|
| Status |
Public on Aug 15, 2023 |
| Title |
MDA231_shEGR1_NT |
| Sample type |
RNA |
| |
|
| Source name |
MDA-MB-231
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: TNBC
cell line: MDA-MB-231
shRNA: shEGR1
treatment: nontreated
|
| Treatment protocol |
MDA-MB-231 cells were transfected with shCT (control) or shEGR1 and splited into two groups. Cells were then serum-starved (0.5% FBS) and treated with vehicle or 10 ng/mL TNF-a for 24 h.
|
| Growth protocol |
MDA-MB-231 cells were cultured in DMEM containing 10% FBS and 1% penicillin/streptomycin.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using NucleoZOL (Macherey-Nagel, Düren, Germany) according to the manufacturer's instructions.
|
| Label |
Cy3
|
| Label protocol |
Amplification and babeling were performed using Agilent’s Low RNA Input Linear Amplification kit PLUS.
|
| |
|
| Hybridization protocol |
Hybridization and washing steps were performed using Agilent’s Gene Expression Hybridization Kit and Agilent’s Gene Expression Wash Buffer Kit, respectively.
|
| Scan protocol |
Microarrays were scanned using Agilent’s DNA microarray scanner and Feature Extraction Software.
|
| Description |
Gene expression of nontreated MSCs
|
| Data processing |
Raw data were processed and normalized using Agilent's GeneSpring Software. First, noise data with signal intensity less than 0.01 were adjusted to 0.01. For normalization, Each probes are divided by the 50th percentile (median) value of all probes. To optain reliable genes, spots with signal intensity lower than the background or insignificant standard deviation of each pixel value were removed by applying flag values.
|
| |
|
| Submission date |
Aug 09, 2023 |
| Last update date |
Aug 15, 2023 |
| Contact name |
Soon Young Shin |
| E-mail(s) |
shinsy@konkuk.ac.kr
|
| Organization name |
Konkuk University
|
| Department |
Department of Biological Sciences
|
| Street address |
120, Neungdong-ro, Gwangjin-gu
|
| City |
Seoul |
| ZIP/Postal code |
05029 |
| Country |
South Korea |
| |
|
| Platform ID |
GPL6480 |
| Series (1) |
| GSE240489 |
Role of EGR1 in vasculogenic mimicry of MDA-MB-231 cells |
|
