|
| Status |
Public on Oct 15, 2008 |
| Title |
Carcinoma (F11C_s40_b16) |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
colon
|
| Organism |
Homo sapiens |
| Characteristics |
disease state: Carcinoma
site: Colorectum
tumor site: Rectum
tnm: pTxN1M1
age: 66
gender: M
platform_id type: bac
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
protocol available on www.vumc.nl/microarrays
|
| Label |
Cy3
|
| Label protocol |
as described by Snijders et al, Nat Genetics, volume 29, p 263-4
|
| |
|
| Channel 2 |
| Source name |
Female Reference DNA
|
| Organism |
Homo sapiens |
| Characteristics |
sample type: A pool of ten normal individuals
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNAzol (Invitrogen) according to manufacturer's protocol
|
| Label |
Cy5
|
| Label protocol |
as described by Snijders et al, Nat Genetics, volume 29, p 263-4
|
| |
|
| |
| Hybridization protocol |
as described by Carvalho et al, Cell Oncol. 2006;28(5-6):283-94.
|
| Scan protocol |
Microarray Scanner G2505B (Agilent Technologies), default settings
|
| Description |
CRC14
|
| Data processing |
Spots were quantified in ImaGene 5.6.1 software using default settings. BAC clones were positioned along the genome according to the July 2003 freeze. After exclusion of flagged spots, the average of the triplicate spots was calculated for each BAC clone and 2log ratios (tumour/normal reference signal) were normalised by subtraction of the mode value of BAC clones on chromosome 1-22. BAC clones with flagged spots were excluded from analysis.
|
| |
|
| Submission date |
Jun 04, 2007 |
| 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 |
GPL3442 |
| Series (2) |
| GSE8067 |
Multiple genes at the chromosome 20q amplicon contribute to colorectal adenoma to carcinoma progression |
| GSE23418 |
Small bowel adenocarcinoma copy number profiles are more closely related to colorectal than to gastric cancers |
|
| Data table header descriptions |
| ID_REF |
|
| Signal Median CH1 |
spot signal channel 1 (Cy3) |
| Background Median CH1 |
background signal of channel 1 (Cy3) |
| Signal Median CH2 |
spot signal channel 2 (Cy5) |
| Background Median CH2 |
background signal of channel 1 (Cy5) |
| Log2ratio |
|
| Flag |
A flag to highlight spots that suffer frmo poor prinitng and other experimental artefacts (0 acceptable; 1-4 not acceptable) |
| VALUE |
same as UNF_VALUE but with flagged values removed |
| UNF_VALUE |
Normalized value of the log2ratio. Flagged features are excluded. Values where also deleted if the each triplicate had a Standard Deviation higher than 0.2. |
