|
| Status |
Public on Apr 10, 2020 |
| Title |
Wt_STZ-1: Renal_WT Diabetic_rep1 |
| Sample type |
RNA |
| |
|
| Source name |
Renal
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: Renal cortical
gendel: Male
|
| Treatment protocol |
Eight-week-old C57BL/6J mice were fed with high fat diet (HFD; 60% of total calories from fat, D12492, Keao Xieli, Beijing, China), while the control group was fed with normal chow diet (NCD; 10% of total calories from fat). After four weeks, mice in the HFD group were intraperitoneally injected with streptozotocin (STZ, S0130, Sigma Aldrich, St Louis, USA) dissolved in 50 mM sodium citrate buffer (pH 4.5, Solarbio, Beijing, China) at 60 mg/kg for three consecutive days, while the NCD group were injected with equivalent amount of vehicle.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted by mirVanaTM RNA Isolation Kit (Applied Biosystem p/n AM1556 ) following the manufacturer's instructions.
|
| Label |
Cy3
|
| Label protocol |
Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 μg RNA using the One-Color Low RNA Input Linear Amplification PLUS 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-1000 Spectrophotometer.
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| |
|
| Hybridization protocol |
0.6 μg of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/μg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 22.5μl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers' instructions. On completion of the fragmentation reaction, 22.5μl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Mouse Gene Expression v2.0 (8×60K) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.
|
| Scan protocol |
Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 4x180k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).
|
| Description |
C57BL/6, sacrificed 26 weeks after STZ induction
|
| Data processing |
The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities as the raw data. Raw data were normalized in quantile algorithm with Genespring 13.0(Agilent). Probe that at least 1 out of 2 samples flagged as Detected were maintained.
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| |
|
| Submission date |
Jul 01, 2019 |
| Last update date |
Apr 10, 2020 |
| Contact name |
Xiao-Qian Li |
| E-mail(s) |
[email protected]
|
| Organization name |
the First Affiliated Hospital of Zhengzhou University
|
| Department |
Nephrology Hospital
|
| Street address |
No. 1, East of Jianshe Street, Erqi District
|
| City |
Zhengzhou |
| State/province |
Henan |
| ZIP/Postal code |
450052 |
| Country |
China |
| |
|
| Platform ID |
GPL21163 |
| Series (2) |
| GSE133597 |
Deficiency of C3a receptor attenuates the development of diabetic nephropathy (Diabetic Group) |
| GSE133598 |
Deficiency of C3a receptor attenuates the development of diabetic nephropathy |
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