GEO DataSets

Analysis of glioblastoma (GBM) tumors from different regions of the brain from patients of various ages. Mutations in H3F3A and IDH1 define distinct epigenetic and biological subgroups of GBM. Results provide insight into heterogeneity of GBM and oncogenic pathways leading to gliomagenesis.

Organism:

Homo sapiens

Type:

Expression profiling by array, count, 27 age, 7 disease state, 5 genotype/variation, 3 other, 13 tissue sets

Platform:

GPL570

Series:

GSE36245

46 Samples

Download data: CEL

(Submitter supplied) Glioblastoma (GBM) is an incurable brain tumor carrying a dismal prognosis, which displays considerable heterogeneity. We have recently identified recurrent H3F3A mutations affecting two critical positions of histone H3.3 (K27, G34) in one-third of pediatric GBM. Here we show that each of these H3F3A mutations defines an epigenetic subgroup of GBM with a distinct global methylation pattern, and are mutually exclusive with IDH1 mutations (characterizing a CpG-Island Methylator Phenotype (CIMP) subgroup). more...

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL13534

142 Samples

Download data: TXT

(Submitter supplied) Glioblastoma (GBM) is an incurable brain tumor carrying a dismal prognosis, which displays considerable heterogeneity. We have recently identified recurrent H3F3A mutations affecting two critical positions of histone H3.3 (K27, G34) in one-third of pediatric GBM. Here we show that each of these H3F3A mutations defines an epigenetic subgroup of GBM with a distinct global methylation pattern, and are mutually exclusive with IDH1 mutation (characterizing a CpG-Island Methylator Phenotype (CIMP) subgroup). more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Dataset:

GDS4470

Platform:

GPL570

46 Samples

Download data: CEL

(Submitter supplied) High-throughput sequencing of numerous patient samples has identified a myriad of frequent mutations of epigenetic regulators in human cancers, including recently discovered mutations in histone-encoding genes. Lysine-to-methionine mutations such as H3K27M and H3K36M share a common mechanism of inhibiting methylation pathways at the genome-wide level to promote tumorigenesis. However, the mechanism underlying the molecular and cellular changes due to H3G34 alterations is yet to be determined. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL21290

22 Samples

Download data: BW

(Submitter supplied) In this study, we aimed to characterize the global DNA methylation pattern of mainly IDH1 wild type survival outliers of glioblastoma.

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL13534

44 Samples

Download data: TXT

(Submitter supplied) We over-expressed an epigenetic regulator in a glioblastoma (GBM) primary culture from an adult patient. These GBM cells have cancer stem cell phenotypes, as they have self-renewal properties and tumor initiation potential when transplanted in immunocompromised mice. ATAC-seq was performed on cells over-expressing the epigenetic regulator and control cells expressing EGFP.

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing; Other

Platform:

GPL16791

12 Samples

Download data: NARROWPEAK

(Submitter supplied) Mutations in the histone 3 variant H3.3 have been identified in one-third of pediatric glioblastomas (GBMs), but not in adult tumors. Here we show that H3.3 is a dynamic determinant of functional properties in adult GBM. H3.3 is repressed by mixed lineage leukemia 5 (MLL5) in self-renewing GBM cells. MLL5 is a global epigenetic repressor that orchestrates reorganization of chromatin structure by punctuating chromosomes with foci of compacted chromatin, favoring tumorigenic and self-renewing properties. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL17586

6 Samples

Download data: CEL, TXT

(Submitter supplied) Genome wide DNA methylation profiling of fourteen adult GBM primary cultures and their comparison to pediatric GBMs [GSE36278; GSE55712]

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL13534

14 Samples

Download data: IDAT, TXT

(Submitter supplied) Oncogenic mutations in two isocitrate dehydrogenase (IDH)-encoding genes (IDH1 and IDH2) have been identified in acute myelogenous leukemia, low-grade glioma, and secondary glioblastoma (GBM). Our in silico and wet-bench analyses indicate that non-mutated IDH1 mRNA and protein are commonly overexpressed in primary GBM. We show that genetic and pharmacologic inactivation of IDH1 decreases GBM cell growth, promotes a more differentiated tumor cell state, increases apoptosis in response to targeted therapies, and prolongs survival of animal subjects bearing patient-derived xenografts (PDXs). more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL18573

7 Samples

Download data: BW

(Submitter supplied) The aim of this study was to perform a genomic profiling of gliomas of Brazilian origin, using array-CGH, MSI analysis and to associate the genomic alterations with TERT and IDH1 mutation status, and correlate the molecular features with clinicopathological characteristics.

Organism:

Homo sapiens

Type:

Genome variation profiling by genome tiling array

Platform:

GPL10152

65 Samples

Download data: TXT

(Submitter supplied) miRNA expression analysis was performed on 14 cases of high grade gliomas and 4 controls obtained from age-matched epileptic patients. After this differentially miRNA analysis has been done among T53,H3F3A,normal and pediatric high grade glioma patient and try to identify the highly altered miRNA expression as well as sno expression pattern.

Organism:

Homo sapiens; synthetic construct

Type:

Non-coding RNA profiling by array

Platform:

GPL16384

18 Samples

Download data: CEL

(Submitter supplied) IDH3a KO in NHAs was demonstrated to exert global DNA methylation changes. These studies were followed by an Illumina EPIC methylation array to evaluate the location of differentially methylated CpGs

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL21145

8 Samples

Download data: IDAT

(Submitter supplied) RNA-seq of NHAs with either wild-type IDH3a expression (control) or IDH3a KO via CRISPR/Cas9

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20301

8 Samples

Download data: TXT

(Submitter supplied) We investigate the role of lactic acid in GBM cells as an epigenetic metabolite in the regulation of pro-survival gene expression.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL27949

12 Samples

Download data: CEL

(Submitter supplied) We had performed the ATAC-seq in mouse and human glioblastoma stem cells to understand the epigenetic regulation of glioblastoma stem cells.

Organism:

Mus musculus; Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL24676 GPL24247

186 Samples

Download data: BED, BW