Investigation of different transcript quantitation tools for high-throughput mapping of brain gene expression using voxelation.
Voxelation is a new approach for genome scale acquisition of brain gene expression patterns. The method employs high-throughput analysis of spatially registered voxels (cubes) to create multiple volumetric images of brain gene expression, similar to those obtained from biomedical imaging systems. The spatial resolution of voxelation depends on voxel size, with smaller voxels giving higher resolution. An important question is the applicability of different transcript profiling tools for the various levels of resolution that can be employed. Here, we describe the use of three methods to analyze voxel transcript abundance: real-time PCR, microarray analysis and linear amplification coupled with microarrays. We show statistically significant concordance between real-time PCR and microarray analysis for the myelin basic protein gene in human brain specimens at differing levels of spatial resolution. In addition, we also demonstrate the feasibility of using linear amplification coupled with microarray analysis to create voxelation maps from the mouse brain at high resolution, 1 microl. These data indicate the suitability of a number of transcript profiling tools for various levels of spatial resolution in voxelation.
Singh
Ram P
RP
Department of Molecular and Medical Pharmacology, UCLA School of Medicine, Los Angeles, CA 90095, USA.
Liu
Dahai
D
Chaudhari
Abhijit
A
Cherry
Simon R
SR
Leahy
Richard M
RM
Smith
Desmond J
DJ
D001921:Brain / Q000502:physiology*; D001923:Brain Chemistry / Q000235:genetics / Q000502:physiology; D001931:Brain Mapping / Q000379:methods*; D020869:Gene Expression Profiling; D005786:Gene Expression Regulation / Q000502:physiology*; D006801:Humans; D007091:Image Processing, Computer-Assisted / Q000379:methods*; D046228:Microarray Analysis; D042282:Microdissection / Q000379:methods; D004676:Myelin Basic Protein / Q000096:biosynthesis* / Q000235:genetics; D016133:Polymerase Chain Reaction; D012333:RNA, Messenger / Q000096:biosynthesis / Q000235:genetics
D004676:Myelin Basic Protein; D012333:RNA, Messenger