|
| Status |
Public on Oct 07, 2009 |
| Title |
SBA_09 |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
small intestinal adenocarcinoma
|
| Organism |
Homo sapiens |
| Characteristics |
age: 59
sex: female
tumor site: duodenum
celiac disease: No
tnm: pT4N0M1
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 |
male reference DNA
|
| Organism |
Homo sapiens |
| Characteristics |
sample type: Pooled DNA from the blood of 10 normal male 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) |
[email protected]
|
| 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 |
