|
| Status |
Public on Jun 01, 2011 |
| Title |
total RNA, doxorubicin plus 17-β estradiol (physiological dose) treated, 10h, biological replicate #3 |
| Sample type |
RNA |
| |
|
| Source name |
MCF7 cells, doxorubicin plus 17-β estradiol (E2) physiological dose treated, 10 hours, total RNA, biological replicate #3
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: MCF7 cells
agent: doxorubicin plus 17-β estradiol (E2) physiological dose
time point: 10 hours
population: total RNA
biological replicate: #3
|
| Biomaterial provider |
ICLC
|
| Treatment protocol |
MCF7 cells were seeded on 10cm Petri dishes and grown in estrogen-depleted conditions, D-MEM w/o Phenol Red, 10% Dextrane-Charcoal treated serum, 2mM glutamine, 1X penicillin/streptomycin. After 24h cells were treated at the same time with doxorubicin and E2 for 10 hours at a final concentration of respectively 1.5 µM and 1 nM.
|
| Growth protocol |
MCF7 cells were cultured in Dulbecco Modified Eagle Medium (D-MEM) without Phenol Red supplemented with 10% Dextrane-Charcoal treated fetal bovine serum (FBS), 2mM glutamine, 100 units/ml penicillin, and 100 mg/ml streptomycin at 37 °C in a humidified atmosphere of 5% CO2.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the Agilent Total RNA Isolation Mini kit according to the manufacturer’s protocol. RNA was quantified using a spectrophotometer and its quality was checked by agarose gel electrophoresis as well as by Agilent 2100 Bioanalyzer platform, following the manifacturer’s guidelines for sample preparation and analysis of data (Agilent 2100 Bioanalyzer 2100 Expert User's Guide, http://www.agilent.com).
|
| Label |
Cy3-CTP
|
| Label protocol |
G4140-90040_One-Color_GE_5.7 (https://www.chem.agilent.com/Library/usermanuals/Public/G4140-90040_GeneExpression_One-Color_v6.0.pdf)
|
| |
|
| Hybridization protocol |
Hybridization, blocking and washing were performed according to Agilent protocol: “One-Color Microarray-Based Gene Expression Analysis (Quick Amp Labeling)”: (https://www.chem.agilent.com/Library/usermanuals/Public/G4140-90040_GeneExpression_One-Color_v6.0.pdf).
|
| Scan protocol |
Hybridized microarray slides were scanned with an Agilent DNA Microarray Scanner (G2505C, Agilent Technologies, Santa Clara, CA) at 5 micron resolution with the manufacturer’s software (Agilent ScanControl 8.1.3). The scanned TIFF images were analyzed numerically using the Agilent Feature Extraction Software version 10.7.7.1 according to the Agilent standard protocol GE1_107_Sep09.
|
| Description |
Total RNA sample extracted from doxorubicin plus 17-β estradiol (E2) (physiological dose) treated MCF7 cells grown in estrogen-depleted conditions.
|
| Data processing |
Agilent Feature Extraction Software version 10.7.7.1 (standard protocol GE1_107_Sep09) was used for data extraction, background correction and flagging of non-uniform features. The output of Feature Extraction was analyzed with the R software environment for statistical computing (http://www.r-project.org/) and the Bioconductor library of biostatistical packages (http://www.bioconductor.org/). Signal intensities across arrays were normalized with the quantile normalization algorithm.
|
| |
|
| Submission date |
Sep 09, 2010 |
| Last update date |
Jun 01, 2011 |
| Contact name |
Toma Tebaldi |
| E-mail(s) |
[email protected]
|
| URL |
http://portale.unitn.it/cibio/portalpage.do?channelId=-54340&channel2Id=-54565&content_OID=269530&page=/jsp/editorial/editorial.jsp&programId=269532
|
| Organization name |
Centre for Integrative Biology
|
| Lab |
Transcriptional Network Lab
|
| Street address |
via delle Regole 101
|
| City |
Mattarello - Trento |
| State/province |
Trento |
| ZIP/Postal code |
38123 |
| Country |
Italy |
| |
|
| Platform ID |
GPL6480 |
| Series (1) |
| GSE24065 |
Crossroads of the p53, ER, NFkB stress response networks |
|
