"strain: K-12 substrain MG1655"	"characteristics_ch1.1"
"tissue: entire bacterial cell"	"characteristics_ch1.2"
"growth phase: logarithmic growth"	"characteristics_ch1.3"
"treated with: 100 µg/ml PGRP for 30min"	"characteristics_ch1.4"
"The hybridization intensity data signals were analyzed, normalized, and corrected for batch effect using Affymetrix GeneChip® Command Console® Software (AGCC v.3.0). Signal average, noise average, scaling factor, % present, and % absent were calculated for each probe, from which the signal intensity of >39 was calculated as reliable expression. Using this cutoff, 5531 probes were classified as present out of total 10208 probes on the array (full_expressed_data.txt)."	"data_processing.1"
"Signal intensities with all probes are shown in Sample data table. The 'expressed_present_probes.txt (available on Series records) contains Signal intensities with present probes.  Average signal intensities from 3 experiments were used to calculate fold increases in gene expression between treated and control groups, with signal intensity of 39 used as a minimum intensity, using the formula: average intensity in treated group/average intensity in control group (the 'Avg' columns). Transformed Ln (signal intensity) values, shown in columns 'Ln', were used for direct statistical comparisons of expression signals between treated and control groups by t-test (columns 't-test' ). The probes in the expressed_present_probes.txt are arranged in descending order from the highest to the lowest ratio of gene induction in PGRP/control (column 'Ratio' in 'expressed_present_probes.txt')."	"data_processing.2"
"RNA was obtained from each culture using Ambion RiboPureTM-bacteria RNA extraction kit according to the manufacturer’s instructions."	"extract_protocol_ch1.1"
"E. coli (OD660 nm = 0.3) was incubated with control protein or antibacterial preparations in 5 mM TRIS (pH 7.6) with 150 mM NaCl, 10 µM ZnSO4, and 2% LB, at 37oC aerobically with shaking."	"growth_protocol_ch1.1"
"Escherichia coli"	"organism_ch1.1"
"E. coli_PGRP_30 min"	"source_name_ch1.1"
"PGRP-3, biological rep3"	"title.1"
"E. coli was treated at 37C aerobically with shaking with BSA (control, 100 µg/ml), PGRP (human recombinant PGLYRP4, 100 µg/ml), or gentamicin (5 µg/ml) for 30 min, or with CCCP (carbonyl cyanide 3-chlorophenylhydrazone, 800 µM) for 15 min. Each experiment was repeated 3 times."	"treatment_protocol_ch1.1"
"strain: K-12 substrain MG1655"	"characteristics_ch1.1"
"tissue: entire bacterial cell"	"characteristics_ch1.2"
"growth phase: logarithmic growth"	"characteristics_ch1.3"
"treated with: 100 µg/ml PGRP for 30min"	"characteristics_ch1.4"
"E. coli (OD660 nm = 0.3) was incubated with control protein or antibacterial preparations in 5 mM TRIS (pH 7.6) with 150 mM NaCl, 10 µM ZnSO4, and 2% LB, at 37oC aerobically with shaking."	"growth_protocol_ch1.1"
"Escherichia coli"	"organism_ch1.1"
"E. coli_PGRP_30 min"	"source_name_ch1.1"
"E. coli was treated at 37C aerobically with shaking with BSA (control, 100 µg/ml), PGRP (human recombinant PGLYRP4, 100 µg/ml), or gentamicin (5 µg/ml) for 30 min, or with CCCP (carbonyl cyanide 3-chlorophenylhydrazone, 800 µM) for 15 min. Each experiment was repeated 3 times."	"treatment_protocol_ch1.1"