Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Evolution of neuronal and endothelial transcriptomes in primates

ABSTRACT: Neurons and endothelial cells were identified by immunohistochemistry in human brains, isolated by laser-capture-microdissection and used to find genes preferentially expressed in the two cell types. Keywords: cell type comparison Laser capture microdissection was used to isolate approximately 1000 neurons and endothelial cells from 6 (for neurons) and 7 (for endothelial cells) human post mortem brain samples. RNA was isolated and amplified (3 linear amplifications) and genome wide expression was measured. This allowed the identification of genes that are differentially expressed between neurons and endothelial cells in the human brain.

ORGANISM(S): Homo sapiens

SUBMITTER: Thomas Giger

PROVIDER: E-GEOD-12293 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Evolution of neuronal and endothelial transcriptomes in primates.

Giger Thomas T Khaitovich Philipp P Somel Mehmet M Lorenc Anna A Lizano Esther E Harris Laura W LW Ryan Margaret M MM Lan Martin M Wayland Matthew T MT Bahn Sabine S Pääbo Svante S

Genome biology and evolution 20100712

The study of gene expression evolution in vertebrates has hitherto focused on the analysis of transcriptomes in tissues of different species. However, because a tissue is made up of different cell types, and cell types differ with respect to their transcriptomes, the analysis of tissues offers a composite picture of transcriptome evolution. The isolation of individual cells from tissue sections opens up the opportunity to study gene expression evolution at the cell type level. We have stained ne ...[more]

PMID: 20624733

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Project description:Retinoic acid (RA), an active derivative of the liposoluble vitamin A (retinol), acts as an important signaling molecule during embryonic development, regulating phenomenons as diverse as anterior-posterior axial patterning, forebrain and optic vesicle development, specification of hindbrain rhombomeres, pharyngeal arches and second heart field, somitogenesis, and differentiation of spinal cord neurons. This small molecule directly triggers gene activation by binding to nuclear receptors (RARs), switching them from potential repressors to transcriptional activators. The repertoire of RA-regulated genes in embryonic tissues is poorly characterized. We performed a comparative analysis of the transcriptomes of murine wild-type and Retinaldehyde Dehydrogenase 2 null-mutant (Raldh2-/-) embryos - unable to synthesize RA from maternally-derived retinol - using Affymetrix DNA microarrays. Transcriptomic changes were analyzed in two embryonic regions: anterior tissues including forebrain and optic vesicle, and posterior (trunk) tissues, at early stages preceding the appearance of overt phenotypic abnormalities. Several genes expected to be downregulated under RA deficiency appeared in the transcriptome data (e.g. Emx2, Foxg1 anteriorly, Cdx1, Hoxa1, Rarb posteriorly), whereas reverse-transcriptase-PCR and in situ hybridization performed for additional selected genes validated the changes identified through microarray analysis. Altogether, the affected genes belonged to numerous molecular pathways and cellular/organismal functions, demonstrating the pleiotropic nature of RA-dependent events. In both tissue samples, genes upregulated were more numerous than those downregulated, probably due to feedback regulatory loops. Bioinformatic clustering analysis allowed us to extract groups of genes displaying similar behaviors in mutant tissue samples. These data give an overview of the gene expression changes occurring under a state of embryonic RA deficiency, and provide new candidate genes and pathways for a better understanding of retinoid-dependent molecular events. Two sets of samples were used for analyzing transcriptome changes in Raldh2-/- embryos. The rostral part of the head (including the anterior forebrain, optic vesicles, and overlying tissues), was collected from wild-type and mutant embryos at the 14 somite stage.The posterior tissues were analyzed at the 4 somite stage, and samples were collected from a transverse section plane excluding all tissues from the level of the first branchial arch.

Dataset Information

Evolution of neuronal and endothelial transcriptomes in primates

Publications

Evolution of neuronal and endothelial transcriptomes in primates.

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