Edit
Preparation of genomics libraries for an emerging next-gen sequencing platform – Course and Conference Office

EMBL Course

Preparation of genomics libraries for an emerging next-gen sequencing platform

Overview

Course overview

This course will focus on the latest state-of-the-art sequencing platform technology and novel library preparation protocols. We will start with experimental design, focusing on the hands-on library preparation (including best practices, standards, and potential pitfalls), concluding with sequencing of libraries, bioinformatic evaluation & best practice. For this purpose we will use, for the first time ever in the settings of the practical course, the cutting-edge sequencing platform AVITI (https://www.elementbiosciences.com/products/aviti), which was developed by Element Biosciences and is currently entering the next-gen sequencing (NGS) field. An evaluation of the technology in conjunction with the newly developed library preparation reagents by New England Biolabs (NEB) will be important for the scientific community and course participants to assist their decision if to adopt the new sequencing technology. The course will cover a complete workflow, such as library preparation and sequencing. The course participants will also learn about its tips and tricks and will also use bioinformatics tools required for data processing, quality control and initial data analysis.

Beside the practical exercises, lectures and discussion sessions, the course will offer the opportunity to learn more about transferring the knowledge gained during the course to the home institute of the participants as well as the implementation of this new technology into the environment of genomics core facilities. During the course participants will prepare two types of NGS libraries, gDNA-Seq and mRNA-Seq. We offer the opportunity to provide a maximum of 2 samples. Those samples must be shipped to Heidelberg prior to the course and must meet quality criteria of EMBL GeneCore. Generated libraries will be used for shallow sequencing.

Audience

This course is directed towards wet-lab molecular biologists, scientists and technicians who want to assess and use the AVITI technology. A focus will be on applicants from member states and their genomics core facilities. This audience can best disseminate the knowledge gained during the course and serve scientists at their home institutes.

Modules/resources

  • Presentation of the latest state-of-the-art sequencing technology (Element Biosciences, the AVITI system)
  • Hands-on training on genomic library preparation with upcoming state-of-the-art reagents
  • Setting up an AVITI sequencing run
  • Basics in data handling and analysis

Learning outcomes

The NGS field is entering a new phase of sequencing platforms available to the community and for their various applications. One crucial eplatform is the Aviti sytem by Element Bioscinces. During the course, its participants will:

  • be exposed to the cutting-edge sequencing technology
  • learn to apply novel NEBNext NGS library preparation reagents and protocols
  • learn about the benefits and bottlenecks of different systems
  • be provided with guidance on the implementation of sequencing technologies into the core facility environment

What past participants say about this course

“I truly recommend this course to anyone interested in RNASeq. We were pushed to go below the limits of RNA input to construct libraries and it was an exciting challenge. The spirit of science “go beyond our limits” was present through all of the course. The knowledge sharing environment with all the participants, trainers, and speakers, made this one of the best courses I have ever attended.” – Anna Sofia Varanda, University of Aveiro, Portugal

Speakers

Speakers, trainers, and staff

Lim De Swert

VIB Nucleomics Core

Belgium

Max Fritsch

New England Biolabs Inc.

UK

Chris Mason

Weill Cornell Medicine

USA

(Virtual Speaker)

Pingfang Liu

New England Biolabs

USA

Chris Mason

Weill Cornell Medicine

USA

(Virtual Speaker)

Matthias Meister

Agilent Technologies

The Netherlands

Michael Petridis

New England Biolabs Inc.

USA

Scientific organisers

John Baeten

Element Biosciences

The Netherlands

Pingfang Liu

New England Biolabs

USA

Course organisers

Luana Ribeiro

EMBL Heidelberg

Germany

Programme

Got something to say? Tweet it! #EMBLSeqLibPrep 

  • Some speakers may need to join virtually to give their lecture or Q&A, and the programme is subject to change.
Day 1 – Monday 6 November 2023
Time (Europe/Berlin)SessionLocation
12:40Bus from ISG Hotel to EMBLHotel Entrance
13:15 – 13:30Welcome of participants / registrationFlex Lab A&B
13:30 – 14:00EMBL introduction, house notes and lab safety
Vladimir Benes – EMBL Heidelberg, Germany
Bjoern Textor – New England Biolabs, USA
John Baeten – Element Biosciences, The Netherlands
Laura Villacorta – EMBL Heidelberg, Germany
Luana Ribeiro – EMBL Heidelberg, Germany
Irena Provaznikova – EMBL Heidelberg, Germany
Flex Lab A&B
14:00 – 14:30Lecture 1: Get familiar with the lab and introduction into the NEBNext Ultra II FS DNA workflow for Element Biosciences
Pingfang Liu – New England Biolabs, USA
Vladimir Benes – EMBL Heidelberg, Germany
Flex Lab A&B
14:30 – 14:45Practical session: Fragmentation & End Prep
Pingfang Liu – New England Biolabs, USA
Michael Petridis – New England Biolabs, USA
Max Fritsch – New England Biolabs, USA
Lim de Swert – VIB Nucleomics Core, Belgium
Hilal Ozgur – EMBL Heidelberg, Germany
Daphne Welter – EMBL Heidelberg, Germany
Training Lab B
14:45 – 16:00Icebreaking activity (Introduction round each participant 2 slides)Flex Lab A&B
16:00 – 17:45Practical session: Adaptor ligation, Cleanup of adaptor-ligated DNA, size selection of adaptor-ligated DNA and setup enrichment PCR
Pingfang Liu – New England Biolabs, USA
Michael Petridis – New England Biolabs, USA
Max Fritsch – New England Biolabs, USA
Lim de Swert – VIB Nucleomics Core, Belgium
Hilal Ozgur – EMBL Heidelberg, Germany
Daphne Welter – EMBL Heidelberg, Germany
Training Lab B
17:45 – 18:30Lecture 2: NEBNext protocol discussion and performance on the Aviti system
Pingfang Liu – New England Biolabs, USA
Vladimir Benes – EMBL Heidelberg, Germany
Flex Lab A&B
18:30 – 19:30Practical session: Clean Up
Pingfang Liu – New England Biolabs, USA
Michael Petridis – New England Biolabs, USA
Max Fritsch – New England Biolabs, USA
Lim de Swert – VIB Nucleomics Core, Belgium
Hilal Ozgur – EMBL Heidelberg, Germany
Daphne Welter – EMBL Heidelberg, Germany
Training Lab B
19:30 – 20:30Dinner at EMBLEMBL Canteen
20:30Departure to hotelEMBL Bus Stop
Day 2 – Tuesday 7 November 2023
Time (Europe/Berlin)SessionLocation
08:40Bus from ISG Hotel to EMBLHotel entrance
09:00 – 09:10Overview of the dayFlex Lab A&B
09:10 – 10:00Lecture 3: The Aviti platform at the VIB Nucleomics Core: from implementation to routine usage
Stefaan Derveaux – VIB Nucleomics, Belgium
Flex Lab A&B
10:00 – 10:15Introduction into RNA library preparation protocol
Pingfang Liu – New England Biolabs, USA
Vladimir Benes – EMBL Heidelberg, Germany
Flex Lab A&B
10:15 – 12:30Practical session: polyA, First, Second, Strand Synthesis
Pingfang Liu – New England Biolabs, USA
Michael Petridis – New England Biolabs, USA
Max Fritsch – New England Biolabs, USA
Lim de Swert – VIB Nucleomics Core, Belgium
Laura Villacorta – EMBL Heidelberg, Germany
Mireia Osuna Lopez – EMBL Heidelberg, Germany
Training Lab B
12:30 – 13:30LunchEMBL Canteen
13:30 – 14:30Practical session: cDNA continues
Pingfang Liu – New England Biolabs, USA
Michael Petridis – New England Biolabs, USA
Max Fritsch – New England Biolabs, USA
Lim de Swert – VIB Nucleomics Core, Belgium
Laura Villacorta – EMBL Heidelberg, Germany
Mireia Osuna Lopez – EMBL Heidelberg, Germany
Training Lab B
14:30 – 15:00Practical session: Set-Up of End/Prep dA Tailing
Pingfang Liu – New England Biolabs, USA
Michael Petridis – New England Biolabs, USA
Max Fritsch – New England Biolabs, USA
Lim de Swert – VIB Nucleomics Core, Belgium
Laura Villacorta – EMBL Heidelberg, Germany
Mireia Osuna Lopez – EMBL Heidelberg, Germany
Training Lab B
15:00 – 16:30Practical session: Ligation and Clean Up, PCR Set-Up
Pingfang Liu – New England Biolabs, USA
Michael Petridis – New England Biolabs, USA
Max Fritsch – New England Biolabs, USA
Lim de Swert – VIB Nucleomics Core, Belgium
Laura Villacorta – EMBL Heidelberg, Germany
Mireia Osuna Lopez – EMBL Heidelberg, Germany
Training Lab B
16:30 – 17:30Lecture 4: Multi-omic profiling methods for astronauts and spaceflight (virtual)
Chris Mason – Weill Cornell, USA
Flex Lab A&B
17:30 – 18:30Practical session: Clean Up
Pingfang Liu – New England Biolabs, USA
Michael Petridis – New England Biolabs, USA
Max Fritsch – New England Biolabs, USA
Lim de Swert – VIB Nucleomics Core, Belgium
Laura Villacorta – EMBL Heidelberg, Germany
Mireia Osuna Lopez – EMBL Heidelberg, Germany
Training Lab B
18:30 – 19:45Tips & Tricks with concurrent Pizza DinnerATC Rooftop Lounge
19:45Departure to HotelEMBL Bus Stop
Day 3 – Wednesday 8 November 2023
Time (Europe/Berlin)SessionLocation
08:40 Bus from ISG Hotel to EMBLHotel Entrance
09:00 – 09:10Overview of the dayFlex Lab A&B
09:10 – 10:00Practical session: Library QC
Pingfang Liu – New England Biolabs, USA
Michael Petridis – New England Biolabs, USA Max Fritsch – New England Biolabs, USA
Lim de Swert – VIB Nucleomics Core, Belgium
Hilal Ozgur – EMBL Heidelberg, Germany
Laura Villacorta – EMBL Heidelberg, Germany
Daphne Welter – EMBL Heidelberg, Germany
Mireia Osuna Lopez – EMBL Heidelberg, Germany
Jessica Sutter – EMBL Heidelberg, Germany
Training Lab B
10:00 – 11:00Lecture 5: Library QC – A perspective from Agilent Technologies
Samina Kaufmann – Agilent Technologies, Germany
Flex Lab A&B
11:00 – 12:30Lecture 6: Aviti System by Element Biosciences
John Baeten – Element Biosciences, The Netherlands
Flex Lab A&B
12:30 – 13:15LunchEMBL Canteen
13:15 – 13:30Group Photo
13:30 – 15:00Set-up of the Aviti Sequencer & Tour through GeneCore Facility
John Baeten – Element Biosciences, The Netherlands
Vladimir Benes – EMBL Heidelberg, Germany
GeneCore Facility
15:00 – 15:30Coffee Break
15:30 – 17:00Lecture 7: Considerations on experimental design and NGS implementation the Core Facility
Vladimir Benes – EMBL Heidelberg, Germany
Flex Lab A&B
17:00Bus Heidelberg downtown and sightseeingATC Entrance
19:30Dinner & Networking (NEB sponsored)Oskar Vinothek and Restaurant
Day 4 – Thursday 9 November 2023
Time (Europe/Berlin)SessionLocation
08:40 Bus from ISG Hotel to EMBL Hotel Entrance
09:00 – 09:10Overview of the dayComputer Training Lab
09:10 – 10:00Practical Lecture: Introduction to NGS Data formats and QC
Jan Provaznik – EMBL Heidelberg, Germany
Jonathan Landry – EMBL Heidelberg, Germany
Computer Training Lab
10:00 – 10:30Coffee break
10:30 – 12:00Practical Lecture: Review – Generated Raw Data: Element Cloud Solution
John Beaten – Element Biosciences, The Netherlands
Computer Training Lab
12:00 – 13:00Lunch EMBL Canteen
13:00 – 14:30Practical session: Light Intro to Genome Mapping / Variant Calling
Jan Provaznik – EMBL Heidelberg, Germany
Jonathan Landry – EMBL Heidelberg, Germany
Tobias Rausch – EMBL Heidelberg, Germany
Computer Training Lab
14:30 – 15:00Feedback round and closing remarksFlex Lab A&B
15:30Bus to Heidelberg train station and city centerEMBL Bus Stop

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 fees include admission, course materials, meals and coffee breaks. Participants are expected to book and pay their own accommodation and travel expenses. 

Academia575 €
PhD Student575 €
Industry1100 €

A letter to support your visa application will be issued, on request, once payment of the registration fee is confirmed. We recommend that you book your visa appointment as soon as possible, to avoid any delay with your visa application.

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 both registration fee waivers and travel grants. Availability is limited to participants attending on-site EMBL Courses and virtual or on-site EMBO Practical Courses in Heidelberg, and will be indicated during the motivation letter submission process.

Your place in the course 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 (EMBO Practical Courses only)

For EMBO Practical Course participants with children, there is the possibility to apply for a childcare grant to offset child care costs incurred by participants or speakers when participating at a course. Eligible costs include fees for a babysitter or child-care facility, travel costs for a caregiver, or travel costs for taking the child to the meeting etc. Please note that priority will be given to early-stage researchers. A maximum amount of €500 can be awarded per participant applying for an EMBO childcare grant. 

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 shuttles

Hotel

Single rooms have been reserved for 5 nights (5-10 November 2023) at the ISG Hotel. After the selection process, selected participants should contact the hotel directly to make a booking (booking code NEB23-01). 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.

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.

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 on-site 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 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.

Social 1080×1920
Social 1080×1080
Social 1600×900
PPT Slide 16 x 9

Date: 6 - 9 Nov 2023

Location: EMBL Heidelberg

Venue: EMBL Advanced Training Centre


Deadline(s):

Application: Closed


Organisers:

  • John Baeten
    Element Biosciences, The Netherlands
    • Vladimir Benes
      EMBL Heidelberg, Germany

What's new on our blog

Edit