|
| Status |
Public on Dec 01, 2021 |
| Title |
m-1 |
| Sample type |
RNA |
| |
|
| Source name |
db/m
|
| Organism |
Mus musculus |
| Characteristics |
tissue: submandibular gland
gender: male
age: 16-week-old
Sex: male
|
| Growth protocol |
The submandibular glands of mice are preserved at -80 degrees Celsius.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using Trizol reagent (Invitrogen Life Technologies, Carlsbad, CA, USA) according to the manufacturer’s instructions.
|
| 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) with minor modifications. Briefly, mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). Then, each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3’ bias utilizing a random priming method (Arraystar Flash 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.
|
| |
|
| Hybridization protocol |
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 × GE Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA 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).
|
| 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 v12.1 software package (Agilent Technologies). After quantile normalization of the raw data, LncRNAs and mRNAs that at least 4 out of 8 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis. Differentially expressed LncRNAs and mRNAs with statistical significance between the two groups were identified through P-value/FDR filtering. Differentially expressed LncRNAs and mRNAs between the two samples were identified through Fold Change filtering.
|
| |
|
| Submission date |
Dec 04, 2019 |
| Last update date |
Dec 01, 2021 |
| Contact name |
huimin liu |
| E-mail(s) |
1811210002@pku.edu.cn
|
| Phone |
13146619655
|
| Organization name |
Peking University
|
| Department |
Peking University Health Science Center
|
| Lab |
Department of Physiology and Pathophysiology
|
| Street address |
38 Xueyuan Rd , Haidian District
|
| City |
Beijing |
| State/province |
Beijing |
| ZIP/Postal code |
100191 |
| Country |
China |
| |
|
| Platform ID |
GPL25454 |
| Series (2) |
| GSE141411 |
MicroRNA-mRNA expression profiles and functional networks of Submandibular Gland in type 2 diabetic db/db mice [array] |
| GSE141412 |
MicroRNA-mRNA expression profiles and functional networks of Submandibular Gland in type 2 diabetic db/db mice |
|
