Vladimir Benes
EMBL Heidelberg
Germany
Overview
Update on cancellation
Thank you for your interest in the EMBL Course on NicE-RNA sequencing for multiomics on open chromatin and transcription.
Unfortunately, due to product release delays, we are not able to host this course in September 2025 and have to cancel the event.
If you would like to receive further details on the product/protocol please feel free to contact the NEB Senior Application Manager Dr. Björn Textor.
To stay in contact with us you can visit www.embl.org/events for a complete list of all EMBL events and subscribe for our newsletter at www.embl.de/events/newsletter.
Course overview
This course will focus on the latest state-of-the-art novel library preparation protocols. We will start with experimental design, focusing on hands-on library preparation (including best practices, standards, and potential pitfalls), concluding with sequencing of libraries, bioinformatic evaluation & best practices.
Multiomic data in scientific projects have become more and more important. NicE-Seq is a novel method enabling detection of open chromatin in fixed low numbers of cells without any additional instrumentation. Combining open chromatin with transcriptome information is crucial for interpretation of cellular states. Therefore, the course participants will also prepare mRNA libraries from the same cell populations.
Participants will carry out a complete workflow, from isolation of DNA & RNA from fixed cells, library preparation for both applications and shallow sequencing. The course will discuss alternative novel approaches, various cell fixatives and their impact on analysis. In addition, we will cover basic bioinformatic 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 participants’ home institutes.
Audience
This course is directed towards wet-lab biologists, scientists and technicians who want to apply the here offered technology.
Modules/resources
- Hands-on training on NGS multiome library preparations with upcoming state-of-the-art reagents
- Setting up a sequencing run
- Basics in data handling and analysis
Learning outcomes
Multiome genomic analyses have become important to understand genome dynamics. Methodology to explore this is still challenging and requires a lot of experience and hands on time.
During the course, its participants will:
- learn to apply novel NEBNext NGS library preparation reagents and protocols
- learn about the benefits and bottlenecks of different library preparations
- be exposed to cutting-edge sequencing technology
What past participants say about this course
“I really enjoyed this course (both practical and invited lectures). This was an interesting course format and I will apply the techniques I learned during the course in my project. This is an extremely valuable course and I recommend this course to my colleagues. Thanks to the EMBL organizers for making such a wonderful event successful.” – Kesava Priyan Parmasamy, Ulmea University, Sweden
Speakers
Speakers, trainers, and staff
Mathias Boulanger
EMBL Heidelberg
Germany
Alicia He
New England Biolabs
Germany
Ferris Jung
EMBL Heidelberg
Germany
Keerthana Krishnan
New England Biolabs
Germany
Chaithanya Ponnaluri
New England Biolabs
Germany
Jan Provaznik
EMBL Heidelberg
Germany
Karin Prummel
EMBL Heidelberg
Germany
Chen Song
New England Biolabs
Germany
Björn Textor
New England Biolabs
Germany
Laura Villacorta
EMBL Heidelberg
Germany
Daphne Welter
EMBL Heidelberg
Germany
Scientific organisers
Vladimir Benes
EMBL Heidelberg
Germany
Björn Textor
New England Biolabs
Germany
Laura Villacorta
EMBL Heidelberg
Germany
Course organisers
Ellen Malovrh
Scientific Training
Officer
EMBL Heidelberg
Germany
Adéla Graf
Course and Conference Officer
EMBL Heidelberg
Germany
Karo Wolkersdorfer
Course and Conference
Officer
EMBL Heidelberg
Germany
Preliminary programme
Are you on social media? Post using #EMBLNicESeq and don’t forget to tag @EMBLEvents.
- The programme will be shared here in due time.
- Some pre-course work (such as watching pre-recordings and protocol reading) with estimated time 0-10 hours will 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.
Day 1 – Monday, 29 September 2025
| Description |
|---|
| Arrival at EMBL + registration |
| Welcome |
| EMBL intro and house notes (incl. safety) + course overview Vladimir Benes – EMBL Heidelberg, Germany Bjoern Textor – New England Biolabs, USA Laura Villacorta – EMBL Heidelberg, Germany |
| Icebreaking activity Introduction round and “Challenges and Expectations” |
| Coffee break |
| Lecture: Sequencing technology overview and how to work in a Core facility Vladimir Benes |
| Practical session: Cell fixation and preparation of DNA and RNA |
| Tips & Tricks with concurrent dinner |
Day 2 – Tuesday, 30 September 2025
| Description |
|---|
| Introduction Lecture: NicE-seq: High Resolution Profiling of Accessible Chromatin of Formaldehyde-fixed Cells Chaithanya Ponnaluri |
| Practical Session: Cytosol Extraction |
| Practical Session: NicE-Seq labeling reaction |
| Lecture: Methods for sequencing cell-free DNA and cell-free RNA from human plasma Chen Song |
| Lunch |
| Practical Session: Decrosslinking |
| Practical Session: Clean-Up |
| Practical Session: EndPrep, Ligation, Buffer Exchange |
| Practical Session: PCR Reaction |
| Lecture: Streamlining processes of automated RNA library prep Ferris Jung |
| Practical Session: Clean Up |
| Practical Session: Library QC, Quantification |
| Dinner |
Day 3 – Wednesday, 1 October 2025
| Description |
|---|
| Lecture: Introduction into strand-specific RNA Library Prep: NicE-Seq application in the field – first hands-on experiences Ulrike Bönisch |
| Practical Session: PolyA Enrichment |
| Practical Session: Fragmentation First Strand Synthesis Second Strand Synthesis |
| Lunch |
| Practical Session: Clean Up |
| Practical Session: End prep of cDNA libraries |
| Practical Session: Adaptor Ligation USER Treatment |
| Practical Session: PCR Enrichment |
| Lecture: NEBNext Product Development: Streamlining workflows & addressing new applications Keerthana Krishnan |
| Coffee Break |
| Practical Session: Clean Up |
| Practical Session: Library QC (Qubit, Bioanalyzer) |
| Dinner |
Day 4 – Thursday, 2 October 2025
| Time | Description | Location |
|---|---|---|
| 09:00 – 10:00 | Introduction & Practical Session: Set-up of Sequencing runs of processed samples | Training Labs |
| 10:00 – 10:45 | Lecture: Epigenomic research Karin Prummel | Flex Labs |
| 10:45 – 11:00 | Coffee Break | Courtyard Foyer |
| 11:00 – 12:00 | Practical Session: Bioinformatics I Introduction to data analysis and QC | |
| 12:00 – 13:00 | Lunch | EMBL Canteen |
| 13:00 – 14:30 | Practical Session: Bioinformatics II NicE-seq examples and pitfalls | |
| 14:30 – 16:00 | Final technical discussion round | Flex Labs |
| 16:00 – 16:45 | Feedback round and closing remarks | Flex Labs |
Sponsors
Sponsorship opportunities
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Warning
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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.
Date: 29 Sep - 2 Oct 2025
Location: EMBL Heidelberg
Venue: EMBL Advanced Training Centre
Deadline(s):
Application: Closed
Organisers:
-
Vladimir Benes
EMBL Heidelberg, Germany -
Björn Textor
New England Biolabs, Germany -
Laura Villacorta
EMBL Heidelberg, Germany -
-
Contact: Adéla Graf