|
| Status |
Public on Aug 10, 2021 |
| Title |
Liver tissue_14 weeks_high fat diet_rep1 |
| Sample type |
RNA |
| |
|
| Source name |
Liver tissue, 14 weeks, high fat diet
|
| Organism |
Rattus norvegicus |
| Characteristics |
disease state: NAFLD
gender: male
age: 22-week-old
treatment: high fat diet
tissue: liver
|
| Treatment protocol |
liver tissues were collected in RNase-free tubes and promptly frozen in liquid nitrogen.
|
| Growth protocol |
The two groups of rats were fed by14 weeks of high fat diet and normal chow diet seperatly
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from the rat liver samples using TRIzol reagent (Invitrogen,Carlsbad,CA,USA) and purified using the RNeasy Mini Qiagen purification kit (QIAGEN,Valencia,CA) according to the manufacturer’s instructions. Integrity and concentration of RNA were assessed after RNA extraction and prior to sample labeling by NanoDrop ND-1000 (Thermo Fisher scientific,Waltham,MA). The integrity of RNA were assessed by Denaturing Agarose Gel Electrophoresis.
|
| 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
|
| |
|
| Hybridization protocol |
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. 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.
|
| Scan protocol |
The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C).1.Assemble the slides into an slide holder. 2.Place assembled slide holders into scanner carousel.3.Verify scan settings for one-color scans.4.Click Scan Slot m-n on the Scan Control main window where the letter m represents the Start slot where the first slide is located and the letter n represents the End slot where the last slide is located.
|
| Description |
Gene expression data from liver tissue of NAFLD rat
N 1-4
|
| 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 with using the GeneSpring GX v11.5.1 software package (Agilent Technologies). After quantile normalization of the raw data, genes that all samples have flags in Detected (“All Targets Value”) were chosen for further data analysis. Differentially expressed genes with statistical significance were identified through Volcano Plot filtering. Hierarchical Clustering was performed using the Agilent GeneSpring GX software (version 11.5.1). GO analysis and Pathway analysis were performed in the standard enrichment computation method.
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| |
|
| Submission date |
Aug 22, 2018 |
| Last update date |
Aug 10, 2021 |
| Contact name |
ting li |
| E-mail(s) |
[email protected]
|
| Phone |
0086-18710708230
|
| Organization name |
Xi’an Jiaotong University
|
| Department |
Health Science Center
|
| Street address |
NO.76 Yanta West Road, Health Science Center, Xi’an Jiaotong University, Xi’an. China
|
| City |
Xi’an. China |
| State/province |
Shaanxi |
| ZIP/Postal code |
710061 |
| Country |
China |
| |
|
| Platform ID |
GPL14746 |
| Series (1) |
| GSE118892 |
Screening of Genes Related to Glucose and Lipid Metabolism in Non-alcoholic Fatty Liver Disease by Gene Microarray |
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