Module 1 Instructor Resources =============================== .. rubric:: Instructor Resources for Module 1: Introduction to the Genome Browser: What is a gene? :class: header1 Cover Page ------------------------------- Submission Details ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. cssclass:: gea-cover-page-table +-----------------------------------+-----------------------------------+ | Submitter: | Anne Rosenwald | | | (rosenwaa@georgetown.edu) | +-----------------------------------+-----------------------------------+ | Submission timestamp: | 2019/07/31 4:07:32 PM EST | +-----------------------------------+-----------------------------------+ | Authors: | - Joyce Stamm, University of | | | Evansville | | | | | | - Jennifer Kennell, Vassar | | | College | | | | | | - Wilson Leung, Washington | | | University in St. Louis | | | | | | - Leocadia Paliulis, Bucknell | | | University | | | | | | - Srebrenka Robic, Agnes Scott | | | College | +-----------------------------------+-----------------------------------+ | Corresponding author: | Anne Rosenwald | | | (rosenwaa@georgetown.edu) | +-----------------------------------+-----------------------------------+ Lesson Overview ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. cssclass:: gea-cover-page-table +-----------------------------------+-----------------------------------+ | Lesson abstract: | This lesson introduces the | | | University of California Santa | | | Cruz genome browser to students, | | | walking them through some of the | | | key features so that it can be | | | used for analysis of gene | | | structure. | +-----------------------------------+-----------------------------------+ | Lesson keywords: | - Genome Browser | | | | | | - Exons | | | | | | - Introns | | | | | | - Evidence Track | | | | | | - Start Codon | | | | | | - Stop Codon | +-----------------------------------+-----------------------------------+ | Organism(s) that are the focus of | Drosophila | | this lesson: | | +-----------------------------------+-----------------------------------+ | Type(s) of student learning | Quiz questions | | assessments: | | +-----------------------------------+-----------------------------------+ | Websites and online databases | GEP UCSC Genome Browser | | used: | (http://gander.wustl.edu) | +-----------------------------------+-----------------------------------+ | Resources in addition to the | Questions to work through | | lesson instructions: | | +-----------------------------------+-----------------------------------+ Learning Topics ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. cssclass:: gea-cover-page-table +-----------------------------------+-----------------------------------+ | Topics in scientific fields: | - Bioinformatics | | | | | | - Genetics | +-----------------------------------+-----------------------------------+ | Topics in mathematics or | - None | | statistics: | | +-----------------------------------+-----------------------------------+ | Topics in bioinformatics or data | - Similarity searches (BLAST, | | science: | Multiple Sequence Alignment) | +-----------------------------------+-----------------------------------+ Student Prerequisites ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. cssclass:: gea-cover-page-table +-----------------------------------+-----------------------------------+ | Recommended prior course work: | - High school level biology | | | | | | - Introductory college biology | | | | | | - Genetics | +-----------------------------------+-----------------------------------+ | Recommended computer skills: | Basic: Familiarity with web | | | browsers, word processing | +-----------------------------------+-----------------------------------+ Instructor Prerequisites ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. cssclass:: gea-cover-page-table +-----------------------------------+-----------------------------------+ | Recommended computer skills: | Basic: Familiarity with web | | | browsers, word processing | +-----------------------------------+-----------------------------------+ | Instructional requirements: | Basic Computer Lab (Access to | | | laptops/desktops, no large memory | | | or CPU requirements) | +-----------------------------------+-----------------------------------+ Implementation Recommendations ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. cssclass:: gea-cover-page-table +-----------------------------------+-----------------------------------+ | Instructional time required: | 1 class period or less | +-----------------------------------+-----------------------------------+ | Students work as individuals or | Either individual or team work is | | teams? | possible | +-----------------------------------+-----------------------------------+ | Number of students in a class: | More than 50 students (assume no | | | TAs and one computer for each | | | student) | +-----------------------------------+-----------------------------------+ Accessibility ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. cssclass:: gea-cover-page-table +-----------------------------------+-----------------------------------+ | Available languages: | English | +-----------------------------------+-----------------------------------+ | Additional materials for students | None | | with disabilities: | | +-----------------------------------+-----------------------------------+ .. meta:: :keywords: Genome Browser, Exons, Introns, Evidence Track, Start Codon, Stop Codon Lesson Plan ------------------------------- Title ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - Introduction to the Genome Browser: What is a Gene? Objectives ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - Demonstrate basic skills in using the UCSC Genome Browser to navigate to a genomic region and to control the display settings for different evidence tracks. - Explain the relationships among DNA, pre-mRNA, mRNA, and protein. - Use the navigation tools in the genome browser to zoom in and zoom out on a given region and identify the genes in that region (:ref:`Section 1.1`). - Determine the orientation, number of exons, and number of introns for any given isoform (:ref:`Section 1.2`). - Use the genome browser to visualize the three possible reading frames on each strand (:ref:`Section 1.3`). - Locate the start codon and stop codon for any given isoform (:ref:`Section 1.3`). - Identify open reading frames using the genome browser (:ref:`Section 1.4`). Pre-requisites: knowledge of... ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - DNA structure (base composition, anti-parallel double-stranded helix, base-pairing properties) - Chromosome structure (a chromosome is a continuous DNA molecule, basic understanding of chromosome arms) - Protein structure (proteins are made up of amino acids) Order ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - Warm Up - Investigation - Exit Homework ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - Discuss the question: What is a gene? (Discuss with a partner, then as a class.) Emphasize the *function* of a gene; consider how the structure of the gene is related to its function. - Work through the genome browser investigation, with pauses to discuss the answers to the questions. - Conclude with an emphasis on the main points: - Genes may run in either direction on a chromosome; - Genes are represented on the genome browser as blocks connected by lines; - Eukaryotic genes are made up of protein-coding exons (the blocks) connected by introns; - Proteins usually begin with a Methionine (M) and end at a stop codon (*) Associated Videos ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - `Genome Browser video `_ - `Tracks video `_ Module 1 Resources ------------------------------- The evidence tracks in the Genome Browser are grouped into three categories: - Mapping and Sequencing Tracks Basically these contain the information obtained from sequencing that region of the chromosome. These tracks show the As, Ts, Cs, and Gs (``Base Position``) and matches to particular sequences of interest (``Short Match``) or to the cleavage sites for different "Restriction Enzymes". - Genes and Gene Prediction Tracks These tracks show the genes as they are reported in the Drosophila Database (``FlyBase Genes``), and as predicted by a couple of computer programs (``Genscan Genes``, ``N-SCAN Genes``). It also contains the transcription start site (TSS) annotations (``TSS Annotations``) and *D. melanogaster* cDNAs that have been mapped to contig1. - RNA Seq Tracks These tracks show the results of sequencing mRNAs derived from a particular tissue and developmental time point. Most of the RNA-Seq reads are derived from processed mRNAs (where the introns have been removed). The mRNAs are broken into smaller fragments (e.g. via nebulization) prior to sequencing (usually using the Illumina HiSeq platform). The short reads (~100--125bp) are then mapped against the *D. melanogaster* genome. The y-axis of the ``RNA-Seq Coverage`` track shows the number of reads that has been mapped to each position of the contig (x-axis); this provides an estimate of the expression level. The ``Exon Junctions`` track shows the predicted locations of the introns. This track is derived from the subset of RNA-Seq reads that map partially to each of two adjacent exons (i.e. spliced RNA-Seq reads). .. tip:: For manipulating tracks, students may need to be reminded to read carefully what is immediately under the displayed tracks: Click on a feature for detail. Click sidebars for track options. Drag side bars or labels up or down to reorder tracks. Drag tracks left or right to a new position.