|
| Status |
Public on Jun 07, 2016 |
| Title |
A-7111476 (met) |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
Epithelial tissue (breast cancer)
|
| Organism |
Homo sapiens |
| Characteristics |
disease state: HRPBC
tumor pair: A
tumor state: Metastasis
age: 45.6
Sex: Female
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
10um tissue sections were deparaffined using heated Xylol and rehidratation was conducted with subsequent lowered EtOH (00%,80%, 50%, H20). Tissue was then treated with sodium thiocyanate. DNA then was extracted with DNA was extracted a tissue protocol from Qiagen Dneasy blood and tissue kit, using EtOH 80% instead of Wash Buffer 2 (according to ULS protocols)
|
| Label |
Cy5
|
| Label protocol |
Labeling protocol was done according to the Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis, ULS labeling for FFPE sections v3.2 (G4410-90020)
|
| |
|
| Channel 2 |
| Source name |
reference
|
| Organism |
Homo sapiens |
| Characteristics |
reference: PROMEGA CONTROL DNA
Sex: Male
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
10um tissue sections were deparaffined using heated Xylol and rehidratation was conducted with subsequent lowered EtOH (00%,80%, 50%, H20). Tissue was then treated with sodium thiocyanate. DNA then was extracted with DNA was extracted a tissue protocol from Qiagen Dneasy blood and tissue kit, using EtOH 80% instead of Wash Buffer 2 (according to ULS protocols)
|
| Label |
Cy3
|
| Label protocol |
Labeling protocol was done according to the Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis, ULS labeling for FFPE sections v3.2 (G4410-90020)
|
| |
|
| |
| Hybridization protocol |
According to protocol, CGH arrays where hybrizdized 24 hours, at 65ºC and 20 rpm
|
| Scan protocol |
Agilent G2565CA scanner was used to scan slides at 3um resolution for both Cy5 and Cy3 channels
|
| Description |
A_Met
|
| Data processing |
Microarray data were extracted and visualized using Feature Extraction software v10.7 and Agilent Genomic Workbench v5.0 (Agilent Technologies). CNA regions were detected using the ADM-2 (set as 6) statistic provided by DNA Analytics, with a minimum number of 10 consecutive probes. The segmentation process was carried out using the dnacopy Bioconductor package. Bioconductor´s CGHcall package was employed for determining the step, and CGHregions and CGHtest packages were used to estimate genomic regions and false discovery rate, respectively.
|
| |
|
| Submission date |
Mar 21, 2016 |
| Last update date |
Jun 07, 2016 |
| Contact name |
Silvana Mouron |
| E-mail(s) |
smouron@cnio.es
|
| Organization name |
CNIO
|
| Department |
Clinical Research
|
| Lab |
Breast Cancer Lab
|
| Street address |
Calle Melchor Fdez Almagro
|
| City |
Madrid |
| State/province |
Madrid |
| ZIP/Postal code |
28029 |
| Country |
Spain |
| |
|
| Platform ID |
GPL21613 |
| Series (1) |
| GSE79446 |
Analysis of Paired Primary-Metastatic Hormone-Receptor Positive Breast Tumors (HRPBC) Uncovers Potential Novel Drivers of Hormonal Resistance |
|
