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Sample GSM140143

Query DataSets for GSM140143

Status

Public on Feb 01, 2007

Title

primary cell culture after 2 weeks from malignant glioma, patient 3446

Sample type

genomic

Channel 1

Source name

3446C

Organism

Homo sapiens

Characteristics

male 34 yo, glioblastoma multiforme, no prior treatment
2-week primary cell culture, trypsinization passage 3

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	1709.722	3029.649	-.825	.59	1
2	1549.532	2708.555	-.806	.54	1
3	1566.907	2752.422	-.813	.47	1
4	315.418	58.785	2.424	.01	0
5	438.903	86.498	2.343	.01	0
6	329.065	47.561	2.791	.01	0
7	8571.736	12832.407	-.582	.99	1	.181
8	8478.693	12508.413	-.561	.99	1	.181
9	8835.437	13084.684	-.567	.99	1	.181
10	207.003	353.924	-.774	.01	0
11	195.764	350.205	-.839	.01	1
12	233.556	393.864	-.754	.02	1
13	3581.656	5655.281	-.659	.98	1	.076
14	3484.317	5535.634	-.668	.74	1	.076
15	3306.662	5347.698	-.694	.97	1	.076
16	142.598	257.808	-.854	.01	0
17	139.315	241.263	-.792	.01	0
18	135.68	234.208	-.788	.01	0
19	9295.624	13633.212	-.553	.99	1	.25
20	9339.932	13608.576	-.543	.99	1	.25

Total number of rows: 19200

Table truncated, full table size 733 Kbytes.

Supplementary file	Size	Download	File type/resource
GSM140143.xls.gz	1.3 Mb	(ftp)(http)	XLS