GEO DataSets

(Submitter supplied) Myelodysplastic syndrome (MDS) is a clonal myeloid neoplasm characterized by ineffective haematopoiesis and cytopenia with frequent epigenetic modifications. Hypomethylating agents (HMA) such as azacitidine (AZA) and decitabine (DEC) are standard therapeutic options in MDS, but drug resistance is not uncommon.To study RNA modification in particular M6A, P39-AZA-S and P39-AZA-R native RNA libraries were prepared using the direct RNA sequencing kit (Oxford Nanopore) following the manufacturer’s protocol (SQK-RNA002). more...

Organism:

Homo sapiens

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL28975

2 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 genome tiling array; Expression profiling by high throughput sequencing

Platforms:

GPL21145 GPL28975 GPL23227

10 Samples

Download data: IDAT

(Submitter supplied) Myelodysplastic syndrome (MDS) is a clonal myeloid neoplasm characterized by ineffective haematopoiesis and cytopenia with frequent epigenetic modifications. Hypomethylating agents (HMA) such as azacitidine (AZA) and decitabine (DEC) are standard therapeutic options in MDS, but drug resistance is not uncommon. Herein, multi-omic analysis is used to identify signaling pathways during MDS HMA resistance using MDS cell line P39 and validated in P39 and Kasumi-1. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23227

4 Samples

Download data: TXT

(Submitter supplied) Myelodysplastic syndrome (MDS) is a clonal myeloid neoplasm characterized by ineffective haematopoiesis and cytopenia with frequent epigenetic modifications. Hypomethylating agents (HMA) such as azacitidine (AZA) and decitabine (DEC) are standard therapeutic options in MDS, but drug resistance is not uncommon. Herein, multi-omic analysis is used to identify signaling pathways during MDS HMA resistance using MDS cell line P39 and validated in P39 and Kasumi-1. more...

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL21145

4 Samples

Download data: IDAT, TXT

(Submitter supplied) Epigenetic therapy, using hypomethylating agents (HMA), is known to be effective in the treatment of high-risk myelodysplastic syndromes (MDS) and acute myeloid leukemia (AML) patients who are not suitable for intensive chemotherapy or allogeneic stem cell transplantation. However, response rates to HMA are low and there is an unmet need in finding prognostic and predictive biomarkers of treatment response. more...

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL13534

166 Samples

Download data: IDAT, TSV

(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) Mx1-Cre/KrasG12D mice were injected with pIpC to induce a myeloproliferative disease resembling human chronic myelomonocytic leukemia (CMML-like MPD). When the disease was fully developed, CD11b-/Ly6G-/c-Kit+ hematopoietic stem and progenitor cells (HSPCs) were isolated and subjected to miR-microarray expression profiling. pIpC-injected CD11b-/Ly6G-/c-Kit+ HSPCs of age matched wildytpe control mice were used as controls.

Organism:

synthetic construct; Mus musculus

Type:

Non-coding RNA profiling by array

Platform:

GPL19117

8 Samples

Download data: CEL

(Submitter supplied) Decitabine (DAC) is used clinically for myelodysplastic syndromes (MDS) and acute myeloid leukemia (AML). Our genome-wide CRISPR-dCas9 activation screen using MDS-derived AML cells shows that mitotic regulation plays a pivotal role in DAC resistance. DAC strongly induces abnormal mitosis (abscission failure or tripolar mitosis) in human myeloid tumors at clinical concentrations, especially in those with TP53 mutations and antecedent hematological disorders. more...

Organism:

Mus musculus

Type:

Other

Platform:

GPL17021

4 Samples

Download data: TXT

(Submitter supplied) Decitabine (DAC) is used clinically for myelodysplastic syndromes (MDS) and acute myeloid leukemia (AML). To elucidate its exact mechanism of action, we performed a genome-wide CRISPR-dCas9 activation screen using MDS-derived AML cells and revealed that mitotic regulation plays a pivotal role in DAC resistance. DAC strongly induces abnormal mitosis (abscission failure or tripolar mitosis) in human myeloid tumors at clinical concentrations, especially in those with TP53 mutations and antecedent hematological disorders. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

12 Samples

Download data: TXT

(Submitter supplied) 5-Aza-2'-deoxycytidine, also known as decitabine, is a DNA hypomethylating agent (HMA) used to treat acute myeloid leukemia (AML) and pre-leukemic disorder myelodysplastic syndrome (MDS). Decitabine activates the transcription of endogenous retroviruses (ERV), which can induce immune response by acting as cellular double-stranded RNAs. Here, we employ an image-based screening system to identify dsRNA-binding factors that mediate the downstream effect of ERV induction. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

11 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) This SuperSeries is composed of the SubSeries listed below.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by genome tiling array

Platforms:

GPL24676 GPL21145

78 Samples

Download data: IDAT

(Submitter supplied) Transcriptomic profiling was performed on six cell lines derived from infants with KMT2A-rearranged ALL following treatment with two hypomethylating drugs (azacitidine and decitabine) administered at low doses for 72 hours in vitro. We identified changes in gene expression following treatment with hypomethylating agents, with decitabine exerting a greater effect than azacitidine.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

54 Samples

Download data: TXT

(Submitter supplied) Genome-wide methylation profiling was performed on six cell lines derived from infants with KMT2A-rearranged ALL following treatment with three hypomethylating drugs (azacitidine, decitabine and zebularine) administered at low doses for 72 hours in vitro. We identified drug-specific and common differentially methylated regions and validated differentially expressed genes located within such regions, indicating commonalities in pathways targeted by azacitidine and decitabine in KMT2A-rearranged infant ALL. more...

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL21145

24 Samples

Download data: IDAT

(Submitter supplied) We investigated the immune-related gene expression signature in the tumor immune-microenvironment associated with response or resistance during immunotherapy, by performing targeted gene expression profiling and gene set enrichment analysis using a custom NanoString panel composed of 579 immune-related genes

Organism:

Homo sapiens

Type:

Other

Platform:

GPL31171

98 Samples

Download data: RCC

(Submitter supplied) High BM plasma S100A8/A9 is associated with a perturbed microenvironment and poor prognosis in myelodysplastic syndromes

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

215 Samples

Download data: CSV