|
| Status |
Public on Jan 15, 2019 |
| Title |
HERS-C2_rep1 |
| Sample type |
RNA |
| |
|
| Source name |
HERS cell line HERS-C2
|
| Organism |
Rattus norvegicus |
| Characteristics |
cell line: HERS cell line HERS-C2
|
| Growth protocol |
Cells was cultured with epithelial cell medium (ScienCell, CA, USA) consisting of basal medium, 2% fetal bovine serum, 1% epithelial cell growth supplement, and 1% penicillin/streptomycin solution.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated by the TRIzol (Invitrogen) method following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies).
|
| Label |
Cy3
|
| Label protocol |
Sample labeling was performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology). Briefly, total RNA from each sample was linearly amplified and labeled with Cy3-UTP. 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 |
Array hybridization was performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology). 1 μg of each labeled cRNA was fragmented by adding 11 μl 10 × Blocking Agent and 2.2 μl of 25 × Fragmentation Buffer, then heated the mixture at 60°C for 30 min, finally 55 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 100 μl of hybridization solution was dispensed into the gasket slide and assembled to the gene 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).
|
| Description |
Gene expression of immortalized HERS cell line HERS-C2
|
| 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, mRNAs that at least 3 out of 9 samples have flags in Detected (“All Targets Value”) were chosen for further data analysis.
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| |
|
| Submission date |
Jan 25, 2018 |
| Last update date |
Jan 15, 2019 |
| Contact name |
Guoqing Chen |
| E-mail(s) |
[email protected]
|
| Organization name |
Sichuan University
|
| Department |
West China Hospital of Stomatology
|
| Street address |
No. 14, 3rd Sec., Ren Min Nan Road
|
| City |
Chengdu |
| ZIP/Postal code |
610041 |
| Country |
China |
| |
|
| Platform ID |
GPL14746 |
| Series (1) |
| GSE109622 |
Comparison of the transcriptomes of immortalized Hertwig’s epithelial root sheath (HERS) cell line HERS-H1 and HERS-C2 |
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