|
| Status |
Public on Nov 27, 2020 |
| Title |
P_SLE_S22 |
| Sample type |
RNA |
| |
|
| Source name |
Plasma, SLE
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Plasma
gender: female
|
| Treatment protocol |
The blood was centrifuged by spinning at 2000 × g for 10 min at room temperature. Plasma was then carefully transferred to a fresh RNase-free tube and stored at –80°C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from plasma by using TRIzol Reagent (Invitrogen, Carlsbad, USA) according to the manufacture’s protocol. The purity and concentration of RNA was evaluated with the NanoDrop ND-1000 (Thermo Fisher Scientific, Wilmington, DE).
|
| Label |
Cy3
|
| Label protocol |
Total RNAs were digested with Rnase R (Epicentre, Inc.) to remove linear RNAs and enrich circular RNAs. Then,circular RNAs were amplified and transcribed into fluorescent cRNA utilizing a random priming method (Arraystar Super RNA Labeling Kit; Arraystar). 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.
|
| Description |
circRNA expression in plasma from patient S22
|
| Data processing |
To asses the array images Agilent Feature Extraction software was applied. Quantile normalization and subsequent data processing were performed with the GeneSpring GX v11.5.1 software package (Agilent Technologies).After quantile normalization of the raw data, circRNAs that at least 4 out of 8 samples have flags in Present or Marginal (“All Targets Value”) were retained for further analyses..Differentially expressed circRNAs with statistical significance were identified through Volcano Plot filtering and Hierarchical Clustering.
|
| |
|
| Submission date |
Nov 26, 2017 |
| Last update date |
Nov 27, 2020 |
| Contact name |
Ming-Yue Zhang |
| Organization name |
Anhui Medical University
|
| Street address |
Anhui Medical University of meishan road 81
|
| City |
Heifei |
| ZIP/Postal code |
230032 |
| Country |
China |
| |
|
| Platform ID |
GPL21825 |
| Series (1) |
| GSE107344 |
Plasma circRNA expression profile in systemic lupus erythematosus and its clinical significance |
|
