Homo sapiens
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA175142 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Treatment of AML patient samples with decitabine
| PRJNA192434 | ENA
Project description:Acute myeloid leukemia (AML), and other myeloid malignancies, are frequently treated with hypomethylating agents like decitabine. Alterations in the epigenome, induced by decitabine, are likely to result in gene expression changes. The effects of decitabine have not been systemically studied using primary AML samples. We cultured 18 different primary AML samples for 7 days, the last 3 days of which included 100 nM decitabine (DAC) or 100 nm cytarabine (AraC). We hypothesized that decitabine treatment would result in detectable and consistent gene expression changes. For comparison, we also analyzed mRNA from cells treated with DMSO control (mock) and mRNA from uncultured cells taken at the time of diagnosis.
2012-12-18 | E-GEOD-40442 | biostudies-arrayexpress
Project description:RNA extracted at 240min. Samples are rRNA depleted. Expression measurement of Homo sapiens genes.
2019-07-31 | GSE114179 | GEO
Project description:Acute myeloid leukemia (AML), and other myeloid malignancies, are frequently treated with hypomethylating agents like decitabine. Alterations in the epigenome, induced by decitabine, are likely to result in gene expression changes. The effects of decitabine have not been systemically studied using primary AML samples.
2012-12-18 | GSE40442 | GEO
Project description:The epigenetic regulation, for example, DNA methylation, controls the development and differentiation of both tumor cells and immunocytes. Treatment with DNA demethylating agent (such as decitabine) has shown a dramatic clinical benefit in hematological malignancies and solid tumors. However, the influence of epigenetic therapy on host immune system remains unclear. To investigate the effects of low-dose decitabine therapy on T cells, We collected whole blood samples from two solid tumor patients pre and post low-dose decitabine therapy, and detected the expression profiles of PBMCs.
2016-06-30 | E-GEOD-72686 | biostudies-arrayexpress
Project description: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. To appreciate the role of differentiation in hypomethylation of some CpG by decitabine treatment but not others, promoter CpGs, analyzed by microarray and mass spectrometry, were categorized by the direction of methylation change during normal myeloid differentiation. In MDS/AML cells, high expression of CEBPa, relatively low expression of CEBPe (a gene target of CEBPa), hypermethylation of CEBPe promoter CpG, and the methylation pattern at differentiation sensitive promoter CpGs analyzed by microarray, suggested lineage-commitment and aberrant epigenetic repression of late differentiation genes. DNA hypomethylation in response to decitabine was greatest at CpGs that are hypomethylated during normal myeloid differentiation. In contrast, normal HSPC treated with decitabine retained immature morphology, and methylation significantly decreased at CpG that are hypermethylated during myeloid differentiation. Partial differentiation at baseline, and repression of key late differentiation genes by epigenetic means, likely plays a role in methylation and phenotype responses of AML cells treated with decitabine. Bisulphite converted DNA from the 208 samples were hybridised to the Illumina Cancel Panel 1 GPL9183 methylation assay
2011-07-01 | E-GEOD-29047 | biostudies-arrayexpress
Project description:It is well established that low-dose Decitabine treatment can sustain long-term antitumor effects by targeting DNA methylation and altering gene expression32. We performed methylated DNA immunoprecipitation (MEDIP) followed by next-generation sequencing in 5637 cells. Daily Decitabine treatment with 100 nM for 72 hr (with or without 100ng/ml cisplatin treatment) reduced the methylation level at CpG-islands in the genome of 5637 cells . However, this low-dose DEC treatment did not cause a significant reduction of DNA methylation in non-CpG islands regions.Our study represents the first detailed analysis of DNA methylome generated by RNA-seq technology in bladder cancer cells treated with low-dose decitabine. This study help to reveal the direct target genes of decitabine in bladder cancer treatement.
2021-04-23 | GSE113537 | GEO
Project description:We found previously that the effect of decitabine (DAC) on hematopoietic stem cell viability differed between Mll5 wildtype and null cells. We therefore investigated the role of MLL5 expression levels on outcome of AML patients who were treated with decitabine. High MLL5 expressing AML patients have improved overall survival when treated with decitabine. In transformed murine cells, loss of Mll5 was associated with resistance to low-dose decitabine, less frequent promoter methylation, and reduced demethylation upon decitabine treatment. These data suggest a biological link between MLL5 expression and decitabine response involving regulation of DNA methylation. Leukemia cell model was generated by co-transfer of HOXA9 and MEIS1 into Mll5 wildtype or knockout mouse bone marrow cells. MeDIP was performed in Mll5+/+ HOXA9/MEIS1 and Mll5-/- HOXA9/MEIS1 leukemic cells, untreated or treated with 3-day exposure of 20 nM decitabine, triplicate for each condition. MeDIP-enriched DNA was amplified with the GenomePlex Complete Whole Genome Amplification (WGA) Kit (Sigma-Aldrich). DNA from three MeDIP and WGA of each cell type and treatment was pooled for subsequent microarray analysis. The enriched DNA and corresponding input genomic DNA was labeled, hybridized and scanned on Agilent custom mouse promoter microarrays (Agilent-025976 AP_1M_Custom_CH3, assembly build mm9). The methylation value of individual probes was defined by the signal intensity ratio of MeDIP DNA (Cy3) compared to input DNA (Cy5) . Methylated DNA immunoprecipitation coupled with Agilent mouse promoter CpG arrays (MeDIP-chip)
2014-07-01 | E-GEOD-52199 | biostudies-arrayexpress
Project description:Gene expression profiling in primary AML cells treated with decitabine and cytarabine
| PRJNA174047 | ENA