|
| Status |
Public on Dec 04, 2019 |
| Title |
Case no. 64; primary GIST |
| Sample type |
RNA |
| |
|
| Source name |
primary GIST
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: gastrointestinal stromal tumor
age: 36
gender: M
primary tumor site: duodenum
metastatic tumor site: ---
risk: very low
tumor stage: I
kit/pdgfra mutation type: KIT
kit/pdgfra mutation site: E11: p.V559A
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Tissue samples were submerged in RNAlater solution (Thermo Fisher Scientific), minced, and stored overnight at 4°C before RNA extraction. Total RNA was extracted from approximately 10 mg of minced tissue samples using the miRNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions. Initially, tissue samples were mixed with QIAzol reagent from the kit and then ground with a TissueLyzer II (Qiagen) using a 5-mm zirconia bead for 10 min at room temperature.
|
| Label |
Cy3
|
| Label protocol |
RNA samples with RNA integrity number ≥ 6.0 was used for microarray analysis. Total RNA (100 ng) was amplified and fluorescence-labeled using the One-Color Low Input Quick Amp Labeling Kit (Agilent Technologies).
|
| |
|
| Hybridization protocol |
600ng of labeled cRNA sample were fragmented at 60ºC for 30 min, and hybridized to Agilent SurePrint G3 Human Gene Expression 8×60K v2 microarrays at 65º C for 17 hours in a rotating Agilent hybridization oven. The hybridized slides were washed using Agilent Gene Expression wash buffers.
|
| Scan protocol |
Slides were scanned immediately after washing on the Agilent G2505C Microarray Scanner System.
|
| Data processing |
The scanned images were analyzed with Feature Extraction Software (version 10.7.3.1, Agilent Technologies) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.
|
| |
|
| Submission date |
Sep 03, 2019 |
| Last update date |
Dec 04, 2019 |
| Contact name |
Keiichi Ohshima |
| E-mail(s) |
k.ohshima@scchr.jp
|
| Phone |
+81-55-989-5222
|
| Organization name |
Shizuoka Cancer Center Research Institute
|
| Department |
Medical Genetics Division
|
| Street address |
1007 Shimonagakubo, Nagaizumi-cho
|
| City |
Sunto-gun |
| State/province |
Shizuoka |
| ZIP/Postal code |
4118777 |
| Country |
Japan |
| |
|
| Platform ID |
GPL17077 |
| Series (1) |
| GSE136755 |
Driver gene alterations and activated signaling pathways toward malignant progression of gastrointestinal stromal tumors |
|
