|
| Status |
Public on May 18, 2022 |
| Title |
203845 |
| Sample type |
genomic |
| |
|
| Source name |
pancreatic acinar cell carcinoma
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: pancreatic acinar cell carcinoma
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was extracted from formol fixed-paraffin embedded fragments using Maxwell FFPE DNA LEV Kit (PROMEGA).
|
| 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.
|
| Data processing |
The array image was acquired using Affymetrix GeneChip® Command Console Software (version 3.2.2). Copy number values for individual SNPs were extracted and converted from CEL files into signal intensities using CHAs (version 4.0). Genomic Smoothing analysis was performed by CHAs
The CNV value is the logarithm base 2 of the sample signal divided by a reference value from the OncoScan_CNV.FFPE.na33.r2.REF_MODEL library. The allelic status is determined accordind the B-Allelic Frequency (BAF = B/(A+B) ; AA : BAF = 0, BB : BAF = 1, AB : BAF = 0,5) or the Allele Difference (Diff = A - B where each A and B allele are 0,5 units. AA : Diff = 1, AB : Diff = 0, BB : Diff = -1)
|
| |
|
| Submission date |
May 17, 2022 |
| Last update date |
May 18, 2022 |
| Contact name |
Thibault FABAS |
| Organization name |
CHU Nice
|
| Lab |
Génétiques des Tumeurs Solides
|
| Street address |
28 av Valombrose
|
| City |
NICE |
| ZIP/Postal code |
06107 |
| Country |
France |
| |
|
| Platform ID |
GPL21558 |
| Series (1) |
| GSE203175 |
AGAP3: a novel BRAF-fusion partner in pediatric pancreatic acinar cell carcinoma |
|
