GEO DataSets

(Submitter supplied) Bisulfite-seq data sets were generated for peripheral blood lymphocyte (PBL) and hair follicle (HF) DNA from each of two healthy males.

Organism:

Homo sapiens

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL11154

4 Samples

Download data: TXT

(Submitter supplied) Purpose: we aimed to gain a genome-wide view of the dynamics in DNA methylation inheritance and define the factors associated with methylation fidelity. Methods: Using mouse embryonic stem cell (ES-E14TG2a) in both undifferentiated and differentiated states as a model system, we exploited the hairpin bisulfite sequencing approach to generate methylation data for DNA double strands simultaneously at single-base resolution. more...

Organism:

Mus musculus

Type:

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

Platform:

GPL13112

4 Samples

Download data: TXT

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

Organism:

Homo sapiens

Type:

Methylation profiling by high throughput sequencing; Methylation profiling by array

4 related Platforms

53 Samples

Download data: IDAT, TXT

(Submitter supplied) We systematically evaluated alternate strategies for WGBS studies, taking into account opportunites around library preparation methods, sequencing platforms and analysis pipeline optimization. We also assessed the performance and precision of the WGBS method relative to the methylation arrays, in an effort to provide data-driven recommendations for future WGBS studies, in particularly with respect to minimum coverage.

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platforms:

GPL13534 GPL23976

12 Samples

Download data: IDAT, TXT

(Submitter supplied) We systematically evaluated alternate strategies for WGBS studies, taking into account opportunites around library preparation methods, sequencing platforms and analysis pipeline optimization. We also assessed the performance and precision of the WGBS method relative to the methylation arrays, in an effort to provide data-driven recommendations for future WGBS studies, in particularly with respect to minimum coverage.

Organism:

Homo sapiens

Type:

Methylation profiling by high throughput sequencing

Platforms:

GPL24676 GPL20795

41 Samples

Download data: TXT

(Submitter supplied) DNA methylation data generated by the Illumina Mouse Methylation Beadchip for comparison to WGBS

Organism:

Mus musculus

Type:

Methylation profiling by array

Platform:

GPL31950

35 Samples

Download data: CSV, IDAT

(Submitter supplied) Methylation of DNA is an essential epigenetic mark in mammals, intimately involved in gene regulation. The extent to which genetics, sex, and life experience influence genomic DNA methylation patterns are matters of intense current interest. We addressed this issue by intercrossing inbred mouse strains and analyzing DNA methylation at the base-pair level across the genome in somatic tissue from parents and from age-matched offspring of multiple families. more...

Organism:

Mus musculus

Type:

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

Platforms:

GPL24247 GPL13112

36 Samples

Download data: BIGWIG, TXT

(Submitter supplied) Sexual dimorphism of gene expression is commonly observed in mammalian tissues, including liver. To assess sexual dimorphisms in gene expression, we profiled the transcriptome of liver tissue from 20-week old male and female mice of the C57BL/6N (B6) and C3H/HeN (C3) inbred mouse strains using RNA-seq. These two inbred mouse strains exhibit phenotypic differences in liver biology, as they are at opposite ends of the spectrum of spontaneous hepatocellular carcinoma incidence; C3 mice are highly susceptible to develop spontaneous liver tumors as a function of age, while B6 mice are extremely resistant. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

20 Samples

Download data: TXT

(Submitter supplied) We present a multi-platform assessment and a global resource for epigenetics research from the FDA's Epigenomics Quality Control (EpiQC) Group. The study design leverages seven human cell lines that are designated as reference materials and publicly available from the National Institute of Standards and Technology (NIST) and Genome in a Bottle (GIAB) consortium. These samples were subject to a variety of genome-wide methylation interrogation approaches across six independent laboratories, with a primary focus on 5-methylcytosine modifications.

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL23976

30 Samples

Download data: IDAT, TXT

(Submitter supplied) We present a multi-platform assessment and a global resource for epigenetics research from the FDA's Epigenomics Quality Control (EpiQC) Group. The study design leverages seven human cell lines that are designated as reference materials and publicly available from the National Institute of Standards and Technology (NIST) and Genome in a Bottle (GIAB) consortium. These samples were subject to a variety of genome-wide methylation interrogation approaches across six independent laboratories, with a primary focus on 5-methylcytosine modifications.

Organism:

Homo sapiens

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL24676

106 Samples

Download data: BEDGRAPH

(Submitter supplied) DNA methylation stabilizes developmentally programmed gene expression states. Aberrant methylation is associated with disease progression and is a common feature of cancer genomes. Presently, few methods enable quantitative, large-scale, single-base resolution mapping of DNA methylation states in desired regions of a complex mammalian genome. Here, we present an approach that combines array-based hybrid selection and massively parallel bisulfite sequencing to profile DNA methylation in genomic regions spanning hundreds of thousands of bases. more...

Organism:

Homo sapiens

Type:

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

Platform:

GPL9115

4 Samples

Download data: BED, TXT

(Submitter supplied) Whole Genome Bisulfite Sequencing (WGBS) is the current standard for DNA methylation profiling; however, WGBS is costly as it requires sequencing coverage over the entire genome. Here we introduce Anchor-Based Bisulfite Sequencing (ABBS). We show that ABBS captures accurate DNA methylation information in Escherichia coli and mammalian cells, while requiring approximately 20 times fewer sequencing reads than WGBS. more...

Organism:

Homo sapiens; Escherichia coli

Type:

Methylation profiling by high throughput sequencing

Platforms:

GPL21222 GPL18573

15 Samples

Download data: BEDGRAPH, BW

(Submitter supplied) DNA methylation is a defining feature of mammalian cellular identity and is essential for normal development. Most cell types, except germ cells and pre-implantation embryos, display relatively stable DNA methylation patterns, with 70-80% of all CpGs being methylated. Despite recent advances we still have a too limited understanding of when, where and how many CpGs participate in genomic regulation. more...

Organism:

Homo sapiens

Type:

Third-party reanalysis; Methylation profiling by high throughput sequencing

Platform:

GPL11154

8 Samples

Download data: BED, TXT

(Submitter supplied) Differentiation of human embryonic stem cells (hESCs) provides a unique opportunity to study the epigenetic mechanisms that facilitate cellular transitions in a human context. To that end, we performed comprehensive transcriptional and epigenetic profiling of early populations derived through directed differentiation of hESCs representing each of the three embryonic germ layers. Integration of whole genome bisulfite sequencing, chromatin immunoprecipitation-sequencing and RNA-Sequencing reveals unique events associated with specification towards each lineage. more...

Organism:

Homo sapiens

Type:

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

Platforms:

GPL11154 GPL16791

10 Samples

Download data: BED, GTF

(Submitter supplied) Bisulfite sequencing is a valuable tool for mapping the position of 5-methylcytosine in the genome at single base resolution. However, the associated chemistry renders the majority of DNA fragments unsequenceable, thus necessitating PCR amplification. Furthermore, bisulfite conversion generates an A,T-rich DNA library that leads to major PCR biases that may confound methylation analysis. Here we report a method that enables accurate methylation analysis, by rebuilding the damaged DNA library after bisulfite treatment. more...

Organism:

Plasmodium berghei ANKA

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL19670

5 Samples

Download data: TXT

(Submitter supplied) Genome-wide DNA methylation mapping uncovers epigenetic changes associated with animal development, environmental adaptation, and species evolution. To address the lack of high-throughput methods for studying DNA methylation in non-model organisms, we developed an integrated approach for studying DNA methylation differences without a reference genome. Experimentally, our method relies on an optimized 96-well protocol for reduced representation bisulfite sequencing (RRBS), which we have validated in nine species (human, mouse, rat, cow, dog, chicken, zebrafish, carp, and sea bass). more...

Organism:

Cyprinus carpio; Bos taurus; Homo sapiens

Type:

Methylation profiling by high throughput sequencing

Platforms:

GPL11154 GPL15749 GPL15136

44 Samples

Download data: BED, FA

(Submitter supplied) LiBis is a novel method for low-input WGBS data alignment. By dynamically clipping initially unmapped reads and remapping clipped fragments, we judiciously rescued those reads and uniquely aligned them to the genome. By substantially increasing the mapping ratio by up to 88%, LiBis improves the number of informative CpGs and the precision to quantify the methylation status of individual CpG sites. The high sensitivity and cost effectiveness afforded by LiBis for low-input samples will allow the discovery of genetic and epigenetic features suitable for downstream analysis and biomarker identification using liquid biopsy.

Organism:

Homo sapiens

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL24676

4 Samples

Download data: BW

(Submitter supplied) DNA methylation plays critical roles in gene regulation and cellular specification without altering DNA sequences. The wide application of reduced representation bisulfite sequencing (RRBS) and whole genome bisulfite sequencing (bis-seq) opens the door to study DNA methylation at single CpG site resolution. One challenging question is how best to test for significant methylation differences between groups of biological samples in order to minimize false positive findings. more...

Organism:

Homo sapiens

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL11154

8 Samples

Download data: TXT

(Submitter supplied) In the study of DNA methylation, genetic variation between species, strains, or individuals can result in CpG sites that are exclusive to a subset of samples, and insertions and deletions can rearrange the spatial distribution of CpGs. How to account for this variation in an analysis of the interplay between sequence variation and DNA methylation is not well understood, especially when the number of CpG differences between samples is large. more...

Organism:

Mus musculus

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL13112

8 Samples

Download data: TXT

(Submitter supplied) This dataset demonstrates scTAM-seq, a method for profiling the methylation state of up to 600 CpGs in 10,000 cells with dropout rates of <7%. Besides CpG methylation, scTAM-seq also profiles the expression of select surface proteins in the same cells. We provide for each sample separate protein and methylation fastq and csv files. Here, scTAM-seq was applied to B cells from human peripheral blood and bone marrow.

Organism:

Homo sapiens

Type:

Methylation profiling by high throughput sequencing; Other

Platform:

GPL24676

7 Samples

Download data: CSV, TSV