|
| Status |
Public on Aug 10, 2016 |
| Title |
5991878040_I |
| Sample type |
RNA |
| |
|
| Source name |
17-rep MCF7 PLKO
|
| Organism |
Homo sapiens |
| Characteristics |
genotype/variation: PLKO
treatment: ethanol
cell line: MCF7
|
| Treatment protocol |
Cells were treated with ethanol or estradiol dissolved in ethanol.
|
| Growth protocol |
Cells were maintained in phenol red free MEM with 5% charcoal dextran treated fetal calf serum for four days and then treated with ethanol or 0.1 nM estradiol for three hours.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was prepared using RNeasy kit (Qiagen, Valencia, CA, USA) and cDNA from two μgs of RNA was synthesized using the cDNA Synthesis kit (Bio- Rad, Hercules, CA, USA). qRT-PCR was performed using SyberGreen on a TaqMan 7900HT instrument (Applied Biosystems, Carlsbad, CA, USA).
|
| Label |
biotin
|
| Label protocol |
Microarray with biological triplicates was performed using Illumina HumanHT-12 V4 expression beadchip. Standard Illumina label protocol was used.
|
| |
|
| Hybridization protocol |
Standard Illumina hybridization protocol
|
| Scan protocol |
Standard Illumina scanning protocol
|
| Description |
MCF7 PLKO
|
| Data processing |
Genes that showed statistically insignificant signals in majority of samples were removed from the microarray data, and only those probes that showed statistically significant signal in at least half of samples of at least one group were retained. The probe level data was then collapsed to gene level data by retaining only the probes, which showed a maximal coefficient of variation across all samples. The data was imported into partek genomics suite for differential expression analysis. ANOVA analysis was performed to identify genes differentially expressed between AKT1KD vs. pLKO, AKT2KD vs. pLKO, and AKT1KD vs. AKT2KD groups.
|
| |
|
| Submission date |
Aug 26, 2014 |
| Last update date |
Aug 10, 2016 |
| Contact name |
Guanglong Jiang |
| Organization name |
Indiana University School of Medicine
|
| Department |
Medical and Molecular Genetics
|
| Street address |
410 W. 10th St. Suite 5000
|
| City |
Indianapolis |
| State/province |
IN |
| ZIP/Postal code |
46202 |
| Country |
USA |
| |
|
| Platform ID |
GPL10558 |
| Series (1) |
| GSE60759 |
AKT Isoform Specificity Downstream of PIK3CA Mutation Impacts Estradiol and PI3K Inhibitor Response in Breast Cancer Cells |
|
