|
| Status |
Public on Jul 15, 2020 |
| Title |
GXA_3054 Type: Patient derived Xenograft Passage: 4 |
| Sample type |
genomic |
| |
|
| Source name |
patient-derived tumor xenograft
|
| Organism |
Homo sapiens |
| Characteristics |
passages: 4
|
| Treatment protocol |
none
|
| Growth protocol |
PDX were passaged from mouse to mouse until DNA extraction
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was extracted from snap frozen tumor xenografts, patient tumors or normal tissues. Samples were digested with proteinase K at 55°C overnight and the lysate was digested with DNAse-free RNAse (Qiagen). DNA was extracted with a mix of phenol:chloroform:isoamylalcohol and precipitated with ethanol. DNA pellets were washed and resuspended in Tris-EDTA buffer. Each DNA preparation was subjected to quality control using a 1.3% agarose gel and using NanoDrop 2000 to control for purity. Only DNA samples with no sign of degradation (a clearly defined high molecular weight band on the agarose gel) and the DNA was pure (260/280 nm and 260/230 nm close to 2.0), were used for the microarray analysis.
|
| Label |
biotin
|
| Label protocol |
standard Affymetrix protocol
|
| |
|
| Hybridization protocol |
standard Affymetrix protocol
|
| Scan protocol |
standard Affymetrix protocol
|
| Data processing |
Affymetrix Genome wide SNP6.0 CEL files were loaded into the Affymetrix Genotyping Console 4.1 Software (Affymetrix). After scanning, arrays were checked for quality using the Affymetrix Genotyping Console. In accordance with Affymetrix guidelines, SNP6.0 arrays with a Contrast QC value above 0.4 and MAPD below 0.35 were excluded from further analysis. Copy number variations were calculated using Affymetrix GTC v4.1 and PICNIC software provided by the Cancer Genome Project from the Welcome Trust Sanger Institute. The PICNIC algorithm (PICNIC - Predicting Integral Copy Numbers In Cancer) includes improved normalisation of the data together with determination of underlying copy numbers for each segment by genome wide analysis of allele ratio and signal strength data. The data was subsequently rescaled and plotted onto its predicted underlying integer value and segmentation was applied. This data analysis procedure also allowed for assignment of a genotype to each SNP. The PICNIC segment files were further compiled to generate a simplified gene matrix. A gene was assigned a deletion (CNV=0) if a deletion segment overlaps with the gene, otherwise the copy number of the most amplified segment overlapping with the gene was assigned.
PICNIC integer copy number score (0 is considered as a gene deletion, values between 1 and 7 are considered as a moderate gene copy alteration, values equal or greater than 8 are considered as a gene amplification)
|
| |
|
| Submission date |
Jun 12, 2018 |
| Last update date |
Jul 15, 2020 |
| Contact name |
Vincent Vuaroqueaux |
| E-mail(s) |
vincent.vuaroqueaux@4hf.eu
|
| Organization name |
4HF Biotec
|
| Department |
Bioinformatics
|
| Street address |
Am Flughafen 14
|
| City |
Freiburg |
| ZIP/Postal code |
79108 |
| Country |
Germany |
| |
|
| Platform ID |
GPL6801 |
| Series (2) |
| GSE115674 |
Genomic data from 48 Asian gastric patient-derived xenograft (PDX) models, 7 Asian gastric patient tumors and the 8 corresponding normal tissues |
| GSE115755 |
Establishment of patient-derived tumor xenografts from Asian gastric adenocarcinoma is characterized by clonal selection and bias in molecular subtypes |
|
