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Sample GSM606514 Query DataSets for GSM606514
Status Public on Jan 30, 2011
Title MDS tumor cells patient 45
Sample type genomic
 
Channel 1
Source name MDS tumor cells, patient 45
Organism Homo sapiens
Characteristics gender: M
International Prognostic Scoring System (IPSS): 0
extract protocol: PC
Treatment protocol Hypotonic treatment to eliminate red blood cells and fixation with methanol-acetic acid (3:1) of white blood cells.
Growth protocol Bone marrow cells were cultured unstimulated 24, 48 or 72 hrs in RPMI or Marrow Max Medium and 10% FCS. Colcemid was used to arrest cell cycle in metaphases.
Extracted molecule genomic DNA
Extraction protocol For samples marked Qiagen: DNA was extracted from methanol-acetic acid fixed cells with QIAamp DNA Blood Midi Kit (Qiagen).
For samples marked PC: DNA was extracted from methanol-acetic acid fixed cells with Proteinase K, SDS and Phenol-Chloroform.
Label Cy5
Label protocol Protocol Version 5.0, June 2007, Agilent.Same gender reference/control DNA was purchased from Promega as pool.
 
Channel 2
Source name control DNA
Organism Homo sapiens
Characteristics reference: Pooled, same gender reference/control DNA (Promega)
Treatment protocol Hypotonic treatment to eliminate red blood cells and fixation with methanol-acetic acid (3:1) of white blood cells.
Growth protocol Bone marrow cells were cultured unstimulated 24, 48 or 72 hrs in RPMI or Marrow Max Medium and 10% FCS. Colcemid was used to arrest cell cycle in metaphases.
Extracted molecule genomic DNA
Extraction protocol For samples marked Qiagen: DNA was extracted from methanol-acetic acid fixed cells with QIAamp DNA Blood Midi Kit (Qiagen).
For samples marked PC: DNA was extracted from methanol-acetic acid fixed cells with Proteinase K, SDS and Phenol-Chloroform.
Label Cy3
Label protocol Protocol Version 5.0, June 2007, Agilent.Same gender reference/control DNA was purchased from Promega as pool.
 
 
Hybridization protocol Protocol Version 5.0, June 2007, Agilent.
Scan protocol Images were quantified using Agilent Feature Extraction Software (version 10.7.1.1).
Description Agilent Feature Extraction file: sample_45.txt
MDS tumor cells
Data processing Agilent Feature Extraction Software (version 10.7.1.1) was used for background subtraction and LOWESS normalization.
 
Submission date Oct 08, 2010
Last update date Jan 30, 2011
Contact name Brigitte Royer-Pokora
E-mail(s) royer@uni-duesseldorf.de
Organization name Institute of Human Genetics and Anthropology, Heinrich-Heine-University Duesseldorf
Street address Universitätsstr. 1
City Duesseldorf
ZIP/Postal code 40225
Country Germany
 
Platform ID GPL10123
Series (1)
GSE24602 Comprehensive array CGH of normal karyotype Myelodysplastic syndrome reveals hidden recurrent and individual genomic copy number aberrations with prognostic relevance

Data table header descriptions
ID_REF
VALUE normalized log10 ratio Cy5/Cy3

Data table
ID_REF VALUE
1 -1.911372923e-002
2 7.848402201e-001
3 0.000000000e+000
4 0.000000000e+000
5 0.000000000e+000
6 0.000000000e+000
7 0.000000000e+000
8 0.000000000e+000
9 0.000000000e+000
10 0.000000000e+000
11 0.000000000e+000
12 0.000000000e+000
13 0.000000000e+000
14 5.078664078e-001
15 0.000000000e+000
16 0.000000000e+000
17 0.000000000e+000
18 0.000000000e+000
19 0.000000000e+000
20 0.000000000e+000

Total number of rows: 180880

Table truncated, full table size 4214 Kbytes.




Supplementary file Size Download File type/resource
GSM606514.txt.gz 51.7 Mb (ftp)(http) TXT
Processed data included within Sample table
Processed data provided as supplementary file

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