Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Transcription profiling of neural stem cells treated with FGF-2, PDGF-AA or in the absence of growth factor (differentiation)

ABSTRACT: We compared the gene expression profiles of neural stem cells treated with FGF-2, PDGF-AA or in the absence of growth factor (differentiation). Cells grown in the presence of FGF-2 were used as a reference.

INSTRUMENT(S): ScanArray scanning hardware, microcentrifuge

ORGANISM(S): Rattus norvegicus

SUBMITTER: Jean-Baptiste Demoulin

PROVIDER: E-TABM-39 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

The gene expression profile of PDGF-treated neural stem cells corresponds to partially differentiated neurons and glia.

Demoulin Jean-Baptiste JB Enarsson Mia M Larsson Jimmy J Essaghir Ahmed A Heldin Carl-Henrik CH Forsberg-Nilsson Karin K

Growth factors (Chur, Switzerland) 20060901 3

We have previously shown that platelet-derived growth factor AA (PDGF-AA) stimulates the expansion of neuronal progenitors from neural stem cells, but is unable to replace fibroblast-growth factor 2 (FGF-2) as a stem cell mitogen. In the present study, we compared gene expression in neural stem cells that were grown in the presence of FGF-2 and in cells cultured with PDGF-AA or in the absence of growth factor, which induces differentiation. The genetic program elicited by PDGF-AA (156 significan ...[more]

PMID: 17079202

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Project description:Subconfluent AG01518 fibroblasts were starved for 16 hours in the presence of 0.1% BSA, and then stimulated for 1, 4, 10 or 24 hours with PDGF-BB (10 ng/ml in starvation medium), or left untreated for the same periods of time. Total RNA was isolated using the RNeasy kit (Qiagen). The RNA quality was checked by formaldehyde agarose gel electrophoresis (RNeasy protocol, Qiagen). Total RNA (40 mg) from cells treated for a given period of time with PDGF or control medium were labelled in reverse transcription reactions (Superscript II kit, Invitrogen) with dCTP-Cy5 and dCTP-Cy3, respectively (Amersham). In every second replicate experiment the fluorescent deoxynucleotides were swapped. Purified cDNA probes labelled with Cy3 and Cy5 were mixed per pair, and hybridized to cDNA microarray chips (Sanger Institute H. sapiens 10K array, Hver1.2.1) from the Sanger Institute/LICR/CRUK Consortium (see http://www.sanger.ac.uk/Projects/Microarrays/ for details and hybridization protocols). For each time point, we performed at least four independent hybridizations, and used at least two different batches of RNA. Chips were scanned in a Perkin Elmer/GSI Lumonics ScanArray 4000 scanner and spot intensities were measured using the QuantArray software (histogram method with background subtraction). Normalization and statistical analysis of the quadruplicate data sets were performed using GeneSpring 5.0 analysis software (Silicon Genetics). A Lowess non-linear normalization was applied and the median of the ratio distribution for each array was set to 1. Regulated spots were selected based on the average ratio values > 1.750 for up-regulated genes and < 0.571 for down-regulated genes. In addition, we considered only genes that were significantly regulated (t-test, p<0.05) based on replicate hybridizations (global error model, GeneSpring). For all features selected using this protocol, the signal was significantly above the background, indicating that the expression of these genes was detectable. Finally, Hver1.2.1 microarrays contain replicate spots (1 to 6) corresponding to the same gene. Genes represented by spots that were not regulated in a similar manner were discarded. We show the average ratio of one representative spot for each regulated gene, with standard error calculated from multiple hybridizations and with the annotation provided by the microarray facility (Hver1.2.1_NCBI33).

Dataset Information

Transcription profiling of neural stem cells treated with FGF-2, PDGF-AA or in the absence of growth factor (differentiation)

Publications

The gene expression profile of PDGF-treated neural stem cells corresponds to partially differentiated neurons and glia.

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