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Series GSE68918 Query DataSets for GSE68918
Status Public on May 16, 2015
Title Identification of KDM3A regulated genes in the ER positive breast cancer cell line MCF-7
Organism Homo sapiens
Experiment type Expression profiling by array
Summary Using a siRNA screen we identified the histone demethylase enzyme KDM3A as a potential positive regulator of ER signalling in breast cancer. To interrogate the full extent of KDM3A regulation on ER signalling we assessed basal and estrogen (E2)- stimulated global gene expression changes in KDM3A-depleted MCF-7 cells by microarray analysis using the Illumina Human HT12 Version 4 BeadChip array. We identified ER regulated genes affected by KDM3A knockdown and determined that KDM3A is required for ER recruitment to estrogen response elements in the promotors of ER regulated genes. We also identified that KDM3A regulates expression of a number of genes involved in proliferation and that knockdown of KDM3A inhibits ER positive breast cancer cell growth.
 
Overall design MCF-7 cells were transfected with either a non-silencing scrambled control siRNA (siSCR) or a KDM3A targeting siRNA (siKDM3A-B) using Lipfectamine RNAiMAX (Invitrogen) to a final concentration of 25 nM in steroid depleted conditions. Cells were grown for 48 hours prior to treatment with vehicle or 10 nM E2 for 4 hours before RNA extraction using TRIzol (Ambion, Life Technologies) and hybridization of triplicate samples to an Illumine HT-12 v4 BeadChip array. One sample failed due to low amounts of cRNA and was therefore not included in the analysis (siKDM3A + E2 Replicate 3). The array for replicates 1 and 2 was performed in August 2013 (Array 1) and replicate 3 in August 2014 (Array 2). When processing the data Array 2 was normalized to Array 1.
 
Contributor(s) Wade MA, Jones D, Wilson L, Stockley J, Coffey K, Robson CN, Gaughan L
Citation(s) 25488809
Submission date May 15, 2015
Last update date Aug 13, 2018
Contact name Mark A Wade
E-mail(s) mark.wade@newcastle.ac.uk
Organization name Newcastle University
Department Northern Institute for Cancer Research
Street address Paul O'Gorman Building, Framlington Place
City Newcastle Upon Tyne
State/province Tyne and Wear
ZIP/Postal code NE2 4HH
Country United Kingdom
 
Platforms (1)
GPL10558 Illumina HumanHT-12 V4.0 expression beadchip
Samples (11)
GSM1686435 siSCR - E2 Replicate 1
GSM1686436 siKDM3A-B - E2 Replicate 1
GSM1686437 siSCR + E2 Replicate 1
Relations
BioProject PRJNA284106

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE68918_RAW.tar 26.2 Mb (http)(custom) TAR
GSE68918_non_normalized.txt.gz 3.3 Mb (ftp)(http) TXT
Processed data included within Sample table
Raw data are available on Series record

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