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
(74)

all
(78)

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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	GSM37063	glucose1	7,312	University of Wisconsin-Madison	2004-12-03	[GeneChip] [Ecoli_ASv2] Affymetrix E. coli Antisense Genome Array (GPL199)	RNA	Escherichia coli	unclassified	source_name:E. coli cell title:glucose1 description:The study investigated the effect of different carbon sources on E. coli global gene expression. We grew MG1655 cells aerobically in MOPS minimal medium with either glucose, glycerol, succinate, L-alanine, acetate, or L-proline as the carbon supply. Samples were taken from each culture at mid log phase and were RNA-stabilized using Qiagen RNAProtect Bacterial Reagent (Qiagen). Total RNA was then isolated using MasterPure kits (Epicentre Technologies). Purified RNA was reverse-transcribed to cDNA, labeled and hybridized to Affymetrix GeneChipÃƒâ€™ E. coli Antisense Genome Arrays as recommended in the technical manual (www.affymetrix.com). This sample is from glucose-grown cells.
2	GSM37064	glucose2	7,312	University of Wisconsin-Madison	2004-12-03	[GeneChip] [Ecoli_ASv2] Affymetrix E. coli Antisense Genome Array (GPL199)	RNA	Escherichia coli	unclassified	source_name:E. coli cell title:glucose2 description:The study investigated the effect of different carbon sources on E. coli global gene expression. We grew MG1655 cells aerobically in MOPS minimal medium with either glucose, glycerol, succinate, L-alanine, acetate, or L-proline as the carbon supply. Samples were taken from each culture at mid log phase and were RNA-stabilized using Qiagen RNAProtect Bacterial Reagent (Qiagen). Total RNA was then isolated using MasterPure kits (Epicentre Technologies). Purified RNA was reverse-transcribed to cDNA, labeled and hybridized to Affymetrix GeneChipÃƒâ€™ E. coli Antisense Genome Arrays as recommended in the technical manual (www.affymetrix.com). This sample is from glucose-grown cells.
3	GSM37065	glucose3	7,312	University of Wisconsin-Madison	2004-12-03	[GeneChip] [Ecoli_ASv2] Affymetrix E. coli Antisense Genome Array (GPL199)	RNA	Escherichia coli	unclassified	source_name:E. coli cell title:glucose3 description:The study investigated the effect of different carbon sources on E. coli global gene expression. We grew MG1655 cells aerobically in MOPS minimal medium with either glucose, glycerol, succinate, L-alanine, acetate, or L-proline as the carbon supply. Samples were taken from each culture at mid log phase and were RNA-stabilized using Qiagen RNAProtect Bacterial Reagent (Qiagen). Total RNA was then isolated using MasterPure kits (Epicentre Technologies). Purified RNA was reverse-transcribed to cDNA, labeled and hybridized to Affymetrix GeneChipÃƒâ€™ E. coli Antisense Genome Arrays as recommended in the technical manual (www.affymetrix.com). This sample is from glucose-grown cells.
4	GSM37066	glucose4	7,312	University of Wisconsin-Madison	2004-12-03	[GeneChip] [Ecoli_ASv2] Affymetrix E. coli Antisense Genome Array (GPL199)	RNA	Escherichia coli	unclassified	source_name:E. coli cell title:glucose4 description:The study investigated the effect of different carbon sources on E. coli global gene expression. We grew MG1655 cells aerobically in MOPS minimal medium with either glucose, glycerol, succinate, L-alanine, acetate, or L-proline as the carbon supply. Samples were taken from each culture at mid log phase and were RNA-stabilized using Qiagen RNAProtect Bacterial Reagent (Qiagen). Total RNA was then isolated using MasterPure kits (Epicentre Technologies). Purified RNA was reverse-transcribed to cDNA, labeled and hybridized to Affymetrix GeneChipÃƒâ€™ E. coli Antisense Genome Arrays as recommended in the technical manual (www.affymetrix.com). This sample is from glucose-grown cells.
5	GSM37067	glucose5	7,312	University of Wisconsin-Madison	2004-12-03	[GeneChip] [Ecoli_ASv2] Affymetrix E. coli Antisense Genome Array (GPL199)	RNA	Escherichia coli	unclassified	source_name:E. coli cell title:glucose5 description:The study investigated the effect of different carbon sources on E. coli global gene expression. We grew MG1655 cells aerobically in MOPS minimal medium with either glucose, glycerol, succinate, L-alanine, acetate, or L-proline as the carbon supply. Samples were taken from each culture at mid log phase and were RNA-stabilized using Qiagen RNAProtect Bacterial Reagent (Qiagen). Total RNA was then isolated using MasterPure kits (Epicentre Technologies). Purified RNA was reverse-transcribed to cDNA, labeled and hybridized to Affymetrix GeneChipÃƒâ€™ E. coli Antisense Genome Arrays as recommended in the technical manual (www.affymetrix.com). This sample is from glucose-grown cells.
6	GSM37068	glycerol1	7,312	University of Wisconsin-Madison	2004-12-03	[GeneChip] [Ecoli_ASv2] Affymetrix E. coli Antisense Genome Array (GPL199)	RNA	Escherichia coli	unclassified	source_name:E. coli cell title:glycerol1 description:The study investigated the effect of different carbon sources on E. coli global gene expression. We grew MG1655 cells aerobically in MOPS minimal medium with either glucose, glycerol, succinate, L-alanine, acetate, or L-proline as the carbon supply. Samples were taken from each culture at mid log phase and were RNA-stabilized using Qiagen RNAProtect Bacterial Reagent (Qiagen). Total RNA was then isolated using MasterPure kits (Epicentre Technologies). Purified RNA was reverse-transcribed to cDNA, labeled and hybridized to Affymetrix GeneChipÃƒâ€™ E. coli Antisense Genome Arrays as recommended in the technical manual (www.affymetrix.com). This sample is from glycerol-grown cells.
7	GSM37069	glycerol2	7,312	University of Wisconsin-Madison	2004-12-03	[GeneChip] [Ecoli_ASv2] Affymetrix E. coli Antisense Genome Array (GPL199)	RNA	Escherichia coli	unclassified	source_name:E. coli cell title:glycerol2 description:The study investigated the effect of different carbon sources on E. coli global gene expression. We grew MG1655 cells aerobically in MOPS minimal medium with either glucose, glycerol, succinate, L-alanine, acetate, or L-proline as the carbon supply. Samples were taken from each culture at mid log phase and were RNA-stabilized using Qiagen RNAProtect Bacterial Reagent (Qiagen). Total RNA was then isolated using MasterPure kits (Epicentre Technologies). Purified RNA was reverse-transcribed to cDNA, labeled and hybridized to Affymetrix GeneChipÃƒâ€™ E. coli Antisense Genome Arrays as recommended in the technical manual (www.affymetrix.com). This sample is from glycerol-grown cells.
8	GSM37070	succinate1	7,312	University of Wisconsin-Madison	2004-12-03	[GeneChip] [Ecoli_ASv2] Affymetrix E. coli Antisense Genome Array (GPL199)	RNA	Escherichia coli	unclassified	source_name:E. coli cell title:succinate1 description:The study investigated the effect of different carbon sources on E. coli global gene expression. We grew MG1655 cells aerobically in MOPS minimal medium with either glucose, glycerol, succinate, L-alanine, acetate, or L-proline as the carbon supply. Samples were taken from each culture at mid log phase and were RNA-stabilized using Qiagen RNAProtect Bacterial Reagent (Qiagen). Total RNA was then isolated using MasterPure kits (Epicentre Technologies). Purified RNA was reverse-transcribed to cDNA, labeled and hybridized to Affymetrix GeneChipÃƒâ€™ E. coli Antisense Genome Arrays as recommended in the technical manual (www.affymetrix.com). This sample is from succinate-grown cells.
9	GSM37071	succinate2	7,312	University of Wisconsin-Madison	2004-12-03	[GeneChip] [Ecoli_ASv2] Affymetrix E. coli Antisense Genome Array (GPL199)	RNA	Escherichia coli	unclassified	source_name:E. coli cell title:succinate2 description:The study investigated the effect of different carbon sources on E. coli global gene expression. We grew MG1655 cells aerobically in MOPS minimal medium with either glucose, glycerol, succinate, L-alanine, acetate, or L-proline as the carbon supply. Samples were taken from each culture at mid log phase and were RNA-stabilized using Qiagen RNAProtect Bacterial Reagent (Qiagen). Total RNA was then isolated using MasterPure kits (Epicentre Technologies). Purified RNA was reverse-transcribed to cDNA, labeled and hybridized to Affymetrix GeneChipÃƒâ€™ E. coli Antisense Genome Arrays as recommended in the technical manual (www.affymetrix.com). This sample is from succinate-grown cells.
10	GSM37072	alanine1	7,312	University of Wisconsin-Madison	2004-12-03	[GeneChip] [Ecoli_ASv2] Affymetrix E. coli Antisense Genome Array (GPL199)	RNA	Escherichia coli	unclassified	source_name:E. coli cell title:alanine1 description:The study investigated the effect of different carbon sources on E. coli global gene expression. We grew MG1655 cells aerobically in MOPS minimal medium with either glucose, glycerol, succinate, L-alanine, acetate, or L-proline as the carbon supply. Samples were taken from each culture at mid log phase and were RNA-stabilized using Qiagen RNAProtect Bacterial Reagent (Qiagen). Total RNA was then isolated using MasterPure kits (Epicentre Technologies). Purified RNA was reverse-transcribed to cDNA, labeled and hybridized to Affymetrix GeneChipÃƒâ€™ E. coli Antisense Genome Arrays as recommended in the technical manual (www.affymetrix.com). This sample is from alanine-grown cells.
11	GSM37073	alanine2	7,312	University of Wisconsin-Madison	2004-12-03	[GeneChip] [Ecoli_ASv2] Affymetrix E. coli Antisense Genome Array (GPL199)	RNA	Escherichia coli	unclassified	source_name:E. coli cell title:alanine2 description:The study investigated the effect of different carbon sources on E. coli global gene expression. We grew MG1655 cells aerobically in MOPS minimal medium with either glucose, glycerol, succinate, L-alanine, acetate, or L-proline as the carbon supply. Samples were taken from each culture at mid log phase and were RNA-stabilized using Qiagen RNAProtect Bacterial Reagent (Qiagen). Total RNA was then isolated using MasterPure kits (Epicentre Technologies). Purified RNA was reverse-transcribed to cDNA, labeled and hybridized to Affymetrix GeneChipÃƒâ€™ E. coli Antisense Genome Arrays as recommended in the technical manual (www.affymetrix.com). This sample is from alanine-grown cells.
12	GSM37074	acetate1	7,312	University of Wisconsin-Madison	2004-12-03	[GeneChip] [Ecoli_ASv2] Affymetrix E. coli Antisense Genome Array (GPL199)	RNA	Escherichia coli	unclassified	source_name:E. coli cell title:acetate1 description:The study investigated the effect of different carbon sources on E. coli global gene expression. We grew MG1655 cells aerobically in MOPS minimal medium with either glucose, glycerol, succinate, L-alanine, acetate, or L-proline as the carbon supply. Samples were taken from each culture at mid log phase and were RNA-stabilized using Qiagen RNAProtect Bacterial Reagent (Qiagen). Total RNA was then isolated using MasterPure kits (Epicentre Technologies). Purified RNA was reverse-transcribed to cDNA, labeled and hybridized to Affymetrix GeneChipÃƒâ€™ E. coli Antisense Genome Arrays as recommended in the technical manual (www.affymetrix.com). This sample is from acetate-grown cells.
13	GSM37075	acetate2	7,312	University of Wisconsin-Madison	2004-12-03	[GeneChip] [Ecoli_ASv2] Affymetrix E. coli Antisense Genome Array (GPL199)	RNA	Escherichia coli	unclassified	source_name:E. coli cell title:acetate2 description:The study investigated the effect of different carbon sources on E. coli global gene expression. We grew MG1655 cells aerobically in MOPS minimal medium with either glucose, glycerol, succinate, L-alanine, acetate, or L-proline as the carbon supply. Samples were taken from each culture at mid log phase and were RNA-stabilized using Qiagen RNAProtect Bacterial Reagent (Qiagen). Total RNA was then isolated using MasterPure kits (Epicentre Technologies). Purified RNA was reverse-transcribed to cDNA, labeled and hybridized to Affymetrix GeneChipÃƒâ€™ E. coli Antisense Genome Arrays as recommended in the technical manual (www.affymetrix.com). This sample is from acetate-grown cells.
14	GSM37076	proline1	7,312	University of Wisconsin-Madison	2004-12-03	[GeneChip] [Ecoli_ASv2] Affymetrix E. coli Antisense Genome Array (GPL199)	RNA	Escherichia coli	unclassified	source_name:E. coli cell title:proline1 description:The study investigated the effect of different carbon sources on E. coli global gene expression. We grew MG1655 cells aerobically in MOPS minimal medium with either glucose, glycerol, succinate, L-alanine, acetate, or L-proline as the carbon supply. Samples were taken from each culture at mid log phase and were RNA-stabilized using Qiagen RNAProtect Bacterial Reagent (Qiagen). Total RNA was then isolated using MasterPure kits (Epicentre Technologies). Purified RNA was reverse-transcribed to cDNA, labeled and hybridized to Affymetrix GeneChipÃƒâ€™ E. coli Antisense Genome Arrays as recommended in the technical manual (www.affymetrix.com). This sample is from proline-grown cells.
15	GSM37077	proline2	7,312	University of Wisconsin-Madison	2004-12-03	[GeneChip] [Ecoli_ASv2] Affymetrix E. coli Antisense Genome Array (GPL199)	RNA	Escherichia coli	unclassified	source_name:E. coli cell title:proline2 description:The study investigated the effect of different carbon sources on E. coli global gene expression. We grew MG1655 cells aerobically in MOPS minimal medium with either glucose, glycerol, succinate, L-alanine, acetate, or L-proline as the carbon supply. Samples were taken from each culture at mid log phase and were RNA-stabilized using Qiagen RNAProtect Bacterial Reagent (Qiagen). Total RNA was then isolated using MasterPure kits (Epicentre Technologies). Purified RNA was reverse-transcribed to cDNA, labeled and hybridized to Affymetrix GeneChipÃƒâ€™ E. coli Antisense Genome Arrays as recommended in the technical manual (www.affymetrix.com). This sample is from proline-grown cells.
16	GSM37885	Aerobic GSNO Chemostat Run 1	4,608	University of Sheffield	2004-12-21	[Oligo Array] MWG E. coli K12 Array (GPL534)	RNA	Escherichia coli	unclassified	source_name:Steady-state continuous cultured control samples in absence of GSNO Steady-state continuous cultured experiment samples in presence of 200uM GSNO for 5 minutes title:Aerobic GSNO Chemostat Run 1 description:Escherichia coli strain MG1655 was grown in a New Brunswick Scientific Bioflow III Biofermentor under continuous culture (chemostat) conditions. Cells were grown in defined media containing 54 mM glycerol as the sole and limiting source of energy and carbon. The working volume was 1 litre, and the dilution rate 0.2 h-1. For aerobic growth, the air-flow rate was 1 l/min, and the dissolved oxygen tension was maintained at 40% air saturation by measuring oxygen dissolved in the culture using a Broadley James D140 OxyProbeÃ‚Â® electrode and automated adjustment of stirring rate. Cells were grown as above to steady-state, At steady-state, GSNO was added to the chemostat culture and to the nutrient feed at a final concentration of 200 uM unless otherwise stated. Samples were taken immediately prior to the addition of GSNO and after a period of 5 min exposure to GSNO for subsequent analysis using microarrays. Cells were harvested directly into RNA Protect (Qiagen) to stabilize RNA, and total RNA was purified using QiagenÃ¢â‚¬â„¢s RNeasy Mini kit as recommended by the suppliers.
17	GSM37886	Aerobic GSNO Chemostat Run 2	4,608	University of Sheffield	2004-12-21	[Oligo Array] MWG E. coli K12 Array (GPL534)	RNA	Escherichia coli	unclassified	source_name:Steady-state continuous cultured experiment samples in presence of 200uM GSNO for 5 minutes Steady-state continuous cultured control samples in absence of GSNO title:Aerobic GSNO Chemostat Run 2 description:Escherichia coli strain MG1655 was grown in a New Brunswick Scientific Bioflow III Biofermentor under continuous culture (chemostat) conditions. Cells were grown in defined media containing 54 mM glycerol as the sole and limiting source of energy and carbon. The working volume was 1 litre, and the dilution rate 0.2 h-1. For aerobic growth, the air-flow rate was 1 l/min, and the dissolved oxygen tension was maintained at 40% air saturation by measuring oxygen dissolved in the culture using a Broadley James D140 OxyProbeÃ‚Â® electrode and automated adjustment of stirring rate. Cells were grown as above to steady-state, At steady-state, GSNO was added to the chemostat culture and to the nutrient feed at a final concentration of 200 uM unless otherwise stated. Samples were taken immediately prior to the addition of GSNO and after a period of 5 min exposure to GSNO for subsequent analysis using microarrays. Cells were harvested directly into RNA Protect (Qiagen) to stabilize RNA, and total RNA was purified using QiagenÃ¢â‚¬â„¢s RNeasy Mini kit as recommended by the suppliers.
18	GSM37887	Aerobic GSNO Chemostat 2 Run 1	4,608	University of Sheffield	2004-12-21	[Oligo Array] MWG E. coli K12 Array (GPL534)	RNA	Escherichia coli	unclassified	source_name:Steady-state continuous cultured control samples in absence of GSNO Steady-state continuous cultured experiment samples in presence of 200uM GSNO for 5 minutes title:Aerobic GSNO Chemostat 2 Run 1 description:Escherichia coli strain MG1655 was grown in a New Brunswick Scientific Bioflow III Biofermentor under continuous culture (chemostat) conditions. Cells were grown in defined media containing 54 mM glycerol as the sole and limiting source of energy and carbon. The working volume was 1 litre, and the dilution rate 0.2 h-1. For aerobic growth, the air-flow rate was 1 l/min, and the dissolved oxygen tension was maintained at 40% air saturation by measuring oxygen dissolved in the culture using a Broadley James D140 OxyProbeÃ‚Â® electrode and automated adjustment of stirring rate. Cells were grown as above to steady-state, At steady-state, GSNO was added to the chemostat culture and to the nutrient feed at a final concentration of 200 uM unless otherwise stated. Samples were taken immediately prior to the addition of GSNO and after a period of 5 min exposure to GSNO for subsequent analysis using microarrays. Cells were harvested directly into RNA Protect (Qiagen) to stabilize RNA, and total RNA was purified using QiagenÃ¢â‚¬â„¢s RNeasy Mini kit as recommended by the suppliers.
19	GSM37888	Aerobic GSNO Chemostat 2 Run 2	4,608	University of Sheffield	2004-12-21	[Oligo Array] MWG E. coli K12 Array (GPL534)	RNA	Escherichia coli	unclassified	source_name:Steady-state continuous cultured experiment samples in presence of 200uM GSNO for 5 minutes Steady-state continuous cultured control samples in absence of GSNO title:Aerobic GSNO Chemostat 2 Run 2 description:Escherichia coli strain MG1655 was grown in a New Brunswick Scientific Bioflow III Biofermentor under continuous culture (chemostat) conditions. Cells were grown in defined media containing 54 mM glycerol as the sole and limiting source of energy and carbon. The working volume was 1 litre, and the dilution rate 0.2 h-1. For aerobic growth, the air-flow rate was 1 l/min, and the dissolved oxygen tension was maintained at 40% air saturation by measuring oxygen dissolved in the culture using a Broadley James D140 OxyProbeÃ‚Â® electrode and automated adjustment of stirring rate. Cells were grown as above to steady-state, At steady-state, GSNO was added to the chemostat culture and to the nutrient feed at a final concentration of 200 uM unless otherwise stated. Samples were taken immediately prior to the addition of GSNO and after a period of 5 min exposure to GSNO for subsequent analysis using microarrays. Cells were harvested directly into RNA Protect (Qiagen) to stabilize RNA, and total RNA was purified using QiagenÃ¢â‚¬â„¢s RNeasy Mini kit as recommended by the suppliers.
20	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.

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