|
| Status |
Public on Sep 30, 2022 |
| Title |
adjacent normal tissues 2 |
| Sample type |
RNA |
| |
|
| Source name |
adjacent normal tissues
|
| Organism |
Homo sapiens |
| Characteristics |
gender: male
age: 57 years
tnm status: T1NOMO
tissue: tongue
|
| Treatment protocol |
2 pairs of tongue squamous cell carcinoma and their matched adjacent tissues taken were obtained from patients undergoing surgery at the Department of Oral and Maxillofacial Surgery, The First Affiliated Hospital of Fujian Medical University. None of the patients received chemotherapy or radiotherapy before surgery. The experimental tissue specimens were diagnosed independently by two experienced clinical pathologists. Specimens were instantly stored in liquid nitrogen and then stored at -80°C after biopsy.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from samples using TRIzol™ reagent (Invitrogen; Thermo Fisher Scientific, Inc., Waltham, MA, USA) following the protocol provided by the manufacturer. Next, RNA was purified with the RNeasy Mini kit (Qiagen) according to the manufacturer's guidelines. A NanoDrop ND-1000 spectrophotometer (Thermo Fisher Scientific, Inc.) was used to measure the concentration of RNA based on the OD260/OD280 ratio.
|
| Label |
Cy3
|
| Label protocol |
Total RNAs were digested with Rnase R (Epicentre, Inc.) to remove linear RNAs and enrich circular RNAs. Then, the enriched circular RNAs were amplified and transcribed into fluorescent cRNA utilizing a random priming method (Arraystar Super 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 × Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the circRNA 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 using the Agilent Scanner G2505C.Scanned images were imported into Agilent Feature Extraction software for raw data extraction.
|
| Description |
PTSCC_2
|
| Data processing |
Data processing, including quantile normalization, was performed using R software.
CircRNAs that were significantly differentially expressed between the tumor and normal tissues were identified using a fold-change cut-off value
|
| |
|
| Submission date |
Sep 14, 2020 |
| Last update date |
Sep 30, 2022 |
| Contact name |
Zexi Chen |
| Organization name |
Fujian Medical University
|
| Street address |
1 Xue Yuan Road,University Town
|
| City |
Fuzhou |
| State/province |
Fujian |
| ZIP/Postal code |
350122 |
| Country |
China |
| |
|
| Platform ID |
GPL21825 |
| Series (1) |
| GSE157918 |
Circular RNA expression in tongue squamous cell carcinoma patients |
|
