|
| Status |
Public on Jan 11, 2013 |
| Title |
small cell MALT lymphoma 6 |
| Sample type |
genomic |
| |
|
| Source name |
small cell MALT lymphoma 6
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: stomach
disease status: small cell MALT lymphoma
sample id: SC6A
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted from freshly frozen tumor tissue using the QIAamp DNA Mini Kit (Qiagen). Content of tumor cells was at least 90%. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer 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 GenomeWide SNP 6.0 array
|
| Data processing |
CEL-files were generated using Affymetrix Command console software
normalized raw data (lin scale) were generated using the R package aroma.affymetrix (H. Bengtsson, R. Irizarry, B. Carvalho & T.P. Speed, Estimation and assessment of raw copy numbers at the single locus level, Bioinformatics 2008, 24, pp759-767)
CHP-files were generated using Affymetrix Genotyping console (BRLMM2)
|
| |
|
| Submission date |
Mar 06, 2012 |
| Last update date |
Jan 11, 2013 |
| Contact name |
Karlheinz Holzmann |
| E-mail(s) |
karlheinz.holzmann@uni-ulm.de
|
| Organization name |
Ulm University
|
| Department |
Medical Faculty
|
| Lab |
Genomics Core Facility
|
| Street address |
Helmholtzstreet 8/1
|
| City |
Ulm |
| ZIP/Postal code |
D-89081 |
| Country |
Germany |
| |
|
| Platform ID |
GPL6801 |
| Series (1) |
| GSE36311 |
High-resolution genomic profiling of marginal zone B-cell lymphomas and variants |
|
