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Sample GSM275658 Query DataSets for GSM275658
Status Public on Oct 30, 2008
Title expression microarray - GBM8
Sample type RNA
 
Source name GBM8 - tumor RNA
Organism Homo sapiens
Characteristics Age: 65; Gender: Female; WHO grade IV
Extracted molecule total RNA
Extraction protocol Total RNA was isolated using the NucleoSpin RNAII Kit (Macherey-Nagel, Düren, DE) and quantified via spectrophotometry (Nanodrop, Labtech). RNA integrity was confirmed using the Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA).
Label Cy3
Label protocol Agilent’s recommended procedures for microarray-based one-color gene expression analysis were followed. Briefly, 350ng of total RNA with control RNA Spike In were amplified and labeled with Cy3-CTP using the T7-based Low RNA Input Linear Amplification Kit, PLUS, One-Color (Agilent Technologies, Santa Clara, CA). After purification (RNeasy Mini Kit, QIAGEN), labeled cRNAs were quantified for yield and dye incorporation using a Nanodrop spectrophotometer.
 
Hybridization protocol 1.65microg of Cy3-labeled RNA were hybridized to each array in a 110microl total volume of hybridization buffer (Agilent Technologies) for 17 hours at 65°C. Washing was performed according to the Agilent protocol.
Scan protocol Arrays were analyzed using the dynamic autofocus Agilent G2565BA microarray scanner and the Agilent Feature Extraction software (FE v9.4.1, GE1-v5_91_0806 protocol).
Description Poor quality spots were flagged according to default FE criteria and corresponding values were removed.
Data processing Median normalization from the processed Multiplicative Detrend FE data was carried out using limma (R package) from Bioconductor. Missing values were imputed by the use of the k-nearest neighbors method implemented in impute (R package).
 
Submission date Mar 18, 2008
Last update date Sep 20, 2008
Contact name Marie de Tayrac
E-mail(s) marie.de-tayrac@univ-rennes1.fr
Phone 0223234776
Organization name CNRS-UMR6061
Lab Regulation of transcription and oncogenesis
Street address 2 avenue du Professeur Léon Bernard
City Rennes
ZIP/Postal code 35000
Country France
 
Platform ID GPL6480
Series (1)
GSE10878 Integrative Genome-wide Analysis of Glioblastoma.

Data table header descriptions
ID_REF
VALUE normalized log10 (Cy3) [gProcessedSignal]

Data table
ID_REF VALUE
A_23_P100001 2.52770308448162
A_23_P100011 2.34582317218545
A_23_P100022 2.62092112146527
A_23_P100056 2.32198587820972
A_23_P100074 3.12143122010074
A_23_P100092 2.40717795827072
A_23_P100103 2.71726401958008
A_23_P100111 2.07219436486636
A_23_P100127 3.14009174933545
A_23_P100133 2.60627594512074
A_23_P100141 2.58183095528128
A_23_P100156 2.92763317054993
A_23_P100177 2.66763978459121
A_23_P100189 1.40734266412817
A_23_P100196 3.63277466374871
A_23_P100203 3.87857205530004
A_23_P100220 2.54488433181286
A_23_P100240 0.744224277306711
A_23_P10025 3.6031325025665
A_23_P100263 4.04675431281198

Total number of rows: 41000

Table truncated, full table size 1187 Kbytes.




Supplementary file Size Download File type/resource
GSM275658.txt.gz 6.6 Mb (ftp)(http) TXT
Processed data included within Sample table

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