|
| Status |
Public on Sep 29, 2011 |
| Title |
Nodal Marginal Zone Lymphoma_02040336 |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
Nodal Marginal Zone Lymphoma
|
| Organism |
Homo sapiens |
| Characteristics |
tissue origin: freshly frozen lymph nodes
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA of frozen-tissue cases was extracted using the standard phenol-chloroform protocol. For CNA, the DNA was hybridized on an Agilent Human Genome CGH Microarray Kit 1 x 44K (Agilent Technologies) following the manufacturer’s instructions. Human female and male pooled gDNA (Promega) was used to normalize the CGH results. Results were considered valuable in 12 cases. The samples (1 μg DNA) were labeled with Cy5 and the DNA donor pool was labeled with Cy3.
|
| Label |
Cy5
|
| Label protocol |
Total DNA amplification and labeling were performed according to the standard Agilent protocol. The samples (1 μg DNA) were labeled with Cy5 and the DNA donor pool was labeled with Cy3.
|
| |
|
| Channel 2 |
| Source name |
Universal Human Reference DNA from Promega
|
| Organism |
Homo sapiens |
| Characteristics |
sample type: reference - Human female and male-pooled gDNA
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA of frozen-tissue cases was extracted using the standard phenol-chloroform protocol. For CNA, the DNA was hybridized on an Agilent Human Genome CGH Microarray Kit 1 x 44K (Agilent Technologies) following the manufacturer’s instructions. Human female and male pooled gDNA (Promega) was used to normalize the CGH results. Results were considered valuable in 12 cases. The samples (1 μg DNA) were labeled with Cy5 and the DNA donor pool was labeled with Cy3.
|
| Label |
Cy3
|
| Label protocol |
Total DNA amplification and labeling were performed according to the standard Agilent protocol. The samples (1 μg DNA) were labeled with Cy5 and the DNA donor pool was labeled with Cy3.
|
| |
|
| |
| Hybridization protocol |
DNA was hybridized on an Agilent Human Genome CGH Microarray Kit 1x44K (Agilent Technologies, Inc., Santa Clara, CA) according to the manufacturer’s instructions.
|
| Scan protocol |
Scanned on an Agilent G2505B scanner.
|
| Description |
02040336
|
| Data processing |
Normalization and DNA copy number alterations (CNA) were performed using CAPweb version 2.0 from the Curie Institute (http://bioinfo-out.curie.fr/CAPweb)
The background subtraction of microarray data was carried out using GEPAS 4.0 (http://gepas.bioinfo.cipf.es). The dataset was normalized by lowess within-array normalization and quantile between-array normalization.
|
| |
|
| Submission date |
Sep 28, 2011 |
| Last update date |
Sep 29, 2011 |
| Contact name |
Alberto Arribas |
| E-mail(s) |
aarribas@sescam.jccm.es
|
| Phone |
925269200
|
| Organization name |
Hospital Virgen de la Salud
|
| Department |
Molecular Pathology Research Unit
|
| Lab |
Genetics
|
| Street address |
Avda Barber, 30
|
| City |
Toledo |
| State/province |
Toledo |
| ZIP/Postal code |
45250 |
| Country |
Spain |
| |
|
| Platform ID |
GPL8841 |
| Series (2) |
| GSE32233 |
Molecular characterization of Nodal marginal zone lymphoma |
| GSE32436 |
Molecular characterization of Nodal marginal zone lymphoma [CGH] |
|
