NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM578940 Query DataSets for GSM578940
Status Public on Aug 17, 2010
Title patient 3
Sample type genomic
 
Channel 1
Source name blood
Organism Homo sapiens
Characteristics gender: Female
patient: 3
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was extracted from peripheral blood using the Qiagen DNA Blood Mini Kit. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer and agarose gel electrophoresis.
Label cy5
Label protocol 1-2 μg of genomic DNA from experimental and gender matched reference samples were digested with AluI (10 units) and RsaI (10 units) (Promega, Madison, WI) at 37°C for 2 hours. The labeling reaction was performed using the Bioprime CGH Labeling Module (Invitrogen, Carlsbad, CA) at 37°C for 2 hours in the presence of cyanine 5-dCTP (for the experimental sample) or cyanine 3-dCTP (for the reference sample) (PerkinElmer, Boston, MA).
 
Channel 2
Source name Blood
Organism Homo sapiens
Characteristics gender: female
reference: gender matched normal reference sample
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was extracted from peripheral blood using the Qiagen DNA Blood Mini Kit. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer and agarose gel electrophoresis.
Label Cy3
Label protocol 1-2 μg of genomic DNA from experimental and gender matched reference samples were digested with AluI (10 units) and RsaI (10 units) (Promega, Madison, WI) at 37°C for 2 hours. The labeling reaction was performed using the Bioprime CGH Labeling Module (Invitrogen, Carlsbad, CA) at 37°C for 2 hours in the presence of cyanine 5-dCTP (for the experimental sample) or cyanine 3-dCTP (for the reference sample) (PerkinElmer, Boston, MA).
 
 
Hybridization protocol The labeled samples were applied to an array, which was placed in a microarray hybridization chamber (Agilent Technologies), hybridized for more than 20 hours at 65°C in a rotating hybridization oven and washed according to the manufacturer’s protocol (Agilent Technologies).
Scan protocol The slides were scanned into image files using a GenePix Model 4000B microarray scanner (Molecular Devices, Sunnyvale, CA) or an Agilent Microarray Scanner (PN G2565BA).
Description Chromosomal microarray analysis with OLIGO V6.1 array discovered chromosome 4p deletion and 11p gain of this patient
Data processing Microarray image files of oligo arrays were quantified using Agilent Feature Extraction software (v9.0) default setting, and text file outputs from the quantitation analysis were converted to BAC-level emulation data by combining oligo data corresponding to regions encompassed by BAC clones (“emulated BAC clone”) and then using our in-house analysis package for copy number analysis.
 
Submission date Aug 13, 2010
Last update date Aug 16, 2010
Contact name zhishuo ou
E-mail(s) zhishuoo@bcm.edu
Phone 7137984365
Organization name Baylor College of medicine
Department Molecular and Human Genetics
Lab Dr Beaudet
Street address One Baylor Plaza
City Houston
State/province TX
ZIP/Postal code 77030
Country USA
 
Platform ID GPL10802
Series (1)
GSE23587 Homologous recombination between nonhomologous chromosomes – Recurrent chromosomal translocations mediated by interchromosomal NAHR

Data table header descriptions
ID_REF
VALUE Normalized log2 ratio (experiment/control)
IntensityCy3
IntensityCy5

Data table
ID_REF VALUE IntensityCy3 IntensityCy5
A_16_P00000036 0.3168 3142.5 4028
A_16_P15001543 -0.1344 459 409
A_16_P00000056 -0.4661 704 512
A_16_P00000060 -0.2478 617 523
A_16_P00000066 -0.0068 1088 1125
A_16_P15001594 -0.2718 722 592
A_16_P00000082 0.0387 720 737
A_16_P15001622 0.257 406 448
A_16_P00000090 0.072 956 1048
A_16_P00000099 0.0148 504 496
A_16_P00000104 0.0522 1578 1567
A_16_P00000112 0.3587 204 207
A_16_P00000114 -0.072 803.5 778
A_16_P00000122 0.1611 751 842
A_16_P00000127 -0.0473 665 648
A_16_P00000136 -0.1186 655 630
A_16_P00000140 0.2536 1538.5 1879
A_16_P15001756 0.0099 864 838
A_16_P15001775 -0.3948 635 501
A_16_P00000165 0.288 1129 1346

Total number of rows: 42640

Table truncated, full table size 1321 Kbytes.




Supplementary file Size Download File type/resource
GSM578940_KCL108001_patient_3.txt.gz 1.6 Mb (ftp)(http) TXT
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap