GEO DataSets

(Submitter supplied) DDX46 is identified to be required at the early step of pre-spliceosome assembly,but whether DDX46 could regulate antiviral transcripts isoform splicing in the nucleus remain elusive.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13112

2 Samples

Download data: XLSX

(Submitter supplied) DDX46 is identified to be required at the early step of pre-spliceosome assembly,but the potential roles of DDX46 in RNA editing and whether DDX46 could regulate antiviral innate immunity by editing antiviral transcripts in the nucleus remain elusive.

Organism:

Mus musculus

Type:

Other

Platform:

GPL13112

4 Samples

Download data: XLSX

(Submitter supplied) To investigate whether the ALKBH5-mediated metabolic changes via demethylation of its target mRNA(s) is important in regulating viral response, we mapped the targeting transcripts and binding sites of ALKBH5 in the virus infected cells and uninfected cells by using iCLIP-seq. Biological replicates of iCLIP-seq confirmed that OGDH is the direct targeting transcript of ALKBH5 and the binding capacity of ALKBH5 to OGDH mRNA was decreased upon viral infection. more...

Organism:

Mus musculus

Type:

Other

Platform:

GPL17021

4 Samples

Download data: BED

(Submitter supplied) By performing RNA sequencing (RNA-seq) analysis on the peritoneal macrophages that derived from ALKBH5-/- mice and littermate mice infected with or without vesicular stomatitis virus (VSV), we want to investigate whether deficiency of ALKBH5 controls viral replication through a more general mechanism such as enhancing innate response, and if not, what's the critical downstream target(s) of ALKBH5. RNA-seq analysis showed that mRNA expression of innate genes remained unchanged or not increased in ALKBH5-deficient cells. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21103

12 Samples

Download data: TXT

(Submitter supplied) By performing m6A-seq analysis on the peritoneal macrophages that derived from ALKBH5-/- mice and littermate mice infected with or without vesicular stomatitis virus (VSV), we want to investigate whether ALKBH5 deficiency-mediated m6A RNA methylation contributes to the regulation of its target genes expression. m6A-seq analysis revealed enriched and specific m6A peaks on the transcript of ALKBH5-targeted gene, which were substantially increased in ALKBH5-deficient peritoneal macrophages than that in wild-type cells whatever infected with or without VSV. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21103

16 Samples

Download data: BED

(Submitter supplied) All major types of interferon (IFN) efficiently inhibit hepatitis C virus (HCV) replication in vitro and in vivo. Remarkably, HCV replication is not sensitive to IFNγ in the hepatoma cell line Huh6, despite an intact signaling pathway. We performed transcriptome analyses between Huh6 and Huh-7 to identify effector genes of the IFNγ response and thereby identified the DExD/H box helicase DDX60L as a restriction factor of HCV replication. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

7 Samples

Download data: CEL

(Submitter supplied) VSV infection affects various gene expression

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13112

2 Samples

Download data: TXT

(Submitter supplied) Wild type or Elf4-/- peritoneal macrophages were infected with VSV, followed by whole genome RNA-seq analysis. 293T cells were transfected with miR-221 or empty vector, followed by whole genome RNA-seq analysis. Conclusions:Overexpression of miR-221 in cells facilitated viral infection and inhibited the production of IFNβ.

Organism:

Mus musculus; Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL13112 GPL11154

4 Samples

Download data: XLS, XLSX

(Submitter supplied) Cytosine-5 methylation (m5C) is one of the most prevalent modifications of RNA, playing important roles in RNA metabolism, nuclear export, and translation. However, the potential role of RNA m5C methylation in innate immunity remains elusive. Here we show that depletion of NSUN2, an m5C methyltransferase, significantly inhibits the replication and gene expression of a wide range of RNA and DNA viruses. more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL24676

44 Samples

Download data: XLSX

(Submitter supplied) Microarry analysis of mouse gene expression profile after transfected with miR-27a mimics (27a-7) and mimic NC (NC-9) Goal was to determine the effects of miR-27a transfection on global gene expression.

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL7202

1 Sample

Download data: TXT

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

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL18573 GPL20301

32 Samples

Download data

(Submitter supplied) The RNA modification N6-methyladenosine (m6A) regulates gene expression through various transcript-specific effects. The overall goal of these experiments was to determine the effects of the m6A methyltransferase complex proteins METTL3 and METTL14 on the expression of interferon stimulated genes. First, we depleted METTL3 and METTL14 in Huh7 cells using siRNAs and treated with Mock or IFN-β to analyze the regulatory effects of METTL3/14 on interferon-stimulated genes' transcript abundance. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL18573 GPL20301

20 Samples

Download data: TXT

(Submitter supplied) The RNA modification N6-methyladenosine (m6A) regulates gene expression through various transcript-specific effects. The goal of this experiment was to identify m6A-modified transcripts during the type I interferon response, with interest in determining which interferon-stimulated genes are modified by m6A. We found that a high percentage of ISGs are m6A-modified, and in follow-up experiments we determined the effects of m6A on the expression of interferon-stimulated genes. more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL20301

12 Samples

Download data: TXT

(Submitter supplied) N6-methyladenosine (m6A) is the most prevalent internal modification of messenger RNA (mRNA) in higher eukaryotes. Here we report ALKBH5 as a new mammalian demethylase that oxidatively removes the m6A modification in mRNA in vitro and inside cells. This demethylation activity of ALKBH5 significantly affects mRNA export and RNA metabolism as well as the assembly of mRNA processing factors in nuclear speckles. more...

Organism:

Homo sapiens; Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL11154 GPL13112

4 Samples

Download data: TXT

(Submitter supplied) Pattern recognition receptors (PRRs)-mediated innate immune responses are critical for host defense against microbial pathogens including RNA/DNA viruses. A growing number of coding genes and genes originally defined as non-coding RNAs (ncRNAs) are found to encode short peptides or proteins, named microproteins. However, the landscape of microproteins in responsive to virus infection and the functions of these microproteins remain uncharacterized. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

2 Samples

Download data: TXT

(Submitter supplied) N6-Methyladenosine (m6A) is the most prevalent internal modification in mammalian mRNAs, and participates in various fundamental bioprocesses as well as cancer. Here we immunoprecipitated m6A methylated poly (A+) RNAs (MeRIP) and then sequenced and profiled mRNA m6A methylation in P493-6 cells.

Organism:

Homo sapiens

Type:

Other

Platform:

GPL11154

3 Samples

Download data: BED

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

Organism:

Homo sapiens; Mus musculus

Type:

Other

Platforms:

GPL13112 GPL21493 GPL11154

38 Samples

Download data: TXT

(Submitter supplied) N6-methyladenosine (m6A) is a dynamic post-transcriptional RNA modification influencing all aspects of mRNA biology. Here, we examined cellular m6A epitranscriptomes during P.aeruginosa infection to identify m6A-regulated innate immune response genes with or without ALKBH5 knockdown. We showed that a significant portion of cellular genes including many innate immune response genes underwent m6A modifications in 5’UTR and 3’UTR, from which we identified common and distinct m6A-modified genes under different stimulating conditions.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21493

28 Samples

Download data: TXT

(Submitter supplied) N6-methyladenosine (m6A) is a dynamic post-transcriptional RNA modification influencing all aspects of mRNA biology. Here, we examined cellular m6A epitranscriptomes during infections of herpes simplex virus type 1 (HSV-1) and lipopolysaccharide (LPS) stimulation to identify m6A-regulated innate immune response genes. We showed that a significant portion of cellular genes including many innate immune response genes underwent m6A modifications in 5’UTR and 3’UTR, from which we identified common and distinct m6A-modified genes under different stimulating conditions.

Organism:

Homo sapiens; Mus musculus

Type:

Other

Platforms:

GPL13112 GPL11154

10 Samples

Download data: TXT