GEO DataSets

(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) 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) 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) Purpose: Oncogenic transformation of hematopoietic stem cells by chimeric fusion kinases causing constitutive activation of FGFR1 leads to a stem cell leukemia/lymphoma (SCLL) syndrome, accompanied by widespread dysregulation of gene activity. The goals of this study are to use NGS-derived transcriptome profiling (RNA-seq) to identify genes regulated by FGFR1 fusion kinase in SCLL. Methods: Three different cell models for SCLL, respectively BBC2 (B cell lymphoblastic leukemia/lymphoma), ZNF112 (B cell lymphoblastic leukemia/lymphoma) and BCRF8C (myloid leukemia) were treated with selective FGFR1 kinase inhibitor,then the total RNA from treatment and viechel control were isolated for RNA-Seq analysis. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL17021 GPL19057

6 Samples

Download data: TXT

(Submitter supplied) Background: In high-grade serous ovarian cancer (HGSOC) intrinsic and/or acquired resistance against platinum-containing chemotherapy is a major obstacle for successful treatment. A low frequency of somatic mutations, but frequent epigenetic alterations including DNA methylation in HGSOC tumors, presents the cancer epigenome as a relevant target for innovative therapy. Patient-derived xenografts (PDXs) supposedly are good preclinical models for identifying novel drug targets. more...

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL13534

22 Samples

Download data: IDAT

(Submitter supplied) RIPK3 locus is methylated in mesothelioma cell lines

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL16791

8 Samples

Download data: TSV

(Submitter supplied) Transciptional profiling of Calu6 tumors comparing 4 pooled untreated tumors to 5-azacytodine or 5-azacytodine + MS-275 (combined therapy) treated tumors

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL4133

9 Samples

Download data: TXT

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

Organism:

Mus musculus

Type:

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

Platform:

GPL21493

24 Samples

Download data: BW, TXT

(Submitter supplied) Malignant transformation depends on genetic and epigenetic events that result in a burst of deregulated gene expression and chromatin changes. To dissect the sequence of events in this process, we used a T cell-specific lymphoma model based on the human oncogenic NPM-ALK translocation. We find that transformation of T cells shifts thymic cell populations to an undifferentiated immunophenotype, which occurs only after a period of latency, accompanied by induction of the MYC-NOTCH1 axis and deregulation of key epigenetic enzymes. more...

Organism:

Mus musculus

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL21493

12 Samples

Download data: BW

(Submitter supplied) Malignant transformation depends on genetic and epigenetic events that result in a burst of deregulated gene expression and chromatin changes. To dissect the sequence of events in this process, we used a T cell-specific lymphoma model based on the human oncogenic NPM-ALK translocation. We find that transformation of T cells shifts thymic cell populations to an undifferentiated immunophenotype, which occurs only after a period of latency, accompanied by induction of the MYC-NOTCH1 axis and deregulation of key epigenetic enzymes. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21493

12 Samples

Download data: TXT

(Submitter supplied) We sorted GFP-labeled 4T1 cells from primary tumor and lung metastases and performed mRNA sequencing.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

8 Samples

Download data: TXT

(Submitter supplied) We sorted GFP-labeled 4T1 cells from primary tumors and lung metastases and performed methylation-seq.

Organism:

Mus musculus

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL17021

8 Samples

Download data: TXT

(Submitter supplied) We sorted GFP-labeled 4T1 cells from lung metastases and performed DNMT3B ChIP-seq.

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL19057

4 Samples

Download data: 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 high throughput sequencing; Methylation profiling by array; Other; Methylation profiling by high throughput sequencing

4 related Platforms

88 Samples

Download data: BED, BW, HIC, IDAT, NARROWPEAK, TXT

(Submitter supplied) Mouse gene express was using Mouse Gene 1.0 ST Array.

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL6246

12 Samples

Download data: CEL, CHP

(Submitter supplied) The Mouse Promoter Array is designed for chromatin immunoprecipitation (ChIP) experiments. Sequences used in the design of the Mouse Promoter array were selected from NCBI human genome assembly (Build 34). Repetitive elements were removed by RepeatMasker.

Organism:

Mus musculus

Type:

Methylation profiling by genome tiling array

Platform:

GPL5811

12 Samples

Download data: CEL, XLSX

(Submitter supplied) The GeneChip® Human Promoter 1.0R Array is designed for chromatin immunoprecipitation (ChIP) experiments. Sequences used in the design of the Human Promoter array were selected from NCBI human genome assembly (Build 34). Repetitive elements were removed by RepeatMasker.

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL5082

40 Samples

Download data: CEL, XLSX

(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