PROGRAM
Day 1 (Wed, Sept. 2) – Welcome and Lectures
Chair: Monika Holubová (Charles University)
| 7:30 – 8:30 | Registration | ||
| Introduction session – chairman: Monika Holubová, Pavel Ostašov | |||
| 8:30 – 10:30 | Welcome and opening | Milena Králíčková (vice-rector, 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 (online) | Valentina Caputo (Imperial College London) | 30 min |
| Searching for rare events – real life struggle from academia and industry (online) | Pavel Pitule (Biomedical Center, Pilsen) | 30 min | |
| 12:00 – 12:50 | Lunch | ||
| Examples of Application – chairman: Lucie Houdová, Iros Barozzi | |||
| 12:50 – 14:30 | Introduction to Application section | Blanka Šedivá (vice-rector, University of West Bohemia) | 10 min |
| Lecture (title will be specified) (online) | Roberto Mantovani (University of Milan) | 30 min | |
| Transcriptional subclone diversity, microenvironmental interactions and treatment responses in refractory multiple myeloma (online) | 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 (online) | Alexandra Poos (University Hospital Heidelberg) | 30 min | |
| 14:30 – 15:00 | Coffee break | ||
| 15:00 – 16:30 | Decoding cell-type specific transcriptomics in neuroinflammation | 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 | |
| Investigating how transcription factor splicing variants steer mouse stem cell fates (online) | 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, Diana Macečková, Karolína Dostálová, Iva Machová (all Charles University); Bashir Sadet, Luca Mazzitelli (10X Genomics - online); Ondřej Pácalt (GeneTICA)
| Group 1 | ||
| 9:00 – 11:00 | Single cell sorting/dead cell removal | |
| 11:00 – 13:00 | 10X company presentation | |
| 14:00 – 16:00 | 10X sample preparation presentation and analytical tool | |
| 16:00 – 18:00 | 10X hands-on training | |
| Group 2 | ||
| 9:00 – 11:00 | 10X sample preparation presentation and analytical tool | |
| 11:00 – 13:00 | 10X hands-on training | |
| 14:00 – 16:00 | 10X company presentation | |
| 16:00 – 18:00 | Single cell sorting/dead cell removal |
Day 3 (Fri, Sept. 4) – Wet lab part 2 & Preparation for In silico lab
Supervisors – wet lab: Valentina Caputo (Imperial College - online), Pavel Ostašov; Co-supervisors: Robin Klieber, Diana Macečková, Eva Kralovcová, Karolína Dostálová (Charles University)
Supervisors – in silico lab: Iros Barozzi (Imperial College), Marcin Tabaka (University of Warsaw), Lucie Houdová (University of West Bohemia)
| Group 1 | ||
| 8:00 – 16:30 | Cell processing for single cell RNAseq (cell lysis and library preparation, quality control, sequencing) | |
| 16:30 – 17:30 | Q/A session with Valentina Caputo | |
| Group 2 | ||
| 8:00 – 11:30 | Introduction to Linux & R programming rudiments | |
| 12:30 – 14:30 | Quality controls & data management for single-cell transcriptomics | |
| 14:30 – 16:00 | GeneTICA presentation |
Day 4 (Sat, Sept. 5) – Wet lab part 2 & Preparation for In silico lab
Supervisors – wet lab: Valentina Caputo (Imperial College - online), Pavel Ostašov; Co-supervisors: Robin Klieber, Diana Macečková, Eva Kralovcová, Karolína Dostálová (Charles University)
Supervisors – in silico lab: Iros Barozzi (Imperial College), Marcin Tabaka (University of Warsaw), Lucie Houdová (University of West Bohemia)
| Group 1 | ||
| 8:00 – 11:30 | Introduction to Linux & R programming rudiments | |
| 12:30 – 14:30 | Quality controls & data management for single-cell transcriptomics | |
| 14:30 – 16:00 | GeneTICA presentation | |
| Group 2 | ||
| 8:00 – 16:30 | Cell processing for single cell RNAseq (cell lysis and library preparation, quality control, sequencing) | |
| 16:30 – 17:30 | Q/A session with Valentina Caputo |
Day-off (Sun, Sept. 6)
Organized tour through Pilsen with visit to the brewery and 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 | Barbecue party |
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.