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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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The intracellular domain of amyloid precursor protein induces the dynamic change of the gene expression profile in P19 cells.

ABSTRACT: As previously reported (Neuroscience letters 444(2008)127-131), we established embryonic carcinoma P19 cell line expressing the intracellular domain of APP (AICD). Although neurons could be differentiated from these cell lines with RA treatment, expression of AICD gave rise to neuron-specific apoptosis. To identify the genes that are involved in this cell death, we evaluated changes of gene expressions that was induced by AICD through this process of cell death. The expression profiles of almost forty thousands transcripts were monitored by DNA microarrays. AICD-expressing P19 cell lines (AICD/P19) and control P19 cell lines (pCDNA/P19) that carry vector alone were used and cultured. To induce neural differentiation of these P19 cell lines, cells were allowed to aggregate in culture medium with 5×10-7 M all-trans-retinoic acid (RA) for 4 days (aggregated state). After aggregation, cells were replated onto cell culture grade dishes or poly-L-Lysine coated cell-disks for two days (differentiated state). RNAs were isolated at each states.

ORGANISM(S): Mus musculus

SUBMITTER: Kohzo Nakayama

PROVIDER: E-GEOD-22690 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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The intracellular domain of amyloid precursor protein induces the dynamic change of the gene expression profile in P19 cells.

Project description:As previously reported (Neuroscience letters 444(2008)127-131), we established embryonic carcinoma P19 cell line expressing the intracellular domain of APP (AICD). Although neurons could be differentiated from these cell lines with RA treatment, expression of AICD gave rise to neuron-specific apoptosis. To identify the genes that are involved in this cell death, we evaluated changes of gene expressions that was induced by AICD through this process of cell death. The expression profiles of almost forty thousands transcripts were monitored by DNA microarrays.

2010-07-14 | GSE22690 | GEO

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Project description:To investigate whether Rbfox3 could alter the expression level of miRNAs during neuronal differentiation of P19 cells, we performed miRNA microarray analysis using the RNAs extracted from untreated (undifferentiated) P19-GFP, RA-treated (neuronally differentiated) P19-GFP, or RA-treated P19-T2 cells. Total 9 samples were analyzed. We compared expression levels of P19-GFP (-) vs P19-GFP (+) vs P19-T2 (+) to identify miRNAs which had changes in expression levels with p < 0.01. From this miRNA list, we compared among P19-GFP (-) vs P19-GFP (+) vs P19-T2 (+) to identify the miRNAs which appeared to correlate with Rbfox3 expression.

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HeLa cell response to overexpression of wild type and mutated forms of the P19 splice variant of c-H-ras

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Differential expression of mature miRNAs in P19 cells during neuronal differentiation and by Rbfox3 depletion.

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Project description:Nervous system (NS) development relies on coherent up-regulation of extensive sets of genes in a precise spatiotemporal manner. How such transcriptome-wide effects are orchestrated at the molecular level remains an open question. Here we show that 3’-untranslated regions (3’UTRs) of multiple neuronal transcripts contain A/U-rich cis-elements (AREs) recognized by tristetraprolin (TTP/Zfp36), an RNA-binding protein previously reported to destabilize mRNAs encoding predominantly cytokines, growth factors and proto-oncogenes. We further demonstrate that the efficiency of ARE-dependent mRNA degradation declines during neural differentiation due to a decrease in the TTP protein expression mediated by the NS-enriched microRNA miR-9. Our experiments with transgenenic cell lines suggest that TTP down-regulation is essential for proper neuronal differentiation. Moreover, inactivation of TTP in neuroblastoma cells or mouse embryonic fibroblasts induces major changes in their transcriptomes accompanied by significantly elevated expression of NS-specific genes. We conclude that the newly identified miR-9/TTP circuitry limits unscheduled accumulation of neuronal mRNAs in non-neuronal cells and ensures coordinated up-regulation of these transcripts in neurons. 3'READS of undifferentiated and 3.5-day differentiated P19 cells

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Transcription profiling of mouse P19 EC differentiating neurons cultured at low and high densities

Project description:P19 differentiating cells were spread a two densities and mRNA from the two densities were compared

2007-06-30 | E-MEXP-1061 | biostudies-arrayexpress

Gene expression data from undifferentiated mouse embryonal carcinoma cell strains (MOE430A and MOE430B)

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2011-01-26 | E-GEOD-26875 | biostudies-arrayexpress

AP2gamma ChIPseq

Project description:As a part of a modelling experiment for transcriptional control of mouse primordial germ cell specification, the transcription factor AP2gamma was stably expressed in the mouse p19 embryonal carcinoma cell line and its genome wide binding sites were defined using ChIPseq.

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Genetic and epigenetic determinants of neurogenesis and myogenesis [expression profiling]

Project description:The regulatory networks of differentiation programs have been partly characterized; however, the molecular mechanisms of lineage-specific gene regulation by highly similar transcription factors remain largely unknown. Here we compare the genome-wide binding and transcription profiles of NEUROD2-mediated neurogenesis with MYOD-mediated myogenesis. We demonstrate that NEUROD2 and MYOD bind a shared CAGCTG E-box motif and E-box motifs specific for each factor: CAGGTG for MYOD and CAGATG for NEUROD2. Binding at factor-specific motifs is associated with gene transcription, whereas binding at shared sites is associated with regional epigenetic modifications but not as strongly associated with gene transcription. Binding is largely constrained to E-boxes pre-set in an accessible chromatin context that determines the set of target genes activated in each cell type. These findings demonstrate that the differentiation program is genetically determined by E-box sequence whereas cell lineage epigenetically determines the availability of E-boxes for each differentiation program. Total RNA samples were collected in triplicate from undifferentiated and differentiated P19 cells and MEFs, and labeled cDNA was made per Affymetrix protocol

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