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Comparative gene expression profiling of the EBV-positive NPC cell line C666.1 and normal primary tonsillar epithelial cells

ABSTRACT: In this study, we have performed comparative gene expression profiling of primary tonsil epithelial cells with the EBV-positive NPC cell line C666.1 using a human gene array.

ORGANISM(S): Homo sapiens

PROVIDER: GSE39826 | GEO | 2013/09/06

SECONDARY ACCESSION(S): PRJNA172824

REPOSITORIES: GEO

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Comparative gene expression profiling of the EBV-positive NPC cell line C666.1 and normal primary tonsillar epithelial cells

Project description:In this study, we have performed comparative gene expression profiling of primary tonsil epithelial cells with the EBV-positive NPC cell line C666.1 using a human gene array. Differences in cellular gene expression was compared using RNA isolated from C666-1 cells and primary tonsil epithelial cells grown in serum-free keratinocyte growth medium (performed in triplicate). RNA isolated from each sample was processed according to the Genechip WT sense target labelling protocol. 1μg of RNA was hybridised to human gene 1.0 ST array chips.

2013-09-06 | E-GEOD-39826 | biostudies-arrayexpress

mRNA expression profiling of ebv-miR-BART7-expressing NPC cells

Project description:Nasopharyngeal carcinoma (NPC) is endemic in Southeast Asia and southern China. The primary treatment for NPC is radiotherapy. Despite of the encouraging results of radiotherapy, local recurrence or distant metastases of NPC after the initial therapy is frequently found due to radioresistance. Therefore, there is an urgent need to identify genes that control radiosensitivty, aiming to reduce disease recurrence. Epstein-Barr virus (EBV) infection was closely associated with undifferentiated NPC. EBV-encoded microRNAs (miRNAs) played crucial roles in the pathogenesis of NPC. Ebv-miR-BART7 belongs to the 44 EBV BART miRNAs and was found to be up-regulated in NPC tissues and plasma. Forced expression of ebv-miR-BART7 enhanced the radiosensitivity of NPC cells. However, the mechanisms underlying the sensitizing effect of ebv-miR-BART7 on radiation remain largely unknown. Given that miRNA exerts biological functions by regulating its targets, we used microarray to identify the targets of ebv-miR-BART7 that regulate radiosensitivity of NPC cells.

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Expression data from EBV-encoded latent membrane protein 2A (LMP2A) positive and negative nasopharyngeal carcinoma (NPC) cell lines

Project description:Latent infection with Epstein-Barr virus (EBV) is recognised as a factor in the pathogenesis of nasopharyngeal carcinoma (NPC). We found that EBV encoded Latent membrane protein 2A (LMP2A) enhances lipid accumulation significantly in NPC cells. We used microarrays to identify differential genes regulated by LMP2A in NPC cell lines.

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ABBERANT GENE EXPRESSION BY EBERs IN EBV-NEGATIVE NPC HK1 CELL LINE

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miRNA-Seq profiling of nasopharyngeal carcinoma (NPC) and normal control samples

Project description:Epstein-Barr virus (EBV) is a ubiquitous human herpesvirus associated with nasopharyngeal carcinoma (NPC). EBV encodes two groups of microRNAs (miRNAs) which are divided into BamHI fragment H rightward open reading frame 1 (BHRF1) and BamHI-A rightward transcripts (BART) microRNAs. EBV miR-BARTs have been found to be involved in the development and progression of NPC. However, the role of EBV-miR-BARTs in NPC progression remains illusive. This study aimed to investigate the role of EBV-miR-BARTs in NPC and explore the underlying mechanisms.

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ABBERANT GENE EXPRESSION BY EBERs IN EBV-NEGATIVE NPC HK1 CELL LINE

Project description:Differential gene expression in RNA isolated from stably-transfected EBERs-negative versus EBERs-positive HK1 cell lines We established stable transfection of EBERs in the EBV-negative NPC cell line, HK1,to elucidate the role of the EBERs in NPC pathogenesis. Microarray gene expression profiling was carried out to investigate candidate genes which expression correlates with the expression of the EBERs. Total RNA was extracted from each cell line and processed using GeneChipÂ® Whole Transcript (WT) Sense Target Labelling Assay and then analyzed with GeneChipÂ® Human Gene 1.0 ST Array, with three repeats. Candidate genes differentially expressed between the two transfected HK1 cell lines were identified using GeneSpring GX 10 (Agilent Technologies).

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Expression data of EBV-positive and EBV-negative subclones of gastric adenocarcinoma cell line AGS

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Expression of EBV miRNAs in numerous EBV-positive cell lines

Project description:EBV-positive cell lines were assayed for expression of EBV miRNAs. The names of the miRNAs are from miRBase from Fall 2007. Microarray probes are tandem complements of the mature miRNA sequence. We assayed Burkitt's lymphoma (BL), Nasopharyngeal carcinoma, post-transplant lymphoproliferative disease (PTLD), primary effusion lymphoma, and lymphoblastoid cell lines. We also assayed primary B cells that were infected with the B95-8 strain of EBV, which was found to express EBV miRNAs as early as 20 hours post infection. We have found PTLD and BLs from HIV-positive donors both express EBV miRNAs. These types of cell lines have not previously been found to express viral miRNAs. We have found that cells that support type I and type II latency express only the BART miRNAs, whereas cells that support type III latency express BART and BHRF1 miRNAs. Furthermore, BL cell lines that spontaneously lose EBV express levels of the viral miRNAs that are at least 5-fold lower than cell lines that do not lose EBV. In total, 48 samples have been assayed and included in this study. EBV-negative control samples are not included in this data set, but raw and processed data may be requested from the contributors. These EBV-negative cell lines include the Burkitt's lymphoma cell lines, BJAB and Akata-negative, the gastric carcinoma cell line, AGS, and uninfected primary B cells. Of the 48 samples, we have assayed 22 different EBV-positive cell lines and 4 different time points after infection of primary B cells with EBV. Replicates of the majority of cell lines is included in this data set. Replicates are from independent RNA isolations that were then hybridized to individual microarrays.

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with and without EBV infection in NPC cell lines

Project description:5 samples with EBV infection vs 5 samples without Keywords: parallel sample

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Expression of EBV miRNAs in numerous EBV-positive cell lines

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