|
| Status |
Public on Dec 23, 2017 |
| Title |
Tumor, Splenic Diffuse Red Pulp Lymphoma, case 14 |
| Sample type |
genomic |
| |
|
| Source name |
Peripheral Blood
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: peripheral blood
cell type: splenic diffuse red pulp lymphoma
gender: male
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted from peripheral blood or spleen samples using the Qiagen DNA Blood Mini/Midi Kit. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer, PicoGreen and agarose gel electrophoresis.
|
| Label |
Biotin
|
| Label protocol |
As per manufacturer (Affymetrix)
|
| |
|
| Hybridization protocol |
DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.
|
| Scan protocol |
The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.
|
| Description |
Hybridized to SNP 6.0
|
| Data processing |
Image data were analysed with Genotyping Console 4.0 to obtain the CEL data files, which were also exported to the Nexus Biodiscovery Edition for data analysis and visualization. Quality controls assessed by Genotyping Console included Contrast Quality Control (CQC>0.4) produced by Birdseed and Median of the Absolute values of all Pairwise Differences (MAPD<0.35). Tumour and normal DNA samples were analysed individually with the Nexus Biodiscovery Edition using the SNP-FASST2 segmentation algorithm and using segment reporting tool filters: minimum of 100 Kb minimum genomic size of a segment, as well as by visual inspection.
|
| |
|
| 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 |
GPL6801 |
| Series (2) |
| GSE64822 |
Clinical and molecular characterization of splenic diffuse red pulp lymphomas |
| GSE65052 |
Affymetrix SNP-array data for splenic diffuse red pulp lymphoma samples |
|
