Location & dates EMBL Heidelberg, Germany 15 - 21 Nov 2020
Deadlines Application closed
organiser_EMBO_Course_2017

EMBL Courses and Conferences during the Coronavirus pandemic

With the onsite programme paused, many of our events are now being offered in virtual formats.


Registration is open as usual for many events, with back-up plans in place to move further courses and conferences online as necessary. Registration fees for any events affected by the COVID-19 disruption are fully refundable.


More information for participants of events at EMBL Heidelberg can be found here.

Programme

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Day 1 - Sunday 15 November 2020
TimeSpeakerLocation
10:00 - 10:15

Welcome and some practicalities by organisers

Flex Lab A

10:15 - 10:30

Laboratory safety introduction

Flex Lab A

10:30 - 11:15

Ice breaking activity (concurrent coffee break)

Flex Lab A

11:15 - 12:15

Interactive Lecture: Flow Cytometry and single cell sampling
Malte Paulsen - EMBL Heidelberg, Germany

Flex Lab A

12:15 - 13:00

Lunch break

Rooftop Lounge

13:00 - 13:45

Lecture: Introduction

Stephen Clark - Babraham Institute, UK

Flex Lab A

13:45 - 15:15

Practical I and II: purification of BS converted DNA and pre-amplification / Cell sampling by FACS

Training Lab B

15:15 - 16:45

Practical I and II: Cell sampling by FACS/ practical I purification of BS converted DNA and pre-amplification

Training Lab B
16:45 - 17:00

Coffee break

Outside Training Lab Area

17:00 - 18:00

Lecture: 

Anders Ståhlberg - Sahlgrenska Academy at University of Gothenburg, Sweden

Flex Lab A

18:00-19:30

Practical III: purification and adaptor tagging

Training Lab B

19:30 - 20:30

Dinner

EMBL Canteen

20:30 - 21:30

Flash talks by participants

Flex Lab A

21:30

Return to Hotel

Day 2 - Monday 16 November 2020
TimeSpeakerLocation
09:00 - 09:15

Overview of the day

Flex Lab A

09:15 - 10:00

Lecture: Single cell transcriptomics – newest advantages and
limitations in the field

Vladimir Benes - EMBL Heidelberg, Germany

Flex Lab A

10:00 - 10:15

Coffee break

Outside Training Lab Area

10:15 - 11:15

Practical (sc-BS-Seq): Purification and library amplification (Stephen Clark, Ferris Jung, Nayara de Azevedo)

Training Lab B

11:15 - 11:45

Practical (scRNA-Seq): workflow overview (Katharina Danielski)

Training Lab B
11:45 - 13:00

Practical (scRNA-Seq): GEM generation and barcoding incl. workflow overview: from cell preparation to reverse transcription set-up (Katharina Danielski, Ferris Jung, Nayara de Azevedo)

Training Lab B
13:00 - 14:00

Lunch break

EMBL Canteen

14:00 - 14:45

Lecture: Single-Cell ATAC Seq and its Applications
Eileen Furlong - EMBL Heidelberg, Germany

Flex Lab A

14:45 - 15:00

Coffee break

Outside Training Lab Area
15:00 - 17:00

Practical (scRNA-Seq): Post Gem RT clean up and cDNA amplification (Katharina Danielski, Ferris Jung, Nayara de Azevedo)

Training Lab B
17:00 - 17:45

Lecture: Single cell analysis in tracking embryo development

Qiaolin Deng - Karolinska Institutet, Sweden

Flex Lab A
17:45 - 18:30

Interactive Lecture: Experimental Design for single cell analysis (all speakers and trainers)

Flex Lab A
18:30 - 21:00

Poster Session with Pizza and drinks & Discussion I

Helix A

21:00

Return to Hotel

Day 3 - Tuesday 17 November 2020
TimeSpeakerLocation
09:00 - 09:15

Overview of the day

Flex Lab A

09:15 - 10:00

Lecture: Spatial transcriptomics – and comparisons to single-cell RNA Seq

Lars Borm - Karolinska Institutet, Sweden

Flex Lab A

10:00 - 10:15

Coffee break

Outside Training Lab Area

10:15 - 12:00

Practical (scRNA-Seq): Library preparation and quality control (Katharina Danielski, Ferris Jung, Nayara de Azevedo)

Training Lab B

12:00 - 13:00

Lunch break

EMBL Canteen

13:00 - 13:45

Single-Cell protein analysis
Johan Reimegård - Uppsala University, Sweden

Flex Lab A

13:45 - 15:45

Practical (scRNA-Seq): Library preparation continues and EMBL Genomics Core Facility Tour (Vladimir Benes, Ferris Jung, Nayara de Azevedo)

Training Lab B/ Core Facilities
16:00 - 16:45

Lecture: Single-cell approaches in stem cell and cancer research using Ab-Seq

Simon Haas - HI-STEM gGmbH/ German Cancer Research Centre, Germany

Flex Lab A
16:45 - 17:45

Discussion-round: Challenges, limitations and “tips and tricks” of single-cell omics applications (all speakers and trainers)

Flex Lab A
17:45 - 19:00

Career-Networking Dinner: participants will be grouped based on their interest with an respective expert (topic examples: funding for postdoc positions, tips for starting your own group)

EMBL Canteen
19:00 - 21:00

Poster Session with drinks and discussion II

Helix A

21:00

Departure to Hotel

Day 4 - Wednesday 18 November 2020
TimeSpeakerLocation
09:00 - 09:15

Overview of the day

Flex Lab A

09:15 - 10:00

Lecture: Single cell genomics
Jan Korbel - EMBL Heidelberg, Germany

Flex Lab A

10:00 - 10:45

Practical Introduction lecture: Strand-Seq technology
introduction and applications

Ashley Sanders - EMBL Heidelberg, Germany

Flex Lab A

10:45 - 11:00

Coffee break

Outside Training Lab Area

11:00 - 12:30

Practical (Strand-Seq): Strand Seq sample prep (nuclei isolation and FACS analysis) (Ashley Sanders, Karen Grimes, Patrick Hasenfeld)

Training Lab B

12:30 - 13:30

Lunch break

EMBL Canteen

13:30 - 15:30

Practical (Strand-Seq) continued: Strand-seq MNase digestion with sample clean up (Ashley Sanders, Karen Grimes, Patrick Hasenfeld)

Training Lab B

15:30 - 16:30

Practical (Strand-Seq): Robotics demonstration of MNase protocol (Ashley Sanders, Karen Grimes, Patrick Hasenfeld)

Training Lab B
16:30 - 16:45

Coffee break

Outside Training Lab Area

16:45 - 18:00

Lecture: Data-preprocessing (focus on generated scRNA-seq datasets)

Raffaele Calogero - University of Torino, Italy

Computer Training Lab

18:00 - 19:30

Bus downtown and guided tour through Heidelberg

downtown Heidelberg

20:00

Dinner

Restaurant downtown

Day 5 - Thursday 19 November 2020
TimeSpeakerLocation
09:00 - 09:15

Overview of the day

Flex Lab A

09:15 - 10:00

Lecture: Single cell RNA Seq data analysis
Raffaele Calogero - University of Torino, Italy

Computer Training Lab

10:00 - 10:15

Coffee break

Outside Computer Training Lab

10:15 - 12:30

Computational practical: Single-cell RNA Seq data analysis (Raffaele Calogero, Francesca Cordero)

Computer Training Lab

12:30 - 13:30

Lunch break

EMBL Canteen

13:30 - 15:00

Computational practical continued: Single-cell RNA Seq data analysis (Raffaele Calogero, Francesca Cordero)

Computer Training Lab

15:00 - 15:30

Coffee break

Outside Training Lab Area

15:30 - 16:15

Lecture: Spatial single-cell metabolomics

Theodore Alexandrov - EMBL Heidelberg, Germany

Computer Training Lab

16:15 - 17:00

Lecture: Data Integration on Spatial Levels

Oliver Stegle - German Cancer Research Centre, Germany

Computer Training Lab
17:00 - 18:00 Group activity: Critical steps in single cell data analysis Computer Training Lab
18:00

Free evening

Day 6 - Friday 20 November 2020
TimeSpeakerLocation
09:00 - 09:15

Overview of the day

Computer Training Lab

09:15 - 10:00

Practical Introduction Lecture: Single-cell genomics data  nalysis

Hyobin Jeong/ David Porubsky 

Computer Training Lab

10:00 - 10:15

Coffee break

Computer Training Lab

10:15 - 12:30

Computational practical: Single-cell genomics data analysis (Hyobin Jeong, David Porubsky)

outside Computer Training Lab

12:30 - 13:30

Lunch break

EMBL Canteen

13:30 - 15:00

Computational practical continued: Single-cell genomics data analysis (David Porubsky, Hyobin Jeong)

Computer Training Lab

15:00 - 15:30

Coffee break

outside Computer Training Lab
15:30 - 16:15

Lecture: Analysis of epigenetic single-cell datasets

Davis McCarthy - The University of Melbourne & St Vincent's Institute of Medical Research, Australia

Computer Training Lab
16:15 - 18:00

Computational practical: scBS-Seq data analysis – Data pre-processing and first analysis steps

Computer Training Lab

18:00

Bus to ISG

19:00

Flammkuchen Dinner

ISG Hotel
Day 7 - Saturday 21 November 2020
TimeSpeakerLocation
09:00 - 09:15

Overview of the day

Computer Training Lab

09:15 - 10:30

Computational practical continued: scBS-Seq data analysis (Davis McCarthy)

Computer Training Lab

10:30 - 10:45

Coffee break

outside Computer Training Lab

12:30 - 13:30

Computational practical: Data integration tools (Raffaele Calogero)

Computer Training Lab

12:30 - 13:30

Lunch break

EMBL Canteen

13:30 - 14:30

Data analysis discussion round

Computer Training Lab
14:30 – 15:00

Wrap up, Poster prize and feedback

Computer Training Lab

15:00

End of course