Open Access Highly Accessed Research article

Gene expression in the rat brain: High similarity but unique differences between frontomedial-, temporal- and occipital cortex

Christine Stansberg12*, Kari M Ersland12, Paul van der Valk3 and Vidar M Steen12

Author Affiliations

1 Dr E. Martens Research Group for Biological Psychiatry, Department of Clinical Medicine, University of Bergen, Norway

2 Center for Medical Genetics and Molecular Medicine, Haukeland University Hospital, Bergen, Norway

3 Department of Pathology, VU University Medical Center, Amsterdam, The Netherlands

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BMC Neuroscience 2011, 12:15  doi:10.1186/1471-2202-12-15

Published: 26 January 2011

Additional files

Additional file 1:

Numbers of regionally enriched genes. This file presents the number of genes enriched in rat cortical regions according to the two microarray platforms and the different comparisons used in the study

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Additional file 2:

Gene expression profiles of regionally enriched genes on the AB1700 system. This file displays the AB1700 gene expression profiles of all 65 regionally enriched genes in rat FMCx, TCx, OCx, hippocampus, striatum, cerebellum, liver, spleen and kidney. Individual samples are placed along the x-axis. The y-axis indicates quantile normalised signal intensities for each gene in each individual sample.

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Additional file 3:

Gene expression profiles of regionally enriched genes on the Illumina system. This file displays the Illumina gene expression profiles of the 59 available probes of regionally enriched genes in rat FMCx, TCx and OCx. Individual samples are placed along the x-axis. The y-axis indicates quantile normalised signal intensities for each gene in each individual sample.

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Additional file 4:

Full list of regionally enriched genes identified in this study. This file presents the full list of 65 genes enriched in FMCx, TCx or OCx, including gene ID, gene symbol, gene name, fold differences, AB1700-, Illumina- and TaqMan probe IDs and significance of differential expression according to each of the three platforms.

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Additional file 5:

Features of regionally enriched genes observed in other data sets. This file lists expression features such as regional co-enrichment and preferences for certain cortical layers or cell types as well as tests for differential expression of regional genes in the different data sets used in the study. Each experiment has a separate data sheet; 1) regional co-enrichment in the rat brain [20], 2) developmental stages of the cortex [10], 3) cortical layers (Allen Mouse Brain Atlas), 4) cortical cell types [28] and 5) neuronal subtypes of the cortex [30].

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Additional file 6:

Gene expression of regionally enriched genes throughout development of the rat cerebral cortex. This file displays gene expression profiles of regionally enriched genes across pre- and postnatal stages of the developing rat cerebral cortex. Individual samples are placed along the x-axis; Cortex E16, E17, E18, E20, P01, P07, P14, P21, P30 and P90, Hippocampus P0, P07, P14, P21, P30 and P90, Hypothalamus E18, E20, P01, P07, P14, P21, P30 and P90; see original publication for details. The y-axis indicates quantile normalised signal intensities for each gene in each individual sample. Raw microarray data were obtained from [10]. 32 of our genes were represented in this data set.

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Additional file 7:

Laminar expression profiles of regionally enriched genes. This file presents in situ hybridisation images demonstrating laminar expression patterns of the 56 regionally enriched genes that were represented in the Allen Mouse Brain Atlas. For FMCx and OCx genes, images presented in this study represent sagittal sections near midline (lateral ~0.7-1.4 mm). For TCx genes, coronal sections between Bregma -3.08 and -3.38 are presented where available. Only sagittal sections were available for Arhgap9, Cabp1, Col13a1, Hhatl, Ikbke and Mox2r, hence the lateral-most sections are presented for these genes.

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Additional file 8:

Expression of regionally enriched genes in astrocytes, oligodendrocytes and neurons. This file shows gene expression profiles of regionally enriched genes across differentiating as well as mature astrocytes, oligodendrocytes and neurons. Individual samples are placed along the x-axis; Cultured Astroglia, Astrocytes P1, P7-P8 and P17, Astrocytes Gray P17, Oligodendrocyte progenitor cells, premyelinating, postmitotic oligodendrocytes (Myelin Oligos), Oligodendrocytes, Neurons P7n, P7, P16n and P16, see original publication for details. The y-axis indicates quantile normalised signal intensities for each gene in each individual sample. Raw microarray data were obtained from Cahoy et al [28]. 42 of our genes were represented in this data set.

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Additional file 9:

Expression of regionally enriched genes in different neuronal subtypes. This file shows gene expression profiles of regionally enriched genes across different subtypes of neocortical neurons. Individual samples are placed along the x-axis; layer 6 glutamatergic neurons from cingulate cortex (CT6 strain), layer 5 glutamatergic neurons from cingulate cortex (YFPH strain), layer 5-6 glutamatergic neurons from somatosensory cortex (YFPH strain), layer 1-6 GABAergic neurons from cingulate cortex (G30 strain), layer 4-6 GABAergic neurons from cingulate cortex (G43 strain), layer 2-4 GABAergic neurons from cingulate cortex (GIN strain) and layer 1-6 GABAergic neurons from somatosensory cortex (G30 strain); see original publication for details. The y-axis indicates quantile normalised signal intensities for each gene in each individual sample. Raw microarray data were obtained from Sugino et al [30]. 51 of our genes were represented in this data set.

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Additional file 10:

Available knock-out mutants and transgenic lines. This file lists available mouse knock-out mutants and transgenic lines and resulting phenotypes for the regionally enriched cortex genes.

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