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
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
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
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/.
Project description:Finding a novel prognostic marker and therapeutic target for aggressive GBM is necessary. By analyzing pre- and post-treatment tumors from a GBM patient who experienced a very aggressive tumor recurrence after receiving concurrent chemoradiotherapy with temozolomide, we discovered a novel prognostic marker for aggressive mesenchymal GBM
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
Project description:In this study, we investigated and compared the miRNA and protein content of the small EVs released by different human GBM established cell lines and by GBM primary CSC lines, to explore the role of EVs in their different tumor behavior and capacities.