|
| Status |
Public on Jul 01, 2022 |
| Title |
231-NC |
| Sample type |
RNA |
| |
|
| Source name |
231-siBTF3
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: breast cancer cell line MDA-MB-231
|
| Treatment protocol |
MDA-MB-231 cells transfected with siRNA are referred as 231-NC and 231-siBTF3.
|
| Growth protocol |
Cells were maintained in L-15 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 |
cDNA samples were amplified, Cy3-labeled with Agilent Quick Amp labeling kit following manufacturer’s protocol.
|
| |
|
| Hybridization protocol |
1.5 μg of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/μg 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 centrifμgation.
|
| 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 Vcap transfected with lentivirus 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 |
Jul 27, 2020 |
| Last update date |
Jul 01, 2022 |
| Contact name |
Jing Hu |
| E-mail(s) |
[email protected]
|
| Organization name |
Shandong University
|
| Department |
Department of Pathology
|
| Street address |
Wenhua xi road
|
| City |
Jinan |
| ZIP/Postal code |
250012 |
| Country |
China |
| |
|
| Platform ID |
GPL13497 |
| Series (1) |
| GSE155168 |
Gene expression by BTF3 knocked down in MDA-MB-231 cells |
|
