|
| Status |
Public on Dec 01, 2014 |
| Title |
Control rep.1 |
| Sample type |
RNA |
| |
|
| Source name |
MCF-7 cells grown in the absence of trichodermin
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: MCF-7 human breast cancer cell line
agent: Control
|
| Treatment protocol |
MCF-7 cells grown for 8 h in without trichodermin (C, control) or presence of 10 µM trichodermin (T).
|
| Growth protocol |
MCF-7 cells were cultured in ATCC-formulated Eagle’s Mininum Essential Medium with 10% FBS. Cell cultures were maintained at 37 ºC in a humidified 5% CO2 incubator.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from MCF-7 cells grown for 8 h in the absence (C) or presence of 10 µM trichodermin (T), using the Mini RNeasy kit (Qiagen, Valencia, CA) according to the manufacturer's protocol. The quality of the RNA was assessed on the Agilent 2100 Bioanalyser (Agilent Technologies, Germany).
|
| Label |
biotin
|
| Label protocol |
cDNAs were synthesized from 1 gµ of total RNA using the ‘‘Reverse Transcription System’’ kit (Promega Biotech Iberica, Alcobendas, Spain), and used for hybridization to Human Gene 1.0 ST expression chips using the Genechip Fluidics Station 450 (Affymetrix) and according to protocols described in the Gene Expression Analysis Technical Manual (http://www.affymetrix.com).
|
| |
|
| Hybridization protocol |
Hybridization was carried out according to protocols described in the Gene Expression Analysis Technical Manual (http://www.affymetrix.com) using the Genechip Fluidics Station 450 (Affymetrix).
|
| Scan protocol |
Chips were washed, stained and scanned using the GeneChip Scanner 3000 7G (Affymetrix).
|
| Description |
1.C1_(HuGene-1_0-st-v1).chp
1.C1_(HuGene-1_0-st-v1).CEL
|
| Data processing |
Affymetrix Expression Console: Background correction, normalization, and expression analysis from the data were performed using the RMA algorithm (Irizarry et al., 2003).
The significance of the differential expression under the two conditions compared was determined by statistical analysis performed with the T-test algorithm (Baldi and Long, 2001).
Transcripts showing significantly differential expression (FC≥2) were annotated Gene Ontology (GO) terms, and analyzed using the Genespring GX program.
|
| |
|
| Submission date |
Dec 05, 2011 |
| Last update date |
Dec 01, 2014 |
| Contact name |
Enrique Monte |
| E-mail(s) |
[email protected]
|
| Phone |
34923294500 (5119)
|
| Organization name |
University of Salamanca
|
| Department |
Spanish-Portuguese Centre for Agricultural Research
|
| Lab |
2
|
| Street address |
Rio Duero
|
| City |
Salamanca |
| State/province |
Salamanca |
| ZIP/Postal code |
37185 |
| Country |
Spain |
| |
|
| Platform ID |
GPL6244 |
| Series (1) |
| GSE34165 |
Comparative study of transcriptome from human breast cancer cell lines MCF7 treated with trichodermin |
|
