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Curr Protoc Mol Biol. 2012 Apr;Chapter 4:Unit 4.13.1-9. doi: 10.1002/0471142727.mb0413s98.

RASL-seq for massively parallel and quantitative analysis of gene expression.

Author information

1
Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, California, USA.

Abstract

Large-scale, quantitative analysis of gene expression can be accomplished by microarray or RNA-seq analysis. While these methods are applicable to genome-wide analysis, it is often desirable to quantify expression of a more limited set of genes in hundreds, thousands, or even tens of thousands of biological samples. For example, some studies may require monitoring a sizable panel of key genes under many different experimental conditions, during development, or following treatment with a large library of small molecules, for which current genome-wide methods are either inefficient or cost-prohibitive. This unit presents a method that permits quantitative profiling of several hundred selected genes in a large number of samples by coupling RNA-mediated oligonucleotide Annealing, Selection, and Ligation with Next-Gen sequencing (RASL-seq). The method even allows direct analysis of RNA levels in cell lysates and is also adaptable to full automation, making it ideal for large-scale analysis of multiple biological pathways or regulatory gene networks in the context of systematic genetic or chemical genetic perturbations.

PMID:
22470064
PMCID:
PMC3325489
DOI:
10.1002/0471142727.mb0413s98
[Indexed for MEDLINE]
Free PMC Article

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