Edit
Methods for analysis of circRNAs: from discovery to function – Course and Conference Office

EMBO Practical Course

Methods for analysis of circRNAs: from discovery to function

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

Circular RNAs (CircRNAs) are a rediscovered class of RNA species that originate from back-splicing events, which have been reported across all domains of life. Many circular RNAs are stable, abundant and conserved between species. They exhibit context-dependent expression patterns, which are often linked to disease states. Validated circular RNA functions are numerous and range from regulation of transcription and splicing to RNA/protein sponging and scaffolding. However, CircRNAs are by and large the most underexplored class of all non-coding RNAs. This course will meet the specific need to explore complexity, distribution, function and mechanisms of circRNA action experimentally and computationally.

The presented methods and approaches are widely applicable to all organisms beyond standard models. Lectures will cover the technological background of circular RNA research and present the latest advancements from biology, chemistry and medicine. The practical part will include detection and quantification of circRNAs by low- and high-throughput methods, data analysis and integration as well as comprehensive computational assessment of circRNA candidates, function prediction and experimental design of follow-up experiments.

Audience

This course is intended for PhD students and young Postdoctoral researchers.

Modules/Resources

  • RNA splicing
  • Computational biology
  • Gene expression
  • RNA localisation
  • Quantitative biology

Learning Outcomes

Participants will go through all wet-lab steps required for preparation of circRNA-seq libraries and will be introduced to basic bioinformatics required for analyses of circRNA-seq data.

Speakers and Trainers

Speakers

Jacqueline Ay

Bio-techne

Germany

Mirco Castoldi

University Hospital Dusseldorf

Germany

Trainers

Jörg Bantin

Bio-Rad

Germany

Alessio Colantoni

University of Rome

Italy

Linda Masante

University of Trento

Italy

Tiziana Santini

University of Rome

Italy

Pia Scheu

Bio-Rad

Germany

Giorgia Susin

University of Trento

Italy

Scientific Organisers

Irene Bozzoni

University of Rome

Italy

Course Organisers

Irena Provaznikova

Training Lab Technician

EMBL Heidelberg

Germany

Aline Schnieder

Course and Conference Officer

EMBL Heidelberg

Germany

Programme

Got something to say? Tweet it with #EMBOCircRNAs

  • Some pre-course work (such as watching pre-recordings, protocol reading and computational exercises) 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.
  • All times in the programme below are shown as the time in Europe/Berlin.
Day 1 – Saturday 23 April 2022
TimeSpeakerLocation
12:30Bus from ISG to EMBLHotel entrance
13:00 – 15:00Welcome and breaking the ice activity incl. speed networking  session and light lunch, housenotes Courtyard room A & B
15:00 – 15:45Lecture 1 with Q&A: Circular RNAs, wet-lab & computational tools to detect and analyze them
Tobias Jakobi – University of Arizona College of Medicine, USA   
Courtyard room A & B
15:45 – 16:30Lecture2 with Q&A: Elucidating the function for circRNA in cancer and neuronal  development
Jørgen Kjems – Aarhus University, Denmark
Courtyard room A & B
16:30 – 17:00Coffee break
17:00 – 17:45Lecture 3 with Q&A: circRNAs role in brain development
Marie-Laure Baudet – University of Trento, Italy 
Courtyard room A & B
17:45 – 18:30Overview of wet-lab practical exercise, Q&A on sample QC criteria
Karim Rahimi – Aarhus University, Denmark
Courtyard room A & B
18:40 – 19:40Dinner
19:40 – 20:40Student presentations ICourtyard room A& B
20:40 – 20:55Departure to HotelATC Entrance
Day 2 – Sunday 24 April 2022
TimeSpeaker Location
08:15Bus from ISG to EMBLHotel entrance
08:30 – 09:00Housekeeping notes, familiarization with the training lab,  protocol introduction, overview of the day
09:00 – 10:30Practical 1: wet-lab practical (cDNA synthesis)
Karim Rahimi – Aarhus University, Denmark
Isabel Naarmann-de Vries – University Hospital Heidelberg, Germany
Laura Villacorta – EMBL Heidelberg, Germany
Nayara Azevedo – EMBL Heidelberg, Germany
Training lab A & B
10:30 – 11:00Coffee break
11:00 – 12:30Practical 1: wet-lab practical (RNase inactivation and setting up first PCR)
Karim Rahimi – Aarhus University, Denmark
Isabel Naarmann-de Vries – University Hospital Heidelberg, Germany
Laura Villacorta – EMBL Heidelberg, Germany
Nayara Azevedo – EMBL Heidelberg, Germany
Training lab A & B
12:30 – 13:30Lunch
13:30 – 15:30Practical 1: wet-lab practical (ExoI treatment, first PCR cleanup, run bioanalyzer and setting up second PCR)
Karim Rahimi – Aarhus University, Denmark
Isabel Naarmann-de Vries – University Hospital Heidelberg, Germany
Laura Villacorta – EMBL Heidelberg, Germany
Nayara Azevedo – EMBL Heidelberg, Germany
Training lab A & B
15:30 – 16:15Lecture 4 with Q&A: solation and characterization of EVs for analysis of circRNAs: Certainties and pitfalls
Mirco Castoldi – University Hospital Dusseldorf, Germany 
Courtyard room A & B
16:15 – 16:45Coffee break
16:45 – 18:45Practical 1: wet-lab practical (Second PCR cleanup, prepare nanopore library, check flowcell and run sequencing)
Karim Rahimi – Aarhus University, Denmark
Isabel Naarmann-de Vries – University Hospital Heidelberg, Germany
Laura Villacorta – EMBL Heidelberg, Germany
Nayara Azevedo – EMBL Heidelberg, Germany
Training lab A & B
18:55 – 19:10Departure to Hotel
19:10 – 20:10Dinner
Day 3 – Monday 25 April 2022
TimeSpeaker Location
08:40Bus from ISG to EMBLHotel entrance
09:00 – 09:05Overview of the day
09:05 – 09:50Lecture 5 with Q&A: Circular RNAs: regulation and function in the vascular system
Stefanie Dimmeler – Goethe University Frankfurt, Germany
Courtyard
room A & B
09:50 – 10:35Lecture 6 with Q&A: Biogenesis and function of circRNAs (remotely)
Irene Bozzoni – Sapienza University of Rome, Italy 
Courtyard
room A & B
10:35 – 11:05Coffee break
11:05 – 12:35Practical session 4: Introduction to command line and R language
Tobias Jakobi – University of Arizona College of Medicine, USA
Alessio Colantoni – University of Rome, Italy
Marieke Vromman – University of Ghent, Belgium
Harald Wilhelmi – University Hospital Heidelberg, Germany
Computer Training Lab
12:35 – 13:35Lunch
13:35 – 14:20Lecture 7 with Q&A (remotely)
Morten Venø – omiics, Denmark
Courtyard
room A & B
14:20 – 16:20Practical session 5: Nanopore data analysis
Tobias Jakobi – University of Arizona College of Medicine, USA
Thiago Britto-Borges – University Hospital Heidelberg, Germany
Alessio Colantoni – University of Rome, Italy
Marieke Vromman – University of Ghent, Belgium
Computer Training Lab
16:20 – 16:50Coffee break
16:50 – 17:35Lecture 7 with Q&A: circPCNX, a circular RNA involved in modulating cell proliferation (remotely)
Myriam  Gorospe – National Institute on Aging, USA
Courtyard
room A & B
17:35 – 18:35Student presentations II Courtyard
room A & B
18:45 – 19:00Departure to Hotel
19:00 – 20:00Dinner
Day 4 – Tuesday 26 April 2022
TimeSpeakerLocation
08:40Bus from ISG to EMBLHotel entrance
09:00 – 09:10Overview of the dayCourtyard room A & B
09:10 – 09:55Lecture 8 with Q&A: Circtools, bioinformatics suite for data analysis
Christoph Dieterich – Heidelberg University  Hospital, Germany
Courtyard room A & B
09:55 – 10:25Coffee break
10:25 – 12:00Practical session 5: Basics of computational NGS data processing (RNA-seq)
Tobias Jakobi – University of Arizona College of Medicine, USA
Thiago Britto-Borges – University Hospital Heidelberg, Germany
Alessio Colantoni – University of Rome, Italy
Marieke Vromman – University of Ghent, Belgium
Computer Training Lab
12:00 – 13:00Lunch 
13:00 – 15:00Practical session 6: Introduction of the circtools workflow and basic back-splice junction detection
Tobias Jakobi – University of Arizona College of Medicine, USA
Thiago Britto-Borges – University Hospital Heidelberg, Germany
Alessio Colantoni – University of Rome, Italy
Marieke Vromman – University of Ghent, Belgium
Computer Training Lab
15:00 – 15:30Coffee break
15:30 – 17:00Practical session 6: Introduction of the circtools workflow and basic back-splice  junction detection
Tobias Jakobi – University of Arizona College of Medicine, USA
Thiago Britto-Borges – University Hospital Heidelberg, Germany
Alessio Colantoni – University of Rome, Italy
Marieke Vromman – University of Ghent, Belgium
Computer Training Lab
17:00 – 17:30Q&A to Introduction of the FISH protocol
Eleonora D’Ambra – University of Rome, Italy Tiziana Santini – University of Rome, Italy
Courtyard room A & B
17:30 – 18:15BaseScope presentation
Jacqueline Ay – Bio-techne, Germany
Courtyard room A & B
18:15 – 19:15Student presentations IIICourtyard room A & B
19:25 – 20:25Dinner
20:25 – 20:40Departure to Hotel
Day 5 – Wednesday 27 April 2022
TimeSpeakerLocation
08:40Bus from ISG to HotelHotel entrance
09:00 – 09:30Practical session 2: Basescope FISH pretreatment part I
Marie-Laure Baudet – University of Trento, Italy
Eleonora D’Ambra – University of Rome, Italy
Tiziana Santini – University of Rome, Italy
Training lab A & B
09:30 – 10:00Coffee break
10:00 – 12:00Practical session 2: Basescope FISH pretreatment part II
Marie-Laure Baudet – University of Trento, Italy
Eleonora D’Ambra – University of Rome, Italy
Tiziana Santini – University of Rome, Italy
Training lab A & B
12:00 – 13:00Lunch
13:00 – 13:30Practical session2: Basescope FISH post-hybridization treatment part I
Marie-Laure Baudet – University of Trento, Italy
Eleonora D’Ambra – University of Rome, Italy
Tiziana Santini – University of Rome, Italy
Training lab A & B
13:30 – 14:00Coffee break
14:00 – 16:30Practical session 2: Basescope FISH post-hybridization treatment part II
Marie-Laure Baudet – University of Trento, Italy
Eleonora D’Ambra – University of Rome, Italy
Tiziana Santini – University of Rome, Italy
Training lab A & B
16:30 – 16:45Short break
16:45 – 19:15Practical session 2: BaseScope FISH
Marie-Laure Baudet – University of Trento, Italy
Eleonora D’Ambra – University of Rome, Italy
Tiziana Santini – University of Rome, Italy
Training lab A & B
19:25 – 19:40Departure to Hotel
19:40 – 20:40Dinner
Day 6 – Thursday 28 April 2022
TimeSpeakerLocation
08:40Bus from ISG to EMBLHotel entrance
09:00 – 11:00Practical session 3: ddPCR
Marie-Laure Baudet – University of Trento, Italy
Linda Masante – University of Trento, Italy
Giorgia Susin – University of Trento, Italy
Joergen Bantin – Bio-Rad, Germany
Pia Scheu – Bio-Rad, Germany
Training lab A & B
11:00 – 11:30Coffee break
11:30 – 13:00Practical session 2: Basescope FISH – observation and result discussion 
Marie-Laure Baudet – University of Trento, Italy
Eleonora D’Ambra – University of Rome, Italy
Tiziana Santini – University of Rome, Italy
Training lab A & B
13:00 – 14:00Lunch
14:00 – 15:30Practical session 7: Advanced use of circtools ‘reconstruct’, ‘exon’ & ‘enrich’  modules
Tobias Jakobi – University of Arizona College of Medicine, USA
Alessio Colantoni – University of Rome, Italy
Christoph Dieterich – University Hospital Heidelberg, Germany
Marieke Vromman – University of Ghent, Belgium
Computer Training Lab
15:30 – 16:00Coffee break
16:00 – 17:00Lecture 10: Molecular and Physiological functions of circRNAs
Sebastian Kadener – Brandeis University, USA 
Courtyard room A & B
17:00 – 18:30Practical session 3: ddPCR
Marie-Laure Baudet – University of Trento, Italy
Linda Masante – University of Trento, Italy
Giorgia Susin – University of Trento, Italy
Joergen Bantin – Bio-Rad, Germany
Pia Scheu – Bio-Rad, Germany
Courtyard room A & B
18:40- 22:00Bus downtown, free time & course dinner
Day 7 – Friday 29 April 2022
TimeSpeakerLocation
08:40Bus from ISG to EMBLHotel entrance
09:00 – 10:00Lecture 10: CircRNAs: Searching for new functions
Albrecht Bindereif – Justus Liebig University Giessen, Germany 
Courtyard room A & B
10:00 – 10:30Coffee break
10:30- 12:00Practical session 8: Design of follow-up experiments with circtools: Targeted  Quantification, Knock-Down and Data Interpretation 
Tobias Jakobi – University of Arizona College of Medicine, USA
Thiago Britto-Borges – University Hospital Heidelberg, Germany
Alessio Colantoni – University of Rome, Italy
Marieke Vromman – University of Ghent, Belgium
Computer Training Lab
12:00 – 13:00Lunch
13:00- 14:30Practical session 8: Design of follow-up experiments with circtools: Targeted  Quantification, Knock-Down and Data Interpretation 
Tobias Jakobi – University of Arizona College of Medicine, USA
Thiago Britto-Borges – University Hospital Heidelberg, Germany
Alessio Colantoni – University of Rome, Italy
Marieke Vromman – University of Ghent, Belgium
Computer Training Lab
14:30- 16:00Final remarks, open Q&A and farewellCourtyard room A & B
16:30Shuttle bus downtown/to Main Station

Practical Information

Registration Fees and Motivation Letter

The course is limited to 12 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.

This EMBO course includes accommodation and transportation to and from the ISG Hotel to the venue.

Academia€500
PhD Student€500
Industry€1000

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

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.

Childcare Grant (EMBO Practical Courses and Workshops only)

For EMBO Practical Course or EMBO Workshop 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 or conference. Eligible costs include fees for a baby-sitter or child-care facility, travel costs for a care giver, 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 EUR can be awarded per participant applying for an EMBO Childcare Grant. In order to apply for this grant for EMBO Workshops, you must be registered by the abstract submission deadline.

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 to 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 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.

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

See 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

Accommodation has been pre-booked for you at the ISG Hotel for the default dates of 23 to 29 (6 nights). Please note that the course registration fee includes coverage of accommodation costs in twin rooms, including breakfasts, for your stay at the ISG but that you will be required to pay an additional cost of 21 EUR per night for a single room. This should be paid by you directly to the ISG during your stay. Any additional nights need to be booked and paid for by you. 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

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 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.

Date: 23 - 29 Apr 2022

Location: EMBL Heidelberg


Deadline(s):

Application: Closed


Organisers:

  • Marie-Laure Baudet
    University of Trento, Italy
    • Vladimir Benes
      EMBL Heidelberg, Germany

Edit