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Quantitative methods for genome-scale analysis of in situ hybridization and correlation with microarray data

Chang-Kyu Lee, Susan M Sunkin, Chihchau Kuan, Carol L Thompson, Sayan Pathak, Lydia Ng, Chris Lau, Shanna Fischer, Marty Mortrud, Cliff Slaughterbeck, Allan Jones, Ed Lein and Michael Hawrylycz*

Author Affiliations

Allen Institute for Brain Science, N. 34th Street, Seattle, WA 98103, USA

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Genome Biology 2008, 9:R23 doi:10.1186/gb-2008-9-1-r23

Published: 30 January 2008

Abstract

With the emergence of genome-wide colorimetric in situ hybridization (ISH) data sets such as the Allen Brain Atlas, it is important to understand the relationship between this gene expression modality and those derived from more quantitative based technologies. This study introduces a novel method for standardized relative quantification of colorimetric ISH signal that enables a large-scale cross-platform expression level comparison of ISH with two publicly available microarray brain data sources.