|
Status |
Public on Jan 11, 2013 |
Title |
large cell MALT lymphoma 17 |
Sample type |
genomic |
|
|
Source name |
large cell MALT lymphoma 17
|
Organism |
Homo sapiens |
Characteristics |
tissue: stomach disease status: large cell MALT lymphoma sample id: LC17
|
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)
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|
|
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 |
|