|
| Status |
Public on Nov 25, 2013 |
| Title |
786-O_knockdown 1_rep3 |
| Sample type |
RNA |
| |
|
| Source name |
clear renal cell carcinoma cell line 786-O, stable transfection with knockdown of S100A6
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: clear cell renal cell carcinoma cell line 786-O
genotype/variation: knockdown of S100A6
|
| Treatment protocol |
The 786-O cells were stable transfection with overexpression and knockdown of S100A6, each treatment had a vector transfection control. The final purity of stable transfection is 99%.
|
| Growth protocol |
The 786-O cells were cultured in RPMI 1640 medium (HyClone), and the culture medium was supplemented with 10% fatal bovin serum (FBS, Gibco). The cells were maintained at 37℃ with 5% CO2.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from each sample was extracted using TRK1001（LC Sciences, Cat. TRK-1001, Total RNA Purification Kit）according to the manufacturer’s instructions. Total RNA was quantified by the NanoDrop ND-2000 (Thermo Scientific) and the RNA integrity was assessed using Agilent Bioanalyzer 2100 (Agilent Technologies).
|
| Label |
cy3
|
| Label protocol |
The sample labeling, microarray hybridization and washing were performed based on the manufacturer’s standard protocols. Briefly, total RNA were transcribed to double strand cDNA, then synthesized into cRNA and labeled with Cyanine-3-CTP.
|
| |
|
| Hybridization protocol |
The labeled cRNAs were hybridized onto the microarray according to the manufacturer’s standard protocols.
|
| Scan protocol |
After washing, the arrays were scanned by the Agilent Scanner G2505C (Agilent Technologies).
|
| Description |
Sample name: SH1
Total 1399 different expression genes (DEGs) including 880 up-regulated and 519 down regulated genes were found in overexpression S100A6 and vector control group.
|
| Data processing |
Feature Extraction software (version10.7.1.1, Agilent Technologies) was used to analyze array images to get raw data. Genesrping were employed to finish the basic analysis with the raw data. To begin with, the raw data was normalized with the quantile algorithm. The probes that at least 1 out of all samples have flags in Detected were chosen for further data analysis. Differentially expressed genes were then identified through fold change as well as P value calculated with t-test. The threshold set for up- and down-regulated genes was a fold change>= 2.0 and a P value<= 0.05. expression pattern among samples.
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| |
|
| Submission date |
Nov 25, 2013 |
| Last update date |
Apr 23, 2018 |
| Contact name |
xu zhang |
| Organization name |
PLA general hospital
|
| Street address |
Fuxing road
|
| City |
Beijing |
| ZIP/Postal code |
100853 |
| Country |
China |
| |
|
| Platform ID |
GPL17077 |
| Series (1) |
| GSE52708 |
The mechanism of elevated S100A6 (Calcyclin) Enhances Tumorigenesis in clear cell renal cell carcinoma |
|
| Relations |
| Reanalyzed by |
GSE113533 |
