Location & dates EMBL Heidelberg, Germany 17 - 22 Nov 2019
Deadlines Application closed
organiser_EMBO_Course_2017

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Programme

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Day 1 - Sunday 17 November 2019
TimeSpeakerLocation
14:00 - 14:30

Arrival & Welcome

ISG Hotel

14:30 - 15:30 Lecture - Circular RNAs, wet-lab & computational tools to detect and analyze them
Christoph Dieterich - Heidelberg University Hospital, Germany

 ISG Hotel

15:30 - 16:00

Coffee break

ISG Hotel

16:00 - 17:00

Lecture - circRNAs role brain development
Marie-Laure Baudet - University of Trento, Italy

ISG Hotel

17:00 - 18:00

Overview of the wet-lab practical exercise, Q&A on sample QC criteria

ISG Hotel

18:00

Get-together & dinner

ISG Hotel

Day 2 - Monday 18 November 2019
TimeSpeakerLocation
07:45

Bus to EMBL

ISG Hotel bus stop

08:00 - 08:30

Housekeeping notes, familiarization with the training lab, protocol introduction

Flex Lab A & B

08:30 - 09:30

RNase digestion, bead clean-up, RNA fragmentation

Training Lab B

09:30 - 10:00

1st strand synthesis preparation

Training Lab B

10:00 - 10:30

Coffee break

Flex Lab A & B

10:30 - 11:00

Review of bead cleanup and 2nd strand synthesis preparation 

Training Lab B

11:00 - 12:00

Lecture - Biogenesis and function of circRNAs
Irene Bozzoni - Sapienza University of Rome, Italy

Flex Lab A & B

12:00 - 13:00

Bead clean-up and set up end repair reaction

Training Lab B

13:00 - 14:00

Lunch break

EMBL Canteen

14:00 - 14:30

Adaptor ligation

Training Lab B
14:30 - 15:00

User enzyme treatment

Training Lab B

15:00 - 15:30

Coffee break

Flex Lab A & B
15:30 - 16:30

Lecture - Biogenesis and function of AUG circRNAs
Thomas Birkballe Hansen - Aarhus University, Denmark

Flex Lab A & B
16:30 - 17:35

Bead clean-up

Training Lab B
17:35 - 18:30 Summary of the day + Q&A Flex Lab A & B
18:30 - 19:30 Tapas Night ATC Rooftop Lounge
19:30 - 21:00 Presentations by participants ATC Rooftop Lounge
21:00 Bus to ISG Hotel ATC entrance
Day 3 - Tuesday 19 November 2019
TimeSpeakerLocation
08:40

Bus to EMBL

ISG Hotel bus stop

09:00 - 09:30

PCR set up

Training Lab B

09:30 - 10:30

Lecture - Circular RNAs modulating myogenic transcription
Myriam Gorospe - National Institute on Aging, USA

Flex Lab A & B

10:30 - 10:35

Group photo

10:35 - 11:20

Final PCR clean-up

Training Lab B

11:20 - 11:40

Coffee Break

Flex Lab A & B

11:40 - 12:30

Library QC: Qubit, Bioanalyzer

Training Lab B
12:30 - 13:30

Lunch break

EMBL Canteen

13:30 - 14:30

Discussion of QC results and pool of final libraries

Training Lab B
14:30 - 15:00

Start sequencing run

Training Lab B

15:00 - 15:30 Coffee Break Flex Lab A & B
15:30 - 17:30

Introduction to qPCR 

Training Lab B
17:30 - 18:30 Q&A session Flex Lab A & B
18:30 - 19:30 Dinner EMBL Canteen
19:30 - 21:00 Presentations by participants ATC Rooftop Lounge
21:00 Bus to ISG Hotel ATC entrance
Day 4 - Wednesday 20 November 2019
TimeSpeakerLocation
08:40

Bus to EMBL

ISG Hotel bus stop

09:00 - 10:00

Lecture - Circtools, bioinformatics suite for data analysis
Tobias Jakobi - Heidelberg University Hospital, Germany

Flex Lab A & B

10:00 - 10:30

Coffee break

Computer Training Lab

10:30 - 13:00

Data analysis, part I (combination of tutorials and hands-on exercise): Introduction to R
NGS data structure, post-sequencing data QC, alignment algorithms (from reads-to-gene lists), interpretation of results

Computer Training Lab

13:00 - 14:00

Lunch break

EMBL Canteen

14:00 - 16:00

Data analysis, part II (combination of tutorials and hands-on exercise):
Starting the circtools workflow: ‘Detect’ module for circRNA detection

Computer Training Lab

16:00 - 16:30

Coffee break

Computer Training Lab

16:30 - 18:00

Data analysis, part II (combination of tutorials and hands-on exercise)

Computer Training Lab

from 18:00

Free evening

18:00

Bus to ISG Hotel

ATC entrance
18:15 Bus to Neckarmünzplatz ISG Hotel bus stop
18:30

Optional - Guided Tour of Heidelberg

Neckarmünzplatz
Day 5 - Thursday 21 November 2019
TimeSpeakerLocation
08:40

Bus to EMBL

ISG Hotel bus stop

09:00 - 10:00

Lecture - Circular RNAs: regulation and function in the vascular system
Stefanie Dimmeler - Goethe-University Frankfurt am Main, Germany

Flex Lab A & B

10:00 - 10:30

Coffee break

Computer Training Lab

10:30 - 13:00

Data analysis, part III (combination of tutorials and hands-on exercise):
Throughout the day, application of ‘quickcheck’, ‘circtest’, ‘reconstruct’, ‘exon’ & ‘enrich’modules from the
‘circtools’ suite and analysis of generated results

Computer Training Lab

13:00 - 14:00

Lunch break

EMBL Canteen

14:00 - 18:00

Data analysis, part III (combination of tutorials and hands-on exercise):
application of ‘quickcheck’, ‘circtest’, ‘reconstruct’, ‘exon’ & ‘enrich’modules from the ‘circtools’ suite and
analysis of generated results

Computer Training Lab

18:00 - 18:30

Summary of the day

Computer Training Lab

18:30

Bus to ISG Hotel

ATC entrance

18:50

Bus to restaurant "Oskar"

ISG Hotel bus stop

19:00

Course Dinner

Restaurant Oskar

Day 6 - Friday 22 November 2019
TimeSpeakerLocation
08:40

Bus to EMBL

ISG Hotel bus stop

09:30 - 10:30

Lecture - Molecular and Physiological functions of circRNAs
Sebastian Kadener - Brandeis University, USA

Flex Lab A & B

10:30 - 11:00

Coffee break

Computer Training Lab

11:00 - 13:00

Data analysis, part IV (hands-on exercise, competition):
Participants independently working with circtools on defined datasets

Computer Training Lab

13:00 - 14:00

Lunch break

EMBL Canteen

14:00 - 16:00

Data analysis, part IV (hands-on exercise):
Participants independently working with circtools on defined datasets, evaluation of the outcome

Computer Training Lab

16:00 - 16:30

Wrap-up and course feedback

Computer Training Lab

16:30

Bus to ISG Hotel, Heidelberg main train station & Lufthansa Shuttle bus

ATC entrance