|
| Status |
Public on Feb 20, 2009 |
| Title |
CIN lesion grade 2/3 VUMC_HGCIN28_b45_s55 |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
uterine cervix
|
| Organism |
Homo sapiens |
| Characteristics |
cervical intraepithelial neoplasia (CIN) lesion, grade 2/3
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
as described in Van zeeburg et al, Cancer Res, volume 65, p 1271-76, 2005
|
| Label |
Cy3
|
| Label protocol |
as described by Snijders et al, Nat Genetics, volume 29, p 263-4
|
| |
|
| Channel 2 |
| Source name |
Reference DNA
|
| Organism |
Homo sapiens |
| Characteristics |
Pooled DNA from the blood of 10 normal male individuals
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
as described in Wilting et al, J Pathol, volume 209, p 220-30
|
| Label |
Cy5
|
| Label protocol |
as ch1, Cy5 in stead of Cy3
|
| |
|
| |
| Hybridization protocol |
Hybridisations were performed as described by Snijders et al, Nat Genetics, volume 29, p 263-4. Both pre-hybridisation and hybridisation were performed in a hybridisation station (HybStation12 – Perkin Elmer Life Sciences).
|
| Scan protocol |
Microarray Scanner G2505B (Agilent Technologies), default settings
|
| Description |
CIN3 lesion, patient age 25 years, contains high risk Human Papilloma Virus
|
| Data processing |
Spots were quantified in ImaGene 5.6.1 software using default settings. BAC clones were positioned along the genome according to the May 2004 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 |
May 28, 2008 |
| Last update date |
Feb 20, 2009 |
| 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 |
GPL2843 |
| Series (1) |
| GSE11573 |
Chromosomal signatures of a subset of high-grade premalignant cervical lesions closely resemble invasive carcinomas |
|
| Data table header descriptions |
| ID_REF |
|
| Signal Median CH1 |
Spot signal in channel 1 (Cy3) |
| Background Median CH1 |
Background signal channel 1 (Cy3) |
| Signal Median CH2 |
Spot signal in channel 2 (Cy5) |
| Background Median CH2 |
Background signal channel 2 (Cy5) |
| Flag |
A flag to highlight spots that suffer from poor printing and other experimental artefacts (0 acceptable; 1-4 not acceptable) |
| Coriell |
BAC clones misbehaving in hybridisations with Coriell cell lines were flagged (0 acceptable; 1 not acceptable) |
| VALUE |
Normalized log2 ratio of the test (Cy3)/ reference (Cy5) sample |
