Advanced Neurogenomics

07 Nov 2022 (2h 00m)

Alessandro Cellerino - Corso (attività didattica) - Mista

Advanced Neurogenomics. Lecture 1. A primer on data distribution and visualization. Definition of probability, frequentist and bayesian approaches. Definition of p-value and Bayesian factor. Binomial distribution, gaussian, Student's-t test. Bayesian alternative to t-test. Sign test as an example of non-parametric test. Box plot, gaussian kernel density, scatterplot, venn diagrams.

11 Nov 2022 (2h 00m)

Alessandro Cellerino - Corso (attività didattica) - Mista

Lecture 2. RNAseq pipeline: RNA purification, purification of mRNA via polyA+ or rRNA depletion, cDNA library synthesis, adapter ligation, bridge amplification, sequencing. Type of sequencing: single end or pair end. How to determine the optimal amount of reads per sample.

14 Nov 2022 (2h 00m)

Alessandro Cellerino - Corso (attività didattica) - Mista

Lecture 3. FASTQ format. Phred score. Filtering and trimming of adapters. Alignment. Coverage vectors. Count tables. Negative binomial. Methods of normalization: RPKM, TPM and DESeq (pseudo counts).

18 Nov 2022 (2h 00m)

Alessandro Cellerino - Corso (attività didattica) - Mista

Lecture 4: variance-mean relationships and p-value calculations in DESeq, DESeq2, empirical bayesian methods, calculation of gene-wise dispersion, fold-change shrinkage, regularized log2, multiple linear regression and generalized linear methods, mitigation of batch effects, correction for multiple testing

21 Nov 2022 (2h 00m)

Alessandro Cellerino - Corso (attività didattica) - Mista

Lecture 5: hierarchical clustering, heat maps, k-means clustering, principal component analysis, effects of feature selection, multi dimensional scaling, an example of machine learning and cross-validation.

25 Nov 2022 (2h 00m)

Alessandro Cellerino - Corso (attività didattica) - Mista

Lecture 6: KEEG,Gene Ontology hierarchical structure and acyclic graph, Reactome, Hypergeometric distribution and Fisher's test, Clusterin of GO terms, Gene Set Enrichment Analysis, GAGE

12 Dic 2022 (2h 00m)

Alessandro Cellerino - Corso (attività didattica) - In presenza

Lecture 7. Network analysis. Types of biological networks: metabolic network, protein-protein interaction network, brain connectome, coexpression networks. Random, Scale free and hierarchical-networks. Measures of centrality. WGCNA. Example of application of WGCNA from Baumgart et al., 2016.

16 Dic 2022 (2h 00m)

Alessandro Cellerino - Corso (attività didattica) - Mista

Lecture 8. Network analysis: case studies. Oldham MC, Horvath S, Geschwind DH. Conservation and evolution of gene coexpression networks in human and chimpanzee brains. Proc Natl Acad Sci U S A. 2006 Nov 21;103(47):17973-8. doi: 10.1073/pnas.0605938103. Epub 2006 Nov 13. PMID: 17101986; PMCID: PMC1693857. Miller JA, Oldham MC, Geschwind DH. A systems level analysis of transcriptional changes in Alzheimer's disease and normal aging. J Neurosci. 2008 Feb 6;28(6):1410-20. doi: 10.1523/JNEUROSCI.4098-07.2008. PMID: 18256261; PMCID: PMC2902235. Winden KD, Oldham MC, Mirnics K, Ebert PJ, Swan CH, Levitt P, Rubenstein JL, Horvath S, Geschwind DH. The organization of the transcriptional network in specific neuronal classes. Mol Syst Biol. 2009;5:291. doi: 10.1038/msb.2009.46. Epub 2009 Jul 28. PMID: 19638972; PMCID: PMC2724976. Hawrylycz MJ, Lein ES, Guillozet-Bongaarts AL, Shen EH, Ng L, Miller JA, van de Lagemaat LN, Smith KA, Ebbert A, Riley ZL, Abajian C, Beckmann CF, Bernard A, Bertagnolli D, Boe AF, Cartagena PM, Chakravarty MM, Chapin M, Chong J, Dalley RA, David Daly B, Dang C, Datta S, Dee N, Dolbeare TA, Faber V, Feng D, Fowler DR, Goldy J, Gregor BW, Haradon Z, Haynor DR, Hohmann JG, Horvath S, Howard RE, Jeromin A, Jochim JM, Kinnunen M, Lau C, Lazarz ET, Lee C, Lemon TA, Li L, Li Y, Morris JA, Overly CC, Parker PD, Parry SE, Reding M, Royall JJ, Schulkin J, Sequeira PA, Slaughterbeck CR, Smith SC, Sodt AJ, Sunkin SM, Swanson BE, Vawter MP, Williams D, Wohnoutka P, Zielke HR, Geschwind DH, Hof PR, Smith SM, Koch C, Grant SGN, Jones AR. An anatomically comprehensive atlas of the adult human brain transcriptome. Nature. 2012 Sep 20;489(7416):391-399. doi: 10.1038/nature11405. PMID: 22996553; PMCID: PMC4243026. Richiardi J, Altmann A, Milazzo AC, Chang C, Chakravarty MM, Banaschewski T, Barker GJ, Bokde AL, Bromberg U, Büchel C, Conrod P, Fauth-Bühler M, Flor H, Frouin V, Gallinat J, Garavan H, Gowland P, Heinz A, Lemaître H, Mann KF, Martinot JL, Nees F, Paus T, Pausova Z, Rietschel M, Robbins TW, Smolka MN, Spanagel R, Ströhle A, Schumann G, Hawrylycz M, Poline JB, Greicius MD; IMAGEN consortium. BRAIN NETWORKS. Correlated gene expression supports synchronous activity in brain networks. Science. 2015 Jun 12;348(6240):1241-4. doi: 10.1126/science.1255905. Epub 2015 Jun 11. PMID: 26068849; PMCID: PMC4829082. Gandal MJ, Haney JR, Parikshak NN, Leppa V, Ramaswami G, Hartl C, Schork AJ, Appadurai V, Buil A, Werge TM, Liu C, White KP; CommonMind Consortium; PsychENCODE Consortium; iPSYCH-BROAD Working Group, Horvath S, Geschwind DH. Shared molecular neuropathology across major psychiatric disorders parallels polygenic overlap. Science. 2018 Feb 9;359(6376):693-697. doi: 10.1126/science.aad6469. PMID: 29439242; PMCID: PMC5898828.

09 Gen 2023 (2h 00m)

Alessandro Cellerino - Corso (attività didattica) - Mista

Analisi di microRNA and Ribosome footprinting. Mapping the human miRNA interactome by CLASH reveals frequent noncanonical binding. Helwak A, Kudla G, Dudnakova T, Tollervey D. Cell. 2013 Apr 25;153(3):654-65. 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. AGO CLIP Reveals an Activated Network for Acute Regulation of Brain Glutamate Homeostasis in Ischemic Stroke. Cell Rep. 2019 Jul 23;28(4):979-991. Ripa R, Dolfi L, Terrigno M, Pandolfini L, Savino A, Arcucci V, Groth M, Terzibasi Tozzini E, Baumgart M, Cellerino A. MicroRNA miR-29 controls a compensatory response to limit neuronal iron accumulation during adult life and aging. BMC Biol. 2017 Feb 13;15(1):9. Eichhorn SW, Guo H, McGeary SE, Rodriguez-Mias RA, Shin C, Baek D, Hsu SH, Ghoshal K, Villén J, Bartel DP. mRNA destabilization is the dominant effect of mammalian microRNAs by the time substantial repression ensues. Mol Cell. 2014 Oct 2;56(1):104-15. Boudreau RL, Jiang P, Gilmore BL, Spengler RM, Tirabassi R, Nelson JA, Ross CA, Xing Y, Davidson BL. Transcriptome-wide discovery of microRNA binding sites in human brain. Neuron. 2014 Jan 22;81(2):294-305. Bartel DP. Metazoan MicroRNAs. Cell. 2018 Mar 22;173(1):20-51. doi: 10.1016/j.cell.2018.03.006. PMID: 29570994; PMCID: PMC6091663. Warnefors M, Liechti A, Halbert J, Valloton D, Kaessmann H. Conserved microRNA editing in mammalian evolution, development and disease. Genome Biol. 2014 Jun 25;15(6):R83. doi: 10.1186/gb-2014-15-6-r83. PMID: 24964909; PMCID: PMC4197820.

13 Gen 2023 (2h 00m)

Alessandro Cellerino - Corso (attività didattica) - Mista

Hands-on lecture: RNAseq analysis using DESeq2

16 Gen 2023 (2h 00m)

Alessandro Cellerino - Corso (attività didattica) - Mista

HAnds on lecture: GO analysis and STRING

30 Gen 2023 (2h 00m)

Alessandro Cellerino - Corso (attività didattica) - In presenza

Single cell (1) The development of single cell techniques. 10X Genomics and SMART-seq: depth vs. cell numerosity. Non linear embeddings of single cell data: t-SNE. Methods for clustering of single cell data. Trajectory reconstruction. RNA velocity.

06 Feb 2023 (2h 00m)

Alessandro Cellerino - Corso (attività didattica) - In presenza

Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets. Macosko EZ, Basu A, Satija R, Nemesh J, Shekhar K, Goldman M, Tirosh I, Bialas AR, Kamitaki N, Martersteck EM, Trombetta JJ, Weitz DA, Sanes JR, Shalek AK, Regev A, McCarroll SA. Cell. 2015 May 21;161(5):1202-1214. doi: 10.1016/j.cell.2015.05.002. Adult mouse cortical cell taxonomy revealed by single cell transcriptomics. Tasic B, Menon V, Nguyen TN, Kim TK, Jarsky T, Yao Z, Levi B, Gray LT, Sorensen SA, Dolbeare T, Bertagnolli D, Goldy J, Shapovalova N, Parry S, Lee C, Smith K, Bernard A, Madisen L, Sunkin SM, Hawrylycz M, Koch C, Zeng H. Nat Neurosci. 2016 Feb;19(2):335-46. doi: 10.1038/nn.4216. Div-Seq: Single-nucleus RNA-Seq reveals dynamics of rare adult newborn neurons. Habib N, Li Y, Heidenreich M, Swiech L, Avraham-Davidi I, Trombetta JJ, Hession C, Zhang F, Regev A. Science. 2016 Aug 26;353(6302):925-8. doi: 10.1126/science.aad7038 Molecular Architecture of the Mouse Nervous System. Zeisel A, Hochgerner H, Lönnerberg P, Johnsson A, Memic F, van der Zwan J, Häring M, Braun E, Borm LE, La Manno G, Codeluppi S, Furlan A, Lee K, Skene N, Harris KD, Hjerling-Leffler J, Arenas E, Ernfors P, Marklund U, Linnarsson S. Cell. 2018 Aug 9;174(4):999-1014.e22. doi: 10.1016/j.cell.2018.06.021

10 Feb 2023 (2h 00m)

Alessandro Cellerino - Corso (attività didattica) - Mista

Exporation of the ISH and single cell datasets of the Allen brain atlas and of the adolescent nervous system of the Linnarson lab database

13 Feb 2023 (2h 00m)

Alessandro Cellerino - Corso (attività didattica) - Mista

Integrated Morphoelectric and Transcriptomic Classification of Cortical GABAergic Cells. Gouwens NW, Sorensen SA, Baftizadeh F, Budzillo A, Lee BR, Jarsky T, Alfiler L, Baker K, Barkan E, Berry K, Bertagnolli D, Bickley K, Bomben J, Braun T, Brouner K, Casper T, Crichton K, Daigle TL, Dalley R, de Frates RA, Dee N, Desta T, Lee SD, Dotson N, Egdorf T, Ellingwood L, Enstrom R, Esposito L, Farrell C, Feng D, Fong O, Gala R, Gamlin C, Gary A, Glandon A, Goldy J, Gorham M, Graybuck L, Gu H, Hadley K, Hawrylycz MJ, Henry AM, Hill D, Hupp M, Kebede S, Kim TK, Kim L, Kroll M, Lee C, Link KE, Mallory M, Mann R, Maxwell M, McGraw M, McMillen D, Mukora A, Ng L, Ng L, Ngo K, Nicovich PR, Oldre A, Park D, Peng H, Penn O, Pham T, Pom A, Popović Z, Potekhina L, Rajanbabu R, Ransford S, Reid D, Rimorin C, Robertson M, Ronellenfitch K, Ruiz A, Sandman D, Smith K, Sulc J, Sunkin SM, Szafer A, Tieu M, Torkelson A, Trinh J, Tung H, Wakeman W, Ward K, Williams G, Zhou Z, Ting JT, Arkhipov A, Sümbül U, Lein ES, Koch C, Yao Z, Tasic B, Berg J, Murphy GJ, Zeng H. Cell. 2020 Nov 12;183(4):935-953.e19. doi: 10.1016/j.cell.2020.09.057. Visualization and analysis of gene expression in tissue sections by spatial transcriptomics. Ståhl PL, et al. Science. 2016. PMID: 27365449 Spatial Transcriptomics and In Situ Sequencing to Study Alzheimer's Disease. Chen WT, et al. Cell. 2020. PMID: 32702314 Three-dimensional intact-tissue sequencing of single-cell transcriptional states Xiao Wang 1, William E Allen 1 2, Matthew A Wright 1 3, Emily L Sylwestrak 1, Nikolay Samusik 4, Sam Vesuna 1, Kathryn Evans 1, Cindy Liu 1, Charu Ramakrishnan 1, Jia Liu 5, Garry P Nolan 6, Felice-Alessio Bava 6, Karl Deisseroth 7 3 8

17 Feb 2023 (2h 00m)

Alessandro Cellerino - Corso (attività didattica) - Mista

Discussion of the papers: Molecular Profiling of Neurons Based on Connectivity Molecular Profiling of Activated Neurons by Phosphorylated Ribosome Capture Warm-Sensitive Neurons that Control Body Temperature High-Throughput Mapping of Single-Neuron Projections by Sequencing of Barcoded RNA The logic of single-cell projections from visual cortex

20 Feb 2023 (2h 00m)

Alessandro Cellerino - Corso (attività didattica) - Mista

Introduction to proteomics.

24 Feb 2023 (2h 00m)

Alessandro Cellerino - Corso (attività didattica) - Mista

RNA localization is a key determinant of neurite-enriched proteome. |DOI: 10.1038/s41467-017-00690-6 Monosomes actively translate synaptic mRNAs in neuronal processes.DOI: 10.1126/science.aay4991 Local protein synthesis is a ubiquitous feature of neuronal pre- and postsynaptic compartments. DOI: 10.1126/science.aau3644 Proteomic Analysis of Unbounded Cellular Compartments: Synaptic Clefts. doi.org/10.1016/j.cell.2016.07.041 Droplet-based transcriptome profiling of individual synapses. https://doi.org/10.1038/s41587-022-01635-1 Dynamic Axonal Translation in Developing and Mature Visual Circuits. http://dx.doi.org/10.1016/j.cell.2016.05.029 On-Site Ribosome Remodeling by Locally Synthesized Ribosomal Proteins in Axons. https://doi.org/10.1016/j.celrep.2019.11.025 The Local Transcriptome in the Synaptic Neuropil Revealed by Deep Sequencing and High-Resolution Imaging. Neuron 74, 453–466, May 10, 2012

06 Mar 2023 (2h 00m)

Alessandro Cellerino - Corso (attività didattica) - In presenza

Epigenetics (1) Methods to profile chromatin accessibility: DNAse hypersensitivity and ATAC-seq MEthods to profile 3-D chromatin structure: Hi-C MEthods to profile DNA methylations: MeDIP. WGBS and RRBS-WGBS Workflow of ChIP-seq Analysis of ChiP-seq Representation in Genome Browsers of ChIP-seq data

16 Mar 2023 (2h 00m)

Alessandro Cellerino - Corso (attività didattica) - Mista

The accessible chromatin landscape of the murine hippocampus at single-cell resolution. http://www.genome.org/cgi/doi/10.1101/gr.243725.118. Global Epigenomic Reconfiguration During Mammalian Brain Development. SCIENCE VOL 341 9 AUGUST 2013 Epigenomic Signatures of Neuronal Diversity in the Mammalian Brain. http://dx.doi.org/10.1016/j.neuron.2015.05.018 Dysregulation of the epigenetic landscape of normal aging in Alzheimer’s disease. Nature Neuroscience | VOL 21 | APRIL 2018 | 497–505