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Sample GSM140165 Query DataSets for GSM140165
Status Public on Feb 01, 2007
Title organotypic spheroid culture after 12 weeks from malignant glioma, patient 60
Sample type genomic
 
Channel 1
Source name 60S3
Organism Homo sapiens
Characteristics male 45 yo, glioblastoma multiforme, prior surgical resection, whole brain irradiation and temozolomide chemotherapy
12-week organotypic spheroid culture
Extracted molecule genomic DNA
Label Cy3
 
Channel 2
Source name reference DNA
Organism Homo sapiens
Characteristics Pooled DNA from the blood of 10 normal individuals
Extracted molecule genomic DNA
Label Cy5
 
 
Hybridization protocol available from http://www.vumc.nl/microarrays
Scan protocol MicroArray Scanner G2505B (Agilent Technologies)
Description DNA copy number information
Data processing Spot analysis and quality control was automated using BlueFuse version 3.2 (BlueGnome, Cambridge, UK). Spots were excluded with quality flag < 1 or confidence value < 0.85. Triplicates of the spot ratios (Cy3/Cy5 intensity signals) were fused within BlueFuse in a confidence weighted fashion. The resulting log2 transformed ratios were normalized to their mode value.
 
Submission date Oct 16, 2006
Last update date Dec 14, 2006
Contact name Philip C De Witt Hamer
E-mail(s) [email protected]
Phone +31 20 5663542
Fax +31 20 5669590
Organization name Academic Medical Center Amsterdam
Department Neurosurgery
Street address PO Box 22660
City Amsterdam
ZIP/Postal code 1100 DD
Country Netherlands
 
Platform ID GPL2843
Series (1)
GSE6042 DNA copy numbers of malignant glioma in culture

Data table header descriptions
ID_REF
AMPCH1 total signal intensity in channel 1 (Cy3)
AMPCH2 total signal intensity in channel 2 (Cy5)
LOG2RAT log2 transformed ratio of AMPCH1/AMPCH2
CONFIDENCE confidence estimate of the AMPCH1/AMPCH2 ratio as calculated by BlueFuse, between 0 and 1
QUALITY A quality flag determined as binary by BlueFuse to differentiate inferior spot quality (0) from sufficient spot quality (1)
VALUE Mode normalized value of the log2 transformed AMPCH1/AMPCH2 ratio after fusion of replicates by BlueFuse, after exclusion of spots with confidence < 0.85 or quality < 1

Data table
ID_REF AMPCH1 AMPCH2 LOG2RAT CONFIDENCE QUALITY VALUE
1 6.935 11.549 -.736 .01 0
2 4.128 3.368 .294 .01 0
3 19.63 34.004 -.793 .01 0
4 20.425 10.502 .96 .01 0
5 4.949 11.071 -1.161 .01 0
6 41.061 12.847 1.676 .01 0
7 4.809 40.904 -3.089 .01 0
8 5.898 24.962 -2.081 .01 0
9 29.531 51.638 -.806 .01 0
10 7.082 20.314 -1.52 .01 0
11 9.496 29.63 -1.642 .01 0
12 11.42 30.309 -1.408 .01 0
13 11.321 28.538 -1.334 .01 0
14 25.107 85.795 -1.773 .01 0
15 16.108 46.176 -1.519 .01 0
16 20.69 55.172 -1.415 .02 0
17 208.753 473.622 -1.182 .62 0
18 73.915 146.506 -.987 .06 0
19 5873.566 11150.839 -.925 .98 0 .385
20 6694 11816.451 -.82 .79 0 .385

Total number of rows: 19200

Table truncated, full table size 708 Kbytes.




Supplementary file Size Download File type/resource
GSM140165.xls.gz 1.3 Mb (ftp)(http) XLS

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