|
| Status |
Public on Oct 02, 2012 |
| Title |
BRCA1 Ovarian cancer sample60 |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
ovarian tumour
|
| Organism |
Homo sapiens |
| Characteristics |
disease subtype: BRCA1
disease state: ovarian carcinoma
tissue: ovarian tumor
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted from three 10-μm-thick FFPE tissue sections per tumour. After deparaffination and rehydration, sections were haematoxylin and eosin (H&E) stained and tumoral areas were delimited by a pathologist and macrodissected with a surgical blade to ensure at least 80% of tumor content. DNA extraction was performed by standard protocols of proteinase-K overnight digestion and using a column-based commercially available kit following manufacturer´s instructions (QIAamp DNA mini kit; Qiagen, Westburg, Leusden, The Netherlands) 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 |
Labeling of test and reference DNA was performed using the Enzo Genomic DNA labeling kit (Enzo Life Sciences ) according to Enzo Life Sciences protocol as described previously (Buffart et al, Genes Chrom and Cancer, 2008).
|
| |
|
| Channel 2 |
| Source name |
pooled blood healthy women
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: blood
sample type: pooled blood healthy women
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted from three 10-μm-thick FFPE tissue sections per tumour. After deparaffination and rehydration, sections were haematoxylin and eosin (H&E) stained and tumoral areas were delimited by a pathologist and macrodissected with a surgical blade to ensure at least 80% of tumor content. DNA extraction was performed by standard protocols of proteinase-K overnight digestion and using a column-based commercially available kit following manufacturer´s instructions (QIAamp DNA mini kit; Qiagen, Westburg, Leusden, The Netherlands) DNA isolation protocol available via www.vumc.nl/microarrays. Also described in Buffart et al, J Pathol. 2007 Jan;211(1):45-51.
|
| Label |
Cy5
|
| Label protocol |
Labeling of test and reference DNA was performed using the Enzo Genomic DNA labeling kit (Enzo Life Sciences ) according to Enzo Life Sciences protocol as described previously (Buffart et al, Genes Chrom and Cancer, 2008).
|
| |
|
| |
| Hybridization protocol |
Hybridization protocol available via www.agilent.com NOTE: Nine samples (highlighted in description) were hybridized using Across Array CGH method with which reference sample is hybridized to an external array while two test samples can be hybridized to the same array (with different channels/fluorochromes) (Buffart et al., Genes Chromosomes and Cancer, 2008 and Voorham et al., Clinical Cancer Research, 2012).
|
| Scan protocol |
Slides were scanned using the Agilent microarray scanner, protocol according to Agilent.
|
| Description |
standard dual color hybridization
|
| Data processing |
Wave smoothing and median normalization in R/Bioconductor.Calling performed with DNAcopy algorithm.
|
| |
|
| Submission date |
Oct 01, 2012 |
| Last update date |
Oct 02, 2012 |
| Contact name |
Maria Jose García |
| E-mail(s) |
[email protected]
|
| Phone |
+ (34) 917 328 000
|
| Organization name |
Centro Nacional de Investigaciones Oncológicas
|
| Department |
Human Cancer Genetics
|
| Street address |
C/ Melchor Fernández Almagro 3
|
| City |
Madird |
| State/province |
Madrid |
| ZIP/Postal code |
28029 |
| Country |
Spain |
| |
|
| Platform ID |
GPL8687 |
| Series (1) |
| GSE41253 |
Copy number analysis of familial and sporadic Epithelial Ovarian Carcinomas (EOC) from FFPE tissue on high resolution Agilent platform. |
|
