"Sequencing reads were mapped to the E. coli genome with bowtie2"	"data_processing.1"
"Read counts per gene determined using HTseq count before normalized using DESeq2"	"data_processing.2"
"PCA analysis was performed using the top 500 genes with the most variations."	"data_processing.3"
"Supplementary_files_format_and_content: The txt file includes the gene expression profiles of all the samples. The xlsx file contains the PC1 and PC2 values of all the samples."	"data_processing.4"
"After exposed under the red light with a specific ON/OFF frequency for 10 hours, 1ml bacterial culture was sampled and the bacterial cells were collected at 4 °C. The total RNA of E. coli was extracted using RNAprep pure Cell/Bacteria Kit (TIANGEN, DP430) and preserved at -80 °C."	"extract_protocol_ch1.1"
"RNA libraries were prepared for sequencing using standard Illumina protocols"	"extract_protocol_ch1.2"
"Plasmid pLCenvZ or pLCenvZM was co-transformed with pPCB into the competent cells of E. coli JW3367 and spread on LB agar plates containing Ampicillin (50 ng/μl) and Chloramphenicol (170 ng/μl) at 37°C overnight. A single colony was diluted in 2.5ml LB medium containing Ampicillin (50 ng/μl) and Chloramphenicol (170 ng/μl) and was shaken at 250 rpm and 37°C overnight."	"growth_protocol_ch1.1"
"Escherichia coli"	"organism_ch1.1"
"BW25113"	"source_name_ch1.1"
"envz600"	"title.1"
"In the 15 ml centrifuge tube (Corning, 430791), the overnight culture was diluted to 2ml in fresh LB medium containing Ampicillin (50 ng/μl), Chloramphenicol (170 ng/μl) and IPTG (0.5mM) to reach OD600 = 0.01. The LED tube was screwed into the centrifuge tube and connected with the control box. Then the power of the control box was turned on and the LED frequency input was generated. At last, the 15 ml centrifuge tube with LED tube was put into the Thermomixer comfort (Eppendorf) and shaken at 650 rpm and 37°C for 10 hours."	"treatment_protocol_ch1.1"
"RNA-Seq"	"library_strategy.1"
"plasmid: pLCenvZ, pPCB (wild type)"	"characteristics_ch1.1"
"strain: JW3367"	"characteristics_ch1.2"
"input signal frequency: 1/600 Hz"	"characteristics_ch1.3"
"Plasmid pLCenvZ or pLCenvZM was co-transformed with pPCB into the competent cells of E. coli JW3367 and spread on LB agar plates containing Ampicillin (50 ng/μl) and Chloramphenicol (170 ng/μl) at 37°C overnight. A single colony was diluted in 2.5ml LB medium containing Ampicillin (50 ng/μl) and Chloramphenicol (170 ng/μl) and was shaken at 250 rpm and 37°C overnight."	"growth_protocol_ch1.1"
"Escherichia coli"	"organism_ch1.1"
"BW25113"	"source_name_ch1.1"
"In the 15 ml centrifuge tube (Corning, 430791), the overnight culture was diluted to 2ml in fresh LB medium containing Ampicillin (50 ng/μl), Chloramphenicol (170 ng/μl) and IPTG (0.5mM) to reach OD600 = 0.01. The LED tube was screwed into the centrifuge tube and connected with the control box. Then the power of the control box was turned on and the LED frequency input was generated. At last, the 15 ml centrifuge tube with LED tube was put into the Thermomixer comfort (Eppendorf) and shaken at 650 rpm and 37°C for 10 hours."	"treatment_protocol_ch1.1"