Laboratory

Chromatin Structure and Function

29 October–08 November 2017

Wellcome Genome Campus, Hinxton, UK

Summary

This popular laboratory- and computer-based course provides training in
experimental and computational approaches that can be used to
mechanistically dissect important aspects of chromatin biology at the
gene and genome-wide levels.

Our understanding of eukaryotic genomes has benefitted tremendously from
whole genome sequencing projects. However, we are only beginning to
systematically understand how the interplay of DNA, proteins and its
biochemical modifications (i.e., chromatin) can influence global
processes which control gene expression, mRNA splicing, and DNA
replication or repair in normal development and in disease.

Learning Outcomes
After attending the course, participants can expect to be able to:

  • Perform chromatin immunoprecipitation, ATAC, 3C and Capture C, and RRBS techniques, including experimental design, end-point analysis and validation (qPCR; FISH)
  • Understand the methods used in the preparation of material for next generation sequencing (NGS)
  • Perform end-to-end analysis of NGS data, derived from the above methods, from raw sequence through to identifying relevant loci.
  • Visualise large-scale datasets in formats suitable for figures for publication
  • Download and install relevant software and manage large datasets.
  • Understand how polymer physics can be used to build models of chromatin structures
Feedback from the 2016 course
“I had never used bioinformatic tools before, and the “step-by-step” introduction we received in the course was, in my opinion, one of the most useful things I learned. Also, I take home nice advice and experience from the ATAC, FISH, RRBS and Capture-C and ChIP.”
“Everything was very organized and useful. Great group of Instructors!”
“Thank you all again for this great opportunity.”
“Thanks you very much for organising such an amazing course!”
“Thanks so much for organizing this course so meticulously! I appreciated every single module and came out of these nine days with a whole new understanding of how I can approach my thesis project. Very grateful for the opportunity to attend, and hope to see you all at some point in the not-so-distant future!”
“Thank you to all the instructors. I’m am really really grateful for all the hard work that they put into planning and executing the course. I feel like I gained a years worth of knowledge in just 9 days. I already feel like a more informed scientist.”
“The course was immensly useful to all the students and all the instructors were perfect mentors to us.”
“All instructors did an exceptionally good job – all material was very well explained and instructors were approachable and friendly – thanks!”

Programme

Participants will receive intensive wet laboratory and computational
training focussed across five broad themes using a variety of
state-of-the-art methods:

  • DNA/transcription factor interactions and histone dynamics
    Methods: Chromatin immunoprecipitation (ChIP)
  • DNA methylation
    Methods: reduced representation bisulfite sequencing (RRBS)
  • Chromatin accessibility
    Methods: Assay for Transposase-Accessible Chromatin (ATAC)
  • Chromatin looping and nuclear organisation
    Methods: Chromosome conformation capture (3C), Capture-C, and fluorescent in situ hybridisation (FISH)
  • Computational analysis/integration of chromatin datasets
    Methods: basic programming in Unix, sequence alignments, data visualisation tools, ChiP-seq analysis, RRBS analysis, 3C analysis

View the full 2017 draft timetable here.

These sessions will be supplemented with informal tutorials and lectures
from the instructors and distinguished invited speakers. Participants
will analyse various genome-wide datasets to complement the wet
laboratory sessions. They will also have an opportunity to discuss their
own research interests and present aspects of their work that are
relevant to the course.

Learning Outcomes
After attending the course, participants can expect to be able to:

  • Perform
    chromatin immunoprecipitation, ATAC, 3C and Capture C, and RRBS
    techniques, including experimental design, end-point analysis and
    validation (qPCR; FISH)
  • Understand the methods used in the preparation of material for next generation sequencing (NGS)
  • Perform end-to-end analysis of NGS data, derived from the above methods, from raw sequence through to identifying relevant loci.
  • Visualise large-scale datasets in formats suitable for figures for publication
  • Download and install relevant software and manage large datasets.
  • Understand how polymer physics can be used to build models of chromatin structures

Instructors and speakers

Course instructors
David
Vetrie
University of Glasgow, UK
Nick
Gilbert
University of Edinburgh, UK
Paul Guilhamon Princess Margaret Cancer Centre,
Canada
Robert Andrews Cardiff University, UK

Guest speakers
Andrew Feber University College London,
UK
Nada Jabado McGill University, USA
Benjamin Rowland Netherlands Cancer Institute, The Netherlands

How to apply

Prerequisites
Applicants should be PhD students, post-doctoral scientists or clinicians
engaged in relevant research.

Cost

The
course is subsidised by the Wellcome Genome Campus
Advanced Courses and Scientific Conferences Programme. This is a
residential
course and there is a fee of £1195 towards
board and lodging for non-commercial applicants. Please contact us for
the commercial fee.

Additional limited bursaries are available (up to 50%
of the course fee)
and are awarded on merit. Please see the “Bursaries”
tab for details.

Applications
Applications for this course can be completed online. Places are limited
and will be awarded on merit. If you have any problems with the online
application process, please contact us.

Please note: Applications
must be supported by a
recommendation from a scientific or clinical sponsor (e.g. supervisor or
head of department). A request for a supporting
statement will be sent
to your nominated sponsor automatically during
the application process.
Applicants must ensure that their sponsor
provides this supporting
statement by the application deadline. Applications without a supporting
statement cannot be considered.

Deadlines
Deadline for Applications: Closed

Travel visas
Please contact the
event organiser if you require a letter to support a travel visa
application. Note that letters will be provided to confirmed attendees.

Non-European Economic Area or Swiss nationals may be required to have a
visa to enter the UK.
Early application is strongly advised, as this process can take 6-8 weeks
or longer.

Please visit the following websites for further information:
UK Border Agency website and information for general visitors and business
visitors.

Cost

Cost
The
course is subsidised by the Wellcome Genome Campus Advanced Courses
and
Scientific Conferences Programme. This is a residential
course and
there is a fee of £1195 towards board and lodging for
non-commercial applicants. Please contact us for the commercial fee.

Bursaries
Advanced Courses are subsidised for non-commercial
applicants from anywhere in the world. Additional, limited bursaries are
available (up to 50% of the course fee) and are awarded on merit. If you
would like to apply for a
bursary, please complete the bursary section
of the online application
form.

Please note that both the applicant
and sponsor are required to provide
a justification for the
bursary as part of the application.

Bursary terms and conditions

UK Courses (held at the Wellcome Genome Campus, Hinxton,
Cambridge)
A
limited number of bursaries are available for each course. These are
awarded by the selection committee according to merit. The bursary
covers a maximum of 50% of the course fee, though in exceptional
circumstances an application for the total course fee may be considered.
Where there are many bursary applications, the selection committee may
issue smaller amounts. We cannot assist with travel costs to attend UK
courses.

Overseas Courses (held outside of the UK)
A
limited number of bursaries are available for each course. These are
awarded on merit to cover travel, accommodation and sustenance. The
maximum award for travel (economy class) will be £750.

Bursaries can be applied for as part of the course application form.
Applicants
will be notified of a bursary award along with their place on
the
course, usually within one month of the application deadline. The
decision of the selection committee is
final.

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