|
| Status |
Public on Aug 14, 2012 |
| Title |
germline SNP array |
| Sample type |
genomic |
| |
|
| Source name |
tail
|
| Organism |
Mus musculus |
| Characteristics |
cell type: connective tissue
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA from diagnostic sorted B cell lymphoma samples derived from Cgamma1-cre; R26StopFLMYC;R26StopFLP110* transplanted animals and germline DNA (tail) was isolated with Dneasy according manufacturer’s recommendations (Qiagen).
|
| Label |
Biotin
|
| Label protocol |
Affymetrix Mouse Diversity Genotyping Arrays were labeled using the Genome Wide Human SNP Nsp/Sty 5.0/6.0 Assay Kit according to the manufacturer’s recommendations (Affymetrix).
|
| |
|
| Hybridization protocol |
Hybridization, washing, and staining protocols, respectively, were performed on Affymetrix GeneChip instruments (Hybridization Oven 640, Fluidics Station FS450) as recommended by the manufacturer.
|
| Scan protocol |
Scanning was performed on Affymetrix GeneChip Scanner GCS3000 instruments as recommended by the manufacturer using default settings. The software used was GCOS 1.2 or higher.
|
| Description |
Hybridized to Mouse Diversity Genotyping Arrays
|
| Data processing |
CEL files were generated the Command_Console Software (Affymetrix) and processed by aroma.affymetrix.
Normalization and detecition of genomic aberrations was carried out using the R packages aroma.affymetrix and DNAcopy (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).
|
| |
|
| Submission date |
Jan 25, 2012 |
| Last update date |
Aug 14, 2012 |
| Contact name |
Lars Bullinger |
| E-mail(s) |
lars.bullinger@charite.de
|
| Phone |
+49-30-450-553111
|
| Organization name |
Charité
|
| Department |
Hematology, Oncology and Tumorimmunology
|
| Street address |
Augustenburger Platz 1
|
| City |
Berlin |
| ZIP/Postal code |
13353 |
| Country |
Germany |
| |
|
| Platform ID |
GPL13147 |
| Series (1) |
| GSE35219 |
Synergy between PI3K Signaling and MYC in Burkitt Lymphomagenesis |
|
