Challenges in Studies of the Postmortem Human Brain

Analyzing the human brain transcriptome and interpreting the outcome of these experiments is a challenging task. Although many of the following considerations are not unique for genomic experiments and apply in general to postmortem brain research, they have a major impact on planning and interpreting the outcome of microarray experiments. A. The Starting Material is Postmortem Tissue In the absence of viable animal models for most of the psychiatric disorders, analysis of human postmortem...

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Scale Normalization

Where g(A) is a loess curve fitted to spots from the MSP series, g (A) is a loess for print-tip group i, and w(A) is usually defined as the proportion of spots less than intensity A. The adjustment is then done as before. The idea is to increasingly use the MSP curve at higher intensities, where there are fewer spots and the print-tip specific curves may be more unreliable. We have discussed normalization within slides, but sometimes there are large differences in scale when comparing data...

Slides and Probes

If one chooses a commercial platform, there is no need to consider slide choice. However, if one prints arrays in-house, choosing appropriate array slides is essential. A typical cDNA microarray consists of densely deposited PCR-amplified cDNA clones or expressed sequence tags (ESTs) onto a solid surface, such as specially coated silicon or glass slides. These amplified elements (probes) are noncovalently deposited on the slide surfaces that are optimized for DNA attachment and minimal...

Volume

Energy Metabolism in the Brain Leif Hertz and Gerald A. Dienel The Cerebral Glucose-Fatty Acid Cycle Evolutionary Roots, Regulation, and (Patho) physiological Importance Kurt Heininger Expression, Regulation, and Functional Role of Glucose Transporters (GLUTs) in Brain Donard S. Dwyer, Susan J. Vannucci, and Ian A. Simpson Insulin-Like Growth Factor-1 Promotes Neuronal Glucose Utilization During Brain Development and Repair Processes CNS Sensing and Regulation of Peripheral Glucose Levels Barry...

Introduction

Over the last decade, huge advances in genome sequencing promoted the development of various techniques aimed at studying gene expression on a genome-wide level. With the introduction of complementary DNA cDNA and oligonucleotide microarrays in 1995 Lockhart et al., 1996 Schena et al., 1995 , high-throughput simultaneous monitoring of gene expression became possible. DNA microarrays allow the simultaneous study of the expression patterns of thousands of genes in the same tissue or cell Karsten...

Microarray Platforms Introduction And Application To Neurobiology

Kudo,y and Daniel H. Geschwind Department of Neurology, Program in Neurogenetics, and yNeuroscience IDP David Geffen School of Medicine, University of California Los Angeles, California 90095 I. Introduction II. Experimental Flow V. Sample Preparation and Labeling VI. Data Analysis VII. Data Interpretation VIII. Confirmation of Microarray Results B. Data Collection, Annotation, and Interpretation Tools D. Metabolic and Regulatory Pathway Databases References