|
| Status |
Public on Mar 02, 2023 |
| Title |
liver_MCT_rep2 |
| Sample type |
RNA |
| |
|
| Source name |
liver tissue, MCT, replicate 2
|
| Organism |
Rattus norvegicus |
| Characteristics |
tissue: liver
gender: male
age: 7-9 weeks
strain: SD rats
|
| Treatment protocol |
Rats were fed adaptively for 7 days before the experiment and randomly divided into two groups (Control, MCT). Hepatic sinusoidal obstruction syndrome was induced 12h after monocrotaline treatment, and the Control group was given with normal saline.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was quantified by the NanoDrop ND-2000 (Thermo Scientific)and the RNA integritywas assessed using Agilent Bioanalyzer 2100 (Agilent Technologies).
|
| Label |
Cy3
|
| Label protocol |
Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 μg RNA using One-Color Low Input Quick Amp Labeling kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.
|
| |
|
| Hybridization protocol |
Total RNA were transcribed to double strand cDNA, then synthesizedinto cRNA and labeled with Cyanine-3-CTP. The labeled cRNAs were hybridized onto the microarray.
|
| Scan protocol |
After washing, the arrays were scanned by the Agilent Scanner G2505C (Agilent Technologies).
|
| Description |
Gene expression in colonic tissue of MCT group
|
| Data processing |
Feature Extraction software (version10.7.1.1, Agilent Technologies) was used to analyzearray images to get raw data. Genespring (version 14.8, Agilent Technologies) were employedto finish the basic analysis with the raw data. To begin with, the raw data was normalizedwith the quantile algorithm. The probes that at least 1 conditions out of 2 conditions haveflags in “Detected” were chosen for further data analysis. Differentially expressed geneswere then identified through fold change as well as P value calculated with t-test. Thethreshold set for up- and down-regulated genes was a fold change>= 2.0 and a P value<= 0.05.Afterwards, GO analysis and KEGG analysis were applied to determine the roles of thesedifferentially expressed mRNAs. Finally, Hierarchical Clustering was performed to displaythe distinguishable genes' expression pattern among samples.
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| |
|
| Submission date |
Sep 09, 2022 |
| Last update date |
Mar 02, 2023 |
| Contact name |
Lixin Sun |
| E-mail(s) |
slxcpu@126.com
|
| Organization name |
China Pharmaceutical University
|
| Street address |
24 Tong Jia Xiang
|
| City |
Nanjing |
| ZIP/Postal code |
210038 |
| Country |
China |
| |
|
| Platform ID |
GPL32651 |
| Series (1) |
| GSE213031 |
LncRNA expression profile and their possible regulatory role in the HSOS induced by monocrotaline in rats |
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