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Sample GSM754377 Query DataSets for GSM754377
Status Public on Dec 27, 2012
Title MCF7-ELF5-rep2
Sample type RNA
 
Source name MCF7, ELF5 induced
Organism Homo sapiens
Characteristics cell line: MCF7
inducible vector: doxycycline inducible pHUSH ProEx vector containing ELF5
phenotype: luminal
treatment: doxycycline
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+3_(HuGene-1_0-st-v1).CEL
RNA from MCF7 cell line, dox 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.

Data table header descriptions
ID_REF
VALUE log2-RMA signal

Data table
ID_REF VALUE
7896736 5.0275
7896738 3.1088
7896740 3.8077
7896742 6.2734
7896744 4.4922
7896746 8.2714
7896748 9.3268
7896750 4.6973
7896752 9.442
7896754 5.6633
7896756 5.5154
7896759 7.1437
7896761 7.1867
7896779 7.3744
7896798 7.3755
7896817 7.0531
7896822 8.2452
7896859 6.0024
7896861 4.3518
7896863 6.3787

Total number of rows: 28829

Table truncated, full table size 421 Kbytes.




Supplementary file Size Download File type/resource
GSM754377.CEL.gz 4.4 Mb (ftp)(http) CEL
Processed data included within Sample table

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