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Sample GSM140135

Query DataSets for GSM140135

Status

Public on Feb 01, 2007

Title

organotypic spheroid culture after 2 weeks from malignant glioma, patient 33

Sample type

genomic

Channel 1

Source name

33S

Organism

Homo sapiens

Characteristics

male 38 yo, glioblastoma multiforme, no prior treatment
2-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	1828.711	2899.717	-.665	.64	1
2	1714.455	2705.09	-.658	.54	1
3	1733.189	2704.127	-.642	.55	1
4	49.481	88.963	-.846	.01	0
5	71.631	118.441	-.726	.01	0
6	56.478	130.554	-1.209	.01	0
7	11415.115	17327.043	-.602	.99	1	.233
8	11046.014	16707.287	-.597	.99	1	.233
9	10857.12	16368.349	-.592	.99	1	.233
10	242.92	379.575	-.644	.02	1
11	240.762	383.818	-.673	.02	1
12	223.394	354.821	-.668	.02	1
13	3904.688	5925.46	-.602	.98	1	.228
14	3698.447	5556.501	-.587	.77	1	.228
15	3783.238	5730.488	-.599	.61	1	.228
16	149.644	217.677	-.541	.01	0
17	156.227	248.872	-.672	.01	0
18	120.189	187.712	-.643	.01	0
19	11793.617	17334.023	-.556	.99	1	.34
20	11521.749	16889.461	-.552	.99	1	.34

Total number of rows: 19200

Table truncated, full table size 734 Kbytes.

Supplementary file	Size	Download	File type/resource
GSM140135.xls.gz	1.3 Mb	(ftp)(http)	XLS