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Status |
Public on Jun 28, 2023 |
Title |
Liver_saline_8W_rep3 |
Sample type |
RNA |
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Source name |
Liver_Wild type mice_8-week saline i.p.
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Organism |
Mus musculus |
Characteristics |
tissue: Liver genotype: Wild type mice age: 8-week agent: saline i.p.
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Treatment protocol |
Liver from liver fibrosis model induced by intraperitoneal injection of thioacetamide (TAA) in C57BL/6J mice for 8 weeks. Control mice received the same volume of normal saline (NS).
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Extracted molecule |
total RNA |
Extraction protocol |
The purity and concentration of total RNA samples were determined with NanoDrop ND-1000. Results were provided in Sample QC report.
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Label |
Cy3
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Label protocol |
Sample labeling was performed according to the manufacturer’s protocol (Arraystar Inc.). The circRNA were treated with Rnase R (Epicentre, Inc.) to remove linear RNAs. Then, each sample was 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.
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Hybridization protocol |
Array hybridization was performed according to the manufacturer’s protocol (Arraystar Inc.). 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.
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Scan protocol |
The hybridized arrays were washed, fixed and scanned using the Axon GenePix 4000B microarray scanner (Molecular Devices, Inc.).
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Description |
A total of 896 spot data on the Arraystar Mouse circRNA Array.
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Data processing |
Scanned images were imported into GenePix Pro 6.0 software (Axon) for grid alignment and raw data extraction. Quantile normalization of raw data and subsequent data processing were performed using the R software package. After quantile normalization of the raw data, low intensity filtering was performed, and the circRNAs that at least 5 out of 10 samples have flag expressed(greater than 2 times background standard deviation) were retained for further analyses. When comparing two groups or samples of profile differences, the “fold change” (i.e. the ratio of the group averages) between the groups or samples for each circRNA is computed. The statistical significance of the difference may be conveniently estimated by t-test. circRNAs having fold changes >= 2.0 and p-values =< 0.05 are selected as the significantly differentially expressed ones.
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Submission date |
Nov 22, 2022 |
Last update date |
Jun 28, 2023 |
Contact name |
shuaijie qian |
E-mail(s) |
qsjbxh1997@outlook.com
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Phone |
13540675514
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Organization name |
West China Hospital, Sichuan University
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Lab |
Lab of Gastroenterology and Hepatology
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Street address |
NO. 1, 4th Keyuan Road, Chengdu,
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City |
chengdu |
State/province |
sichuan |
ZIP/Postal code |
610041 |
Country |
China |
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Platform ID |
GPL32873 |
Series (2) |
GSE218574 |
The angiogenic role of circRNA-007371 in liver fibrosis [circRNA Microarray] |
GSE218581 |
The angiogenic role of circRNA-007371 in liver fibrosis |
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