|
| Status |
Public on Aug 01, 2023 |
| Title |
DM+RYGB, rep1 |
| Sample type |
RNA |
| |
|
| Source name |
Renal cortex
|
| Organism |
Rattus norvegicus |
| Characteristics |
disease state: DM
treatment: RYGB
|
| Treatment protocol |
SD rats are as controls, and type 1 diabetes was induced by STZ. 4 weeks later, control and diabetes rats were treated with Sham or RYGB surgery. Then renal cortex was collected 4 weeks later.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from the frozen tissues by using TRIzol (Invitrogen). The RNA quantity and quality were measured with a NanoDrop ND-1000. RNA integrity was assessed by using standard denaturing agarose gel electrophoresis.
|
| Label |
Cy3
|
| Label protocol |
The Rat 4 × 44 K Gene Expression Array was manufactured by Agilent. The updated content provided full coverage of rat genes and transcripts. Sample labeling and array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology). Briefly, the total RNA from each sample was linearly amplified and labeled with Cy3-UTP. The labeled cRNAs were purified with a RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μgcRNA) were measured with a NanoDrop ND-1000. Each labeled cRNA (1 μg) was fragmented in 11 μl of 10 × Blocking Agent and 2.2 μl of 25 × Fragmentation Buffer. Then, the mixture was heated at 60 ℃ for 30 min.
|
| |
|
| Hybridization protocol |
Finally, 55 μl of 2 × GE Hybridization buffer was added to dilute the labeled cRNA. One hundred microliters of hybridization solution were dispensed into the gasket slide and assembled to create the gene expression microarray slide. The slides were incubated for 17 h at 65 °C in an Agilent Hybridization Oven.
|
| Scan protocol |
The hybridized arrays were washed, fixed and scanned with the Agilent DNA Microarray Scanner (part number G2505C). Agilent Feature Extraction software (version 11.0.1.1) was used to analyze the acquired array images.
|
| Data processing |
Quantile normalization and subsequent data processing were performed using the Gene Spring GX v12.1 software package (Agilent Technologies). After quantile normalization of the raw data, genes for which at least 46 out of 92 samples had Detected (“All Targets Value”) flags were chosen for further analysis. Differentially expressed genes with a statistically significant difference between the two groups were identified through Volcano Plot filtering.
Differentially expressed genes between the two samples were identified through Fold Change filtering.
|
| |
|
| Submission date |
Aug 26, 2020 |
| Last update date |
Aug 01, 2023 |
| Contact name |
Xiao Wei |
| E-mail(s) |
[email protected]
|
| Organization name |
Daping Hospital, Army Medical University of PLA
|
| Department |
Department of Hypertension and Endocrinology, Center for Hypertension and Metabolic Diseases
|
| Street address |
ChangJiang Zhi Road 10, YuZhong District
|
| City |
ChongQing |
| ZIP/Postal code |
400003 |
| Country |
China |
| |
|
| Platform ID |
GPL14746 |
| Series (1) |
| GSE156908 |
Reducing NADPH synthesis counteracts diabetic nephropathy through restoration of AMPK activity |
|
