|
| Status |
Public on Dec 27, 2012 |
| Title |
MCF7-vehicle-rep2 |
| Sample type |
RNA |
| |
|
| Source name |
MCF7, untreated
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: MCF7
inducible vector: doxycycline inducible pHUSH ProEx vector containing ELF5
phenotype: luminal
treatment: vehicle
batch: 2
|
| Treatment protocol |
T47D and MCF7 cells were treated with doxycycline (Clontech) at 0.1 μg/ml, R5020 (Du Pont) at 10 nM or 17β-estradiol (Sigma) at 10 mM. Dox-containing medium was changed every 24 hours to ensure optimum Dox activity.
|
| Growth protocol |
Human breast carcinoma MCF7-EcoR and T47D-EcoR (Brummelkamp et al, 2002, Science 296) cell lines were grown in RPMI 1640 medium (Invitrogen) supplemented with 10 % Tet System Approved fetal bovine serum (FBS) (Clontech). Cells were infected with pHUSH-ProEX-based produced by the Platinum E cell line (Morita et al., 2000). Transient transfection with Elf5-containing plasmid constructs used FuGENE reagent (Roche) or Lipofectamine LTX (Invitrogen) according to manufacturer’s instructions. Cells were maintained in the presence of puromycin (Sigma) at a concentration of 1μg/ml for MCF7-EcoR and 2μg/ml for T47D-EcoR.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted with the RNeasy Minikit (Qiagen) and DNase-treated with the DNase kit (Qiagen) according to manufacturer’s instructions. RNA quality was assessed by RNA Nano LabChip analysis on an Agilent Bioanalyzer 2100 (Agilent Technologies).
|
| Label |
biotin
|
| Label protocol |
RNA was fragmented, biotin labeled at the Ramaciotti Centre for Gene Function Analysis at the University of New South Wales (UNSW, Sydney, NSW, Australia), following manufacturers instructions.
|
| |
|
| Hybridization protocol |
Labeled, fragmented RNA hybridized to Affymetrix Human Gene 1.0 ST Gene Arrays at the Ramaciotti Centre for Gene Function Analysis at the University of New South Wales (UNSW, Sydney, NSW, Australia), following manufacturers instructions.
|
| Scan protocol |
Arrays were scanned at the Ramaciotti Centre for Gene Function Analysis at the University of New South Wales (UNSW, Sydney, NSW, Australia), following manufacturers instructions.
|
| Description |
MK_MV-2_(HuGene-1_0-st-v1).CEL
RNA from MCF7 cell line, vehicle treated, replicate 2
|
| Data processing |
Within each batch, data was RMA normalised using NormalizeAffymetrixST (version 1) GenePattern module from the Peter Wills Bioinformatics Centre's GenePattern Server: http://pwbc.garvan.unsw.edu.au/gp. T47D and MCF7 arrays were normalised within the context of a larger set of microarrays, so if you re-normalise these data using the 8 arrays here, the value will differ slightly.
|
| |
|
| Submission date |
Jul 05, 2011 |
| Last update date |
Dec 27, 2012 |
| Contact name |
Mark Cowley |
| E-mail(s) |
m.cowley@garvan.org.au
|
| Organization name |
Garvan Institute of Medical Research
|
| Department |
Genome Informatics & Clinical Genomics
|
| Lab |
Dinger lab
|
| Street address |
384 Victoria St.
|
| City |
Darlinghurst |
| State/province |
NSW |
| ZIP/Postal code |
2010 |
| Country |
Australia |
| |
|
| Platform ID |
GPL6244 |
| Series (2) |
| GSE30405 |
The ets transcription factor ELF5 suppresses the estrogen sensitive phenotype and contributes to antiestrogen resistance in luminal breast cancer. [human] |
| GSE30407 |
The ets transcription factor ELF5 suppresses the estrogen sensitive phenotype and contributes to antiestrogen resistance in luminal breast cancer. |
|
