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	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.
2	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.
3	GSM35285	Spanish soil sample S5, replicate 2	1,200	University of British Columbia	2004-11-13	[Oligo Array] SARST microarray (GPL1705)	genomic	Bacteria	unclassified	source_name:Soil sample from Portugalete title:Spanish soil sample S5, replicate 2 description:Comparison of hexachlorocyclohexane (HCH) contaminated soils from Spain with a community-specific microarray. Location Portugalete Depth 10 alpha-HCH (ppm) 4.36 Total HCH (ppm) 8.95 Heterotrophic counts 9.20E+06 Fungal counts 2.20E+04 pH 8.4 Organic matter 3.27
4	GSM35280	Spanish soil sample S5, replicate 1	1,200	University of British Columbia	2004-11-13	[Oligo Array] SARST microarray (GPL1705)	genomic	Bacteria	unclassified	source_name:Soil sample from Portugalete title:Spanish soil sample S5, replicate 1 description:Comparison of hexachlorocyclohexane (HCH) contaminated soils from Spain with a community-specific microarray. Location Portugalete Depth 10 alpha-HCH (ppm) 4.36 Total HCH (ppm) 8.95 Heterotrophic counts 9.20E+06 Fungal counts 2.20E+04 pH 8.4 Organic matter 3.27
5	GSM35279	Spanish soil sample S4, replicate 2	1,200	University of British Columbia	2004-11-13	[Oligo Array] SARST microarray (GPL1705)	genomic	Bacteria	unclassified	source_name:Soil sample from Ansio title:Spanish soil sample S4, replicate 2 description:Comparison of hexachlorocyclohexane (HCH) contaminated soils from Spain with a community-specific microarray. Location Ansio Depth 100 alpha-HCH (ppm) 3580 Total HCH (ppm) 3750 Heterotrophic counts 5.14E+05 Fungal counts 3.51E+03 pH 5.9 Organic matter 3.96
6	GSM35278	Spanish soil sample S4, replicate 1	1,200	University of British Columbia	2004-11-13	[Oligo Array] SARST microarray (GPL1705)	genomic	Bacteria	unclassified	source_name:Soil sample from Ansio title:Spanish soil sample S4, replicate 1 description:Comparison of hexachlorocyclohexane (HCH) contaminated soils from Spain with a community-specific microarray. Location Ansio Depth 100 alpha-HCH (ppm) 3580 Total HCH (ppm) 3750 Heterotrophic counts 5.14E+05 Fungal counts 3.51E+03 pH 5.9 Organic matter 3.96
7	GSM35277	Spanish soil sample S16, replicate 2	1,200	University of British Columbia	2004-11-13	[Oligo Array] SARST microarray (GPL1705)	genomic	Bacteria	unclassified	source_name:Soil sample from Artxanda title:Spanish soil sample S16, replicate 2 description:Comparison of hexachlorocyclohexane (HCH) contaminated soils from Spain with a community-specific microarray. Location Artxanda Depth 10 alpha-HCH (ppm) 17.7 Total HCH (ppm) 53.3 Heterotrophic counts 4.30E+06 Fungal counts 1.05E+04 pH 7.2 Organic matter 31.9
8	GSM35276	Spanish soil sample S16, replicate 1	1,200	University of British Columbia	2004-11-13	[Oligo Array] SARST microarray (GPL1705)	genomic	Bacteria	unclassified	source_name:Soil sample from Artxanda title:Spanish soil sample S16, replicate 1 description:Comparison of hexachlorocyclohexane (HCH) contaminated soils from Spain with a community-specific microarray. Location Artxanda Depth 10 alpha-HCH (ppm) 17.7 Total HCH (ppm) 53.3 Heterotrophic counts 4.30E+06 Fungal counts 1.05E+04 pH 7.2 Organic matter 31.9
9	GSM35275	Spanish soil sample S15, replicate 2	1,200	University of British Columbia	2004-11-13	[Oligo Array] SARST microarray (GPL1705)	genomic	Bacteria	unclassified	source_name:Soil sample from Artxanda title:Spanish soil sample S15, replicate 2 description:Comparison of hexachlorocyclohexane (HCH) contaminated soils from Spain with a community-specific microarray. Location Artxanda Depth 10 alpha-HCH (ppm) 1900 Total HCH (ppm) 21800 Heterotrophic counts 6.61E+06 Fungal counts 4.63E+04 pH 4.4 Organic matter 18.6
10	GSM35274	Spanish soil sample S15, replicate 1	1,200	University of British Columbia	2004-11-13	[Oligo Array] SARST microarray (GPL1705)	genomic	Bacteria	unclassified	source_name:Soil sample from Artxanda title:Spanish soil sample S15, replicate 1 description:Comparison of hexachlorocyclohexane (HCH) contaminated soils from Spain with a community-specific microarray. Location Artxanda Depth 10 alpha-HCH (ppm) 1900 Total HCH (ppm) 21800 Heterotrophic counts 6.61E+06 Fungal counts 4.63E+04 pH 4.4 Organic matter 18.6
11	GSM35273	Spanish soil sample S14, replicate 2	1,200	University of British Columbia	2004-11-13	[Oligo Array] SARST microarray (GPL1705)	genomic	Bacteria	unclassified	source_name:Soil sample from Artxanda title:Spanish soil sample S14, replicate 2 description:Comparison of hexachlorocyclohexane (HCH) contaminated soils from Spain with a community-specific microarray. Location Artxanda Depth 10 alpha-HCH (ppm) 1270 Total HCH (ppm) 13500 Heterotrophic counts 5.43E+05 Fungal counts 4.18E+04 pH 3.6 Organic matter 96.4
12	GSM35272	Spanish soil sample S14, replicate 1	1,200	University of British Columbia	2004-11-13	[Oligo Array] SARST microarray (GPL1705)	genomic	Bacteria	unclassified	source_name:Soil sample from Artxanda title:Spanish soil sample S14, replicate 1 description:Comparison of hexachlorocyclohexane (HCH) contaminated soils from Spain with a community-specific microarray. Location Artxanda Depth 10 alpha-HCH (ppm) 1270 Total HCH (ppm) 13500 Heterotrophic counts 5.43E+05 Fungal counts 4.18E+04 pH 3.6 Organic matter 96.4
13	GSM35271	Spanish soil sample S12, replicate 2	1,200	University of British Columbia	2004-11-13	[Oligo Array] SARST microarray (GPL1705)	genomic	Bacteria	unclassified	source_name:Soil sample from Artxanda title:Spanish soil sample S12, replicate 2 description:Comparison of hexachlorocyclohexane (HCH) contaminated soils from Spain with a community-specific microarray. Location Artxanda Depth 8 alpha-HCH (ppm) 0.17 Total HCH (ppm) 0.4 Heterotrophic counts 4.01E+06 Fungal counts 6.41E+03 pH 7.6 Organic matter 31.8
14	GSM35270	Spanish soil sample S12, replicate 1	1,200	University of British Columbia	2004-11-13	[Oligo Array] SARST microarray (GPL1705)	genomic	Bacteria	unclassified	source_name:Soil sample from Artxanda title:Spanish soil sample S12, replicate 1 description:Comparison of hexachlorocyclohexane (HCH) contaminated soils from Spain with a community-specific microarray. Location Artxanda Depth 8 alpha-HCH (ppm) 0.17 Total HCH (ppm) 0.4 Heterotrophic counts 4.01E+06 Fungal counts 6.41E+03 pH 7.6 Organic matter 31.8
15	GSM35269	Spanish soil sample S11, replicate 2	1,200	University of British Columbia	2004-11-13	[Oligo Array] SARST microarray (GPL1705)	genomic	Bacteria	unclassified	source_name:Soil sample from Artxanda title:Spanish soil sample S11, replicate 2 description:Comparison of hexachlorocyclohexane (HCH) contaminated soils from Spain with a community-specific microarray. Location Artxanda Depth 10 alpha-HCH (ppm) 0 Total HCH (ppm) 0.01 Heterotrophic counts 1.07E+07 Fungal counts 9.31E+03 pH 8.1 Organic matter 9.1
16	GSM35268	Spanish soil sample S11, replicate 1	1,200	University of British Columbia	2004-11-13	[Oligo Array] SARST microarray (GPL1705)	genomic	Bacteria	unclassified	source_name:Soil sample from Artxanda title:Spanish soil sample S11, replicate 1 description:Comparison of hexachlorocyclohexane (HCH) contaminated soils from Spain with a community-specific microarray. Location Artxanda Depth 10 alpha-HCH (ppm) 0 Total HCH (ppm) 0.01 Heterotrophic counts 1.07E+07 Fungal counts 9.31E+03 pH 8.1 Organic matter 9.1
17	GSM35267	Spanish soil sample S10, replicate 2	1,200	University of British Columbia	2004-11-13	[Oligo Array] SARST microarray (GPL1705)	genomic	Bacteria	unclassified	source_name:Soil sample from Artxanda title:Spanish soil sample S10, replicate 2 description:Comparison of hexachlorocyclohexane (HCH) contaminated soils from Spain with a community-specific microarray. Location Artxanda Depth 15 alpha-HCH (ppm) 0 Total HCH (ppm) 0.03 Heterotrophic counts 2.17E+06 Fungal counts 7.43E+03 pH 5.4 Organic matter 21.2
18	GSM35266	Spanish soil sample S10, replicate 1	1,200	University of British Columbia	2004-11-13	[Oligo Array] SARST microarray (GPL1705)	genomic	Bacteria	unclassified	source_name:Soil sample from Artxanda title:Spanish soil sample S10, replicate 1 description:Comparison of hexachlorocyclohexane (HCH) contaminated soils from Spain with a community-specific microarray. Location Artxanda Depth 15 alpha-HCH (ppm) 0 Total HCH (ppm) 0.03 Heterotrophic counts 2.17E+06 Fungal counts 7.43E+03 pH 5.4 Organic matter 21.2
19	GSM35164	Spanish soil composite	973	University of British Columbia	2004-11-11	[Other] SARST:Bacteria (GPL919)	SARST	Bacteria	unclassified	source_name:Soils from the Basque region of Spain differing in HCH contamination title:Spanish soil composite description:Ribosomal sequence tag (RST) data from a composite soil sample from hexachlorocyclohexane (HCH) contaminated and uncontaminated soils. Sites include Artxanda, Portugalete, and Ansio. Predominant RST sequences used to design oligonucleotide probes for microarray application.
20	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.

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