Similar studies for GEO DataSets (Select 200017512) - GEO DataSets

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Items: 20

Select item 2000175121.

Detection of aberrant DNA methylation in colorectal carcinoma samples compared to normal human colon

(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

Series

Accession:: GSE17512

ID:: 200017512

Select item 2000175102.

Detection of aberrant DNA methylation in acute leukemia samples compared to normal human monocytes

(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

Series

Accession:: GSE17510

ID:: 200017510

Select item 2000174553.

Detection of aberrant DNA methylation in AML cell lines compared to normal human monocytes

(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

Series

Accession:: GSE17455

ID:: 200017455

Select item 2000160784.

Detection of transcription factor NRF1, YY1 and SP1 bound regions in human peripheral blood monocytes

(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

Series

Accession:: GSE16078

ID:: 200016078

Select item 2000160765.

Transcriptome analysis of myelid cell types (normal and leukemic)

(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

Series

Accession:: GSE16076

ID:: 200016076

Select item 2000040096.

Methylation profiling of leukemia cell lines

(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

Download data

Series

Accession:: GSE4009

ID:: 200004009

Select item 2000032807.

Expression profiling of leukemia cell lines

(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

Download data

Series

Accession:: GSE3280

ID:: 200003280

Select item 22518.

Myeloid leukemia cell lines

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

Download data

DataSet

Accession:: GDS2251

ID:: 2251

Select item 2000381429.

Molecular rules governing de novo methylation in cancer

(Submitter supplied) De novo methylation of CpG islands is seen in many tumors, but the general rules governing this process are not known. By analyzing DNA from tumors, as well as normal tissues, and by utilizing a wide range of published data, we have been able to identify a well-defined set of tumor targets, each of which has its own “coefficient” of methylation that is largely determined by its inherent relative ability to recruit the polycomb complex. more...

Organism:: Homo sapiens

Type:: Methylation profiling by genome tiling array

Platforms:: GPL10878 GPL4126
34 Samples

Download data: TXT

Series

Accession:: GSE38142

ID:: 200038142

Select item 20009693610.

Microarray analysis of gene expression in the livers of C57BL/6J mice fed a choline- and folate-deficient diet

(Submitter supplied) Non-alcoholic steatohepatitis (NASH) is becoming one of the leading causes of hepatocellular carcinoma (HCC), replacing viral HBV-, HCV-, and alcohol-related chronic liver diseases as major etiological risk of factors for HCC. The goal of the present study was to investigate transcriptomic alterations in the livers of male C57BL/6J mice fed a choline- and folate-deficient (CFD) diet. Feeding mice a CFD diet for 12 weeks caused NASH-like liver injury exhibiting uniform morphological features of human NASH. more...

Organism:: Mus musculus

Type:: Expression profiling by array

Platform:: GPL4134
6 Samples

Download data: TXT

Series

Accession:: GSE96936

ID:: 200096936

Select item 20003835411.

Genome-Wide DNA Methylation Profiles in Hematopoietic Stem and Progenitor Cells Reveal Over-Representation of ETS Transcription Factor Binding Sites

(Submitter supplied) DNA methylation is an essential epigenetic mark that is required for normal development. Knockout of the DNA methyltransferase enzymes in the mouse hematopoietic compartment reveals that methylation is critical for hematopoietic differentiation. To better understand the role of DNA methylation in hematopoiesis, we characterized genome-wide DNA methylation in primary mouse hematopoietic stem cells (HSC), common myeloid progenitors (CMP), and erythroblasts (ERY). more...

Organism:: Mus musculus

Type:: Methylation profiling by high throughput sequencing

Platform:: GPL9185
6 Samples

Download data: BED

Series

Accession:: GSE38354

ID:: 200038354

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 20006417112.

The effects of cytosine methylation on general transcription factors

(Submitter supplied) DNA methylation (mC) on CpG sites is the most common epigenetic modification. Recently methylation on non-CpG context was found to widely occur on genomic DNA. However, how non-CpG methylation influences DNA/protein interaction and regulates transcription is unknown. Using single-molecule assays, we studied the interactions of transcription factors (TFs) GR, ER and BMAL1-CLOCK with methylated or unmethylated cognate DNA binding sequences. more...

Organism:: Homo sapiens

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

Platform:: GPL11154
4 Samples

Download data: TXT

Series

Accession:: GSE64171

ID:: 200064171

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 20006393813.

Targeted CpG island methylation in human pluripotent stem cells

(Submitter supplied) In our manuscript, we describe novel methodologies for bidirectional DNA methylation editing at targeted genomic loci through homologous recombination (HR) in human pluripotent stem cells. In order to gain insights on the applicability of these methodologies towards modeling epigenetic alterations, as well as for the development of platforms for cell transplantation upon epigenetic correction.

Organism:: Homo sapiens

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

Platform:: GPL16791
29 Samples

Download data: BEDGRAPH, FA

Series

Accession:: GSE63938

ID:: 200063938

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 20007627014.

DNA methylome analysis of pediatric acute lymphoblastic leukemia cells reveals stochastic de novo DNA methylation in CpG islands.

(Submitter supplied) We used whole genome bisulfite sequencing (WGBS) to determine the DNA methylation levels at single base-pair resolution of four patients with different subtypes of pediatric ALL together with RNA-sequencing to increase our understanding of the leukemic transformation in ALL.

Organism:: Homo sapiens

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

Platform:: GPL10999
49 Samples

Download data: BED, BEDGRAPH, TXT

Series

Accession:: GSE76270

ID:: 200076270

PubMed Full text in PMC Similar studies

Select item 20021368615.

High-resolution Nanopore methylome-maps reveal random hyper-methylation at CpG-poor regions as driver of chemoresistance in leukemias.

(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:: GPL28975 GPL24676
23 Samples

Download data: TSV

Series

Accession:: GSE213686

ID:: 200213686

PubMed Full text in PMC Similar studies

Select item 20021368516.

High-resolution Nanopore methylome-maps reveal random hyper-methylation at CpG-poor regions as driver of chemoresistance in leukemias. [methylation]

(Submitter supplied) Aberrant DNA-methylation at CpG dinucleotides is a hallmark of cancer and is associated with the emergence of resistance to anti-cancer treatment, though molecular mechanisms and biological signifi- cance remain elusive. Genome-scale methylation maps by currently used methods are based on chemical modification of DNA and are best suited for analyses of methylation at CpG-rich regions (CpG islands). more...

Organism:: Homo sapiens

Type:: Methylation profiling by high throughput sequencing

Platform:: GPL28975
6 Samples

Download data: TSV

Series

Accession:: GSE213685

ID:: 200213685

PubMed Full text in PMC Similar studies

Select item 20021368417.

High-resolution Nanopore methylome-maps reveal random hyper-methylation at CpG-poor regions as driver of chemoresistance in leukemias.[RNA-Seq]

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing

Platform:: GPL24676
17 Samples

Download data: XLSX

Series

Accession:: GSE213684

ID:: 200213684

PubMed Full text in PMC Similar studies

Select item 20015840618.

De novo DNA methyltransferase activity in colorectal cancer is directed towards H3K36me3 marked CpG island

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

Organism:: Homo sapiens

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

Platforms:: GPL21697 GPL18573
50 Samples

Download data: BIGWIG, COV

Series

Accession:: GSE158406

ID:: 200158406

PubMed Full text in PMC Similar studies

Select item 20015840519.

De novo DNA methyltransferase activity in colorectal cancer is directed towards H3K36me3 marked CpG island (T7-DNMT3B ChIP-Rx_seq)

(Submitter supplied) The aberrant gain of DNA methylation at CpG islands (CGIs) is frequently observed in colorectal tumours and may silence the expression of tumour suppressors such as MLH1. Current models propose that these CGIs are targeted by de novo DNA methyltransferases (DNMTs) in a sequence-specific manner but this has not been tested. Using ectopically integrated CGIs, we find that aberrantly methylated CGIs are subject to low levels of de novo DNMT activity in colorectal cancer cells. more...