GEO DataSets

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

Organism:

Mus musculus

Type:

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

Platforms:

GPL21103 GPL19057

48 Samples

Download data: TXT

(Submitter supplied) Investigation into changes in the methylome in rapamycin and caloric restriction in aged mice.

Organism:

Mus musculus

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL21103

16 Samples

Download data: TXT

(Submitter supplied) Investigation into changes in the methylome in young (2 months) and aged (22 months) Ames dwarf (Prop1 Hom) and WT (Prop1 Het) mice

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

16 Samples

Download data: CSV

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

Organism:

Mus musculus

Type:

Methylation profiling by high throughput sequencing; Third-party reanalysis

Platforms:

GPL21103 GPL17021

549 Samples

Download data: CSV, TXT

(Submitter supplied) Human DNA-methylation data have been used to develop highly accurate biomarkers of aging ("epigenetic clocks"). Recent studies demonstrate that similar epigenetic clocks for mice (Mus Musculus) can be slowed by gold standard anti-aging interventions such as calorie restriction and growth hormone receptor knock-outs. Using DNA methylation data from previous publications with data collected in house for a total 1189 samples spanning 193,651 CpG sites, we developed 4 novel epigenetic clocks by choosing different regression models (elastic net- versus ridge regression) and by considering different sets of CpGs (all CpGs vs highly conserved CpGs). more...

Organism:

Mus musculus

Type:

Methylation profiling by high throughput sequencing; Third-party reanalysis

Download data: TXT

(Submitter supplied) Human DNA-methylation data have been used to develop highly accurate biomarkers of aging ("epigenetic clocks"). Recent studies demonstrate that similar epigenetic clocks for mice (Mus Musculus) can be slowed by gold standard anti-aging interventions such as calorie restriction and growth hormone receptor knock-outs. Using DNA methylation data from previous publications with data collected in house for a total 1189 samples spanning 193,651 CpG sites, we developed 4 novel epigenetic clocks by choosing different regression models (elastic net- versus ridge regression) and by considering different sets of CpGs (all CpGs vs highly conserved CpGs). more...

Organism:

Mus musculus

Type:

Methylation profiling by high throughput sequencing

Platforms:

GPL17021 GPL21103

549 Samples

Download data: TXT

(Submitter supplied) Background: DNA-methylation changes at a discrete set of sites in the human genome are predictive of chronological and biological age. However, it is not known whether these changes are causative or a consequence of an underlying ageing programme. It has also not been shown whether this ‘epigenetic clock’ is unique to humans or conserved in other animals such as the experimentally tractable mouse. Results: We have generated a comprehensive set of whole genome base-resolution methylation maps from multiple mouse tissues spanning a wide range of ages. more...

Organism:

Mus musculus

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL13112

62 Samples

Download data: TXT

(Submitter supplied) Background Chronological aging-associated changes in the human DNA methylome are studied by multiple epigenome-wide association studies (EWAS); however, the aging-associated DNAmet changes identified among different age groups and tissues vary and especially the rates of aging-associated alterations in the epigenome during adulthood remain unclear. Here, we further explore and characterize CpG-sites where DNA methylation levels alter at a constant rate during adulthood and are also independent of blood cell type heterogeneity. more...

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL13534

184 Samples

Download data: TXT

(Submitter supplied) Background: Genetic and epigenetic variability contributes to the susceptibility and pathogenesis of autoimmune diseases. T cells play an important role in several autoimmune conditions, including lupus, which is more common and more severe in people of African descent. To investigate inherent epigenetic differences in T cells between ethnicities, we characterized genome-wide DNA methylation patterns in naïve CD4+ T cells in healthy African-Americans and European-Americans, and then confirmed our findings in lupus patients. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL13534

66 Samples

Download data: TXT

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

Organism:

Homo sapiens

Type:

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

Platforms:

GPL10999 GPL11154

111 Samples

Download data: BED

(Submitter supplied) Chronic lymphocytic leukemia (CLL) is a biologically and clinically heterogeneous disease. The somatic hypermutation status of the immunoglobulin heavy chain variable (IGHV) genes has been identified as one of the most robust prognostic markers in CLL. Patients with unmutated IGHV status (U-CLL) typically experience an inferior outcome compared to those whose clones express mutated IGHV genes (M-CLL). more...

Organism:

Homo sapiens

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL11154

42 Samples

Download data: BED

(Submitter supplied) Chronic lymphocytic leukemia (CLL) is a biologically and clinically heterogeneous disease. The somatic hypermutation status of the immunoglobulin heavy chain variable (IGHV) genes has been identified as one of the most robust prognostic markers in CLL. Patients with unmutated IGHV status (U-CLL) typically experience an inferior outcome compared to those whose clones express mutated IGHV genes (M-CLL). more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

52 Samples

Download data: TXT

(Submitter supplied) We performed affinity-based enrichment with methyl-CpG binding domain protein followed by high-throughput sequencing (MBD-seq) to assay DNA methylation in mouse liver tissue.

Organism:

Mus musculus

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL21103

70 Samples

Download data: CSV

(Submitter supplied) DNA methylation plays an important role in development of disease and the process of aging. In this study we examine DNA methylation at 476,366 sites throughout the genome of white blood cells from a population cohort (N = 421) ranging in age from 14 to 94 years old. Age affects DNA methylation at almost one third (29%) of the sites (Bonferroni adjusted P-value <0.05), of which 60.5% becomes hypomethylated and 39.5% hypermethylated with increasing age. more...

Organism:

Homo sapiens

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL13534

732 Samples

Download data: IDAT, TXT, XLSX

(Submitter supplied) DNA methylation data for 479 women from 130 families including 66 monozygotic twin pairs, 66 dizygotic twin pairs and 215 sisters of twins.

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL13534

479 Samples

Download data: TXT

(Submitter supplied) The Illumina Infinium 27k Human DNA methylation Beadchip v1.2 was used to obtain DNA methylation profiles across approximately 27,000 CpGs in whole blood samples from 172 normal female twins. See Bell, Tsai et al. Plos Genet. 2012;8(4):e1002629.

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL8490

172 Samples

Download data: TXT

(Submitter supplied) We recently identified a novel protein, Rearranged L-myc fusion (Rlf), that is required for DNA hypomethylation (and transcriptional activity) at certain regions of the mouse genome known to be sensitive to epigenetic gene silencing. Here we report the analysis of 12 whole genome bisulphite sequencing datasets across three different embryonic tissues/stages from mice with and without Rlf. We find that its absence has effects at thousands of differentially methylated regions.

Organism:

Mus musculus

Type:

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

Platforms:

GPL13112 GPL19057

22 Samples

Download data: BW, TAB

(Submitter supplied) The impact of STAT5 on liver DNA methylation was assessed by performing RRBS analysis on male and female mouse liver with a hepatocyte-specific loss of STAT5a and STAT5b. Extensive changes in CpG-methylation were seen in STAT5-deficient liver, where sex differences were abolished at 88% of ~1,500 sex-differentially methylated regions, largely due to increased DNA methylation upon STAT5 loss. STAT5-dependent CpG-hypomethylation was rarely found at proximal promoters of STAT5-dependent genes. more...

Organism:

Mus musculus

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL17021

23 Samples

Download data: XLSX

(Submitter supplied) rRNA-depleted RNA isolated from livers of control male and female mice and from male mice with hepatocyte-specific STAT5ab-KO was analyzed by RNA-seq. This study revealed a substantial, albeit incomplete loss of liver sex bias in hepatocyte-specific STAT5a/STAT5b (collectively, STAT5)-deficient mouse liver. Notably, in male liver, many male-biased genes were down regulated in direct association with the loss of STAT5 binding; many female-biased genes, which show low STAT5 binding, were de-repressed, indicating an indirect mechanism for repression by STAT5. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

8 Samples

Download data: XLSX

(Submitter supplied) Age predictors based on DNA methylation levels at a small set of CpG sites, DNAm clocks, have been developed for humans and extended to several other species. Three currently available versions of mouse DNAm clocks were either created for individual tissues or tuned towards young ages. Here, we constructed a robust multi-tissue age predictor based on 435 CpG sites, which covers the entire mouse lifespan and remains unbiased with respect to any particular age group. more...

Organism:

Mus musculus

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL21273

81 Samples

Download data: COV