Gene Expression Omnibus (GEO) Overview

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DataSet	:	Series(GSE) x Platform(GPL). A set of related gene expression data.
Sample	:	Biological materials.
platform	:	Methods or instruments used for the gene expression profilings.

Human
(2,851)

Bacteria
(78)

Viruses
(0)

Phages
(0)

Unclassified
(120)

All
(6,302)

SAGE NlaIII
(0)

SAGE RsaI
(0)

SAGE Sau3A
(0)

MPSS
(0)

GeneChip
(15)

Tiling Array
(0)

cDNA Array
(6)

Oligo Array
(50)

Bead Array
(0)

Protein Array
(0)

Antibody
(0)

RT-PCR
(0)

HT-Seq
(0)

Other
(7)

All
(78)

brain
(0)

blood
(4)

connective
(0)

reproductive
(0)

muscular
(0)

digestive
(0)

liver
(0)

lung
(0)

urinary
(0)

endo/exo-crine
(0)

embryo
(0)

adult aerial structure
(0)

young aerial structure
(0)

root
(0)

meristem/growing tissue
(0)

flower/sexual organ
(0)

seed/fruit/grain
(0)

pooled
(0)

unclassified
(46)

all
(50)

1 | 2 | 3 »

	Sample ID	Title	Number of Data	Institute	Submission date	Platform	Sample type	Species	Organ class	Reasoning of the classification Keywords used for the classification are shown with bold font.
1	GSM33583	JRS4 9-29A	7,344	University of Maryland, College Park	2004-10-26	[Oligo Array] M1, M3, M18 GAS Array (GPL1482)	RNA	Streptococcus pyogenes	unclassified	source_name:CsCl total RNA from M6 serotype GAS JRS4 genomic DNA from M6 serotype GAS JRS4 title:JRS4 9-29A description:Total RNA was isolated by CsCl method, cDNA was labled using CyScribe Post labeling kit from Amersham. Genomic DNA was labeled using Nick Translation kit from Amersham. Labeled probes were purified with GFX columns and incorporation rates were determined using a nanodrop. Approximately equal amounts of cDNA/gDNA were denatured and hybridized to arrays at 50C overnight followed by subsequent washes. Arrays were scanned using GenePix software. Output data (F635 mean-B635, F532 mean-B532, flags) from gpr file was analyzed to remove spots that did not exceed 2SD above a background threshold. Remaining spots were normalized and ratios of cDNA to gDNA were calculated.
2	GSM33597	JRS4 9-29B	7,344	University of Maryland, College Park	2004-10-27	[Oligo Array] M1, M3, M18 GAS Array (GPL1482)	RNA	Streptococcus pyogenes	unclassified	source_name:CsCl total RNA from M6 serotype GAS JRS4 genomic DNA from M6 serotype GAS JRS4 title:JRS4 9-29B description:Total RNA was isolated by CsCl method, cDNA was labeled using CyScribe Post Lbeleing kit from Amersham. Genomic DNA was labeled using Nick Translation kit from Amersham. Labeled probes were purified with GFX columns and incorporation rates were determined using a nanodrop. Approximately equal amounts of cDNA/gDNA were denatured and hybridized to arrays at 50C overnight followed by subsequent washes. Arrays were scanned using GenePix software. Output data (F635 mean -B635, F532 mean -B532, flags) from gpr file were analyzed to remove spots that did not exceed 2SD above a background threshold. Remaining spots were normalized and ratios of cDNA to gDNA were calculated.
3	GSM33598	JRS4 1-2A	7,344	University of Maryland, College Park	2004-10-27	[Oligo Array] M1, M3, M18 GAS Array (GPL1482)	RNA	Streptococcus pyogenes	unclassified	source_name:CsCl total RNA from M6 serotype GAS JRS4 genomic DNA from M6 serotype GAS JRS4 title:JRS4 1-2A description:Total RNA was isolated by CsCl method, cDNA was labeled using CyScribe Post Lbeleing kit from Amersham. Genomic DNA was labeled using Nick Translation kit from Amersham. Labeled probes were purified with GFX columns and incorporation rates were determined using a nanodrop. Approximately equal amounts of cDNA/gDNA were denatured and hybridized to arrays at 50C overnight followed by subsequent washes. Arrays were scanned using GenePix software. Output data (F635 mean -B635, F532 mean -B532, flags) from gpr file were analyzed to remove spots that did not exceed 2SD above a background threshold. Remaining spots were normalized and ratios of cDNA to gDNA were calculated.
4	GSM33599	JRS4 1-2B	7,344	University of Maryland, College Park	2004-10-27	[Oligo Array] M1, M3, M18 GAS Array (GPL1482)	RNA	Streptococcus pyogenes	unclassified	source_name:CsCl total RNA from M6 serotype GAS JRS4 genomic DNA from M6 serotype GAS JRS4 title:JRS4 1-2B description:Total RNA was isolated by CsCl method, cDNA was labeled using CyScribe Post Lbeleing kit from Amersham. Genomic DNA was labeled using Nick Translation kit from Amersham. Labeled probes were purified with GFX columns and incorporation rates were determined using a nanodrop. Approximately equal amounts of cDNA/gDNA were denatured and hybridized to arrays at 50C overnight followed by subsequent washes. Arrays were scanned using GenePix software. Output data (F635 mean -B635, F532 mean -B532, flags) from gpr file were analyzed to remove spots that did not exceed 2SD above a background threshold. Remaining spots were normalized and ratios of cDNA to gDNA were calculated.
5	GSM33600	JRS519 9-29A	7,344	University of Maryland, College Park	2004-10-27	[Oligo Array] M1, M3, M18 GAS Array (GPL1482)	RNA	Streptococcus pyogenes	unclassified	source_name:CsCl total RNA from M6 serotype GAS JRS519 genomic DNA from M6 serotype GAS JRS4 title:JRS519 9-29A description:Total RNA was isolated by CsCl method, cDNA was labeled using CyScribe Post Lbeleing kit from Amersham. Genomic DNA was labeled using Nick Translation kit from Amersham. Labeled probes were purified with GFX columns and incorporation rates were determined using a nanodrop. Approximately equal amounts of cDNA/gDNA were denatured and hybridized to arrays at 50C overnight followed by subsequent washes. Arrays were scanned using GenePix software. Output data (F635 mean -B635, F532 mean -B532, flags) from gpr file were analyzed to remove spots that did not exceed 2SD above a background threshold. Remaining spots were normalized and ratios of cDNA to gDNA were calculated.
6	GSM33601	JRS519 9-29B	7,344	University of Maryland, College Park	2004-10-27	[Oligo Array] M1, M3, M18 GAS Array (GPL1482)	RNA	Streptococcus pyogenes	unclassified	source_name:CsCl total RNA from M6 serotype GAS JRS519 genomic DNA from M6 serotype GAS JRS4 title:JRS519 9-29B description:Total RNA was isolated by CsCl method, cDNA was labeled using CyScribe Post Lbeleing kit from Amersham. Genomic DNA was labeled using Nick Translation kit from Amersham. Labeled probes were purified with GFX columns and incorporation rates were determined using a nanodrop. Approximately equal amounts of cDNA/gDNA were denatured and hybridized to arrays at 50C overnight followed by subsequent washes. Arrays were scanned using GenePix software. Output data (F635 mean -B635, F532 mean -B532, flags) from gpr file were analyzed to remove spots that did not exceed 2SD above a background threshold. Remaining spots were normalized and ratios of cDNA to gDNA were calculated.
7	GSM33602	JRS519 1-2A	7,344	University of Maryland, College Park	2004-10-27	[Oligo Array] M1, M3, M18 GAS Array (GPL1482)	RNA	Streptococcus pyogenes	unclassified	source_name:CsCl total RNA from M6 serotype GAS JRS519 genomic DNA from M6 serotype GAS JRS4 title:JRS519 1-2A description:Total RNA was isolated by CsCl method, cDNA was labeled using CyScribe Post Lbeleing kit from Amersham. Genomic DNA was labeled using Nick Translation kit from Amersham. Labeled probes were purified with GFX columns and incorporation rates were determined using a nanodrop. Approximately equal amounts of cDNA/gDNA were denatured and hybridized to arrays at 50C overnight followed by subsequent washes. Arrays were scanned using GenePix software. Output data (F635 mean -B635, F532 mean -B532, flags) from gpr file were analyzed to remove spots that did not exceed 2SD above a background threshold. Remaining spots were normalized and ratios of cDNA to gDNA were calculated.
8	GSM33603	JRS519 1-2B	7,344	University of Maryland, College Park	2004-10-27	[Oligo Array] M1, M3, M18 GAS Array (GPL1482)	RNA	Streptococcus pyogenes	unclassified	source_name:CsCl total RNA from M6 serotype GAS JRS519 genomic DNA from M6 serotype GAS JRS4 title:JRS519 1-2B description:Total RNA was isolated by CsCl method, cDNA was labeled using CyScribe Post Lbeleing kit from Amersham. Genomic DNA was labeled using Nick Translation kit from Amersham. Labeled probes were purified with GFX columns and incorporation rates were determined using a nanodrop. Approximately equal amounts of cDNA/gDNA were denatured and hybridized to arrays at 50C overnight followed by subsequent washes. Arrays were scanned using GenePix software. Output data (F635 mean -B635, F532 mean -B532, flags) from gpr file were analyzed to remove spots that did not exceed 2SD above a background threshold. Remaining spots were normalized and ratios of cDNA to gDNA were calculated.
9	GSM33606	SF370 6-23A	7,344	University of Maryland, College Park	2004-10-27	[Oligo Array] M1, M3, M18 GAS Array (GPL1482)	RNA	Streptococcus pyogenes	unclassified	source_name:CsCl total RNA from M1 serotype GAS SF370 genomic DNA from M1 serotype GAS SF370 title:SF370 6-23A description:Total RNA was isolated by CsCl method, cDNA was labeled using CyScribe Post Lbeleing kit from Amersham. Genomic DNA was labeled using Nick Translation kit from Amersham. Labeled probes were purified with GFX columns and incorporation rates were determined using a nanodrop. Approximately equal amounts of cDNA/gDNA were denatured and hybridized to arrays at 50C overnight followed by subsequent washes. Arrays were scanned using GenePix software. Output data (F635 mean -B635, F532 mean -B532, flags) from gpr file were analyzed to remove spots that did not exceed 2SD above a background threshold. Remaining spots were normalized and ratios of cDNA to gDNA were calculated.
10	GSM33607	SF370 6-23B	7,344	University of Maryland, College Park	2004-10-27	[Oligo Array] M1, M3, M18 GAS Array (GPL1482)	RNA	Streptococcus pyogenes	unclassified	source_name:CsCl total RNA from M1 serotype GAS SF370 genomic DNA from M1 serotype GAS SF370 title:SF370 6-23B description:Total RNA was isolated by CsCl method, cDNA was labeled using CyScribe Post Lbeleing kit from Amersham. Genomic DNA was labeled using Nick Translation kit from Amersham. Labeled probes were purified with GFX columns and incorporation rates were determined using a nanodrop. Approximately equal amounts of cDNA/gDNA were denatured and hybridized to arrays at 50C overnight followed by subsequent washes. Arrays were scanned using GenePix software. Output data (F635 mean -B635, F532 mean -B532, flags) from gpr file were analyzed to remove spots that did not exceed 2SD above a background threshold. Remaining spots were normalized and ratios of cDNA to gDNA were calculated.
11	GSM33608	SF370 12-31A	7,344	University of Maryland, College Park	2004-10-27	[Oligo Array] M1, M3, M18 GAS Array (GPL1482)	RNA	Streptococcus pyogenes	unclassified	source_name:CsCl total RNA from M1 serotype GAS SF370 genomic DNA from M1 serotype GAS SF370 title:SF370 12-31A description:Total RNA was isolated by CsCl method, cDNA was labeled using CyScribe Post Lbeleing kit from Amersham. Genomic DNA was labeled using Nick Translation kit from Amersham. Labeled probes were purified with GFX columns and incorporation rates were determined using a nanodrop. Approximately equal amounts of cDNA/gDNA were denatured and hybridized to arrays at 50C overnight followed by subsequent washes. Arrays were scanned using GenePix software. Output data (F635 mean -B635, F532 mean -B532, flags) from gpr file were analyzed to remove spots that did not exceed 2SD above a background threshold. Remaining spots were normalized and ratios of cDNA to gDNA were calculated.
12	GSM33609	SF370 12-31B	7,344	University of Maryland, College Park	2004-10-27	[Oligo Array] M1, M3, M18 GAS Array (GPL1482)	RNA	Streptococcus pyogenes	unclassified	source_name:CsCl total RNA from M1 serotype GAS SF370 genomic DNA from M1 serotype GAS SF370 title:SF370 12-31B description:Total RNA was isolated by CsCl method, cDNA was labeled using CyScribe Post Lbeleing kit from Amersham. Genomic DNA was labeled using Nick Translation kit from Amersham. Labeled probes were purified with GFX columns and incorporation rates were determined using a nanodrop. Approximately equal amounts of cDNA/gDNA were denatured and hybridized to arrays at 50C overnight followed by subsequent washes. Arrays were scanned using GenePix software. Output data (F635 mean -B635, F532 mean -B532, flags) from gpr file were analyzed to remove spots that did not exceed 2SD above a background threshold. Remaining spots were normalized and ratios of cDNA to gDNA were calculated.
13	GSM33610	KSM165L 6-23A	7,344	University of Maryland, College Park	2004-10-27	[Oligo Array] M1, M3, M18 GAS Array (GPL1482)	RNA	Streptococcus pyogenes	unclassified	source_name:CsCl total RNA from M1 serotype GAS KSM165L genomic DNA from M1 serotype GAS SF370 title:KSM165L 6-23A description:Total RNA was isolated by CsCl method, cDNA was labeled using CyScribe Post Lbeleing kit from Amersham. Genomic DNA was labeled using Nick Translation kit from Amersham. Labeled probes were purified with GFX columns and incorporation rates were determined using a nanodrop. Approximately equal amounts of cDNA/gDNA were denatured and hybridized to arrays at 50C overnight followed by subsequent washes. Arrays were scanned using GenePix software. Output data (F635 mean -B635, F532 mean -B532, flags) from gpr file were analyzed to remove spots that did not exceed 2SD above a background threshold. Remaining spots were normalized and ratios of cDNA to gDNA were calculated.
14	GSM33611	KSM165L 6-23B	7,344	University of Maryland, College Park	2004-10-27	[Oligo Array] M1, M3, M18 GAS Array (GPL1482)	RNA	Streptococcus pyogenes	unclassified	source_name:CsCl total RNA from M1 serotype GAS KSM165L genomic DNA from M1 serotype GAS SF370 title:KSM165L 6-23B description:Total RNA was isolated by CsCl method, cDNA was labeled using CyScribe Post Lbeleing kit from Amersham. Genomic DNA was labeled using Nick Translation kit from Amersham. Labeled probes were purified with GFX columns and incorporation rates were determined using a nanodrop. Approximately equal amounts of cDNA/gDNA were denatured and hybridized to arrays at 50C overnight followed by subsequent washes. Arrays were scanned using GenePix software. Output data (F635 mean -B635, F532 mean -B532, flags) from gpr file were analyzed to remove spots that did not exceed 2SD above a background threshold. Remaining spots were normalized and ratios of cDNA to gDNA were calculated.
15	GSM33612	KSM165L 12-31A	7,344	University of Maryland, College Park	2004-10-27	[Oligo Array] M1, M3, M18 GAS Array (GPL1482)	RNA	Streptococcus pyogenes	unclassified	source_name:CsCl total RNA from M1 serotype GAS KSM165L genomic DNA from M1 serotype GAS SF370 title:KSM165L 12-31A description:Total RNA was isolated by CsCl method, cDNA was labeled using CyScribe Post Lbeleing kit from Amersham. Genomic DNA was labeled using Nick Translation kit from Amersham. Labeled probes were purified with GFX columns and incorporation rates were determined using a nanodrop. Approximately equal amounts of cDNA/gDNA were denatured and hybridized to arrays at 50C overnight followed by subsequent washes. Arrays were scanned using GenePix software. Output data (F635 mean -B635, F532 mean -B532, flags) from gpr file were analyzed to remove spots that did not exceed 2SD above a background threshold. Remaining spots were normalized and ratios of cDNA to gDNA were calculated.
16	GSM33613	KSM165L 12-31B	7,344	University of Maryland, College Park	2004-10-27	[Oligo Array] M1, M3, M18 GAS Array (GPL1482)	RNA	Streptococcus pyogenes	unclassified	source_name:CsCl total RNA from M1 serotype GAS KSM165L genomic DNA from M1 serotype GAS SF370 title:KSM165L 12-31B description:Total RNA was isolated by CsCl method, cDNA was labeled using CyScribe Post Lbeleing kit from Amersham. Genomic DNA was labeled using Nick Translation kit from Amersham. Labeled probes were purified with GFX columns and incorporation rates were determined using a nanodrop. Approximately equal amounts of cDNA/gDNA were denatured and hybridized to arrays at 50C overnight followed by subsequent washes. Arrays were scanned using GenePix software. Output data (F635 mean -B635, F532 mean -B532, flags) from gpr file were analyzed to remove spots that did not exceed 2SD above a background threshold. Remaining spots were normalized and ratios of cDNA to gDNA were calculated.
17	GSM38212	LL2-Cy3+LL14-Cy5 (expt 1)	5,408	Nagoya University	2004-12-28	[Oligo Array] T. elongatus 2.5k oligoarray (GPL1771)	RNA	Thermosynechococcus elongatus BP-1	peripheral blood	Strain and culture conditions. We grew wild-type T. elongatus (Yamaoka et al., Plant Cell Physiol. 19, 943-954) at 50oC under constant light from white fluorescent lamps at 38 micromol m-2 sec-1 (hereafter called LL conditions) in BG-11 liquid medium (Rippka et al., J. Gen. Microbiol. 111, 1-61) with bubbling of air containing 5% (v/v) CO2. We subjected the cells to 12 h of darkness to synchronize the circadian clock, and transferred them back to LL. We collected cells for RNA isolation at 2 h (LL2) and 14 h (LL14) after the transfer. Microarray experiments. We isolated total RNAs from two independent cultures by the hot-phenol method (Kucho et al., Genes Genet. Syst. 79, 189-197) and purified them using the SV total RNA isolation system (Promega, WI, USA). We used a mixture of the total RNAs from the two cultures for labeling reactions. We synthesized fluorescence-labeled cDNA by direct incorporation of Cy3-dUTP or Cy5-dUTP (Amersham Bioscience, NJ, USA) during random-primed reverse transcription, using 5.9 microgram total RNA and an RNA fluorescence labeling core kit (M-MLV version 2.0, TaKaRa, Japan). We prehybridized the microarray for 1 h at 42oC in a solution containing 5 X SSC (1 X SSC is 0.15 M NaCl, 0.015 M sodium citrate), 0.1% sodium lauryl sulfate (SDS), and 10 mg/ml bovine serum albumin. We washed the microarray at room temperature in distilled water 3 times for 1 min, rinsed it in 2-propanol, and dried it by centrifugation at 150 X g for 2 min. We performed hybridization for 16 h at 42oC in 12-mL solution containing 5 X SSC, 0.1% SDS, 30% formamide, and heat-denatured labeled cDNA. We then washed the microarray at room temperature with 2 X SSC containing 0.1% SDS for 4 min, with 0.1 X SSC containing 0.1% SDS for 4 min, and 3 times with 0.1 X SSC for 1 min. We dried the microarray by centrifugation. We obtained fluorescence images of Cy3 and Cy5 dye channels using a GenePix 4000B scanner (Axon Instruments, CA, USA). Data analysis. We used GenePix Pro 5.0 software (Axon Instruments) to determine the signal intensity of each spot and its local background. We calculated net signal intensity by subtracting the median signal intensity of all pixels within the local background area from the median signal intensity of all pixels within the spot area. We visually confirmed the correct recognition of all spot areas by the automatic alignment function of the GenePix Pro. We flagged spots and did not use them for data analysis when any of following occurred: (i) the GenePix Pro did not find the spot area automatically, (ii) the net signal intensity was <= 0, (iii) the percentage of saturated pixels in the spot area was >= 25, and (iv) severe noise was present. We normalized biases in signal intensity between the two fluorescent dye channels in a microarray by locally weighted linear regression analysis (lowess normalization) (Yang et al., Nucleic Acids Res. 30, e15) using MIDAS software (http://www.tigr.org/software/tm4/midas.html). For all normalization, we set the smoothing parameter to 0.33. Keywords = circadian clock Keywords = thermophilic cyanobacteria
18	GSM38213	LL2-Cy5+LL14-Cy3 (expt 1, dye swap)	5,408	Nagoya University	2004-12-28	[Oligo Array] T. elongatus 2.5k oligoarray (GPL1771)	RNA	Thermosynechococcus elongatus BP-1	peripheral blood	Strain and culture conditions. We grew wild-type T. elongatus (Yamaoka et al., Plant Cell Physiol. 19, 943-954) at 50oC under constant light from white fluorescent lamps at 38 micromol m-2 sec-1 (hereafter called LL conditions) in BG-11 liquid medium (Rippka et al., J. Gen. Microbiol. 111, 1-61) with bubbling of air containing 5% (v/v) CO2. We subjected the cells to 12 h of darkness to synchronize the circadian clock, and transferred them back to LL. We collected cells for RNA isolation at 2 h (LL2) and 14 h (LL14) after the transfer. Microarray experiments. We isolated total RNAs from two independent cultures by the hot-phenol method (Kucho et al., Genes Genet. Syst. 79, 189-197) and purified them using the SV total RNA isolation system (Promega, WI, USA). We used a mixture of the total RNAs from the two cultures for labeling reactions. We synthesized fluorescence-labeled cDNA by direct incorporation of Cy3-dUTP or Cy5-dUTP (Amersham Bioscience, NJ, USA) during random-primed reverse transcription, using 5.9 microgram total RNA and an RNA fluorescence labeling core kit (M-MLV version 2.0, TaKaRa, Japan). We prehybridized the microarray for 1 h at 42oC in a solution containing 5 X SSC (1 X SSC is 0.15 M NaCl, 0.015 M sodium citrate), 0.1% sodium lauryl sulfate (SDS), and 10 mg/ml bovine serum albumin. We washed the microarray at room temperature in distilled water 3 times for 1 min, rinsed it in 2-propanol, and dried it by centrifugation at 150 X g for 2 min. We performed hybridization for 16 h at 42oC in 12-mL solution containing 5 X SSC, 0.1% SDS, 30% formamide, and heat-denatured labeled cDNA. We then washed the microarray at room temperature with 2 X SSC containing 0.1% SDS for 4 min, with 0.1 X SSC containing 0.1% SDS for 4 min, and 3 times with 0.1 X SSC for 1 min. We dried the microarray by centrifugation. We obtained fluorescence images of Cy3 and Cy5 dye channels using a GenePix 4000B scanner (Axon Instruments, CA, USA). Data analysis. We used GenePix Pro 5.0 software (Axon Instruments) to determine the signal intensity of each spot and its local background. We calculated net signal intensity by subtracting the median signal intensity of all pixels within the local background area from the median signal intensity of all pixels within the spot area. We visually confirmed the correct recognition of all spot areas by the automatic alignment function of the GenePix Pro. We flagged spots and did not use them for data analysis when any of following occurred: (i) the GenePix Pro did not find the spot area automatically, (ii) the net signal intensity was <= 0, (iii) the percentage of saturated pixels in the spot area was >= 25, and (iv) severe noise was present. We normalized biases in signal intensity between the two fluorescent dye channels in a microarray by locally weighted linear regression analysis (lowess normalization) (Yang et al., Nucleic Acids Res. 30, e15) using MIDAS software (http://www.tigr.org/software/tm4/midas.html). For all normalization, we set the smoothing parameter to 0.33. Keywords = circadian clock Keywords = thermophilic cyanobacteria
19	GSM38214	LL2-Cy3+LL14-Cy5 (expt 2)	5,408	Nagoya University	2004-12-28	[Oligo Array] T. elongatus 2.5k oligoarray (GPL1771)	RNA	Thermosynechococcus elongatus BP-1	peripheral blood	Strain and culture conditions. We grew wild-type T. elongatus (Yamaoka et al., Plant Cell Physiol. 19, 943-954) at 50oC under constant light from white fluorescent lamps at 38 micromol m-2 sec-1 (hereafter called LL conditions) in BG-11 liquid medium (Rippka et al., J. Gen. Microbiol. 111, 1-61) with bubbling of air containing 5% (v/v) CO2. We subjected the cells to 12 h of darkness to synchronize the circadian clock, and transferred them back to LL. We collected cells for RNA isolation at 2 h (LL2) and 14 h (LL14) after the transfer. Microarray experiments. We isolated total RNAs from two independent cultures by the hot-phenol method (Kucho et al., Genes Genet. Syst. 79, 189-197) and purified them using the SV total RNA isolation system (Promega, WI, USA). We used a mixture of the total RNAs from the two cultures for labeling reactions. We synthesized fluorescence-labeled cDNA by direct incorporation of Cy3-dUTP or Cy5-dUTP (Amersham Bioscience, NJ, USA) during random-primed reverse transcription, using 5.9 microgram total RNA and an RNA fluorescence labeling core kit (M-MLV version 2.0, TaKaRa, Japan). We prehybridized the microarray for 1 h at 42oC in a solution containing 5 X SSC (1 X SSC is 0.15 M NaCl, 0.015 M sodium citrate), 0.1% sodium lauryl sulfate (SDS), and 10 mg/ml bovine serum albumin. We washed the microarray at room temperature in distilled water 3 times for 1 min, rinsed it in 2-propanol, and dried it by centrifugation at 150 X g for 2 min. We performed hybridization for 16 h at 42oC in 12-mL solution containing 5 X SSC, 0.1% SDS, 30% formamide, and heat-denatured labeled cDNA. We then washed the microarray at room temperature with 2 X SSC containing 0.1% SDS for 4 min, with 0.1 X SSC containing 0.1% SDS for 4 min, and 3 times with 0.1 X SSC for 1 min. We dried the microarray by centrifugation. We obtained fluorescence images of Cy3 and Cy5 dye channels using a GenePix 4000B scanner (Axon Instruments, CA, USA). Data analysis. We used GenePix Pro 5.0 software (Axon Instruments) to determine the signal intensity of each spot and its local background. We calculated net signal intensity by subtracting the median signal intensity of all pixels within the local background area from the median signal intensity of all pixels within the spot area. We visually confirmed the correct recognition of all spot areas by the automatic alignment function of the GenePix Pro. We flagged spots and did not use them for data analysis when any of following occurred: (i) the GenePix Pro did not find the spot area automatically, (ii) the net signal intensity was <= 0, (iii) the percentage of saturated pixels in the spot area was >= 25, and (iv) severe noise was present. We normalized biases in signal intensity between the two fluorescent dye channels in a microarray by locally weighted linear regression analysis (lowess normalization) (Yang et al., Nucleic Acids Res. 30, e15) using MIDAS software (http://www.tigr.org/software/tm4/midas.html). For all normalization, we set the smoothing parameter to 0.33. Keywords = circadian clock Keywords = thermophilic cyanobacteria
20	GSM38215	LL2-Cy5+LL14-Cy3 (expt 2, dye swap)	5,408	Nagoya University	2004-12-28	[Oligo Array] T. elongatus 2.5k oligoarray (GPL1771)	RNA	Thermosynechococcus elongatus BP-1	peripheral blood	Strain and culture conditions. We grew wild-type T. elongatus (Yamaoka et al., Plant Cell Physiol. 19, 943-954) at 50oC under constant light from white fluorescent lamps at 38 micromol m-2 sec-1 (hereafter called LL conditions) in BG-11 liquid medium (Rippka et al., J. Gen. Microbiol. 111, 1-61) with bubbling of air containing 5% (v/v) CO2. We subjected the cells to 12 h of darkness to synchronize the circadian clock, and transferred them back to LL. We collected cells for RNA isolation at 2 h (LL2) and 14 h (LL14) after the transfer. Microarray experiments. We isolated total RNAs from two independent cultures by the hot-phenol method (Kucho et al., Genes Genet. Syst. 79, 189-197) and purified them using the SV total RNA isolation system (Promega, WI, USA). We used a mixture of the total RNAs from the two cultures for labeling reactions. We synthesized fluorescence-labeled cDNA by direct incorporation of Cy3-dUTP or Cy5-dUTP (Amersham Bioscience, NJ, USA) during random-primed reverse transcription, using 5.9 microgram total RNA and an RNA fluorescence labeling core kit (M-MLV version 2.0, TaKaRa, Japan). We prehybridized the microarray for 1 h at 42oC in a solution containing 5 X SSC (1 X SSC is 0.15 M NaCl, 0.015 M sodium citrate), 0.1% sodium lauryl sulfate (SDS), and 10 mg/ml bovine serum albumin. We washed the microarray at room temperature in distilled water 3 times for 1 min, rinsed it in 2-propanol, and dried it by centrifugation at 150 X g for 2 min. We performed hybridization for 16 h at 42oC in 12-mL solution containing 5 X SSC, 0.1% SDS, 30% formamide, and heat-denatured labeled cDNA. We then washed the microarray at room temperature with 2 X SSC containing 0.1% SDS for 4 min, with 0.1 X SSC containing 0.1% SDS for 4 min, and 3 times with 0.1 X SSC for 1 min. We dried the microarray by centrifugation. We obtained fluorescence images of Cy3 and Cy5 dye channels using a GenePix 4000B scanner (Axon Instruments, CA, USA). Data analysis. We used GenePix Pro 5.0 software (Axon Instruments) to determine the signal intensity of each spot and its local background. We calculated net signal intensity by subtracting the median signal intensity of all pixels within the local background area from the median signal intensity of all pixels within the spot area. We visually confirmed the correct recognition of all spot areas by the automatic alignment function of the GenePix Pro. We flagged spots and did not use them for data analysis when any of following occurred: (i) the GenePix Pro did not find the spot area automatically, (ii) the net signal intensity was <= 0, (iii) the percentage of saturated pixels in the spot area was >= 25, and (iv) severe noise was present. We normalized biases in signal intensity between the two fluorescent dye channels in a microarray by locally weighted linear regression analysis (lowess normalization) (Yang et al., Nucleic Acids Res. 30, e15) using MIDAS software (http://www.tigr.org/software/tm4/midas.html). For all normalization, we set the smoothing parameter to 0.33. Keywords = circadian clock Keywords = thermophilic cyanobacteria

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