|
| Status |
Public on May 28, 2009 |
| Title |
MCF-7 cells_luciferase knockdown_E2_replicate 1 |
| Sample type |
RNA |
| |
|
| Source name |
MCF-7 cells, luciferase knockdown, E2 treatment 3 hours
|
| Organism |
Homo sapiens |
| Characteristics |
MCF-7 cells, luciferase knockdown, E2 treatment 3 hours
|
| Treatment protocol |
MCF-7 cells were cultured in estrogen-free media for 72 hours prior to hormone treatment. E2 samples were treated with 10-7M estradiol for 3 hours.
|
| Growth protocol |
MCF-7 cells were maintained in Eagle's minimum essential medium supplemented with 5% calf serum and antibiotics.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was prepared using Trizol reagent according to the manufacturer's instructions (Invitrogen) and was further purified using RNeasy columns (Qiagen)
|
| Label |
Biotin
|
| Label protocol |
Seven µg of total RNA were subjected to One-cycle Target Labeling Assay (Affymetrix) to generate biotinylated cRNA targets for hybridization to Affymetrix U133A 2.0 microarray
|
| |
|
| Hybridization protocol |
Standard hybridization to Affymetrix U133A 2.0 microarray
|
| Scan protocol |
Standard scanning protocol using GeneChip Scanner
|
| Description |
MCF-7 cells_luciferase knockdown_E2_replicate 1
|
| Data processing |
The raw data were processed by Affymetrix GCOS software to obtain detection calls and signal values, and then normalized by scaling. Signals were subsequently normalized through the following steps: common probe sets on both U133 A2.0 and U133 Plus2.0 platforms were selected; within each sample group hybridized to the same microarray platform, the signal values were log2 transformed, median centered for the array, and median centered for each gene; the data sets were further adjusted using the parametric empirical Bayes method (Combat R).
|
| |
|
| Submission date |
Nov 03, 2008 |
| Last update date |
May 28, 2009 |
| Contact name |
W. Lee Kraus |
| E-mail(s) |
lee.kraus@utsouthwestern.edu
|
| Organization name |
UT Southwestern Medical Center
|
| Street address |
5323 Harry Hines Blvd.
|
| City |
Dallas |
| State/province |
TX |
| ZIP/Postal code |
75390-8511 |
| Country |
USA |
| |
|
| Platform ID |
GPL571 |
| Series (2) |
| GSE13458 |
Expression analysis upon NMNAT1 knockdown in MCF-7 cells |
| GSE13577 |
SIRT1-Dependent Gene Regulation Through Promoter-Directed Recruitment of a Nuclear NAD+ Synthase |
|
