GEO DataSets

(Submitter supplied) Methylation of CpG islands is associated with transcriptional repression and, in cancer, leads to the abnormal silencing of tumor-suppressor genes. We developed a novel and robust technique that allows the unbiased, genome wide detection of CpG-methylation in limited DNA samples, without applying methylation-sensitive restriction endonucleases or bisulfite-treatment. The approach is based on a recombinant, methyl-CpG binding protein that efficiently binds CpG-methylated DNA depending on its degree of CpG methylation. more...

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL2040

10 Samples

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(Submitter supplied) Methylation of CpG islands is associated with transcriptional repression and, in cancer, leads to the abnormal silencing of tumor-suppressor genes. Genome wide methylation profiling of myeloid leukemia cell lines identified a large number of genes with aberrantly methylated CpG islands. Comparative mRNA expression analysis suggests that more than half of these genes show extremely low or absent expression in normal cells, suggesting that hypermethylation in cancer may be independent of the transcriptional status of the affected gene. more...

Organism:

Homo sapiens

Type:

Expression profiling by array; Methylation profiling by array

Dataset:

GDS2251

Platform:

GPL570

4 Samples

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Comparison of myeloid leukemia cells to normal monocytes. Transcriptional status of each gene compared to its CpG methylation state. The methylation of CpG islands is associated with transcriptional repression and, in cancer, leads to the abnormal silencing of tumor suppressor genes.

Organism:

Homo sapiens

Type:

Expression profiling by array, count, 4 cell line, 2 disease state sets

Platform:

GPL570

Series:

GSE3280

4 Samples

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(Submitter supplied) To globally define methylation-’prone’ and -’protected’ CpG islands in colorectal carcinoma we analyzed the methylation status of 23,000 CpG islands of the human genome in ten coleorectal carcinoma samples as well as normal colon using our previously described methyl-CpG immunoprecipitation (MCIp) technique (Gebhard et al. 2006; Schilling and Rehli 2007). This method enriches for highly CpG methylated DNA that can be directly applied to fluorescent labeling and oligonucleotide microarray hybridization without an additional amplification step. more...

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array; Genome variation profiling by genome tiling array

Platform:

GPL8544

10 Samples

Download data: TXT

(Submitter supplied) To globally define methylation-’prone’ and -’protected’ CpG islands in leukemia, we analyzed the methylation status of 23,000 CpG islands of the human genome in eight acute leukemia samples as well as normal blood monocytes using our previously described methyl-CpG immunoprecipitation (MCIp) technique (Gebhard et al. 2006; Schilling and Rehli 2007). This method enriches for highly CpG methylated DNA that can be directly applied to fluorescent labeling and oligonucleotide microarray hybridization without an additional amplification step. more...

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array; Genome variation profiling by genome tiling array

Platform:

GPL8544

8 Samples

Download data: TXT

(Submitter supplied) To globally define methylation-’prone’ and -’protected’ CpG islands in leukemia, we analyzed the methylation status of 23,000 CpG islands of the human genome in two acute leukemia cell lines as well as normal blood monocytes using our previously described methyl-CpG immunoprecipitation (MCIp) technique (Gebhard et al. 2006; Schilling and Rehli 2007). This method enriches for highly CpG methylated DNA that can be directly applied to fluorescent labeling and oligonucleotide microarray hybridization without an additional amplification step. more...

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL8544

6 Samples

Download data: TXT

(Submitter supplied) To study the correlation between sequence motif appearance, transcription factor binding and aberrant hypermethylation in the cell lines, we performed ChIP-on-chip analyses (on CpG island microarrays) for the transcription factors Sp1, NRF1 and YY1 in normal peripheral blood monocytes. Keywords: ChIP-on-Chip; comparative genomic hybridization

Organism:

Homo sapiens

Type:

Genome variation profiling by genome tiling array

Platform:

GPL8544

6 Samples

Download data: TXT

(Submitter supplied) Transcriptome analysis of freshly sorted human CD34+ hematopoietic progenitor cells, human CD14+ peripheral blood monocytes and the human cell line U937 Keywords: one-color based gene expression

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6480

6 Samples

Download data: TXT

(Submitter supplied) Understanding cell-type-specific epigenetic codes on a global level is a major challenge after the sequencing of the human genome has been completed. Here we applied methyl-CpG immunoprecipitation (MCIp) to obtain comparative methylation profiles of coding and noncoding genes in three human tissues, testis, brain, and monocytes. Forty-four mainly testis-specific promoters were independently validated using bisulfite sequencing or single-gene MCIp, confirming the results obtained by the MCIp microarray approach. more...

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platforms:

GPL4089 GPL4090

8 Samples

Download data: TIFF, TXT

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

Organism:

Homo sapiens

Type:

Expression profiling by array; Methylation profiling by genome tiling array

Platforms:

GPL2040 GPL16100

45 Samples

Download data: CEL, GPR

(Submitter supplied) Genome-wide expression and methylation profiling identifies novel targets with aberrant hypermethylation and reduced expression in low-risk myelodysplastic syndromes (MDSs). Gene expression profiling signatures may be used to classify the subtypes of Myelodysplastic syndrome (MDS) patients. However, there are few reports on the global methylation status in MDS. The integration of genome-wide epigenetic regulatory marks with gene expression levels would provide additional information regarding the biological differences between MDS and healthy controls. more...

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL2040

20 Samples

Download data: GPR

(Submitter supplied) Genome-wide expression and methylation profiling identifies novel targets with aberrant hypermethylation and reduced expression in low-risk myelodysplastic syndromes (MDSs). Gene expression profiling signatures may be used to classify the subtypes of Myelodysplastic syndrome (MDS) patients. However, there are few reports on the global methylation status in MDS. The integration of genome-wide epigenetic regulatory marks with gene expression levels would provide additional information regarding the biological differences between MDS and healthy controls. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL16100

25 Samples

Download data: CEL

(Submitter supplied) Efficient and sustained knockdown of DNMT1 transcript and protein was achieved using a consecutive transfection protocol in the mouse pituitary adenoma cell line, AtT-20. Genome wide microarray analysis identified 91 transcripts that were significantly differentially expressed relative to cells treated with a non-targeting control. Keywords: Differential expression

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL1261

6 Samples

Download data: CEL, CHP

(Submitter supplied) We found frequent epigenetic silencing of microRNA-34b/c in human colorectal cancer. Introduction of miR-34b/c into a colorectal cancer cell line induced significant changes in gene expression profile. We also found overlap between the genes downregulated by miR-34b/c and those downregulated by DAC. Keywords: dose response

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL4133

5 Samples

Download data: TXT

(Submitter supplied) CpG island promoter hypermethylation of tumor suppressor genes is a common hallmark of human cancer, and new large-scale epigenomic technologies might be useful in our attempts to define the complete DNA hypermethylome of tumor cells. Here we report a functional search for hypermethylated CpG islands using the colorectal cancer cell line HCT-116, in which two major DNA methyltransferases, DNMT1 and DNMT3b, have been genetically disrupted (DKOcells). more...

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platforms:

GPL4089 GPL4090

4 Samples

Download data: TXT

(Submitter supplied) This experiment series sought to detect genome-wide methylation in sporadic amyotrophic lateral sclerosis brains and compare it to normal control brains. Methylation across the whole genome was measured in brain DNA of 10 SALS patients and 10 neurologically-normal controls. Methylated DNA was immunoprecipitated and interrogated by Affymetrix GeneChip Human Tiling 2.0R Array Sets. Methylation calls were compared between SALS patients and controls at each methylated site. more...

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

7 related Platforms

148 Samples

Download data: BAR, CEL, TXT

(Submitter supplied) Identification and characterization of epigenetically silenced genes is very important for cancer research. Particularly, information of hypermethylated genes provides clues to understand roles of epigenetics in tumorigeneses, and genes frequently methylated in a tumor-specific manner can be used as tumor markers. DNA methylation inhibitors such as 5-aza-cytidine or 5-aza-2’-deoxycytidine were widely used to search epigenetically silenced genes. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6480

8 Samples

Download data: TXT

(Submitter supplied) Four cervical carcinoma cell lines (C4I, CaSki, HeLa, SiHa) were treated with epigenetic modifying drugs 5-aza-2’-deoxycytidine and trichostatin A. Such treatment leads to reactivation of genes that are epigenetically silenced in cancer by aberrant methylation; reactivated genes were then identified by microarray profiling. Subsets consist of 2 biological repeats and 2 dye-flip experiments for each repeat for CaSki cell line, and 3 repeats, each with 2 dye-flip experiments for C4I, HeLa, Caski cell lines. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL1753

22 Samples

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(Submitter supplied) Agilent CpG microarray in combination with enriched methylated DNA by a MBD protein were carried out in each pool of genomic DNA from primary breast tumor and matched adjacent normal tissues.

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL9767

2 Samples

Download data: TXT

(Submitter supplied) Genome wide DNA methylation profiling of normal and cancer tissue samples in prostate cancer. The Illumina Infinium 27k Human DNA methylation Beadchip v1.2 was used to obtain DNA methylation profiles across approximately 27,000 CpGs. Samples are pool of 12 normal and 12 cancer tissues.

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL8490

2 Samples

Download data: TXT