hw - High- Throughput Gene Expression Assays: Microarrays...

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Unformatted text preview: High- Throughput Gene Expression Assays: Microarrays and Sequencing High- Throughput Gene Expression Assays Microarrays Sequencing Sequencing vs. Microarrays Statistical and Computational Challenges References High-Throughput Gene Expression Assays: Microarrays and Sequencing PB HLTH C240D/STAT C245D/STAT 246 Sandrine Dudoit Division of Biostatistics and Department of Statistics University of California, Berkeley www.stat.berkeley.edu/~sandrine Spring 2009 Version: 16/01/2009, 22:58 High- Throughput Gene Expression Assays: Microarrays and Sequencing High- Throughput Gene Expression Assays Microarrays Sequencing Sequencing vs. Microarrays Statistical and Computational Challenges References Outline 1 High-Throughput Gene Expression Assays 2 Microarrays 3 Sequencing 4 Sequencing vs. Microarrays 5 Statistical and Computational Challenges High- Throughput Gene Expression Assays: Microarrays and Sequencing High- Throughput Gene Expression Assays Microarrays Sequencing Sequencing vs. Microarrays Statistical and Computational Challenges References High-Throughput Gene Expression Assays High-throughput biotechnologies, such as microarray and sequencing assays, have revolutionized biology by providing genome-wide measures of transcription levels (mRNA-Chip/mRNA-Seq); alternative splicing events; protein-nucleic acid interactions, e.g., transcription factor binding sites (ChIP-Chip/ChIP-Seq 1 ); DNA methylation status; DNA copy numbers; genotypes, etc. These novel assays have also provided a great impetus for the development of new and not so new statistical and computational methodologies . 1 ChIP: Chromatin immunoprecipitation. High- Throughput Gene Expression Assays: Microarrays and Sequencing High- Throughput Gene Expression Assays Microarrays Sequencing Sequencing vs. Microarrays Statistical and Computational Challenges References Microarrays High- Throughput Gene Expression Assays: Microarrays and Sequencing High- Throughput Gene Expression Assays Microarrays Sequencing Sequencing vs. Microarrays Statistical and Computational Challenges References Microarrays Microarray experiments are high-throughput biological assays for measuring the abundance of DNA or RNA sequences in different types of cell samples, for thousands of sequences simultaneously. For the past decade, microarrays have been the assays of choice for high-throughput genome-wide studies of gene expression . Microarrays exploit the availability of sequence data to get information on gene expression. Microarrays rely on the hybridization properties of nucleic acids to monitor DNA or RNA abundance. The ancestor of cDNA microarrays is the Northern blot . Probes : DNA sequences spotted on the microarray, immobile substrate. High- Throughput Gene Expression Assays: Microarrays and Sequencing High- Throughput Gene Expression Assays Microarrays Sequencing Sequencing vs....
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This note was uploaded on 03/14/2010 for the course C 240D, C24 taught by Professor S.dudoit during the Spring '09 term at University of California, Berkeley.

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hw - High- Throughput Gene Expression Assays: Microarrays...

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