NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM578938 Query DataSets for GSM578938
Status Public on Aug 17, 2010
Title patient 2
Sample type genomic
 
Channel 1
Source name blood
Organism Homo sapiens
Characteristics gender: Female
patient: 2
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 Genomic DNAs from patient samples and controls were differentially labeled with cyanin-3 (Cy3) and Cy5 (Perkin Elmer,Boston, MA) using a Bioprime DNA direct labeling kit (Invitrogen, Carlsbad, CA)
 
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 Genomic DNAs from patient samples and controls were differentially labeled with cyanin-3 (Cy3) and Cy5 (Perkin Elmer,Boston, MA) using a Bioprime DNA direct labeling kit (Invitrogen, Carlsbad, CA)
 
 
Hybridization protocol Labeled probes hybridized onto the arrays at 37°C for 24 hours.
Scan protocol The slides were washed and fluorescent signals on the slides were scanned into image files using an Axon microarray scanner and ScanArray software (GenePix 4000B from Axon Instruments, Union City, CA).
Description Chromosomal microarray analysis with BAC V5.1 array discovered chromosome 4p deletion and 11p gain of this patient
Data processing Individual microarray LogRatio values were normalized using lowess smoothing to correct for intensity and spatially structured variation in the logRatio values. The logRatio values for replicate spots were then averaged within each array. These within array averaged values were then scaled by array using the median absolute deviation (MAD) of the smoothed, averaged logRatios. The scale factor for each array is determined to make the post scaling MAD values equivalent in between arrays using the geometric mean method. Finally, the dye-reversed pair of arrays are sign corrected and averaged to create a final statistic for determing segmental events and a final combined log-ratio value -- and this value is reported as the combined logRatio.
 
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 GPL10801
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)

Data table
ID_REF VALUE
1 -0.042
2 0.058
3 -0.449
4 0.032
5 0.053
6 -0.044
7 -0.062
8 0.041
9 0.016
10 0.043
11 0.026
12 0.048
13 -0.193
14 0
15 -0.021
16 0.017
17 0.009
18 -0.038
19 0.004
20 -0.069

Total number of rows: 1792

Table truncated, full table size 18 Kbytes.




Supplementary file Size Download File type/resource
GSM578938_102980Cy5vsNFCy3_output_post_patient_2.txt.gz 123.3 Kb (ftp)(http) TXT
Processed data included within Sample table
Processed data are available on Series record

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