00.0 Introduction to Epigenetics [Loi] - 02/11/2025
00.1 Ubuntu and basic Linux command part 1 [Huy] - 02/11/2025
01.0 Gene Expression and Chromatin 1 [Loi] - 09/11/2025
01.1 Ubuntu and basic Linux command part 2 [Huy] - 09/11/2025
02.0 Gene Expression and Chromatin 2 [Loi] - 16/11/2025
02.1 Bash Script 1 [Huy] - 16/11/2025
03.0 The Basal Transcriptional Machinery [Loi] - 23/11/2025
03.1 Bash Script 2 [Huy] - 23/11/2025
04.0 Transcription Factors and Signal Transduction [Loi] - 30/11/2025
04.1 Awk and practice part 1 [Huy] - 30/11/2025
05.0 A Key Transcription Factor Family: Nuclear Receptors [Loi] - 07/12/2025
05.1 Awk and practice part 2 [Huy] - 7/12/2025
- [PDF] [HOMEWORK] YOUTUBE
06.0 Oral Midterm Exam I Part 1 for Module I: Fundamentals of Epigenetics [Loi] - 14/12/2025
06.1 Introduction to R 0 [Phuc] - 14/12/2025
07 Introduction to R 1 [Phuc] - 21/12/2025
08 Introduction to R 2 [Phuc] - 28/12/2025
09 Introduction to R 3 [Phuc] - 04/01/2026
- Practice:
- PDF [HOMEWORK]
10.0 Oral Midterm Exam I Part 2 for Module I: Fundamentals of Epigenetics [Loi] - 11/01/2026
10.1 Introduction to R 4 [Phuc] - 11/01/2026
11.0 Principles of epigenetics [Loi] - 21/02/2026
11.1 Epigenomics and Encode Project [Loi] - 28/02/2026
12.0 Chromatin based epigenetic control I - 14+07/3/2026
13.0 Fundamental concepts of RNA sequencing experiments - 21/3/2026
13.1 Best Practice for RNA-seq analysis [Loi] - 28/3/2026
14.0 Chromatin based epigenetic control II [Loi] - 04+11/4/2026
- Chromatin organisation and histone methylation: setting, removing and reading
- Chromatin organisation and histone modifications: inheritance
15.0 ChIP-seq for Histone modifications and Transcription Factors Profiling [Loi] - 18/4/2026
15.1 ChIP-seq for DNAaseI Hypersensitivity and ATAC-seq Analysis [Loi]
- Exercise 1. Explain Figure 1 in the paper
- Exercise 2. Explain Figure 7A in the paper
- Exercise 3. Explain Figure 5E in the paper
- Exercise 4. Explain Figure 4C and 4D in the paper
- Exercise 5. Explain Figure 1F and 1H in the paper
15.2 3C, 4C, 5C and Hi-C for Chromatin Conformation [Loi]
16 Hands-on: ATACSeq Analysis [Nhu] - 25/4/2026
- Practice:
17.0 DNA-methylation and epigenetic control [Loi] - 09/5/2026
- Exercise 1. Explain Figure 5 in the paper
- Exercise 2. Explain Figure 3 in the paper
- Exercise 3. Explain Figure 4 in the paper
- Exercise 4. Explain Figure 5 in the paper
- Exercise 5. Explain Figure 2 & 3 in the paper
17.1 DNA methylation analysis with DMRcate [Thien/Hoang/Quan] - 16/5/2026
- Introduction to DMR
- Data - LINK1
- Data.gz - LINK2
- 00.Install_packages:
- 01.GSE2IDAT_&_IDAT2Table:
- 02.DMRcate:
- 03.Plotting:
- 04.Annotation:
- 05.Gene ontology analysis: