limited and N-limited treatment, respectively.<\/li>\n<\/ul>\n<p>&nbsp;<\/p>\n<p><strong><em>Ochromonas\u00a0<\/em>sp. str. BG-1 transcriptomes<\/strong><\/p>\n<p>We sequenced transcriptomes of three treatments, three replicates for each treatment, totaling 176.8 Gb of data.<\/p>\n<p>Original sequences have been deposited at\u00a0<a href=\"http:\/\/www.ncbi.nlm.nih.gov\/sra\" target=\"_blank\" rel=\"noopener\">NCBI Sequence Read Archive<\/a>\u00a0(SRA) under the accession numbers SRX965527 (exponential phase samples), SRX968591 (stationary phase samples), and SRX970036 (dark treatment samples).<\/p>\n<p><strong>\u00a0<\/strong><\/p>\n<p><strong>Protist single-cell transcriptomes<\/strong><\/p>\n<p>We sequenced single-cell transcriptomes of two species,\u00a0<em>Karlodium veneficum<\/em>\u00a0(10 cells) and\u00a0<em>Prymnesium parvum<\/em>(18 cells), isolated using two methods, and their batch culture transcriptomes for comparison, totaling 121.2 Gb of data.<\/p>\n<p>Original sequences have been deposited at\u00a0<a href=\"http:\/\/www.ncbi.nlm.nih.gov\/sra\" target=\"_blank\" rel=\"noopener\">NCBI SRA<\/a>\u00a0under the accession numbers SRX1430089 (<em>P. parvum<\/em>\u00a0batch culture), SRX1430091 (<em>P. parvum<\/em>\u00a0single cells isolated manually), SRX1431799 (<em>P. parvum\u00a0<\/em>single cells isolated using microfluidics), SRX1434822 (<em>K. veneficum<\/em>\u00a0batch culture), SRX1434823 (<em>K. veneficum\u00a0<\/em>single cells isolated manually).<\/p>\n<p>Transcriptome assemblies generated using these data are being uploaded to\u00a0<a href=\"http:\/\/www.ncbi.nlm.nih.gov\/genbank\/tsa\" target=\"_blank\" rel=\"noopener\">NCBI Transcriptome Shotgun Assembly Database<\/a>.<\/p>\n<p>&nbsp;<\/p>\n<hr style=\"color: #00000012;\" \/>\n<p>&nbsp;<\/p>\n<h4>For more information, please see:<\/h4>\n<p><a class=\"cta-link\" href=\"https:\/\/dornsife.usc.edu\/caron\/moore-mixotrophy\/\" target=\"_self\">Project overview<\/a><\/p>\n<p><a class=\"cta-link\" href=\"https:\/\/dornsife.usc.edu\/caron\/moore-objective\/\">Project objectives<\/a><\/p>\n<p><a class=\"cta-link\" href=\"https:\/\/dornsife.usc.edu\/caron\/moore-publications\/\">Publications related to this project<\/a><\/p>\n<p><a class=\"cta-link\" href=\"https:\/\/dornsife.usc.edu\/caron\/moore-protocols-sequence\/\" target=\"_self\">Protocols &amp; sequence data<\/a><\/p>\n<p><a class=\"cta-link\" href=\"https:\/\/dornsife.usc.edu\/caron\/moore-gallery\/\">Video<\/a><\/p>\n<p>&nbsp;<\/p>\n\n\n\n<\/div>\n\n\n  <\/div><\/div>\n","protected":false},"excerpt":{"rendered":"","protected":false},"author":584,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"page-content-detail.php","meta":{"_acf_changed":false,"footnotes":""},"class_list":["post-479","page","type-page","status-publish","hentry"],"acf":[],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v27.1.1 - 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