(精选)transcriptomics教学课件.pptVIP

RNA-Seq Lockhart and Winzeler 2000 Wang et al. 2009 RNA-Seq Whole Transcriptome Shotgun Sequencing Sequencing cDNA Using NexGen technology Revolutionary Tool for Transcriptomics More precise measurements Ability to do large scale experiments with little starting material RNA-Seq Experiment Wang et al. 2009 Mapping Place reads onto a known genomic scaffold Requires known genome and depends on accuracy of the reference / Mapping Create unique scaffolds Harder algorithms with such short reads Comparisons Wang et al. 2009 Comparisons Wang et al. 2009 Biases Wang et al. 2009 Transcriptomics:A general overviewBy Todd, Mark, and Tom Intro Transcriptomics = RNA in a cell Either coding or non-coding (ncRNA). mRNA vs microRNA, siRNA Also non-functional RNA (pseudo-genes) Transcriptomics focuses sets on:howwherewhenwhyAlso diagnosing :developmental stagestissue differentialsvirusesresponse to stimuli Microarray Used for Biological Assays DNA Microarrays MMChips Protein Microarrays Tissue Microarrays Antibody Microarrays DNA Microarray Can be used to measure Expression levels SNPs Genotyping Comparative Genome Hybridization Basic DNA Microarray Experiment / Labeling Lockhart and Winzeler 2000 Probes and Targets Probes Known sequence bonded to substrate Target Sample obtained to wash over chip See what and how much is hybridized Results Lockhart and Winzeler 2000 Tiling Array Genome array consisting of overlapping probes Finer Resolution Better at finding RNA in the cell mRNA Alternative splicing Not Polyadenylated miRNA Tiling Arrays / Tiling Array / Microarray Wheelan et al. 2008 Gene expression profiling predicts clinical outcome of breast cancerLaura J. van t Veer1,2, Hongyue Dai2,3, Marc J. van de Vijver1,2, Yudong D. He3, Augustinus A. M. Hart1, Mao Mao3, Hans L. Peterse1, Karin van der Kooy1, Matthew J. Marton3, Anke T. Witteveen1, George J. Schreiber3, Ron M. Kerkhoven1, Chris Roberts3, Peter S. Linsley3, René Bernards1 and Stephen H. Friend3