|
| Status |
Public on Oct 15, 2008 |
| Title |
Carcinoma (F54C_expr_s15_b34) |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
colon
|
| Organism |
Homo sapiens |
| Characteristics |
Carcinoma
|
| Extracted molecule |
total RNA |
| Extraction protocol |
protocol available on wwww.vumc.nl/microarrays/
|
| Label |
Cy3
|
| Label protocol |
As described in Muris et al, Br J Haematol. 2007 Jan;136(1):38-47.
|
| |
|
| Channel 2 |
| Source name |
universal human reference RNA, Stratagene
|
| Organism |
Homo sapiens |
| Characteristics |
comprised of 10 cell lines for human giving broad gene coverage
|
| Extracted molecule |
total RNA |
| Extraction protocol |
See www.stratagene.com
|
| Label |
Cy5
|
| Label protocol |
As described in Muris et al, Br J Haematol. 2007 Jan;136(1):38-47
|
| |
|
| |
| Hybridization protocol |
As described in Muris et al, Br J Haematol. 2007 Jan;136(1):38-47
|
| Scan protocol |
Microarray Scanner G2505B (Agilent Technologies), default settings
|
| Description |
n/a
|
| Data processing |
Spots were quantified in ImaGene 5.6.1 software using default settings, as described in Carvalho et al, submitted
|
| |
|
| Submission date |
Jun 07, 2007 |
| Last update date |
Oct 15, 2008 |
| 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 |
GPL3055 |
| Series (1) |
| GSE8067 |
Multiple genes at the chromosome 20q amplicon contribute to colorectal adenoma to carcinoma progression |
|
| 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 from 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. |
