Gene Expression Omnibus (GEO) Overview

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.

Bacteria
(39,082)

Viruses
(1,266)

Phages
(101)

Unclassified
(5,242)

All
(898,944)

SAGE NlaIII
(0)

SAGE RsaI
(0)

SAGE Sau3A
(0)

MPSS
(0)

Bead Array
(0)

Protein Array
(0)

Antibody
(0)

All
(39,082)

blood
(706)

adult aerial structure
(0)

young aerial structure
(0)

root
(0)

meristem/growing tissue
(0)

flower/sexual organ
(0)

seed/fruit/grain
(0)

pooled
(217)

unclassified
(36,324)

all
(39,082)

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	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	GSM832329	Yersinia pestis KIM6+ TraSH Microarry Analysis Output (Cy3) vs Input (Cy5) #1	4,829	Stony Brook University	2011-11-13	[Oligo Array] JCVI PFGRC Yersinia pestis 30K v2 array designed primarily based on strain KIM (GPL4199)	genomic	Yersinia pestis	peripheral blood	Yersinia pestis KIM6+ transposon library unselected input Yersinia pestis KIM6+ transposon library output after selection inside macrophage
2	GSM832330	Yersinia pestis KIM6+ TraSH Microarry Analysis Output (Cy3) vs Input (Cy5) #2	4,829	Stony Brook University	2011-11-13	[Oligo Array] JCVI PFGRC Yersinia pestis 30K v2 array designed primarily based on strain KIM (GPL4199)	genomic	Yersinia pestis	peripheral blood	Yersinia pestis KIM6+ transposon library unselected input Yersinia pestis KIM6+ transposon library output after selection inside macrophage
3	GSM832337	Yersinia pestis KIM6+ TraSH Microarry Analysis Output (Cy5) vs Input (Cy3)#1	4,829	Stony Brook University	2011-11-13	[Oligo Array] JCVI PFGRC Yersinia pestis 30K v2 array designed primarily based on strain KIM (GPL4199)	genomic	Yersinia pestis	peripheral blood	Yersinia pestis KIM6+ transposon library output after selection inside macrophage Yersinia pestis KIM6+ transposon library unselected input
4	GSM832338	Yersinia pestis KIM6+ TraSH Microarry Analysis Output (Cy5) vs Input (Cy3)#2	4,829	Stony Brook University	2011-11-13	[Oligo Array] JCVI PFGRC Yersinia pestis 30K v2 array designed primarily based on strain KIM (GPL4199)	genomic	Yersinia pestis	peripheral blood	Yersinia pestis KIM6+ transposon library output after selection inside macrophage Yersinia pestis KIM6+ transposon library unselected input
5	GSM885543	HC1	5,925	University of South Florida	2012-03-04	[Oligo Array] Combimatrix Thiomicrospira crunogena array (GPL15301)	RNA	Thiomicrospira crunogena	peripheral blood	HC1
6	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
7	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
8	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
9	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
10	GSM348486	WH8102_bsy89255d0025_copper-shock_rep4	19,200	Macquarie University	2008-12-08	[Oligo Array] JCVI Synechococcus sp. WH 8102 19K v1.0 (GPL7448)	RNA	Synechococcus sp. WH 8102	lymphnode	CD44r(2)-WH8102 in normal SOW-CuEDTA shock CD43r(2)-WH8102 in normal SOW- Control of CD44r(2)
11	GSM348542	WH8102_bsy89280d0056_copper-shock_rep5	19,200	Macquarie University	2008-12-08	[Oligo Array] JCVI Synechococcus sp. WH 8102 19K v2.0 (GPL7449)	RNA	Synechococcus sp. WH 8102	lymphnode	CD44r(2)-WH8102 in normal SOW-CuEDTA shock CD43r(2)-WH8102 in normal SOW-Control of CD44r(2)
12	GSM348544	WH8102_bsy89280d0057_copper-shock_rep6	19,200	Macquarie University	2008-12-08	[Oligo Array] JCVI Synechococcus sp. WH 8102 19K v2.0 (GPL7449)	RNA	Synechococcus sp. WH 8102	lymphnode	CD43r(2)-WH8102 in normal SOW-Control of CD44r(2) CD44r(2)-WH8102 in normal SOW-CuEDTA shock
13	GSM329374	Early_log_phase_phosphate_stress_bsy89255d0021_rep1	15,156	Macquarie University	2008-10-10	[Oligo Array] JCVI Synechococcus sp. WH 8102 19K v1.0 (GPL7448)	RNA	Synechococcus sp. WH 8102	lymphnode	wild type in 5 micromolar phosphate SOW medium, early log phase CD39r wild type in 87 micromolar phosphate SOW medium, early log phase CD40r
14	GSM329375	Early_log_phase_phosphate_stress_bsy89255d0022_rep4	15,156	Macquarie University	2008-10-10	[Oligo Array] JCVI Synechococcus sp. WH 8102 19K v1.0 (GPL7448)	RNA	Synechococcus sp. WH 8102	lymphnode	wild type in 5 micromolar phosphate SOW medium, early log phase CD43r wild type in 87 micromolar phosphate SOW medium, early log phase CD44r
15	GSM329376	Early_log_phase_phosphate_stress_bsy89280d0048_rep2	15,156	Macquarie University	2008-10-10	[Oligo Array] JCVI Synechococcus sp. WH 8102 19K v2.0 (GPL7449)	RNA	Synechococcus sp. WH 8102	lymphnode	wild type in 5 micromolar phosphate SOW medium, early log phase CD39r wild type in 87 micromolar phosphate SOW medium, early log phase CD40r
16	GSM329378	Early_log_phase_phosphate_stress_bsy89280d0049_rep3	15,156	Macquarie University	2008-10-10	[Oligo Array] JCVI Synechococcus sp. WH 8102 19K v2.0 (GPL7449)	RNA	Synechococcus sp. WH 8102	lymphnode	wild type in 87 micromolar phosphate SOW medium, early log phase CD40r wild type in 5 micromolar phosphate SOW medium, early log phase CD39r
17	GSM329379	Early_log_phase_phosphate_stress_bsy89280d0050_rep5	15,156	Macquarie University	2008-10-10	[Oligo Array] JCVI Synechococcus sp. WH 8102 19K v2.0 (GPL7449)	RNA	Synechococcus sp. WH 8102	lymphnode	wild type in 5 micromolar phosphate SOW medium, early log phase CD43r wild type in 87 micromolar phosphate SOW medium, early log phase CD44r
18	GSM329380	Early_log_phase_phosphate_stress_bsy89280d0051_rep6	15,156	Macquarie University	2008-10-10	[Oligo Array] JCVI Synechococcus sp. WH 8102 19K v2.0 (GPL7449)	RNA	Synechococcus sp. WH 8102	lymphnode	wild type in 87 micromolar phosphate SOW medium, early log phase CD44r wild type in 5 micromolar phosphate SOW medium, early log phase CD43r
19	GSM65501	M145 gDNA vs. 380 gDNA	10,368	Stanford Microarray Database (SMD)	2005-07-25	[cDNA Array] ScoKao_02-08-14 (GPL2619)	genomic	Streptomyces coelicolor	lymphnode	M145 gDNA 380 gDNA
20	GSM26678	wt JRS4 cy3 vs mt JRS550 cy5 early exp (slide1)	10,935	National Institute of Allergy and Infectious Diseases	2004-07-09	[cDNA Array] NIAID Group A Streptococcus (GPL1338)	RNA	Streptococcus pyogenes M1 GAS	peripheral blood	Wild-type (JRS4) and irr mutant (JRS550) Group A Streptococcus (GAS) strains Wild-type (JRS4) and irr mutant (JRS550) Group A Streptococcus (GAS) strains were cultured in Todd-Hewitt broth containing 0.5% yeast extract to early (OD600 0.35) and late (OD600 0.75) exponential phases of growth. Bacteria (2.5 x 109) were lysed with 700 Ã‚Âµl RLT buffer (Qiagen, Valencia, CA) and the lysate was homogenized with an FP120 FastPrep system (Qbiogene Inc., Carlsbad, CA). Total RNA was isolated with RNeasy kits (Qiagen). First-strand cDNA synthesis to incorporate Cy3 and Cy5 labels, and tyramide signal amplification (TSA(tm)), was performed for RNA samples using a Micromax(tm) TSA(tm) Labeling and Detection Kit (Perkin Elmer Life Sciences). cDNA labeled with Cy3 (mutant GAS strain) and Cy5 (wild-type GAS strain) were combined (50 Ã‚Âµl total) and then diluted 1:1 with SlideHyb 3 (Ambion, Austin, TX). Samples were denatured at 95Ã‚ÂºC for 2 min and incubated with a DNA microarray containing 1705 (of 1752) M1 GAS ORFs based on strain SF370, and unique M18 and M3 ORFs. PCR products derived from each ORF were printed onto CMT-GAPS Corning glass slides (Acton, MA) with a Chipwriter robotic arrayer (Bio-Rad, Hercules, CA) in at least quadruplicate. Hybridization of cDNA samples to microarray slides was conducted overnight in a 45Ã‚ÂºC water bath. Slide signal was amplified with TSA (tm) and slides were scanned with a ScanArray 5000 instrument (PE Biosystems, San Diego, CA). Slides were normalized to equal fluorescence intensity against serial dilutions of MGAS8232 genomic DNA standards by adjusting laser power and/or photomultiplier gain. Spot location and array alignment were adjusted with QuantArray (PE Biosystems). To compare gene expression between the wild-type and irr mutant GAS strains, fold-changes for each gene were determined by the ratio of median fluorescence intensity of microarray spots derived from RNA samples of wild-type and irr mutant strains. Analysis of microarrays was done with GENESPRING software, version 4.2 (Silicon Genetics, Redwood City, CA). Microarray experiments were performed in duplicate. Slides 1 and 2 compare mutant and wild-type GAS strains during early exponential growth (OD600 0.35). Slides 3 and 4 compare mutant and wild-type GAS strains during late exponential growth (OD600 0.75). Each microarray slide contained 4Ã¢â‚¬â€œ12 spots per gene for a total of at least 8 spots for each gene. Keywords = Human Keywords = Neutrophils Keywords = Bacterial Keywords = Gene Regulation Keywords = Inflammation

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