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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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

ABSTRACT: The c-H-ras proto-oncogene undergoes alternative splicing of the exon termed IDX giving rise to a novel protein of the Ras family, p19 (H-RasIDX). The experiment tests the effect on the transcriptome of overexpressing the wild type and W164A mutated forms of p19. Keywords: genetic modification Three-condition experiment, where wild type p19 H-ras transfection or transfection with a mutated form (p19W164A) were compared to transfection with the negative control (empty pRK5 expression vector) which was used as the common reference. Biological replicates: 3 of each set of treatments, independently grown and harvested. Two technical replicates with dye swapping per comparison.

ORGANISM(S): Homo sapiens

SUBMITTER: Lauro Sumoy

PROVIDER: E-GEOD-12059 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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P19 H-ras induces G1/S phase delay maintaining cells in a reversible quiescence state.

Camats Maria M Kokolo Mariette M Heesom Kate J KJ Ladomery Michael M Bach-Elias Montse M

PloS one 20091230 12

<h4>Background</h4>Three functional c-ras genes, known as c-H-ras, c-K-ras, and c-N-ras, have been largely studied in mammalian cells with important insights into normal and tumorigenic cellular signal transduction events. Two K-Ras mRNAs are obtained from the same pre-mRNA by alternative splicing. H-Ras pre-mRNA can also be alternatively spliced in the IDX and 4A terminal exons, yielding the p19 and p21 proteins, respectively. However, despite the Ras gene family's established role in tumorigen ...[more]

PMID: 20046837

Similar Datasets

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

Project description:The c-H-ras proto-oncogene undergoes alternative splicing of the exon termed IDX giving rise to a novel protein of the Ras family, p19 (H-RasIDX). The experiment tests the effect on the transcriptome of overexpressing the wild type and W164A mutated forms of p19. Keywords: genetic modification

2009-12-30 | GSE12059 | GEO

A dataset describing a suite of novel antibody reagents for the RAS signaling network

Project description:RAS genes are frequently mutated in cancer and have for decades eluded effective therapeutic attack. The National Cancer Institute’s RAS Initiative has a focus on understanding pathways and discovering therapies for RAS-driven cancers. Part of these efforts is the generation of novel reagents to enable the quantification of RAS network proteins. Here we present a dataset describing the development, validation (following consensus principles developed by the broader research community), and distribution of 104 monoclonal antibodies (mAbs) enabling detection of 27 phosphopeptides and 69 unmodified peptides from 20 proteins in the RAS network. The dataset characterizes the utility of the antibodies in a variety of applications, including Western blotting, immunoprecipitation, protein array, immunohistochemistry, and targeted mass spectrometry. All antibodies and characterization data are publicly available through the CPTAC Antibody Portal, Panorama Public Repository, and/or PRIDE databases. These reagents will aid researchers in discerning pathways and measuring expression changes in the RAS signaling network.

2019-07-18 | PXD012130 | Pride

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

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.

2014-09-21 | E-GEOD-52377 | biostudies-arrayexpress

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. 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.

2010-07-14 | E-GEOD-22690 | biostudies-arrayexpress

Gene expression profiling by DNA microarray in Colo741 cell line transfected by KRas-G12D or KRas-G12V

Project description:Mutations of the proto-oncogene KRas, together with the inactivation of the onco-suppressor genes APC and TP53, are considered to have an important role both in the carcinogenesis and in the colorectal tumor progression. The oncogene K-ras has activating mutations, especially in codon 12, in about 40% to 50% of colorectal carcinomas (Andreyev et al., 1998). The mechanism by which oncogenic K-ras alone contribuites to tumor progression in colon cancer is largely unknown. To this end, we have developed a model system where the colorectal adenocarcinoma cell line Colo741 has been stably trasfected with the Kras-G12V or Kras-G12D mutated oncogenes. Our results demonstrate how expression profiling data can be used to interpret changes in cellular characteristics induced by transfection and hence provide some clues as to the mechanisms by which different activated K-Ras impair processes mediated by endogenous wild-type KRas proteins. We made for the production of cell clones that could be utilized as useful in vitro models. The adenocarcinoma cell line Colo741 has been chosen to produce stable transfectants for two mutant forms of KRas2 (Gly12Val and Gly12Asp) and the wild-type coding sequence (as experiment control). After the transfection, the cells have been selected (with G418), cloned (by limited dilutions) and screened (by RT-PCR). The total RNAs, Dnase-treated, from five cell clones per condition, have been pooled. The samples, constituted by biotin-labeled cRNA, derived from a pool of five cell clones obtained from transfection of the adenocarcinoma cell line Colo741 with either pcDNA3.1-KRas2(Wt) or pcDNA3.1-KRas2(Gly12Val) or pcDNA3.1KRas2(Gly12Asp). They were hybridized to a Human Gene 1.0 ST array (Affymetrix). Two technical replicates have been performed for each condition.

2008-12-17 | E-GEOD-12398 | biostudies-arrayexpress

MicroRNA profiling of human HeLa cells overexpressing p19 H-Ras

Project description:MicroRNA miRNA expression profiles for human HeLa cells (Cervical cancer), overexpressing p19 H-Ras, were examined to investigate the miRNA regulation by p19 H-Ras. miRNA microarray analysis identified statistical unique profiles, which could discriminate miRNAs regulated by p19 H-Ras and not regulated by the p19 mutant (W164A) H-Ras.

2008-12-12 | E-TABM-494 | biostudies-arrayexpress

High-resolution analysis of SRSF3 and SRSF4 binding sites by iCLIP

Project description:Endogenous SRSF3 and SRSF4 RNA binding sites were identified genome-wide by iCLIP in P19 BAC trangenic cell lines using GFP-epitope tag.

2012-03-21 | E-MTAB-747 | biostudies-arrayexpress

Expression signatures of human HeLa cells with RNAi targetting A1 hnRNP, FUS, H hnRNP and p68-DDX5

Project description:Transcription profiling of human HeLa cells (cervical cancer cell line) transfected with a plasmid expressing shRNAs cloned into the pSuper expression vector compared to emprty vector negative controls for transfection. Four different RNA interference treatments targetted: A1 hnRNP (HNRNPA1, Heterogeneous nuclear ribonucleoprotein A1); FUS (fusion gene, involved in t(12;16) in malignant liposarcoma); H hnRNP (HNRNPH1); and p68 helicase (DDX5, DEAD (Asp-Glu-Ala-Asp) box polypeptide 5). Keywords: genetic modification Five-condition experiment, where HNRNPA1, FUS, HNRNPH1 and DDX5 gene product levels were inhibited by siRNA transfection and compared to transfection with the negative control (scrambled siRNA). Biological replicates: 2 of each of the first three treatments and 3 of the treatment against DDX5, all independently grown and harvested. No technical replicates were performed.

2008-08-20 | E-GEOD-12058 | biostudies-arrayexpress

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

Proteome profiling of GC1-spg cells over-expressing DYNLT1

Project description:This study was designed to evaluate the proteome profiles of GC1-spg cells transfected with pEGFPN1-dynlt1 (experiment) and empty vector (control). The cells were harvested 48 hrs after transfection and the proteins were profiled.

2015-11-03 | PXD002593 | Pride

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