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Sample GSM710314 Query DataSets for GSM710314
Status Public on Oct 05, 2011
Title ROC_deletion_characterization
Sample type genomic
 
Channel 1
Source name wholeblood leukocytes
Organism Homo sapiens
Characteristics tissue: wholeblood leukocytes
genotype/variation: ROC_deletion
Extracted molecule genomic DNA
Extraction protocol High-molecular-weight DNAs from patients and healthy donors were prepared by standard proteinase K digestion followed by phenol-chloroform extraction from wholeblood leukocytes.
The quantity and quality of the DNA samples were assessed with Nanodrop technology (Coleman Technologies, Orlando, FL) and verified by electrophoresis through agarose gels and staining with ethidium bromide.
Label Cy5
Label protocol Genomic DNA from each sample was double digested with AluI and RsaI (Promega, Madison, WI) for 2 hours at 37°C. The digested DNAs were labeled by random priming with the Agilent Genomic DNA Labeling Kit Plus (Agilent technologies) for 2 hours at 37°C, according to the manufacturer’s instructions (Protocol v6.3, October 2010, Agilent technologies). Patients’ DNA and pooled normal control DNAs (reference) were labeled with Cy5-dUTP and Cy3-dUTP, respectively.
 
Channel 2
Source name Pool of six normal control DNAs from six healthy donors
Organism Homo sapiens
Characteristics tissue: wholeblood leukocytes
reference sample: Pool of six normal control DNAs from six healthy donors
Extracted molecule genomic DNA
Extraction protocol High-molecular-weight DNAs from patients and healthy donors were prepared by standard proteinase K digestion followed by phenol-chloroform extraction from wholeblood leukocytes.
The quantity and quality of the DNA samples were assessed with Nanodrop technology (Coleman Technologies, Orlando, FL) and verified by electrophoresis through agarose gels and staining with ethidium bromide.
Label Cy3
Label protocol Genomic DNA from each sample was double digested with AluI and RsaI (Promega, Madison, WI) for 2 hours at 37°C. The digested DNAs were labeled by random priming with the Agilent Genomic DNA Labeling Kit Plus (Agilent technologies) for 2 hours at 37°C, according to the manufacturer’s instructions (Protocol v6.3, October 2010, Agilent technologies). Patients’ DNA and pooled normal control DNAs (reference) were labeled with Cy5-dUTP and Cy3-dUTP, respectively.
 
 
Hybridization protocol Labeled products were purified with Microcon YM-30 filters (Millipore, Billerica, MA). Patient and normal control DNAs (reference) were mixed and hybridized with Human Cot I DNA (Invitrogen) at 65°C for 40 hours. The sandwiched slides were hybridized for 40 hours at 65°C with 15 rotations per minute and washed according to the Agilent protocol.
Scan protocol Arrays were scanned with an Agilent DNA Microarray Scanner (G2565BA).
Description Reference sample: Pool of six normal control DNAs from six healthy donors
Data processing Log2 ratios were determined with Agilent Feature Extraction software (v 9.1.3.1). Results were visualized and analyzed with Agilent’s Genomic Workbench 5.0 software, and copy number aberrations were detected with the Aberration Detection Method 2 (ADM-2) algorithm using a threshold value of 6.0. This threshold value of the altered copy number was determined from the normal variation in the control hybridization.
 
Submission date Apr 18, 2011
Last update date Oct 05, 2011
Contact name Eric Pasmant
E-mail(s) eric.pasmant@gmail.com
Organization name Paris Descartes University
Department EA7331
Street address Faculté de Pharmacie de Paris, 4 avenue de l’Observatoire
City Paris
ZIP/Postal code 75006
Country France
 
Platform ID GPL9777
Series (1)
GSE28676 Molecular characterization of two unrelated patients ABCB4 deletions

Data table header descriptions
ID_REF
VALUE Normalized log2 ratio (Cy5/Cy3) representing test/reference

Data table
ID_REF VALUE
1 1.09E-01
2 0.00E+00
3 0.00E+00
4 -4.52E-02
5 -8.26E-02
6 -3.52E-02
7 8.16E-02
8 3.91E-02
9 -3.12E-03
10 -6.87E-02
11 6.52E-02
12 1.38E-01
13 -3.75E-02
14 1.03E-02
15 -6.44E-02
16 -3.17E-02
17 -4.53E-03
18 2.60E-01
19 -7.37E-02
20 3.20E-02

Total number of rows: 420288

Table truncated, full table size 6658 Kbytes.




Supplementary file Size Download File type/resource
GSM710314_US84600241_252185013210_ROC.txt.gz 43.3 Mb (ftp)(http) TXT
Processed data included within Sample table

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