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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

Speakers

Dirk Jürgensen

10X Genomics

Germany

Katharina Zirngibl

Heidelberg University

Germany

Scientific organisers

Course organisers

Programme

Are you on social media? Post using #EMBLATAC and don’t forget to tag @EMBLEvents
Day 1 – Monday 8 April 2024
TimeSpeakerLocation
08:40Bus from ISG Hotel to EMBLISG Hotel entrance
09:00 – 09:45Welcome, introduction and safety briefing
Vladimir Benes – EMBL Heidelberg, Germany
Ulrike Litzenburger – Nuvisan Innovation Campus Berlin, Germany
Judith Zaugg – EMBL Heidelberg, Germany
Courtyard Room A & B
09:45 – 10:45Participants flash talksCourtyard Room A & B
10:45 – 11:00Coffee break
11:00 – 11:45Experimental practical:
Introduction and preparation to experimental practical

Gwen Bauersachs – EMBL Heidelberg, Germany
Ulrike Litzenburger – Nuvisan Innovation Campus Berlin, Germany
Training Lab A & B
11:45 – 12:45LunchEMBL Canteen
12:45 – 14:45 Experimental practical:
Sample preparation and transposition

Gwen Bauersachs – EMBL Heidelberg, Germany
Juan Jauregui – EMBL Heidelberg, Germany
Sara Lobato Moreno – EMBL Heidelberg, Germany
Hilal Ozgur – EMBL Heidelberg, Germany
Karin Prummel – EMBL Heidelberg, Germany
Daphne Welter – EMBL Heidelberg, Germany
Training Lab A & B
14:45 – 17:30Experimental practical (with flexible coffee break):
GEM formation and elongation

Gwen Bauersachs – EMBL Heidelberg, Germany
Juan Jauregui – EMBL Heidelberg, Germany
Sara Lobato Moreno – EMBL Heidelberg, Germany
Hilal Ozgur – EMBL Heidelberg, Germany
Karin Prummel – EMBL Heidelberg, Germany
Daphne Welter – EMBL Heidelberg, Germany
Training Lab A & B
17:30-17:45Coffee break
17:45 – 18:15Seminar: Nuclei isolation: Tips and Tricks Karin Prummel – EMBL Heidelberg, GermanyCourtyard Room A & B
18:15 – 19:00Lecture: Single cells ATAC-Seq introduction Ulrike Litzenburger – Nuvisan Innovation Campus Berlin, GermanyEMBL Canteen
19:00 – 20:15DinnerEMBL Canteen
20:15Bus from EMBL to ISG Hotel
Day 2 – Tuesday 9 April 2024
TimeSpeakerLocation
08:40 Bus from ISG Hotel to EMBLISG Hotel entrance
09:00 – 12:00Experimental practical (with flexible coffee break): Breaking GEMs and library preparation
Gwen Bauersachs – EMBL Heidelberg, Germany
Juan Jauregui – EMBL Heidelberg, Germany
Sara Lobato Moreno – EMBL Heidelberg, Germany
Hilal Ozgur – EMBL Heidelberg, Germany
Karin Prummel – EMBL Heidelberg, Germany
Daphne Welter – EMBL Heidelberg, Germany
Training Lab A & B
12:00 – 13:00LunchEMBL Canteen
13:00 – 13:10Results explanation
Ulrike Litzenburger – Nuvisan Innovation Campus Berlin, Germany
Training Lab A & B
13:10 – 14:00 Lecture:
Cyndie Forestier – Element Biosciences, France
Courtyard Room A & B
14:00 – 15:40 Bioanalyzer results explained
Gwen Bauersachs – EMBL Heidelberg, Germany
Karin Prummel – EMBL Heidelberg, Germany
Hilal Ozgur – EMBL Heidelberg, Germany
Courtyard Room A & B
15:00 – 15:40Coffee break and GeneCore tourGeneCore
15:40 – 16:00Start of sequencing run
16:00- 16:30Coffee break and Q&AFoyer
16:30 – 19:30Students presentations & pizzaCourtyard Room A & B
19:30Bus from EMBL to ISG HotelATC entrance
Day 3 – Wednesday 10 April 2024
TimeSpeakerLocation
08:40Bus from ISG Hotel to EMBLISG Hotel entrance
09:00 – 10:00Lecture: Sample Preparation for scATAC Assay: What are important factors
Dirk Jürgensen – 10X Genomics, Germany
Courtyard Room A & B
10:00 – 10:45Lecture: A multimodal approach to identify molecular drivers of follicular lymphoma transformation
Kristy Ou– EMBL Heidelberg, Germany
Courtyard Room A & B
10:45– 11:00Coffee break
11:00 – 11:45Lecture: Overview of computational methods for integrating scATAC-Seq and scRNA-seq
Judith Zaugg – EMBL Heidelberg, Germany
Courtyard Room A & B
11:45 – 12:30Lecture: sequencing technologies
Vladimir Benes – EMBL Heidelberg Germany
Courtyard Room A & B
12:30 – 13:30LunchEMBL Canteen
13:30 – 14:00Students presentations IICourtyard Room A & B
14:00 – 14:30Group photo and coffee break
14:30 – 16:00Computational practical:
Introduction to Linux, R and computational analyses

Christian Arnold – EMBL Heidelberg, Germany
Ivan Berest – ETH Zürich, Switzerland
Annique Claringbould – EMBL Heidelberg, Germany
Maksim Kholmatov – EMBL Heidelberg, Germany
Computer Training Lab
16:00-16:30Lecture: AVITI data pre-processing
Jan Provaznik – EMBL Heidelberg, Germany
Computer Training Lab
16:30 – 18:30Computational practical:
Start computational analysis overnight
Christian Arnold – EMBL Heidelberg, Germany
Ivan Berest – ETH Zürich, Switzerland
Annique Claringbould – EMBL Heidelberg, Germany
Maksim Kholmatov – EMBL Heidelberg, Germany
Computer Training Lab
18:30 – 19:30DinnerEMBL Canteen
19:30 Bus from EMBL to ISG HotelATC entrance
Day 4 – Thursday 11 April 2024
TimeSpeakerLocation
08:40Bus from ISG Hotel to EMBLISG Hotel entrance
09:00 – 10:30 Computational 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
Katharina Zirngibl – University Heidelberg, Germany
Charles Dussiau – EMBL Heidelberg, Germany
Evi Vlachou – 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
Katharina Zirngibl – University Heidelberg, Germany
Charles Dussiau – EMBL Heidelberg, Germany
Evi Vlachou – EMBL Heidelberg, Germany
Computer Training Lab
12:30 – 13:30LunchEMBL Canteen
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
Katharina Zirngibl – University Heidelberg, Germany
Charles Dussiau – EMBL Heidelberg, Germany
Evi Vlachou – EMBL Heidelberg, Germany
Computer Training Lab
16:00 – 16:30Coffee break
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
Katharina Zirngibl – University Heidelberg, Germany
Charles Dussiau – EMBL Heidelberg, Germany
Evi Vlachou – EMBL Heidelberg, Germany
Computer Training Lab
18:40Bus from EMBL to downtownATC entrance
19:30Course dinner downtown at Oskar restaurantRestaurant
Day 5 – Friday 12 April 2024
TimeSpeakerLocation
08:40Bus from ISG Hotel to EMBLISG Hotel entrance
09:00 – 09:30Lecture: Applications of (sc)ATAC-seq to understand zebra fish in development
Mike Dorrity – 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
Katharina Zirngibl – University Heidelberg, Germany
Charles Dussiau – EMBL Heidelberg, Germany
Evi Vlachou – EMBL Heidelberg, Germany
Computer Training Lab
12:00 – 13:00 LunchEMBL Canteen
13:00 – 14:00Participants prepare for presentationsComputer Training Lab
14:00 – 14:30Coffee break
14:30 – 16:00Presentation of results by participantsComputer Training Lab
16:00 – 16:30Wrap-up, end of the course and departureComputer Training Lab
16:30Bus downtown to Heidelberg train stationATC entrance

Practical information

Registration fees and motivation letter

The course is limited to 18 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€715
PhD Student€715
Industry€1225

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 detailed instructions, please watch 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

Financial assistance

Limited financial assistance is provided by the EMBL Advanced Training Centre Corporate Partnership Programme and EMBO in the form of registration fee waiverstravel grants and childcare grants

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.

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 within Europe.

– up to €1000 for participants travelling to an EMBL Course from outside Europe.

– up to €500 for any participant travelling to an EMBO Practical Course.

– up to €1000 for any participant working in Chile, India, Singapore or Taiwan travelling to an EMBO Practical Course.

– up to €700 for any participant working in Croatia, Czech Republic, Estonia, Greece, Hungary, Italy, Lithuania, Luxembourg, Poland, Slovenia, and Turkey travelling to an EMBO Practical Course.

*Registration fees are only covered for EMBO Practical Courses

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.

Childcare grant

There is the possibility to apply for a childcare grant to offset child care costs incurred by participants, speakers, trainers and organisers when attending a course. Eligible costs include (but are not limited to) fees for a babysitter or child-care facility and travel costs for a caregiver. Please note that priority will be given to early-stage researchers. There is a limited amount of funding available for the childcare grants and funds will be distributed amongst eligible applicants.

Boehringer Ingelheim Fonds travel grant

Applies to selected courses only. Availability will be indicated during the 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. 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 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 course. Selection is based on scientific merit, 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

See our list of external funding opportunities and for further information about financial assistance please refer to the FAQ page.

Accommodation and travel

Travel information

For travel information, please see here.

If you are travelling to the conference within Germany then you are eligible for the Deutsche Bahn ‘Event Ticket’ (called the ‘Veranstaltungsticket’ in German). This will result in a lower ticket price if your travel distance to Heidelberg is more than 100 km. You need to provide proof of your event attendance when purchasing the ticket.

For more information in English see here or in German see here.

You can book your ticket here.

Accommodation is not included in the registration fee. Participants are expected to book and pay for their own accommodation. A mix of single and twin rooms have been reserved for 5 nights (7 – 12 April 2024) at the ISG Hotel.  Single rooms are limited and will be available on a first come, first served basis. After the selection process, selected participants should contact the hotel directly to make a booking with a booking code ATA24-01 by the deadline of 11 March 2024. We recommend that all course participants stay in 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 more information about accommodation and travel, please refer to the FAQ page.

On-site information

Catering

All meals and coffee breaks are included in the registration fee. Our catering staff will prepare a wide variety of vegetarian meals, meat and fish dishes, soups, pasta, fresh fruit and vegetables, as well as a variety of desserts.

Please wear your badge at all times when serving yourself.

No food or drinks are allowed in the laboratories.

Electricity and charging station

In most places the electricity is 220 volts AC (50 cycles). An adaptor and a plug that fits the German socket may be needed for your appliances/laptop (i.e. American, Japanese, etc.). A USB charging station for electronic devices is available at the registration desk.

EMBL Merchandise

If you are interested in purchasing an EMBL souvenir (products presented in the glass display in the registration area), please ask at the registration desk for more information.

Health and safety notes

Please read EMBL’s COVID-19 safety policy for on-site events.
Do not smoke in any EMBL building.
Eating and drinking is prohibited in all laboratories.
Do not enter any restricted areas or the laboratories unless instructed to do so.

If first aid is required …

  • The first aid room is located next to the ATC Registration Desk (room 10- 205).
  • Dial the Emergency number 222 from any EMBL internal phone only.
  • Where is the accident? What happened? How many injured?
  • Emergency number 06221-387 7821 from mobile phones.
  • Please report all accidents to the conference officer at the registration desk.

In case of fire …

  • Press the nearest fire alarm button or the Emergency number 222 from any internal phone.
  • A loud fire alarm will go off if an evacuation is required. On hearing the alarm leave the building immediately following the escape route and fire wardens and head to one of the meeting points
  • Do not use the lifts.

Beyond first aid…

Please remember to bring your own medication, if needed, to the conference. Note that the next pharmacy is a 4-minute drive from the EMBL, but for many medications you will be required to see a doctor to get a prescription.

Ensure in advance that your medical insurance will cover you during your visit in the event that you do need to see a doctor while in Heidelberg. In any case, the EMBL Course and Conference Office will assist you to get to the pharmacy and a doctor of your choice if necessary.

Internet

Wi-Fi is available on campus. Log in using the EMBL-Events network and the event specific password, which will be provided on site. The eduroam network (secure, worldwide roaming access service developed for the international research and education community) is also available.

Lost and found

‘’Lost and Found’’ items are kept at the registration desk until the end of the conference.

Luggage

There are lockers available on-site to store your luggage, which require a 2 EURO coin to operate. There is another luggage room on level E0, which is free to use but remains unlocked during the conference.

Nursing room

There is a nursing room available in the ATC Rooftop Lounge on level A29.

Photography

During the conference, an EMBL Photographer may be taking photos. If you would not like to appear in these, please inform the photographer or a member of the Course and Conference Office.

Printing

We can help to print your boarding pass/train ticket. Please send it to events@embl.de and collect your print-outs at the registration desk.

Room for prayer, yoga, and meditation

There is a room for prayer, meditation, and yoga located on level E0 behind the Auditorium. Please be respectful of others using the room.

Sightseeing

A variety of activities in Heidelberg can be found on the website of Heidelberg Marketing.

Travel to and from the venue

During the event, we provide conference shuttle buses to and from EMBL. In addition, there is the public bus 39A that serves the EMBL campus and taxis can be easily booked at any time. Information on the shuttle buses can be found on the individual event website and more detailed information on travelling to EMBL can be found on our Travel Information page.

Additional information

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

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

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 on-site events at EMBL Heidelberg can be found in our COVID-19 FAQs.

Sponsors

course partner

course sponsor

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 events, 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.

Warning

EMBL wishes to warn sponsors of EMBL conferences and courses of fraudulent schemes purporting to offer sponsorship opportunities on behalf of EMBL or affiliated with EMBL officials. One current scam campaign of which we are aware is conducted using the name ‘Judy Eastman’ (judy@gopcontact.a2hosted.com) and entails approaches to sponsors offering sponsorship opportunities on EMBL’s behalf. Please be kindly advised that all relevant communication regarding sponsorship of EMBL conferences, symposia and courses is handled by EMBL directly and is sent from an official EMBL account. EMBL does not work with any external providers on sponsorship acquisition.

Please also note that:

  • EMBL never provides attendee lists for purchase. Any offers of such are fraudulent.
  • EMBL will never call or email you to ask for your credit card details or to request a payment.
  • All payments are on invoice.

Suspicious communications purportedly from, for or on behalf of EMBL should be reported to EMBL at the following email address sponsorship@embl.de.

Media kit

Want to let others know you’re attending this event? Take a look at our shareable media and feel free to use them in your social media channels or presentations.

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Date: 8 - 12 Apr 2024

Location: EMBL Heidelberg

Venue: EMBL Advanced Training Centre


Deadline(s):

Application: Closed


Organisers:


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