|
| Status |
Public on Sep 17, 2013 |
| Title |
ALL 6646 initial |
| Sample type |
genomic |
| |
|
| Source name |
6646
|
| Organism |
Homo sapiens |
| Characteristics |
individual: 6646
disease: B-acute lymphoblastic leukemia
disease status: initial
|
| Treatment protocol |
None
|
| Growth protocol |
None
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was isolated from mononuclear cells from peripheral blood or bone marrow using the Qiagen DNA Blood Mini Kit. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer.
|
| 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 7G.
|
| Description |
pediatric B-ALL sample before treatment
|
| Data processing |
The array image was acquired using Affymetrix Command Console Software (version 2.0.1). Processing of the raw signals and raw copy-number calculation were performed using the CRMAv2 procedure of the aroma.affymetrix package (version 2.0.0) for R Statistical platform (version 2.12.1) according to the aroma.affymetrix vignette for paired total copy-number analysis. Circular Binary Segmentation (Ohlsen et al., 2004) was then applied using DNAcopy package for R Bioconductor to perform the segmentation. Affymetrix "GenomeWideSNP_6.na30.annot.csv" annotation (Genome Build version hg18) was used.
Primary data description: Smoothed copy-number signal ratios and detected segments and segment mean values. Genome Build version hg18 was used.
|
| |
|
| Submission date |
Nov 06, 2012 |
| Last update date |
Sep 18, 2013 |
| Contact name |
Thomas Streichert |
| Organization name |
University Medical Center Hamburg-Eppendorf
|
| Department |
Institute For Clinical Chemistry / Central Laboratories
|
| Street address |
Martinistr. 52, Campus Forschung N27, 2. OG
|
| City |
Hamburg |
| ZIP/Postal code |
D-20246 |
| Country |
Germany |
| |
|
| Platform ID |
GPL6801 |
| Series (1) |
| GSE42056 |
Affymetrix SNP array data for acute lymphoblastic leukemia samples |
|
