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scATAC-seq: attacking open chromatin in single cells – Course and Conference Office

EMBL Course

scATAC-seq: attacking open chromatin in single cells

Overview

Course overview

ATAC-Seq stands for Assay of Transposase Accessible Chromatin and is a widespread method to profile open chromatin on a genome-scale. The goal of this introductory course is to teach the entire workflow of a single cell 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 single cell 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 joint analysis of scRNA and scATAC-seq data, how to use these joint modalities to generate gene regulatory networks, and give an outlook on future perspectives and applications – including ways for multiplexing scRNA/scATAC assays and high-throughput cost-effective options.

Audience

This course is directed towards molecular biologists who want to perform scATAC-Seq experiments and/or analysis in their lab.

Learning outcomes

After this course you should be able to:

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

What past participants say about the course

A very well tailored course with fantastic speakers who take you on an exciting journey from wet lab to data analysis!” – Mahdi, Adam Mickiewicz University, Poland

It was an intense but very informative and motivating week. Both the theoretical and practical parts were perfectly organised. Thank you for the price-worthy experience!” – Kristyna Zavacka, Masaryk University, Czech Republic

Date: 8 - 12 Apr 2024

Location: EMBL Heidelberg

Venue: EMBL Advanced Training Centre


Deadline(s):

Application: Closed


Organisers:


EMBL Courses and Conferences are kindly supported by our Corporate Partnership Programme

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