Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Cross-species transcriptomic comparison of in vitro and in vivo mammalian neural cells

ABSTRACT: We report the first RNA profiing of mammalian neural cells grown in vitro. About 50 million reads are generated by RNA-seq from rat astrocytes, neurons and oligodendrocyte precursor cells in primary culture. These data are compared with theose generated from the correponding mouse neural cells that are acutely purified from brains. Cross-species RNA-seq data analysis revealed hundreds of genes that are differentially expressed between cultured and acutely purified cells. Astrocytes have more such genes compared to neurons and oligodendrocyte precursor cells, indicating that signalling pathways are greatly perturbed in cultured astrocytes. mRNA profiles of rat astrocytes, neurons and oligodendrocyte precursor cells cultured in vitro

ORGANISM(S): Rattus norvegicus

SUBMITTER: FENG CUI

PROVIDER: E-GEOD-72739 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:A Transcriptome Database for Astrocytes, Neurons, and Oligodendrocytes: A New Resource for Understanding Brain Development and Function Understanding the cell-cell interactions that control CNS development and function has long been limited by the lack of methods to cleanly separate astrocytes, neurons, and oligodendrocytes. Here we describe the first method for the isolation and purification of developing and mature astrocytes from mouse forebrain. This method takes advantage of the expression of S100β by astrocytes. We used fluorescent activated cell sorting (FACS) to isolate EGFP positive cells from transgenic mice that express EGFP under the control of an S100β promoter. By depletion of astrocytes and oligodendrocytes we obtained purified populations of neurons, while by panning with oligodendrocyte-specific antibodies we obtained purified populations of oligodendrocytes. Using GeneChip Arrays we then created a transcriptome database of the expression levels of over 20,000 genes by gene profiling these three main CNS neural cell types at postnatal ages day 1 to 30. This database provides the first global characterization of the genes expressed by mammalian astrocytes in vivo and is the first direct comparison between the astrocyte, neuron, and oligodendrocyte transcriptomes. We demonstrate that Aldh1L1, a highly expressed astrocyte gene, is a highly specific antigenic marker for astrocytes with a substantially broader, and therefore potentially more useful, pattern of astrocyte expression than the traditional astrocyte marker GFAP. This transcriptome database of acutely isolated and highly pure populations of astrocytes, neurons and oligodendrocytes provides a resource to the neuroscience community by providing improved cell type specific markers and for better understanding of neural development, function, and disease. We acutely purified mouse astrocytes from early postnatal ages (P1) to later postnatal ages (P30), when astrocyte differentiation is morphologically complete (Bushong et al., 2004), and acutely purified mouse OL-lineage cells from stages ranging from OPCs to newly differentiated OLs to myelinating OLs. We extracted RNA from each of these highly purified, acutely isolated cell types and used GeneChip Arrays to determine the expression levels of over 20,000 genes and construct a comprehensive database of cell type specific gene expression in the mouse forebrain. Analysis of this database confirms cell type specific expression of many well characterized and functionally important genes. In addition, we have identified thousands of new cell type enriched genes, thereby providing important new information about astrocyte, OL, and neuron interactions, metabolism, development, and function. This database provides a comparison of the genome-wide transcriptional profiles of the main CNS cell types and is a resource to the neuroscience community for better understanding the development, physiology, and pathology of the CNS. Keywords: Developmental CNS Cell type comparision

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Cross-species transcriptomic comparison of in vitro and in vivo mammalian neural cells

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