deposited data can be found in the gene expression omnibus ( geo ) database : http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=gse77286 a. thaliana ecotype columbia ( col-0 ) , and an arabidopsis t - dna insertion double mutant ( bzip19 bzip23 ) , were grown in a climate chamber with a long day photoperiod ( 16  h light at 22  c , 8  h dark at 20  c ) , at 120  mol photon m s , and 50% relative humidity . before germination , seeds were subjected to a 3-day stratification treatment in a cold room at 4  c , in the dark , to promote uniform germination . seeds were sown onto 0.55% ( w / v ) agar - filled microtubes , and grown in hydropony on a modified half - strength hoagland 's nutrient solution   containing 2  m znso4 ( zn  + ) . the hydroponic system consisted of 8-l - capacity containers ( 46    31    8  cm ) , with a non - translucent 3-mm - thick plastic lid containing holes for placement of agar - filled tubes . the nutrient solution was replaced once in the first week , and twice a week in weeks thereafter . the two genotypes , i.e. , wild - type ( col-0 ) and double mutant ( bzip19 bzip23 ) , were grown for three weeks with normal zinc supply ( zn  + , 2  m znso4 ) and then one week with low ( zn- , 0.05  m znso4 ) , normal ( zn  + ) or excess zinc supply ( zn  + + , 25  m znso4 ) . for each genotype and treatment ( zn  /zn  + /zn + + ) , roots or shoots of six plants ( two containers ) were pooled . plant tissue was snap frozen into liquid nitrogen and stored at   80  c . rna was extracted with the rneasy plant mini kit ( qiagen ) . for cdna synthesis , targets were prepared with the one - cycle cdna synthesis kit followed by biotin - labeling with the ivt labeling kit ( genechip one - cycle target labeling and control reagents ; affymetrix ) , and hybridized to the ath1 gene chip for 16  h , as recommended by the supplier ( gene expression analysis manual ; affymetrix ) . four and three hybridizations were performed for independent biological replicates of the root and shoot material , respectively . raw data files were processed in bioconductor / r using packages affy   and limma . background correction and quantile normalization were performed using the robust multichip average ( rma ) function . principal component analysis ( pca ) was conducted using multi experiment viewer v4.0 ( www.tm4.org/mev.html ) . a. thaliana ecotype columbia ( col-0 ) , and an arabidopsis t - dna insertion double mutant ( bzip19 bzip23 ) , were grown in a climate chamber with a long day photoperiod ( 16  h light at 22  c , 8  h dark at 20  c ) , at 120  mol photon m s , and 50% relative humidity . before germination , seeds were subjected to a 3-day stratification treatment in a cold room at 4  c , in the dark , to promote uniform germination . seeds were sown onto 0.55% ( w / v ) agar - filled microtubes , and grown in hydropony on a modified half - strength hoagland 's nutrient solution   containing 2  m znso4 ( zn  + ) . the hydroponic system consisted of 8-l - capacity containers ( 46    31    8  cm ) , with a non - translucent 3-mm - thick plastic lid containing holes for placement of agar - filled tubes . the nutrient solution was replaced once in the first week , and twice a week in weeks thereafter . the two genotypes , i.e. , wild - type ( col-0 ) and double mutant ( bzip19 bzip23 ) , were grown for three weeks with normal zinc supply ( zn  + , 2  m znso4 ) and then one week with low ( zn- , 0.05  m znso4 ) , normal ( zn  + ) or excess zinc supply ( zn  + + , 25  m znso4 ) . for each genotype and treatment ( zn  /zn  + /zn + + ) , roots or shoots of six plants ( two containers ) were pooled . plant tissue was snap frozen into liquid nitrogen and stored at   80  c . rna was extracted with the rneasy plant mini kit ( qiagen ) . for cdna synthesis , targets were prepared with the one - cycle cdna synthesis kit followed by biotin - labeling with the ivt labeling kit ( genechip one - cycle target labeling and control reagents ; affymetrix ) , and hybridized to the ath1 gene chip for 16  h , as recommended by the supplier ( gene expression analysis manual ; affymetrix ) . four and three hybridizations were performed for independent biological replicates of the root and shoot material , respectively . raw data files were processed in bioconductor / r using packages affy   and limma . background correction and quantile normalization were performed using the robust multichip average ( rma ) function . principal component analysis ( pca ) knowledge on of the molecular network modulating the response to zinc nutrition in the arabidopsis plant model system is a timely subject , and will contribute to the development of plant - based solutions addressing nutrient use efficiency and adaptation to nutrient - limited or toxic soils , , , . previously , the transcription factors bzip19 and bzip23 were identified as essential regulators of the response to micronutrient zinc deficiency in arabidopsis . here , we describe a microarray dataset that provides a comparative analysis between arabidopsis wild - type and the bzip19 bzip23 double mutant , the latter displaying a hypersensitive response to zinc deficiency . the experimental conditions include analysis of root and shoot tissues , and plant growth in varying zinc supply , i.e. , deficient , normal and excess zinc ( fig . this dataset extends significantly on the previously reported transcriptomics study , by including shoot tissue analysis and the expression profile under sufficient and excess zinc supplementation . the quality of the dataset was demonstrated by the homogenous distribution of spot intensity values across replicates and even between traits ( zn levels ) , as depicted by boxplot graphs in roots ( fig . 1b , c ) and shoots ( fig . 1d , e ) , where the effectiveness of the quantile normalization can be checked as well . subsequently , we used pca to analyze variance in the datasets for each of the 42 hybridizations , allowing us to infer on 1 ) quality of the datasets , 2 ) length of transcriptional rearrangements given the three working variables ( zinc supply , genotype , tissue type ) ( fig . 1f replicates within the 12 experimental conditions clearly clustered together across pca components 13 , demonstrating the quality of hybridization and data normalization procedures , and ensuring the biological significance of future differential expression analysis on these datasets . regarding the latter , results demonstrate that variance in component 1 clearly reflects root vs. shoot datasets ( fig . 1f ) , with at least 85% of gene expression variability being attributed to this variable ( fig . even though components 2 and 3 still demonstrate the weight of the tissue type variable on transcriptional data , they also resolve datasets across a gradient of zinc supply , indicating that this is the second most significant variable affecting transcription variance ( fig . the impact of the bzip19 bzip23 mutant genotype on transcription is therefore likely to be less extensive than remaining variables , which is foreseeable given that a reduce number of genes seems to be transcriptionally regulated by bzip19/23 . this dataset is a resource that can provide valuable information , generate extensive differential expression comparisons , or complement results of other experiments . ultimately , it can contribute to a better understanding of the regulatory network modulating the response to zinc nutrition in arabidopsis . in addition , it should provide further insight onto the particular roles that bzip19 and bzip23 transcription factors play in zinc homeostasis .