Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

PrPC-dependent gene expression and cell signalling signature in Neuro2a cells. Role on mitogenic stimulation and cell morphology.

ABSTRACT: In this work we present the PrPC-dependent gene expression signature in N2A cells and its implication on the most overrepresented functions; cell cycle, cell growth and proliferation and cell morphology. To evaluate the genes whose transcription was regulated after Prnp modulation, RNA samples were analyzed with Illumina mouse whole genome beadarrays. cell type comparison; genetic modification; RNA interference

ORGANISM(S): Mus musculus

SUBMITTER: Lauro Sumoy

PROVIDER: E-GEOD-38887 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

PrP(C) regulates epidermal growth factor receptor function and cell shape dynamics in Neuro2a cells.

Llorens Franc F Carulla Patricia P Villa Ana A Torres Juan M JM Fortes Puri P Ferrer Isidre I del Río José A JA

Journal of neurochemistry 20130528 1

The prion protein (PrP) plays a key role in prion disease pathogenesis. Although the misfolded and pathologic variant of this protein (PrP(SC)) has been studied in depth, the physiological role of PrP(C) remains elusive and controversial. PrP(C) is a cell-surface glycoprotein involved in multiple cellular functions at the plasma membrane, where it interacts with a myriad of partners and regulates several intracellular signal transduction cascades. However, little is known about the gene expressi ...[more]

PMID: 23638794

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Project description:Epidermal growth factor (EGF) is a key regulatory growth factor activating a myriad of processes affecting cell proliferation and survival that are relevant to normal development and disease. Here we have used a combined approach to study the EGF dependent transcriptome of HeLa cells. We obtained mRNA expression profiles using multiple long oligonucleotide based microarray platforms (from Agilent, Operon, Febit, and Illumina) in combination with digital gene expression profiling (DGE) with the Illumina Genome Analyzer I (GA-I). By applying a procedure for cross-platform data meta-analysis based on rank product and global ancova tests, we establish a well validated gene set with transcript levels altered after EGF treatment. We used this robust gene list to build higher order networks of gene interaction by interconnecting associated networks, supporting and extending the important role of the EGF signaling pathway in cancer. In addition, we found a whole new set of genes previously unrelated to the currently accepted EGF associated cellular functions, among which are metallothionein genes. We propose the use of global genomic cross-validation to generate more reliable datasets derived from high content technologies (microarrays or deep sequencing). This approach should help to improve the confidence of downstream in silico functional inference analyses based on high content data. Keywords: treated vs. untreated comparison, time course Time course experiment comparing HeLa gene expression in response to EGF analyzed on different microarray platforms (Agilent, IMPPC, Illumina, and Operon) and by digital gene expression using short read high throughput tag sequencing. Three independent experiments were performed where HeLa cells were serum deprived for 24 hours and were either left untreated or treated with EGF for 6, and 24 h and harvested for RNA extraction. Technical dye swap duplicates were performed for each of the three biological replicates in both time points. Comparative genomic hybridization of HeLa cell genomic DNA versus poooled genomic DNA from blood obtained from human females conducted on commercial oligonucleotide microarrays (Human Genome CGH Microarray Kit 244A, Agilent Technologies) in order to assess DNA dosage dependence of gene expression levels and response to EGF. Digital gene expression using short read high throughput tag sequencing data submitted to NCBI's SRA

Dataset Information

PrPC-dependent gene expression and cell signalling signature in Neuro2a cells. Role on mitogenic stimulation and cell morphology.

Publications

PrP(C) regulates epidermal growth factor receptor function and cell shape dynamics in Neuro2a cells.

Similar Datasets

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