GEO DataSets

(Submitter supplied) To address the role of miRNAs in Hirschsprund disease (HSCR), we carried out microRNA (miRNA) array analysis by using human intestinal samples obtained from HSCR patients and controls, and identified dysregulated miRNAs involved in the pathogenesis of HSCR.

Organism:

Homo sapiens; Human alphaherpesvirus 1; Human betaherpesvirus 5; Human immunodeficiency virus 1; Human betaherpesvirus 6B; Merkel cell polyomavirus; Herpesvirus saimiri (strain 11); JC polyomavirus; Human gammaherpesvirus 8

Type:

Non-coding RNA profiling by array

Platform:

GPL32145

10 Samples

Download data: GPR, TXT

(Submitter supplied) Within the first 15 minutes of infection, herpes simplex virus 1 (HSV-1) immediate early proteins repurpose cellular RNA polymerase (Pol II) for viral transcription. An important role of the viral infected cell protein 27 (ICP27) is to facilitate viral pre-mRNA processing and export of viral mRNA to the cytoplasm. Here, we use precision nuclear run-on followed by deep sequencing (PRO-seq) to characterize transcription of a viral ICP27 null mutant. more...

Organism:

Drosophila melanogaster; Human alphaherpesvirus 1; Homo sapiens

Type:

Other

Platform:

GPL29914

12 Samples

Download data: BW

(Submitter supplied) The mechanism by which aging induces aortic aneurysm and dissection (AAD) remains unclear. A total of 430 subjects were recruited for screening of differentially expressed plasma microRNAs. We found that miR-1204 was significantly increased in both plasma and aorta of elder patients with AAD, and was positively correlated with age. Cell senescence induced the expression of miR-1204 through p53 interaction with plasmacytoma variant translocation 1, and miR-1204 induced vascular smooth muscle cell (VSMC) senescence to form a positive feedback loop. more...

Organism:

Herpesvirus saimiri (strain 11); JC polyomavirus; Human gammaherpesvirus 8; Betapolyomavirus hominis; Human alphaherpesvirus 2; human gammaherpesvirus 4; Human betaherpesvirus 6B; Betapolyomavirus macacae; Homo sapiens; Human alphaherpesvirus 1; Macacine alphaherpesvirus 1; Human betaherpesvirus 5; Human immunodeficiency virus 1; Merkel cell polyomavirus

Type:

Non-coding RNA profiling by array

Platform:

GPL21439

12 Samples

Download data: GPR, XLSX

(Submitter supplied) Excessive alcohol consumption adversely affects the immune system and triggers the activation of peripheral blood (PB) monocytes and tissue macrophages, contributing to alcohol- related organ damage. This study aimed to analyze the M1/M2 and inflammatory phenotypes of circulating monocytes and macrophage-derived monocytes (MDMs). This single-center cross- sectional study included 20 excessive alcohol drinkers (EADs) and 22 healthy controls. more...

Organism:

Murid gammaherpesvirus 4; Betapolyomavirus hominis; human gammaherpesvirus 4; JC polyomavirus; Human gammaherpesvirus 8; Betapolyomavirus macacae; Homo sapiens; Mus musculus; Human alphaherpesvirus 1; Human betaherpesvirus 5; Murid betaherpesvirus 1; Human immunodeficiency virus 1; Rattus norvegicus; Human alphaherpesvirus 2; Merkel cell polyomavirus; Mus musculus cytomegalovirus 2

Type:

Non-coding RNA profiling by array

Platform:

GPL11434

22 Samples

Download data: GPR, TXT

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

Organism:

Homo sapiens; Human alphaherpesvirus 1

Type:

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

Platforms:

GPL23890 GPL24676

72 Samples

Download data

(Submitter supplied) Herpes simplex virus replicates and forms progeny in the nucleus where it must overcome host chromatin to establish a successful infection. During lytic infection, newly formed viral capsids navigate through heterochromatin channels at the nuclear periphery to egress out of the nucleus. In uninfected cells, specific histone marks such as trimethylation on histone H3 lysine 27 (H3K27me3) and the histone variant macroH2A1 delineate heterochromatin regions, or repressed chromatin, that are predominantly located in the nuclear periphery. more...

Organism:

Homo sapiens; Human alphaherpesvirus 1

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL23890

48 Samples

Download data: BW

(Submitter supplied) Silencing of the adaptor SH3BP2 impairs Gastrointestinal stromal tumors growth through miRNAs We dissected SH3BP2 pathway in Gastrointestinal Stromal Tumor cells (GIST) performing a miRNA array in SH3BP2-silenced GIST cells

Organism:

Human alphaherpesvirus 1; Human betaherpesvirus 5; human gammaherpesvirus 4; Human betaherpesvirus 6B; Betapolyomavirus macacae; Human alphaherpesvirus 2; Betapolyomavirus hominis; Herpesvirus saimiri (strain 11); JC polyomavirus; Human immunodeficiency virus 1; Human gammaherpesvirus 8; Homo sapiens; Macacine alphaherpesvirus 1; Merkel cell polyomavirus

Type:

Non-coding RNA profiling by array

Platform:

GPL21599

12 Samples

Download data: TXT, XLSX

(Submitter supplied) SAFA showed stronger binding with HSV-1 RNA than with human RNA

Organism:

Homo sapiens; Human alphaherpesvirus 1

Type:

Other

Platform:

GPL26733

1 Sample

Download data: TXT

(Submitter supplied) Genome wide RNA-Seq screen was did to detect gene expression of HSV-1 and Hela . We constructed a HeLa cell line that stably expresses the plasmids of SAFA or SAFA-ADAR1 catalytic domain(SAFA-ADAR1cd) or SAFA-ADAR1 catalytic domain E488Q(SAFA-ADAR1cd E488Q) . The RNAs were harvested followed by RNA sequencing to identify the edited RNA.

Organism:

Homo sapiens; Human alphaherpesvirus 1

Type:

Other

Platform:

GPL26733

3 Samples

Download data: TXT

(Submitter supplied) Characterization of pluripotent states, in which cells can both self-renew or differentiate, with the irreversible loss of pluripotency, are important research areas in developmental biology. Although microRNAs (miRNAs) have been shown to be crucial for embryonic stem (ES) self-renewal maintenance and cellular differentiation, the role of miRNAs integrated into gene regulatory networks and its dynamic changes during these state transitions remain elusive. more...

Organism:

human gammaherpesvirus 4; Human gammaherpesvirus 8; Betapolyomavirus macacae; Mus musculus; Rattus norvegicus; Murid betaherpesvirus 1; JC polyomavirus; Human immunodeficiency virus 1; Merkel cell polyomavirus; Homo sapiens; Human alphaherpesvirus 1; Human betaherpesvirus 5; Betapolyomavirus hominis; Human alphaherpesvirus 2; Murid gammaherpesvirus 4

Type:

Non-coding RNA profiling by array

Platform:

GPL18658

12 Samples

Download data: TXT

(Submitter supplied) These data files consist of Illumina next seq 500 sequencing data from precision nuclear run-on and global nuclear run-on experiments conducted with human epithelial Hep2 cells that have been infected with human herpes simplex virus-1 (F) strain mutants. The results of these studies suggest that ICP22 is necessary for reducing Pol II processivity on the viral genome which results in its maintenance on the viral genome over the course of infection. more...

Organism:

Human alphaherpesvirus 1; Drosophila melanogaster; Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL29914

32 Samples

Download data: BW

(Submitter supplied) We describe the cellular response to HSV-1 infection in human iPSC-derived brain organoids

Organism:

Homo sapiens; Human alphaherpesvirus 1

Type:

Expression profiling by high throughput sequencing

6 related Platforms

40 Samples

Download data: CSV, FA, GTF, RDS, TXT

(Submitter supplied) An improved mechanistic understanding of the thyroid hormone (TH) action on bile acid (BA) synthetic pathway, the major route for cholesterol elimination, will facilitate the identification of novel therapeutic targets for hypercholesterolemia. Here, we show that hepatic miR-378 is positively regulated by TH. Transient overexpression of miR-378 in the liver of mice reduces the serum cholesterol levels, which is accompanied with an upregulation of key enzymes involved in the intrahepatic conversion of cholesterol to BAs. more...

Organism:

Rattus norvegicus; human gammaherpesvirus 4; JC polyomavirus; Human gammaherpesvirus 8; Betapolyomavirus macacae; Murid gammaherpesvirus 4; Betapolyomavirus hominis; Homo sapiens; Mus musculus; Human alphaherpesvirus 1; Human betaherpesvirus 5; Murid betaherpesvirus 1; Human immunodeficiency virus 1

Type:

Non-coding RNA profiling by array

Platform:

GPL20794

1 Sample

Download data: TXT, XLS

(Submitter supplied) In other parts of this study we identified Foxc1 as a host target of miR-138 and found that Foxc1 can promote herpes simplex virus-1 (HSV-1) replication. To understand the mechanisms of this function, we performed an RNAseq experiment comparing vector (pcDNA) and pFoxchuman transfected Neuro-2a cells. After transfection, these cells were infected with HSV-1 for 5 hours at an MOI of 1 to identify viral genes regulated by Foxc1 as well as host genes.

Organism:

Mus musculus; Human alphaherpesvirus 1

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28172

6 Samples

Download data: TXT

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

Organism:

Mus musculus; Human alphaherpesvirus 1; Homo sapiens

Type:

Expression profiling by high throughput sequencing; Other

5 related Platforms

36 Samples

Download data: TXT

(Submitter supplied) This is a part of the study that shows that a host microRNA, miR-138, represses herpes simplex virus 1 (HSV-1) gene expression through both viral and host targets. These PAR-CLIP analyses identified viral and host targets of miR-138 in Neuro-2a (mouse neuroblastoma) and 293T (human embryonic kidney) cells. We constructed two cell lines derived from Neuro-2a cells, one overexpressing miR-138 (N2A138) and one antagonizing miR-138 (N2Aanti138). more...

Organism:

Homo sapiens; Mus musculus; Human alphaherpesvirus 1

Type:

Other

Platforms:

GPL19057 GPL26236

6 Samples

Download data: TXT

(Submitter supplied) We previously showed that miR-138 can repress herpes simplex virus 1 (HSV-1) ICP0 expression by binding to ICP0 mRNA. However, in this study we found that miR-138 can also repress viral gene expression independent of ICP0. Therefore we conducted this RNAseq experiment to assess the effects of miR-138 on expression of each individual viral gene to search for other viral targets of miR-138

Organism:

Mus musculus; Human alphaherpesvirus 1

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26237

12 Samples

Download data: TXT

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

Organism:

Human alphaherpesvirus 1 strain 17; Homo sapiens

Type:

Other

4 related Platforms

28 Samples

Download data

(Submitter supplied) Primary human foreskin fibroblasts (HFF) were infected with wild-type simplex virus 1 (HSV-1) strain 17 at a multiplicity of infection (MOI) of 10. Sequencing libraries were prepared using the cRNA-seq and dRNA-seq protocol from the indicated time points of infection.

Organism:

Homo sapiens; Human alphaherpesvirus 1 strain 17

Type:

Other

4 related Platforms

18 Samples

Download data: TSV

(Submitter supplied) Primary human foreskin fibroblasts (HFF) were infected with wild-type simplex virus 1 (HSV-1) strain 17 at a multiplicity of infection (MOI) of 10. Ribosome profiling was performed at various times during infection with minor modification to the protocol described in Stern-Ginossar N et al., Science 2012. Translation start site profiling was performed by culturing cells in presence of Harringtonin or Lactimidomycin for 30 min prior to cell harvest.

Organism:

Human alphaherpesvirus 1 strain 17; Homo sapiens

Type:

Other

Platforms:

GPL26303 GPL11154

10 Samples

Download data: TSV