|
| Status |
Public on Jun 12, 2010 |
| Title |
SCLC2008 |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
DNA from formalin fixed paraffin embedded(FFPE) NSCLC sample SCLC2008
|
| Organism |
Homo sapiens |
| Characteristics |
age: 82
gender: female
history: SCLC stage ED nine years.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA isolation protocol available via www.vumc.nl/microarrays. Also described in Buffart et al, J Pathol. 2007 Jan;211(1):45-51
|
| Label |
Cy3
|
| Label protocol |
DNA labeling protocol according to Enzo Life Sciences
|
| |
|
| Channel 2 |
| Source name |
Pooled DNA from the blood of 18 normal individuals
|
| Organism |
Homo sapiens |
| Characteristics |
reference: female reference DNA
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNAzol (Invitrogen) according to manufacturer's protocol
|
| Label |
cy5
|
| Label protocol |
DNA labeling protocol according to Enzo Life Sciences
|
| |
|
| |
| Hybridization protocol |
Hybridization protocol available via www.agilent.com
|
| Scan protocol |
Slides were scanned using the Agilent microarray scanner, protocol according to Agilent.
|
| Description |
protocols according to manufacturer (Enzo Life Sciences or www.Agilent.com
|
| Data processing |
Dewaving: The data have been de-waved as described in Van de Wiel et al. (2009) using the R package "NoWaves". This is available from www.few.vu.nl/~mavdwiel/nowaves.html. Agilent 105K normals were used as calibration.
Normalization: mode normalization
Segmentation: R-package DNAcopy (Olshen et al., 2004) using default settings. This is available from www.bioconductor.org.
van de Wiel MA, Brosens R, Eilers PHC, Kumps C, Meijer GA, Menten B, Sistermans E, Speleman F, Timmerman ME, Ylstra B (2009). Smoothing waves in array CGH tumor profiles. Bioinformatics, 25, 1099-1104.
Olshen, A.B., E.S. Venkatraman, R. Lucito, and M. Wigler (2004). Circular binary segmentation for the analysis of array-based DNA copy number data. Biostatistics, 5, 557{572.
|
| |
|
| Submission date |
Jun 12, 2009 |
| Last update date |
Jun 18, 2009 |
| 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 |
GPL8693 |
| Series (1) |
| GSE16575 |
An 82-Year old woman with a palpable lymph node |
|
