GEO DataSets

(Submitter supplied) Purpose: Decitabine is a deoxycytidine nucleoside derivative inhibitor of DNA-methyltransferases indicated for treatment of myelodysplastic syndrome (MDS). Laboratory evidence shows that pretreatment of AML cell lines can sensitize leukemia cells to chemotherapy and inhibit clonogenic potential. We conducted a randomized study of decitabine when used as priming before standard induction therapy in children with newly diagnosed acute myelogenous leukemia (AML) to evaluate the safety, pharmacokinetics, and any potential early efficacy signal. more...

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL13534

36 Samples

Download data: TXT

(Submitter supplied) Genome-wide CpG-island methylation profiling on pediatric AML samples was performed to identify specific methylation patterns discriminating particular AML subgroups from the rest of AML samples based on the methylation profile.

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL9767

152 Samples

Download data: TXT

(Submitter supplied) Epigenetic changes play a role in the pathogenesis of myeloid malignancies and hypomethylating agents have shown efficacy in these diseases. We studied the apoptotic effect, the genome-wide methylation and gene expression profiles in HL60 cells following decitabine treatment, using micro-array technologies. Decitabine treatment resulted in a decrease in global DNA methylation, corresponding to 4876 probeset IDs with significantly reduced methylation levels, while expression of 2583 IDs was induced. more...

Organism:

Homo sapiens

Type:

Expression profiling by array; Methylation profiling by genome tiling array

Platforms:

GPL570 GPL5082

12 Samples

Download data: CEL, TXT

(Submitter supplied) The Affymetrix Human Genome U133 Plus 2.0 Array was used to examine the Genome wide transcriptional changes which follow the treatment of AML xenografts with either PBS control or combination of decitabine (DAC) and cytarabine (Ara-C). Animals were treated with PBS, DAC alone, Ara-C alone, DAC and Ara-C combined (D+A), DAC followed by Ara-C (D/A) or Ara-C followed by DAC (A/D).

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

18 Samples

Download data: CEL, XLSX

(Submitter supplied) The DNA hypomethylating drug decitabine maintains normal hematopoietic stem and progenitor cell (HSPC) self-renewal but induces terminal differentiation in acute myeloid leukemia (AML) cells. To better understand the basis for this contrasting treatment effect, the baseline expression of key lineage-specifying transcription factor (TF) (eg., CEBPa) and key late differentiation TF (CEBPe), was examined in normal, myelodysplastic (MDS) and AML primary cells and cell lines. more...

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL9183

208 Samples

Download data: TXT

(Submitter supplied) DNMT inhibitors (DNMTi) are finally approved for AML/MDS, also based on their activity in patients with high-risk cytogenetics (often monosomal karyotype) such as -5/del(5q) or -7/del(7q), often - but not always - harboring TP53-mutations. Several studies provided evidence for aberrant hypermethylation/silencing on monoallelic gene loci, including tumor suppressor genes. We hypothesized that transcriptional repression on monosomal gene loci may be preferentially reversed by DNMTi. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

24 Samples

Download data: TXT

(Submitter supplied) DNMT inhibitors (DNMTi) are finally approved for AML/MDS, also based on their activity in patients with high-risk cytogenetics (often monosomal karyotype) such as -5/del(5q) or -7/del(7q), often - but not always - harboring TP53-mutations. Several studies provided evidence for aberrant hypermethylation/silencing on monoallelic gene loci, including tumor suppressor genes. We hypothesized that transcriptional repression on monosomal gene loci may be preferentially reversed by DNMTi. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL17586

80 Samples

Download data: CEL

(Submitter supplied) DNMT inhibitors (DNMTi) are finally approved for AML/MDS, also based on their activity in patients with high-risk cytogenetics (often monosomal karyotype) such as -5/del(5q) or -7/del(7q), often - but not always - harboring TP53-mutations. Several studies provided evidence for aberrant hypermethylation/silencing on monoallelic gene loci, including tumor suppressor genes. We hypothesized that transcriptional repression on monosomal gene loci may be preferentially reversed by DNMTi. more...

Organism:

Homo sapiens

Type:

Genome variation profiling by SNP array

Platforms:

GPL18637 GPL6801

4 Samples

Download data: CEL, CNCHP, CYCHP

(Submitter supplied) Guadecitabine is a second generation DNA methylation inhibitor with improved pharmacokinetics and clinical activity in relapsed/refractory AML (rrAML). Here we report genome-wide DNA methylation profiles in pre-treatment samples from 116 rrAML patients treated at therapeutic doses of guadecitabine in a phase I/II study. Response rate to guadecitabine was 22 % (16CR, 42 12CRi/CRp). There were no strong mutation or methylation predictors of response. more...

Organism:

Homo sapiens

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL16791

121 Samples

Download data: CSV, TXT

(Submitter supplied) Early epigenetic changes and DNA damage do not predict clinical response in an overlapping schedule of 5-azacytidine and entinostat in patients with myeloid malignancies. The patients with MDS, chronic myelomonocytic leukemia (CMMoL), and high risk AML were treated with sequential administration of methylation inhibitor drugs (5AC and entinostat). To study gene expresion regulation in treated patients, microarray analysis was done on RNA samples extracted from CD34+ cells from 18 patients before and 15 days after treatment using Affymetrix U133Plus2.0.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

24 Samples

Download data: CEL

(Submitter supplied) Genome wide demethylation by DNMT1 inhibitors GSK3685032 results in up-regulation of epigenetically-silenced genes.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

156 Samples

Download data: TXT

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

Organism:

Homo sapiens

Type:

Methylation profiling by array; Expression profiling by high throughput sequencing

Platforms:

GPL24676 GPL21145

221 Samples

Download data: IDAT

(Submitter supplied) Genome wide demethylation by DNMT1 inhibitor GSK3484862 results in up-regulation of epigenetically-silenced genes. Methylation was assayed for each cell line following DNMT1 inhibitor or vehicle treatment. Global methylation distributions were compared between treated and untreated samples.

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL21145

14 Samples

Download data: IDAT, TXT

(Submitter supplied) Genome wide demethylation by DNMT1 inhibitor GSK3685032 results in up-regulation of epigenetically-silenced genes

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL21145

51 Samples

Download data: IDAT, TXT

(Submitter supplied) The therapeutic effect of DNA-hypomethylating agents (HMAs) in AML/MDS is discussed to be via its effects on aberrant gene silencing by reactivation (e.g. through promoter demethylation). While this has been broadly studied in cell line models, only very few studies have addressed the global effects of HMAs in primary blasts serially isolated from AML patients (pts) undergoing HMA treatment (Claus et al., Leuk. more...

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL13534

132 Samples

Download data: IDAT, TXT

(Submitter supplied) The therapeutic effect of DNA-hypomethylating agents (HMAs) in AML/MDS is discussed to be via its effects on aberrant gene silencing by reactivation (e.g. through promoter demethylation). While this has been broadly studied in cell line models, only very few studies have addressed the global effects of HMAs in primary blasts serially isolated from AML patients (pts) undergoing HMA treatment (Claus et al., Leuk. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL17586

133 Samples

Download data: CEL, CSV

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

Organism:

blank sample; Homo sapiens

Type:

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

4 related Platforms

355 Samples

Download data: COV

(Submitter supplied) Global changes in DNA methylation are observed in several developmental and disease contexts, and single-cell analyses are beginning to reveal the heterogeneous regulation of these processes. However, these studies are limited by the poor alignment rates and high sequencing demands associated with single-cell analysis of DNA methylation. We present single-cell transposable element methylation sequencing (scTEM-seq) for cost-effective estimation of global DNA methylation levels. more...

Organism:

Homo sapiens

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL15520

2 Samples

Download data: COV

(Submitter supplied) Global changes in DNA methylation are observed in several developmental and disease contexts, and single-cell analyses are beginning to reveal the heterogeneous regulation of these processes. However, these studies are limited by the poor alignment rates and high sequencing demands associated with single-cell analysis of DNA methylation. We present single-cell transposable element methylation sequencing (scTEM-seq) for cost-effective estimation of global DNA methylation levels. more...

Organism:

blank sample; Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL29107 GPL18573

161 Samples

Download data: TXT

(Submitter supplied) Global changes in DNA methylation are observed in several developmental and disease contexts, and single-cell analyses are beginning to reveal the heterogeneous regulation of these processes. However, these studies are limited by the poor alignment rates and high sequencing demands associated with single-cell analysis of DNA methylation. We present single-cell transposable element methylation sequencing (scTEM-seq) for cost-effective estimation of global DNA methylation levels. more...

Organism:

blank sample; Homo sapiens

Type:

Methylation profiling by high throughput sequencing

Platforms:

GPL15520 GPL27039

96 Samples

Download data: COV