{"id":496,"date":"2023-06-30T18:02:38","date_gmt":"2023-07-01T01:02:38","guid":{"rendered":"https:\/\/dornsife.usc.edu\/carlslab\/?page_id=496"},"modified":"2023-08-13T16:42:00","modified_gmt":"2023-08-13T23:42:00","slug":"data-protocols","status":"publish","type":"page","link":"https:\/\/dornsife.usc.edu\/carlslab\/data-protocols\/","title":{"rendered":"Data &#038; Protocols"},"content":{"rendered":"\n        \n  \n    \n\n\n\n\n\n\n<div\n  class=\"cc--component-container cc--full-width-cta \"\n\n  \n  \n  \n  \n  \n  \n  >\n  <div class=\"c--component c--full-width-cta\"\n    \n      >\n\n    \n<div class=\"inner-wrapper\">\n      <div class=\"header-container\">\n  \n                  \n<div class=\"f--field f--section-title\">\n\n    \n  <h2>\n          Protocols\n      <\/h2>\n\n\n<\/div>\n                        \n<div class=\"f--field f--description\">\n\n    \n  <p>The CEE Lab is committed to increasing access to information and bettering the scientific community by sharing data and protocols whenever possible. Below are links to resources we have developed, including tips and techniques for colony-level 3D photogrammetry, measuring phenotypic data in MeshLab, and protocols for isolating and culturing algal and bacterial partners.<\/p>\n\n\n\n<\/div>\n          <\/div>\n    \n      <div class=\"links-container\">\n        \n            \n<div class=\"f--field f--link\">\n\n    \n    \n  \n<a \n  class=\"link\"\n  href= https:\/\/www.protocols.io\/view\/image-capture-and-pre-filtering-for-3d-photogramme-bgdcjs2w\n  target=\"_blank\"  aria-label=\"Read more about Photogrammetry\"  \n>\n    Photogrammetry \n  <svg version=\"1.1\" xmlns=\"http:\/\/www.w3.org\/2000\/svg\" xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" x=\"0px\" y=\"0px\" viewBox=\"0 0 35 35\" enable-background=\"new 0 0 35 35\" width=\"25\" height=\"25\" xml:space=\"preserve\"><polygon fill-rule=\"evenodd\" clip-rule=\"evenodd\" fill=\"#FC0\" points=\"19.3,27.5 29.3,17.5,19.3,7.5 16.3,10.4 21.4,15.4 6.7,15.4 6.7,19.6 21.4,19.6 16.3,24.6 \"\/><\/svg>\n<\/a>\n\n\n<\/div>\n        \n            \n<div class=\"f--field f--link\">\n\n    \n    \n  \n<a \n  class=\"link\"\n  href= https:\/\/www.protocols.io\/view\/phenotyping-3d-coral-models-in-meshlab-bgbpjsmn\n  target=\"_blank\"  aria-label=\"Read more about Phenotyping\"  \n>\n    Phenotyping \n  <svg version=\"1.1\" xmlns=\"http:\/\/www.w3.org\/2000\/svg\" xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" x=\"0px\" y=\"0px\" viewBox=\"0 0 35 35\" enable-background=\"new 0 0 35 35\" width=\"25\" height=\"25\" xml:space=\"preserve\"><polygon fill-rule=\"evenodd\" clip-rule=\"evenodd\" fill=\"#FC0\" points=\"19.3,27.5 29.3,17.5,19.3,7.5 16.3,10.4 21.4,15.4 6.7,15.4 6.7,19.6 21.4,19.6 16.3,24.6 \"\/><\/svg>\n<\/a>\n\n\n<\/div>\n        \n            \n<div class=\"f--field f--link\">\n\n    \n    \n  \n<a \n  class=\"link\"\n  href= https:\/\/www.protocols.io\/view\/isolating-non-axenic-monoclonal-symbiodinium-cultu-rm7vzb89rvx1\/v1\n  target=\"_blank\"  aria-label=\"Read more about Isolating Algal Symbionts\"  \n>\n    Isolating Algal Symbionts \n  <svg version=\"1.1\" xmlns=\"http:\/\/www.w3.org\/2000\/svg\" xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" x=\"0px\" y=\"0px\" viewBox=\"0 0 35 35\" enable-background=\"new 0 0 35 35\" width=\"25\" height=\"25\" xml:space=\"preserve\"><polygon fill-rule=\"evenodd\" clip-rule=\"evenodd\" fill=\"#FC0\" points=\"19.3,27.5 29.3,17.5,19.3,7.5 16.3,10.4 21.4,15.4 6.7,15.4 6.7,19.6 21.4,19.6 16.3,24.6 \"\/><\/svg>\n<\/a>\n\n\n<\/div>\n        \n            \n<div class=\"f--field f--link\">\n\n    \n    \n  \n<a \n  class=\"link\"\n  href= https:\/\/www.protocols.io\/view\/isolating-bacteria-from-algal-monocultures-261ge3okyl47\/v1\n  target=\"_blank\"  aria-label=\"Read more about Isolating Bacteria Protocols\"  \n>\n    Isolating Bacteria Protocols \n  <svg version=\"1.1\" xmlns=\"http:\/\/www.w3.org\/2000\/svg\" xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" x=\"0px\" y=\"0px\" viewBox=\"0 0 35 35\" enable-background=\"new 0 0 35 35\" width=\"25\" height=\"25\" xml:space=\"preserve\"><polygon fill-rule=\"evenodd\" clip-rule=\"evenodd\" fill=\"#FC0\" points=\"19.3,27.5 29.3,17.5,19.3,7.5 16.3,10.4 21.4,15.4 6.7,15.4 6.7,19.6 21.4,19.6 16.3,24.6 \"\/><\/svg>\n<\/a>\n\n\n<\/div>\n          <\/div>\n  <\/div>\n\n\n\n  <\/div><\/div>\n\n\n\n  \n    \n\n\n\n\n\n\n<div\n  class=\"cc--component-container cc--signup-form dark\"\n\n  \n  \n  \n  \n  \n  \n  >\n  <div class=\"c--component c--signup-form\"\n    \n      >\n\n    \n<div class=\"text-image-container\">\n  <div class=\"text-container\">\n\n              \n<div class=\"f--field f--section-title\">\n\n    \n  <h2>\n          2bRAD Reference Libraries\n      <\/h2>\n\n\n<\/div>\n    \n              \n<div class=\"f--field f--description\">\n\n    \n  <p><span style=\"font-weight: 400;\">The link below will take you to the Dropbox folder containing the data for four species of Pseudo-nitzschia. To download remotely, copy the link and use the wget command.<\/span><\/p>\n<p><a href=\"https:\/\/commons.wikimedia.org\/wiki\/File:Pseudo-nitzschia-multiseries.jpg\">Image credit &amp; licensing<\/a><\/p>\n<p>&nbsp;<\/p>\n\n\n\n<\/div>\n    \n              \n<div class=\"f--field f--link\">\n\n    \n    \n  \n<a \n  class=\"link\"\n  href= https:\/\/www.dropbox.com\/s\/bnm4p9sstrn9zl7\/Pseudonitzschia2bRADref.tar.gz\n  target=\"_blank\"  aria-label=\"Read more about Pseudo-nitzschia spp. Dropbox\"  \n>\n    Pseudo-nitzschia spp. Dropbox \n  <svg version=\"1.1\" xmlns=\"http:\/\/www.w3.org\/2000\/svg\" xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" x=\"0px\" y=\"0px\" viewBox=\"0 0 35 35\" enable-background=\"new 0 0 35 35\" width=\"25\" height=\"25\" xml:space=\"preserve\"><polygon fill-rule=\"evenodd\" clip-rule=\"evenodd\" fill=\"#000\" points=\"19.3,27.5 29.3,17.5,19.3,7.5 16.3,10.4 21.4,15.4 6.7,15.4 6.7,19.6 21.4,19.6 16.3,24.6 \"\/><\/svg>\n<\/a>\n\n\n<\/div>\n\n      <\/div>\n\n      <div class=\"image-container\">\n          \n<div class=\"f--field f--image\">\n\n    \n    \n    \n    \n    \n    \n              \n      <img\n                            data-src=\"https:\/\/dornsife.usc.edu\/carlslab\/wp-content\/uploads\/sites\/216\/2023\/06\/Pseudo-nitzschia-multiseries.jpg\"\n                    data-sizes=\"(min-width:1024px) 50vw, (min-width:768px) 100vw, 100vw\"          class=\"lazyload\"\n        \n                  role=\"none\"\n        \n        \n                                      \/>\n\n    \n    \n  \n  \n\n<\/div>\n    <\/div>\n  \n<\/div>\n\n\n  <\/div><\/div>\n\n\n\n          \n  \n    \n\n\n\n\n\n\n<div\n  class=\"cc--component-container cc--link-list \"\n\n  \n  \n  \n  \n  \n  \n  >\n  <div class=\"c--component c--link-list\"\n    \n      >\n\n    \n      <div class=\"header-container\">\n\n                  \n<div class=\"f--field f--section-title\">\n\n    \n  <h2>\n          Transcriptome Assemblies\n      <\/h2>\n\n\n<\/div>\n                        \n<div class=\"f--field f--description\">\n\n    \n  <p><span style=\"font-weight: 400;\">Links will take you to the Dropbox folder containing the transcriptome assemblies for each species. To download remotely, copy the link and use the wget command.<\/span><\/p>\n\n\n\n<\/div>\n          <\/div>\n  \n      <div class=\"links-container\">\n\n                        \n        \n          \n            <div class=\"column\">\n                <ul>\n                                                                  <li>\n                                \n<div class=\"f--field f--link\">\n\n    \n    \n  \n<a \n  class=\"link\"\n  href= https:\/\/www.dropbox.com\/s\/a4i9m61h1mrcxj8\/Plob.tar.gz\n  target=\"_blank\"  aria-label=\"Read more about Porites lobata\"  \n>\n    Porites lobata \n  <svg version=\"1.1\" xmlns=\"http:\/\/www.w3.org\/2000\/svg\" xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" x=\"0px\" y=\"0px\" viewBox=\"0 0 35 35\" enable-background=\"new 0 0 35 35\" width=\"25\" height=\"25\" xml:space=\"preserve\"><polygon fill-rule=\"evenodd\" clip-rule=\"evenodd\" fill=\"#000\" points=\"19.3,27.5 29.3,17.5,19.3,7.5 16.3,10.4 21.4,15.4 6.7,15.4 6.7,19.6 21.4,19.6 16.3,24.6 \"\/><\/svg>\n<\/a>\n\n\n<\/div>\n\n                                                    <\/li>\n                                                                                        <li>\n                                \n<div class=\"f--field f--link\">\n\n    \n    \n  \n<a \n  class=\"link\"\n  href= https:\/\/www.dropbox.com\/s\/m09q503xxohfznz\/Gach.tar.gz\n  target=\"_blank\"  aria-label=\"Read more about Galaxea acrhelia\"  \n>\n    Galaxea acrhelia \n  <svg version=\"1.1\" xmlns=\"http:\/\/www.w3.org\/2000\/svg\" xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" x=\"0px\" y=\"0px\" viewBox=\"0 0 35 35\" enable-background=\"new 0 0 35 35\" width=\"25\" height=\"25\" xml:space=\"preserve\"><polygon fill-rule=\"evenodd\" clip-rule=\"evenodd\" fill=\"#000\" points=\"19.3,27.5 29.3,17.5,19.3,7.5 16.3,10.4 21.4,15.4 6.7,15.4 6.7,19.6 21.4,19.6 16.3,24.6 \"\/><\/svg>\n<\/a>\n\n\n<\/div>\n\n                                                    <\/li>\n                                                                                        <li>\n                                \n<div class=\"f--field f--link\">\n\n    \n    \n  \n<a \n  class=\"link\"\n  href= https:\/\/www.dropbox.com\/s\/4id5hyjh0412xmi\/Gast.tar.gz\n  target=\"_blank\"  aria-label=\"Read more about Galaxea astreata\"  \n>\n    Galaxea astreata \n  <svg version=\"1.1\" xmlns=\"http:\/\/www.w3.org\/2000\/svg\" xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" x=\"0px\" y=\"0px\" viewBox=\"0 0 35 35\" enable-background=\"new 0 0 35 35\" width=\"25\" height=\"25\" xml:space=\"preserve\"><polygon fill-rule=\"evenodd\" clip-rule=\"evenodd\" fill=\"#000\" points=\"19.3,27.5 29.3,17.5,19.3,7.5 16.3,10.4 21.4,15.4 6.7,15.4 6.7,19.6 21.4,19.6 16.3,24.6 \"\/><\/svg>\n<\/a>\n\n\n<\/div>\n\n                                                    <\/li>\n                                                          <\/ul>\n            <\/div>\n\n          \n          \n        \n          \n            <div class=\"column\">\n                <ul>\n                                                                  <li>\n                                \n<div class=\"f--field f--link\">\n\n    \n    \n  \n<a \n  class=\"link\"\n  href= https:\/\/www.dropbox.com\/s\/eyjtuswown9rjs7\/Gcol.tar.gz\n  target=\"_blank\"  aria-label=\"Read more about Goniopora columna\"  \n>\n    Goniopora columna \n  <svg version=\"1.1\" xmlns=\"http:\/\/www.w3.org\/2000\/svg\" xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" x=\"0px\" y=\"0px\" viewBox=\"0 0 35 35\" enable-background=\"new 0 0 35 35\" width=\"25\" height=\"25\" xml:space=\"preserve\"><polygon fill-rule=\"evenodd\" clip-rule=\"evenodd\" fill=\"#000\" points=\"19.3,27.5 29.3,17.5,19.3,7.5 16.3,10.4 21.4,15.4 6.7,15.4 6.7,19.6 21.4,19.6 16.3,24.6 \"\/><\/svg>\n<\/a>\n\n\n<\/div>\n\n                                                    <\/li>\n                                                                                        <li>\n                                \n<div class=\"f--field f--link\">\n\n    \n    \n  \n<a \n  class=\"link\"\n  href= https:\/\/www.dropbox.com\/s\/7tmlzfwrdicuy2v\/Maqe.tar.gz\n  target=\"_blank\"  aria-label=\"Read more about Montipora aequituberculata\"  \n>\n    Montipora aequituberculata \n  <svg version=\"1.1\" xmlns=\"http:\/\/www.w3.org\/2000\/svg\" xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" x=\"0px\" y=\"0px\" viewBox=\"0 0 35 35\" enable-background=\"new 0 0 35 35\" width=\"25\" height=\"25\" xml:space=\"preserve\"><polygon fill-rule=\"evenodd\" clip-rule=\"evenodd\" fill=\"#000\" points=\"19.3,27.5 29.3,17.5,19.3,7.5 16.3,10.4 21.4,15.4 6.7,15.4 6.7,19.6 21.4,19.6 16.3,24.6 \"\/><\/svg>\n<\/a>\n\n\n<\/div>\n\n                                                    <\/li>\n                                                          <\/ul>\n            <\/div>\n\n          \n          \n        \n\n\n\n    <\/div>\n  \n\n  <\/div><\/div>\n","protected":false},"excerpt":{"rendered":"","protected":false},"author":392,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"_acf_changed":false,"footnotes":""},"class_list":["post-496","page","type-page","status-publish","hentry"],"acf":[],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v27.1.1 - https:\/\/yoast.com\/product\/yoast-seo-wordpress\/ -->\n<title>Data &amp; Protocols - Cnidarian Evolutionary Ecology Lab<\/title>\n<meta name=\"robots\" content=\"index, follow, max-snippet:-1, max-image-preview:large, max-video-preview:-1\" \/>\n<link rel=\"canonical\" href=\"https:\/\/dornsife.usc.edu\/carlslab\/data-protocols\/\" \/>\n<meta property=\"og:locale\" content=\"en_US\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Data &amp; Protocols - Cnidarian Evolutionary Ecology Lab\" \/>\n<meta property=\"og:url\" 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