Filters
Technology
Platform
SRP003764
Homo sapiens
1 Downloadable Sample
IlluminaGenomeAnalyzerII
Description
RNASeq was used to evaluate the Epstein-Barr virus transcriptome. A pipeline was developed for the analysis of EBV specific transcripts and applied to EBV positive Burkitt's lymphoma cells exhibiting type I latency. PolyA fractions of whole cell RNA was sequenced using 74b single-end reads on an Illumina GA2x machine.
Publication Title
Quantitative and qualitative RNA-Seq-based evaluation of Epstein-Barr virus transcription in type I latency Burkitt's lymphoma cells.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 5 Downloadable Samples
- Illumina HiSeq 2000
Description
Certain peripheral T-cell lymphomas (PTCLs) have been associated with viral infection, particularly infection with Epstein-Barr virus (EBV). However, a comprehensive virome analysis across PTCLs has not previously been reported, and viral gene expression profiles have been studied only in certain PTCL subtypes. In this study we utilized published RNA-seq data sets from seven different PTCL studies as well as new RNA-seq data from our laboratory to screen for virus association, to analyze viral gene expression, and to assess B- and T-cell receptor diversity paradigms across these tumor types. In addition to identifying EBV in angioimmunoblastic T-cell lymphoma (AITL) and extranodal NK/T cell lymphoma (ENKTL), two PTCL subtypes with well-established EBV associations, we also detected EBV in several cases of anaplastic large cell lymphoma (ALCL), and we found evidence of infection by the oncogenic viruses KSHV and HTLV-1 in isolated PTCL cases. In AITLs, EBV gene expression analysis showed expression of immediate early, early and late lytic genes, suggesting either abortive lytic replication and/or productive infection in a subset of the EBV infected infiltrating B-lymphocytes. Deconvolution of immune cell subpopulations demonstrated a greater B-cell signal in AITLs than in other PTCL subtypes, consistent with a larger role for B-cell support in the pathogenesis of AITL. T-cell receptor (TCR) and B-cell receptor (BCR) repertoires reconstructed from RNA-seq data demonstrated increased BCR diversity in AITLs, consistent with a possible EBV-driven polyclonal response. These findings indicate potential alternative roles for EBV in PTCLs in addition to the canonical oncogenic mechanisms associated with EBV latent infection. The findings also suggest the involvement of other viruses in T-cell lymphoma pathogenesis and demonstrate immunological alterations associated with these cancers. Overall design: RNA sequencing of five extranodal NK/T-cell lymphoma (ENKTL)-derived cell lines
Publication Title
High-Throughput Sequence Analysis of Peripheral T-Cell Lymphomas Indicates Subtype-Specific Viral Gene Expression Patterns and Immune Cell Microenvironments.
Sample Metadata Fields
Specimen part, Subject
View Samples- Homo sapiens
- 4 Downloadable Samples
- Illumina HiSeq 2500
Description
deepCAGE was used in conjunction with Pacific Biosciences Iso-Seq and Illumina RNA-Seq to globally resolve transcript structures in replicating Epstein-Barr virus. Overall design: deepCAGE of replicating Epstein-Barr virus in Akata cells to identify transcript 5'' ends
Publication Title
Global transcript structure resolution of high gene density genomes through multi-platform data integration.
Sample Metadata Fields
Specimen part, Subject
View Samples- Homo sapiens
- 4 Downloadable Samples
Illumina HumanHT-12 V4.0 expression beadchip
Description
The Kaposi sarcoma-associated herpesvirus (KSHV) is the causative agent of Kaposi sarcoma (KS), the most common HIV/AIDS-associated tumor worldwide. Involvement of the oral cavity portends a poor prognosis for patients with KS, but mechanisms for KSHV regulation of the oral tumor microenvironment are largely unknown. Infiltrating fibroblasts are found with KS lesions, and KSHV establishes latent infection within human primary fibroblasts in vitro, but contributions for KSHV-infected fibroblasts to the KS microenvironment have not been previously characterized. In the present study, we used Illumina microarray to detect the global gene profile altered in KSHV-infected primary human fibroblasts (PDLF and HGF) isolated from the oral cavity.
Publication Title
Transcriptomic analysis of KSHV-infected primary oral fibroblasts: The role of interferon-induced genes in the latency of oncogenic virus.
Sample Metadata Fields
Specimen part
View Samples- Homo sapiens
- 10 Downloadable Samples
- IlluminaHiSeq2000
Description
We confirmed immune response as the key mechanism and provided solid evidence for novel genes (e.g., FCAR and CUX1) and distinct biological processes (e.g., endocytosis, cytokine production and apoptosis) as potentially new important factors/mechanisms contributing to chronic periodontitis pathogenesis. Overall design: We performed an RNA-sequencing (RNA-seq) study of peripheral blood monocytes (PBMs) in 5 non-smoking moderate to severe CP (case) subjects vs. 5 controls. We replicated the DEx transcripts/isoforms using an independent microarray dataset. We also pathway-based analysis on the identified/replicated DEx transcripts/isoforms using DAVID performed (Database for Annotation, Visualization and Integrated Discovery).
Publication Title
RNA-sequencing study of peripheral blood monocytes in chronic periodontitis.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 4 Downloadable Samples
- IlluminaHiSeq2000
Description
RNA Sequencing performed on EBV positive gastric cancer biopsies and cells lines to study expression of EBV specific genes. Overall design: Examination of two EBV postitive gastric carcinoma biopsies and two EBV positive gastric cancer cell lines, NCC24 and YCCEL1 by RNA-Seq.
Publication Title
Latent Expression of the Epstein-Barr Virus (EBV)-Encoded Major Histocompatibility Complex Class I TAP Inhibitor, BNLF2a, in EBV-Positive Gastric Carcinomas.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 2 Downloadable Samples
- Illumina HiSeq 2000
Description
Our goal of this study was to perform quantitative and global assessment of EBV gene expression in gastric carcinomas and assess EBV associated cellular pathway alterations. Overall design: Examination of a gastric carcinoma cell line naturally infected with EBV, SNU-719 using poly-A and ribodepletion RNA-seq data sets
Publication Title
Latent Expression of the Epstein-Barr Virus (EBV)-Encoded Major Histocompatibility Complex Class I TAP Inhibitor, BNLF2a, in EBV-Positive Gastric Carcinomas.
Sample Metadata Fields
Cell line, Subject
View Samples- Mus musculus
- 1 Downloadable Sample
- Illumina HiSeq 2500
Description
Strand-specific Illumina RNA-Seq was used in conjunction with Pacific Biosciences Iso-Seq and deepCAGE to globally resolve transcript structures in lytic murine gammaherpesvirus 68. Overall design: Strand-specific Illumina RNA-Seq of MHV68-infected fibroblasts
Publication Title
Genome-wide Transcript Structure Resolution Reveals Abundant Alternate Isoform Usage from Murine Gammaherpesvirus 68.
Sample Metadata Fields
Specimen part, Subject
View Samples- Homo sapiens
- 13 Downloadable Samples
- IlluminaHiSeq2000
Description
Using strand specific RNA-seq to assess the EBV transcriptome during reactivation of Akata cells, we found extensive bidirectional transcription extending across nearly the entire genome. Overall design: Illumina strand-specific RNA-seq of BCR-activated Akata cells at 9 time points
Publication Title
The Epstein Barr virus circRNAome.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 6 Downloadable Samples
- Affymetrix Mouse Gene 1.0 ST Array (mogene10st)
Description
IL-10 is an anti-inflammatory cytokine that has been shown to be produced by antigen-specific CD8 T cells at the peak of viral encephalitis. We found that IL-10+CD8 T cells are more activated and cytolytic than IL-10-CD8 T cells.
Publication Title
Highly activated cytotoxic CD8 T cells express protective IL-10 at the peak of coronavirus-induced encephalitis.
Sample Metadata Fields
Specimen part
View Samples