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Sample GSM578540 Query DataSets for GSM578540
Status Public on Aug 17, 2010
Title patient 6 [SNP]
Sample type genomic
 
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 Biotin
Label protocol As per manufacturer (Affymetrix)
 
Hybridization protocol DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.
Scan protocol The Arrays were scanned using a GeneChip® Scanner 3000 7G (Affymetrix, Inc.)
Description Breakpoints of chromosomal translocations were fine mapped with the Affymetrix Genome-Wide SNP Array 6.0 arrays
Data processing Data were analyzed using Genotyping Console version 2.1 software.
primary data description: Copy number state
 
Submission date Aug 12, 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 GPL6801
Series (1)
GSE23587 Homologous recombination between nonhomologous chromosomes – Recurrent chromosomal translocations mediated by interchromosomal NAHR

Data table header descriptions
ID_REF
VALUE CN STATE
CHROMOSOME
POSITION
LOG2 RATIO
SMOOTH SIGNAL
LOH
ALLELE DIFFERENCE

Data table
ID_REF VALUE CHROMOSOME POSITION LOG2 RATIO SMOOTH SIGNAL LOH ALLELE DIFFERENCE
CN_473963 3.000000 1 51586 0.610128 2.514544 nan nan
CN_473964 3.000000 1 51659 0.064948 2.514523 nan nan
CN_473965 3.000000 1 51674 0.374487 2.514519 nan nan
CN_473981 3.000000 1 52771 -0.525395 2.514217 nan nan
CN_473982 3.000000 1 52788 0.472736 2.514213 nan nan
CN_497981 3.000000 1 62627 0.282949 2.511731 nan nan
CN_502615 3.000000 1 75787 0.017980 2.509100 nan nan
CN_502613 3.000000 1 75849 0.575499 2.509089 nan nan
CN_502614 3.000000 1 76175 0.196339 2.509035 nan nan
CN_502616 3.000000 1 76192 -0.530142 2.509032 nan nan
CN_502843 3.000000 1 88453 0.425175 2.507406 nan nan
CN_466171 3.000000 1 218557 1.085563 5.691730 nan nan
CN_468414 3.000000 1 218926 0.317491 5.690787 nan nan
CN_468412 3.000000 1 219009 1.196955 5.690576 nan nan
CN_468413 3.000000 1 219024 1.189413 5.690537 nan nan
CN_470565 3.000000 1 219470 1.361063 5.689398 nan nan
CN_468424 3.000000 1 225521 0.404864 5.673903 nan nan
CN_468425 3.000000 1 225579 0.264978 5.673754 nan nan
CN_460512 2.000000 1 346294 -0.472066 1.783679 nan nan
CN_460513 2.000000 1 346393 0.276861 1.783680 nan nan

Total number of rows: 1813441

Table truncated, full table size 114240 Kbytes.




Supplementary file Size Download File type/resource
GSM578540.CEL.gz 29.5 Mb (ftp)(http) CEL
GSM578540.CHP.gz 35.1 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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