|
| Status |
Public on Jan 01, 2017 |
| Title |
BHK21 cell_Cirp−/−_48h_rep3 |
| Sample type |
RNA |
| |
|
| Source name |
BHK21 cell,Cirp−/−,48h
|
| Organism |
Mus musculus |
| Characteristics |
cell line: BHK21
treatment: Cirp−/− knockdown
time: 48h
|
| Treatment protocol |
Before RNA extract, the cells were washed three times by the phosphate buffer solution (PBS).
|
| Growth protocol |
Cirp−/−, or control BHK21 cells at a density of 2.0×105 cells/mL were inoculated into six-well plates containing 2.5 mL of Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum and then cultured at 37 °C in a humidified incubator with 5% CO2.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from Cirp−/− and control BHK21 cells at 24, 48, and 72 h was extracted using TRIzol reagent (Applied Biosystems Inc., Carlsbad, CA) according to the manufacturer’s instructions.
|
| Label |
Cy3
|
| Label protocol |
Total RNA of each sample was used for labeling and array hybridization as the following steps: 1) Reverse transcription with by Invitrogen Superscript ds-cDNA synthesis kit; 2) ds-cDNA labeling with NimbleGen one-color DNA labeling kit.
|
| |
|
| Hybridization protocol |
Array hybridization using the NimbleGen Hybridization System and followed by washing with the NimbleGen wash buffer kit.
|
| Scan protocol |
Array scanning using the Axon GenePix 4000B microarray scanner (Molecular Devices Corporation).
|
| Description |
Cirp−/− BHK21 cell
|
| Data processing |
Scanned images (TIFF format) were then imported into NimbleScan software (version 2.5.26) for grid alignment and expression data analysis. Expression data were normalized through quantile normalization and the Robust Multichip Average (RMA) algorithm included in the NimbleScan software. The Probe level (*_norm_RMA.pair) files and Gene level (*_RMA.calls) files were generated after normalization.
|
| |
|
| Submission date |
Jan 27, 2014 |
| Last update date |
Jan 01, 2017 |
| Contact name |
Cheng TANG |
| Organization name |
Southwest University for Nationalities
|
| Street address |
No 16 Yihuan Lu South Sect.4,
|
| City |
Chengdu |
| State/province |
Sichuan |
| ZIP/Postal code |
610041 |
| Country |
China |
| |
|
| Platform ID |
GPL15887 |
| Series (1) |
| GSE54425 |
Analysis of gene expression profiles of the cold-inducible RNA-binding protein knockdown BHK21 (Cirp−/−BHK21) cells |
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