Schedule
Monday (22 September 2025)
DNA methylation with Illumina array and Bisulfite-seq
09:00 - 09:30 Welcome
09:30 - 10:15 Introduction to DNA methylation + Overview Array Exercises
10:15 - 10:30 Uppmax set up + break
10:30 - 12:00 Exercises Array Workflow
12:00 - 13:00 lunch (offline)
13:00 - 14:00 Methylation methods & technologies (Jessica Nordlund)
14:00 - 14:15 Break
14:15 - 14:30 Methylation Exercises Overview II: Methylation Sequencing
14:30 - 16:00 Exercises Methylation Sequencing
16:00 - 17:00 Daily challenge (offline)
Tuesday (23 September 2025)
ATAC-seq: data processing and analysis principles
09:00 - 09:30 Recap previous day
09:30 - 10:15 Introduction to ATAC-seq data analysis
10:30 - 11.30 Exercise: Data preprocessing and general QC and ATACseq QC
11:30 - 12:00 Exercise: ATAC-seq data analysis
12:00 - 13:00 lunch (offline)
13:00 - 13.45 Presentation and Q&A with National Genomics Infrastructure (Orlando Contreras Lopez and Michelle Ljungmark)
13:45 - 14:00 Break
14:00 - 15:30 Exercise: ATAC-seq data analysis
15:30 - 17:00 Exercise (offline support)
16:00 - 17:00 Daily challenge (offline)
Wednesday (24 September 2025)
New methods and quantitative ChIP-seq (Simon Elsässer and Carmen Navarro Luzón)
09:00 - 10:00 Recap previous day
10.00 - 11.00 ChIP-seq methods
11.00 - 12.00 ChIP-seq alternatives
12:00 - 13:00 lunch (offline)
13:00 - 13:30 Introduction to exercises
13:30 - 16:00 Principles of ChIP-seq and Advanced ChIP Methods
16:00 - 17:00 Exercises (offline support)
16:00 - 17:00 Daily challenge (offline)
Thursday (25 September 2025)
Downstream analyses
09:00 - 09:30 Recap previous day
09:30 - 10:00 Introduction to transcription factors and gene regulation (slides)
10:00 - 10:30 Exercises: Representing transcription factor binding sites (online session)
10:30 - 10:45 break (offline)
10:45 - 12:00 Exercises: Predicting relevant motifs (online session)
12:00 - 13:00 lunch (offline)
13:00 - 15:00 Additional downstream exercises (online support)
15:00 - 17:00 Exercises (offline support)
16:00 - 17:00 Daily challenge (offline)
Friday (26 September 2025)
Integrative and single cell omics
09:00 - 09:30 Recap previous day
09.30 - 10.20 Single cell methods
10.20 - 10.35 Break
10.35 - 11.15 Integration of genomics data
11:15 - 11:20 Introduction to exercises
11.20 - 12.00 Single cell and data integration exercises
12:00 - 13:00 lunch (offline)
13.00 - 14.00 Single cell and data integration exercises
14.00 - 15.00 Inspirational talk: Marek Bartosovic (Stockholm University). Deciphering the epigenetic landscape of the brain: Innovations in chromatin profiling with single-cell nano-CUT&Tag. Join by Zoom.
15:00 - 16:00 Daily challenge
15:00 - 16:00 Short term feedback form
15.00 - 16.00 Course wrap-up