|
| Status |
Public on Nov 26, 2012 |
| Title |
H321 |
| Sample type |
genomic |
| |
|
| Source name |
Sample from patient with diffuse large B-cell lymphoma
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: sample of diffuse large B-cell lymphoma
|
| Treatment protocol |
None
|
| Growth protocol |
None
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
The tumor sample was after removal snap frozen and stored in OCT at - 80 oC. From each OCT block, 3x20 µm cuts were obtained using a microtome; the slices were washed twice in PBS and homogenized using the TissueLyser II (Qiagen). DNA extraction was performed using the DNeasy Blood & Tissue kit (Qiagen). From one of the patients (H380) a peripheral blood sample was included as a normal control sample (BB39). Mononuclear cells were isolated from the blood sample by Ficoll-Paque Plus (GE Health Care, Uppsala, Sweden) and stored in 10 % DMSO and 20 % serum at – 80 oC. For DNA extraction, the cells were thawed, washed twice in PBS and genomic DNA extracted using the DNeasy Blood & Tissue kit (Qiagen). The DNA was eluted in water and the concentration measured using a Nanodrop (Thermo Scientific)
|
| 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 SNP6.0
|
| Data processing |
The SNP6.0 CEL files were imported in Genotyping Console version 4.1 (Affymetrix) and copy number/LOH analysis performed using regional GC correction and the CN baseline file generated from 270 HapMap samples; GenomeWideSNP_6.hapmap270.na32.r1.a5.ref (downloaded from Affymetrix webpage). Individual SNPs were not assessed. The resulting CNCHP-files were viewed using the software; Chromosome Analysis Suite, version 1.1 (Affymetrix). TXT files of normalized data were exported from the Chromosome Analysis Suite software. All genomic positions were annotated to the hg19 version of the human genome (NCBI build 37).
Detection of CNVs larger than 200 kb with size being the only restriction.
|
| |
|
| Submission date |
May 14, 2012 |
| Last update date |
Nov 26, 2012 |
| Contact name |
Julie Støve Bødker |
| E-mail(s) |
j.boedker@rn.dk
|
| Organization name |
Aalborg University Hospital
|
| Department |
Department of Heamatology
|
| Lab |
Research Laboratory
|
| Street address |
Sdr. Skovvej 15
|
| City |
Aalborg |
| ZIP/Postal code |
9000 |
| Country |
Denmark |
| |
|
| Platform ID |
GPL6801 |
| Series (2) |
| GSE37977 |
SNP6.0 copy number analysis of eight diffuse large B-cell samples and one matched blood sample |
| GSE37979 |
Performance Comparison of the Affymetrix SNP6.0 and Cytogenetic 2.7M Whole-genome Microarrays in Complex Cancer Samples |
|
