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Sample GSM388008 Query DataSets for GSM388008
Status Public on Oct 07, 2009
Title SBA_14
Sample type genomic
 
Channel 1
Source name small intestinal adenocarcinoma
Organism Homo sapiens
Characteristics age: 34
sex: male
tumor site: Jejunum
celiac disease: No
tnm: pT3N1Mx
platform_id type: oligo
Extracted molecule genomic DNA
Extraction protocol DNA extraction was performed using the the QIAmp DNA Micro Kit (Qiagen).
Label Cy3
Label protocol According Van den IJssel et al, Nucleic Acids Res. 2005 Dec 16;33(22):e192
 
Channel 2
Source name female reference DNA
Organism Homo sapiens
Characteristics sample type: Pooled DNA from the blood of 10 normal female individuals
Extracted molecule genomic DNA
Extraction protocol DNAzol (Invitrogen) according to manufacturer's protocol
Label Cy5
Label protocol According Van den IJssel et al, Nucleic Acids Res. 2005 Dec 16;33(22):e192
 
 
Hybridization protocol According Van den IJssel et al, Nucleic Acids Res. 2005 Dec 16;33(22):e192
Scan protocol Microarray Scanner G2505B (Agilent Technologies), default settings
Description 600ng of tumor and normal DNA were combined with 10 µg Cot-1 DNA and precipitated by adding 2.5 volumes of ice-cold 100% ethanol and 0.1 volume of 3M sodium acetate (pH 5.2). The DNA was collected by centrifugation at 14000 rpm for 30 minutes at 4 °C. The pellet was dissolved in 130 µl hybridization solution and incubated at 73°C for 10 minutes to denature the DNA, followed by 60-120 minute incubation at 37°C. Next, the hybridization mixture was added to the array in a hybridization station (HybArray12TM, Perkin Elmer Life Sciences, Zaventum, Belgium) and incubated for 38 hours at 37°C. After hybridization the slides were washed in six washing steps and dried by centrifugation for 3 minutes at 1000 g.
Data processing The raw signal intensities were obtained with Bluefuse. The unreliable and morphologically corrupted measurement spots were removed from the data. We used the global mode normalization.
 
Submission date Mar 31, 2009
Last update date Aug 09, 2010
Contact name Daoud Sie
E-mail(s) d.sie@vumc.nl
Phone +31 20 4442428
Organization name Vrije Universiteit Medical Center
Department Pathology
Lab Microarray Core Facility
Street address De Boelelaan 1117
City Amsterdam
ZIP/Postal code 1081 HV
Country Netherlands
 
Platform ID GPL8368
Series (2)
GSE15470 Array comparative genomic hybridization in sporadic and coeliac disease-related small bowel adenocarcinomas
GSE23418 Small bowel adenocarcinoma copy number profiles are more closely related to colorectal than to gastric cancers

Data table header descriptions
ID_REF
AMPCH1 Total signal in channel 1 (Cy3)
AMPCH2 Total signal in channel 2 (Cy5)
LOG2RATIO CH1/CH2 Log, base 2, of the ratio of total signal in channel 1 divided by total signal in channel 2
CONFIDENCE The Confidence Estimate in the calculated ratio, between 0 and 1, calculated by BlueFuse
QUALITY A flag to highlight spots that suffer from poor printing and other experimental artefacts (1 acceptable; 0 not acceptable), estimated by BlueFuse
VALUE normalized log2 ratio (CH1/CH2) but with flagged values removed
UNF_VALUE normalized log2 ratios

Data table
ID_REF AMPCH1 AMPCH2 LOG2RATIO CH1/CH2 CONFIDENCE QUALITY VALUE UNF_VALUE
1 330.203 397.898 -0.269 0.94 1 0.291 0.291
2 96.689 138.318 -0.517 0.8 1 0.043 0.043
3 84.841 133.792 -0.657 0.75 1 -0.097 -0.097
4 1126.699 1626.797 -0.53 0.98 1 0.03 0.03
5 2192.67 2935.851 -0.421 0.99 1 0.139 0.139
6 977.168 1190.099 -0.284 0.89 1 0.276 0.276
7 88.342 125.054 -0.501 0.76 1 0.059 0.059
8 735.529 1053.314 -0.518 0.93 1 0.042 0.042
9 80.128 94.366 -0.236 0.63 1 0.324 0.324
10 181.126 233.269 -0.365 0.92 1 0.195 0.195
11 79.714 130.814 -0.715 0.72 1 -0.155 -0.155
12 398.558 468.584 -0.234 0.85 1 0.326 0.326
13 83.675 116.883 -0.482 0.75 1 0.078 0.078
14 81.27 145.896 -0.844 0.74 1 -0.284 -0.284
15 204.474 289.402 -0.501 0.92 1 0.059 0.059
16 177.995 214.71 -0.271 0.89 1 0.289 0.289
17 367.492 422.424 -0.201 0.94 1 0.359 0.359
18 280.513 268.733 0.062 0.92 1 0.622 0.622
19 64.607 105.733 -0.711 0.68 1 -0.151 -0.151
20 77.576 144.782 -0.9 0.77 1 -0.34 -0.34

Total number of rows: 29999

Table truncated, full table size 1292 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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