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| Status |
Public on Jun 23, 2020 |
| Title |
BV_LPS_1 (circRNA) |
| Sample type |
RNA |
| |
|
| Source name |
blood vessel, LPS
|
| Organism |
Rattus norvegicus |
| Characteristics |
strain: Wistar
tissue: blood vessel
gender: male
age: 7 week
treatment: LPS
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using Trizol reagent (Invitrogen Life Technologies, Carlsbad, CA, USA) according to the manufacturer’s instructions.
|
| Label |
Cy3
|
| Label protocol |
Sample labeling and array hybridization were performed according to the manufacturer’s protocol (Arraystar Inc.) Briefly, 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).
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| |
|
| Hybridization protocol |
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. 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. The hybridized arrays were washed, fixed and scanned using the Agilent Scanner G2505C.
|
| 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.
|
| 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. Differentially expressed circRNAs with statistical significance between two groups were identified through Volcano Plot filtering. Differentially expressed circRNAs between two samples were identified through Fold Change filtering. Hierarchical Clustering was performed to show the distinguishable circRNAs expression pattern among samples.
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| |
|
| Submission date |
Mar 30, 2020 |
| Last update date |
Jun 23, 2020 |
| Contact name |
Jinghua Yang |
| E-mail(s) |
yangjh@xy-data.net
|
| Organization name |
Beijing Zhiyun data technology co. LTD
|
| Street address |
32 North Third Ring Road West, Haidian District, Beijing
|
| City |
Beijing |
| ZIP/Postal code |
100098 |
| Country |
China |
| |
|
| Platform ID |
GPL21828 |
| Series (2) |
| GSE147772 |
Identification of circRNA and mRNA expression profiles and functional networks of vascular tissue in lipopolysaccharide-induced rat septic shock model [circRNA] |
| GSE147775 |
Identification of circRNA and mRNA expression profiles and functional networks of vascular tissue in lipopolysaccharide-induced rat septic shock model |
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