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Sample GSM140156

Query DataSets for GSM140156

Status

Public on Feb 01, 2007

Title

organotypic spheroid culture after 2 weeks from malignant glioma, patient 58

Sample type

genomic

Channel 1

Source name

58S1

Organism

Homo sapiens

Characteristics

male 81 yo, glioblastoma multiforme, prior surgical resection and whole brain irradiation
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	9.893	29.07	-1.555	.01	0
2	7.788	43.216	-2.472	.01	0
3	22.021	70.119	-1.671	.01	0
4	10.037	52.689	-2.392	.01	0
5	31.97	108.117	-1.758	.01	0
6	5.676	77.359	-3.769	.01	0
7	8.985	133.394	-3.892	.01	0
8	17.14	149.076	-3.121	.02	0
9	27.156	235.589	-3.117	.02	0
10	29.252	114.799	-1.972	.01	0
11	41.572	122.634	-1.561	.01	0
12	7.055	97.285	-3.785	.01	0
13	1383.822	1569.392	-.182	.01	0
14	18.815	206.606	-3.457	.08	0
15	9.077	188.588	-4.377	.01	0
16	25.711	168.928	-2.716	.01	0
17	63.478	530.373	-3.063	.37	0
18	95.847	906.796	-3.242	.57	0
19	8376.03	13608.734	-.7	.89	0	.237
20	7870.266	12833.528	-.705	.91	0	.237

Total number of rows: 19200

Table truncated, full table size 695 Kbytes.

Supplementary file	Size	Download	File type/resource
GSM140156.xls.gz	1.3 Mb	(ftp)(http)	XLS