Dataset features

Specifications


Application: Gene expression microarray analysis, aCGH data analysis, ChIP-on-chip analysis
Number of samples: 171
Release date: Apr 22 2010
Last update date: May 17 2017
Access: Public
Diseases: Glioblastoma, Glioma, Sleep Initiation and Maintenance Disorders, Neoplasms
Genes: PROM1, PTEN
Dataset link A Hierarchy of Self-Renewing Tumor-Initiating Cell Types in Glioblastoma

Experimental Protocol


DNA analysis and Expression profiling: DNA from patient tumor mincates was profiled for copy number changes on Affymetrix 500k chips and sequenced for mutations in exons 4-8 of p53 and exons 5&6 of PTEN. For determination of amplification, samples with mean relative copy number estimates of >3 for SNPs residing within the locus were scored as amplified. Copy number losses were determined using data from 30 SNPs within or immediately flanking the locus of interest. Relative copy number losses that were statistically significant at the p<.001 level were scored as losses regardless of the magnitude of the alteration. DNA from neurosphere lines was analyzed for copy number alterations by profiling on Agilent 244K arrays. Relative copy number estimates were determined using the GLAD segmentation algorithm. For expression profiling, RNA was extracted as previously described (Phillips et al., 2006) and profiled on Agilent WHG (for patient samples) or WHG 4x44 chips (for neurosphere lines and grafts) according to the manufacturer's (Agilent technologies, Palo Alto CA) protocol.

Repositories


GEO

GSE19612

ArrayExpress

E-GEOD-19612

BioProject

PRJNA122451

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