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Attacking open chromatin with ATAC sequencing – Course and Conference Office

EMBL Course

Attacking open chromatin with ATAC sequencing

Overview

Proof of COVID-19 vaccination or recovery is required to attend this on-site course. Please see EMBL’s COVID-19 safety policy for on-site events.

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 and bulk 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 and bulk 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, comparison of bulk and single-cell data, 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 aimed at molecular biologists who want to perform ATAC-Seq experiments and/or analysis in their lab. Knowledge of bulk ATACseq, 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 single cell and bulk ATAC-Seq library preparation
  • Best practices of single cell and bulk ATAC-Seq data processing and quality control
  • Basic data analysis and visualisation of single cell and bulk 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 and trainers

Speakers and trainers

Scientific organisers

Course organisers

Lisa Trinh

Course and Conference

Officer

EMBL Heidelberg

Germany

Programme

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  • Some pre-course work (such as watching pre-recordings, protocol reading and computational exercises) may be required and will be shared in advance of the course.
  • Some speakers may need to join virtually to give their lecture or Q&A, and the programme is subject to change.
  • All times in the programme below are shown as the time in Europe/Berlin.
Day 1 – Monday 9 May 2022
TimeSpeakerLocation
08:40Bus from ISG Hotel to EMBLISG Hotel entrance
09:00 – 09:45Welcome, introduction and safety briefing
Yvonne Yeboah – EMBL Heidelberg, Germany
Vladimir Benes – EMBL Heidelberg, Germany
Ulrike Litzenburger – Nuvisan Innovation Campus Berlin, Germany
Judith Zaugg – EMBL Heidelberg, Germany
Irena Provaznikova – EMBL Heidelberg, Germany
Lisa Trinh – EMBL Heidelberg, Germany		Courtyard Room A & B
09:45 – 10:45Participant flash talksCourtyard Room A & B
10:45 – 11:00Coffee breakFlex Lab A & B
11:00 – 11:45Experimental practical:
Introduction and preparation to experimental practical
Daria Bunina – EMBL Heidelberg, Germany
Ulrike Litzenburger – Nuvisan Innovation Campus Berlin, Germany		Training Lab A & B
11:45 – 12:45LunchEMBL Canteen Outdoor Tent
12:45 – 14:45Experimental practical:
Sample preparation and transposition
Nayara Azevedo – EMBL Heidelberg, Germany
Daria Bunina – EMBL Heidelberg, Germany
Sara Lobato Moreno – EMBL Heidelberg, Germany
Karin Prummel – EMBL Heidelberg, Germany
Umut Yildiz – EMBL Heidelberg, Germany
Laura Villacorta – EMBL Heidelberg, Germany 		Training Lab A & B
14:45 – 18:45Experimental practical (with flexible coffee break):
GEM formation and elongation
Nayara Azevedo – EMBL Heidelberg, Germany
Daria Bunina – EMBL Heidelberg, Germany
Sara Lobato Moreno – EMBL Heidelberg, Germany
Karin Prummel – EMBL Heidelberg, Germany
Umut Yildiz – EMBL Heidelberg, Germany
Laura Villacorta – EMBL Heidelberg, Germany 		Training Lab A & B
18:45 – 19:15Lecture: Single cells ATAC-Seq introduction
Ulrike Litzenburger – Nuvisan Innovation Campus Berlin, Germany 		Courtyard Room A & B
19:20Bus from EMBL to ISG HotelATC entrance
19:30 – 20:30DinnerISG Hotel Restaurant
Day 2 – Tuesday 10 May 2022
TimeSpeakerLocation
08:35Bus from ISG Hotel to EMBLISG Hotel entrance
09:00 – 12:30Experimental practical (with flexible coffee break):
Breaking GEMs and library preparation
Nayara Azevedo – EMBL Heidelberg, Germany
Daria Bunina – EMBL Heidelberg, Germany
Sara Lobato Moreno – EMBL Heidelberg, Germany
Karin Prummel – EMBL Heidelberg, Germany
Umut Yildiz – EMBL Heidelberg, Germany
Laura Villacorta – EMBL Heidelberg, Germany 		Training Lab A & B
12:30 – 13:30LunchEMBL Canteen Outdoor Tent
13:30 – 14:15Seminar: Nuclei isolation: Tips and Tricks
Dirk Jürgensen – 10X Genomics		Courtyard Room A & B
14:15 – 16:45Experimental practical (with flexible coffee break):
Library quantification, QC check and sequencing start,
includes tour of EMBL Genomics Core Facility
Nayara Azevedo – EMBL Heidelberg, Germany
Daria Bunina – EMBL Heidelberg, Germany
Sara Lobato Moreno – EMBL Heidelberg, Germany
Karin Prummel – EMBL Heidelberg, Germany
Umut Yildiz – EMBL Heidelberg, Germany
Laura Villacorta – EMBL Heidelberg, Germany 		Training Lab A & B
16:45 – 18:15Student presentations 1Courtyard Room A & B
18:15 – 19:15DinnerOperon Foyer and Outdoor Tent
19:20Bus from EMBL to ISG HotelATC entrance
Day 3 – Wednesday 11 May 2022
TimeSpeakerLocation
08:35Bus from ISG Hotel to EMBLISG Hotel entrance
09:00 – 09:45Q&A session and wrap up of experimental part
Daria Bunina – EMBL Heidelberg, Germany
Ulrike Litzenburger – Nuvisan Innovation Campus Berlin, Germany		Courtyard Room A & B
09:45 – 10:30Lecture: Applications of (sc)ATAC-seq and related methods in drug-discovery: from drug mechanism of action to genetics-driven target discovery
James Reddington – GlaxoSmithKline Cellzome, Germany		Courtyard Room A & B
10:30 – 11:00Coffee breakFlex Lab A & B
11:00 – 11:45Lecture: Overview of computational methods for ATAC-Seq
Judith Zaugg – EMBL Heidelberg, Germany		Courtyard Room A & B
11:45 – 12:30Lecture
Vladimir Benes – EMBL Heidelberg, Germany		Courtyard Room A & B
12:30 – 13:30LunchEMBL Canteen Outdoor Tent
13:30 – 14:00Lecture
Umut Yildiz – EMBL Heidelberg, Germany		Courtyard Room A & B
14:00 – 14:30Group photo and coffee breakFlex Lab A & B
14:30 – 16:30Computational practical:
Introduction to Linux and computational analyses
Christian Arnold – EMBL Heidelberg, Germany
Ivan Berest – ETH Zürich, Switzerland		Computer Training Lab
16:30 – 18:30Computational practical:
Start computational analysis overnight
Christian Arnold – EMBL Heidelberg, Germany
Ivan Berest – ETH Zürich, Switzerland 		Computer Training Lab
18:30 – 19:30DinnerEMBL Canteen
19:30 – 21:00Student presentations 2
Courtyard Room A & B
21:15Bus from EMBL to ISG HotelATC entrance

Day 4 – Thursday 12 May 2022
TimeSpeakerLocation
08:35Bus from ISG Hotel to EMBLISG Hotel entrance
09:00 – 10:30Computational practical (with flexible coffee break)
Christian Arnold – EMBL Heidelberg, Germany
Ivan Berest – ETH Zürich, Switzerland
Annique Claringbould – EMBL Heidelberg, Germany
Maksim Kholmatov – EMBL Heidelberg, Germany
Kristy Ou – EMBL Heidelberg, Germany
Nila Servaas – EMBL Heidelberg, Germany		Computer Training Lab
10:30 – 12:30Computational practical
Christian Arnold – EMBL Heidelberg, Germany
Ivan Berest – ETH Zürich, Switzerland
Annique Claringbould – EMBL Heidelberg, Germany
Maksim Kholmatov – EMBL Heidelberg, Germany
Kristy Ou – EMBL Heidelberg, Germany
Nila Servaas – EMBL Heidelberg, Germany 		Computer Training Lab
12:30 – 13:30LunchEMBL Canteen Outdoor Tent
13:30 – 14:00Lecture: Overview of scATAC computational analyses
Ivan Berest – ETH Zürich, Switzerland		Computer Training Lab
14:00 – 16:00Computational practical
Christian Arnold – EMBL Heidelberg, Germany
Ivan Berest – ETH Zürich, Switzerland
Annique Claringbould – EMBL Heidelberg, Germany
Maksim Kholmatov – EMBL Heidelberg, Germany
Kristy Ou – EMBL Heidelberg, Germany
Nila Servaas – EMBL Heidelberg, Germany 		Computer Training Lab
16:00 – 16:30Coffee breakFlex Lab A & B
16:30 – 18:30Computational practical
Christian Arnold – EMBL Heidelberg, Germany
Ivan Berest – ETH Zürich, Switzerland
Annique Claringbould – EMBL Heidelberg, Germany
Maksim Kholmatov – EMBL Heidelberg, Germany
Kristy Ou – EMBL Heidelberg, Germany
Nila Servaas – EMBL Heidelberg, Germany 		Computer Training Lab
18:40Bus from EMBL to downtownATC entrance
19:30Course dinnerRestaurant
Day 5 – Friday 13 May 2022
TimeSpeakerLocation
08:40Bus from ISG Hotel to EMBLISG Hotel entrance
09:00 – 09:30Lecture
Daria Bunina – EMBL Heidelberg, Germany		Computer Training Lab
09:30 – 12:00Computational practical (with flexible coffee break)
Christian Arnold – EMBL Heidelberg, Germany
Ivan Berest – ETH Zürich, Switzerland
Annique Claringbould – EMBL Heidelberg, Germany
Maksim Kholmatov – EMBL Heidelberg, Germany
Kristy Ou – EMBL Heidelberg, Germany
Nila Servaas – EMBL Heidelberg, Germany 		Computer Training Lab
12:00 – 13:00LunchEMBL Canteen Outdoor Tent
13:00 – 14:00Participants prepare for presentationsCourtyard Room A & B
14:00 – 14:30Coffee breakFlex Lab A & B
14:30 – 16:00Presentation of results by participantsCourtyard Room A & B
16:00 – 16:30Wrap-up, end of the course and departureCourtyard Room A & B
17:00Bus downtown to Heidelberg Train StationATC entrance

Practical information

Registration Fees and Motivation Letter

The course is limited to 16 participants. For selection purposes, please note that your application will not be considered without a letter of motivation.

Registration

Registration Fees include admission, course materials, COVID-19 safety measures, meals and coffee breaks.

Participants are expected to book and pay their own accommodation and travel expenses.

Academia€690
PhD Student€690
Industry€1100

NO visa support letters will be issued until payment of the registration fee is confirmed.

Confirmation and Payment

The registration fee should be paid only after acceptance to the course. The results will be announced approximately 2-3 weeks after the application deadline.

Motivation letter submission

After you have logged in and successfully registered, you will receive an email asking you to submit your motivation letter. Click on the link provided and enter your motivation letter in the text box provided. Alternatively you can submit your motivation letter by clicking on the link on the confirmation page directly after registering.

Instructions

  1. Include your relevant skills, experience and qualifications showing why you would be suitable for the course.
  2. Explain why you would like to attend, including what you can contribute and how you think you will benefit from the course.

Please note:

  • The limit of 2000 characters refers to manually typed text and excludes spaces. If an error occurs try using a different web browser (preferably Google Chrome or Mozilla Firefox).
  • If you copy-paste the text into the form, hidden formatting might still be included which may cause the text to exceed the 2,000 character limit resulting in an error message. We recommend you clear all formatting before pasting in the text.
  • If you have special symbols in your text, make sure you are using Unicode characters, otherwise these will not be recognised.

For more detailed information, follow the instructions provided in our video on how to submit a course motivation letter.

Further details

For further information about registration and motivation letter submission please refer to the FAQ page.

Financial Assistance

Limited financial assistance is provided by the EMBL Advanced Training Centre Corporate Partnership Programme and EMBO in the form of both registration fee waivers and travel grants. Availability is limited to participants attending on-site events in Heidelberg and will be indicated during the abstract or motivation letter submission process.

Your place in the meeting is only confirmed by paying the registration fee, which is mandatory even when receiving a fee waiver.

Registration fee waiver

The fee waiver will cover the registration sum that you have paid to attend the course or conference.

Travel grant

The travel grant will cover the cost of travel (airfare, train, bus, taxi, accommodation, visa, and/or registration fees*) and is provided up to specified caps which are normally as follows:

– up to €400 for participants travelling to an EMBL Course, EMBL Conference or EMBO|EMBL Symposium from within Europe.
– up to €1000 for participants travelling to an EMBL Course, EMBL Conference or EMBO|EMBL Symposium from outside Europe.
– up to €500 for any participant travelling to an EMBO Practical Course or EMBO Workshop.
– up to €1000 for any participant working in Chile, India, Singapore or Taiwan travelling to an EMBO Practical Course or EMBO Workshop.

*Registration fees are only covered for EMBO Practical Courses or EMBO Workshops

The organisers may reduce the grant cap to accommodate more participants. Recipients will be notified of their travel cap amount when they are informed of the outcome of their application. Original receipts must be provided with your signature for all costs incurred within two months of completion of travel. Scanned copies cannot be accepted.

Boehringer ingelheim fonds travel grant

Applies to selected courses only. Availability will be indicated during the abstract or motivation letter submission process.

This grant covers costs related to your attendance at the course (registration, travel and accommodation costs). The grant is restricted to PhD students and postdocs who conduct basic biomedical research.
Whether you are eligible to apply for a travel grant, depends on when you received your university entrance qualification (e.g. Abitur, A-Levels, High School Diploma, Final State Examination):

– for PhD and MD students, as well as graduates, the university entrance qualification must not have been obtained more than 11 years ago at the time of the envisaged course
– for postdocs, the university entrance qualification must not have been obtained more than 13 years ago at the time of the envisaged course

Application

You may apply for financial assistance when submitting your motivation letter for courses, and abstract for conferences. In your application, you will be asked to answer questions regarding why your lab cannot fund your attendance and how your attendance will make a difference to your career. Application for financial support will not affect the outcome of your registration application.

For the Boehringer Ingelheim Fonds Travel Grant, there is a pre-application question during the motivation letter submission process, and if selected you will be requested to complete a standard form and documentation consisting of your travel expense estimation.

Selection

The scientific organisers will select the recipients of all financial assistance during the motivation letter or abstract selection process. Results will be announced approximately 6-8 weeks before the event start date, however for some events this may be delayed. Selection results do not impact your admission to the meeting. Selection is based on your current work or study location, the reasons for needing financial support and the impact this event will have on your career.

Reimbursement

Costs will be reimbursed after the meeting only once a reimbursement form and original receipts (from travel costs) have been received.

Further details

View our list of external funding opportunities and information on attending a conference as an event reporter.

For further information about financial assistance please refer to the FAQ page.

Accommodation and Shuttles

Hotel

Single rooms have been reserved for 5 nights (8-13 May 2022) at the ISG Hotel. After the selection process, selected participants should contact the hotel directly to make a booking (booking code ATA22-01). We recommend that all course participants stay at the ISG Hotel which is the dedicated hotel for the course.

Local transport

Shuttle buses will go from the ISG Hotel to EMBL and back, mornings and evenings. A bus schedule and location of the bus stops will be made available prior to the meeting.

Further details

Address: EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany

For further information on getting to EMBL Heidelberg visit our Travel Information page.

For enquiries about accommodation and local transportation please refer to the FAQ page.

Technical Requirements and Event Software

Technical requirements

Below you will find the software and technical requirements for this course.

  • Participants need to bring their own laptops, which will be used to remotely access EMBL virtual machines with pre-installed software.
  • You will need admin rights to install the software required to access the virtual machines. If you do not have admin rights, please contact your technical support team in advance to make sure the software can be installed.
  • If you have a non-standard HDMI port (other than type A), you need to bring an adaptor.
  • Keyboard and PC mouse are available for use with a standard USB port. If you have a different port type, such as USB-C, you will need to bring your own.

Event software

The EMBL eCampus learning platform will be used to collaborate, communicate and network with all of the course participants. All participants will receive information on how to join shortly before the course. We recommend using Chrome, Safari or Mozilla Firefox browsers for eCampus. 

Additional Information

Please find additional information including FAQs, terms and conditions, COVID-19 safety policy and travelling to EMBL on our Information for Participants page.

COVID-19 Related Questions

COVID-19 information for onsite events at EMBL Heidelberg can be found in our COVID-19 FAQs.

Sponsors

Sponsorship opportunities

We offer a variety of event sponsoring possibilities, with the flexibility to select a set sponsorship package or combine individual sponsorship options to suit your event budget. Discounts are available for companies sponsoring multiple events at EMBL Heidelberg. View other conferences, or contact sponsorship@embl.de for further information.

If you are interested in becoming a media partner of this event, please visit our media partnerships webpage.

Date: 9 - 13 May 2022

Location: EMBL Heidelberg

Venue: EMBL Advanced Training Centre

Deadline(s):

Application: Closed

Organisers:

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