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Sample GSM873375 Query DataSets for GSM873375
Status Public on Feb 10, 2012
Title 18207patient
Sample type genomic
 
Source name patient
Organism Homo sapiens
Characteristics cell type: white blood cell
cell source: patient
Treatment protocol None
Growth protocol None
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was extracted from sorted cells obtained from peripheral blood using the Qiagen Puregen Kit and buccal epithelia using Oragene DNA 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 whole-genome amplified, purified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.
Scan protocol The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000 7G.
Description Hybridized to Affymetrix Cytogenetics Array
Data processing CEL files generated by Affymetrix Command Console and CYCHP files generated byAffymetrix Chromosome Analysis Suite software (ChAS). DNA copy number and allele analysis were performed using Affymetrix ChAS, which compares all hybridization intensities against a built-in reference data set.
Primary data description: copy number, allele peaks.
The allele peaks data are included in the cychp files in addition to copy number.
 
Submission date Feb 09, 2012
Last update date Feb 10, 2012
Contact name JIANMING PEI
E-mail(s) jianming.pei@fccc.edu
Phone 2157282898
Fax 2152141623
Organization name Fox Chase Cancer Center
Department Population Science
Lab Testa's Lab
Street address 333 Cottman Ave.
City Philadelphia
State/province PA
ZIP/Postal code 19111
Country USA
 
Platform ID GPL11157
Series (1)
GSE35674 Affymetrix Cytogenetics array data for a study of D45-deficiency resulting from uniparental disomy: a novel cause of SCID

Data table header descriptions
ID_REF
VALUE LOG2 RATIO (copy number in log)
WEIGHTED LOG2 RATIO
SMOOTH SIGNAL smoothed copy number

Data table
ID_REF VALUE WEIGHTED LOG2 RATIO SMOOTH SIGNAL
C-0HT3C -0.133984 -0.124645 2.056324
C-0HT3D -0.124645 -0.124645 2.056765
C-0HT3E -0.328988 -0.124645 2.056902
C-0HT3F 0.006548 0.006548 2.056842
C-0HT3I 0.064145 0.021599 2.057294
C-0HT48 0.478648 0.064145 2.058018
C-0HT4C 0.021599 0.064145 2.058869
S-2K62M 0.117269 0.079862 2.059703
C-0HT4G -0.157613 0.065429 2.060407
C-0HT4K 0.079862 0.065429 2.060929
C-0HT4L 0.065429 0.053868 2.060850
C-0HT4M 0.053868 0.053868 2.061138
C-0HT4O -0.125409 0.053868 2.060885
C-0HT4P -0.051370 -0.051370 2.061482
C-0HT4R 0.135423 -0.103624 2.062287
S-2H4KY -0.103624 -0.051370 2.062271
C-0HT4U -0.162277 0.063920 2.064859
S-2K3DK 0.174395 0.063920 2.066034
C-0HT4X 0.063920 0.063920 2.066371
S-2KEV0 0.162502 0.063920 2.066629

Total number of rows: 2141361

Table truncated, full table size 74531 Kbytes.




Supplementary file Size Download File type/resource
GSM873375.CEL.gz 20.8 Mb (ftp)(http) CEL
GSM873375.cychp.gz 37.6 Mb (ftp)(http) CYCHP
Processed data included within Sample table
Processed data provided as supplementary file

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