|
| Status |
Public on Jun 23, 2020 |
| Title |
BV_LPS_3 (mRNA) |
| 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 Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology). Briefly, total RNA from each sample was linearly amplified and labeled with Cy3-UTP. 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 11 μl 10 × Blocking Agent and 2.2 μl of 25 × Fragmentation Buffer, then heated the mixture at 60°C for 30 min, finally 55 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA.
|
| |
|
| Hybridization protocol |
100 μl of hybridization solution was dispensed into the gasket slide and assembled to the gene 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 with using the Agilent DNA Microarray Scanner (part number G2505C).
|
| Scan protocol |
The hybridized arrays were washed, fixed and scanned using the Agilent DNA Microarray Scanner .Scanned images were imported into Agilent Feature Extraction software for raw data extraction. Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images.
|
| Data processing |
Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies). After quantile normalization of the raw data, LncRNAs and mRNAs that at least 5 out of 10 samples have flags in Detected (“All Targets Value”) were chosen for further data analysis. Differentially expressed genes with statistical significance between the two groups were identified through Volcano Plot filtering. Differentially expressed genes between the two samples were identified through Fold Change filtering. Hierarchical Clustering was performed using the R scripts. GO analysis and Pathway analysis were performed in the standard enrichment computation method.
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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 |
GPL14746 |
| Series (2) |
| GSE147774 |
Identification of circRNA and mRNA expression profiles and functional networks of vascular tissue in lipopolysaccharide-induced rat septic shock model [mRNA] |
| 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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