|
| Status |
Public on Oct 19, 2016 |
| Title |
LSCC-Tumor-9515T |
| Sample type |
RNA |
| |
|
| Source name |
early stage lung squamous cell carcinoma tissues
|
| Organism |
Homo sapiens |
| Characteristics |
gender: male
age: 66
tnm stage: IIa
tissue: early stage lung squamous cell carcinoma tissues
|
| Treatment protocol |
Paired LSCC and adjacent normal lung tissues from each subject were snap-frozen in liquid nitrogen immediately after resection and stored at -80 °C until later use.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was purified from total RNA after removal of rRNA using mRNA-ONLYTM Eukaryotic mRNA Isolation Kit (Epicentre, Madison, WI, USA).
|
| Label |
Cy3
|
| Label protocol |
Cyanine-3 (Cy3) labeled cRNA was prepared from 1 ug RNA using the Quick Amp Labeling Kit, One-Color (Agilent p/n 5190-0442) according to the manufacturer's instructions,
|
| |
|
| Hybridization protocol |
1.5 ug of cyanine 3-labeled, linearly amplified cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2xgGEx Hybridization Buffer HI-RPM was added to the fragmentation mixture and hybridized to Hybridization Chamber gasket slides (Agilent p/n G2534-60003) for 17 hours at 65°C in a rotating Agilent hybridization oven.
|
| Scan protocol |
Slides were scanned immediately after washing on the Agilent Microarray Scanner (Agilent p/n G2565BA) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5 um, Dye channel is set to Green and Green PMT is set to 100%).
|
| Description |
lncRNA and mRNA expression profile in tumor tissues
|
| Data processing |
The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
|
| |
|
| Submission date |
Oct 18, 2016 |
| Last update date |
Oct 19, 2016 |
| Contact name |
cheng zule |
| Organization name |
Shanghai Institute of Microsystem And Information Technology,Chinese Academy of Sciences
|
| Street address |
NO.865 Changning Street
|
| City |
Shanghai |
| ZIP/Postal code |
200050 |
| Country |
China |
| |
|
| Platform ID |
GPL16956 |
| Series (1) |
| GSE88862 |
Examine the expression profiles of lncRNAs in early stage lung squamous cell carcinoma |
|
