|
| Status |
Public on Apr 25, 2018 |
| Title |
Patient 3 CP-7 |
| Sample type |
RNA |
| |
|
| Source name |
CD117IHC+/KITmutant GIST
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: CD117IHC+/KITmutant GIST
status after 5 years: alive
histology: spindle
age: 72 years
Sex: Female
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated with the Total RNA Purification Kit (Norgen Biotek Corporation, Thorold, Canada) according to the manufacture's instructions
|
| Label |
Cy5
|
| Label protocol |
Labeling of total RNA was performed according to the protocol from LC Science for a single-color experiment with no modification.
|
| |
|
| Hybridization protocol |
Hybridization was performed overnight on a μParaflo microfluidic chip using a micro-circulation pump (Atactic Technologies) (1). On the microfluidic chip, each detection probe consisted of a chemically modified nucleotide coding segment complementary to target microRNA (from miRBase, http://www.mirbase.org/) or other RNA (control or customer defined sequences) and a spacer segment of polyethylene glycol to extend the coding segment away from the substrate. The detection probes were made by in situ synthesis using PGR (photogenerated reagent) chemistry. The hybridization melting temperatures were balanced by chemical modifications of the detection probes. Hybridization used 100 L 6xSSPE buffer (0.90 M NaCl, 60 mM Na2HPO4, 6 mM EDTA, pH 6.8) containing 25% formamide at 34 °C.
|
| Scan protocol |
Fluorescence images were collected using a laser scanner (GenePix 4000B, Molecular Device) and digitized using Array-Pro image analysis software (Media Cybernetics)
|
| Description |
paraffin tissue
|
| Data processing |
Data were analyzed by first subtracting the background, then the signals were normalized using a Lowess (locally weighted regression) filter. The raw microarray data set was filtered according to a standard procedure to exclude spots with minimum intensity. It was arbitrarily set to an intensity parameter of P100 for the miRNA microarray data. Spots with diameters less than 10 μm and flagged spots were also excluded from the analyses.
|
| |
|
| Submission date |
Sep 23, 2015 |
| Last update date |
Apr 25, 2018 |
| Contact name |
Yu Wang |
| E-mail(s) |
tongjisiyu@163.com
|
| Organization name |
Institute of Pathology
|
| Street address |
1095 Jiefang Dadao
|
| City |
Wuhan |
| State/province |
Hubei |
| ZIP/Postal code |
430030 |
| Country |
China |
| |
|
| Platform ID |
GPL20948 |
| Series (1) |
| GSE73346 |
Function annotation and clinical implications of KIT mutation and overexpression associated microRNAs in gastrointestinal stromal tumours |
|
