Schedule
Monday (16 September 2024)
DNA methylation with Illumina 450K arrays 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 - 16:30 Exercises Methylation Sequencing
16:30 - 17:00 Daily challenge
Tuesday (17 September 2024)
ATAC-seq: data processing and analysis principles
09:00 - 09:30 Recap previous day (online session)
09:30 - 10:15 Introduction to ATAC-seq data analysis (online session)
10:30 - 11.30 Exercise: Data preprocessing and general QC and ATACseq QC (online support)
11:30 - 12:00 Exercise: ATAC-seq data analysis (online support)
12:00 - 13:00 lunch (offline)
13:00 - 13.45 Presentation and Q&A with National Genomics Infrastructure (Orlando Contreras Lopez and Anja Metzger) (online session)
13:30 - 15:30 Exercise: ATAC-seq data analysis (online support)
15:30 - 17:00 Exercise (offline)
16:00 - 17:00 Daily challenge
Wednesday (18 September 2024)
New methods and quantitative ChIP-seq (Simon Elsässer and Carmen Navarro Luzón)
09:00 - 10:00 Recap previous day (online session)
10.00 - 11.00 ChIP-seq methods (online session)
11.00 - 12.00 ChIP-seq alternatives (online session)
12:00 - 13:00 lunch (offline)
13:00 - 13:30 Introduction to exercises (online session)
13:30 - 16:00 Principles of ChIP-seq and Advanced ChIP Methods (online support)
16:00 - 17:00 Exercises (offline)
16:00 - 17:00 Daily challenge
Thursday (19 September 2024)
Workflow Management Systems & Downstream Analyses
09:00 - 09:30 Recap previous day (online session)
09:30 - 10:00 Introduction to Workflow Management (online session)
10:00 - 10:15 break (offline)
10:15 - 12:00 nf-core exercises (online support)
12:00 - 13:00 lunch (offline)
13:00 - 13:15 Introduction to Downstream analyses exercises (online session)
13:15 - 15:00 Downstream analyses exercises (online support)
15:00 - 17:00 Exercises (offline)
16:00 - 17:00 Daily challenge
Friday (20 September 2024)
Integrative and single cell omics & inspirational talk
09:00 - 09:30 Recap previous day (online session)
09.30 - 10.20 Single cell methods (online session)
10.20 - 10.35 Break
10.35 - 11.15 Integration of genomics data (online session)
11:15 - 11:20 Introduction to exercises (online session)
11.20 - 12.00 Single cell and data integration exercises and optional exercise on Multi-OMICs Factor Analysis (online support)
12:00 - 13:00 lunch (offline)
13.00 - 14.00 Inspirational talk: How does epigenetic mechanisms impact Type 2 diabetes? (Charlotte Ling) Zoom link: https://lu-se.zoom.us/j/67681656100
14.00 - 14.10 Break
14.10 - 15.00 Single cell and data integration exercises and optional exercise on Multi-OMICs Factor Analysis (online support)
15:00 - 16:00 Daily challenge
15:00 - 16:00 Short term feedback form
15.00 - 16.00 Course wrap-up