|
| Status |
Public on Jul 15, 2020 |
| Title |
GXA_3039 |
| Sample type |
RNA |
| |
|
| Source name |
patient-derived tumor xenograft
|
| Organism |
Homo sapiens |
| Characteristics |
passage: 5
|
| Growth protocol |
PDX were passaged from mouse to mouse until RNA extraction
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA were extracted from four pieces of snap frozen tumor xenografts from four individual xenografts of the same tumors in the same or different passages using the mirVana kit (Ambion) according to the manufacturer’s instructions. A DNAse digest was performed. Each RNA preparation was subjected to quality control using NanoDrop 2000 to control for purity and Bioanalyzer (Agilent) to control for RNA integrity. Only the RNA samples with an integrity number (RIN) between 6.5 and 10 and a ratio between 28s and 18 sRNA between 1.0 and 2.0, and the RNA 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 |
All analyses were carried out using the “R” statistical computing environment and associated modules from Biobase (affy, simpleaffy, affyPLM). Gene expression signal values were extracted directly from the CEL files using robust multiarray average analysis algorithm (‘gcrma’ R package from Bioconductor; justGCRMA function with default parameters)
|
| |
|
| Submission date |
Jun 11, 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 |
GPL570 |
| Series (2) |
| GSE115637 |
Expression data from 27 Asian gastric patient-derived xenograft (PDX) models |
| GSE115755 |
Establishment of patient-derived tumor xenografts from Asian gastric adenocarcinoma is characterized by clonal selection and bias in molecular subtypes |
|
