SCHEDULE for BL8048 The Genome: Expression & Dynamics (GED), 15 hp, HT 2018

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1 New version 1/ SCHEDULE for BL8048 The Genome: Expression & Dynamics (GED), 15 hp, HT 2018 The course begins: Monday November 5, in D508 Course leaders: Lars Wieslander LW Neus Visa NV Teachers: Ylva Engström YE Marc Friedländer MF Mattias Mannervik MM Klas Udekwu KU Uli Theopold UT Lab assistants: Kajsa Fritzell KF Li He LH Wenjing Kang WK Dan Liu DL Victor Karlström VK +? Venues: Lectures: D508 Svante Arrhenius väg 18B Laboratory excercises: D247 Svante Arrhenius väg 18B Computer exercises: D508 Literature: Molecular Biology of the gene, 7 th edition, Watson et al. + materials handed out during the course Examination: See separate document Exam: The final written exam will take place on January 18, 2019, Room:? The Written exam will be anonymous, register for the exam at the Department of Biology Education to obtain a code. The exam will be returned/reviewed? Retake of exam: If requested, a second exam will be arranged. Time and place will be decided later. The course is organized by the Department of Molecular Biosciences, The WennerGren Institue. It runs from November 5, 2018 to January 18, The course is based on lectures, individual studies, practical laboratory exercises and an individual project work. Lectures will be given by senior scientists, both in house and invited from the Stockholm-Uppsala region. This will ensure high quality and coverage of a broad range of aspects of genomes and genome research, from basic science to medical and technical applications. In addition to the course book,we will provide review articles for updated information and for filling gaps in the book content. Material such as computer-based presentations from lecturers will either be sent to you by or by using the web-based learning platform Mondo, under the label GED H18. All material is provided solely for your own individual studies during the course and cannot be copied or given further to others.

2 Day Time Venue Content and teacher Monday D508 Introduction 05 November D508 Individual project work: information and subjects D508 Coffee with teachers, sign up for project plan Tuesday D508 Lecture: Genome Sequence Dynamics LW 06 November D334 Individual studies: chapter 3-5, textbook Wednesday D508 Invited speaker: Genome analyses 07 November Björn Nystedt, SciLifeLab F402 Lecture: How to write a project plan LW/NV Thursday D508 Tutorial: Computer-based genome analysis UT 08 November Individual studies: read chapter 6-7 in the book Friday 09 November Invited speaker: Chromosome dynamics and DNA topology Camilla Björkegren, KI Monday D508 Lecture: The functional organization of the cell 12 November nucleus LW Individual studies: chapter 8-10, textbook Tuesday 13 November Individual studies: project work Wednesday Individual studies, read chapter November D508 Individual studies: review articles on cell nucleus Thursday D508 Lecture: How to study the Genome in situ NV 15 November D508 Individual studies: review articles on cell nucleus

3 Friday D508 Review discussion: The cell nucleus NV 16 November Monday Read review articles, Epigenetics 19 November D508 Lab: Introduction to ChIP NV D247 Lab: Chromatin Immuno-Precipitation; prepare buffers DL/LH Tuesday 9:30-12:00 Lecture: Transcriptional regulation 20 November in eukaryotes MM Lecture: Chromatin and epigenetics MM Lab: ChIP; Preparation of chromatin DL/LH Wednesday D247 Lab: ChIP; immunoprecipitation 21 November Read review articles, Epigenetics Thursday 9: D247 Lab: ChIP; DNA purification DL/LH 22 November D508 Review discussion: Epigenetics MM Friday D247 Lab: ChIP; dissolve DNA and PCR DL/LH 23 November D313 Lab: ChIP; electrophoresis and analysis DL/LH Monday 9: Individual studies: Project work 26 November D508 Diagnostic test1: Genome structure, chromatin LW Tuesday D508 Lecture: RNA processing as a regulatory event LW 27 November D508 Lab: Alternative RNA processing; transfection KF/VK Wednesday D508 Individual studies: read review articles on non-coding 28 November RNA Review discussion: non-coding RNA LW? Thursday D247 Lab: Alternative RNA processing; RNA prep., RT-PCR 29 November KF/VK Friday D508 Lecture: Regulatory RNAs MF 30 November D247 Lab: Alternative RNA processing; gel electrophoresis/ sequence analysis KF/VK

4 Monday D508 Methods lecture: Transcriptome analysis MF 03 December Individual studies: Prepare for seminar on project work Tuesday D508 Tutorial: Computational biology MF 04 December Individual studies: prepare for seminar on project work Turn in abstract for seminar on project Wednesday Individual studies: prepare for seminar on project work 05 December Thursday D508 Student seminar UT/NV 06 December D508 Student seminar NV/LW Friday D508 Student seminar YE/UT 07December Individual studies: read chapter Monday D508 Tutorial: Gene expression methodology YE 10 December D508 Diagnostic test 2: Regulation of the transcriptome NV/MF Tuesday Individual studies: Project work 11 December Wednesday D508 Lecture: Systems Biology and Genetic screens UT 12 December Individual studies: read chapter Thursday 13 December D508 Invited speaker: Functional genome analysis and functional adaptation Anthony Wright, KI Friday D508 Lecture: Metabolomics UT 14 December Monday D508 Invited speaker: Plasmodium and the impact of 17 December genome variability Mats Wahlgren, KI Tuesday D508 Individual studies: Project work 18 December D508 Tutorial: mrna quality control NV Wednesday Invited speaker: Domestic Animal Genome 19 December Analysis Göran Andersson, SLU Thursday D508 Methods lecture: Metagenomics KU 20 December Individual studies: Project work Friday Invited speaker: Metagenomics of complex 21 December microbial communities Daniel Lundin, SciLifeLab

5 Last day to turn in first draft of Project work to supervisor Winter break Monday D January D508 Diagnostic test 3: Functional genomics UT Tuesday Individual studies: Project work 08 January Wednesday Individual studies: Project work 09 January Thursday Individual studies: Project work 10 January Friday 11 January Individual studies: Project work Monday Individual studies: Project work/meet with supervisor 14 January, 2016 Tuesday Individual studies: Project work/meet with supervisor 15 January Wednesday-Thursday January Study for final written exam, finish project work 8-11 January Friday P232 Final exam and deadline for Project work 18 January