Design of 240,000 orthogonal 25mer DNA barcode probes

Xu, Q., Schlabach, M. R., Hannon, G. J., Elledge, S. J. (2009) Design of 240,000 orthogonal 25mer DNA barcode probes. Proceedings of the National Academy of Sciences of the United States of America, 106 (7). pp. 2289-2294. ISSN 00278424 (ISSN)

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DOI: 10.1073/pnas.0812506106


DNA barcodes linked to genetic features greatly facilitate screening these features in pooled formats using microarray hybridization, and new tools are needed to design large sets of barcodes to allow construction of large barcoded mammalian libraries such as shRNA libraries. Here we report a framework for designing large sets of orthogonal barcode probes. We demonstrate the utility of this framework by designing 240,000 barcode probes and testing their performance by hybridization. From the test hybridizations, we also discovered new probe design rules that significantly reduce cross-hybridization after their introduction into the framework of the algorithm. These rules should improve the performance of DNA microarray probe designs for many applications. © 2009 by The National Academy of Sciences of the USA.

Item Type: Paper
Uncontrolled Keywords: Deconvolution Hybridization Library screen shRNA article controlled study DNA barcoding DNA probe gene library genetic analysis microarray analysis nonhuman priority journal Algorithms Automatic Data Processing DNA DNA Probes Gene Expression Profiling Nucleic Acid Conformation Nucleic Acid Hybridization Oligonucleotide Array Sequence Analysis Oligonucleotide Probes RNA Sequence Analysis, DNA Software Temperature Mammalia
Subjects: Investigative techniques and equipment
Investigative techniques and equipment > probes > DNA probes
Investigative techniques and equipment > probes
CSHL Authors:
Communities: CSHL labs > Hannon lab
Depositing User: Matt Covey
Date: 2009
Date Deposited: 09 Jan 2013 16:50
Last Modified: 05 Jan 2018 20:25
PMCID: PMC263107
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