title	geo_accession	status	submission_date	last_update_date	type	channel_count	source_name_ch1	organism_ch1	characteristics_ch1	characteristics_ch1.1	characteristics_ch1.2	characteristics_ch1.3	growth_protocol_ch1	molecule_ch1	extract_protocol_ch1	label_ch1	label_protocol_ch1	taxid_ch1	hyb_protocol	scan_protocol	description	description.1	data_processing	platform_id	contact_name	contact_email	contact_institute	contact_address	contact_city	contact_state	contact_zip/postal_code	contact_country	supplementary_file	data_row_count	culture type:ch1	genotype/variation:ch1	treatment duration:ch1	treatment:ch1
Pseudomonas syringae pv. tomato DC3000 Wild type Dark Rep1	GSM2715489	Public on Oct 01 2018	Jul 23 2017	Oct 01 2018	RNA	1	Wild type 10 min Dark	Pseudomonas syringae pv. tomato str. DC3000	genotype/variation: Wild type	culture type: Liquid	treatment: Darkness	treatment duration: 10 min	Transcriptomic analyses were done with cultures grown in liquid KB medium. Total RNA was extracted from cell cultures collected at O.D.=0.5 after a 10 min treatment with either white, blue or red light. Cultures maintained in the darkness were used as controls.	total RNA	Total RNA from four biological replicates from each treatment was extracted with TRI Reagent (Ambion) as recommended by the manufacturer. RNA was pre-treated with RNase-free DNase I (Roche) plus RNaseOUT (Invitrogen), followed by purification with RNeasy columns (Qiagen).	Cy3	cDNA was labeled with Cy3 by using the SuperScript III indirect cDNA labeling system (Invitrogen) as described in the instruction manual (One-Color Microarray Based Gene Expression Analysis Manual).	223283	600 ng of Cy3 probes were mixed and added to 5 μl of 10x Blocking Agent and Nuclease-free water in a 25 μl reaction. Then, we added 25 μl from 2x GExHybridization buffer and mixed carefully. The samples were placed on ice and quickly loaded onto arrays, hybridized at 65 ºC for 17 h and then washed once in GE wash buffer 1 at room temperature (1 min) and once in GE Wash Buffer 2 at 37 ºC (1 min).	Images from Cy3 channel were equilibrated and captured with a High resolution Scanner (Agilent) and spots quantified using Feature Extraction software (Agilent).	G0	Gene expression after 10 min darkness treatment.	For local background correction and normalization, the methods normexp and loess in LIMMA were used, respectively. Log-ratio values were scaled using as scale estimator the median-absolute-value. Linear model methods were used for determining differentially expressed genes. Each probe was tested for changes in expression over replicates by using an empirical Bayes moderated t-statistic. To control the false discovery rate, p-values were corrected by using the method of Benjamani and Hochberg, 1995. The expected false discovery rate (FDR) was controlled to be less than 1%.	GPL23823	Emilia,,López Solanilla	emilia.lopez@upm.es	CBGP-Universidad Politécnica de Madrid (UPM)	Parque Científico y Tecnológico UPM, Campus de Montegancedo, Ctra. M-40, km 38	Pozuelo de Alarcon	Madrid	28223	Spain	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM2715nnn/GSM2715489/suppl/GSM2715489_Dark_Rep_1_Raw.txt.gz	15744	Liquid	Wild type	10 min	Darkness
Pseudomonas syringae pv. tomato DC3000 Wild type Dark Rep2	GSM2715490	Public on Oct 01 2018	Jul 23 2017	Oct 01 2018	RNA	1	Wild type 10 min Dark	Pseudomonas syringae pv. tomato str. DC3000	genotype/variation: Wild type	culture type: Liquid	treatment: Darkness	treatment duration: 10 min	Transcriptomic analyses were done with cultures grown in liquid KB medium. Total RNA was extracted from cell cultures collected at O.D.=0.5 after a 10 min treatment with either white, blue or red light. Cultures maintained in the darkness were used as controls.	total RNA	Total RNA from four biological replicates from each treatment was extracted with TRI Reagent (Ambion) as recommended by the manufacturer. RNA was pre-treated with RNase-free DNase I (Roche) plus RNaseOUT (Invitrogen), followed by purification with RNeasy columns (Qiagen).	Cy3	cDNA was labeled with Cy3 by using the SuperScript III indirect cDNA labeling system (Invitrogen) as described in the instruction manual (One-Color Microarray Based Gene Expression Analysis Manual).	223283	600 ng of Cy3 probes were mixed and added to 5 μl of 10x Blocking Agent and Nuclease-free water in a 25 μl reaction. Then, we added 25 μl from 2x GExHybridization buffer and mixed carefully. The samples were placed on ice and quickly loaded onto arrays, hybridized at 65 ºC for 17 h and then washed once in GE wash buffer 1 at room temperature (1 min) and once in GE Wash Buffer 2 at 37 ºC (1 min).	Images from Cy3 channel were equilibrated and captured with a High resolution Scanner (Agilent) and spots quantified using Feature Extraction software (Agilent).	G0	Gene expression after 10 min darkness treatment.	For local background correction and normalization, the methods normexp and loess in LIMMA were used, respectively. Log-ratio values were scaled using as scale estimator the median-absolute-value. Linear model methods were used for determining differentially expressed genes. Each probe was tested for changes in expression over replicates by using an empirical Bayes moderated t-statistic. To control the false discovery rate, p-values were corrected by using the method of Benjamani and Hochberg, 1995. The expected false discovery rate (FDR) was controlled to be less than 1%.	GPL23823	Emilia,,López Solanilla	emilia.lopez@upm.es	CBGP-Universidad Politécnica de Madrid (UPM)	Parque Científico y Tecnológico UPM, Campus de Montegancedo, Ctra. M-40, km 38	Pozuelo de Alarcon	Madrid	28223	Spain	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM2715nnn/GSM2715490/suppl/GSM2715490_Dark_Rep_2_Raw.txt.gz	15744	Liquid	Wild type	10 min	Darkness
Pseudomonas syringae pv. tomato DC3000 Wild type Dark Rep3	GSM2715491	Public on Oct 01 2018	Jul 23 2017	Oct 01 2018	RNA	1	Wild type 10 min Dark	Pseudomonas syringae pv. tomato str. DC3000	genotype/variation: Wild type	culture type: Liquid	treatment: Darkness	treatment duration: 10 min	Transcriptomic analyses were done with cultures grown in liquid KB medium. Total RNA was extracted from cell cultures collected at O.D.=0.5 after a 10 min treatment with either white, blue or red light. Cultures maintained in the darkness were used as controls.	total RNA	Total RNA from four biological replicates from each treatment was extracted with TRI Reagent (Ambion) as recommended by the manufacturer. RNA was pre-treated with RNase-free DNase I (Roche) plus RNaseOUT (Invitrogen), followed by purification with RNeasy columns (Qiagen).	Cy3	cDNA was labeled with Cy3 by using the SuperScript III indirect cDNA labeling system (Invitrogen) as described in the instruction manual (One-Color Microarray Based Gene Expression Analysis Manual).	223283	600 ng of Cy3 probes were mixed and added to 5 μl of 10x Blocking Agent and Nuclease-free water in a 25 μl reaction. Then, we added 25 μl from 2x GExHybridization buffer and mixed carefully. The samples were placed on ice and quickly loaded onto arrays, hybridized at 65 ºC for 17 h and then washed once in GE wash buffer 1 at room temperature (1 min) and once in GE Wash Buffer 2 at 37 ºC (1 min).	Images from Cy3 channel were equilibrated and captured with a High resolution Scanner (Agilent) and spots quantified using Feature Extraction software (Agilent).	G0	Gene expression after 10 min darkness treatment.	For local background correction and normalization, the methods normexp and loess in LIMMA were used, respectively. Log-ratio values were scaled using as scale estimator the median-absolute-value. Linear model methods were used for determining differentially expressed genes. Each probe was tested for changes in expression over replicates by using an empirical Bayes moderated t-statistic. To control the false discovery rate, p-values were corrected by using the method of Benjamani and Hochberg, 1995. The expected false discovery rate (FDR) was controlled to be less than 1%.	GPL23823	Emilia,,López Solanilla	emilia.lopez@upm.es	CBGP-Universidad Politécnica de Madrid (UPM)	Parque Científico y Tecnológico UPM, Campus de Montegancedo, Ctra. M-40, km 38	Pozuelo de Alarcon	Madrid	28223	Spain	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM2715nnn/GSM2715491/suppl/GSM2715491_Dark_Rep_3_Raw.txt.gz	15744	Liquid	Wild type	10 min	Darkness
Pseudomonas syringae pv. tomato DC3000 Wild type Dark Rep4	GSM2715492	Public on Oct 01 2018	Jul 23 2017	Oct 01 2018	RNA	1	Wild type 10 min Dark	Pseudomonas syringae pv. tomato str. DC3000	genotype/variation: Wild type	culture type: Liquid	treatment: Darkness	treatment duration: 10 min	Transcriptomic analyses were done with cultures grown in liquid KB medium. Total RNA was extracted from cell cultures collected at O.D.=0.5 after a 10 min treatment with either white, blue or red light. Cultures maintained in the darkness were used as controls.	total RNA	Total RNA from four biological replicates from each treatment was extracted with TRI Reagent (Ambion) as recommended by the manufacturer. RNA was pre-treated with RNase-free DNase I (Roche) plus RNaseOUT (Invitrogen), followed by purification with RNeasy columns (Qiagen).	Cy3	cDNA was labeled with Cy3 by using the SuperScript III indirect cDNA labeling system (Invitrogen) as described in the instruction manual (One-Color Microarray Based Gene Expression Analysis Manual).	223283	600 ng of Cy3 probes were mixed and added to 5 μl of 10x Blocking Agent and Nuclease-free water in a 25 μl reaction. Then, we added 25 μl from 2x GExHybridization buffer and mixed carefully. The samples were placed on ice and quickly loaded onto arrays, hybridized at 65 ºC for 17 h and then washed once in GE wash buffer 1 at room temperature (1 min) and once in GE Wash Buffer 2 at 37 ºC (1 min).	Images from Cy3 channel were equilibrated and captured with a High resolution Scanner (Agilent) and spots quantified using Feature Extraction software (Agilent).	G0	Gene expression after 10 min darkness treatment.	For local background correction and normalization, the methods normexp and loess in LIMMA were used, respectively. Log-ratio values were scaled using as scale estimator the median-absolute-value. Linear model methods were used for determining differentially expressed genes. Each probe was tested for changes in expression over replicates by using an empirical Bayes moderated t-statistic. To control the false discovery rate, p-values were corrected by using the method of Benjamani and Hochberg, 1995. The expected false discovery rate (FDR) was controlled to be less than 1%.	GPL23823	Emilia,,López Solanilla	emilia.lopez@upm.es	CBGP-Universidad Politécnica de Madrid (UPM)	Parque Científico y Tecnológico UPM, Campus de Montegancedo, Ctra. M-40, km 38	Pozuelo de Alarcon	Madrid	28223	Spain	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM2715nnn/GSM2715492/suppl/GSM2715492_Dark_Rep_4_Raw.txt.gz	15744	Liquid	Wild type	10 min	Darkness
Pseudomonas syringae pv. tomato DC3000 Wild type Blue Rep 1	GSM2715493	Public on Oct 01 2018	Jul 23 2017	Oct 01 2018	RNA	1	Wild type 10 min under Blue light	Pseudomonas syringae pv. tomato str. DC3000	genotype/variation: Wild type	culture type: Liquid	treatment: Blue light	treatment duration: 10 min	Transcriptomic analyses were done with cultures grown in liquid KB medium. Total RNA was extracted from cell cultures collected at O.D.=0.5 after a 10 min treatment with either white, blue or red light. Cultures maintained in the darkness were used as controls.	total RNA	Total RNA from four biological replicates from each treatment was extracted with TRI Reagent (Ambion) as recommended by the manufacturer. RNA was pre-treated with RNase-free DNase I (Roche) plus RNaseOUT (Invitrogen), followed by purification with RNeasy columns (Qiagen).	Cy3	cDNA was labeled with Cy3 by using the SuperScript III indirect cDNA labeling system (Invitrogen) as described in the instruction manual (One-Color Microarray Based Gene Expression Analysis Manual).	223283	600 ng of Cy3 probes were mixed and added to 5 μl of 10x Blocking Agent and Nuclease-free water in a 25 μl reaction. Then, we added 25 μl from 2x GExHybridization buffer and mixed carefully. The samples were placed on ice and quickly loaded onto arrays, hybridized at 65 ºC for 17 h and then washed once in GE wash buffer 1 at room temperature (1 min) and once in GE Wash Buffer 2 at 37 ºC (1 min).	Images from Cy3 channel were equilibrated and captured with a High resolution Scanner (Agilent) and spots quantified using Feature Extraction software (Agilent).	G1	Gene expression after 10 min blue light treatment.	For local background correction and normalization, the methods normexp and loess in LIMMA were used, respectively. Log-ratio values were scaled using as scale estimator the median-absolute-value. Linear model methods were used for determining differentially expressed genes. Each probe was tested for changes in expression over replicates by using an empirical Bayes moderated t-statistic. To control the false discovery rate, p-values were corrected by using the method of Benjamani and Hochberg, 1995. The expected false discovery rate (FDR) was controlled to be less than 1%.	GPL23823	Emilia,,López Solanilla	emilia.lopez@upm.es	CBGP-Universidad Politécnica de Madrid (UPM)	Parque Científico y Tecnológico UPM, Campus de Montegancedo, Ctra. M-40, km 38	Pozuelo de Alarcon	Madrid	28223	Spain	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM2715nnn/GSM2715493/suppl/GSM2715493_Blue_Rep_1_Raw.txt.gz	15744	Liquid	Wild type	10 min	Blue light
Pseudomonas syringae pv. tomato DC3000 Wild type Blue Rep 2	GSM2715494	Public on Oct 01 2018	Jul 23 2017	Oct 01 2018	RNA	1	Wild type 10 min under Blue light	Pseudomonas syringae pv. tomato str. DC3000	genotype/variation: Wild type	culture type: Liquid	treatment: Blue light	treatment duration: 10 min	Transcriptomic analyses were done with cultures grown in liquid KB medium. Total RNA was extracted from cell cultures collected at O.D.=0.5 after a 10 min treatment with either white, blue or red light. Cultures maintained in the darkness were used as controls.	total RNA	Total RNA from four biological replicates from each treatment was extracted with TRI Reagent (Ambion) as recommended by the manufacturer. RNA was pre-treated with RNase-free DNase I (Roche) plus RNaseOUT (Invitrogen), followed by purification with RNeasy columns (Qiagen).	Cy3	cDNA was labeled with Cy3 by using the SuperScript III indirect cDNA labeling system (Invitrogen) as described in the instruction manual (One-Color Microarray Based Gene Expression Analysis Manual).	223283	600 ng of Cy3 probes were mixed and added to 5 μl of 10x Blocking Agent and Nuclease-free water in a 25 μl reaction. Then, we added 25 μl from 2x GExHybridization buffer and mixed carefully. The samples were placed on ice and quickly loaded onto arrays, hybridized at 65 ºC for 17 h and then washed once in GE wash buffer 1 at room temperature (1 min) and once in GE Wash Buffer 2 at 37 ºC (1 min).	Images from Cy3 channel were equilibrated and captured with a High resolution Scanner (Agilent) and spots quantified using Feature Extraction software (Agilent).	G1	Gene expression after 10 min blue light treatment.	For local background correction and normalization, the methods normexp and loess in LIMMA were used, respectively. Log-ratio values were scaled using as scale estimator the median-absolute-value. Linear model methods were used for determining differentially expressed genes. Each probe was tested for changes in expression over replicates by using an empirical Bayes moderated t-statistic. To control the false discovery rate, p-values were corrected by using the method of Benjamani and Hochberg, 1995. The expected false discovery rate (FDR) was controlled to be less than 1%.	GPL23823	Emilia,,López Solanilla	emilia.lopez@upm.es	CBGP-Universidad Politécnica de Madrid (UPM)	Parque Científico y Tecnológico UPM, Campus de Montegancedo, Ctra. M-40, km 38	Pozuelo de Alarcon	Madrid	28223	Spain	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM2715nnn/GSM2715494/suppl/GSM2715494_Blue_Rep_2_Raw.txt.gz	15744	Liquid	Wild type	10 min	Blue light
Pseudomonas syringae pv. tomato DC3000 Wild type Blue Rep 3	GSM2715495	Public on Oct 01 2018	Jul 23 2017	Oct 01 2018	RNA	1	Wild type 10 min under Blue light	Pseudomonas syringae pv. tomato str. DC3000	genotype/variation: Wild type	culture type: Liquid	treatment: Blue light	treatment duration: 10 min	Transcriptomic analyses were done with cultures grown in liquid KB medium. Total RNA was extracted from cell cultures collected at O.D.=0.5 after a 10 min treatment with either white, blue or red light. Cultures maintained in the darkness were used as controls.	total RNA	Total RNA from four biological replicates from each treatment was extracted with TRI Reagent (Ambion) as recommended by the manufacturer. RNA was pre-treated with RNase-free DNase I (Roche) plus RNaseOUT (Invitrogen), followed by purification with RNeasy columns (Qiagen).	Cy3	cDNA was labeled with Cy3 by using the SuperScript III indirect cDNA labeling system (Invitrogen) as described in the instruction manual (One-Color Microarray Based Gene Expression Analysis Manual).	223283	600 ng of Cy3 probes were mixed and added to 5 μl of 10x Blocking Agent and Nuclease-free water in a 25 μl reaction. Then, we added 25 μl from 2x GExHybridization buffer and mixed carefully. The samples were placed on ice and quickly loaded onto arrays, hybridized at 65 ºC for 17 h and then washed once in GE wash buffer 1 at room temperature (1 min) and once in GE Wash Buffer 2 at 37 ºC (1 min).	Images from Cy3 channel were equilibrated and captured with a High resolution Scanner (Agilent) and spots quantified using Feature Extraction software (Agilent).	G1	Gene expression after 10 min blue light treatment.	For local background correction and normalization, the methods normexp and loess in LIMMA were used, respectively. Log-ratio values were scaled using as scale estimator the median-absolute-value. Linear model methods were used for determining differentially expressed genes. Each probe was tested for changes in expression over replicates by using an empirical Bayes moderated t-statistic. To control the false discovery rate, p-values were corrected by using the method of Benjamani and Hochberg, 1995. The expected false discovery rate (FDR) was controlled to be less than 1%.	GPL23823	Emilia,,López Solanilla	emilia.lopez@upm.es	CBGP-Universidad Politécnica de Madrid (UPM)	Parque Científico y Tecnológico UPM, Campus de Montegancedo, Ctra. M-40, km 38	Pozuelo de Alarcon	Madrid	28223	Spain	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM2715nnn/GSM2715495/suppl/GSM2715495_Blue_Rep_3_Raw.txt.gz	15744	Liquid	Wild type	10 min	Blue light
Pseudomonas syringae pv. tomato DC3000 Wild type Blue Rep 4	GSM2715496	Public on Oct 01 2018	Jul 23 2017	Oct 01 2018	RNA	1	Wild type 10 min under Blue light	Pseudomonas syringae pv. tomato str. DC3000	genotype/variation: Wild type	culture type: Liquid	treatment: Blue light	treatment duration: 10 min	Transcriptomic analyses were done with cultures grown in liquid KB medium. Total RNA was extracted from cell cultures collected at O.D.=0.5 after a 10 min treatment with either white, blue or red light. Cultures maintained in the darkness were used as controls.	total RNA	Total RNA from four biological replicates from each treatment was extracted with TRI Reagent (Ambion) as recommended by the manufacturer. RNA was pre-treated with RNase-free DNase I (Roche) plus RNaseOUT (Invitrogen), followed by purification with RNeasy columns (Qiagen).	Cy3	cDNA was labeled with Cy3 by using the SuperScript III indirect cDNA labeling system (Invitrogen) as described in the instruction manual (One-Color Microarray Based Gene Expression Analysis Manual).	223283	600 ng of Cy3 probes were mixed and added to 5 μl of 10x Blocking Agent and Nuclease-free water in a 25 μl reaction. Then, we added 25 μl from 2x GExHybridization buffer and mixed carefully. The samples were placed on ice and quickly loaded onto arrays, hybridized at 65 ºC for 17 h and then washed once in GE wash buffer 1 at room temperature (1 min) and once in GE Wash Buffer 2 at 37 ºC (1 min).	Images from Cy3 channel were equilibrated and captured with a High resolution Scanner (Agilent) and spots quantified using Feature Extraction software (Agilent).	G1	Gene expression after 10 min blue light treatment.	For local background correction and normalization, the methods normexp and loess in LIMMA were used, respectively. Log-ratio values were scaled using as scale estimator the median-absolute-value. Linear model methods were used for determining differentially expressed genes. Each probe was tested for changes in expression over replicates by using an empirical Bayes moderated t-statistic. To control the false discovery rate, p-values were corrected by using the method of Benjamani and Hochberg, 1995. The expected false discovery rate (FDR) was controlled to be less than 1%.	GPL23823	Emilia,,López Solanilla	emilia.lopez@upm.es	CBGP-Universidad Politécnica de Madrid (UPM)	Parque Científico y Tecnológico UPM, Campus de Montegancedo, Ctra. M-40, km 38	Pozuelo de Alarcon	Madrid	28223	Spain	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM2715nnn/GSM2715496/suppl/GSM2715496_Blue_Rep_4_Raw.txt.gz	15744	Liquid	Wild type	10 min	Blue light
Pseudomonas syringae pv. tomato DC3000 Wild type Red Rep 1	GSM2715497	Public on Oct 01 2018	Jul 23 2017	Oct 01 2018	RNA	1	Wild type 10 min under Red light	Pseudomonas syringae pv. tomato str. DC3000	genotype/variation: Wild type	culture type: Liquid	treatment: Red light	treatment duration: 10 min	Transcriptomic analyses were done with cultures grown in liquid KB medium. Total RNA was extracted from cell cultures collected at O.D.=0.5 after a 10 min treatment with either white, blue or red light. Cultures maintained in the darkness were used as controls.	total RNA	Total RNA from four biological replicates from each treatment was extracted with TRI Reagent (Ambion) as recommended by the manufacturer. RNA was pre-treated with RNase-free DNase I (Roche) plus RNaseOUT (Invitrogen), followed by purification with RNeasy columns (Qiagen).	Cy3	cDNA was labeled with Cy3 by using the SuperScript III indirect cDNA labeling system (Invitrogen) as described in the instruction manual (One-Color Microarray Based Gene Expression Analysis Manual).	223283	600 ng of Cy3 probes were mixed and added to 5 μl of 10x Blocking Agent and Nuclease-free water in a 25 μl reaction. Then, we added 25 μl from 2x GExHybridization buffer and mixed carefully. The samples were placed on ice and quickly loaded onto arrays, hybridized at 65 ºC for 17 h and then washed once in GE wash buffer 1 at room temperature (1 min) and once in GE Wash Buffer 2 at 37 ºC (1 min).	Images from Cy3 channel were equilibrated and captured with a High resolution Scanner (Agilent) and spots quantified using Feature Extraction software (Agilent).	G2	Gene expression after 10 min red light treatment.	For local background correction and normalization, the methods normexp and loess in LIMMA were used, respectively. Log-ratio values were scaled using as scale estimator the median-absolute-value. Linear model methods were used for determining differentially expressed genes. Each probe was tested for changes in expression over replicates by using an empirical Bayes moderated t-statistic. To control the false discovery rate, p-values were corrected by using the method of Benjamani and Hochberg, 1995. The expected false discovery rate (FDR) was controlled to be less than 1%.	GPL23823	Emilia,,López Solanilla	emilia.lopez@upm.es	CBGP-Universidad Politécnica de Madrid (UPM)	Parque Científico y Tecnológico UPM, Campus de Montegancedo, Ctra. M-40, km 38	Pozuelo de Alarcon	Madrid	28223	Spain	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM2715nnn/GSM2715497/suppl/GSM2715497_Red_Rep_1_Raw.txt.gz	15744	Liquid	Wild type	10 min	Red light
Pseudomonas syringae pv. tomato DC3000 Wild type Red Rep 2	GSM2715498	Public on Oct 01 2018	Jul 23 2017	Oct 01 2018	RNA	1	Wild type 10 min under Red light	Pseudomonas syringae pv. tomato str. DC3000	genotype/variation: Wild type	culture type: Liquid	treatment: Red light	treatment duration: 10 min	Transcriptomic analyses were done with cultures grown in liquid KB medium. Total RNA was extracted from cell cultures collected at O.D.=0.5 after a 10 min treatment with either white, blue or red light. Cultures maintained in the darkness were used as controls.	total RNA	Total RNA from four biological replicates from each treatment was extracted with TRI Reagent (Ambion) as recommended by the manufacturer. RNA was pre-treated with RNase-free DNase I (Roche) plus RNaseOUT (Invitrogen), followed by purification with RNeasy columns (Qiagen).	Cy3	cDNA was labeled with Cy3 by using the SuperScript III indirect cDNA labeling system (Invitrogen) as described in the instruction manual (One-Color Microarray Based Gene Expression Analysis Manual).	223283	600 ng of Cy3 probes were mixed and added to 5 μl of 10x Blocking Agent and Nuclease-free water in a 25 μl reaction. Then, we added 25 μl from 2x GExHybridization buffer and mixed carefully. The samples were placed on ice and quickly loaded onto arrays, hybridized at 65 ºC for 17 h and then washed once in GE wash buffer 1 at room temperature (1 min) and once in GE Wash Buffer 2 at 37 ºC (1 min).	Images from Cy3 channel were equilibrated and captured with a High resolution Scanner (Agilent) and spots quantified using Feature Extraction software (Agilent).	G2	Gene expression after 10 min red light treatment.	For local background correction and normalization, the methods normexp and loess in LIMMA were used, respectively. Log-ratio values were scaled using as scale estimator the median-absolute-value. Linear model methods were used for determining differentially expressed genes. Each probe was tested for changes in expression over replicates by using an empirical Bayes moderated t-statistic. To control the false discovery rate, p-values were corrected by using the method of Benjamani and Hochberg, 1995. The expected false discovery rate (FDR) was controlled to be less than 1%.	GPL23823	Emilia,,López Solanilla	emilia.lopez@upm.es	CBGP-Universidad Politécnica de Madrid (UPM)	Parque Científico y Tecnológico UPM, Campus de Montegancedo, Ctra. M-40, km 38	Pozuelo de Alarcon	Madrid	28223	Spain	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM2715nnn/GSM2715498/suppl/GSM2715498_Red_Rep_2_Raw.txt.gz	15744	Liquid	Wild type	10 min	Red light
Pseudomonas syringae pv. tomato DC3000 Wild type Red Rep 3	GSM2715499	Public on Oct 01 2018	Jul 23 2017	Oct 01 2018	RNA	1	Wild type 10 min under Red light	Pseudomonas syringae pv. tomato str. DC3000	genotype/variation: Wild type	culture type: Liquid	treatment: Red light	treatment duration: 10 min	Transcriptomic analyses were done with cultures grown in liquid KB medium. Total RNA was extracted from cell cultures collected at O.D.=0.5 after a 10 min treatment with either white, blue or red light. Cultures maintained in the darkness were used as controls.	total RNA	Total RNA from four biological replicates from each treatment was extracted with TRI Reagent (Ambion) as recommended by the manufacturer. RNA was pre-treated with RNase-free DNase I (Roche) plus RNaseOUT (Invitrogen), followed by purification with RNeasy columns (Qiagen).	Cy3	cDNA was labeled with Cy3 by using the SuperScript III indirect cDNA labeling system (Invitrogen) as described in the instruction manual (One-Color Microarray Based Gene Expression Analysis Manual).	223283	600 ng of Cy3 probes were mixed and added to 5 μl of 10x Blocking Agent and Nuclease-free water in a 25 μl reaction. Then, we added 25 μl from 2x GExHybridization buffer and mixed carefully. The samples were placed on ice and quickly loaded onto arrays, hybridized at 65 ºC for 17 h and then washed once in GE wash buffer 1 at room temperature (1 min) and once in GE Wash Buffer 2 at 37 ºC (1 min).	Images from Cy3 channel were equilibrated and captured with a High resolution Scanner (Agilent) and spots quantified using Feature Extraction software (Agilent).	G2	Gene expression after 10 min red light treatment.	For local background correction and normalization, the methods normexp and loess in LIMMA were used, respectively. Log-ratio values were scaled using as scale estimator the median-absolute-value. Linear model methods were used for determining differentially expressed genes. Each probe was tested for changes in expression over replicates by using an empirical Bayes moderated t-statistic. To control the false discovery rate, p-values were corrected by using the method of Benjamani and Hochberg, 1995. The expected false discovery rate (FDR) was controlled to be less than 1%.	GPL23823	Emilia,,López Solanilla	emilia.lopez@upm.es	CBGP-Universidad Politécnica de Madrid (UPM)	Parque Científico y Tecnológico UPM, Campus de Montegancedo, Ctra. M-40, km 38	Pozuelo de Alarcon	Madrid	28223	Spain	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM2715nnn/GSM2715499/suppl/GSM2715499_Red_Rep_3_Raw.txt.gz	15744	Liquid	Wild type	10 min	Red light
Pseudomonas syringae pv. tomato DC3000 Wild type Red Rep 4	GSM2715500	Public on Oct 01 2018	Jul 23 2017	Oct 01 2018	RNA	1	Wild type 10 min under Red light	Pseudomonas syringae pv. tomato str. DC3000	genotype/variation: Wild type	culture type: Liquid	treatment: Red light	treatment duration: 10 min	Transcriptomic analyses were done with cultures grown in liquid KB medium. Total RNA was extracted from cell cultures collected at O.D.=0.5 after a 10 min treatment with either white, blue or red light. Cultures maintained in the darkness were used as controls.	total RNA	Total RNA from four biological replicates from each treatment was extracted with TRI Reagent (Ambion) as recommended by the manufacturer. RNA was pre-treated with RNase-free DNase I (Roche) plus RNaseOUT (Invitrogen), followed by purification with RNeasy columns (Qiagen).	Cy3	cDNA was labeled with Cy3 by using the SuperScript III indirect cDNA labeling system (Invitrogen) as described in the instruction manual (One-Color Microarray Based Gene Expression Analysis Manual).	223283	600 ng of Cy3 probes were mixed and added to 5 μl of 10x Blocking Agent and Nuclease-free water in a 25 μl reaction. Then, we added 25 μl from 2x GExHybridization buffer and mixed carefully. The samples were placed on ice and quickly loaded onto arrays, hybridized at 65 ºC for 17 h and then washed once in GE wash buffer 1 at room temperature (1 min) and once in GE Wash Buffer 2 at 37 ºC (1 min).	Images from Cy3 channel were equilibrated and captured with a High resolution Scanner (Agilent) and spots quantified using Feature Extraction software (Agilent).	G2	Gene expression after 10 min red light treatment.	For local background correction and normalization, the methods normexp and loess in LIMMA were used, respectively. Log-ratio values were scaled using as scale estimator the median-absolute-value. Linear model methods were used for determining differentially expressed genes. Each probe was tested for changes in expression over replicates by using an empirical Bayes moderated t-statistic. To control the false discovery rate, p-values were corrected by using the method of Benjamani and Hochberg, 1995. The expected false discovery rate (FDR) was controlled to be less than 1%.	GPL23823	Emilia,,López Solanilla	emilia.lopez@upm.es	CBGP-Universidad Politécnica de Madrid (UPM)	Parque Científico y Tecnológico UPM, Campus de Montegancedo, Ctra. M-40, km 38	Pozuelo de Alarcon	Madrid	28223	Spain	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM2715nnn/GSM2715500/suppl/GSM2715500_Red_Rep_4_Raw.txt.gz	15744	Liquid	Wild type	10 min	Red light
Pseudomonas syringae pv. tomato DC3000 Wild type White Rep 1	GSM2715501	Public on Oct 01 2018	Jul 23 2017	Oct 01 2018	RNA	1	Wild type 10 min under White light	Pseudomonas syringae pv. tomato str. DC3000	genotype/variation: Wild type	culture type: Liquid	treatment: White light	treatment duration: 10 min	Transcriptomic analyses were done with cultures grown in liquid KB medium. Total RNA was extracted from cell cultures collected at O.D.=0.5 after a 10 min treatment with either white, blue or red light. Cultures maintained in the darkness were used as controls.	total RNA	Total RNA from four biological replicates from each treatment was extracted with TRI Reagent (Ambion) as recommended by the manufacturer. RNA was pre-treated with RNase-free DNase I (Roche) plus RNaseOUT (Invitrogen), followed by purification with RNeasy columns (Qiagen).	Cy3	cDNA was labeled with Cy3 by using the SuperScript III indirect cDNA labeling system (Invitrogen) as described in the instruction manual (One-Color Microarray Based Gene Expression Analysis Manual).	223283	600 ng of Cy3 probes were mixed and added to 5 μl of 10x Blocking Agent and Nuclease-free water in a 25 μl reaction. Then, we added 25 μl from 2x GExHybridization buffer and mixed carefully. The samples were placed on ice and quickly loaded onto arrays, hybridized at 65 ºC for 17 h and then washed once in GE wash buffer 1 at room temperature (1 min) and once in GE Wash Buffer 2 at 37 ºC (1 min).	Images from Cy3 channel were equilibrated and captured with a High resolution Scanner (Agilent) and spots quantified using Feature Extraction software (Agilent).	G3	Gene expression after 10 min white light treatment.	For local background correction and normalization, the methods normexp and loess in LIMMA were used, respectively. Log-ratio values were scaled using as scale estimator the median-absolute-value. Linear model methods were used for determining differentially expressed genes. Each probe was tested for changes in expression over replicates by using an empirical Bayes moderated t-statistic. To control the false discovery rate, p-values were corrected by using the method of Benjamani and Hochberg, 1995. The expected false discovery rate (FDR) was controlled to be less than 1%.	GPL23823	Emilia,,López Solanilla	emilia.lopez@upm.es	CBGP-Universidad Politécnica de Madrid (UPM)	Parque Científico y Tecnológico UPM, Campus de Montegancedo, Ctra. M-40, km 38	Pozuelo de Alarcon	Madrid	28223	Spain	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM2715nnn/GSM2715501/suppl/GSM2715501_White_Rep_1_Raw.txt.gz	15744	Liquid	Wild type	10 min	White light
Pseudomonas syringae pv. tomato DC3000 Wild type White Rep 2	GSM2715502	Public on Oct 01 2018	Jul 23 2017	Oct 01 2018	RNA	1	Wild type 10 min under White light	Pseudomonas syringae pv. tomato str. DC3000	genotype/variation: Wild type	culture type: Liquid	treatment: White light	treatment duration: 10 min	Transcriptomic analyses were done with cultures grown in liquid KB medium. Total RNA was extracted from cell cultures collected at O.D.=0.5 after a 10 min treatment with either white, blue or red light. Cultures maintained in the darkness were used as controls.	total RNA	Total RNA from four biological replicates from each treatment was extracted with TRI Reagent (Ambion) as recommended by the manufacturer. RNA was pre-treated with RNase-free DNase I (Roche) plus RNaseOUT (Invitrogen), followed by purification with RNeasy columns (Qiagen).	Cy3	cDNA was labeled with Cy3 by using the SuperScript III indirect cDNA labeling system (Invitrogen) as described in the instruction manual (One-Color Microarray Based Gene Expression Analysis Manual).	223283	600 ng of Cy3 probes were mixed and added to 5 μl of 10x Blocking Agent and Nuclease-free water in a 25 μl reaction. Then, we added 25 μl from 2x GExHybridization buffer and mixed carefully. The samples were placed on ice and quickly loaded onto arrays, hybridized at 65 ºC for 17 h and then washed once in GE wash buffer 1 at room temperature (1 min) and once in GE Wash Buffer 2 at 37 ºC (1 min).	Images from Cy3 channel were equilibrated and captured with a High resolution Scanner (Agilent) and spots quantified using Feature Extraction software (Agilent).	G3	Gene expression after 10 min white light treatment.	For local background correction and normalization, the methods normexp and loess in LIMMA were used, respectively. Log-ratio values were scaled using as scale estimator the median-absolute-value. Linear model methods were used for determining differentially expressed genes. Each probe was tested for changes in expression over replicates by using an empirical Bayes moderated t-statistic. To control the false discovery rate, p-values were corrected by using the method of Benjamani and Hochberg, 1995. The expected false discovery rate (FDR) was controlled to be less than 1%.	GPL23823	Emilia,,López Solanilla	emilia.lopez@upm.es	CBGP-Universidad Politécnica de Madrid (UPM)	Parque Científico y Tecnológico UPM, Campus de Montegancedo, Ctra. M-40, km 38	Pozuelo de Alarcon	Madrid	28223	Spain	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM2715nnn/GSM2715502/suppl/GSM2715502_White_Rep_2_Raw.txt.gz	15744	Liquid	Wild type	10 min	White light
Pseudomonas syringae pv. tomato DC3000 Wild type White Rep 3	GSM2715503	Public on Oct 01 2018	Jul 23 2017	Oct 01 2018	RNA	1	Wild type 10 min under White light	Pseudomonas syringae pv. tomato str. DC3000	genotype/variation: Wild type	culture type: Liquid	treatment: White light	treatment duration: 10 min	Transcriptomic analyses were done with cultures grown in liquid KB medium. Total RNA was extracted from cell cultures collected at O.D.=0.5 after a 10 min treatment with either white, blue or red light. Cultures maintained in the darkness were used as controls.	total RNA	Total RNA from four biological replicates from each treatment was extracted with TRI Reagent (Ambion) as recommended by the manufacturer. RNA was pre-treated with RNase-free DNase I (Roche) plus RNaseOUT (Invitrogen), followed by purification with RNeasy columns (Qiagen).	Cy3	cDNA was labeled with Cy3 by using the SuperScript III indirect cDNA labeling system (Invitrogen) as described in the instruction manual (One-Color Microarray Based Gene Expression Analysis Manual).	223283	600 ng of Cy3 probes were mixed and added to 5 μl of 10x Blocking Agent and Nuclease-free water in a 25 μl reaction. Then, we added 25 μl from 2x GExHybridization buffer and mixed carefully. The samples were placed on ice and quickly loaded onto arrays, hybridized at 65 ºC for 17 h and then washed once in GE wash buffer 1 at room temperature (1 min) and once in GE Wash Buffer 2 at 37 ºC (1 min).	Images from Cy3 channel were equilibrated and captured with a High resolution Scanner (Agilent) and spots quantified using Feature Extraction software (Agilent).	G3	Gene expression after 10 min white light treatment.	For local background correction and normalization, the methods normexp and loess in LIMMA were used, respectively. Log-ratio values were scaled using as scale estimator the median-absolute-value. Linear model methods were used for determining differentially expressed genes. Each probe was tested for changes in expression over replicates by using an empirical Bayes moderated t-statistic. To control the false discovery rate, p-values were corrected by using the method of Benjamani and Hochberg, 1995. The expected false discovery rate (FDR) was controlled to be less than 1%.	GPL23823	Emilia,,López Solanilla	emilia.lopez@upm.es	CBGP-Universidad Politécnica de Madrid (UPM)	Parque Científico y Tecnológico UPM, Campus de Montegancedo, Ctra. M-40, km 38	Pozuelo de Alarcon	Madrid	28223	Spain	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM2715nnn/GSM2715503/suppl/GSM2715503_White_Rep_3_Raw.txt.gz	15744	Liquid	Wild type	10 min	White light
Pseudomonas syringae pv. tomato DC3000 Wild type White Rep 4	GSM2715504	Public on Oct 01 2018	Jul 23 2017	Oct 01 2018	RNA	1	Wild type 10 min under White light	Pseudomonas syringae pv. tomato str. DC3000	genotype/variation: Wild type	culture type: Liquid	treatment: White light	treatment duration: 10 min	Transcriptomic analyses were done with cultures grown in liquid KB medium. Total RNA was extracted from cell cultures collected at O.D.=0.5 after a 10 min treatment with either white, blue or red light. Cultures maintained in the darkness were used as controls.	total RNA	Total RNA from four biological replicates from each treatment was extracted with TRI Reagent (Ambion) as recommended by the manufacturer. RNA was pre-treated with RNase-free DNase I (Roche) plus RNaseOUT (Invitrogen), followed by purification with RNeasy columns (Qiagen).	Cy3	cDNA was labeled with Cy3 by using the SuperScript III indirect cDNA labeling system (Invitrogen) as described in the instruction manual (One-Color Microarray Based Gene Expression Analysis Manual).	223283	600 ng of Cy3 probes were mixed and added to 5 μl of 10x Blocking Agent and Nuclease-free water in a 25 μl reaction. Then, we added 25 μl from 2x GExHybridization buffer and mixed carefully. The samples were placed on ice and quickly loaded onto arrays, hybridized at 65 ºC for 17 h and then washed once in GE wash buffer 1 at room temperature (1 min) and once in GE Wash Buffer 2 at 37 ºC (1 min).	Images from Cy3 channel were equilibrated and captured with a High resolution Scanner (Agilent) and spots quantified using Feature Extraction software (Agilent).	G3	Gene expression after 10 min white light treatment.	For local background correction and normalization, the methods normexp and loess in LIMMA were used, respectively. Log-ratio values were scaled using as scale estimator the median-absolute-value. Linear model methods were used for determining differentially expressed genes. Each probe was tested for changes in expression over replicates by using an empirical Bayes moderated t-statistic. To control the false discovery rate, p-values were corrected by using the method of Benjamani and Hochberg, 1995. The expected false discovery rate (FDR) was controlled to be less than 1%.	GPL23823	Emilia,,López Solanilla	emilia.lopez@upm.es	CBGP-Universidad Politécnica de Madrid (UPM)	Parque Científico y Tecnológico UPM, Campus de Montegancedo, Ctra. M-40, km 38	Pozuelo de Alarcon	Madrid	28223	Spain	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM2715nnn/GSM2715504/suppl/GSM2715504_White_Rep_4_Raw.txt.gz	15744	Liquid	Wild type	10 min	White light