SUMMER SCHOOL OF SINGLE CELL

FROM THE LAB TO DATA ANALYSIS

September 2 – 9, 2020, Pilsen, Czech Republic

Charles University, University of West Bohemia,

Imperial College London, University of Milan, University of Warsaw, Heidelberg University, University Hospital Heidelberg and German Cancer Research Center

PROGRAM

The program is preliminary and might change.

Day 1 (Wed, Sept. 2) – Welcome and Lectures

Chair: Monika Holubová (Charles University)

7:30 – 8:30 Registration
Introduction session
8:45 – 10:30 Welcome Monika Holubová (Charles University) 15 min
Introduction to single-cell analysis and its role in today’s research Pavel Ostašov (Charles University) 30 min
Connecting computer scientists and biologists in the design and implementation of single cell experiments Lucie Houdová (University of West Bohemia) 30 min
Single-cell transcriptomics data analysis: an introduction by examples Iros Barozzi (Imperial College London) 30 min
10:30 – 10:50 Coffee break
10:50 – 11:00 Company presentation: iBioTech Petr Táborský (iBioTech) 10 min
11:00 – 12:00 scRNA -seq experimental design: Dos and Don'ts Valentina Caputo (Imperial College London) 30 min
Searching for rare events – real life struggle from academia and industry Pavel Pitule (Biomedical Center, Pilsen) 30 min
12:00 – 13:00 Lunch
Examples of Application
13:00 – 14:30 Lecture (title will be specified) Roberto Mantovani (University of Milan) 30 min
Transcriptional subclone diversity, microenvironmental interactions and treatment responses in refractory multiple myeloma Stephan Tirier (German Cancer Research Center) 30 min
Integrative analysis of chromatin accessibility and gene expression to understand the gene regulatory mechanisms underlying treatment response in multiple myeloma Alexandra Poos (University Hospital Heidelberg) 30 min
14:30 – 15:00 Coffee break
15:00 – 16:30 Lecture (title will be specified) Lucas Schirmer (Heidelberg University) 30 min
What can single cell analysis provide to non-alcoholic fatty liver disease research? Lucie Vištejnová (Biomedical Center, Pilsen) 30 min
Lecture (title will be specified) Diletta Dolfini (University of Milan) 30 min
16:30 – 18:00 Welcome drink and networking

Day 2 (Thu, Sept. 3) – Wet lab part 1

Supervisors: Monika Holubová, Pavel Ostašov (both Charles University)

8:00 – 9:00 Introduction to laboratory work
9:00 – 18:00 Single cell preparation - Participants will be split to 2 groups and will rotate.
Cell sorting and dead cells removal
Company presentation: GeneTiCA
Company presentation: 10XGenomics - Presentation with sample preparation

Day 3 (Fri, Sept. 4) – Wet lab part 2 & Preparation for In silico lab

Supervisors – wet lab: Valentina Caputo (Imperial College), Pavel Ostašov (Charles University)

Supervisors – in silico lab: Iros Barozzi (Imperial College), Marcin Tabaka (University of Warsaw), Lucie Houdová (University of West Bohemia)

Group 1 – Wet lab part 2
8:00 – 16:30 Cell processing for single cell RNAseq (cell lysis and library preparation, quality control, sequencing)
Group 2 – Preparation for In silico lab
8:00 – 11:30 Introduction to Linux & R programming rudiments
11:30 – 12:30 Lunch
12:30 – 14:30 Quality controls & data management for single-cell transcriptomics
14:30 – 16:30 Company presentation: 10XGenomics analysis tool

Day 4 (Sat, Sept. 5) – Wet lab part 2 & Preparation for In silico lab

Supervisors – wet lab: Valentina Caputo (Imperial College), Pavel Ostašov (Charles University).

Supervisors – in silico lab: Iros Barozzi (Imperial College), Marcin Tabaka (University of Warsaw), Lucie Houdová (University of West Bohemia)

Group 1 – Preparation for In silico lab
8:00 – 11:30 Introduction to Linux & R programming rudiments
11:30 – 12:30 Lunch
12:30 – 14:30 Quality controls & data management for single-cell transcriptomics
14:30 – 16:30 Company presentation: 10XGenomics analysis tool
Group 2 – Wet lab part 2
8:00 – 16:30 Cell processing for single cell RNAseq (cell lysis and library preparation, quality control, sequencing)

Day-off (Sun, Sept. 6)

Organized tour through Pilsen with beer tasting.

Day 5 (Mon, Sept. 7) – Data analysis part 1

Supervisors: Lucie Houdová (University of West Bohemia), Iros Barozzi (Imperial College), Ewa Szczurek, Marcin Tabaka (both University of Warsaw)

Theoretical and Tutorial Day
8:00 – 11:30 Theoretical introduction to analytical approaches
11:30 – 12:30 Lunch
12:30 – 16:30 Tutorial: how to approach single-cell RNA-seq datasets, using published data (preprocessing & mapping, QC, normalization, dimensionality reduction, clustering, differential expression)

Day 6 (Tue, Sept. 8) – Data analysis part 2

Supervisors: Lucie Houdová (University of West Bohemia), Iros Barozzi (Imperial College), Ewa Szczurek, Marcin Tabaka (both University of Warsaw)

Practical Day
8:00 – 16:30 Analysis of the data generated during the summer school
18:00 – 22:00 Dinner event

Day 7 (Wed, Sept. 9) – Goodbye

9:00 – 12:00 Conclusion with the announcement of the best presented project, discussion and goodbye

Note: Unless specified directly in the program Lunch and coffee breaks will be determined according to the current situation.