ALLELE Consortium GBM Project
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ABSTRACT:
PROVIDER: PRJNA862248 | ENA |
REPOSITORIES: ENA
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Project description:This SuperSeries is composed of the SubSeries listed below. Consortium contacts: Maria Pedersen: mpedersen@nygenome.org Hemali Phatnani: hphatnani@nygenome.org NYGC ALS Consortium: cgndhelp@nygenome.org
2019-09-20 | GSE137810 | GEO
Project description:This SuperSeries is composed of the following subset Series: GSE24446: Genetic abnormalities in GBM brain tumors GSE24452: Genetic abnormalities in various cell subpopulations of GBM brain tumors GSE24557: Exon-level expression profiles of GBM brain tumors Refer to individual Series
2010-11-21 | E-GEOD-24558 | biostudies-arrayexpress
Project description:The mission of expO is to build on the technologies and outcomes of the Human Genome Project to accelerate improved clinical management of cancer patients. IGC's Expression Project for Oncology (expO) seeks to integrate longitudinal clinical annotation with gene expression data for a unique and powerful portrait of human malignancies, providing critical perspective on diagnostic markers, prognostic indicators, and therapeutic targets. The goal of expO and its consortium supporters is to procure tissue samples under standard conditions and perform gene expression analyses on a clinically annotated set of deidentified tumor samples. The tumor data is updated with clinical outcomes and is released into the public domain without intellectual property restriction. Series-matrices are available at ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/SeriesMatrix/GSE2109/. For more information, see http://www.intgen.org/ Keywords: cancer portraits
2005-01-15 | GSE2109 | GEO
Project description:The Mammalian Methylation Consortium aimed to characterize the relationship between cytosine methylation levels and a) species characteristics such as maximum lifespan and b) individual sample characteristics such as age, sex, tissue type. Both supervised machine learning approaches and unsupervised machine learning approaches were applied to the data as described in the citations. To facilitate comparative analyses across species, the mammalian methylation consortium applied a single measurement platform (the mammalian methylation array, GPL28271) to n=15216 DNA samples derived from 70 tissue types of 348 different mammalian species (331 eutherian-, 15 marsupial-, and 2 monotreme species). Most of the CpGs are located in highly conserved stretches of DNA but not all CpGs apply to all species as detailed in the description of the platform, GPL28271 and on https://github.com/shorvath/MammalianMethylationConsortium/.
2023-08-05 | GSE223748 | GEO
Project description:Single RNA-Seq on GBM cells from human GBM sample
| PRJNA820777 | ENA
Project description:We performed RNA-Seq as part of the ENCODE project in order to determine sites of allele-specific expression This was done in the GM12878 cell line which was genotyped as part of the pilot II phase of the 1000 genomes project. There is a matching ChIP-Seq experiments for a number of transcription factors were also performed on the same cell line. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf
2011-07-09 | GSE30400 | GEO
Project description:Glioblastoma multiforme (GBM) is the most aggressive form of brain tumors. Despite radical surgery and radiotherapy supported by chemotherapy, the disease still remains incurable with extremely low median survival rate of 12-15 months from the time of initial diagnosis. The main cause of treatment failure is considered to be the presence of cells that are resistant to such treatment. MicroRNAs (miRNAs) as regulators of gene expression are involved in the tumor pathogenesis, including GBM. MiR-338 is a brain specific miRNA which has been described to target pathways involved in proliferation and differentiation. In our study, miR-338-3p and -5p were differentially expressed in GBM tissue in comparison to non-tumor brain tissue. Overexpression of miR-338-3p with miRNA mimic did not show any changes in proliferation rates in GBM cell lines (A172, T98G, U87MG). On the other hand, pre-miR-338-5p notably decreased proliferation and caused cell cycle arrest. Since radiation is currently the main treatment modality in GBM, we combined overexpression of pre-miR-338-5p with radiation, which led to significantly decreased of cell proliferation, and increased cell cycle arrest and apoptosis in comparison to only irradiated cells. To better elucidate the mechanism of action, we performed gene expression profiling analysis that revealed targets of miR-338-5p being Ndfip1, Rheb, ppp2R5a. These genes have been described to be involved in DNA damage response, proliferation and cell cycle regulation. To our knowledge, this is the first study to describe role of miR-338-5p in GBM and its potential to improve sensitivity of GBM to radiation. Study was performed on three glioblastoma multiforme cell lines A172, T98G and U87MG. This experiment was performed on Affymetrix GeneChip Human Gene ST 1.0 to elucidate the targets of miRNA-338-5p. Cell lines were seeded 24 hours prior transfection. After transfection with pre-miR338-5p or negative control cell were cultured for 24 hours and harvested. RNA was isolated using MirVana miRNA Isolation Kit (Ambion, USA) and checked for RNA integrity by Bioanalyzer 2100 and purity by ratios 260/280>1.8 and 260/230>1.8 by Nanodrop2000.
2015-12-10 | E-GEOD-75789 | biostudies-arrayexpress