|
| Status |
Public on Oct 21, 2016 |
| Title |
Para-carcinoma_patient 4 |
| Sample type |
RNA |
| |
|
| Source name |
Adjacent normal tissue
|
| Organism |
Homo sapiens |
| Characteristics |
patient id: patient 4
patient diagnosis: bladder cancer
tissue: Adjacent normal
gender: male
age: 79y
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from frozen tissues stored in liquid nitrogen using TRIzol (Invitrogen) according to manufacturer’s recommendations. RNA quantity and quality were determined by OD260 using a NanoDrop ND-1000 spectrophotometer and RNA integrity was assessed by electrophoresis on a denaturing agarose gel.
|
| Label |
Cy3
|
| Label protocol |
RNA 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 |
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.
|
| Scan protocol |
The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C).
|
| Data processing |
Scanned images were imported into Agilent Feature Extraction software for raw data extraction. Quantile normalization of raw data and subsequent data processing were performed using the R software package.
|
| |
|
| Submission date |
Oct 20, 2016 |
| Last update date |
Oct 21, 2016 |
| Contact name |
Zhenyu Zhong |
| E-mail(s) |
mylifeemail@sina.com
|
| Organization name |
Chongqing Medical University
|
| Street address |
No. 1 Yixueyuan Road
|
| City |
Chongqing |
| ZIP/Postal code |
400016 |
| Country |
China |
| |
|
| Platform ID |
GPL16956 |
| Series (1) |
| GSE89006 |
Expression profiles of lncRNAs in bladder cancer |
|
