Pilsen Summer School of Single Cell
from the lab to data analysis
September 2 – 10, 2026, Pilsen, Czech Republic
Charles University, University of West Bohemia, Medical University of Vienna, London South Bank University, University of Warsaw, Nencki Institute
| DAY 1, September 2, 2026 – Hotel U Pramenů | |||
| 16:00–17:00 | Registration + PC Troubleshooting | ||
| 17:00–17:15 | Welcome and opening | ||
| 17:15–20:00 | Networking with welcome drink | ||
| DAY 2, September 3, 2026 – Biomedical Center | |||
| GROUP 1 | Single-cell sample preparation and 10X Genomics training (supervisors: Eliška Jandová, Valentina Caputo, BD representative, Robin Klieber) | ||
| GROUP 2 | BD Rhapsody training and Singleron Biotechnologies training (supervisors: Eva Sánchez Quant, Ritika Kulshreshtha) | ||
| DAY 3, September 4, 2026 – Biomedical Center | |||
| GROUP 1 | BD Rhapsody training and Singleron Biotechnologies training (supervisors: Eva Sánchez Quant, Ritika Kulshreshtha) | ||
| GROUP 2 | Single-cell sample preparation and 10X Genomics training (supervisors: Eliška Jandová, Valentina Caputo, BD representative, Robin Klieber) | ||
| DAY 4, September 5, 2026 – Biomedical Center | |||
| Morning session | |||
| GROUP 1 + 2 | Experiment design workshop (supervisor: Valentina Caputo, Monika Holubová, Pavel Ostašov) Wet lab quiz (supervisor: Valentina Caputo) |
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| Afternoon session | |||
| GROUP 1 + 2 | Basic training for data analysis – Introduction to R (supervisors: Kateřina Wolf, Bartosz Wojtaś, Pavel Ostašov) - optional | ||
| DAY 5, September 6, 2026 | |||
| Organized tour through Pilsen and Pilsner Urquel brewery tour with beer tasting |
| DAY 6, September 7, 2026 – NTIS Research Centre | |||
| Supervisors: Iros Barozzi, Aleksander Jankowski; co-supervisors: Bartosz Wojtaś, Kateřina Wolf, Pavel Ostašov, Tomáš Honzík | |||
| Morning session | |||
| GROUP 1 + 2 | Basic Lecture Short intro to coding (also use of AI/LLM) | ||
| Single-cell RNA-seq (Technologies, raw data analysis) | |||
| Afternoon session | |||
| GROUP 1 + 2 | Single-cell RNA-seq tutorial (QC, filtering, normalization) | ||
| Single-cell RNA-seq tutorial (Dimensionality reduction, clustering) | |||
| DAY 7, September 8, 2026 – NTIS Research Centre | |||
| Supervisors: Iros Barozzi, Aleksander Jankowski; co-supervisors: Bartosz Wojtaś, Kateřina Wolf, Pavel Ostašov, Tomáš Honzík | |||
| Morning session | |||
| GROUP 1 + 2 | Single-cell RNA-seq tutorial (Marker genes, cell cycle annotation) | ||
| Single-cell RNA-seq tutorial (Cell type annotation) | |||
| Afternoon session | |||
| GROUP 1 + 2 | Data visualization | ||
| Short introduction to Group Projects, Working on Group Projects | |||
| DAY 8, September 9, 2026 – NTIS Research Centre | |||
| Supervisors Iros Barozzi, Aleksander Jankowski; co-supervisors: Kateřina Wolf, Pavel Ostašov, Tomáš Honzík | |||
| Morning session | |||
| GROUP 1 + 2 | Agentic AI for Single-Cell Analysis | ||
| Working on Group Projects | |||
| Afternoon session | |||
| GROUP 1 + 2 | Working on Group Projects | ||
| Barbecue party at Hotel U Pramenů | |||
| DAY 9, September 10, 2026 – NTIS Research Centre | |||
| Morning session | |||
| GROUP 1 + 2 | Group project presentation and awards | ||
| Certification and conclusion | |||