Předmět Methods of Functional Genomics (KMB / 217)

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Materiál	Typ	Datum	Počet stažení

Obsah

Content of lectures:Proteomics:Mass spectrometry: what's the purpose?MS instrumentationPeptide fingerprinting: protein identification by MSPeptide sequencing by MSIdentification of post-translational modificationsLC-MSMS and large-scale proteomics, incl. examplesStable-isotope labeling and quantitative proteomicsAnalysis of intact proteinsMass spectrometry as a discovery tool in proteomicsMass spectrometry as a screening tool - from research to clinic?Mass spectrometry for structural biologyBioinformatics:Introduction: Biologists and Bioinformatics - What bioinformatics is- What bioinformatics can do- What it can't do- Current Challenges for bioinformatics- Data sizes, Read lengthsApplication 1: Microarrays- Analysis- Normalization- Design- Data Repositories and MiningApplication 2: Next Generation Sequencing- The range of applications- Data analysis by application- What can go wrong and biases with countsFlow cytometry: The principles of flow cytometryTechnology overviewAssays, applicationsGenomics: Microarrays - overview of technologies & applications;Massively parallel sequencing - overview of technologies &applications; comparison with microarraysPrinciples of MPS data analysisDiscovery and implications of genome structural variantsqPCR - principles, applications, data.RNAi technology:Overview about silencing reagents used in RNAi screenssiRNA designTransfection methods used for RNAiGenome-wide RNAi screen to identify cell division genes as anexample for high-throughput applicationsValidation of RNAi results

Literatura

Ahrens CH, Brunner E, Qeli E, Basler K & Aebersold R: Generating and navigating proteome maps using mass spectrometry. Nature ReviewsMol Cell Bio (2010), 12, 789-801. Erfle H, Neumann B, Rogers J, Bulkescher J, Ellenberg J and Pepperkok R: Work Flow for Multiplexing siRNA Assays by Solid-Phase Reverse Transfection in Multiwell Plates. J Biomol Screening (2008), 13, 575-80. Gibson & Muse: A Primer of Genome Science, the 3rd edition (Sinauer Associates, 2009, ISBN 978-0-87893-236-8). Han X, Aslanian A & Yates III JR: Mass spectrometry for proteomics. Current Opinion Chem Biol (2008), 12, 483-490. Herzenberg LA, Parks D, Sahaf B, Perez O, Roederer M & Herzenberg LA: The history and future of fluoresence activated cell sorter and flow cytometry. Clinical Chemistry (2002), 48, 1819-1827. Choudhary C & Mann M: Decoding signalling networks by mass-spectrometry-based proteomics. Nature ReviewsMol Cell Bio (2010), 12, 427-439. Mann M: Functional and quantitative proteomics using SILAC. Nature ReviewsMol Cell Bio (2006), 7, 952-8. Mardis ER: A decade s perspective on DNA sequencing technology. Nature (2011), 470, 198-203. Medvedev P, Stanciu M, Brudno M: Computational Methods for Discovering Structural Variation with Next Generation Sequencing, Nature Methods (2009), 6:S13-S20, 2009. Moffa J, Sabatini DM: Building mammalian signalling pathways with RNAi screens. Nature Reviews Mol Cell Bio (2006), 7, 177-87. Neumann B, Walter T, Hériché JK, Bulkescher J, Erfle H, Conrad C, Rogers P, Poser I, Held M, Liebel U, Cetin C, Sieckmann F, Pau G, Kabbe R, Wünsche A, Satagopam V, Schmitz MH, Chapuis C, Gerlich DW, Schneider R, Eils R, Huber W, Peters JM, Hyman AA, Durbin R, Pepperkok R, Ellenberg J: Phenotypic profiling of the human genome by time-lapse microscopy reveals cell division genes. Nature (2010), 464, 721-7.

Požadavky

Periodicity: each academic year.(alternation between Praque and České Budějovice)Speciální kurz doktorského studijního oboru Molekulární a buněčná biologie a genetika

Garant

RNDr. Vladimír Beneš, CSc.Mgr. David Doležel, Ph.D.