Abstract
Dental pulp tissue can be damaged by a range of irritants, however, if the irritation is removed and/or the tooth is adequately restored, pulp regeneration is possible (Mjör and Tronstad, 1974 [1]). At present, dental restorative materials limit healing by impairing mineralization and repair processes and as a result new biologically-based materials are being developed (Ferracane et al., 2010 [2]). Previous studies have highlighted the benefit of epigenetic modification by histone deacetylase inhibitor (HDACi) application to dental pulp cells (DPCs), which induces changes to chromatin architecture, promoting gene expression and cellular-reparative events (Duncan et al., 2013 [3]; Paino et al., 2014 [4]). In this study a genome-wide transcription profiling in epigenetically-modified mineralizing primary DPC cultures was performed, at relatively early and late time-points, to identify differentially regulated transcripts that may provide novel therapeutic targets for use in restorative dentistry. Here we provide detailed methods and analysis on these microarray data which has been deposited in Gene Expression Omnibus (GEO): GSE67175.
Highlights
Dental pulp tissue can be damaged by a range of irritants, if the irritation is removed and/or the tooth is adequately restored, pulp regeneration is possible (Mjör and Tronstad, 1974 [1])
Previous studies have highlighted the benefit of epigenetic modification by histone deacetylase inhibitor (HDACi) application to dental pulp cells (DPCs), which induces changes to chromatin architecture, promoting gene expression and cellular-reparative events (Duncan et al, 2013 [3]; Paino et al, 2014 [4])
The DPCs were seeded in supplemented α-MEM for 3 days, and either cultured for 24 h in supplemented mineralizing medium containing 1 μM suberoylanilide hydroxamic acid (SAHA) prior to harvest (24 h samples) or incubated with an HDACi-free mineralizing medium for a further 13 days (14 day samples)
Summary
The DPCs were seeded in supplemented α-MEM for 3 days (experimental day 0), and either cultured for 24 h in supplemented mineralizing medium containing 1 μM SAHA prior to harvest (24 h samples) or incubated with an HDACi-free mineralizing medium for a further 13 days (14 day samples). The cRNA was purified using the RNeasy mini kit (Qiagen) and Cy3, Cy5 concentration, RNA absorbance 260/ 280 nm and cRNA concentrations determined spectrophotometrically (Nanodrop 2000, Wilmington, DE, USA). This enabled specific activity and target yields to be calculated prior to microarray experimentation
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