Programme
All sessions will take place using Zoom, please join using the ‘Join Zoom’ button. Password: SingCell
If you have any problems using Zoom, please first check the Zoom help sheet.
If you have watched the pre-recordings before the course, then the times marked in the programme for the pre-recorded sessions are for you to use as you wish. Please make sure you add any questions from the pre-recording to the course Q&A document.
All programme times are in GMT, to make sure you join sessions at the correct time, you can check the current GMT time here.
Data and containers from the course can be found in the EBI FTP, available for all to download.
| Time | Topic | Trainer |
| Day one – Monday 17 February – Planning the experiment | ||
| 09:00 — 09:45 | Introduction to EMBL-EBI and icebreaker | Piv Gopalasingam |
| 09:45 — 10:00 | Break | |
| 10:00 — 10:45 | Introduction to Single Cell Technologies | Silvie Fexova |
| 10:45 — 12:15 | Wet-lab overview | Wendi Bacon |
| 12:15 — 13:15 | Lunch break | |
| 13:15 — 14:30 | Dry-lab overview | Wendi Bacon |
| 14:30 — 15:00 | Break | |
| 15:00 — 16:30 | Experimental design and Q&A | Tallulah Andrews |
| Day two – Tuesday 18 February – Processing data | ||
| 08:00 — 09:00 | Designing your analysis (pre-recorded) | Tallulah Andrews |
| 09:00 — 09:40 | Getting set up: data set, workflow and environment setup | Anna Vathrakokoili Pournara |
| 09:40 – 10:00 | Break | |
| 10:00 — 11:00 | Raw reads to expression matrix — Talk and Q&A | Jiawei Wang and Jinzheng Ren |
| 11:00 — 12:30 | QC, Pre-processing, & Normalisation (pre-recorded talk and practical demo) | Yuyao Song, Hugo Tavares and Iris Yu |
| 12:30 — 13:30 | Lunch break | |
| 13:30 — 14:20 | Feature selection and dimensionality reduction — Talk and Q&A | Anna Vathrakokoili Pournara |
| 14:20 —15:00 | Batch correction and data set integration — Talk and Q&A | Yuyao Song |
| 15:00 — 15:30 | Break | |
| 15:30 — 16:30 | Posters and Networking | |
| Day three – Wednesday 19 February – Analysing data | ||
| 09:00 — 10:00 | Feature Selection, Dimensionality Reduction, and Data Integration — Practicals | Yuyao Song |
| 10:00 — 10:20 | Break | |
| 10:20 — 11:30 | Clustering and Cluster Marker Genes — Practicals | Anna Vathrakokoili Pournara |
| 11:30 — 12:30 | Differential Expression and Abundance Analysis — Talk and Q&A | Andrian Yang |
| 12:30 — 13:30 | Lunch break | |
| 13:30 — 14:30 | Differential Expression — Practical | Andrian Yang |
| 14:30 — 15:30 | Abundance Analysis — Practical | Andrian Yang |
| 15:30— 16:30 | Poster and Networking | |
| Day four – Thursday 20 February – Applying the pipeline | ||
| 09:00 — 09:40 | Spatial transcriptomics — Talk and Q&A | Nadav Yayon |
| 09:40 — 10:00 | Break | |
| 10:00 — 12:00 | Spatial transcriptiomics — Practical | Nadav Yayon |
| 12:00 — 13:00 | Lunch break | |
| 13:00 — 14:00 | Single cell Expression Atlas and single cell data submission | Liora Vilmovsky and Silvie Fexova |
| 14:00 — 15:00 | Project work | Project mentors |
| 15:00 — 15:30 | Break | |
| 15:30 — 16:00 | Project work | Project mentors |
| Day five – Friday 21 February – Putting it into practice | ||
| 09:00 — 10:00 | Project work | Project mentors |
| 10:00 — 10:20 | Break | |
| 10:20 — 12:00 | Project work | Project mentors |
| 12:00 — 13:00 | Lunch break | |
| 13:00 — 14:00 | Project work wrap-up | Project mentors |
| 14:00 — 15:00 | Final Q&A with project mentors | |
| 15:00 — 15:30 | Course wrap-up and survey | Piv Gopalasingam |