GEO DataSets

(Submitter supplied) Purpose: to compare different Methyl Binding Domain (MBD) based kits for DNA-methylation sequencing using Reduced Representation Bisulfite Sequencing (RRBS) data for validation, and to determine whether data quality can also be derived from inherent sequence data characteristics

Organism:

Homo sapiens

Type:

Methylation profiling by high throughput sequencing

Platforms:

GPL10999 GPL11154

18 Samples

Download data: TXT

(Submitter supplied) Methylome-wide association studies (MWAS) are typically performed using microarray technologies that assay only a very small fraction of the CG methylome and entirely miss two forms of methylation that are common in brain and likely of particular relevance for neuroscience and psychiatric disorders. The alternative is the use whole genome bisulfite sequencing, but this approach is not yet practically feasible with the sample sizes required for adequate statistical power. more...

Organism:

Homo sapiens

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL18573

26 Samples

Download data: CSV, TAR

(Submitter supplied) DNA methylation in CpG context is fundamental to the epigenetic regulation of gene expression in high eukaryotes. Disorganization of methylation status is implicated in many diseases, cellular differentiation, imprinting, and other biological processes. Techniques that enrich for biologically relevant CpG-rich genomic regions are desired since, depending on the size of an oragnism's methylome, the depth of sequencing required to cover all CpGs can be prohibitively expensive. more...

Organism:

Homo sapiens

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL16791

7 Samples

Download data: TXT

(Submitter supplied) DNA methylation analysis of 68 glioblastoma specimen of patients treated within clinical trials, 5 samples of normal brain tissue (non-tumor brain) and 4 tumor-derived glioma sphere lines. The data was used to identify changes in DNA methylation which contribute to the aberrant of expression of HOX transcription factors. Our group had previously demonstrated that expression of HOX genes was associated with increased resistance to chemo-radiotherapy and worse outcome in GBM patients Keywords: Disease state comparison

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL13534

77 Samples

Download data: IDAT

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

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array; Methylation profiling by high throughput sequencing

Platforms:

GPL21145 GPL24676

16 Samples

Download data: COV, IDAT

(Submitter supplied) Background: Epigenome-wide association studies (EWAS) have been widely applied to identify methylation CpG sites associated with human disease. To date, the Infinium Methylation EPIC array (EPIC) is commonly used for high-throughput DNA methylation profiling. However, the EPIC array covers only 30% of the human methylome. Methylation Capture bisulfite sequencing (MC-seq) captures target regions of methylome and has advantages of extensive coverage in the methylome at an affordable price. more...

Organism:

Homo sapiens

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL24676

12 Samples

Download data: COV

(Submitter supplied) Background: Epigenome-wide association studies (EWAS) have been widely applied to identify methylation CpG sites associated with human disease. To date, the Infinium Methylation EPIC array (EPIC) is commonly used for high-throughput DNA methylation profiling. However, the EPIC array covers only 30% of the human methylome. Methylation Capture bisulfite sequencing (MC-seq) captures target regions of methylome and has advantages of extensive coverage in the methylome at an affordable price. more...

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL21145

4 Samples

Download data: IDAT, TXT

(Submitter supplied) Here, we report an enrichment-based ultra-low input cfDNA methylation profiling method using methyl-CpG binding proteins capture, termed cfMBD-seq. We optimized the conditions of cfMBD capture by adjusting the amount of MethylCap protein along with using methylated filler DNA. Our data showed that cfMBD-seq performs equally to the standard MBD-seq (>1000 ng input) even when using 1 ng DNA as the input. more...

Organism:

Homo sapiens

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL21697

43 Samples

Download data: TXT, WIG, XLSX

(Submitter supplied) Methylated DNA enrichment is a key step in a microarray based genome-wide methylation profiling study, and even for future high-throughput sequencing based methylome analysis. In order to evaluate the sensitivity and accuracy of methylated DNA enrichment, we investigated and optimized a number of important parameters to improve the performance of several enrichment assays, including differential methylation hybridization (DMH), microarray-based methylation assessment of single samples (MMASS), and methylated DNA immunoprecipitation (MeDIP). more...

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL9952

17 Samples

Download data: LSR

(Submitter supplied) Using 1 melanocyte and 6 melanoma cell line (3 pair of primary and metastatic), we generated base-resolution DNA methylation maps to document DNA methylation drivers of melanoma metastasis.

Organism:

Homo sapiens

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL16791

7 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; Expression profiling by array

Platforms:

GPL570 GPL10999

24 Samples

Download data: BED, CEL, WIG

(Submitter supplied) 8 neuroblastoma (NB) cell lines (CLB-GA, IMR-32, SH-SY5Y, N206, CHP-902R, LAN-2, SK-N-AS, SJNB-1) their methylome is determined by sequencing after MBD2-capture using MethylCollector (ActiveMotif)

Organism:

Homo sapiens

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL10999

8 Samples

Download data: BED, WIG

(Submitter supplied) 8 neuroblastoma (NB) cell lines (CLB-GA, IMR-32, SH-SY5Y, N206, CHP-902R, LAN-2, SK-N-AS, SJNB-1) were profiled on the Affymetrix HGU-133plus2,0 platform before and after treatment with DAC (2'-deoxy-5-azacytidine) to investigate the influence on expression after inhibiting DNA-methylation

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

16 Samples

Download data: CEL

(Submitter supplied) This study aimed at identifying a methylation signature for a hypermethylation phenotype in endometrial cancer. Specifically, this data set consisting of 9 primary endometrial cancer tissue samples was investigated with a Illumina Infinium 450k Human Methylation Beadchip in order to technically validate the findings from the larger MethylCap-Seq study deposited in BioProject PRJNA360573.

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL13534

9 Samples

Download data: IDAT, TSV

(Submitter supplied) We applied the solution hybrid selection approach to the enrichment of CpG islands (CGIs) and promoter sequences from the human genome for targeted high-throughput bisulfite sequencing. A single lane of Illumina sequences allowed accurate and quantitative analysis of 1 million CpGs in more than 21,408 CGIs and 15,946 transcriptional regulatory regions. More than 85% of capture probes successfully yielded quantitative DNA methylation information of targeted regions. more...

Organism:

Homo sapiens

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL10999

8 Samples

Download data: TXT

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

Organism:

Canis lupus familiaris

Type:

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

Platform:

GPL25760

6 Samples

Download data

(Submitter supplied) MethylCap-seq was performed to characterize the genome-wide DNA methylation in CLBL-1 8.0, a doxorubicin-resistant cDLBCL cell line, and CLBL-1 as control, and aimed to investigate underlying mechanisms of doxorubicin resistance in cDLBCL. Strong difference in methylation pattern of both promoter and gene-body regions was detected between CLBL-1 8.0 and CLBL-1. Methylated peaks with fold-change greater than 4 and a P value of less than 0.01 were defined as differentially methylated regions (DMRs); there were a total of 20289 hypermethylated and 38362 hypomethylated DMRs detected. more...

Organism:

Canis lupus familiaris

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL25760

4 Samples

Download data: XLSX

(Submitter supplied) To analyze the biological relevance of methylation changes, gene expression from both CLBL-1 and CLBL-1 8.0, a doxorubicin-resistanct cDLBCL cell line, were examined. In total, we obtained 24.8 M and 23.7 M sequence reads for CLBL-1 and CLBL-1 8.0, respectively. After filtering out low-quality bases and reads from the datasets prior to read mapping, 19.8 M reads for CLBL-1 and 19.1 M reads for CLBL-1 8.0 were mapped to canine genome. more...

Organism:

Canis lupus familiaris

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25760

2 Samples

Download data: XLSX

(Submitter supplied) Lung macrophages are major participants in the pulmonary innate immune response. In the cystic fibrosis (CF) lung, the inability of lung macrophages to successfully regulate the exaggerated inflammatory response suggests dysfunctional innate immune cell function. In this study, we aim to gain insight into innate immune cell dysfunction in CF by investigating alterations in DNA methylation in bronchoalveolar lavage (BAL) cells, composed primarily of lung macrophages of CF subjects compared with healthy controls. more...

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL21145

16 Samples

Download data: IDAT

(Submitter supplied) To better characterize smoking–associated methylation changes in whole blood, we used Illumina HumanMethylation450 BeadChip to assess DNA samples from current (SM, n=172) and never smokers (NS, n=81).

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL13534

253 Samples

Download data: IDAT, TXT