CB 399: Transposon-Insertion Sequencing: the design and analysis of a new approach for bacterial genetics Spring 2015

Transposon-Insertion Sequencing: the design and analysis of a new approach for bacterial genetics

Course Instructors: Dr. Matthew K. Waldor (PI), Dr. Michael Chao (postdoc), Troy Hubbard (graduate student), Kasia Baranowski (graduate student), Karen Kieser (graduate student)
Curriculum Fellow: Zofia Gajdos, Zofia_Gajdos@hms.harvard.edu

Day 1: 1 hour introductory lecture to TIS followed by a 2-hour interactive presentation that covers the implementation of TIS and relevant experimental considerations for every step of the process. 

Day 2: A 3-hour hands-on workshop that focuses on how to use custom programs in Python and Matlab to visualize and analyze important TIS experimental metrics.  Attendees will also utilize several methods to analyze existing TIS data and generate biologically meaningful results.

Overview:

Transposon-Insertion Sequencing (TIS) is a revolutionary microbial genetic technique that unites high-density genome-wide transposon mutagenesis with high-throughput parallel sequencing to identify genes and regulatory networks necessary for bacterial growth under virtually any experimental condition.  As a computational approach, there are many experimental factors that can affect the applicability of the TIS technique and also impact the accuracy of downstream analysis methods.  This course aims to introduce and discuss the implications of these experimental parameters and offer practical experience in the analysis of TIS data using a variety of computational platforms.  There are two components to this course: a 3-hour lecture-based seminar and a 3-hour hands-on data analysis workshop.  The lecture will present experimental considerations for different types of TIS studies, and examine their respective merits and pitfalls, relevant quality controls, and impact on downstream statistical analyses.  In the follow-up workshop, participants will be introduced to the Python and Matlab platforms and use a variety of custom scripts to carry out a full analysis of existing TIS data, including mapping raw sequence information, normalizing the data for experimental biases, and finally performing statistical analyses and generating biologically meaningful results.

Goal:

Participants should leave this course with an understanding of fundamental experimental and statistical considerations that can affect the accurate implementation of the TIS approach.  Through hands-on training, the participant will be familiarized with the tools necessary to perform a TIS study from start to finish and assess the quality of the resulting data.

Schedule:

First Session: Thursday, January 29, 2015 1 – 4 PM  
Location: NRB 1031

Second Session: Wednesday, February 4, 2015 1 – 4 PM
Location: Countway Library, Room 403

 

DROP DEADLINE: Thursday, January 22, 2015

 

AUDITORS (Post-Docs, Faculty, or Staff) DO NOT NEED TO SIGN UP TO ATTEND THE 1st SESSION.  PLEASE DO NOT ENROLL.