|
| Status |
Public on May 20, 2021 |
| Title |
22Rv1 cell as control |
| Sample type |
RNA |
| |
|
| Source name |
22Rv1_NC
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: 22Rv1
genotype/variation: negative control
|
| Treatment protocol |
22Rv1 cells transfected with siRNA are referred as 22Rv1_NC and 22Rv1_siKIF15.
|
| Growth protocol |
Cells were maintained in 1640 medium supplemented with 10% fetal bovine serum (FBS) and 100 U/mL penicillin and streptomycin. Cell cultures were held in a humid, 37℃ and 5% CO2 cell culture incubator.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from each sample was quantified by the NanoDrop ND-1000 and RNA integrity was assessed by standard denaturing agarose gel electrophoresis.
|
| Label |
CY3
|
| Label protocol |
Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.
|
| |
|
| Hybridization protocol |
1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.
|
| Scan protocol |
After being washed in an ozone-free environment, image capture was performed with Ageilent DNA Microarray Scanner and uploaded into Agilent Feature Extraction (v11.0.0.1), and Cy3 label intensities determined.
|
| Description |
This sample is of 22Rv1 transfected with siRNA of negtive control.
|
| Data processing |
The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the Agilent GeneSpring GX software package, version 12.1 .
|
| |
|
| Submission date |
Mar 14, 2020 |
| Last update date |
May 20, 2021 |
| Contact name |
Lin Gao |
| E-mail(s) |
gaolin90@aliyun.com
|
| Organization name |
shandong university
|
| Street address |
No.44, Wenhua Xi Road
|
| City |
Jinan |
| ZIP/Postal code |
250012 |
| Country |
China |
| |
|
| Platform ID |
GPL13497 |
| Series (2) |
| GSE146984 |
KIF15 confers resistance to enzalutamide in castration resistant prostate cancer [array] |
| GSE150896 |
KIF15 promotes AR and AR-V7 protein stabilization in contribution to enzalutamide resistance of prostate cancers |
|
