early passage dpscs ( p1p2 ) isolated from deciduous teeth have been obtained from dr .
songtao shi ( univ . of southern california ) and cultured in alpha - mem supplemented with 20% fetal bovine serum ( v / v ) , 2  mm l - glutamine , 100  m l - ascorbate-2-phosphate , 50  u / ml penicillin and 50  g / ml streptomycin .
exponentially growing dpscs were treated with different concentrations of ethanol diluted from absolute ethanol ( fw  =  21.7  m ) . for acute exposure
, cells were fed with media containing given concentrations of ethanol ( 0 , 1 , 5 , 10 , 20 , 50  mm ) for 24 or 48  h. total rna was isolated from dpscs treated with ethanol ( 0 , 1 , 5 , 10 , 20 , 50  mm ) for 24 or 48  h. rna was extracted using rneasy purification kit , following the manufacturer 's instruction ( qiagen , valencia , ca ) .
isolated rna was further purified by dnase treatment ( ambion / life technologies , grand island , ny ) . rna purity and concentration
were determined by nanodrop , nd-1000 spectrophotometer ( thermo scientific , indianapolis , in ) and microfluidics - based platform 2100 bioanalyzer ( agilent technologies , santa clara , ca ) .
the sensitivity of the system was measured by % p using the 3 biased affymetrix hg - u133a 2.0 arrays .
% p ranged from 41.1 to 45.1% demonstrating the ability to detect a large number of transcripts across a wide range of abundance .
all 24 arrays were assessed for recommended standard quality control metrics by affymetrix including image quality , signal distribution and pair wise scatter plots and passed .
mas5.chp files were generated for each array by mas 5.0 ( affymetrix , santa clara , ca ) and combined to a final results.mas5.txt file .
degradation plot was prepared with each curve corresponding to a single chip and visualizing the chip - averaged dependency between probe intensity and probe position ( fig . 
raw data was initially analyzed for the quality of microarray analysis by log density estimates of the data across all arrays ( fig . 
2 ) , quantile normalization and log transformation with robust multi - array average ( rma ) approach on affymetrix gene expression data using  affy  r package ( fig .  3 ) .
we removed probes with expression lower than the overall sample median ; 27,327 out of 54,676 probes were kept for further analysis ( fig .  3 ) . given that the sensitivity of array platforms is generally considered lower than deep sequencing ( with enough sequence depth ) , clearly a significant percentage of genes are either not expressed or beyond the detection limit in a typical array experiment .
filtering out this group of genes would potentially be beneficial to deg ( differentially expressed gene ) detection .
principal component analysis was performed to detect expression data separation by etoh treatment time ( fig . 
treatment time shows quite consistent grouping irrespective of doses , but doses in combination of treatment time show high degree of variations in gene expression .
we constructed linear regression models to evaluate the effect of dose and time on gene expression ( fig . 
we fit a separate model in terms of dose , time , and the dose by time interaction effect . in these models dose was treated as a continuous variable .
in addition to the linear model , we performed a regression spline analysis with moderated f - test to detect the probes differentially expressed over time with increasing dose , with the assumption that expression changes smoothly along with the increasing of the dose rather than making discrete jumps from one dose to another .  limma
q - values were generated to control the false discovery rate using  qvalue  r package ( http://www.bioconductor.org/packages/release/bioc/html/qvalue.html ) .
a set of significant probes with cut - off of p <  0.05 for interaction effects was selected from each model for further functional analysis .
early passage dpscs ( p1p2 ) isolated from deciduous teeth have been obtained from dr .
songtao shi ( univ . of southern california ) and cultured in alpha - mem supplemented with 20% fetal bovine serum ( v / v ) , 2  mm l - glutamine , 100  m l - ascorbate-2-phosphate , 50  u / ml penicillin and 50  g / ml streptomycin .
exponentially growing dpscs were treated with different concentrations of ethanol diluted from absolute ethanol ( fw  =  21.7  m ) . for acute exposure
, cells were fed with media containing given concentrations of ethanol ( 0 , 1 , 5 , 10 , 20 , 50  mm ) for 24 or 48  h.
total rna was isolated from dpscs treated with ethanol ( 0 , 1 , 5 , 10 , 20 , 50  mm ) for 24 or 48  h. rna was extracted using rneasy purification kit , following the manufacturer 's instruction ( qiagen , valencia , ca ) .
isolated rna was further purified by dnase treatment ( ambion / life technologies , grand island , ny ) . rna purity and concentration
were determined by nanodrop , nd-1000 spectrophotometer ( thermo scientific , indianapolis , in ) and microfluidics - based platform 2100 bioanalyzer ( agilent technologies , santa clara , ca ) .
the sensitivity of the system was measured by % p using the 3 biased affymetrix hg - u133a 2.0 arrays .
% p ranged from 41.1 to 45.1% demonstrating the ability to detect a large number of transcripts across a wide range of abundance .
all 24 arrays were assessed for recommended standard quality control metrics by affymetrix including image quality , signal distribution and pair wise scatter plots and passed .
mas5.chp files were generated for each array by mas 5.0 ( affymetrix , santa clara , ca ) and combined to a final results.mas5.txt file .
degradation plot was prepared with each curve corresponding to a single chip and visualizing the chip - averaged dependency between probe intensity and probe position ( fig . 
raw data was initially analyzed for the quality of microarray analysis by log density estimates of the data across all arrays ( fig . 
2 ) , quantile normalization and log transformation with robust multi - array average ( rma ) approach on affymetrix gene expression data using  affy  r package ( fig .  3 ) .
we removed probes with expression lower than the overall sample median ; 27,327 out of 54,676 probes were kept for further analysis ( fig .  3 ) . given that the sensitivity of array platforms is generally considered lower than deep sequencing ( with enough sequence depth ) , clearly a significant percentage of genes are either not expressed or beyond the detection limit in a typical array experiment .
filtering out this group of genes would potentially be beneficial to deg ( differentially expressed gene ) detection .
principal component analysis was performed to detect expression data separation by etoh treatment time ( fig . 
treatment time shows quite consistent grouping irrespective of doses , but doses in combination of treatment time show high degree of variations in gene expression .
we constructed linear regression models to evaluate the effect of dose and time on gene expression ( fig . 
we fit a separate model in terms of dose , time , and the dose by time interaction effect . in these models
in addition to the linear model , we performed a regression spline analysis with moderated f - test to detect the probes differentially expressed over time with increasing dose , with the assumption that expression changes smoothly along with the increasing of the dose rather than making discrete jumps from one dose to another .  limma
q - values were generated to control the false discovery rate using  qvalue  r package ( http://www.bioconductor.org/packages/release/bioc/html/qvalue.html ) .
a set of significant probes with cut - off of p <  0.05 for interaction effects was selected from each model for further functional analysis .
 human dental pulp stem cells ( dpscs ) isolated from adult dental pulp are multipotent mesenchymal stem cells that can be directed to differentiate into osteogenic / odontogenic cells and also trans - differentiate into neuronal cells . 
 the utility of dpsc has been explored in odontogenic differentiation for tooth regeneration . 
 alcohol abuse appears to lead to periodontal disease , tooth decay and mouth sores that are potentially precancerous . 
 persons who abuse alcohol are at high risk of having seriously deteriorated teeth , gums and compromised oral health in general . 
 it is currently unknown if alcohol exposure has any impact on adult stem cell maintenance , stem cell fate determination and plasticity , and stem cell niche environment . 
 here we provide detailed experimental methods , analysis and information associated with our data deposited into gene expression omnibus ( geo ) under gse57255 . 
 our data provide transcriptomic changes that are occurring by etoh treatment of dpscs at 24-hour and 48-hour time point . 