GEO DataSets

(Submitter supplied) Thirty-seven (37) human cell lines were submitted to HTG Molecular for analysis using the HTG EdgeSeq Oncology Biomarker Panel. The goal of this work is to characterize the gene expression pattern of different cell lines bearing sensitivity or resistance for specific drugs.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

36 Samples

Download data: TXT

(Submitter supplied) Inhibition of estrogen related receptor alpha (ERRa) with C29 decreases global levels of DNA methylation and sensitizes breast cancer cells to the cytostatic effect of the DNMT inhibitor 5-aza-2'-deoxycytidine. We performed RRBS to understand the mechanisms behind the tumor suppression effect observed upon cotreatment with C29 and 5-azadC . We observed distinct patterns of differentially methylated regions in promoters for each condition and discovered that IRF4 was hypomethylated specifically in the condition with drug combination. more...

Organism:

Mus musculus

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL21103

8 Samples

Download data: TSV

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

Organism:

Homo sapiens

Type:

Expression profiling by array; Methylation profiling by array

Platforms:

GPL13534 GPL10558

13 Samples

Download data: IDAT

(Submitter supplied) Dacogen (DAC/ 5-aza-2’deoxycitidine/Aza) is currently used to treat myeloid dysplastic syndrome (MDS) and is in trials for Acute Myeloid Leukaemia (AML) and some solid cancers. As a hypomethylating agent it is thought to act by inhibiting the enzymes which add methyl groups to DNA, chief among them DNMT1. Improved targeting has been hindered by a lack of understanding of the off-target effects following treatment. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL10558

6 Samples

Download data: IDAT

(Submitter supplied) Dacogen (DAC/ 5-aza-2’deoxycitidine/Aza) is currently used to treat myeloid dysplastic syndrome (MDS) and is in trials for Acute Myeloid Leukaemia (AML) and some solid cancers. As a hypomethylating agent it is thought to act by inhibiting the enzymes which add methyl groups to DNA, chief among them DNMT1. Improved targeting has been hindered by a lack of understanding of the off-target effects following treatment. more...

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL13534

7 Samples

Download data: IDAT, TXT

(Submitter supplied) To investigate the knockdown effect of STAT3 on DNA methylation on gastric cancer cells, genome wide DNA methylation profiling of AGS transfected with pLKO.1-puro-shGFP or shSTAT3 generated from Illumina Infinium MethylationEPIC.

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL21145

4 Samples

Download data: IDAT, TXT

(Submitter supplied) Characteristic extinguishing of B-cell phenotype in cHL is believed to be a result of transcription factor network deregulation due to the overexpression of repressor proteins ID2 and ABF-1. KLF4 is a versatile transcription factor, participating in regulation of differentiation processes in various tissues. Epigenetic silencing of KLF4 in cHL hints that KLF4 is involved in the complex mechanism of extinguishing of B-cell phenotype in cHL. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6244

8 Samples

Download data: CEL

(Submitter supplied) MLL-r infant acute lymphoblastic leukemia (ALL) has largely unclear oncogenesis. It has been shown unrelated to copy number change or mutations in the tyrosine kinome. We therefore, explored the possible role of genome wide CpG island hypermethylation in MLL-r infant ALL. We employed the HpaII-tiny fragment Enrichment by Ligation-mediated PCR (HELP) assay to examine MLL-r infant leukemia samples (n=5), other common childhood ALL (n=5) and normals (n=5). more...

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL6604

15 Samples

Download data: PAIR

(Submitter supplied) Diffuse large B-cell lymphoma (DLBCL) is the most common type of lymphoid neoplasm in the world representing 30-40% of all lymphomas. Standard immunochemotherapy (cyclophosphamide, doxorubicin, vincristine, prednisone and rituximab) ensures cure in 60 to 65% of patients, while the rest progress or relapse. While advances have been made in the treatment of DLBCL, especially with the addition of rituximab, it is now apparent that there may be significant differences in prognosis that are related to the cell of origin, and that this disease is heterogeneous and novel treatment options are needed. more...

Organism:

Homo sapiens

Type:

Expression profiling by array; Methylation profiling by array

Dataset:

GDS4006

Platforms:

GPL8490 GPL6947

24 Samples

Download data: TXT

Analysis of three large B-cell lymphoma cell lines treated with the histone deacetylase inhibitor panobinostat, hypomethylating agent decitabine, or both for 48hrs. Panobinostat synergizes with decitabine in DLBCL cells. Results provide insight into the molecular basis for this synergistic effect.

Organism:

Homo sapiens

Type:

Expression profiling by array, count, 4 agent, 3 cell line sets

Platform:

GPL6947

Series:

GSE27226

12 Samples

Download data

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

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Methylation profiling by genome tiling array

Platforms:

GPL21145 GPL28038

30 Samples

Download data: IDAT, TXT

(Submitter supplied) DNA methylation is a fundamental epigenetic modification regulating gene expression. Aberrant DNA methylation is the most common molecular lesion in cancer cells. However, medical intervention has been limited to the use of broadly acting, small molecule-based demethylating drugs with significant side-effects and toxicities. To allow for targeted DNA demethylation, we integrated two novel nucleic acid-based approaches: DNMT1 interacting RNA (DiR) and RNA aptamer strategy. more...

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL21145

15 Samples

Download data: IDAT

(Submitter supplied) DNA methylation is a fundamental epigenetic modification regulating gene expression. Aberrant DNA methylation is the most common molecular lesion in cancer cells. However, medical intervention has been limited to the use of broadly acting, small molecule-based demethylating drugs with significant side-effects and toxicities. To allow for targeted DNA demethylation, we integrated two novel nucleic acid-based approaches: DNMT1 interacting RNA (DiR) and RNA aptamer strategy. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28038

15 Samples

Download data: TXT

(Submitter supplied) DNA methylation is a fundamental epigenetic modification regulating gene expression. Aberrant DNA methylation is the most common molecular lesion in cancer cells. However, medical intervention has been limited to the use of demethylating drugs that act indiscriminately on the genome and come with a toll of high toxicity and low specificity. Aptamers are novel targeting molecules considered high affinity ligands. more...

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL21145

6 Samples

Download data: IDAT, TXT