|
| Status |
Public on Dec 23, 2017 |
| Title |
Tumor, Splenic Diffuse Red Pulp Lymphoma, case 16 |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
Tumor, Splenic Diffuse Red Pulp Lymphoma, case 16
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: splenic diffuse red pulp lymphoma
gender: female
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted form formalin fixed paraffin embedded (FFPE) tissues by phenol chloroform method. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer, and agarose gel electrophoresis.
|
| Label |
Cy5
|
| Label protocol |
Following manufacturer instructions (Agilent)
|
| |
|
| Channel 2 |
| Source name |
pool normal DNA
|
| Organism |
Homo sapiens |
| Characteristics |
gender: F
age: 22
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted form formalin fixed paraffin embedded (FFPE) tissues by phenol chloroform method. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer, and agarose gel electrophoresis.
|
| Label |
Cy3
|
| Label protocol |
Following manufacturer instructions (Agilent)
|
| |
|
| |
| Hybridization protocol |
The protocol Oligonucleotide Array-Based CGH for Genomic DNA Analysis (ULS labeling for Blood, Cells, Tissues or FFPE) was used.
|
| Scan protocol |
Scanned on an Agilent G2565AA scanner.
|
| Description |
Tumor vs normal
|
| Data processing |
Raw data were generated from scanned images using Agilent Feature Extraction Software (10.10.1.1). Log2ratios of background corrected values for tumour over normal DNA were calculated. Normalization was carried out on Agilent's CGH Analytics, integrated on the Agilent Genomic Workbench Standard Edition 6.5.0.58, using data from the internal set of control probes included in the microarray. Detection of Copy Number Alterations (CNAs) was performed using the ADM-2 algorithm, also implemented within the Agilent's genomics suite Genomic Workbench v5.0, with a threshold of 6.5 and a minimum of 5 consecutive probes and Nexus 6.0 Discovery Edition (Biodiscovery, El segundo, CA).
|
| |
|
| Submission date |
Jan 16, 2015 |
| Last update date |
Dec 23, 2017 |
| Contact name |
Alba Navarro |
| E-mail(s) |
ANAVARRL@clinic.ub.es
|
| Organization name |
IDIBAPS - Hospital Clínic
|
| Department |
Pathology
|
| Lab |
Molecular Pathology
|
| Street address |
Villaroel, 170
|
| City |
Barcelona |
| ZIP/Postal code |
08036 |
| Country |
Spain |
| |
|
| Platform ID |
GPL8736 |
| Series (2) |
| GSE64822 |
Clinical and molecular characterization of splenic diffuse red pulp lymphomas |
| GSE65060 |
Clinical and molecular characterization of splenic diffuse red pulp lymphomas [Agilent] |
|
