RAMPAGE: Promoter activity profiling by paired-end sequencing of 5'-complete cDNAs

Batut, P., Gingeras, T. R. (2013) RAMPAGE: Promoter activity profiling by paired-end sequencing of 5'-complete cDNAs. Current Protocols in Molecular Biology (SUPPL). Unit25B. ISSN 19343639 (ISSN)

URL: http://www.ncbi.nlm.nih.gov/pubmed/24510412
DOI: 10.1002/0471142727.mb25b11s104

Abstract

RNA annotation and mapping of promoters for analysis of gene expression (RAMPAGE) is a method that harnesses highly specific sequencing of 5'-complete complementary DNAs to identify transcription start sites (TSSs) genome-wide. Although TSS mapping has historically relied on detection of 5'-complete cDNAs, current genome-wide approaches typically have limited specificity and provide only scarce information regarding transcript structure. RAMPAGE allows for highly stringent selection of 5'-complete molecules, thus allowing base-resolution TSS identification with a high signal-to-noise ratio. Paired-end sequencing of medium-length cDNAs yields transcript structure information that is essential to interpreting the relationship of TSSs to annotated genes and transcripts. As opposed to standard RNA-seq, RAMPAGE explicitly yields accurate and highly reproducible expression level estimates for individual promoters. Moreover, this approach offers a streamlined 2-to 3-day protocol that is optimized for extensive sample multiplexing, and is therefore adapted for large-scale projects. This method has been applied successfully to human and Drosophila samples, and in principle should be applicable to any eukaryotic system. © 2013 by John Wiley & Sons, Inc.

Item Type: Paper
Uncontrolled Keywords: Expression profiling High-throughput sequencing Promoter Rampage Transcription start site
Subjects: bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > DNA expression
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification
bioinformatics > genomics and proteomics > annotation > gene expression profiling annotation
Investigative techniques and equipment > assays > next generation sequencing
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > DNA expression > promoter
Investigative techniques and equipment > assays > whole genome sequencing
CSHL Authors:
Communities: CSHL labs > Gingeras lab
Watson School > Publications
Depositing User: Matt Covey
Date: 2013
Date Deposited: 04 Feb 2014 15:41
Last Modified: 06 Apr 2015 18:58
PMCID: PMC4372803
Related URLs:
URI: http://repository.cshl.edu/id/eprint/29467

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