{"id":3752,"date":"2026-01-03T13:38:26","date_gmt":"2026-01-03T18:38:26","guid":{"rendered":"https:\/\/www.bowdish.ca\/lab\/?page_id=3752"},"modified":"2026-01-03T13:38:26","modified_gmt":"2026-01-03T18:38:26","slug":"general-biochemistry-molecular-biology","status":"publish","type":"page","link":"https:\/\/www.bowdish.ca\/lab\/general-biochemistry-molecular-biology\/","title":{"rendered":"General Biochemistry &#038; Molecular Biology"},"content":{"rendered":"\n<h2 class=\"wp-block-heading\"><a>Cloning &amp; Transfection<\/a><\/h2>\n\n\n\n<p><a href=\"https:\/\/www.bowdish.ca\/lab\/wp-content\/uploads\/2014\/11\/Molecular-Cloning.pdf\">Cloning<\/a><\/p>\n\n\n\n<p><a href=\"https:\/\/www.bowdish.ca\/lab\/wp-content\/uploads\/2014\/04\/Site-Directed-Mutagenesis-Protocol.pdf\">Site-directed\nmutagenesis<\/a><\/p>\n\n\n\n<p><a href=\"https:\/\/www.bowdish.ca\/lab\/wp-content\/uploads\/2013\/01\/PEI_Transfection_Bowdish_v2.pdf\">Transfection\nof HEK293T cells with PEI<\/a><\/p>\n\n\n\n<ul class=\"wp-block-list\"><li>This\n     is a cheap and effective protocol for transfecting HEK293T cells using\n     PEI. &nbsp;<em>Note: In Jan 2013 we posted an updated version (version 2)\n     with clarifications requested by users.&nbsp;<\/em>We have another\n     variant&nbsp;<a href=\"https:\/\/www.bowdish.ca\/lab\/wp-content\/uploads\/2014\/11\/PEI-transfection.pdf\">here<\/a>.&nbsp;We\n     have adapted this protocol for 24 well plates. To see the adapted version\n     click&nbsp;<a href=\"https:\/\/www.bowdish.ca\/lab\/wp-content\/uploads\/2013\/01\/Protocol-for-24-Well-Plates.pdf\">Protocol\n     for 24-Well Plates<\/a><\/li><\/ul>\n\n\n\n<p>&nbsp;<a>PCR<\/a><\/p>\n\n\n\n<p><a href=\"https:\/\/www.bowdish.ca\/lab\/wp-content\/uploads\/2017\/04\/qPCR-Bible.pdf\">The\nPCR resource manual.<\/a><\/p>\n\n\n\n<ul class=\"wp-block-list\"><li>The\n     how-to guide:qPCR from primer design to testing those primers in\n     preparation for quantitative PCR<\/li><\/ul>\n\n\n\n<p><a href=\"https:\/\/www.bowdish.ca\/lab\/wp-content\/uploads\/2023\/04\/Updated-cDNA-Synthesis-Protocol-Aunika-Venables.pdf\">cDNA\nsynthesis<\/a><\/p>\n\n\n\n<ul class=\"wp-block-list\"><li>This\n     protocol is used to synthesis cDNA from isolated RNA using the SuperScript\n     II reverse transcriptase enzyme with the aim to use the synthesized cDNA\n     in subsequent 2-stage RT-qPCR reactions.<\/li><\/ul>\n\n\n\n<p><a href=\"https:\/\/www.bowdish.ca\/lab\/wp-content\/uploads\/2017\/08\/qPCR-Primer-Design.pdf\">Designing\nprimers for qPCR<\/a><\/p>\n\n\n\n<p><a href=\"https:\/\/www.bowdish.ca\/lab\/wp-content\/uploads\/2023\/04\/Updated-qPCR-Protocol-Aunika-Venables.pdf\">Two-step\nqPCR<\/a><\/p>\n\n\n\n<p>Two-step reverse transcription quantitative polymerase chain\nreaction, often abbreviated as 2-Step RT-qPCR or simply as qPCR, is a\nhigh-throughput assay design that allows the real-time measurement of the\nexpression level of specific genes at the RNA level. This protocol was written\nfor SYBR green.<\/p>\n\n\n\n<h2 class=\"wp-block-heading\"><a>Protein<\/a> <\/h2>\n\n\n\n<p><a href=\"https:\/\/www.bowdish.ca\/lab\/wp-content\/uploads\/2012\/10\/Immunoprecipitation.pdf\">Immunoprecipitation<\/a><\/p>\n\n\n\n<ul class=\"wp-block-list\"><li>This\n     protocol demonstrates how to immunoprecipitate a protein from a cell\n     lysate.<\/li><\/ul>\n\n\n\n<p><a href=\"https:\/\/www.bowdish.ca\/lab\/wp-content\/uploads\/2014\/11\/Co-Immunoprecipitation.pdf\">Co-immunoprecipitation<\/a><\/p>\n\n\n\n<p><a href=\"https:\/\/www.bowdish.ca\/lab\/wp-content\/uploads\/2019\/08\/Updated-Western-blot-protocol.pdf\">Western\nimmunoblotting<\/a><\/p>\n\n\n\n<ul class=\"wp-block-list\"><li>This\n     includes running the gel, transferring to PVDF membrane and preparing\n     antibodies.<\/li><\/ul>\n\n\n\n<p>&nbsp;<a href=\"https:\/\/www.bowdish.ca\/lab\/wp-content\/uploads\/2016\/05\/Coomassie-Blue-Stain-Protocol.pdf\">Coommassie\nblue staining of protein gels<\/a><\/p>\n\n\n\n<h2 class=\"wp-block-heading\"><a>RNA<\/a><\/h2>\n\n\n\n<p><a href=\"https:\/\/www.bowdish.ca\/lab\/wp-content\/uploads\/2023\/04\/Updated-TRIzol-RNA-Extraction-Protocol-Aunika-Venables.pdf\">RNA\nextraction using TRIzol&nbsp;<\/a><\/p>\n\n\n\n<p>This protocol is used to extract the RNA from tissue or a\ncell sample using TRIzol and also includes recommendations for 260\/280 and\n260\/230 values when measuring the concentration of extracted RNA using a\nnanodrop spectrometer.<\/p>\n\n\n\n<p><a href=\"https:\/\/www.bowdish.ca\/lab\/wp-content\/uploads\/2011\/07\/RNA_extraction_lungs.pdf\">RNA\nextraction \u2013 lungs<\/a><\/p>\n\n\n\n<p><a href=\"https:\/\/www.bowdish.ca\/lab\/wp-content\/uploads\/2011\/07\/RNA_extraction-nasopharnyx.pdf\">RNA\nextraction \u2013 nasopharynx<\/a><\/p>\n\n\n\n<p><a href=\"https:\/\/www.bowdish.ca\/lab\/wp-content\/uploads\/2013\/06\/RNA-Extraction-For-RNAseq.pdf\">RNA\nExtraction for RNAseq<\/a><\/p>\n\n\n\n<ul class=\"wp-block-list\"><li>This\n     protocol is for isolating RNA from cell lines or tissues for RNA\n     sequencing.<\/li><\/ul>\n\n\n\n<p><a href=\"https:\/\/www.bowdish.ca\/lab\/wp-content\/uploads\/2013\/09\/Sample-Preparation-For-RNAseq.pdf\">RNA\npreparation for RNAseq<\/a>&nbsp;(RNA sequencing\/transcriptomics)<\/p>\n\n\n\n<ul class=\"wp-block-list\"><li>The\n     protocol details the steps required fro processing (eukaryote) RNA for RNA\n     sequencing experiments including ribosomal RNA depletion, quality control\n     and quantification, cDNA preparation and labelling with adaptors.&nbsp;<\/li><\/ul>\n\n\n\n<h2 class=\"wp-block-heading\"><a>Other (e.g., bacterial sugars, SDS contamination)<\/a>\n<\/h2>\n\n\n\n<p><a href=\"https:\/\/www.bowdish.ca\/lab\/wp-content\/uploads\/2012\/08\/Methylene-Green-SDS-Detection-Assay-4.pdf\">Methylene\nGreen SDS Detection Assay<\/a><\/p>\n\n\n\n<ul class=\"wp-block-list\"><li>&nbsp;Is\n     there SDS contamination in your reagent? Quantitate the amount of SDS\n     using this assay based off of the traditional Methylene Blue assay.<\/li><\/ul>\n\n\n\n<p><a href=\"https:\/\/www.bowdish.ca\/lab\/wp-content\/uploads\/2016\/05\/Mannose-Detection-Protocol.pdf\">Phenol-sulfuric\nacid Mannose detection assay<\/a>.<\/p>\n\n\n\n<ul class=\"wp-block-list\"><li>This\n     assay is sensitive to mannose from 1 \u2013 100 ?g but will also\n     detect&nbsp;other carbohydrates. We use this assay to&nbsp;quantify of\n     complex carbohydrates in the bacterial cell wall<\/li><\/ul>\n","protected":false},"excerpt":{"rendered":"<p>Cloning &amp; Transfection Cloning Site-directed mutagenesis Transfection of HEK293T cells with PEI This is a cheap and effective protocol for transfecting HEK293T cells using PEI. &nbsp;Note: In Jan 2013 we posted an updated version (version 2) with clarifications requested by &hellip; <a href=\"https:\/\/www.bowdish.ca\/lab\/general-biochemistry-molecular-biology\/\">Continue reading <span class=\"meta-nav\">&rarr;<\/span><\/a><\/p>\n","protected":false},"author":2,"featured_media":3584,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-3752","page","type-page","status-publish","has-post-thumbnail","hentry"],"_links":{"self":[{"href":"https:\/\/www.bowdish.ca\/lab\/wp-json\/wp\/v2\/pages\/3752","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.bowdish.ca\/lab\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/www.bowdish.ca\/lab\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/www.bowdish.ca\/lab\/wp-json\/wp\/v2\/users\/2"}],"replies":[{"embeddable":true,"href":"https:\/\/www.bowdish.ca\/lab\/wp-json\/wp\/v2\/comments?post=3752"}],"version-history":[{"count":1,"href":"https:\/\/www.bowdish.ca\/lab\/wp-json\/wp\/v2\/pages\/3752\/revisions"}],"predecessor-version":[{"id":3753,"href":"https:\/\/www.bowdish.ca\/lab\/wp-json\/wp\/v2\/pages\/3752\/revisions\/3753"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/www.bowdish.ca\/lab\/wp-json\/wp\/v2\/media\/3584"}],"wp:attachment":[{"href":"https:\/\/www.bowdish.ca\/lab\/wp-json\/wp\/v2\/media?parent=3752"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}