|
| Status |
Public on Dec 31, 2020 |
| Title |
intestine_normal_rep3 [NC-1C] |
| Sample type |
RNA |
| |
|
| Source name |
intestine_normal
|
| Organism |
Mus musculus |
| Characteristics |
strain: Kunming (KM)
gender: female
age: 2month
sample group: normal mice
tissue: intestine
|
| Treatment protocol |
The tissue blocks were ground into a tissue homogenate to extract RNA
|
| Growth protocol |
Gastric and intestinal tissues were removed from euthanized mice and stored at -80 ° c in a refrigerator
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA containing small RNA was extracted from stomach and intestine by using the Trizol reagent (Invitrogen) and purified with mirVana miRNA Isolation Kit (Ambion, Austin,TX, USA) according to manufacter’s protocol. The purity and concentration of RNA were determined from OD260/280 readings using spectrophotometer (NanoDrop ND-1000). RNA integrity was determined by 1% formaldehyde denaturing gel electrophoresis.
|
| Label |
Cy3
|
| Label protocol |
cDNA labeled with a fluorescent dye (Cy3-dCTP) was produced by Eberwine’s linear RNA amplification method and subsequent enzymatic reaction. This procedure has been previously described, 2 and the procedure has been improved by using CapitalBio cRNA Amplification and Labeling Kit (CapitalBio) for producing higher yields of labeled cDNA.
|
| |
|
| Hybridization protocol |
DNA in hybridization solution was denatured at 95℃ for 3 min prior to loading onto a microarray. Arrays were hybridized was preformed in a Agilent Hybridization Oven overnight at a rotation speed of 20 rpm and a temperature of 42℃ and washed with two consecutive solutions (0.2% SDS, 2× SSC at 42℃ for 5 min, and 0.2× SSC for 5 min at room temperature).
|
| Scan protocol |
Agilent chip scanner (G2565CA) was used to scan the cleaned chip and obtain hybrid images.
|
| Data processing |
The lncRNA+mRNA array data were analyzed for data summarization, normalization and quality control by using the GeneSpring software V13.0 (Agilent). To select the differentially expressed genes, we used threshold values of ≥2 and ≤−2-fold change and a Benjamini-Hochberg corrected p vlaue of 0.05. The data was Log2 transformed and median centered by genes using the Adjust Data function of CLUSTER 3.0 software then further analyzed with hierarchical clustering with average linkage (Eisen et al., 1998).
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| |
|
| Submission date |
Nov 25, 2019 |
| Last update date |
Jan 01, 2021 |
| Contact name |
Jie Meng |
| E-mail(s) |
meng_jie0216@126.com
|
| Organization name |
Gansu University of Chinese Medicene
|
| Street address |
35 Dingxi dong lu, Chengguan district, Lanzhou city, Gansu province, China
|
| City |
Lanzhou |
| State/province |
Gansu |
| ZIP/Postal code |
730000 |
| Country |
China |
| |
|
| Platform ID |
GPL22782 |
| Series (1) |
| GSE140949 |
The effects of codonopsis pilosula on RNA expression profile in digestive system of D-galactose-induced aging mice |
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