Advanced Neurogenomics

13 Nov 2023 (2h 00m)

Alessandro Cellerino - Corso (attività didattica) - Mista

Lecture 1 - a primer on data distribution and visualization

17 Nov 2023 (2h 00m)

Alessandro Cellerino - Corso (attività didattica) - Mista

Lecture 2 RNA sequencing methods

20 Nov 2023 (2h 00m)

Alessandro Cellerino - Corso (attività didattica) - Mista

Lecture 3 - Quality control, mapping and normalization

24 Nov 2023 (2h 00m)

Alessandro Cellerino - Corso (attività didattica) - Mista

Lecture 4 - Analysis of differential gene expression. DESeq and DESeq2

27 Nov 2023 (2h 00m)

Alessandro Cellerino - Corso (attività didattica) - Mista

Lecture 5. Clustering methods and as primer on machine learning

01 Dic 2023 (2h 00m)

Alessandro Cellerino - Corso (attività didattica) - Mista

Lecture 6: KEGG, Gene Ontology, Reactome, Overrepresentation analysis and Gene Set Enrichment Analysis

05 Dic 2023 (2h 00m)

Alessandro Cellerino - Corso (attività didattica) - Mista

Lecture 7: Network theory and applications to connectome and gene co-expression network analysis.

18 Dic 2023 (2h 00m)

Alessandro Cellerino - Corso (attività didattica) - Mista

Lecture 8: case studies of network analysis applied to the brain Conservation and evolution of gene coexpression networks in human and chimpanzee brains. Oldham MC, Horvath S, Geschwind DH. Proc Natl Acad Sci U S A. 2006 Nov 21;103(47):17973-8 The organization of the transcriptional network in specific neuronal classes Kellen D Winden 1, Michael C Oldham, Karoly Mirnics, Philip J Ebert, Christo H Swan, Pat Levitt, John L Rubenstein, Steve Horvath, Daniel H Geschwind An anatomically comprehensive atlas of the adult human brain transcriptome Michael J Hawrylycz Correlated gene expression supports synchronous activity in brain networks Jonas Richiardi Gandal et al., "Shared molecular neuropathology across major psychiatric disorders parallels polygenic overlap Integrated systems approach identifies genetic nodes and networks in late-onset Alzheimer's disease Bin Zhang

08 Gen 2024 (2h 00m)

Alessandro Cellerino - Corso (attività didattica) - Mista

Lecture 9 Riboseq and microRNAs Developmental dynamics of RNA translation in the human brain. Duffy EE, Finander B, Choi G, Carter AC, Pritisanac I, Alam A, Luria V, Karger A, Phu W, Sherman MA, Assad EG, Pajarillo N, Khitun A, Crouch EE, Ganesh S, Chen J, Berger B, Sestan N, O'Donnell-Luria A, Huang EJ, Griffith EC, Forman-Kay JD, Moses AM, Kalish BT, Greenberg ME. Nat Neurosci. 2022 Oct;25(10):1353-1365 Metazoan MicroRNAs. Bartel DP. Cell. 2018 Mar 22;173(1):20-51 mRNA destabilization is the dominant effect of mammalian microRNAs by the time substantial repression ensues. Eichhorn SW, Guo H, McGeary SE, Rodriguez-Mias RA, Shin C, Baek D, Hsu SH, Ghoshal K, Villén J, Bartel DP. Mol Cell. 2014 Oct 2;56(1):104-15. Conserved microRNA editing in mammalian evolution, development and disease. Warnefors M, Liechti A, Halbert J, Valloton D, Kaessmann H. Genome Biol. 2014 Jun 25;15(6):R83 Transcriptome-wide discovery of microRNA binding sites in human brain. Boudreau RL, Jiang P, Gilmore BL, Spengler RM, Tirabassi R, Nelson JA, Ross CA, Xing Y, Davidson BL. Neuron. 2014 Jan 22;81(2):294-305. MicroRNA miR-29 controls a compensatory response to limit neuronal iron accumulation during adult life and aging. Ripa R, Dolfi L, Terrigno M, Pandolfini L, Savino A, Arcucci V, Groth M, Terzibasi Tozzini E, Baumgart M, Cellerino A. BMC Biol. 2017 Feb 13;15(1):9 AGO CLIP Reveals an Activated Network for Acute Regulation of Brain Glutamate Homeostasis in Ischemic Stroke. Kobayashi M, Benakis C, Anderson C, Moore MJ, Poon C, Uekawa K, Dyke JP, Fak JJ, Mele A, Park CY, Zhou P, Anrather J, Iadecola C, Darnell RB. Cell Rep. 2019 Jul 23;28(4):979-991.e6.

14 Gen 2024 (2h 00m)

Alessandro Cellerino - Corso (attività didattica) - Mista

LEcture 10 DESeq2 Description and pratical excerise with dedicated R script to perform explotatory data analysis and differential gene expression analysis using Bioconductor and DESeq2

22 Gen 2024 (2h 00m)

Alessandro Cellerino - Corso (attività didattica) - Mista

Lecture 11: Practical examples to analysis of GO terms. WEBGESTALT STRING. Analysis of a dataset GSE95649

26 Gen 2024 (2h 00m)

Alessandro Cellerino - Corso (attività didattica) - Mista

Lecture 12 SingleCellRNAseq(1): General characteristics of RNAseq. 10X Genomics vs. SMART. Feature selection. t-SNE and UMAP. Louvain method for cluster separation. RNA velocity.

29 Gen 2024 (2h 00m)

Alessandro Cellerino - Corso (attività didattica) - Mista

Lecture 13: seminal papers on the applications of single cell RNAseq to the study of the brain - Molecular Architecture of the Mouse Nervous System - Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets - Adult mouse cortical cell taxonomy revealed by single cell transcriptomics - A high-resolution transcriptomic and spatial atlas of cell types in the whole mouse brain - Transcriptomic cytoarchitecture reveals principles of human neocortex organization - Transcriptomic diversity of cell types across the adult human brain - Div-Seq: Single-nucleus RNA-Seq reveals dynamics of rare adult newborn neurons

02 Feb 2024 (2h 00m)

Alessandro Cellerino - Corso (attività didattica) - Mista

Lecture 14: practical lecture on data analysis in the Allen Brain atlas

05 Feb 2024 (2h 00m)

Alessandro Cellerino - Corso (attività didattica) - Mista

Lecture 15 Spatial transcriptomics - Visualization and analysis of gene expression in tissue sections by spatial transcriptomics - Atlas of the aging mouse brain reveals white matter as vulnerable foci Conservation and divergence of cortical cell organization in human and mouse revealed by MERFISH - Three-dimensional intact-tissue sequencing of single-cell transcriptional states - Integrative in situ mapping of single-cell transcriptional states and tissue histopathology in a mouse model of Alzheimer’s disease

12 Feb 2024 (2h 00m)

Alessandro Cellerino - Corso (attività didattica) - Mista

Lecture 16 Patchseq and MAPseq - Embryonic Origin of Postnatal Neural Stem Cells - Integrated Morphoelectric and Transcriptomic Classification of Cortical GABAergic Cells - High-Throughput Mapping of Single-Neuron Projections by Sequencing of Barcoded RNA - Signature morphoelectric properties of diverse GABAergic interneurons in the human neocortex - The logic of single-cell projections from visual cortex

23 Feb 2024 (2h 00m)

Alessandro Cellerino - Corso (attività didattica) - Mista

Lecture 17 Principles and applications of mass-spectroscopy based proteomics.

26 Feb 2024 (2h 00m)

Alessandro Cellerino - Corso (attività didattica) - Mista

Lecture 18 Proteomic and transcriptomics of the synapse, local protein translation On-Site Ribosome Remodeling by Locally Synthesized Ribosomal Proteins in Axons. Shigeoka T, Koppers M, Wong HH, Lin JQ, Cagnetta R, Dwivedy A, de Freitas Nascimento J, van Tartwijk FW, Ströhl F, Cioni JM, Schaeffer J, Carrington M, Kaminski CF, Jung H, Harris WA, Holt CE. Cell Rep. 2019 Dec 10;29(11):3605-3619 Dynamic Axonal Translation in Developing and Mature Visual Circuits. Shigeoka T, Jung H, Jung J, Turner-Bridger B, Ohk J, Lin JQ, Amieux PS, Holt CE. Cell. 2016 Jun 30;166(1):181-92 Monosomes actively translate synaptic mRNAs in neuronal processes. Biever A, Glock C, Tushev G, Ciirdaeva E, Dalmay T, Langer JD, Schuman EM. Science. 2020 Jan 31;367(6477) Local protein synthesis is a ubiquitous feature of neuronal pre- and postsynaptic compartments. Hafner AS, Donlin-Asp PG, Leitch B, Herzog E, Schuman EM. Science. 2019 May 17;364(6441):eaau3644 The local transcriptome in the synaptic neuropil revealed by deep sequencing and high-resolution imaging. Cajigas IJ, Tushev G, Will TJ, tom Dieck S, Fuerst N, Schuman EM. Neuron. 2012 May 10;74(3):453-66 RNA localization is a key determinant of neurite-enriched proteome. Zappulo A, van den Bruck D, Ciolli Mattioli C, Franke V, Imami K, McShane E, Moreno-Estelles M, Calviello L, Filipchyk A, Peguero-Sanchez E, Müller T, Woehler A, Birchmeier C, Merino E, Rajewsky N, Ohler U, Mazzoni EO, Selbach M, Akalin A, Chekulaeva M. Nat Commun. 2017 Sep 19;8(1):583 Sleep-wake cycles drive daily dynamics of synaptic phosphorylation. Brüning F, Noya SB, Bange T, Koutsouli S, Rudolph JD, Tyagarajan SK, Cox J, Mann M, Brown SA, Robles MS. Science. 2019 Oct 11;366(6462):eaav3617 The forebrain synaptic transcriptome is organized by clocks but its proteome is driven by sleep. Noya SB, Colameo D, Brüning F, Spinnler A, Mircsof D, Opitz L, Mann M, Tyagarajan SK, Robles MS, Brown SA. Science. 2019 Oct 11;366(6462):eaav2642

01 Mar 2024 (2h 00m)

Alessandro Cellerino - Corso (attività didattica) - In presenza

Epigenetics: ATAC-seq, Chip-seq, Bisulfite sequencing, data visualization using multiple tracks

04 Mar 2024 (2h 00m)

Alessandro Cellerino - Corso (attività didattica) - In presenza

Epigenetics 2: examples from the nervous system Global epigenomic reconfiguration during mammalian brain development. Lister R, Mukamel EA, Nery JR, Urich M, Puddifoot CA, Johnson ND, Lucero J, Huang Y, Dwork AJ, Schultz MD, Yu M, Tonti-Filippini J, Heyn H, Hu S, Wu JC, Rao A, Esteller M, He C, Haghighi FG, Sejnowski TJ, Behrens MM, Ecker JR. Science. 2013 Aug 9;341(6146):1237905 Epigenomic Signatures of Neuronal Diversity in the Mammalian Brain. Mo A, Mukamel EA, Davis FP, Luo C, Henry GL, Picard S, Urich MA, Nery JR, Sejnowski TJ, Lister R, Eddy SR, Ecker JR, Nathans J. Neuron. 2015 Jun 17;86(6):1369-84 Dysregulation of the epigenetic landscape of normal aging in Alzheimer's disease. Nativio R, Donahue G, Berson A, Lan Y, Amlie-Wolf A, Tuzer F, Toledo JB, Gosai SJ, Gregory BD, Torres C, Trojanowski JQ, Wang LS, Johnson FB, Bonini NM, Berger SL. Nat Neurosci. 2018 Apr;21(4):497-505 The accessible chromatin landscape of the murine hippocampus at single-cell resolution. Sinnamon JR, Torkenczy KA, Linhoff MW, Vitak SA, Mulqueen RM, Pliner HA, Trapnell C, Steemers FJ, Mandel G, Adey AC. Genome Res. 2019 May;29(5):857-869