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| Status |
Public on Jan 22, 2016 |
| Title |
Diffuse Large B Cell Lymphoma tumor sample 78 |
| Sample type |
genomic |
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| Source name |
TUMOR, Diffuse Large B Cell Lymphoma sample
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| Organism |
Homo sapiens |
| Characteristics |
diagnosis: Diffuse large B cell lymphoma de novo
type of sample: Tumoral sample
gender: Female
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Tumor DNA was extracted from diagnostic samples. High-molecular weight (HMW) DNA from fresh samples was isolated using the DNAzol reagent (MRC, Cincinnati, OH, USA). DNA extraction on formalin-fixed paraffin-embedded (FFPE) tissue was done with the RecoverAll™ Total Nucleic Acid Isolation Kit (AmbionInc-Applied Biosystems, Foster City, CA, USA) or QuickExtract™ FFPE DNA Extraction Kit (Epicenter Biotechnologies, Madison, WI, USA). DNA from non-tumoral matched samples was isolated using DNAzolor theMagNA Pure LC system (Roche Diagnostics GmbH, Mannheim, Germany).
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| Label |
Biotin
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| Label protocol |
As per manufacturer (Affymetrix)
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| Hybridization protocol |
Affymetrix Genome-Wide Human SNP 6.0 Array
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| Scan protocol |
The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.
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| Description |
78T
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| Data processing |
Gains and losses were evaluated with visual inspection by 2 different observers using Nexus Biodiscovery software (Biodiscovery, El Segundo, CA, USA). The CNAs with a minimum size of 100kb were considered real. Loss of heterozigosity regions where considered when size was >5Mb. CNAs were considered germinal CNAs by analyzing the corresponding constitutional DNA of each sample. In cases in which normal DNA was not available, alterations were cross checked in copy number variation database (http://dgv.tcag.ca/dgv/app/). Physiological deletions of the immunoglobulin heavy and light chain loci (IGH@14q32, IGK@2p11, and [email protected]) were excluded from the analysis. Results on both arrays were integrated in a unique database.
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| Submission date |
Jul 27, 2015 |
| Last update date |
Jan 22, 2016 |
| Contact name |
Elena Sebastián |
| Organization name |
Hospital Universitario de Salamnca
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| Department |
Hematology
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| Lab |
Molecular Biology
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| Street address |
Paseo de San Vicente
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| City |
Salamanca |
| ZIP/Postal code |
38007 |
| Country |
Spain |
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| Platform ID |
GPL15315 |
| Series (2) |
| GSE71389 |
Paired copy number analysis of DLBCL Diffuse Large B Cell Lymphoma [SNP 6.0 Array] |
| GSE71394 |
Paired copy number analysis of Diffuse Large B Cell Lymphoma |
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| Supplementary file |
Size |
Download |
File type/resource |
| GSM1833534_78T_TUMOR_GenomeWideSNP_6_.CEL.gz |
30.3 Mb |
(ftp)(http) |
CEL |
| Processed data are available on Series record |
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