Stefaan Derveaux
VIB Nucleomics Core
Belgium
EMBL Course
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.
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.
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:
“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
VIB Nucleomics Core
Belgium
VIB Nucleomics Core
Belgium
New England Biolabs Inc.
UK
Agilent Technologies
Germany
EMBL Heidelberg
Germany
Weill Cornell Medicine
USA
(Virtual Speaker)
New England Biolabs
USA
Weill Cornell Medicine
USA
(Virtual Speaker)
Agilent Technologies
The Netherlands
EMBL Heidelberg
Germany
EMBL Heidelberg
Germany
New England Biolabs Inc.
USA
EMBL Heidelberg
Germany
EMBL Heidelberg
Germany
EMBL Heidelberg
Germany
Element Biosciences
The Netherlands
EMBL Heidelberg
Germany
New England Biolabs
Germany
EMBL Heidelberg
Germany
EMBL Heidelberg
Germany
Training Lab Technician
EMBL Heidelberg
Germany
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Time (Europe/Berlin) | Session | Location |
12:40 | Bus from ISG Hotel to EMBL | Hotel Entrance |
13:15 – 13:30 | Welcome of participants / registration | Flex Lab A&B |
13:30 – 14:00 | EMBL 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 – 14:30 | Lecture 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 – 14:45 | Practical 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 – 16:00 | Icebreaking activity (Introduction round each participant 2 slides) | Flex Lab A&B |
16:00 – 17:45 | Practical 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 – 18:30 | Lecture 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 – 19:30 | Practical 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 – 20:30 | Dinner at EMBL | EMBL Canteen |
20:30 | Departure to hotel | EMBL Bus Stop |
Time (Europe/Berlin) | Session | Location |
08:40 | Bus from ISG Hotel to EMBL | Hotel entrance |
09:00 – 09:10 | Overview of the day | Flex Lab A&B |
09:10 – 10:00 | Lecture 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 – 10:15 | Introduction into RNA library preparation protocol Pingfang Liu – New England Biolabs, USA Vladimir Benes – EMBL Heidelberg, Germany | Flex Lab A&B |
10:15 – 12:30 | Practical 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 – 13:30 | Lunch | EMBL Canteen |
13:30 – 14:30 | Practical 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 – 15:00 | Practical 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 – 16:30 | Practical 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 – 17:30 | Lecture 4: Multi-omic profiling methods for astronauts and spaceflight (virtual) Chris Mason – Weill Cornell, USA | Flex Lab A&B |
17:30 – 18:30 | Practical 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 – 19:45 | Tips & Tricks with concurrent Pizza Dinner | ATC Rooftop Lounge |
19:45 | Departure to Hotel | EMBL Bus Stop |
Time (Europe/Berlin) | Session | Location |
08:40 | Bus from ISG Hotel to EMBL | Hotel Entrance |
09:00 – 09:10 | Overview of the day | Flex Lab A&B |
09:10 – 10:00 | Practical 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 – 11:00 | Lecture 5: Library QC – A perspective from Agilent Technologies Samina Kaufmann – Agilent Technologies, Germany | Flex Lab A&B |
11:00 – 12:30 | Lecture 6: Aviti System by Element Biosciences John Baeten – Element Biosciences, The Netherlands | Flex Lab A&B |
12:30 – 13:15 | Lunch | EMBL Canteen |
13:15 – 13:30 | Group Photo | |
13:30 – 15:00 | Set-up of the Aviti Sequencer & Tour through GeneCore Facility John Baeten – Element Biosciences, The Netherlands Vladimir Benes – EMBL Heidelberg, Germany | GeneCore Facility |
15:00 – 15:30 | Coffee Break | |
15:30 – 17:00 | Lecture 7: Considerations on experimental design and NGS implementation the Core Facility Vladimir Benes – EMBL Heidelberg, Germany | Flex Lab A&B |
17:00 | Bus Heidelberg downtown and sightseeing | ATC Entrance |
19:30 | Dinner & Networking (NEB sponsored) | Oskar Vinothek and Restaurant |
Time (Europe/Berlin) | Session | Location |
08:40 | Bus from ISG Hotel to EMBL | Hotel Entrance |
09:00 – 09:10 | Overview of the day | Computer Training Lab |
09:10 – 10:00 | Practical Lecture: Introduction to NGS Data formats and QC Jan Provaznik – EMBL Heidelberg, Germany Jonathan Landry – EMBL Heidelberg, Germany | Computer Training Lab |
10:00 – 10:30 | Coffee break | |
10:30 – 12:00 | Practical Lecture: Review – Generated Raw Data: Element Cloud Solution John Beaten – Element Biosciences, The Netherlands | Computer Training Lab |
12:00 – 13:00 | Lunch | EMBL Canteen |
13:00 – 14:30 | Practical 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 – 15:00 | Feedback round and closing remarks | Flex Lab A&B |
15:30 | Bus to Heidelberg train station and city center | EMBL Bus Stop |
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.
Academia | 575 € |
PhD Student | 575 € |
Industry | 1100 € |
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.
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.
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
Please note:
For detailed instructions, please watch our video on how to submit a course motivation letter.
For further information about registration and motivation letter submission please refer to the FAQ page.
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.
The fee waiver will cover the registration sum that you have paid to attend the course.
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.
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.
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
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.
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.
Costs will be reimbursed after the meeting only once a reimbursement form and original receipts (from travel costs) have been received.
See our list of external funding opportunities and for further information about financial assistance please refer to the FAQ page.
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.
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.
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.
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.
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.
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.
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 …
In case of fire …
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.
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’’ items are kept at the registration desk until the end of the conference.
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.
There is a nursing room available in the ATC Rooftop Lounge on level A29.
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.
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.
There is a room for prayer, meditation, and yoga located on level E0 behind the Auditorium. Please be respectful of others using the room.
A variety of activities in Heidelberg can be found on the website of Heidelberg Marketing.
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.
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.
Below you will find the software and technical requirements for this course.
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.
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 information for on-site events at EMBL Heidelberg can be found in our COVID-19 FAQs.
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.
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:
Suspicious communications purportedly from, for or on behalf of EMBL should be reported to EMBL at the following email address sponsorship@embl.de.
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Date: 6 - 9 Nov 2023
Location: EMBL Heidelberg
Venue: EMBL Advanced Training Centre
Deadline(s):
Application: Closed
Organisers:
Contact: Luana Ribeiro