GEO DataSets

(Submitter supplied) We aimed to investigate whether EBV exosomes will affect gene expression in primary fibroblasts. By obtaining normalized read counts of genes generated from RNA-sequencing, we compared the transcriptomic alterations between fibroblasts treated with HK1EBV exosomes and untreated fibroblasts.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

3 Samples

Download data: TXT

(Submitter supplied) Epstein-Barr virus (EBV) related nasopharyngeal carcinoma (NPC) is an epithelial malignancy with higher incidence in Asian endemic area (EA) than in non-endemic area (NEA), where frequency is below 1/105/year. The causes of such difference are unclear and might be related to viral, environmental (e.g. diet) and genomic factors. We aimed at dissecting the gene expression (GE) and microenvironment landscape in NPC leading to the identification of molecular subtypes explaining the differences between EA and NEA.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

50 Samples

Download data: TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing

Platform:

GPL20301

22 Samples

Download data

(Submitter supplied) 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. more...

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL20301

11 Samples

Download data: TSV

(Submitter supplied) To understand the genes and pathways that may potentially drive nasopharyngeal carcinoma (NPC) pathogenesis, we sought out to analyze the transcriptomic data from the disease and control samples. We used RNA-sequencing based gene expression data to identify genes differentially expressed between NPC and normal controls and then characterize the gene ontology and pathways down- or up-regulated in the disease samples.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20301

11 Samples

Download data: TSV

(Submitter supplied) Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are using mRNA and microRNA sequencing analysis to evaluate the effects of EBV-encoded microRNA BART2-5p mimics on the mRNA and microRNA profiles of human nasopharyngeal carcinoma cell line 6-10B. Methods: 6-10B cells were transfected with either EBV microRNA BART2-5p mimics or negative control (NC) mimics for 48 hours. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing

Platform:

GPL24676

8 Samples

Download data: TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Other

Platforms:

GPL18573 GPL24676 GPL18460

26 Samples

Download data: BEDGRAPH, BIGWIG, HIC

(Submitter supplied) We analyzed the gene expressions around the host genomic regions where EBV and host genomic interactions were obsearved in nasopharyngeal carcinoma cell lines.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

6 Samples

Download data: TXT

(Submitter supplied) We analyzed the compartment status and chromatin interactions in nasopharyngeal epithelial cell lines and nasopharyngeal carcinoma cell lines by performing Hi-C.

Organism:

Homo sapiens

Type:

Other

Platforms:

GPL24676 GPL18460

2 Samples

Download data: HIC

(Submitter supplied) We analyzed active enhancers of nasopharyngeal epithelial cell lines and nasopharyngeal carcinoma cell lines by performing ChIP-seq on H3K4me1, H3K4me3, and H3K27ac.

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL18573

12 Samples

Download data: BIGWIG

(Submitter supplied) We detected the EBV interaction regions and the genomic loops from TSS of PLA2G4A in nasopharyngeal carcinoma cell lines by 4C-seq analysis.

Organism:

Homo sapiens

Type:

Other

Platforms:

GPL18573 GPL24676

6 Samples

Download data: BEDGRAPH

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Homo sapiens

Type:

Methylation profiling by high throughput sequencing

Platforms:

GPL20795 GPL24676

32 Samples

Download data: BIGWIG

(Submitter supplied) Nasopharyngeal carcinoma (NPC) is enedemic in Southeast Asia but is uncommon worldwide. In Hong Kong, approximately 95% of NPC cases are associated with Esptein-Barr Virus (EBV). EBV has been shown to induce changes in the epigenetics of EBV-malignancies. Epigenetics in NPC may thus play an important role in NPC pathogensis. We performed whole-genome bisulfite sequencing (WGBS) to profile the methylation changes in NPC and investigate the role of abberant methylation pattern in NPC.

Organism:

Homo sapiens

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL20795

20 Samples

Download data: BIGWIG

(Submitter supplied) Nasopharyngeal carcinoma (NPC) is enedemic in Southeast Asia but is uncommon worldwide. In Hong Kong, approximately 95% of NPC cases are associated with Esptein-Barr Virus (EBV). EBV has been shown to induce changes in the epigenetics of EBV-malignancies. Epigenetics in NPC may thus play an important role in NPC pathogensis. We performed targeted bisulfite sequencing to accurately profile the methylation changes in NPC and investigate the role of abberant methylation pattern in NPC.

Organism:

Homo sapiens

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL24676

12 Samples

Download data: BIGWIG

(Submitter supplied) To investigate the effect of TNFα and EBV on invadopodia formation, we treated the EBV-positive and -negative NPC43 cells seeded on gelatin with or without TNFα We then performed gene expression profiling analysis using data obtained from RNA-seq of 4 different groups

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

4 Samples

Download data: TXT

(Submitter supplied) Nasopharyngeal carcinoma (NPC), a cancer that is etiologically associated with the Epstein-Barr virus (EBV), is endemic in Southern China and Southeast Asia. The scarcity of representative NPC cell lines owing to the frequent loss of EBV episomes following prolonged propagation and compromised authenticity of previous models underscores the critical need for new EBV-positive NPC models. Herein, we describe the establishment of a new EBV-positive NPC cell line, designated NPC268 from a primary non-keratinizing, differentiated NPC tissue. more...

Organism:

Homo sapiens

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL24676

1 Sample

Download data: BIGWIG

(Submitter supplied) In this single arm non-randomized phase II trial, 40 patients with recurrent/metastatic EBV-positive nasopharyngeal carcinoma who failed prior chemotherapy received nivolumab 3 mg/kg every 2 weeks and ipilimumab 1 mg/kg every 6 weeks. The best overall objective response rate was 38% with a median progression-free and overall survival of 5.3 and 19.5 months, respectively. This regimen was well-tolerated and treatment-related adverse events requiring discontinuation were low. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL33087

41 Samples

Download data: RCC, XLSX

(Submitter supplied) Understanding of the downstream mechanism of CD70-CD27 signaling in Tregs

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

2 Samples

Download data: H5

(Submitter supplied) Understanding of the spatial architecture of the primary NPC microenvironment as well as the co-localization and cell-cell communication between tumor and immune cells

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

2 Samples

Download data: H5, TAR

(Submitter supplied) The tumor microenvironment (TME) of nasopharyngeal carcinoma (NPC) harbors a heterogeneous and dynamic stromal population. A comprehensive understanding of this tumor-specific ecosystem is necessary to enhance cancer diagnosis, therapeutics, and prognosis. However, recent advances based on bulk RNA sequencing remain insufficient to construct an in-depth landscape of infiltrating stromal cells in NPC. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL24676

35 Samples

Download data: CSV, FASTA, MTX, TSV