{"id":73,"date":"2022-03-31T14:20:29","date_gmt":"2022-03-31T13:20:29","guid":{"rendered":"https:\/\/sites.dundee.ac.uk\/dundee-daffodil\/?page_id=73"},"modified":"2026-03-26T10:42:34","modified_gmt":"2026-03-26T10:42:34","slug":"school-resources","status":"publish","type":"page","link":"https:\/\/sites.dundee.ac.uk\/dundee-daffodil\/school-resources\/","title":{"rendered":"School Resources"},"content":{"rendered":"\n<h2 class=\"wp-block-heading\">Overview pdf Summarising all 8 Steps<\/h2>\n\n\n\n<div class=\"wp-block-media-text alignwide is-stacked-on-mobile\" style=\"grid-template-columns:44% auto\"><figure class=\"wp-block-media-text__media\"><img loading=\"lazy\" decoding=\"async\" width=\"763\" height=\"1024\" src=\"https:\/\/sites.dundee.ac.uk\/dundee-daffodil\/wp-content\/uploads\/sites\/190\/2022\/11\/Henderson-Summary-11-11-2022-763x1024.jpg\" alt=\"\" class=\"wp-image-637 size-full\" srcset=\"https:\/\/sites.dundee.ac.uk\/dundee-daffodil\/wp-content\/uploads\/sites\/190\/2022\/11\/Henderson-Summary-11-11-2022-763x1024.jpg 763w, https:\/\/sites.dundee.ac.uk\/dundee-daffodil\/wp-content\/uploads\/sites\/190\/2022\/11\/Henderson-Summary-11-11-2022-224x300.jpg 224w, https:\/\/sites.dundee.ac.uk\/dundee-daffodil\/wp-content\/uploads\/sites\/190\/2022\/11\/Henderson-Summary-11-11-2022-768x1030.jpg 768w, https:\/\/sites.dundee.ac.uk\/dundee-daffodil\/wp-content\/uploads\/sites\/190\/2022\/11\/Henderson-Summary-11-11-2022-1145x1536.jpg 1145w, https:\/\/sites.dundee.ac.uk\/dundee-daffodil\/wp-content\/uploads\/sites\/190\/2022\/11\/Henderson-Summary-11-11-2022-1527x2048.jpg 1527w, https:\/\/sites.dundee.ac.uk\/dundee-daffodil\/wp-content\/uploads\/sites\/190\/2022\/11\/Henderson-Summary-11-11-2022-scaled.jpg 1909w\" sizes=\"auto, (max-width: 763px) 100vw, 763px\" \/><\/figure><div class=\"wp-block-media-text__content\">\n<pre class=\"wp-block-code\"><code><p><code><strong><u><a href=\"https:\/\/sites.dundee.ac.uk\/dundee-daffodil\/wp-content\/uploads\/sites\/190\/2024\/11\/Henderson-Summary-2024.pdf\" data-type=\"URL\" data-id=\"https:\/\/sites.dundee.ac.uk\/dundee-daffodil\/wp-content\/uploads\/sites\/190\/2022\/11\/Henderson-Summary-10-10-2022.pdf\" target=\"_blank\" rel=\"noreferrer noopener\">Getting Started - Overview pdf <\/a><\/u><\/strong><\/code><\/p><\/code><\/pre>\n<\/div><\/div>\n\n\n\n<h2 class=\"wp-block-heading\">DaffDNA Extraction Protocol<\/h2>\n\n\n\n<figure class=\"wp-block-image size-large\"><img loading=\"lazy\" decoding=\"async\" width=\"1024\" height=\"724\" src=\"https:\/\/sites.dundee.ac.uk\/dundee-daffodil\/wp-content\/uploads\/sites\/190\/2024\/11\/DaffDNA-extraction-protocol-visualisation-1024x724.jpg\" alt=\"\" class=\"wp-image-665\" srcset=\"https:\/\/sites.dundee.ac.uk\/dundee-daffodil\/wp-content\/uploads\/sites\/190\/2024\/11\/DaffDNA-extraction-protocol-visualisation-1024x724.jpg 1024w, https:\/\/sites.dundee.ac.uk\/dundee-daffodil\/wp-content\/uploads\/sites\/190\/2024\/11\/DaffDNA-extraction-protocol-visualisation-300x212.jpg 300w, https:\/\/sites.dundee.ac.uk\/dundee-daffodil\/wp-content\/uploads\/sites\/190\/2024\/11\/DaffDNA-extraction-protocol-visualisation-768x543.jpg 768w, https:\/\/sites.dundee.ac.uk\/dundee-daffodil\/wp-content\/uploads\/sites\/190\/2024\/11\/DaffDNA-extraction-protocol-visualisation-424x300.jpg 424w, https:\/\/sites.dundee.ac.uk\/dundee-daffodil\/wp-content\/uploads\/sites\/190\/2024\/11\/DaffDNA-extraction-protocol-visualisation.jpg 1121w\" sizes=\"auto, (max-width: 1024px) 100vw, 1024px\" \/><\/figure>\n\n\n\n<h2 class=\"wp-block-heading\">DaffDNA Extraction Tube Organisation Sheet<\/h2>\n\n\n\n<figure class=\"wp-block-image size-large\"><img loading=\"lazy\" decoding=\"async\" width=\"724\" height=\"1024\" src=\"https:\/\/sites.dundee.ac.uk\/dundee-daffodil\/wp-content\/uploads\/sites\/190\/2024\/11\/DaffDNA-extraction-tube-organisation-sheet-724x1024.jpg\" alt=\"\" class=\"wp-image-667\" srcset=\"https:\/\/sites.dundee.ac.uk\/dundee-daffodil\/wp-content\/uploads\/sites\/190\/2024\/11\/DaffDNA-extraction-tube-organisation-sheet-724x1024.jpg 724w, https:\/\/sites.dundee.ac.uk\/dundee-daffodil\/wp-content\/uploads\/sites\/190\/2024\/11\/DaffDNA-extraction-tube-organisation-sheet-212x300.jpg 212w, https:\/\/sites.dundee.ac.uk\/dundee-daffodil\/wp-content\/uploads\/sites\/190\/2024\/11\/DaffDNA-extraction-tube-organisation-sheet-768x1086.jpg 768w, https:\/\/sites.dundee.ac.uk\/dundee-daffodil\/wp-content\/uploads\/sites\/190\/2024\/11\/DaffDNA-extraction-tube-organisation-sheet.jpg 793w\" sizes=\"auto, (max-width: 724px) 100vw, 724px\" \/><\/figure>\n\n\n\n<hr class=\"wp-block-separator has-alpha-channel-opacity\" \/>\n\n\n\n<hr class=\"wp-block-separator has-alpha-channel-opacity\" \/>\n\n\n\n<h1 class=\"wp-block-heading\">STEP 1: Extracting Daffodil Chloroplast DNA<\/h1>\n\n\n\n<div class=\"wp-block-media-text alignwide is-stacked-on-mobile is-vertically-aligned-center\" style=\"grid-template-columns:45% auto\"><figure class=\"wp-block-media-text__media\"><img loading=\"lazy\" decoding=\"async\" width=\"723\" height=\"1024\" src=\"https:\/\/sites.dundee.ac.uk\/dundee-daffodil\/wp-content\/uploads\/sites\/190\/2022\/03\/RES119_bep_5-723x1024.jpg\" alt=\"\" class=\"wp-image-108 size-full\" srcset=\"https:\/\/sites.dundee.ac.uk\/dundee-daffodil\/wp-content\/uploads\/sites\/190\/2022\/03\/RES119_bep_5-723x1024.jpg 723w, https:\/\/sites.dundee.ac.uk\/dundee-daffodil\/wp-content\/uploads\/sites\/190\/2022\/03\/RES119_bep_5-212x300.jpg 212w, https:\/\/sites.dundee.ac.uk\/dundee-daffodil\/wp-content\/uploads\/sites\/190\/2022\/03\/RES119_bep_5-768x1088.jpg 768w, https:\/\/sites.dundee.ac.uk\/dundee-daffodil\/wp-content\/uploads\/sites\/190\/2022\/03\/RES119_bep_5-1085x1536.jpg 1085w, https:\/\/sites.dundee.ac.uk\/dundee-daffodil\/wp-content\/uploads\/sites\/190\/2022\/03\/RES119_bep_5-1446x2048.jpg 1446w, https:\/\/sites.dundee.ac.uk\/dundee-daffodil\/wp-content\/uploads\/sites\/190\/2022\/03\/RES119_bep_5-scaled.jpg 1808w\" sizes=\"auto, (max-width: 723px) 100vw, 723px\" \/><\/figure><div class=\"wp-block-media-text__content\">\n<p><a href=\"https:\/\/sites.dundee.ac.uk\/dundee-daffodil\/wp-content\/uploads\/sites\/190\/2022\/03\/RES119_bep_5.pdf\" target=\"_blank\" rel=\"noreferrer noopener\" data-type=\"URL\" data-id=\"https:\/\/sites.dundee.ac.uk\/dundee-daffodil\/wp-content\/uploads\/sites\/190\/2022\/03\/RES119_bep_5.pdf\"><code><strong><u>Extracting chloroplasts using ultracentrifugation protocol with buffer instructions pdf<\/u><\/strong><\/code><\/a><\/p>\n<\/div><\/div>\n\n\n\n<hr class=\"wp-block-separator has-alpha-channel-opacity\" \/>\n\n\n\n<hr class=\"wp-block-separator has-alpha-channel-opacity\" \/>\n\n\n\n<h2 class=\"wp-block-heading\"><strong>STEP 2. Choosing the Best DNA<\/strong><\/h2>\n\n\n\n<h2 class=\"wp-block-heading\">Using Gel Electrophoresis to Select the Cleanest DNA sample<\/h2>\n\n\n\n<figure class=\"wp-block-embed is-type-video is-provider-youtube wp-block-embed-youtube wp-embed-aspect-16-9 wp-has-aspect-ratio\"><div class=\"wp-block-embed__wrapper\">\n<iframe loading=\"lazy\" title=\"blueGel\u2122 electrophoresis by miniPCR bio\u2122\" width=\"1290\" height=\"726\" src=\"https:\/\/www.youtube.com\/embed\/BnPSn1SI43g?start=13&#038;feature=oembed\" frameborder=\"0\" allow=\"accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share\" referrerpolicy=\"strict-origin-when-cross-origin\" allowfullscreen><\/iframe>\n<\/div><figcaption class=\"wp-element-caption\">For more information visit the mini pcr website at <a href=\"https:\/\/www.minipcr.com\/products\/bluegel\/\">https:\/\/www.minipcr.com\/products\/bluegel\/<\/a><\/figcaption><\/figure>\n\n\n\n<div class=\"wp-block-media-text alignwide is-stacked-on-mobile\" style=\"grid-template-columns:46% auto\"><figure class=\"wp-block-media-text__media\"><img loading=\"lazy\" decoding=\"async\" width=\"1024\" height=\"765\" src=\"https:\/\/sites.dundee.ac.uk\/dundee-daffodil\/wp-content\/uploads\/sites\/190\/2022\/03\/minipcr-1024x765.jpg\" alt=\"\" class=\"wp-image-129 size-full\" srcset=\"https:\/\/sites.dundee.ac.uk\/dundee-daffodil\/wp-content\/uploads\/sites\/190\/2022\/03\/minipcr-1024x765.jpg 1024w, https:\/\/sites.dundee.ac.uk\/dundee-daffodil\/wp-content\/uploads\/sites\/190\/2022\/03\/minipcr-300x224.jpg 300w, https:\/\/sites.dundee.ac.uk\/dundee-daffodil\/wp-content\/uploads\/sites\/190\/2022\/03\/minipcr-768x574.jpg 768w, https:\/\/sites.dundee.ac.uk\/dundee-daffodil\/wp-content\/uploads\/sites\/190\/2022\/03\/minipcr-1536x1148.jpg 1536w, https:\/\/sites.dundee.ac.uk\/dundee-daffodil\/wp-content\/uploads\/sites\/190\/2022\/03\/minipcr-401x300.jpg 401w, https:\/\/sites.dundee.ac.uk\/dundee-daffodil\/wp-content\/uploads\/sites\/190\/2022\/03\/minipcr.jpg 1796w\" sizes=\"auto, (max-width: 1024px) 100vw, 1024px\" \/><\/figure><div class=\"wp-block-media-text__content\">\n<p><code><strong><a href=\"https:\/\/www.minipcr.com\/downloads\/\" target=\"_blank\" rel=\"noreferrer noopener\" data-type=\"URL\" data-id=\"https:\/\/www.minipcr.com\/downloads\/\"><u>To program the thermocycler<\/u>, download the software at https:\/\/www.minipcr.com\/downloads\/<\/a><\/strong><\/code><\/p>\n<\/div><\/div>\n\n\n\n<hr class=\"wp-block-separator has-alpha-channel-opacity\" \/>\n\n\n\n<hr class=\"wp-block-separator has-alpha-channel-opacity\" \/>\n\n\n\n<h2 class=\"wp-block-heading\"><strong>STEP 3: DNA Library Preparation<\/strong><\/h2>\n\n\n\n<p><em>Walkthrough Video 1:<\/em> DNA Extraction using Qiagen DNeasy Plant Mini Kit<\/p>\n\n\n\n<figure class=\"wp-block-embed aligncenter is-type-video is-provider-youtube wp-block-embed-youtube wp-embed-aspect-4-3 wp-has-aspect-ratio\"><div class=\"wp-block-embed__wrapper\">\n<iframe loading=\"lazy\" title=\"Video 1: DNA Extraction using Qiagen DNeasy Plant Mini Kit\" width=\"1290\" height=\"968\" src=\"https:\/\/www.youtube.com\/embed\/c1WOBy5vSg8?feature=oembed\" frameborder=\"0\" allow=\"accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share\" referrerpolicy=\"strict-origin-when-cross-origin\" allowfullscreen><\/iframe>\n<\/div><\/figure>\n\n\n\n<div class=\"wp-block-media-text alignwide is-stacked-on-mobile\" style=\"grid-template-columns:46% auto\"><figure class=\"wp-block-media-text__media\"><img loading=\"lazy\" decoding=\"async\" width=\"793\" height=\"1024\" src=\"https:\/\/sites.dundee.ac.uk\/dundee-daffodil\/wp-content\/uploads\/sites\/190\/2022\/03\/HB-0542-003-1101205_PCard_DNY_Plant_Spin_0316_WW_WEB-793x1024.jpg\" alt=\"\" class=\"wp-image-121 size-full\" srcset=\"https:\/\/sites.dundee.ac.uk\/dundee-daffodil\/wp-content\/uploads\/sites\/190\/2022\/03\/HB-0542-003-1101205_PCard_DNY_Plant_Spin_0316_WW_WEB-793x1024.jpg 793w, https:\/\/sites.dundee.ac.uk\/dundee-daffodil\/wp-content\/uploads\/sites\/190\/2022\/03\/HB-0542-003-1101205_PCard_DNY_Plant_Spin_0316_WW_WEB-232x300.jpg 232w, https:\/\/sites.dundee.ac.uk\/dundee-daffodil\/wp-content\/uploads\/sites\/190\/2022\/03\/HB-0542-003-1101205_PCard_DNY_Plant_Spin_0316_WW_WEB-768x992.jpg 768w, https:\/\/sites.dundee.ac.uk\/dundee-daffodil\/wp-content\/uploads\/sites\/190\/2022\/03\/HB-0542-003-1101205_PCard_DNY_Plant_Spin_0316_WW_WEB-1190x1536.jpg 1190w, https:\/\/sites.dundee.ac.uk\/dundee-daffodil\/wp-content\/uploads\/sites\/190\/2022\/03\/HB-0542-003-1101205_PCard_DNY_Plant_Spin_0316_WW_WEB-1586x2048.jpg 1586w, https:\/\/sites.dundee.ac.uk\/dundee-daffodil\/wp-content\/uploads\/sites\/190\/2022\/03\/HB-0542-003-1101205_PCard_DNY_Plant_Spin_0316_WW_WEB.jpg 1748w\" sizes=\"auto, (max-width: 793px) 100vw, 793px\" \/><\/figure><div class=\"wp-block-media-text__content\">\n<p><code><strong><a href=\"https:\/\/sites.dundee.ac.uk\/dundee-daffodil\/wp-content\/uploads\/sites\/190\/2022\/03\/HB-0542-003-1101205_PCard_DNY_Plant_Spin_0316_WW_WEB.pdf\" target=\"_blank\" rel=\"noreferrer noopener\" data-type=\"URL\" data-id=\"https:\/\/sites.dundee.ac.uk\/dundee-daffodil\/wp-content\/uploads\/sites\/190\/2022\/03\/HB-0542-003-1101205_PCard_DNY_Plant_Spin_0316_WW_WEB.pdf\"><u>Extract DNA Qiagen Instructions pdf<\/u><\/a><\/strong><\/code><\/p>\n<\/div><\/div>\n\n\n\n<hr class=\"wp-block-separator has-alpha-channel-opacity\" \/>\n\n\n\n<hr class=\"wp-block-separator has-alpha-channel-opacity\" \/>\n\n\n\n<h2 class=\"wp-block-heading\">STEP 4: DNA Sequencing using MinION Oxford Nanopore Technology<\/h2>\n\n\n\n<p><em><em>Walkthrough Video 2:<\/em><\/em> DNA Library Preparation Minion Flow Cell Loading &amp; Set up<\/p>\n\n\n\n<figure class=\"wp-block-embed aligncenter is-type-video is-provider-youtube wp-block-embed-youtube wp-embed-aspect-16-9 wp-has-aspect-ratio\"><div class=\"wp-block-embed__wrapper\">\n<iframe loading=\"lazy\" title=\"STEM Workshop 2024\" width=\"1290\" height=\"726\" src=\"https:\/\/www.youtube.com\/embed\/CmAYkPPwdOk?feature=oembed\" frameborder=\"0\" allow=\"accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share\" referrerpolicy=\"strict-origin-when-cross-origin\" allowfullscreen><\/iframe>\n<\/div><\/figure>\n\n\n\n<div class=\"wp-block-media-text alignwide is-stacked-on-mobile\" style=\"grid-template-columns:49% auto\"><figure class=\"wp-block-media-text__media\"><img loading=\"lazy\" decoding=\"async\" width=\"789\" height=\"1024\" src=\"https:\/\/sites.dundee.ac.uk\/dundee-daffodil\/wp-content\/uploads\/sites\/190\/2022\/03\/Rapid-Lambda-Control-Experiment-SQK-RAD004-minion-789x1024.jpg\" alt=\"\" class=\"wp-image-116 size-full\" srcset=\"https:\/\/sites.dundee.ac.uk\/dundee-daffodil\/wp-content\/uploads\/sites\/190\/2022\/03\/Rapid-Lambda-Control-Experiment-SQK-RAD004-minion-789x1024.jpg 789w, https:\/\/sites.dundee.ac.uk\/dundee-daffodil\/wp-content\/uploads\/sites\/190\/2022\/03\/Rapid-Lambda-Control-Experiment-SQK-RAD004-minion-231x300.jpg 231w, https:\/\/sites.dundee.ac.uk\/dundee-daffodil\/wp-content\/uploads\/sites\/190\/2022\/03\/Rapid-Lambda-Control-Experiment-SQK-RAD004-minion-768x996.jpg 768w, https:\/\/sites.dundee.ac.uk\/dundee-daffodil\/wp-content\/uploads\/sites\/190\/2022\/03\/Rapid-Lambda-Control-Experiment-SQK-RAD004-minion-1184x1536.jpg 1184w, https:\/\/sites.dundee.ac.uk\/dundee-daffodil\/wp-content\/uploads\/sites\/190\/2022\/03\/Rapid-Lambda-Control-Experiment-SQK-RAD004-minion-1579x2048.jpg 1579w, https:\/\/sites.dundee.ac.uk\/dundee-daffodil\/wp-content\/uploads\/sites\/190\/2022\/03\/Rapid-Lambda-Control-Experiment-SQK-RAD004-minion-scaled.jpg 1973w\" sizes=\"auto, (max-width: 789px) 100vw, 789px\" \/><\/figure><div class=\"wp-block-media-text__content\">\n<p><code><strong><a href=\"https:\/\/sites.dundee.ac.uk\/dundee-daffodil\/wp-content\/uploads\/sites\/190\/2022\/03\/Rapid-Lambda-Control-Experiment-SQK-RAD004-minion.pdf\" target=\"_blank\" rel=\"noreferrer noopener\" data-type=\"URL\" data-id=\"https:\/\/sites.dundee.ac.uk\/dundee-daffodil\/wp-content\/uploads\/sites\/190\/2022\/03\/Rapid-Lambda-Control-Experiment-SQK-RAD004-minion.pdf\"><u>Lambda quality assurance protocol pdf<\/u><\/a><\/strong><\/code><\/p>\n<\/div><\/div>\n\n\n\n<div class=\"wp-block-media-text alignwide is-stacked-on-mobile\" style=\"grid-template-columns:49% auto\"><figure class=\"wp-block-media-text__media\"><img loading=\"lazy\" decoding=\"async\" width=\"749\" height=\"1024\" src=\"https:\/\/sites.dundee.ac.uk\/dundee-daffodil\/wp-content\/uploads\/sites\/190\/2022\/03\/rapid-sequencing-sqk-rad004-RSE_9046_v1_revY_14Aug2019-minion-749x1024.jpg\" alt=\"\" class=\"wp-image-133 size-full\" srcset=\"https:\/\/sites.dundee.ac.uk\/dundee-daffodil\/wp-content\/uploads\/sites\/190\/2022\/03\/rapid-sequencing-sqk-rad004-RSE_9046_v1_revY_14Aug2019-minion-749x1024.jpg 749w, https:\/\/sites.dundee.ac.uk\/dundee-daffodil\/wp-content\/uploads\/sites\/190\/2022\/03\/rapid-sequencing-sqk-rad004-RSE_9046_v1_revY_14Aug2019-minion-219x300.jpg 219w, https:\/\/sites.dundee.ac.uk\/dundee-daffodil\/wp-content\/uploads\/sites\/190\/2022\/03\/rapid-sequencing-sqk-rad004-RSE_9046_v1_revY_14Aug2019-minion-768x1051.jpg 768w, https:\/\/sites.dundee.ac.uk\/dundee-daffodil\/wp-content\/uploads\/sites\/190\/2022\/03\/rapid-sequencing-sqk-rad004-RSE_9046_v1_revY_14Aug2019-minion-1123x1536.jpg 1123w, https:\/\/sites.dundee.ac.uk\/dundee-daffodil\/wp-content\/uploads\/sites\/190\/2022\/03\/rapid-sequencing-sqk-rad004-RSE_9046_v1_revY_14Aug2019-minion-1497x2048.jpg 1497w, https:\/\/sites.dundee.ac.uk\/dundee-daffodil\/wp-content\/uploads\/sites\/190\/2022\/03\/rapid-sequencing-sqk-rad004-RSE_9046_v1_revY_14Aug2019-minion-scaled.jpg 1871w\" sizes=\"auto, (max-width: 749px) 100vw, 749px\" \/><\/figure><div class=\"wp-block-media-text__content\">\n<p><code><a href=\"https:\/\/sites.dundee.ac.uk\/dundee-daffodil\/wp-content\/uploads\/sites\/190\/2022\/03\/rapid-sequencing-sqk-rad004-RSE_9046_v1_revY_14Aug2019-minion.pdf\" target=\"_blank\" rel=\"noreferrer noopener\" data-type=\"URL\" data-id=\"https:\/\/sites.dundee.ac.uk\/dundee-daffodil\/wp-content\/uploads\/sites\/190\/2022\/03\/rapid-sequencing-sqk-rad004-RSE_9046_v1_revY_14Aug2019-minion.pdf\"><strong><u>Library prep and flow cell loading instructions pdf<\/u><\/strong><\/a><\/code><\/p>\n<\/div><\/div>\n\n\n\n<hr class=\"wp-block-separator has-alpha-channel-opacity\" \/>\n\n\n\n<hr class=\"wp-block-separator has-alpha-channel-opacity\" \/>\n\n\n\n<h2 class=\"wp-block-heading\">STEP 5: <strong>Base Calling <\/strong><\/h2>\n\n\n\n<p>Base calling is the process of translating the electronic raw signal of the sequencer into bases. <\/p>\n\n\n\n<p><em>Walkthrough Video 3:<\/em> <\/p>\n\n\n\n<pre class=\"wp-block-code\"><code><\/code><\/pre>\n\n\n\n<hr class=\"wp-block-separator has-alpha-channel-opacity\" \/>\n\n\n\n<hr class=\"wp-block-separator has-alpha-channel-opacity\" \/>\n\n\n\n<h2 class=\"wp-block-heading\">STEP 6: <strong>Assembling the DNA sequence with Geneious Prime<\/strong><\/h2>\n\n\n\n<p><em>Walkthrough Video 4:<\/em> Geneious Prime Sequence Assembly Instructions<\/p>\n\n\n\n<figure class=\"wp-block-embed is-type-video is-provider-youtube wp-block-embed-youtube wp-embed-aspect-16-9 wp-has-aspect-ratio\"><div class=\"wp-block-embed__wrapper\">\n<iframe loading=\"lazy\" title=\"Video 4: Geneious Prime Sequence Assembly Instructions\" width=\"1290\" height=\"726\" src=\"https:\/\/www.youtube.com\/embed\/7CPt7WDU2NA?feature=oembed\" frameborder=\"0\" allow=\"accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share\" referrerpolicy=\"strict-origin-when-cross-origin\" allowfullscreen><\/iframe>\n<\/div><\/figure>\n\n\n\n<hr class=\"wp-block-separator has-alpha-channel-opacity\" \/>\n\n\n\n<hr class=\"wp-block-separator has-alpha-channel-opacity\" \/>\n\n\n\n<h2 class=\"wp-block-heading\">STEP 7: <strong>Viewing and Analysising the DNA Sequence in Jalview<\/strong><\/h2>\n\n\n\n<p>Jalview is one of the most widely used programs for visualizing and analyzing DNA, RNA and protein multiple sequence alignments. It uses an interactive multi-window interface for viewing sequences, trees, and three-dimensional structures. It has a number of analysis tools for aligning sequences, measuring similarities and comparing structures.<\/p>\n\n\n\n<div class=\"wp-block-media-text alignwide is-stacked-on-mobile\" style=\"grid-template-columns:42% auto\"><figure class=\"wp-block-media-text__media\"><img loading=\"lazy\" decoding=\"async\" width=\"591\" height=\"836\" src=\"https:\/\/sites.dundee.ac.uk\/dundee-daffodil\/wp-content\/uploads\/sites\/190\/2022\/03\/Daffodil-Workbook.jpeg\" alt=\"\" class=\"wp-image-101 size-full\" srcset=\"https:\/\/sites.dundee.ac.uk\/dundee-daffodil\/wp-content\/uploads\/sites\/190\/2022\/03\/Daffodil-Workbook.jpeg 591w, https:\/\/sites.dundee.ac.uk\/dundee-daffodil\/wp-content\/uploads\/sites\/190\/2022\/03\/Daffodil-Workbook-212x300.jpeg 212w\" sizes=\"auto, (max-width: 591px) 100vw, 591px\" \/><\/figure><div class=\"wp-block-media-text__content\">\n<p><code><a href=\"https:\/\/sites.dundee.ac.uk\/dundee-daffodil\/wp-content\/uploads\/sites\/190\/2022\/03\/Daffodil-Workbook-v001-18Mar2022.pdf\" target=\"_blank\" rel=\"noreferrer noopener\" data-type=\"URL\" data-id=\"https:\/\/sites.dundee.ac.uk\/dundee-daffodil\/wp-content\/uploads\/sites\/190\/2022\/03\/Daffodil-Workbook-v001-18Mar2022.pdf\"><strong><u>Jalview Workbook for viewing and analysing the daffodil chloroplast sequences pdf<\/u><\/strong><\/a><\/code><\/p>\n<\/div><\/div>\n\n\n\n<p><em>W<\/em><em><em>alkthrough Video 5:<\/em><\/em> Trimming the Sequence Assembly using Jalview<\/p>\n\n\n\n<figure class=\"wp-block-embed is-type-video is-provider-youtube wp-block-embed-youtube wp-embed-aspect-16-9 wp-has-aspect-ratio\"><div class=\"wp-block-embed__wrapper\">\n<iframe loading=\"lazy\" title=\"Video 5: Trimming the Sequence Assembly using Jalview\" width=\"1290\" height=\"726\" src=\"https:\/\/www.youtube.com\/embed\/Vy2M615oImQ?feature=oembed\" frameborder=\"0\" allow=\"accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share\" referrerpolicy=\"strict-origin-when-cross-origin\" allowfullscreen><\/iframe>\n<\/div><\/figure>\n\n\n\n<p><em><em>Walkthrough Video <\/em>6:<\/em> Reviewing the Assembled Sequences using Jalview<\/p>\n\n\n\n<figure class=\"wp-block-embed is-type-video is-provider-youtube wp-block-embed-youtube wp-embed-aspect-16-9 wp-has-aspect-ratio\"><div class=\"wp-block-embed__wrapper\">\n<iframe loading=\"lazy\" title=\"Video 6: Reviewing the Assembled Sequences using Jalview\" width=\"1290\" height=\"726\" src=\"https:\/\/www.youtube.com\/embed\/yV-bnGQ_cbQ?feature=oembed\" frameborder=\"0\" allow=\"accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share\" referrerpolicy=\"strict-origin-when-cross-origin\" allowfullscreen><\/iframe>\n<\/div><\/figure>\n\n\n\n<p><em><em>Walkthrough Video 7<\/em>:<\/em> Create a Tree of Daffodil Chloroplast DNA Sequences<\/p>\n\n\n\n<figure class=\"wp-block-embed is-type-video is-provider-youtube wp-block-embed-youtube wp-embed-aspect-16-9 wp-has-aspect-ratio\"><div class=\"wp-block-embed__wrapper\">\n<iframe loading=\"lazy\" title=\"Video 7: Create a Tree of Daffodil Chloroplast DNA Sequences from Different Cultivars\" width=\"1290\" height=\"726\" src=\"https:\/\/www.youtube.com\/embed\/Opj_emB1Tgo?feature=oembed\" frameborder=\"0\" allow=\"accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share\" referrerpolicy=\"strict-origin-when-cross-origin\" allowfullscreen><\/iframe>\n<\/div><\/figure>\n\n\n\n<hr class=\"wp-block-separator has-alpha-channel-opacity\" \/>\n\n\n\n<hr class=\"wp-block-separator has-alpha-channel-opacity\" \/>\n\n\n\n<h2 class=\"wp-block-heading\">STEP 8: <strong>Viewing <\/strong>the Daffodil Chloroplast Genome using OGDRAW<\/h2>\n\n\n\n<p><em><em>Walkthrough Video <\/em>8:<\/em> Using OGDRAW to Create Graphical Gene Maps<\/p>\n\n\n\n<figure class=\"wp-block-embed is-type-video is-provider-youtube wp-block-embed-youtube wp-embed-aspect-16-9 wp-has-aspect-ratio\"><div class=\"wp-block-embed__wrapper\">\n<iframe loading=\"lazy\" title=\"Video 8: Using OGDRAW to Create Graphical Gene Maps\" width=\"1290\" height=\"726\" src=\"https:\/\/www.youtube.com\/embed\/0iwm_DwwwgQ?feature=oembed\" frameborder=\"0\" allow=\"accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share\" referrerpolicy=\"strict-origin-when-cross-origin\" allowfullscreen><\/iframe>\n<\/div><\/figure>\n\n\n\n<hr class=\"wp-block-separator has-alpha-channel-opacity\" \/>\n\n\n\n<hr class=\"wp-block-separator has-alpha-channel-opacity\" \/>\n\n\n\n<h2 class=\"wp-block-heading\">Why do we need Bioinformatics Software such as Jalview?<\/h2>\n\n\n\n<figure class=\"wp-block-embed is-type-video is-provider-youtube wp-block-embed-youtube wp-embed-aspect-16-9 wp-has-aspect-ratio\"><div class=\"wp-block-embed__wrapper\">\n<iframe loading=\"lazy\" title=\"School Video 1: Bioinformatics and Big Data\" width=\"1290\" height=\"726\" src=\"https:\/\/www.youtube.com\/embed\/f2PAQh17viM?feature=oembed\" frameborder=\"0\" allow=\"accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share\" referrerpolicy=\"strict-origin-when-cross-origin\" allowfullscreen><\/iframe>\n<\/div><\/figure>\n\n\n\n<hr class=\"wp-block-separator has-alpha-channel-opacity\" \/>\n\n\n\n<hr class=\"wp-block-separator has-alpha-channel-opacity\" \/>\n\n\n\n<h2 class=\"wp-block-heading\">Pressing Daffodils<\/h2>\n\n\n\n<p>Kevin Frediani has kindly shared herbarium protocols for pressing daffodils, if you would like to preserve your specimens.<br><\/p>\n\n\n\n<div data-wp-interactive=\"core\/file\" class=\"wp-block-file\"><object data-wp-bind--hidden=\"!state.hasPdfPreview\" hidden class=\"wp-block-file__embed\" data=\"https:\/\/sites.dundee.ac.uk\/dundee-daffodil\/wp-content\/uploads\/sites\/190\/2026\/03\/Narcissus_Herbarium_Preperation_KF.pdf\" type=\"application\/pdf\" style=\"width:100%;height:600px\" aria-label=\"Embed of Narcissus_Herbarium_Preperation_KF.\"><\/object><a id=\"wp-block-file--media-6d5aa197-d3a2-471f-a929-182db08a27ff\" href=\"https:\/\/sites.dundee.ac.uk\/dundee-daffodil\/wp-content\/uploads\/sites\/190\/2026\/03\/Narcissus_Herbarium_Preperation_KF.pdf\">Narcissus_Herbarium_Preperation_KF<\/a><a href=\"https:\/\/sites.dundee.ac.uk\/dundee-daffodil\/wp-content\/uploads\/sites\/190\/2026\/03\/Narcissus_Herbarium_Preperation_KF.pdf\" class=\"wp-block-file__button wp-element-button\" download aria-describedby=\"wp-block-file--media-6d5aa197-d3a2-471f-a929-182db08a27ff\">Download<\/a><\/div>\n\n\n\n<h2 class=\"wp-block-heading\">Miscellaneous<\/h2>\n\n\n\n<div class=\"wp-block-media-text alignwide is-stacked-on-mobile\"><figure class=\"wp-block-media-text__media\"><img loading=\"lazy\" decoding=\"async\" width=\"970\" height=\"1024\" src=\"https:\/\/sites.dundee.ac.uk\/dundee-daffodil\/wp-content\/uploads\/sites\/190\/2022\/05\/pipette-970x1024.jpg\" alt=\"\" class=\"wp-image-252 size-full\" srcset=\"https:\/\/sites.dundee.ac.uk\/dundee-daffodil\/wp-content\/uploads\/sites\/190\/2022\/05\/pipette-970x1024.jpg 970w, https:\/\/sites.dundee.ac.uk\/dundee-daffodil\/wp-content\/uploads\/sites\/190\/2022\/05\/pipette-284x300.jpg 284w, https:\/\/sites.dundee.ac.uk\/dundee-daffodil\/wp-content\/uploads\/sites\/190\/2022\/05\/pipette-768x811.jpg 768w, https:\/\/sites.dundee.ac.uk\/dundee-daffodil\/wp-content\/uploads\/sites\/190\/2022\/05\/pipette-1455x1536.jpg 1455w, https:\/\/sites.dundee.ac.uk\/dundee-daffodil\/wp-content\/uploads\/sites\/190\/2022\/05\/pipette-1940x2048.jpg 1940w\" sizes=\"auto, (max-width: 970px) 100vw, 970px\" \/><\/figure><div class=\"wp-block-media-text__content\">\n<p><code><a href=\"https:\/\/sites.dundee.ac.uk\/dundee-daffodil\/wp-content\/uploads\/sites\/190\/2022\/05\/daffodil-pipette-template-scaled.jpg\" target=\"_blank\" rel=\"noreferrer noopener\" data-type=\"URL\" data-id=\"https:\/\/sites.dundee.ac.uk\/dundee-daffodil\/wp-content\/uploads\/sites\/190\/2022\/05\/daffodil-pipette-template-scaled.jpg\">Download the daffodil pipette template pdf<\/a><\/code><\/p>\n<\/div><\/div>\n","protected":false},"excerpt":{"rendered":"<p>Overview pdf Summarising all 8 Steps DaffDNA Extraction Protocol DaffDNA Extraction Tube Organisation Sheet STEP 1: Extracting Daffodil Chloroplast DNA Extracting chloroplasts using ultracentrifugation protocol with buffer instructions pdf STEP 2. Choosing the Best DNA Using Gel Electrophoresis to Select the Cleanest DNA sample To program the thermocycler, download the software at https:\/\/www.minipcr.com\/downloads\/ STEP 3: [&hellip;]<\/p>\n","protected":false},"author":8,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-73","page","type-page","status-publish","hentry"],"blocksy_meta":[],"_links":{"self":[{"href":"https:\/\/sites.dundee.ac.uk\/dundee-daffodil\/wp-json\/wp\/v2\/pages\/73","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/sites.dundee.ac.uk\/dundee-daffodil\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/sites.dundee.ac.uk\/dundee-daffodil\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/sites.dundee.ac.uk\/dundee-daffodil\/wp-json\/wp\/v2\/users\/8"}],"replies":[{"embeddable":true,"href":"https:\/\/sites.dundee.ac.uk\/dundee-daffodil\/wp-json\/wp\/v2\/comments?post=73"}],"version-history":[{"count":211,"href":"https:\/\/sites.dundee.ac.uk\/dundee-daffodil\/wp-json\/wp\/v2\/pages\/73\/revisions"}],"predecessor-version":[{"id":693,"href":"https:\/\/sites.dundee.ac.uk\/dundee-daffodil\/wp-json\/wp\/v2\/pages\/73\/revisions\/693"}],"wp:attachment":[{"href":"https:\/\/sites.dundee.ac.uk\/dundee-daffodil\/wp-json\/wp\/v2\/media?parent=73"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}