GEO DataSets

(Submitter supplied) Epitranscriptomic RNA modifications have emerged as important regulators of the fate and function of both cellular and viral RNAs. One prominent modification, the cytidine methylation 5-methylcytidine (m5C), is found on the RNA of HIV-1, where m5C enhances the translation and splicing of HIV-1 RNA. However, whether m5C functionally enhances the RNA of other pathogenic viruses remain elusive. Here, we report that the RNA of hepatitis B virus (HBV) is enriched with a high level of m5C, mediated mainly through the cellular methyltransferase NSUN2. more...

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL18573

1 Sample

Download data: BED

(Submitter supplied) We studied the DNA methylation profiles of 93 LBCL cases: Diffuse large B-cell lymphoma not otherwise specified (DLBCL, n=66), High-grade B-cell lymphoma (n=7), Primary CNS lymphoma (n=8), and transformation of indolent B-cell lymphoma (n=12). One sample of normal GC B-cells from tonsils was included as a control. LBCL cases had a particularly aberrant semimethylated pattern with large intertumor variation and overall low hypermethylation. more...

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL23976

97 Samples

Download data: IDAT, TXT

(Submitter supplied) Epitranscriptomic RNA modifications have emerged as important regulators of the fate and function of both cellular and viral RNAs. One prominent modification, the cytidine methylation 5-methylcytidine (m5C), is found on the RNA of HIV-1, where m5C enhances the translation and splicing of HIV-1 RNA. However, whether m5C functionally enhances the RNA of other pathogenic viruses remain elusive. Here, we report that the RNA of hepatitis B virus (HBV) is enriched with a high level of m5C, mediated mainly through the cellular methyltransferase NSUN2. more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL18573

2 Samples

Download data: BED

(Submitter supplied) Epitranscriptomic RNA modifications have emerged as important regulators of the fate and function of both cellular and viral RNAs. One prominent modification, the cytidine methylation 5-methylcytidine (m5C), is found on the RNA of HIV-1, where m5C enhances the translation and splicing of HIV-1 RNA. However, whether m5C functionally enhances the RNA of other pathogenic viruses remain elusive. Here, we report that the RNA of hepatitis B virus (HBV) is enriched with a high level of m5C, mediated mainly through the cellular methyltransferase NSUN2. more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL16791

2 Samples

Download data: BED

(Submitter supplied) Epitranscriptomic RNA modifications have emerged as important regulators of the fate and function of both cellular and viral RNAs. One prominent modification, the cytidine methylation 5-methylcytidine (m5C), is found on the RNA of HIV-1, where m5C enhances the translation and splicing of HIV-1 RNA. However, whether m5C functionally enhances the RNA of other pathogenic viruses remain elusive. Here, we report that the RNA of hepatitis B virus (HBV) is enriched with a high level of m5C, mediated mainly through the cellular methyltransferase NSUN2. more...

Organism:

Homo sapiens

Type:

Other

Platforms:

GPL16791 GPL18573

4 Samples

Download data: BED

(Submitter supplied) Epitranscriptomic RNA modifications have emerged as important regulators of the fate and function of both cellular and viral RNAs. One prominent modification, the cytidine methylation 5-methylcytidine (m5C), is found on the RNA of HIV-1, where m5C enhances the translation and splicing of HIV-1 RNA. However, whether m5C functionally enhances the RNA of other pathogenic viruses remain elusive. Here, we report that the RNA of hepatitis B virus (HBV) is enriched with a high level of m5C, mediated mainly through the cellular methyltransferase NSUN2. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

2 Samples

Download data: BED

(Submitter supplied) We did whole-genome methylation sequencing for 21 Vaccinium samples. This project attempts to analyze the improvement breeding process of cultivated blueberry from two aspects of heredity and epigenetic inheritance.

Organism:

Vaccinium corymbosum; Vaccinium darrowii

Type:

Methylation profiling by high throughput sequencing; Expression profiling by high throughput sequencing

Platforms:

GPL33280 GPL33769

36 Samples

Download data: BW, CGMAP

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

Organism:

Homo sapiens

Type:

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

Platforms:

GPL16791 GPL18573

11 Samples

Download data: BED

(Submitter supplied) We designed and introduced a new methylation array concentrating on human trait screening and discovery. The new MSA (Methylation Screening Array) leveraged the massive Infinium platform-based data from epigenome-wide association studies, combined with updated knowledge from the latest single cell and cell type-resolution whole genome methylome profiles, to achieve scalable screening of epigenetics-trait association in an ultra-high sample-throughput. more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL24676

3 Samples

Download data: BEDGRAPH

(Submitter supplied) Background: Chronic stress significantly contributes to mood- and anxiety disorders. Previous data suggest a correlative connection between vitamin B12 supplementation, depression, and stress resilience. However, the underlying mechanisms are still poorly understood. Methods: Using the chronic variable stress mouse model coupled with RNA-sequencing, we determined vitamin B12-induced transcriptional changes related to stress resilience. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

16 Samples

Download data: TSV

(Submitter supplied) We performed an epigenome-wide association study (EWAS) of allergic sensitization using nasal epithelial cell DNA from 474 subjects.

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL32946

474 Samples

Download data: IDAT, TXT

(Submitter supplied) Arginine methylation is catalyzed by protein arginine methyltransferases (PRMTs) and is involved in various cellular processes, including cancer development. PRMT2 expression is increased in several cancer types although its role in acute myeloid leukemia (AML) remains unknown. Here, we investigate the role of PRMT2 in a cohort of patients with AML, PRMT2 knockout AML cell lines as well as a Prmt2 knockout mouse model. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

9 Samples

Download data: TAB, TSV

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

Organism:

Homo sapiens

Type:

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

Platforms:

GPL16791 GPL17692

27 Samples

Download data: BW, CEL, NARROWPEAK

(Submitter supplied) Epithelial cells are the first point of contact for bacteria entering the respiratory tract. Streptococcus pneumoniae is an obligatory human pathobiont of the nasal mucosa, carried asymptomatically but also the cause of severe pneumoniae. The role of the epithelium in maintaining homeostatic interactions or mounting an inflammatory response to invasive S. pneumoniae is currently poorly understood. However, studies have shown that chromatin modifications, at the histone level, induced by bacterial pathogens interfere with the host transcriptional program and promote infection. In this study, we demonstrate that S. pneumoniae actively induces di-methylation of histone H3 on lysine 4 (H3K4me2), which persists for at least 9 days upon clearance of bacteria with antibiotics. We show that infection establishes a unique epigenetic program affecting the transcriptional response of epithelial cells, rendering them more permissive upon secondary infection. Our results establish H3K4me2 as a unique modification induced by infection, distinct from H3K4me3, which localizes to enhancer regions genome-wide. Therefore, this study reveals evidence that bacterial infection leaves a memory in epithelial cells after bacterial clearance, in an epigenomic mark, thereby altering cellular responses for subsequent infections.

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL16791

15 Samples

Download data: BW, NARROWPEAK

(Submitter supplied) Epithelial cells are the first point of contact for bacteria entering the respiratory tract. Streptococcus pneumoniae is an obligatory human pathobiont of the nasal mucosa, carried asymptomatically but also the cause of severe pneumoniae. The role of the epithelium in maintaining homeostatic interactions or mounting an inflammatory response to invasive S. pneumoniae is currently poorly understood. However, studies have shown that chromatin modifications, at the histone level, induced by bacterial pathogens interfere with the host transcriptional program and promote infection. In this study, we demonstrate that S. pneumoniae actively induces di-methylation of histone H3 on lysine 4 (H3K4me2), which persists for at least 9 days upon clearance of bacteria with antibiotics. We show that infection establishes a unique epigenetic program affecting the transcriptional response of epithelial cells, rendering them more permissive upon secondary infection. Our results establish H3K4me2 as a unique modification induced by infection, distinct from H3K4me3, which localizes to enhancer regions genome-wide. Therefore, this study reveals evidence that bacterial infection leaves a memory in epithelial cells after bacterial clearance, in an epigenomic mark, thereby altering cellular responses for subsequent infections. Transcriptome analysis aimed at testing whether cells respond differently in the primary (1°) and secondary (2°) infection. Differential gene expression and gene set enrichment analysis performed.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL17692

12 Samples

Download data: CEL

(Submitter supplied) Advances in next generation sequencing have expanded our understanding of the molecular drivers of prostate cancer progression from curable androgen-sensitive disease to metastatic castration-resistant prostate cancer (mCRPC). The focus to date has been on the linear genome, but the impact of variations in the 3D structure of the genome on tumor development and progression has been increasingly recognized. more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL24676

80 Samples

Download data: MATRIX

(Submitter supplied) To identify a set of methylation biomarkers capable of reliably distinguishing breast cancer patients from healthy controls, we performed DNA methylation profiling on germline DNA from peripheral blood samples for a predominantly Asian population comprising 256 ethnic Chinese breast cancer patients recruited from genetic testing clinics and 268 age- and ethnicity-matched non-cancer controls.

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL21145

524 Samples

Download data: IDAT, TSV

(Submitter supplied) Eukaryotes employ a set of conserved transcription elongation factors to modulate the behavior of RNA polymerase II (RNAPII). Disruptions of one such factor, the Paf1 complex (Paf1C), generate subunit-specific phenotypes, including distinct changes to co-transcriptional histone modifications. How individual Paf1C subunits impact transcription and coupled processes remains ambiguous. By comparing conditional depletion and steady-state deletion of Paf1C subunits, we determine direct and indirect contributions of Paf1C to gene expression in Saccharomyces cerevisiae. more...

Organism:

Saccharomyces cerevisiae; Schizosaccharomyces pombe

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28173

12 Samples

Download data: BW

(Submitter supplied) Eukaryotes employ a set of conserved transcription elongation factors to modulate the behavior of RNA polymerase II (RNAPII). Disruptions of one such factor, the Paf1 complex (Paf1C), generate subunit-specific phenotypes, including distinct changes to co-transcriptional histone modifications. How individual Paf1C subunits impact transcription and coupled processes remains ambiguous. By comparing conditional depletion and steady-state deletion of Paf1C subunits, we determine direct and indirect contributions of Paf1C to gene expression in Saccharomyces cerevisiae. more...

Organism:

Saccharomyces cerevisiae; Kluyveromyces lactis

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL34174

16 Samples

Download data: BW

(Submitter supplied) Eukaryotes employ a set of conserved transcription elongation factors to modulate the behavior of RNA polymerase II (RNAPII). Disruptions of one such factor, the Paf1 complex (Paf1C), generate subunit-specific phenotypes, including distinct changes to co-transcriptional histone modifications. How individual Paf1C subunits impact transcription and coupled processes remains ambiguous. By comparing conditional depletion and steady-state deletion of Paf1C subunits, we determine direct and indirect contributions of Paf1C to gene expression in Saccharomyces cerevisiae. more...

Organism:

Saccharomyces cerevisiae; Schizosaccharomyces pombe

Type:

Other

Platform:

GPL28173

50 Samples

Download data: BW