| When | What | Who |
|---|---|---|
| 09:00-09:45 | Introduction round #1 | |
| 09:45-10:45 | Lecture: Overview of different single-cell platforms and assays | Susan Kloet |
| 10:45-11:00 | break | |
| 11:00-12:00 | Lecture: scRNA-seq platforms | Miao-Ping Chien |
| 12:00-13:00 | lunch | |
| 13:00-14:00 | Lecture: Preprocessing | Roberta Menafra |
| 14:00-14:15 | break | |
| 14:15-15:15 | Lecture: Quality control and normalization | Ahmed Mahfouz |
| 15:15-15:30 | break | |
| 15:30-17:00 | Practical: Quality control and normalization | TAs (Qirong, Remco) |
| When | What | Who |
|---|---|---|
| 09:00-09:45 | Introduction round #2 | |
| 09:45-10:45 | Lecture: Experimental design & sample preparation | Susan Kloet |
| 10:45-11:00 | break | |
| 11:00-12:00 | Lecture: Single-cell multi-omics | Miao-Ping Chien |
| 12:00-13:00 | lunch | |
| 13:00-14:00 | Lecture: Dimensionality reduction | Alexander Vieth |
| 14:00-14:15 | break | |
| 14:15-15:45 | Practical: Dimensionality reduction | TAs (Mohammed, Gregory) |
| 15:45-16:00 | break | |
| 16:00-17:00 | Lecture: Spatial Transcriptomics | Laura Heezen |
| When | What | Who |
|---|---|---|
| 09:00-10:00 | Lecture: Clustering and cell annotation | Marcel Reinders |
| 10:00-10:15 | break | |
| 10:15-12:00 | Practical: Clustering and cell annotation | TAs (Qirong, Remco) |
| 12:00-13:00 | lunch | |
| 13:00-14:00 | Lecture: Data integration | Tamim Abdelaal |
| 14:00-14:15 | break | |
| 14:15-15:45 | Practical: Data integration | TAs (Qirong, Remco) |
| 15:45-16:00 | break | |
| 16:00-17:00 | Practical: Spatial transcriptomics | TAs (Qirong, Remco) |
| When | What | Who |
|---|---|---|
| 09:00-10:00 | Lecture: Trajectory inference | Mohammed Charrout |
| 10:00-10:15 | break | |
| 10:15-12:00 | Practical: Trajectory inference | TAs (Mohammed, Gregory) |
| 12:00-13:00 | lunch | |
| 13:00-14:00 | Lecture: Differential expression analysis | Ahmed Mahfouz |
| 14:00-14:15 | break | |
| 14:15-15:45 | Practical: Differential expression analysis | TAs (Mohammed, Gregory) |
| 15:45-16:00 | break | |
| 16:00-17:00 | Open discussion, bring your own data | Ahmed Mahfouz, Susan Kloet, Miao-Ping Chien |
| When | What | Who |
|---|---|---|
| 09:00-09:45 | Machine learning for predicting cell type and response to perturbation from single-cell multi-omics | Stavros Makrodimitris (EMC) |
| 09:45-10:00 | break | |
| 10:00-10:45 | Exploring the tissue inflammatory landscape in chronic inflammation and cancer | Yvonne Vercoulen (UMCU) |
| 10:45-11:00 | break | |
| 11:00-11:45 | Single-cell immune profiling reveals novel thymus-seeding populations, T cell commitment, and multi-lineage development in the human thymus | Martijn Cordes (LUMC) |
| 11:45-12:00 | break | |
| 12:00-12:45 | UMCU Cell typing in the complex molecular landscape of the midbrain | Onur Basak (UMCU) |
| 12:45- | lunch |