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Sample GSM579028 Query DataSets for GSM579028
Status Public on Aug 17, 2010
Title patient 6
Sample type genomic
 
Channel 1
Source name blood
Organism Homo sapiens
Characteristics gender: Female
patient: 6
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 V6.4 array discovered chromosome 8p deletion and 12p 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 GPL10804
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 0.1543 7528 10277
A_16_P15001543 -0.0571 1783 2242
A_16_P00000056 -0.0659 1578 1937
A_16_P00000060 -0.1657 2214 2528
A_16_P15001622 0.1257 1258 1766
A_16_P00000090 -0.1361 3433 4010
A_16_P00000099 0.0583 1699 2254
A_16_P00000104 -0.1605 5342.5 5836
A_16_P00000112 -0.0758 690.5 886
A_16_P00000127 -0.0254 1390 1777
A_16_P00000140 0.159 1429.5 1961
A_16_P15001775 -0.0958 2002 2216
A_16_P00000165 -0.0523 3545 4373
A_16_P00000173 0.0715 678 921
A_16_P00000179 -0.1157 2178 2524
A_16_P15001816 -0.0632 3437.5 4070
A_16_P00000200 0.12 6866 9094
A_16_P00000209 0.1311 6414 8635
A_16_P00000211 -0.2456 775 900
A_16_P15001886 0.0397 2342 3012

Total number of rows: 42892

Table truncated, full table size 1375 Kbytes.




Supplementary file Size Download File type/resource
GSM579028_KCL115581_patient_6.txt.gz 1.7 Mb (ftp)(http) TXT
Processed data included within Sample table

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