|
| Status |
Public on Jun 07, 2021 |
| Title |
Patient16_adjacent non-tumor |
| Sample type |
RNA |
| |
|
| Source name |
Liver
|
| Organism |
Homo sapiens |
| Characteristics |
disease: hepatocellular carcinoma
tissue: Adjacent non-tumor
gender: F
age: 70
|
| Treatment protocol |
N.A.
|
| Growth protocol |
N.A.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The frozen tissues were added with RLT buffer (Qiagen, Germany) with 1% β-mercaptoethanol and then homogenized by gentleMACS dissociator (Miltenyi Biotec). RNeasy mini kit (Qiagen, Germany) was used to extract the total RNA following the manufacturer’s protocol.
|
| 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 scanning was performed using Agilent DNA Microarray Scanner (part number G2505C) after washing and fixing the hybridized arrays.
|
| Description |
NA
|
| 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 using the R software limma package.
|
| |
|
| Submission date |
Aug 10, 2020 |
| Last update date |
Jun 07, 2021 |
| Contact name |
Caroline G. Lee |
| E-mail(s) |
bchleec@nus.edu.sg
|
| Organization name |
National University of Singapore
|
| Department |
Biochemistry
|
| Street address |
MD7, Level 2, 8 Medical Drive
|
| City |
Singapore |
| ZIP/Postal code |
117597 |
| Country |
Singapore |
| |
|
| Platform ID |
GPL21825 |
| Series (2) |
| GSE155949 |
circRNA expression profile in hepatocellular carcinoma patient paired tissues |
| GSE156088 |
Expression profile in hepatocellular carcinoma patient paired tissues |
|
