{"id":600,"date":"2020-08-13T11:44:53","date_gmt":"2020-08-13T11:44:53","guid":{"rendered":"https:\/\/lepdata.org\/monteiro\/?page_id=600"},"modified":"2026-07-17T10:02:05","modified_gmt":"2026-07-17T10:02:05","slug":"lab-protocols","status":"publish","type":"page","link":"https:\/\/lepdata.org\/monteiro\/lab-protocols\/","title":{"rendered":"Lab Protocols"},"content":{"rendered":"\t\t<div data-elementor-type=\"wp-page\" data-elementor-id=\"600\" class=\"elementor elementor-600\">\n\t\t\t\t\t\t<section class=\"elementor-section elementor-top-section elementor-element elementor-element-275b89c elementor-section-boxed elementor-section-height-default elementor-section-height-default\" data-id=\"275b89c\" 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-12d0a06f\" data-id=\"12d0a06f\" 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-586c7144 elementor-widget elementor-widget-text-editor\" data-id=\"586c7144\" 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><\/p>\n<h2 class=\"wp-block-heading\"><a href=\"https:\/\/github.com\/tdblab\/NEO-CRISPR\" target=\"_blank\" rel=\"noreferrer noopener\">In situ hybridization probe preparation<\/a><\/h2>\n<p><\/p>\n<h2><a href=\"https:\/\/youtu.be\/UDAW2cfxanI\">How to use the eppendorf Femtojet 4i to inject Bicyclus anynana embryos<\/a><\/h2>\n<p class=\"wp-block-paragraph\">H<b>ow do design CRISPR guides using a new genome and annotation files:<\/b><\/p>\n<p>\u00a0<span style=\"color: #000000; font-family: Aptos, Aptos_EmbeddedFont, Aptos_MSFontService, Calibri, Helvetica, sans-serif; font-size: 12pt;\">If you are working on an organism for which your genome is not available for CRISPR guide design in traditional sites like CRISPR Direct or chopchop. Tirtha Banerjee created a new app that is very helpful. It filters out the best guide for the target region and scans the entire genome in a couple of seconds using GPU acceleration.<\/span><\/p>\n<div style=\"font-size: 12pt; font-family: Aptos, Aptos_EmbeddedFont, Aptos_MSFontService, Calibri, Helvetica, sans-serif; color: #000000;\"><span style=\"font-size: 12pt;\">Just download the app (<\/span><a style=\"font-size: 16px; outline-width: medium;\" href=\"https:\/\/github.com\/tdblab\/NEO-CRISPR\">https:\/\/github.com\/tdblab\/NEO-CRISPR<\/a><span style=\"font-size: 12pt;\">)<\/span><span style=\"font-size: 12pt;\">, drop your genome.fa (the genome file) and annotation.gtf (the annotation file) in the data\/organism_name folder of the app, and it will run nicely in your web browser.<\/span><\/div>\n<p><\/p>\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>In situ hybridization probe preparation How to use the eppendorf Femtojet 4i to inject Bicyclus anynana embryos How do design CRISPR guides using a new genome and annotation files: \u00a0If you are working on an organism for which your genome is not available for CRISPR guide design in traditional sites like CRISPR Direct or chopchop. [&hellip;]<\/p>\n","protected":false},"author":1,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-600","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/lepdata.org\/monteiro\/wp-json\/wp\/v2\/pages\/600","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/lepdata.org\/monteiro\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/lepdata.org\/monteiro\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/lepdata.org\/monteiro\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/lepdata.org\/monteiro\/wp-json\/wp\/v2\/comments?post=600"}],"version-history":[{"count":9,"href":"https:\/\/lepdata.org\/monteiro\/wp-json\/wp\/v2\/pages\/600\/revisions"}],"predecessor-version":[{"id":1883,"href":"https:\/\/lepdata.org\/monteiro\/wp-json\/wp\/v2\/pages\/600\/revisions\/1883"}],"wp:attachment":[{"href":"https:\/\/lepdata.org\/monteiro\/wp-json\/wp\/v2\/media?parent=600"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}