Genome-scale technologies 1000-715TSG

1. Introduction - traditional sequencing methods for DNA (Sanger), RNA (EST and microarrays) and peptides (Edman degradation).
Lab: intro to galaxy
2. Next generation DNA sequencing methods, library preparation and quality control.
Lab: NGS quality control, filtering and trimming reads
3. Mapping NGS reads to genomes
Lab: read mapping in practice
4. DNA methylation sequencing
Lab: Maping reads from bisulfite-seq, calling methylated sites
5. RNA sequencing
Lab: read counting for genes and transcripts, differential gene expression
6. Histone modifications and ChIP-Seq
Lab: identification of enriched regions in ChIP-Seq data
7. DNA Variant identification from NGS
Lab: SNP detection in NGS data
8. Metagenomics
Lab: metagenomic read assignment to phylogenetic clades
9. Qualitative proteomics, mass spectrometry
Lab: peptide identification in MSMS spectra
10. Quantitative proteomics
Lab. differential MS spectra analysis
11. Gene networks (genetic, PPI, coexpression, etc), functional annotation
Lab. Network visualization and ontology annotations
12. Test
Lab. Project work
13. Sequence assembly based on NGS reads
Lab. Project work
14. Single cell omics techniques
Lab. Single cell RNA-Seq analysis with Seurat