Advanced Neurogenomics
Prerequisiti
PhD students
Programma
1) A primer on regulation of gene expression and statistical considerations
2) RNA-seq: how it works
3) Sequence quality control and mapping algorithms
4) Introduction to long-read sequencing (L. Pandolfini)
5) Hands-on: Long Read Sequencing Data Formats (L. Pandolfini)
6) Detection of differential gene expression
7) Clustering and other methods to reduce dimensionality
8) Gene Ontology and Gene Set Enrichment
9) Network analysis
10) RNA metabolism: splicing, stability & decay (L. Pandolfini)
11) Epitranscriptomics (L. Pandolfini)
12) Applications of network analysis to the brain
13) Hands-on: Analysis of differential expression using DESeq2
14) Hands-on: Analysis of GO terms and pathways using WebGestalt
15) Riboseq e miRNAs
16) Single-cell RNA-seq, methods and analysis
17) Single-cell RNA-seq, applications to the nervous system
18) Methods for spatial transcriptomics
19) ScRNA and vertebrate brain evolution (L. Pandolfini)
20) Patchseq and STARMAP
21) hands-on: exploration of ScRNAseq data
22) Proteome analysis by mass-spectroscopy
23) Local synaptic translation
24) Epigenetic analysis: DNA methylation and
ChIP-seq
25) Chromatin 3D conformation and evolution (L. Pandolfini)
26) Examples of epigenetic studies in the nervous system
27) Hands-on: Exploration of ENCODE datasets (L. Pandolfini)
28) - Comparative Genomics 1/3: from Assembly to Evolution (L. Pandolfini)
29) - Comparative Genomics 2/3: Gene Synteny (L. Pandolfini)
30) - Comparative Genomics 3/3: Advanced Transgenesis (L. Pandolfini)
Obiettivi formativi
Aims of the course are: 1) to educate students in the critical reading of omics-based publication both for the experimental and data analysis parts 2) to illustrate how these technologies have provided novel insights into the functional organization of the nervous system and 3) to provide students with the knowledge necessary to design their own omics-based projects, perform initial data analysis and interact with bioinformaticians for more complex anaylsis
Riferimenti bibliografici
Cellerino & Sanguanini "Transcriptome analysis" Ed. Scuola Normale and articles from scientific journals