|
| Status |
Public on Dec 21, 2013 |
| Title |
ALL_Remission_of_Patient_L296_Nsp_Array |
| Sample type |
genomic |
| |
|
| Source name |
bone marrow
|
| Organism |
Homo sapiens |
| Characteristics |
disease stage: Remission
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted from bone marrow aspirates using the Qiagen DNAeasy blood and tissue kit. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer and agarose gel eletrophoresis.
|
| Label |
biotin
|
| Label protocol |
DNA was labelled according to the standard Affymetrix protocol for the Affymetrix GeneChip Human Mapping 500K Array Set.
|
| |
|
| Hybridization protocol |
Labelled DNA was hybridised according to manufacturer’s protocol.
|
| Scan protocol |
Arrays were scanned according to manufacturer’s protocol.
|
| Data processing |
The microarray data was processed using Affymetrix Genotyping Console (GTC) v4.0 to determine data quality. Genotype data was checked using the Concordance Check function within GTC to ensure no sampling errors had occurred during array processing. Copy number alterations were determined for 10 patients using the paired remission sample and the Hapmap894 reference 5 set within Partek Genomics Suite v6.5 (Partek, USA) as the reference for the remaining sample (L625). Further analysis, visualization and identification of genomic gains and losses were performed using Partek Genomics Suite v6.5 (Partek, USA) and SNPView2 v2.6 (Ilixa, UK). Regions of aberration were mapped according to the human reference sequence GRCh37.
|
| |
|
| Submission date |
Dec 20, 2012 |
| Last update date |
Dec 21, 2013 |
| Contact name |
Vikki Rand |
| E-mail(s) |
vikki.rand@newcastle.ac.uk
|
| Organization name |
Newcastle University
|
| Department |
Northern Institute for Cancer Research
|
| Lab |
Lymphoma Genomics
|
| Street address |
Paul O'Gorman Building, Newcastle University
|
| City |
Newcastle Upon Tyne |
| State/province |
Tyne and Wear |
| ZIP/Postal code |
NE12 4HH |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL3718 |
| Series (1) |
| GSE43060 |
Genomic analysis of relapsed Acute Lymphoblastic Leukaemia in children |
|
