"strain: K12"	"characteristics_ch1.1"
"genotype: ybjN mutant"	"characteristics_ch1.2"
"growing condition: M9 minimal medium"	"characteristics_ch1.3"
"Stage: logarithm phase"	"characteristics_ch1.4"
"Microarray data normalization"	"data_processing.1"
"Microarray normalization is carried out using maanova function in R program version 2.2.1. Eight arrays in one slide were globally normalized using glowess method."	"data_processing.2"
"1. library(maanova)"	"data_processing.3"
"go to the directory:"	"data_processing.4"
"setwd(\"C:\\Documents and Settings\\Wang\\Desktop\\Erwinia in vivo\\rcsC MBMA\")"	"data_processing.5"
"2. Read data:"	"data_processing.6"
"Data = read.madata(\"NormInput.txt\", designfile=\"Designfile1.txt\", header=TRUE, spotflag=TRUE, metarow=1, metacol=2, row=3, col=4, geneID=5, pmt=6)"	"data_processing.7"
"3. Log transformation:"	"data_processing.8"
"LogData = createData(Data, n.rep=1, log.trans=TRUE)"	"data_processing.9"
"4. Normalization by Glowess method:"	"data_processing.10"
"NormalData=transform.madata(LogData, method=c(\"glowess\"))"	"data_processing.11"
"5. Save the plot files"	"data_processing.12"
"postscript(file=\"PlotRawData.ps\")"	"data_processing.13"
"riplot(LogData, onScreen=FALSE)"	"data_processing.14"
"postscript(file=\"PlotGLOWESS.ps\")"	"data_processing.15"
"riplot(NormalData, onScreen=FALSE)"	"data_processing.16"
"6. close the graph:"	"data_processing.17"
"graphics.off()"	"data_processing.18"
"norm.temp<-cbind(NormalData$metarow, NormalData$metacol,NormalData$row, NormalData$col, NormalData$geneID, NormalData$data)"	"data_processing.19"
"7. output:"	"data_processing.20"
"write.table(norm.temp, file=\"Normal_Data.csv\", sep=\",\", row.names=FALSE, col.names=TRUE, quote=FALSE)"	"data_processing.21"
""	"data_processing.22"
"Data selection"	"data_processing.23"
"Statistical comparisons were performed using multiple testing procedures to evaluate statistical significance for differentially expressed genes. A modified t-test (p-value) was computed to measure the significance associated with each differential expression value. A gene expression value was decided to be significantly different in the mutant and over-expression strains when the p-value was less than 0.05 (except otherwise mentioned) and the expression ratio was ≥ 2.0or ≤ 0.5. Gene functions were assigned using data from EcoCyc (http://ecocyc.org/)."	"data_processing.24"
"Total RNA isolation was performed using the RNeasy Protect Bacteria system from Qiagen."	"extract_protocol_ch1.1"
""	"extract_protocol_ch1.2"
"Sample collection from M9 medium"	"extract_protocol_ch1.3"
"Grow bacteria overnight in LB medium, reinoculate in M9 minimal medium at an initial OD600 of 0.005. After eight hours growth at 34°C in M9 medium, 2 mL of RNA Protect Reagent (Qiagen) was added to 1 ml bacterial cultures (at OD600 of about 0.5-0.8) to stabilize RNA. Centrifuge for 10 min at 4000 g. Decant the supernatant."	"extract_protocol_ch1.4"
""	"extract_protocol_ch1.5"
"Bacterial lysis"	"extract_protocol_ch1.6"
"Add 100 μl 1 mg/ml lysozyme buffer (TE buffer: 10 mM Tris-HCL, 1 mM EDTA pH=8.0 containing 1 mg/ml lysozyme). Vortex for 10 s and incubate at RT for at least 15 min. Add 350 μl Buffer RLT and vortex vigorously. Add 250 μl 100% ethanol, mix by pipetting."	"extract_protocol_ch1.7"
""	"extract_protocol_ch1.8"
"Column purification"	"extract_protocol_ch1.9"
"Transfer 700 μl lysate into RNeasy Mini column place in a 2 ml collection tube and centrifuge for 30 s at highest speed. Add 350 μl Buffer RW1 to the column and centrifuge for 30 s. Discard flow-through and reuse the collection tube. Add 10 μl DNase stock solution to 70 μ l RDD Buffer. Add the DNase I solution into the column and incubate at RT for 15 min. Add 350 μl Buffer RW1 to the column and wait for 5 min, centrifuge for 30 s. Discard the flow-through and collection tubes. Place the RNeasy Mini spin column in a new 2 ml collection tube. Add 500 μl Buffer RPE to the column. Centrifuge for 30 s. Place the column in a new 1.5 ml tube, and centrifuge for 1 min to eliminate any residue ethanol. Place the column in a new collection tube. Add 50 μl RNase free water, centrifuge for 1 min. Store RNA samples at -20°C."	"extract_protocol_ch1.10"
"Escherichia coli"	"organism_ch1.1"
"E. coli K12 ybjN mutant cells, M9, 8 h"	"source_name_ch1.1"
"E. coli K12_ybjN_MUTANT_M9_rep1"	"title.1"
"strain: K12"	"characteristics_ch1.1"
"genotype: ybjN mutant"	"characteristics_ch1.2"
"growing condition: M9 minimal medium"	"characteristics_ch1.3"
"Stage: logarithm phase"	"characteristics_ch1.4"
"Escherichia coli"	"organism_ch1.1"
"E. coli K12 ybjN mutant cells, M9, 8 h"	"source_name_ch1.1"