|
| Status |
Public on Mar 01, 2016 |
| Title |
B-lineage acute lymphoblastic leukemia_4A |
| Sample type |
genomic |
| |
|
| Source name |
genomic DNA extracted from bone marrow of patient 4 affected by B-lineage acute lymphoblastic leukemia sampled at diagnosi
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: bone marrow sampled at diagnosis
|
| Treatment protocol |
Not applicable
|
| Growth protocol |
Not applicable
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted from bone marrow cells (>70% leukemic blasts) at diagnosis or at complete remission using the Promega Wizard® Genomic DNA Purification Kit. Genomic DNA from saliva was extracted using the NucleoSpin Tissue – (MACHEREY-NAGEL). 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 washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.
|
| Description |
Hybridized to Affymetrix SNP 6.0 Array
|
| Data processing |
CEL files, CHP files and TXT files (generated by Affymetrix Genotyping Console using the Birdseed v2 algorithm) were processed by dChip and model-based expression performed using the PM/MM model. Normalization was performed using the reference normalization algorithm developed at St Jude and described in Mullighan et al Nature 2007;446:758. The data matrix contains the normalized expression values produced by that algorithm (see Matrix sheet and attached .cnmz file)
Genotype Call (SNP call): AA, AB, BB, NC, and NoCall; 'Signal' = Summarized signal
|
| |
|
| Submission date |
Mar 30, 2015 |
| Last update date |
Mar 01, 2016 |
| Contact name |
Monica Messina |
| E-mail(s) |
messina@bce.uniroma1.it
|
| Organization name |
Sapienza University
|
| Department |
Department of Cellular Biotechnologies and Hematology
|
| Lab |
Genomics
|
| Street address |
Via Benevento 26
|
| City |
Rome |
| ZIP/Postal code |
00161 |
| Country |
Italy |
| |
|
| Platform ID |
GPL6801 |
| Series (1) |
| GSE67405 |
Affymetrix SNP array data for B-lineage acute lymphoblastic leukemia |
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