Attacking Open Chromatin with ATAC Sequencing

Overview

Course Overview

ATAC-Seq stands for Assay of Transposase Accessible Chromatin and is, despite its recent invention, already a widespread method to profile open chromatin on a genome-scale. The goal of this introductory course is to teach the entire workflow of an ATAC-Seq experiment including library preparation, sequencing, data processing, and downstream analysis by addressing a real biological question that will be answered at the end of the course.

We will start with the experimental ATAC-Seq protocol, highlighting the critical steps, potential pitfalls, and the most up-to-date tweaks to improve the quality of the results. After sequencing the samples we will go through the basic quality control and preprocessing steps using multiple analysis tools for next generation sequencing data. Finally, we will perform different types of analysis on the processed data, including visualisation, differential peak calling, and differential transcription factor activity profiling to come to a biological conclusion. In addition, we will discuss recent advancements in technology development and algorithms for analysis and give an outlook on future perspectives and applications.

Audience

This course is directed towards molecular biologists who want to perform ATAC-Seq experiments and/or analysis in their lab. Knowledge of next generation sequencing technology and/or basic bioinformatics skills is desirable.

Modules/Resources

During this course we will focus on the following aspects:

• Wet lab training and best practices for ATAC-Seq library preparation
• Best practices of ATAC-Seq data processing and quality control
• Basic data analysis and visualisation of ATAC-Seq data
• Overview of advanced data analysis tools for ATAC-Seq data

Learning Outcomes

After this course you should be able to:

• Perform complete flow for ATAC-Seq experiments
• Process and quality control ATAC-Seq data
• Visualise the data and call differences between samples
• Analyse and interpret the data using existing tools.

Speakers

Speakers and Trainers

Christian Arnold

EMBL Heidelberg

Germany

Nayara Azevedo

EMBL Heidelberg

Germany

Vladimir Benes

EMBL Heidelberg

Germany

Ivan Berest

EMBL Heidelberg

Germany

Daria Bunina

EMBL Heidelberg

Germany

Neha Daga

EMBL Heidelberg

Germany

Emilia Esposito

EMBL Heidelberg,

Germany

Mang Ching Lai

EMBL Heidelberg

Germany

Ulrike Litzenburger

Celgene

USA

James Reddington

EMBL Heidelberg

Germany

Yvonne Yeboah

EMBL Heidelberg,

Germany

Judith Zaugg

EMBL Heidelberg

Germany

Scientific Organisers

Vladimir Benes

EMBL Heidelberg

Germany

Ulrike Litzenburger

Celgene

USA

Judith Zaugg

EMBL Heidelberg

Germany

Course Organisers

George Luca-Ruse

EMBL Heidelberg

Germany

Programme