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Sample GSM1923051 Query DataSets for GSM1923051
Status Public on Mar 10, 2016
Title Tumor28
Sample type genomic
 
Channel 1
Source name glioblastoma tissue
Organism Homo sapiens
Characteristics clinical_subgroup: short-term survivor (STS)
tissue type: glioblastoma
Growth protocol Not applicable
Extracted molecule genomic DNA
Extraction protocol Tumor tissue was snap-frozen and stored at -80°C until further processing. DNA was extracted with the QIAmp DNA Mini Kit (Qiagen) from samples found eligible in terms of tumor cell content (>60%) and necrosis (<20%). Analyte concentration and quality were determined using the Nanodrop 2000 spectrophotometer (Thermo Scientific) and Bioanalyzer 2100 (Agilent). For enrichment of hypermethylated DNA fractions, Methyl-CpG-binding domain (MBD)-Fc protein was produced and MCIp performed as previously described (Schilling et al., Genomics 2007). Briefly, 75 µg of MBD-Fc protein was coupled to 50 µl SIMAG protein A magnetic beads (Chemicell) at 4°C overnight. After binding of 2 µg sonicated DNA, the DNA was eluted with increasing NaCl concentrations (300-1000 mM) using the MagnetoPure-Micro bead separator (Chemicell). Lowly and highly methylated DNA was eluted at the lowest and highest concentrations, respectively. DNA enrichment was monitored by real-time PCR targeting known unmethylated and methylated DNA regions.
Label Cy5
Label protocol Highly methylated glioblastoma and normal brain control DNA were labeled with Alexa Fluor 5 and Alexa Fluor 3, respectively.
 
Channel 2
Source name normal brain tissue
Organism Homo sapiens
Characteristics tissue type: normal brain
Growth protocol Not applicable
Extracted molecule genomic DNA
Extraction protocol Tumor tissue was snap-frozen and stored at -80°C until further processing. DNA was extracted with the QIAmp DNA Mini Kit (Qiagen) from samples found eligible in terms of tumor cell content (>60%) and necrosis (<20%). Analyte concentration and quality were determined using the Nanodrop 2000 spectrophotometer (Thermo Scientific) and Bioanalyzer 2100 (Agilent). For enrichment of hypermethylated DNA fractions, Methyl-CpG-binding domain (MBD)-Fc protein was produced and MCIp performed as previously described (Schilling et al., Genomics 2007). Briefly, 75 µg of MBD-Fc protein was coupled to 50 µl SIMAG protein A magnetic beads (Chemicell) at 4°C overnight. After binding of 2 µg sonicated DNA, the DNA was eluted with increasing NaCl concentrations (300-1000 mM) using the MagnetoPure-Micro bead separator (Chemicell). Lowly and highly methylated DNA was eluted at the lowest and highest concentrations, respectively. DNA enrichment was monitored by real-time PCR targeting known unmethylated and methylated DNA regions.
Label Cy3
Label protocol Highly methylated glioblastoma and normal brain control DNA were labeled with Alexa Fluor 5 and Alexa Fluor 3, respectively.
 
 
Hybridization protocol Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential
Scan protocol Scanned on an Agilent G2505B scanner.
Images were quantified using Agilent Feature Extraction Software.
Description DNA was enriched for hypermethylated fractions by Methyl-CpG Immunoprecipitation (MCIp)
Data processing Scanning raw data were processed using the statistical environment R. Background correction and log2 transformation were performed according to the NormExp method with offset = 50 (Ritchie et al., Bioinformatics 2007). Intensity-based LOESS normalization was applied to rank-invariant probes and negative controls in order to reduce technical noise between samples (Tseng et al., Nucleic Acids Res 2001). For intra-array normalization, log-intensity ratios (M-value) and log-intensity averages (A-values) were scaled to have the same median-absolute value across the array.
 
Submission date Nov 02, 2015
Last update date Mar 10, 2016
Contact name Christel Herold-Mende
Organization name Heidelberg University Hospital
Department Department of Neurosurgery
Lab Experimental Neurosurgery
Street address Im Neuenheimer Feld 400
City Heidelberg
ZIP/Postal code 69117
Country Germany
 
Platform ID GPL9767
Series (1)
GSE74561 LOC283731 promoter hypermethylation prognosticates survival after radiochemotherapy in IDH1 wild-type glioblastoma patients

Data table header descriptions
ID_REF
VALUE Normalized log10 ratio (Cy5/Cy3) representing test/reference. For details: see data processing.

Data table
ID_REF VALUE
A_17_P00000030 -0.010965
A_17_P15006585 0.385039
A_17_P15006586 0.408716
A_17_P00000058 0.023965
A_17_P00000077 -0.470361
A_17_P00000078 -0.55859
A_17_P00000079 0.031118
A_17_P15006611 -0.169467
A_17_P15006612 -0.098098
A_17_P00000131 0.901383
A_17_P00000132 0.591206
A_17_P00000133 0.554435
A_17_P15006642 0.281067
A_17_P00000171 -0.039191
A_17_P15006648 -0.037345
A_17_P00000172 -0.018836
A_17_P15006650 0.048746
A_17_P15006651 0.004454
A_17_P15006652 0.087905
A_17_P15006654 -0.004617

Total number of rows: 199416

Table truncated, full table size 4733 Kbytes.




Supplementary file Size Download File type/resource
GSM1923051_cmc_251479117330_S01_ChIP_105_Dec08.txt.gz 57.7 Mb (ftp)(http) TXT
Processed data included within Sample table
Processed data are available on Series record

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