"strain: O2"	"characteristics_ch1.1"
"condition: in vivo"	"characteristics_ch1.2"
"The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100."	"data_processing.1"
"Total RNA from both the in vitro and in vivo samples of APEC E058 was extracted with the RNAiso Plus kit (Takara, Dalian, China) and further purified with NucleoSpin RNA Clean-up (Macherey-Nagel, Germany), according to the manufacturers’ instructions."	"extract_protocol_ch1.1"
"To prepare the in vitro samples, APEC strain E058 was grown statically at 37 °C in 10 mL of LB broth until the absorbance at 600 nm (A600) reached 0.4. To prepare the in vivo samples, the bacteria was harvested from cardiac blood  in 1-day-old chickens at 5 hours post infection."	"growth_protocol_ch1.1"
"Escherichia coli APEC O2"	"organism_ch1.1"
"bacteria harvested from blood of chickens"	"source_name_ch1.1"
"E058 in vivo, biological rep3"	"title.1"
"The in vitro bacterial samples were harvested by centrifugation (5000 × g, 10 min, 4 °C) and the pellet was frozen at −70 °C until RNA extraction. The in vivo bacterial samples were harvested with two-step centrifugation. We first centrifuged the collected anticoagulated blood samples at low speed to remove the abundant red and white blood cells and collected the upper serum layer. We then used high-speed centrifugation to precipitate the bacteria from the serum."	"treatment_protocol_ch1.1"
"strain: O2"	"characteristics_ch1.1"
"condition: in vivo"	"characteristics_ch1.2"
"To prepare the in vitro samples, APEC strain E058 was grown statically at 37 °C in 10 mL of LB broth until the absorbance at 600 nm (A600) reached 0.4. To prepare the in vivo samples, the bacteria was harvested from cardiac blood  in 1-day-old chickens at 5 hours post infection."	"growth_protocol_ch1.1"
"Escherichia coli APEC O2"	"organism_ch1.1"
"bacteria harvested from blood of chickens"	"source_name_ch1.1"
"The in vitro bacterial samples were harvested by centrifugation (5000 × g, 10 min, 4 °C) and the pellet was frozen at −70 °C until RNA extraction. The in vivo bacterial samples were harvested with two-step centrifugation. We first centrifuged the collected anticoagulated blood samples at low speed to remove the abundant red and white blood cells and collected the upper serum layer. We then used high-speed centrifugation to precipitate the bacteria from the serum."	"treatment_protocol_ch1.1"