Advanced Neurogenomics

05 Nov 2021 (2h 00m)

Alessandro Cellerino - Corso (attività didattica) - Mista

Lecture 1: Primer on data distribution and visualization. Definition of probability, Poisson's distribution, gaussian distribution, definition of p-value, one sample t-test, two samples t-test, sign test as an example of non-parametric test. Box plot, gaussian kernel, violin plot. 2D plot. log-transform. Venn diagrams.

08 Nov 2021 (2h 00m)

Alessandro Cellerino - Corso (attività didattica) - Mista

Lecture 2: RNA-sequencing. Illumina method. RNA isolation and quality check, removal of unwanted RNAs, cDNA synthesis, library construction, bridge amplification, sequencing on flow cell, paired end vs. single end, sequencing depth and optimal experimental design. Pacific Bioscience and Oxford Nanopore.

16 Nov 2021 (2h 00m)

Alessandro Cellerino - Corso (attività didattica) - Mista

Quality check, FASTQ, alignment, BWT, SAM files, coverage vectors

19 Nov 2021 (2h 00m)

Alessandro Cellerino - Corso (attività didattica) - Mista

Detection of differentially expressed genes. Negative binomial distribution. DESeq. Linear regression generalized linear models. DESeq2. Type I and Type II errors. Correction for multiple testing. Benjamini-Hochberg. Block design.

29 Nov 2021 (2h 00m)

Alessandro Cellerino - Corso (attività didattica) - Mista

Hierarchical clustering, heat maps, K-means clustering, principal component analysis, multi dimensional scaling, elements of machine learning: overfitting, cross-validation, elastic net regression, epigenetic clock, linear discriminant analysis

03 Dic 2021 (2h 00m)

Alessandro Cellerino - Corso (attività didattica) - Mista

Kyoto Encyclopedia of Genes and Genomes, Reactome, Gene Ontology, GO as an acyclic graph, the problem of redundancy, clustering of GO terms. Hypergeometric distribution, Gene Set Enrichment Analysis, Generally Applicable Gene Enrichment analysis

06 Dic 2021 (2h 00m)

Alessandro Cellerino - Corso (attività didattica) - Mista

Network theory and application. Edges and NOdes. Random netrowrs and scale-free networks. Types of biological networks: metabolic network, protein-protein interaction, connectome. Correlation-based networks: gene co-expression and neural activity correlation. Metrics of centrality and modularity. Weighted-gene coexpression network analysis. Example of application of WGCNA to identify pathways controlling longevity.

10 Dic 2021 (2h 00m)

Alessandro Cellerino - Corso (attività didattica) - Mista

WGCNA applications in Neuroscience: Conservation and evolution of gene coexpression networks in human and chimpanzee brains. Networks associated to neuronal activity and mitochondria. Allen brain atlas. Concordance of functional and transcriptomic networks. Networks in psychiatric disorders.

13 Dic 2021 (2h 00m)

Alessandro Cellerino - Corso (attività didattica) - Mista

Use of DESeq2: data import, exploratory analysis, data normalization, plotting of counts, differential expression analysis with single and multiple factors

21 Dic 2021 (2h 00m)

Alessandro Cellerino - Corso (attività didattica) - Mista

Practical exercises with WEBGESTALT and REVIGO

10 Gen 2022 (2h 00m)

Alessandro Cellerino - Corso (attività didattica) - Mista

Biology of microRNAs. Ribosome footprinting. Assay of translational efficiency. Small RNA sequencing. IsomiRs. Examples of microRNA-29 biological functions. CLIP and CLASH.

18 Gen 2022 (2h 00m)

Alessandro Cellerino - Corso (attività didattica) - Mista

Single-cell RNA-seq (1): Library construction, trade-off between depth and number of cells, quality control.10x vs. Smart-seq, non-linear embeddings: t-SNE and UMAP. Clustering for single cells. Trajectory reconstruction.

21 Gen 2022 (2h 00m)

Alessandro Cellerino - Corso (attività didattica) - Mista

Molecular diversity of retinal cells (Drop-seq), molecular taxonomy of visual cortical neurons (Smart-seq), single nuclei sequencing and Div-seq, molecular taxonomy of the mouse nervous system

24 Gen 2022 (2h 00m)

Alessandro Cellerino - Corso (attività didattica) - Mista

Practical exercises with Loupe browser and the Allen Brain Atlas single cell collection

28 Gen 2022 (2h 00m)

Alessandro Cellerino - Corso (attività didattica) - Mista

ScRNAseq of pallial neurons in reptiles: comparison with mammals. Patch-seq. In situ sequencing of visual cortex. Spatial transcriptomics and in situ sequencing

31 Gen 2022 (2h 00m)

Alessandro Cellerino - Corso (attività didattica) - Mista

Immunoprecipitation of ribosomes to measure the translatome of defined cell types. Immunoprecipitation of phosphoryated S6 to study the translatome of activated neurons. Example of warm-sensitive neurons. Transcriptional profiling of neurons with defined connections.

04 Feb 2022 (2h 00m)

Alessandro Cellerino - Corso (attività didattica) - Mista

Basis of mass-spectorscopy-based proteomics. Proteome complexity, post-translational modifications and protein localization. Principles of mass spectrometry. Workflow of proteomics: protein isolation, digestion, chromatography, tandem mass spectrometry. Example of proteome/transcriptome decoupling during aging. Analysis of post-translational modifications. Example of phosphoproteome changes in response to depolarization.

07 Feb 2022 (2h 00m)

Alessandro Cellerino - Corso (attività didattica) - Mista

Synaptic RNAs, local translation, local RNa as the principal source of synaptic proteins, ribosome remodelling, analysis of synaptic interaction by BIO-ID and APEX

14 Feb 2022 (2h 00m)

Alessandro Cellerino - Corso (attività didattica) - Mista

Epigenetics. Basics of epigenetic regulation: DNA methylation, association to nuclear envelope and histone remodelling. Chromatin Immunoprecipitation, whole genome bisulfite sequencing, reduced representation bisulfite sequencing. Data analysis for epigenetics: peak calling and correlation between different marks. Use of UCSC Genome browser to visualize Chip-seq tracks.

18 Feb 2022 (2h 00m)

Alessandro Cellerino - Corso (attività didattica) - Mista

Epigenetic remodelling in the nervous system, patterns of methylation in CH and its association with DNMT3A activity. Epigenetic characteristics of neuronal types. Single-cell ATAC-seq in the hippocampus.