cd1 female mice ( 3035  g bw ) were purchased from harlan ( italy ) and kept under standard laboratory conditions ( 22    0.5  c , 5060% relative humidity , 12  h dark  light alternation with 1214 air changes / h ) with water and food ( 4rf25 glp  top certificate  diet purchased from mucedola , milan ,
after 1  week of acclimatization , females were bred with cd sires of proven fertility .
a sperm - positive vaginal plug served to define the gestational day ( gd ) 0 .
pregnant mice were treated daily p.o . by gavage with 0 ( vehicle only  =  olive oil ; sigma - aldrich , milan , italy ) , 0.5 or 50  mg / kg bw pro die of bpa ( cas
80 - 05 - 7 , purity   99% , sigma - aldrich ) , named bpa05 and bpa50 respectively , dissolved in olive oil , from gd1 to gd11 , a period covering implantation through early placentation phase .
on gd 12 the dams were sacrificed by asphyxiation with co2 , followed by cervical dislocation .
four placentae per litter / group were flash frozen in liquid nitrogen then stored at    80  c .
placenta samples were homogenized and total rna was extracted by using the rnaeasy mini kit ( qiagen ) , containing -mercaptoethanol diluted 1:100 .
rna quantity was assessed with nanodrop ( nanodrop , wilmington , de , usa ) , purity was assessed by uv absorbance ratio measurement at 260  nm and 280  nm whereas integrity was evaluated by 1% agarose gel electrophoresis .
cdna and crna synthesis , amplification and labeling were performed using the quick amp labeling kit , two colors ( agilent , santa clara , ca , usa ) with spike - in internal controls ( agilent ) following manufacturer 's protocol . labeled samples and controls were co - hybridized following a dye swap experimental protocol ( control and treatment samples alternatively labeled with cy5 and cy3 ) on agilent 4    44k whole mouse genome microarray g4122f at 65  c for 17  h , with a 10  rpm rotation in an agilent hybridization oven .
after washing with gene expression wash buffers ( agilent ) , slides were scanned by the agilent g2505b microarray scanner system , extracting data through the agilent feature extraction 9.5 software .
normalization and differential expression analysis were performed using the r bioconductor package limma 
 , , .
1a ) and background subtracted , then a global loess was performed to normalize each array .
a quantile between - array normalization was performed to obtain the same distribution of probe signal intensities across arrays ( fig . 
arrays quality was also evaluated   and obtained array weights were applied to the statistical model , a simple linear model fit and moderated t - statistic , thus obtaining two lists of significant differentially expressed genes in the bpa - treated placentas at the two doses in comparison to controls .
a total of 1220 genes were found differently expressed with a p - value  <  0.01 ; in particular 582 were modulated by bpa05 and 701 by bpa50 ; only 77 genes were shared by the two groups ( fig .  2 ) .
hierarchical clustering with euclidean distance and average linkage was performed to discriminate between the two gene expression profiles .
functional analysis of enriched go terms and kegg pathways was performed to determine the biological significance of the differentially expressed genes .
transcription factor binding analysis was performed using five different tools to minimize false positives to identify potential gene expression regulators .
real - time pcr was performed on critical differentially expressed genes to validate microarray data .
cd1 female mice ( 3035  g bw ) were purchased from harlan ( italy ) and kept under standard laboratory conditions ( 22    0.5  c , 5060% relative humidity , 12  h dark  light alternation with 1214 air changes / h ) with water and food ( 4rf25 glp  top certificate  diet purchased from mucedola , milan ,
after 1  week of acclimatization , females were bred with cd sires of proven fertility .
a sperm - positive vaginal plug served to define the gestational day ( gd ) 0 .
pregnant mice were treated daily p.o . by gavage with 0 ( vehicle only  =  olive oil ; sigma - aldrich , milan , italy ) , 0.5 or 50  mg / kg bw pro die of bpa ( cas
80 - 05 - 7 , purity   99% , sigma - aldrich ) , named bpa05 and bpa50 respectively , dissolved in olive oil , from gd1 to gd11 , a period covering implantation through early placentation phase .
on gd 12 the dams were sacrificed by asphyxiation with co2 , followed by cervical dislocation .
four placentae per litter / group were flash frozen in liquid nitrogen then stored at    80  c .
placenta samples were homogenized and total rna was extracted by using the rnaeasy mini kit ( qiagen ) , containing -mercaptoethanol diluted 1:100 .
rna quantity was assessed with nanodrop ( nanodrop , wilmington , de , usa ) , purity was assessed by uv absorbance ratio measurement at 260  nm and 280  nm whereas integrity was evaluated by 1% agarose gel electrophoresis .
cdna and crna synthesis , amplification and labeling were performed using the quick amp labeling kit , two colors ( agilent , santa clara , ca , usa ) with spike - in internal controls ( agilent ) following manufacturer 's protocol . labeled samples and controls were co - hybridized following a dye swap experimental protocol ( control and treatment samples alternatively labeled with cy5 and cy3 ) on agilent 4    44k whole mouse genome microarray g4122f at 65  c for 17  h , with a 10  rpm rotation in an agilent hybridization oven . after washing with gene expression wash buffers ( agilent ) ,
slides were scanned by the agilent g2505b microarray scanner system , extracting data through the agilent feature extraction 9.5 software .
normalization and differential expression analysis were performed using the r bioconductor package limma 
 , , .
1a ) and background subtracted , then a global loess was performed to normalize each array .
a quantile between - array normalization was performed to obtain the same distribution of probe signal intensities across arrays ( fig . 
arrays quality was also evaluated   and obtained array weights were applied to the statistical model , a simple linear model fit and moderated t - statistic , thus obtaining two lists of significant differentially expressed genes in the bpa - treated placentas at the two doses in comparison to controls .
a total of 1220 genes were found differently expressed with a p - value  <  0.01 ; in particular 582 were modulated by bpa05 and 701 by bpa50 ; only 77 genes were shared by the two groups ( fig .  2 ) .
hierarchical clustering with euclidean distance and average linkage was performed to discriminate between the two gene expression profiles .
functional analysis of enriched go terms and kegg pathways was performed to determine the biological significance of the differentially expressed genes .
transcription factor binding analysis was performed using five different tools to minimize false positives to identify potential gene expression regulators .
real - time pcr was performed on critical differentially expressed genes to validate microarray data .
we describe here a data set relative to gene expression profiles of mice placenta samples upon exposure to two different doses of bpa , namely 0.5 or 50  mg / kg bw day , during early gestation ( gd1gd11 ) .
the two doses altered two quite distinct patterns of genes which were associated with different effects on placental morphology and development , as supported by histological , histomorphometrical and immunohistochemical analyses as reported in detail in .
 bisphenol a ( bpa ) , a widespread endocrine disrupter mainly used in food contact plastics , may induce adverse effects especially on susceptible lifestages , first of all pregnancy . the present study considered placental development as a potential target of bpa and investigated potential differences in the modes of action of two doses of bpa by a toxicogenomic approach . 
 pregnant cd-1 mice were administered with vehicle , 0.5 ( bpa05 ) or 50  mg / kg ( bpa50 ) body weight ( bw)/die of bpa , from gestational day ( gd ) 1 to gd11 . at gd12 dams were sacrificed and transcriptomic analysis was performed on placenta samples . 
 histological , histomorphometrical and immunohistochemical analyses were also performed to phenotypically anchor transcriptional changes associated with bpa exposure . the interpretation and description of the overall data 
 are included in a manuscript under revision [ 1 ] . here 
 we describe the experimental design and the analysis performed on the gene expression data which are publicly available through the gene expression omnibus ( geo ) database with accession number gse63852 . 