|
| Status |
Public on Dec 15, 2016 |
| Title |
MCF-7_control rep.2 |
| Sample type |
RNA |
| |
|
| Source name |
MCF-7 cells non treated control
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: MCF-7
cell type: breast cancer
gender: female
|
| Treatment protocol |
No special treatments before harvesting were carried out.
|
| Growth protocol |
Cells were maintained in Dulbecco’s Modified Eagle’s Medium (DMEM) supplemented with 10% fetal calf serum, 2% glutamine, 1% penicillin and 1% streptomycin stock solutions. Cells were incubated at 37°C/ 95% air/ 5% CO2 and the media was changed every two days.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were washed 3 times using PBS and total RNA was collected from adherent tissue culture cells using Trizol (Invitrogen) according to the manufacturer’s instructions. RNA was quantified (A260) using a Nanodrop-1000 spectrophotometer (Nanodrop Technologies).
|
| Label |
biotin
|
| Label protocol |
Complimentary RNA (cRNA) was produced according to Affymetrix geneChip® 3' IVT Express kit Technical Manual (http://media.affymetrix.com/support/downloads/manuals/3_ivt_express_kit_manual.pdf)
|
| |
|
| Hybridization protocol |
Following fragmentation, 5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip® PrimeView™ Human . GeneChips were washed and stained in the Affymetrix Fluidics Station 400. Hybridization reactions to Affymetrix Maize GeneChip expression arrays were done using the services of Expression Analysis Inc. (http://www.expressionanalysis.com/).
|
| Scan protocol |
Scanning of the Affymetrix GeneChip® PrimeView™ Human expression arrays were done using the services of Expression Analysis Inc. (http://www.expressionanalysis.com/).
|
| Description |
Gene expression data from MCF_7 breast cancer cells (24 day incubation)
|
| Data processing |
Data extraction was also performed by Expression Analysis Inc. Expression values were calculated using the Affymetrix GeneChip Operating System (GCOS) and were based on the difference of the PM (Perfect Match) signal and MM (Mismatch) signal at each of the probe pairs. The fluorescent signal values from each array were normalized to achieve similar overall intensity between arrays. The fluorescent signal values of any hybridization reaction were then multiplied by a scaling factor to make their (trimmed) mean intensity equal to 500. The scaling factor is unique to each hybridization reaction and is in general below 10
|
| |
|
| Submission date |
Dec 01, 2015 |
| Last update date |
Dec 15, 2016 |
| Contact name |
Mariya Khodakovskaya |
| E-mail(s) |
m_khod@yahoo.com
|
| Organization name |
University of Arkansas at Little Rock
|
| Department |
Biology
|
| Street address |
2801 S. University Avenue
|
| City |
Little Rock |
| State/province |
AR |
| ZIP/Postal code |
72204 |
| Country |
USA |
| |
|
| Platform ID |
GPL15207 |
| Series (1) |
| GSE75570 |
Expression data from MCF-7 breast cancer cells treated with CNTs, ginsenosides (Rb1 and Rg1) and conjugates (Rb-CNTs and Rg-CNTs) |
|
