--- tags: ebook --- # Sequencing of phage genomes ## Chapter type: Course-based research * Lab Management and Prep (ordering, accounts, reagents, equipment) * Flavors: Quick start * Molecular biology (a specific lab protocol, e.g., DNA extraction, library prep) * Flavors: Tutorial, Lesson * Bioinformatics (data management and analysis) * Flavors: Quick start, tutorials, lessons ## Flavor: * Quick start: usually a page, focuses on achieving one goal, does not cover background information * Tutorial: walks through a demonstration of a technique with the goal of helping the learner understand * Lesson: Provides ample background information, has questions and answers to test learner understanding ## Media: * Videos, animations, figures LAB MANAGEMENT TEMPLATE (QUICK START) TITLE: Laboratory Materials ## SUMMARY: This tutorial can be used to isolate phages from soil and sequence their genomes using Nanopore sequencing technology. ## MATERIALS: ### For phage isolation from soil: [SEA-PHAGES Ordering Guide](https://seaphagesphagediscoveryguide.helpdocsonline.com/9-1-protocol) ### For Nanopore sequencing: #### DNA Extraction Supplies * 1 ml phage lysate (titer ≥ 5 x 10<sup>9</sup> pfu/ml) * Nuclease mix * EDTA (0.5 M) (optional) * Proteinase K (20 mg/ml) and SDS (10 %) (optional) * 2 ml DNA clean-up resin (Promega Wizard DNA Clean-Up Kit) * 2 DNA clean-up columns (Promega Wizard DNA Clean-Up Kit) * 3 ml syringes * 6 ml 80 % isopropanol, freshly prepared * ddH2O pre-warmed (95 &deg;C) #### Library preparation and sequencing: * Ligation sequencing gDNA - Native Barcoding Kit 24 V14 (SQK-NBD114.24) * MinION or MinIONmk1C ## PROTOCOL ### SEA-PHAGES protocol for phage isolation * [Collecting Environmental Samples](https://seaphagesphagediscoveryguide.helpdocsonline.com/5-1-protocol) * [Direct Isolation](https://seaphagesphagediscoveryguide.helpdocsonline.com/5-2-protocol) * [Plaque Assay](https://seaphagesphagediscoveryguide.helpdocsonline.com/5-3-protocol) * [Picking a Plaque](https://seaphagesphagediscoveryguide.helpdocsonline.com/5-4-protocol) * [Enriched Isolation](https://seaphagesphagediscoveryguide.helpdocsonline.com/5-5-protocol) * [Spot Test](https://seaphagesphagediscoveryguide.helpdocsonline.com/5-6-protocol) ### SEA-PHAGES protocol for phage purification [Phage purification](https://seaphagesphagediscoveryguide.helpdocsonline.com/6-0-toc) ### SEA-PHAGES protocol for DNA extraction [DNA Extraction](https://seaphagesphagediscoveryguide.helpdocsonline.com/9-1-protocol) ### Library Preparation [Ligation sequencing gDNA - Native Barcoding Kit 24 V14 (SQK-NBD114.24)](https://seaphagesphagediscoveryguide.helpdocsonline.com/9-1-protocol) Optional elements Media (Figures, animations, videos) Admonitions (Warnings, tips, etc.) MOLECULAR BIOLOGY (TUTORIAL) TITLE: Phage Isolation SUMMARY: Students will collect soil samples to isolate phages TIME: Estimated time to complete this activity Learning Objectives: 1-2 Learning objectives After completing this tutorial, you will be able to… 1. collect soil samples to use for their research project 2. isolate phages from the soil MATERIALS BACKGROUND Short explanation of background information PROTOCOL 1. Numbered instructions * Most steps should have some explanation SUMMARY * Key points and takeaway messages Optional elements Media (Figures, animations, videos) Admonitions (Warnings, tips, etc.) MOLECULAR BIOLOGY (Lesson) TITLE: DNA Extraction of Phage samples SUMMARY: 1-2 sentences on the purpose TIME: Estimated time to complete this activity Learning Objectives: 3-4 Learning objectives After completing this lesson, you will be able to… MATERIALS BACKGROUND Short explanation of background information Slides or other teaching materials PROTOCOL 1. Numbered instructions * Most steps should have some explanation QUESTIONS * Each learning objective should be paired with questions that demonstrate understanding SUMMARY * Key points and takeaway messages Optional elements Media (Figures, animations, videos) Admonitions (Warnings, tips, etc.) MOLECULAR BIOLOGY (Lesson) TITLE: DNA Extraction of Phage samples SUMMARY: 1-2 sentences on the purpose TIME: Estimated time to complete this activity Learning Objectives: 3-4 Learning objectives After completing this lesson, you will be able to… MATERIALS BACKGROUND Short explanation of background information Slides or other teaching materials PROTOCOL 1. Numbered instructions * Most steps should have some explanation QUESTIONS * Each learning objective should be paired with questions that demonstrate understanding SUMMARY * Key points and takeaway messages Optional elements Media (Figures, animations, videos) Admonitions (Warnings, tips, etc.) BIOINFORMATICS (TUTORIAL) TITLE: Genome assembly SUMMARY: 1-2 sentences on the purpose TIME: Estimated time to complete this activity Learning Objectives: 1-2 Learning objectives After completing this tutorial, you will be able to… SOFTWARE * Links to software * Container/Docker image (Github) BACKGROUND Short explanation of background information PROTOCOL 1. Numbered instructions * Most steps should have some explanation SUMMARY * Key points and takeaway messages Optional elements Media (Figures, animations, videos) Admonitions (Warnings, tips, etc.) BIOINFORMATICS (TUTORIAL) TITLE: Genome annotation SUMMARY: 1-2 sentences on the purpose TIME: Estimated time to complete this activity Learning Objectives: 1-2 Learning objectives After completing this tutorial, you will be able to… SOFTWARE * Links to software * Container/Docker image (Github) BACKGROUND Short explanation of background information PROTOCOL 1. Numbered instructions * Most steps should have some explanation SUMMARY * Key points and takeaway messages Optional elements Media (Figures, animations, videos) Admonitions (Warnings, tips, etc.) BIOINFORMATICS (TUTORIAL) TITLE: Genome Comparison SUMMARY: 1-2 sentences on the purpose TIME: Estimated time to complete this activity Learning Objectives: 1-2 Learning objectives After completing this tutorial, you will be able to… SOFTWARE * Links to software * Container/Docker image (Github) BACKGROUND Short explanation of background information PROTOCOL 1. Numbered instructions * Most steps should have some explanation SUMMARY * Key points and takeaway messages Optional elements Media (Figures, animations, videos) Admonitions (Warnings, tips, etc.) BIOINFORMATICS (TUTORIAL) TITLE: Phylogenetics SUMMARY: 1-2 sentences on the purpose TIME: Estimated time to complete this activity Learning Objectives: 1-2 Learning objectives After completing this tutorial, you will be able to… SOFTWARE * Links to software * Container/Docker image (Github) BACKGROUND Short explanation of background information PROTOCOL 1. Numbered instructions * Most steps should have some explanation SUMMARY * Key points and takeaway messages Optional elements Media (Figures, animations, videos) Admonitions (Warnings, tips, etc.)