wild - type and rpa12   cells were grown to stationary phase in a synthetic complete medium .
we used microarrays to study the effect of rpa12 deletion on the cellular metabolism of yeast and identified that distinct class of genes were up - regulated in rpa12   strain . yeast wild - type and deletion strains : euroscarftrizol : invitrogen , cat .
no . 10 - 296 - 028synthetic complete mediayeast nitrogenous base : difcoyeast drop - out : sigma - aldrich yeast wild - type and deletion strains : euroscarf trizol : invitrogen , cat .
no . 10 - 296 - 028 synthetic complete media yeast nitrogenous base : difco yeast drop - out : sigma - aldrich wild - type and rpa12   cells were first inoculated in yeast extract , peptone and 2% dextrose ( ypd ) medium .
stationary phase cells were subcultured in a synthetic complete ( sc ) medium containing 2% dextrose as a carbon source along with kanamycin ( 50  g / ml ) at 30  c .
after 24  h , the cells were pelleted and washed with phosphate - buffered saline to remove the remaining medium .
these samples were hybridized to the affymetrix yeast genome 2.0 array according to the manufacturer 's instructions .
all the original microarray data or raw data ( cel file ) were first normalized using the robust multiarray average ( rma ) method   that consisted of three steps : a background adjustment , quantile normalization and finally summarization .
all above procedures were done by rma algorithm in gene springgx11.5 software from agilent technologies .
the genes of low intensity information content in each data set were filtered as follows : first , the probes of intensities <  20.0 percentile in the raw data were excluded and then the probes whose intensities ' coefficient of variation ( cv ) <  50.0% at least 1 out of 4 types remained . in differential gene expression ( dge ) analyses , we identified many genes involved in cellular metabolism are differentially expressed in rpa12   strain .
normalized data were filtered for probe sets between 20 and 100 percentile . fold change ( fc ) analysis
was performed in gene spring 11.0 using the threshold fc    1.0 and fc    2.0 .
fold change    2.0 was selected because the number of gene lists were large in fc    1.0 .
wild - type and rpa12   cells were grown to stationary phase in a synthetic complete medium .
we used microarrays to study the effect of rpa12 deletion on the cellular metabolism of yeast and identified that distinct class of genes were up - regulated in rpa12   strain .
no . 10 - 296 - 028synthetic complete mediayeast nitrogenous base : difcoyeast drop - out : sigma - aldrich yeast wild - type and deletion strains : euroscarf trizol : invitrogen , cat .
no . 10 - 296 - 028 synthetic complete media yeast nitrogenous base : difco yeast drop - out : sigma - aldrich
wild - type and rpa12   cells were first inoculated in yeast extract , peptone and 2% dextrose ( ypd ) medium . stationary phase cells were subcultured in a synthetic complete ( sc ) medium containing 2% dextrose as a carbon source along with kanamycin ( 50  g / ml ) at 30  c . after 24  h , the cells were pelleted and washed with phosphate - buffered saline to remove the remaining medium .
these samples were hybridized to the affymetrix yeast genome 2.0 array according to the manufacturer 's instructions .
all the original microarray data or raw data ( cel file ) were first normalized using the robust multiarray average ( rma ) method   that consisted of three steps : a background adjustment , quantile normalization and finally summarization .
all above procedures were done by rma algorithm in gene springgx11.5 software from agilent technologies .
the genes of low intensity information content in each data set were filtered as follows : first , the probes of intensities <  20.0 percentile in the raw data were excluded and then the probes whose intensities ' coefficient of variation ( cv ) <  50.0% at least 1 out of 4 types remained . in differential gene expression ( dge ) analyses , we identified many genes involved in cellular metabolism are differentially expressed in rpa12   strain .
normalized data were filtered for probe sets between 20 and 100 percentile . fold change ( fc ) analysis
was performed in gene spring 11.0 using the threshold fc    1.0 and fc    2.0 .
fold change    2.0 was selected because the number of gene lists were large in fc    1.0 .
to identify the rpa12-regulated genes , the expression profiles of rpa12   strain with wild - type ( by4741 ) were compared . on the basis of microarray data analyses , we observed that there are significant changes in the gene expression profile in rpa12   as compared to wild - type .
the upregulation of all metabolic genes in rpa12 strain suggested that rpa12 could be a master regulator of whole cellular metabolism .
 the ribosomal rna ( rrna ) biosynthesis is the most energy consuming process in all living cells and the majority of total transcription activity is dedicated for synthesizing rrna . 
 the cells may adjust the synthesis of rrna with the availability of resources . 
 rrna is mainly synthesized by rna polymerase i that is composed of 14 subunits . 
 deletion of rpa12 , 14 , 39 and 49 are viable . 
 rpa12 is a very small protein ( 13.6  kda ) , and the amount of protein in the cells is very high ( 12,000 molecules per cell ) , but the role of this protein is unknown in other cellular metabolic processes ( kulak et al . , 2014 [ 1 ] ) . 
 rpa12 consists of two zinc - binding domains and it is required for the termination of rrna synthesis ( mullem et al . , 2002 [ 2 ] ) . 
 deletions of rpa12 in saccharomyces cerevisiae and schizosaccharomyces pombe cause a conditional growth defect ( nogi et al . , 1993 
 [ 3 ] ) . in s. pombe , c - terminal deletion behaves like wild - type ( imazawa et al . , 
 2001 [ 4 ] ) . 
 this prompted us to investigate in detail the physiological role of rpa12 in s. cerevisiae , we performed the microarray of rpa12   strain and deposited into gene expression omnibus under gse68731 . 
 the analysis of microarray data revealed that the expression of major cellular metabolism genes is high . 
 the amino acid biosynthesis , nonpolar lipid biosynthesis and glucose metabolic genes are highly expressed . 
 the analyses also revealed that the rpa12   cells have an uncontrolled synthesis of cell metabolites , so rpa12 could be a master regulator for whole cellular metabolism . 
Direct link to deposited data
Experimental design, materials and methods
Experimental design
Materials
Sample preparation
Statistical analysis of the microarray data
Results