|
| Status |
Public on Oct 26, 2016 |
| Title |
pancreasRNA_PDAC_rep2 |
| Sample type |
RNA |
| |
|
| Source name |
pancreasRNA, PDAC
|
| Organism |
Homo sapiens |
| Characteristics |
individual: patient 2
tissue: PDAC
age: 53
gender: Female
|
| Treatment protocol |
PDAC tissue samples and their matched adjacent non-tumor samples were taken during surgery, immediately frozen in liquid nitrogen, and stored at -80˚C for microarry analysis.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol extraction of total RNA was performed according to the manufacturer's instructions.
|
| Label |
Cy3
|
| Label protocol |
Sample labeling was performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology) with minor modifications. Briefly, mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). Then, each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3' bias utilizing a random priming method (Arraystar Flash RNA Labeling Kit, Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.
|
| |
|
| Hybridization protocol |
Sample array hybridization was performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology) with minor modifications.Briefly, 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60°C for 30 min, finally 25 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven,and then the hybridized arrays were washed and fixed.
|
| Scan protocol |
The hybridized arrays were scanned with the Agilent DNA Microarray Scanner (part number G2505C).
|
| Description |
lncRNA expression data from PDAC
|
| Data processing |
Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies).
|
| |
|
| Submission date |
Oct 25, 2016 |
| Last update date |
Oct 26, 2016 |
| Contact name |
Shikai Zhu |
| Organization name |
Sichuan Academy of Medical Sciences & Sichuan Provincial People’s Hospital
|
| Street address |
No.32 West Second Section First Ring Road
|
| City |
Chengdu |
| ZIP/Postal code |
610000 |
| Country |
China |
| |
|
| Platform ID |
GPL16956 |
| Series (1) |
| GSE89139 |
Expression data from pancreatic ductal adenocarcinoma |
|
