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Genome-wide methylation analyses in glioblastoma multiforme (GBM)

ABSTRACT: Our main objective was to study genome-wide differential methylation in de novo glioblastoma multiforme (GBM, grade IV glioma). We evaluated CpG sites in gene promoters of 26,000+ genes using an array-based chip. We retrieved 54 GBM from biorepositories of two institutions(40 from Columbia University and 14 from Case Western Reserve University) and 24 control brain tissues from the New York Brain Bank, which collected control brain tissues from consented subjects without history of neurological diseases at autopsy.

ORGANISM(S): Homo sapiens

PROVIDER: GSE50923 | GEO | 2013/10/18

SECONDARY ACCESSION(S): PRJNA219380

REPOSITORIES: GEO

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Genome-wide methylation analyses in glioblastoma multiforme (GBM)

Project description:Our main objective was to study genome-wide differential methylation in de novo glioblastoma multiforme (GBM, grade IV glioma). We evaluated CpG sites in gene promoters of 26,000+ genes using an array-based chip. We retrieved 54 GBM from biorepositories of two institutions(40 from Columbia University and 14 from Case Western Reserve University) and 24 control brain tissues from the New York Brain Bank, which collected control brain tissues from consented subjects without history of neurological diseases at autopsy. Bisulfite modified DNA was extracted from 54 GBM and 24 control brain tissue. The HumanMethylation27 Analysis Bead-Chips (Illumina) were used to interrogate 26,486 informative CpG sites in the autosomes.

2013-10-18 | E-GEOD-50923 | biostudies-arrayexpress

Unique RNA Expression Patterns in Serum Exosomes from Patients with Glioblastoma Multiforme

Project description:Comparative expression analysis of RNA isolated from microvesicles from serum from glioblastoma multiforme (GBM) patients and normal healthy individuals. Blood samples from 9 patients diagnosed with de-novo primary GBM were collected immediately prior to surgery. Blood from 7 normal healthy controls was collected from volunteers recruited at the MGH blood bank. From each sample, RNA was isolated from microvesicles isolated from 1 mL of serum, and the RNA was linearly amplified and labeled with Cy3. The amplified and labeled RNA was hybridized to 16 individual Agilent Arrays.

2011-12-01 | E-GEOD-24084 | biostudies-arrayexpress

INC280 Combined With Bevacizumab in Patients With Glioblastoma Multiforme

Project description:The purpose of this study is to determine whether the combination of two agents, INC280 and bevacizumab, is safe and effective when administered to patients with Glioblastoma Multiforme (GBM) who have progressed after receiving prior therapy or who have unresectable GBM.

| 2185625 | ecrin-mdr-crc

LncRNA and mRNA expression data from human glioblastoma multiforme

Project description:Glioblastoma multiforme(GBM) is the most common and lethal malignant primary brain tumor. Long non-coding RNAs (lncRNAs) are aberrantly expressed in many cancers and are involved in their cell proliferation, apoptosis, angiogenesis, and invasion. To systematically study the role of lncRNAs in GBM, we built gene expression profiles of GBM and non-tumor tissues using lncRNA and mRNA gene expression microarrays.

2020-06-30 | GSE100675 | GEO

The gene expression profiling of human Glioblastoma multiforme and normal brain tissues

Project description:We used microarrays to investigate the whole genome gene expression level changes of LncRNAs in human Glioblastoma multiforme (GBM) and normal brain tissues, and try to find out some LncRNA associated with the tumorigenesis of GBM. The human LncRNA microarray analysis of 9 samples (5 GBM and 4 normal brain tissues) were completed. Total RNA from each sample was quantified and RNA integrity was assessed using standard denaturing agarose gel electrophoresis. Total RNA of each sample was used for labeling and array hybridization. Array scanning using the Agilent Scanner G250C. Scanned images were then imported into NimbleScan software (version 2.5) for expression data analysis. Differentially expressed LncRNAs were filtered out for further study.

2013-09-26 | E-GEOD-51146 | biostudies-arrayexpress

The gene expression profiling of human Glioblastoma multiforme and normal brain tissues

2013-09-26 | GSE51146 | GEO

head and neck squamous cell carcinoma samples

Project description:Patient selection and specimen collection. Thirty-six freshly frozen tumor samples were prospectively collected from patients undergoing surgery or biopsy for HNSCC at the University of North Carolina (UNC) at Chapel Hill (21 patients) and Vanderbilt University (15 patients). All tissues were snap-frozen in liquid nitrogen within 30 minutes of surgical resection or biopsy, and kept at -80oC until further processing. All patients consented to participation in this study under protocols approved by IRB at the two institutions. This set includes the samples previously deposited into GEO including 8 additional samples and adjustment for protocol changes. The original 36 before protocol changes (and thus unadjusted) are here: Slebos RJ, Yi Y, Ely K, et al. Gene expression differences associated with human papillomavirus status in head and neck squamous cell carcinoma. Clin Cancer Res 2006;12(3 Pt 1):701-9. Keywords: disease state analysis

2009-03-22 | GSE10300 | GEO

Major MLL fusion partners regulate promoter-proximal pausing and release of RNA polymerase II

Project description:1Sheng Yushou Center of Cell Biology and Immunology, Department of Genetics and Developmental Biology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China. 2Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, NY 10065, USA. 3Systems Biology Center, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA. 4CCTS Bioinformatic Program, The Rockefeller University, New York, NY 10065, USA. 5State Key Laboratory of Genetic Engineering & Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai, 200438, China

2021-06-30 | GSE84157 | GEO

Transcriptional profiling of Myotonic dystrophy muscle and heart

Project description:Autopsy and biopsy muscle and heart tissue was collected from consented human subjects with and without confirmed myotonic dystrophy type 1, myotonic dystrophy type 2, or Duchenne muscular dystrophy. RNA was isolated for preparation of RNAseq libraries and sequenced on the Illumina platform.

2016-09-29 | GSE86356 | GEO

Transcription profiling of human head and neck squamous cell carcinoma samples reveals a feed-forward loop involving protein kinase Calpha and microRNAs regulates tumor cell cycle

2009-03-28 | E-GEOD-10300 | biostudies-arrayexpress

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