SUMMER SCHOOL OF SINGLE CELL

FROM THE LAB TO DATA ANALYSIS

September 7 – 14, 2022, Pilsen, Czech Republic

Charles University, University of West Bohemia,

Medical University of Vienna, London South Bank University, University of Milan, University of Warsaw, Heidelberg University and University of Copenhagen

PROGRAM

Day 1 (Wed, Sept. 7) - LECTURES DAY

8:00 - 8:45 REGISTRATION
8:45 - 9:00 WELCOME
Milena Králíčková (Rector of Charles University)
9:00 - 12:30 SESSION 1: IMMUNE CELLS AND SINGLE-CELL ANALYSIS

PART 1 - Chair: Valentina Caputo (London South Bank University) and Monika Holubová (Charles University)

Microenvironmental control of innate lymphoid cell responses Ana Stojanovic (University of Heidelberg) 30 min
iNKT and dogs: a ride from bench to bed with the help of man’s best friend Antonia Rotolo (University of Pennsylvania) 30 min
CAR-iNKT cells: Another blade for the swiss army knife Emmanuelle Moraes Ribeiro (Schneidawind Lab, University Hospital Tubinghen) 30 min
Chaperon presentation Petr Hošek (Charles University) 10 min
Coffee break (10:40 - 11:00)

PART 2 - Chair: Valentina Caputo (London South Bank University) and Pavel Ostašov (Charles University)

Single cell applications in the decade of CART therapy Agnieszka Ciesielska (10X Genomics) 30 min
Profiling of immune cells in bacterial sepsis Lucie Kraftová (Charles University) 30 min
Empowering stem cell therapy for Huntington's disease using single-cell genomics Vittoria Bocchi (University of Milan) 30 min
12:30 - 13:20 LUNCH BREAK
13:20 - 16:30 SESSION 2: THE APPROACHES FOR THE STUDY OF BIOLOGICAL PROCESSES

PART 1 - Chair: Daniel Georgiev (University of West Bohemia) and Lucie Houdová (University of West Bohemia)

Possibilities for bioinformatic support of biological research and data analysis with ELIXIR CZ research infrastructure Karel Berka (ELIXIR Czech Republic, Palacký University Olomouc) 20 min
Spatial genomics: Digital approaches to study the Society of Cells Kyoung Jae Won (University of Copenhagen) 30 min
Single Cell Transcriptomics (as of Today) Giulio Pavesi (University of Milan) 30 min
Coffee break (14:40 - 15:00)

PART 2 - Chair: Daniel Georgiev (University of West Bohemia) and Pavel Ostašov (Charles University)

Variation in gene expression at single-cell level Aleksander Jankowski (University of Warsaw) 30 min
Harnessing cells to analyse cells: a massively parallel method for rare cell detection Daniel Georgiev (Sampling Human, Inc.) 30 min
Genome-wide quantification of transcription factor binding at single-DNA-molecule resolution Guido Barzaghi (Arnaud Krebs Lab, EMBL) 30 min
17:30 - 20:00 NETWORKING WITH WELCOME DRINK

Day 2 (Thu, Sept. 8)

8:00 - 17:00

Group A Cloning of CAR receptors (main supervisor: Valentina Caputo, co-supervisors: Diana Macečková, Monika Holubová)
Group B Single-cell sample preparation and 10XGenomics training (supervisors: Pavel Ostašov, Robin Klieber, Lenka Vaňková)

Day 3 (Fri, Sept. 9)

8:00 - 17:00

Group A Single-cell sample preparation and 10XGenomics training (supervisors: Pavel Ostašov, Robin Klieber, Lenka Vaňková)
Group B Cloning of CAR receptors (main supervisor: Valentina Caputo, co-supervisors: Diana Macečková, Monika Holubová)

Day 4 (Sat, Sept. 10)

8:00 - 18:00

NGS solutions for single cell and immune profiling (Explorea/Takara representative)
Experimental design is crucial: New technologies in NGS (IAB representative)
Experimental design is crucial: Advanced data analysis platforms (IAB representative)
In silico training (R, tidyverse and bioconductor) (main supervisor: Iros Barozzi; co-supervisor: Aleksander Jankowski)
Theoretical introduction to scRNA-seq (and multi-modal) data analysis (main supervisor: Iros Barozzi; co-supervisor: Aleksander Jankowski)

Day 5 - day-off (Sun, Sept. 11)

Organized tour through Pilsen with visit to the brewery and beer tasting.

Day 6 (Mon, Sept. 12)

9:00 - 17:00

Data analysis part 1 - Tutorial on scRNA-seq data analysis with R (main supervisor: Iros Barozzi; co-supervisor: Aleksander Jankowski)

Day 7 (Tue, Sept. 13)

9:00 - 17:00

Data analysis part 2 - Tutorial on multi-modal data analysis with R (main supervisor: Iros Barozzi; co-supervisor: Aleksander Jankowski)
Barbecue party: cloning evaluation, best project evaluation - submitted videos (18:00 - 22:00)

Day 8 (Wed, Sept. 14)

9:00 - 13:00

Data analysis part 3 – group projects (short quest with prize)
Conclusion and certification

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