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| 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
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| 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.
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| 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.
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| 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
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| Organization name |
Newcastle University
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| Department |
Northern Institute for Cancer Research
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| Street address |
Paul O'Gorman Building, Framlington Place
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| City |
Newcastle Upon Tyne |
| State/province |
Tyne and Wear |
| ZIP/Postal code |
NE2 4HH |
| Country |
United Kingdom |
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| Platforms (1) |
| GPL10558 |
Illumina HumanHT-12 V4.0 expression beadchip |
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| Samples (11)
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| Relations |
| BioProject |
PRJNA284106 |
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