GEO DataSets

(Submitter supplied) Prevalence of the members of herpesvirus family in oral inflammatory diseases is increasingly acknowledged suggesting their likely role as etiological factor. However, the underlying mechanisms remains obscure. In our recent miRNA profiling of healthy and diseased human tooth pulpal, elevated expression of HHV encoded v-miRs were identified. Based on the fold induction and significance values, we selected three v-miRs namely miR-K12-3-3p (KSHV), miR-H1 (HSV-1), and miR-UL-70-3p (HCMV) to further examine their impact on host cellular functions. more...

Organism:

synthetic construct; Homo sapiens

Type:

Non-coding RNA profiling by array

Platform:

GPL17107

32 Samples

Download data: TXT

(Submitter supplied) We investigated the impact of on miR-H1 and miR-K12-3-3p- on host transcriptome focusing on gingival epithelial cells that are target sites for various HHV. Results: More than 1300 genes were altered by miR-H1 and miR-K12-3-3p expressing HOK.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL16686

12 Samples

Download data: CEL

(Submitter supplied) Background: Kaposi’s sarcoma associated herpes virus (KSHV) is associated with tumors of endothelial and lymphoid origin. During latent infection, KSHV expresses miR-K12-11, an ortholog of the human tumor gene hsa-miR-155. Both gene products are microRNAs (miRNAs), which are important post-transcriptional regulators that contribute to tissue specific gene expression. Advances in target identification technologies and molecular interaction databases have allowed a systems biology approach to unravel the gene regulatory networks (GRNs) triggered by miR-K12-11 in endothelial and lymphoid cells. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

32 Samples

Download data: CEL

(Submitter supplied) KS lesions consist of endothelial cells latently infected with KSHV which express the KSHV miRNAs. Identifying the targets of the KSHV miRNAs will help us understand their role in viral oncogenesis. Cross-Linking and Sequencing of Hybrids (CLASH) is a method for unambiguously identifying miRNA targetomes. We developed a streamlined version of CLASH, called quick CLASH (qCLASH). qCLASH requires a lower initial input of cells than its parent protocol. more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL16791

9 Samples

Download data: TXT

(Submitter supplied) Marek’s disease virus 1 (MDV-1), an oncogenic -herpesvirus that induces T-cell lymphomas in chickens, serves as model system to study transformation by lymphotropic herpesviruses. Like the oncogenic human -herpesviruses Kaposi’s sarcoma-associated herpesvirus (KSHV) and Epstein-Barr virus (EBV), MDV-1 encodes several viral microRNAs (miRNAs). One MDV-1 miRNA, miR-M4, shares the same “seed” targeting sequence with both a KSHV miRNA, miR-K11, and cellular miR-155. more...

Organism:

Gallus gallus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16133

1 Sample

Download data: TXT

(Submitter supplied) Transcriptional profiling of BJAB cells expressing miR-K12-6-5p. To identify host RNA targets of KSHV miRNAs, we took advantage of the observation that RNAs targeted by miRNAs often display small reductions in their steady-state levels, perhaps as a result of their impaired translation. Accordingly, we examined cellular transcript accumulation by array-based expression profiling under four sets of conditions in which KSHV miRNAs were expressed.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6848

4 Samples

Download data: TXT

(Submitter supplied) All metazoan eukaryotes express microRNAs (miRNAs), ~22 nt long regulatory RNAs that can repress the expression of mRNAs bearing complementary sequences. Several DNA viruses also express miRNAs in infected cells, suggesting a role in viral replication and pathogenesis. While specific viral miRNAs have been shown to autoregulate viral mRNAs or downregulate cellular mRNAs via novel target sites, the function of the majority of viral miRNAs remains unknown. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL5770

23 Samples

Download data: GPR

(Submitter supplied) MicroRNAs are small, non-coding RNAs that post-transcriptionally regulate gene expression by binding to 3’UTRs of target mRNAs. Kaposi’s sarcoma-associated herpesvirus (KSHV), a virus linked to malignancies including primary effusion lymphoma (PEL), encodes 12 miRNA genes, but only a few regulatory targets are known. We found that KSHV-miR-K12-11 shares 100% seed-sequence homology with hsa-miR-155, a miRNA frequently found up-regulated in lymphomas and critically important for B cell development. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Dataset:

GDS3007

Platform:

GPL570

12 Samples

Download data: CEL, EXP

Analysis of cells expressing microRNA (miR) K12-11 from Kaposi's sarcoma-associated herpesvirus. miR-K12-11 shares sequence homology with hsa-miR-155, a miRNA up-regulated in lymphomas and important in B cell development. Results provide insight into the biological activity of miR-K12-11.

Organism:

Homo sapiens

Type:

Expression profiling by array, count, 3 protocol sets

Platform:

GPL570

Series:

GSE9264

12 Samples

Download data: CEL, EXP

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

Organism:

Homo sapiens

Type:

Expression profiling by array; Non-coding RNA profiling by high throughput sequencing; Third-party reanalysis

Platforms:

GPL5770 GPL6244 GPL9115

20 Samples

Download data: BED, CEL, GPR

(Submitter supplied) Primary effusion lymphoma (PEL) is caused by Kaposi's sarcoma-associated herpesvirus (KSHV) and frequently also harbors Epstein-Barr virus (EBV). The expression of KSHV- and, often, EBV-encoded microRNAs (miRNAs) in PELs suggests a role for these miRNAs in viral latency and lymphomagenesis. Here we report the direct and transcriptome-wide identification of miRNA target sites for all miRNAs expressed in PEL cell lines. more...

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL9115

6 Samples

Download data: BED

(Submitter supplied) BJAB cells were infected with pNL-SIN-CMV-AcGFP (see accession number GSE8867 for data) or pNL-SIN-CMV-AcGFP expressing KSHV miR-K1, miR-K12-11 or miR-K4-3p and sorted 48 hours after infection. 12 or 16 days after transduction, cytoplasmic RNA was harvested and gene expression analysis of independent BJAB cell pools was performed using Human Operon v3.0.2 arrays. Each sample was run against Universal Human Reference RNA, Stratagene. more...

Organism:

Homo sapiens

Type:

Expression profiling by array; Third-party reanalysis

Platform:

GPL5770

12 Samples

Download data: GPR, TXT

(Submitter supplied) Microarray analysis of primary effusion lymphoma cell lines BC-1 and BC-3

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6244

2 Samples

Download data: CEL

(Submitter supplied) The viral miRNA miR-K6-5p encoded by the DNA tumor virus Kaposi’s sarcoma-associated herpesvirus exhibits offset, sequence similarity with the tumor suppressive cellular miR-15/16 family, as well as sharing a short seed match to the cellular miR-214 (nts 2-7). We investigated how gene regulation by the viral miR-K6-5p is related to regulation by these cellular miRNAs by performing transcriptome analysis. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20301

15 Samples

Download data: TXT

(Submitter supplied) Transcriptional profiling of BJAB cells expressing miR-K10a and BCBL cells treated with miR-K10a inhibitor. To identify host RNA targets of KSHV miRNAs, we took advantage of the observation that RNAs targeted by miRNAs often display small reductions in their steady-state levels, perhaps as a result of their impaired translation. Accordingly, we examined cellular transcript accumulation by array-based expression profiling under three sets of conditions in which KSHV miRNAs were expressed or inhibited.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6848

6 Samples

Download data: TXT

(Submitter supplied) We performed Ago HITS-CLIP to identify targets of viral and human miRNAs in latently KSHV-infected PEL cells

Organism:

Homo sapiens

Type:

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

Platform:

GPL10999

7 Samples

Download data: BED, TXT

(Submitter supplied) Small RNA deep sequencing analysis was conducted on primary human fibroblasts infected with human cytomegalovirus (HCMV). HCMV-encoded miRNAs accumulated to ~20% of the total smRNA population at late stages of infection, and our analysis led to improvements in viral miRNA annotations and identification of novel HCMV miRNAs. Through crosslinking and immunoprecipitation of Argonaute-bound RNAs from infected cells, followed by high-throughput sequencing (Ago CLIP-seq), we obtained direct evidence for incorporation of all HCMV miRNAs into the endogenous host silencing machinery. more...

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by high throughput sequencing; Other

Platform:

GPL10999

12 Samples

Download data: BED

(Submitter supplied) To examine the trascriptome profiling in monocytes-derived dendritic cells transfected with miR-142-3p by Affymetrix HTA-2_0 arrays

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL17586

7 Samples

Download data: CEL, TXT, XLSX

(Submitter supplied) We report the application of size selection of small RNA species isolated from Jjhan cells harboring the human herpesvirus 6A genome. We ammassed >3.4million reads of sequence from three different sources: Normal Brain cell total RNA, Jjhan total RNA and HHV-6A BAC transfected Jjhan total RNA. Sequences were mapped to the HHV-6A Uganda 1102 strain genome (GenBank: X83413.1) with no less than 100% match for reads >20nt and <23nt. more...

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL10999

1 Sample

Download data: TXT

(Submitter supplied) Transcriptional profiling of mouse brain regions (microdissection of cerebellum and hippocampus regions) comparing control, untreated brain tissue with HSV-1 infected brain tissue. Two viral tires, 10^3 and 10^6 plaque forming units of HSV-1 strain F, were intracerebrally inoculated into the brain of SJL/J strain of mice. The goal was to assess global transcriptional dynamics in HSV-1 infected mice, a model of herpes simplex encephalitis, as compared to controls (either PBS or Vero cell suspension). more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL4134

23 Samples

Download data: TXT