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Sample GSM706880 Query DataSets for GSM706880
Status Public on Nov 18, 2011
Title AB010
Sample type genomic
 
Channel 1
Source name Genomic DNA from tumor
Organism Homo sapiens
Characteristics age: 61
gender: M
site: Tongue
tumor size (cm): 1.5
tumor thickness: 1.5
node status (clinical): X
histology: MD
recurrence: None
follow up months: 126
vital status: Alive
tumor status: Free
node status (path): 0
tobacco use: None
alcohol use: None
Extracted molecule genomic DNA
Extraction protocol Total DNA extracted from microdissected formalin fixed paraffin embedded tissue sections by digestion with proteinase K followed by a phenol chloroform extraction
Label Cy3
Label protocol Test and reference samples labeled with Cy3 and Cy5 respectively using a random priming reaction in a 25 μL reaction to label genomic DNA
 
Channel 2
Source name Normal human genomic DNA
Organism Homo sapiens
Characteristics gender: Male
Extracted molecule genomic DNA
Extraction protocol Total DNA extracted from microdissected formalin fixed paraffin embedded tissue sections by digestion with proteinase K followed by a phenol chloroform extraction
Label Cy5
Label protocol Test and reference samples labeled with Cy3 and Cy5 respectively using a random priming reaction in a 25 μL reaction to label genomic DNA
 
 
Hybridization protocol Labeled test (600ng) and reference (600ng) DNA was hybridized with human Cot-1 DNA for ~ 48 hours at 37°C to arrays of 2464 BAC clones spotted in triplicate (HumArray3.2, UCSF Helen Diller Family Comprehensive Cancer Center Microarray Core). Slides were washed with 50% formamide, 2X SSC for 15 minutes at 45°C followed by a 15 minute wash in PN buffer (0.1M phosphate buffer in 0.1% Nonidet P40) at room temperature. Slides were mounted in a DAPI solution to stain the array spots (90% glycerol, 10% PBS, 1μM DAPI) and imaged.
Scan protocol DAPI, Cy3 and Cy5 images were acquired using a custom CCD camera system
Description oral SCC
DNA isolated from banked blood (buffy coat)
Data processing Array image quantitation was done with UCSF Spot. After quality filtering on spots and clones, an in-house SpotCorrection algorithm was used to remove systematic geometric and GC content effects. Replicate spot averaging and median centering were then performed. A remaining 'paraffin-embedded effect' was removed as follows. For tumor profiles with paired normals, we applied noise reduction using the normal sample as template. The magnitude of the effect was estimated using the derivative log ratio spread (DLRS) [Agilent]. For the two tumor profiles without a paired normal (and AB029 and AB067), we employed the per-probe median of the normal profiles as a normal template, with DLRS scaling as above. Clones without mapping information were excluded. Also, clones of possibly poor quality where more than 50% of the samples had missing data were excluded. Then replicate clones were averaged.
The paired normals for the tumor samples did not have processed normalized data; therefore, these Samples are tableless. The normal data only played a role in the pre-processing stage that generated the processed tumor data.
 
Submission date Apr 12, 2011
Last update date Nov 18, 2011
Contact name Taku Tokuyasu
E-mail(s) [email protected]
Organization name UCSF
Department Helen Diller Family Comprehensive Cancer Center
Street address 1450 3rd Street, HD555
City San Francisco
State/province CA
ZIP/Postal code 94158-9001
Country USA
 
Platform ID GPL6359
Series (1)
GSE28407 Diverse routes to oral cancer differing in genome instability and risk for cervical node metastasis

Data table header descriptions
ID_REF
VALUE log2 ratio of test over reference hybridization signal after preprocessing as described above

Data table
ID_REF VALUE
HA3.2P2_P36 0.15544
HA3.2P2_R24 0.07505
HA3.2P1_D28 0.09887
HA3.2P1_H36 0.05025
HA3.2P1_H28 0.03729
HA3.2P1_L28 -0.05737
HA3.2P1_D25 -0.01571
HA3.2P1_P28 -0.00615
HA3.2P1_B16 0.00232
HA3.2P1_F16 0.01085
HA3.2P1_J16 0.00906
HA3.2P1_A30 -0.00412
HA3.2P1_N16 -0.07947
HA3.2P1_R16 -0.05112
HA3.2P2_H46 -0.11345
HA3.2P1_A8 -0.1214
HA3.2P1_H25 -0.19347
HA3.2P1_Z16 -0.01565
HA3.2P1_V16 -0.09376
HA3.2P1_AD16 -0.00827

Total number of rows: 2322

Table truncated, full table size 45 Kbytes.




Supplementary file Size Download File type/resource
GSM706880.txt.gz 729.2 Kb (ftp)(http) TXT
Processed data included within Sample table

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