"genotype/variation: null polyphosphate metabolism"	"characteristics_ch1.1"
"genotype/variation: wild type (control)"	"characteristics_ch2.1"
"Microarray data analysis was performed with free software genArise, developed in the Computing Unit of Cellular Physiology Institute of UNAM (http://www.ifc.unam.mx/genarise/). GenArise carry out a number of transformations: background correction, normalization, intensity filter, replicates analysis and selecting differentially expressed genes. The goal of genArise is to identify which genes show good evidence of being differentially expressed. The software identifies differential expressed genes by calculating an intensity-dependent z-score. Using a sliding window algorithm to calculate the mean and standard deviation within a window surrounding each data point, and define a z-score where z measures the number of standard deviations a data is from the mean."	"data_processing.1"
"zi = (Ri – mean(R)) / sd(R), where zi is the z-score for each element, Ri is the log-ratio for each element, and sd(R) is the standard deviation of the log-ratio. With this criterion, the elements with a z-score > 2 standard deviations would be the significantly differentially expressed genes."	"data_processing.2"
"Briefly, total RNA were isolated from cell culture with Total RNA Extraction Kit (RBC Bioscience) according to manufacturer's specifications. DNA was degraded by DNAse (Promega)."	"extract_protocol_ch1.1"
"Briefly, total RNA were isolated from cell culture with Total RNA Extraction Kit (RBC Bioscience) according to manufacturer's specifications. DNA was degraded by DNAse (Promega)."	"extract_protocol_ch2.1"
"Escherichia coli K-12"	"organism_ch1.1"
"Escherichia coli K-12"	"organism_ch2.1"
"double mutant (PPK1 and PPX)"	"source_name_ch1.1"
"control"	"source_name_ch2.1"
"PPK1-PPX double mutant"	"title.1"
"genotype/variation: null polyphosphate metabolism"	"characteristics_ch1.1"
"genotype/variation: wild type (control)"	"characteristics_ch2.1"
"Escherichia coli K-12"	"organism_ch1.1"
"Escherichia coli K-12"	"organism_ch2.1"
"double mutant (PPK1 and PPX)"	"source_name_ch1.1"
"control"	"source_name_ch2.1"