|
| Status |
Public on May 01, 2018 |
| Title |
Breast tumor T0175_A |
| Sample type |
genomic |
| |
|
| Source name |
Breast tumor DNA T0175
|
| Organism |
Homo sapiens |
| Characteristics |
Sex: Female
atm status: Heterozygote
variant type: truncating variant
molecular suptype: Unknown
tissue: breast tumor
|
| Treatment protocol |
No treatment was performed
|
| Growth protocol |
All samples were formamid-fixed paraffin-embedded tumors.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Tumor tissues were microdissected from four 10μm section and tumor DNA was extracted from the Macherey-Nagel Nucleospin Tissue protocol according to the manufacturer's instruction. DNA quality and quantity was assessed using Qubit andq-PCR.
|
| Label |
Biotin
|
| Label protocol |
Performed according to manufacturer's protocols.
|
| |
|
| Hybridization protocol |
Probes annealing and ligation on tumor DNA, amplification by PCR, probes digestion and DNA hybridization on each array were performed according to the manufacturer's instructions.
|
| Scan protocol |
The Arrays were then washed using fluidics wash, and scanned using the Gene Chip Scanner 3000.
|
| Description |
T0175_A
|
| Data processing |
Each sample has two CEL files (= array fluorescence intensity files generated per sample by the Affymetrix GeneChip® Command Console (version 4.0, 2013)) , as it was hybridized with two arrays: the A/T array and with the G/C array to obtain the genotype for each SNP present on the OncoScan. Therefore sample name descriptors _A and _C correspond to the CEL file for the A/T array and for the G/C array, respectively. Copy number values for individual SNPs were extracted and converted from CEL file and processed using the Genome Alteration Print (GAP) method (Popoval et al., Genome Biol, 2009) to determine the ploidy of each tumour and CNV.
|
| |
|
| Submission date |
Mar 12, 2018 |
| Last update date |
May 01, 2018 |
| Contact name |
Fabienne Lesueur |
| Organization name |
Institut Curie
|
| Department |
U900
|
| Street address |
11-13 rue Pierre et Marie Curie
|
| City |
Paris |
| ZIP/Postal code |
75005 |
| Country |
France |
| |
|
| Platform ID |
GPL21558 |
| Series (1) |
| GSE111711 |
OncoScan analysis to investigate CNV in breast tumors developed by ATM mutation carriers |
|
