|
| Status |
Public on Feb 01, 2011 |
| Title |
Marginal zone B-cell lymphoma patient sample 08-667_3 |
| Sample type |
genomic |
| |
|
| Source name |
MZL patient sample 08-667_3
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: marginal zone lymphoma
diagnosis: MZL
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
All clinical specimens were derived from involved sites and obtained in the course of routine diagnostic procedures before therapy initiation. Cases were selected based upon the availability of frozen material with a fraction of neoplastic cells in the specimen representing >70% of overall cellularity as determined by morphologic and/or immunophenotypic studies. Genomic DNA was extracted using the QIAamp DNA Mini Kit.
|
| 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 |
08-667_3.CEL
Hybridized to 250K_Nsp
|
| Data processing |
Data acquisition was performed using the GeneChip Operating Software (GCOS) v1.4 and Genotyping Analysis Software (GTYPE) v4.1. Genotype calls were calculated using the BRLMM algorithm. Mapping data for probes were derived from the National Center for Biotechnology Information (NCBI) Human Genome Build 36, as provided by Affymetrix, which was used for all subsequent analyses. The modified Bayesian Piecewise Regression (mBPCR) method was used to estimate the copy number (CN) starting from raw CN values obtained with Affymetrix CNAT 4.01 using a Gaussian bandwidth of 0 Kb and 46 Caucasian normal female samples of the HapMap Project as reference samples.
signal = log2ratio; loh = 0 or 1
|
| |
|
| Submission date |
Oct 21, 2010 |
| Last update date |
Feb 01, 2011 |
| Contact name |
Francesco Bertoni |
| E-mail(s) |
francesco.bertoni@ior.usi.ch
|
| Phone |
+41 91 820 0367
|
| Organization name |
IOR
|
| Department |
Lymphoma & Genomics Research Program
|
| Street address |
Via V. Vela 6
|
| City |
Bellinzona |
| State/province |
Ticino |
| ZIP/Postal code |
6500 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL3718 |
| Series (1) |
| GSE24881 |
Affymetrix SNP array data for Marginal Zone Lymphoma samples |
|
