GEO DataSets

(Submitter supplied) This study reports clinical, genetic, epigenetic, gene expression, and cellular features distinguishing meningioma DNA methylation subgroups within meningioma DNA methylation groups. We present these data in the context of molecular and clinical models predicting postoperative outcomes across 565 meningiomas with comprehensive clinical follow-up from independent discovery and validation institutions. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

302 Samples

Download data: TAR

(Submitter supplied) A custom Nanostring nCounter panel of 100 or 75 meningioma related genes and reference genes was developed, and performed on human frozen and FFPE meningioma samples. This was done as part of a study developing and validating a targeted gene expression biomarker for meningioma outcomes after surgey and benefit from raditherapy.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL32994

1202 Samples

Download data: RCC, XLSX

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

Organism:

Homo sapiens

Type:

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

Platforms:

GPL20301 GPL24676 GPL21145

760 Samples

Download data: IDAT, MTX, TSV

(Submitter supplied) We report single-cell RNA sequencing of 57,114 cells from 8 meningioma samples and 2 dura samples, which are used to analyze the inter- and intra-meningioma heterogeneity across DNA methylation groups.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

10 Samples

Download data: MTX, TSV

(Submitter supplied) We report RNA sequencing of 185 meningiomas, which are used to interrogate the biology underlying DNA methylation groups of meningioma.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20301

185 Samples

Download data: CSV

(Submitter supplied) We report DNA methylation profiling on 565 meningiomas integrated with genetic, transcriptomic, biochemical, proteomic, and single-cell approaches to show meningiomas are comprised of 3 groups with distinct clinical outcomes, biological drivers, and therapeutic vulnerabilities. Merlin-intact meningiomas have the best outcomes and are distinguished by NF2/Merlin regulation of glucocorticoid signaling, apoptosis, and susceptibility to cytotoxic therapy. more...

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL21145

565 Samples

Download data: CSV, IDAT

(Submitter supplied) Multiple stereotatically separate sites from human meningioma were processed for methlyation profiling Meningiomas are the most common primary intracranial tumors, but the molecular drivers of meningioma tumorigenesis are poorly understood. We hypothesized that investigating intratumor heterogeneity in meningiomas would elucidate biologic drivers and reveal new targets for molecular therapy. To test this hypothesis, we performed multiplatform molecular profiling of 86 spatially-distinct samples from 13 human meningiomas. more...

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL23976

88 Samples

Download data: IDAT, TXT

(Submitter supplied) Genome wide DNA methylation profiling of malignant, atypical and benign meningiomas samples. The Illumina infinium HumanMethylation450 beadchip kit was used, which assayed 450,000 potential methylation sites.

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL13534

23 Samples

Download data: TXT

(Submitter supplied) We performed RNA-seq on 42 meningioma samples isolated from human patients to characterize the transcriptome of these tumors

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

42 Samples

Download data: XLSX

(Submitter supplied) Genome wide DNA methylation profiling of formalin-fixed paraffin-embedded (FFPE) meningioma samples. The Illumina Infinium MethylationEPIC BeadChip was used to obtain DNA methylation profiles across approximately 850,000 methylation sites across the genome at single-nucleotide resolution.

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL23976

64 Samples

Download data: IDAT, TXT

(Submitter supplied) Meningiomas are frequent central nervous system tumors. Although most meningiomas are benign (WHO grade I) and curable by surgery, WHO grade II and III tumors remain therapeutically challenging due to frequent recurrence. Interestingly, relapse also occurs in some WHO grade I meningiomas. Hence, we investigated the transcriptional features defining aggressive (recurrent, malignantly progressing or WHO grade III) meningiomas in 144 cases. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL10558

62 Samples

Download data: TXT

(Submitter supplied) Background: A feature of glioblastoma (GBM) is the cellular and molecular heterogeneity, both within and between tumors. This variability results in a risk for sampling bias and potential tumor escape from future targeted therapy. Heterogeneous gene expression within GBM is well documented, but little is known regarding the epigenetic heterogeneity. We therefore aimed to profile the intra-tumor DNA methylation heterogeneity in GBM. more...

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL21145

47 Samples

Download data: IDAT

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

Organism:

Homo sapiens

Type:

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

Platforms:

GPL20301 GPL23976

220 Samples

Download data: IDAT

(Submitter supplied) Purpose: Clustering of meningiomas using DNA methylation and RNA-sequencing data yields groups which predict clinical behavior than the current clinical standard of histopathologic grading. Both techniques segregate many common genomic features seen in meningiomas similarly, raising the question of whether they were identifying the same underyling groups. Methods: DNA methylation profiling (EPIC 850K array) and RNA-sequencing of 110 primary meningiomas was performed. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20301

110 Samples

Download data: CSV, XLSX

(Submitter supplied) Purpose: Clustering of meningiomas using DNA methylation and RNA-sequencing data yields groups which predict clinical behavior than the current clinical standard of histopathologic grading. Both techniques segregate many common genomic features seen in meningiomas similarly, raising the question of whether they were identifying the same underyling groups. Methods: DNA methylation profiling (EPIC 850K array) and RNA-sequencing of 110 primary meningiomas was performed. more...

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL23976

110 Samples

Download data: CSV, IDAT, XLSX

(Submitter supplied) RNA Nanostring from human meningioma samples This set of data pertains to RNA extracted from 2mm core punches from the representative FFPE blocks, on which a custom codeset was run.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL33289

16 Samples

Download data: RCC

(Submitter supplied) DNA methylation from human meningioma samples that were also profiled for spatial heterogeneity analysis. Some samples represent spatially distinct regions, punched using a 2mm core punch from FFPE blocks in a given tumor. Other samples represent serial tumor samples at index treatment and then recurrence.

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL21145

16 Samples

Download data: IDAT, TXT

(Submitter supplied) Methylation analysis of meningioma samples. Genomic DNA isolated directly from fresh-frozen human meningioma specimens.

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL23976

121 Samples

Download data: IDAT, TXT

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

Organism:

Homo sapiens

Type:

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

Platforms:

GPL10558 GPL11154 GPL16791

184 Samples

Download data: BED, FPKM_TRACKING

(Submitter supplied) RNA polymerase II mediates the transcription of all protein-coding genes in eukaryotic cells, a process that is fundamental to life. Genomic mutations in this enzyme have not been previously linked to any pathology in humans, a testament to its indispensable role in cell biology. Based on a combination of next-generation genomic analyses of 775 meningiomas, we report that recurrent somatic p.Gln403Lys or p.Leu438_His439del mutations in POLR2A, which encodes the catalytic subunit of RNA polymerase II, are sufficient to hijack this essential enzyme and drive neoplasia. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

19 Samples

Download data: FPKM_TRACKING