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
(1,690)

Viruses
(78)

Phages
(8)

Unclassified
(430)

All
(11,831)

SAGE NlaIII
(0)

SAGE RsaI
(0)

SAGE Sau3A
(0)

MPSS
(0)

GeneChip
(91)

Tiling Array
(51)

cDNA Array
(284)

Oligo Array
(1,084)

Bead Array
(0)

Protein Array
(0)

Antibody
(0)

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	Platform ID	Title	Number of the probes	Institute	Submission date	Manufacturer	Species	Platform class	Reasoning of the classification Keywords used for the classification are shown with bold font.
1	GPL9192	Nimblegen/NCSU Zymomonas mobilis array	5,850	Science Apps, L3C	2009-09-14	Nimblegen	Zymomonas mobilis	cDNA Array	spotted DNA/cDNA, Nimblegen/NCSU Zymomonas mobilis array,
2	GPL11443	Yersinia pestis cDNA microarray	8,010	Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China	2011-01-12	Beijing Institute of Microbiology and Epidemiology, Beijing, China	Yersinia pestis	cDNA Array	spotted DNA/cDNA, Yersinia pestis cDNA microarray,
3	GPL5937	AMMS_PBS_Y. pestis 201	4,005	Institute of Microbiology and Epidemiology	2007-09-27	State Key laboratory of Pathogen and Biosecurity, Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences	Yersinia pestis	cDNA Array	spotted DNA/cDNA, AMMS_PBS_Y. pestis 201,
4	GPL793	CAGE-Xylella USP - v.1	9,216	Institute for Systems Biology	2003-12-22		Xylella fastidiosa	cDNA Array	spotted DNA/cDNA, CAGE-Xylella USP - v.1, DNA Microarray Construction. PCR primers were designed to amplify unique internal fragments of 200-1000 bp of each predicted CDS described in the annotated genome sequence of X. fastidiosa strain 9a5c (http://aeg.lbi.ic.unicamp.br/xf). Primers (18-23mers) with equivalent predicted melting temperature were designed with the use of a perl program that ran PRIMER3 (http://www-genome.wi.mit.edu/genome_software/other/primer3.html) for the complete CDS list, automatically testing many parameter settings and also guaranteeing that primers hybridized only to a single genome location. Oligonucleotides were synthesized by MWG and Operon Technologies. Genomic or cosmid DNA, obtained in the X. fastidiosa genome sequencing project (Simpson et al. 2000), were used as template in the first round of PCR amplification, and 200-fold-diluted PCR products were used as templates for PCR reamplification to increase product concentration when necessary. The reactions were done in 96-well plates. The mixture in each well contained 100 ng of DNA, 0.5 U of Biolase Taq polymerase (Bioline), 0.2 mM of each dNTP (Invitrogen), 1.5 mM MgCl2 and the primers at 0.5 uM, in a total volume of 100 ul. A 5min denaturing step at 95oC was applied, followed by 40 cycles of 95oC for 45s, 50oC for 30s, 72oC for 1min and a final step at 72oC for 10min. 4 ul of each PCR reaction were checked for product size and concentration by electrophoresis in 1.2% agarose gels. The amplicons were then purified with 96-well MultiScreen purification plates (Millipore) and an equal volume of dimethyl sulfoxide was added to the purified products (~100 ng/ul final concentration). Generation III DNA spotter (Amersham Biosciences) was used to array the samples onto coated type-7 glass slides (Amersham Biosciences). After deposition, the probes were crosslinked to the slides by applying 50 mJ of UV light and the slides were stored desiccated at ~10% relative humidity at room temperature until use. Keywords = xylella fastidiosa Keywords = genomotyping Keywords = DNA microarray Keywords = comparative genomics
5	GPL794	CAGE-Xylella USP - v.2	9,216	Institute for Systems Biology	2003-12-22		Xylella fastidiosa	cDNA Array	spotted DNA/cDNA, CAGE-Xylella USP - v.2, DNA Microarray Construction. PCR primers were designed to amplify unique internal fragments of 200-1000 bp of each predicted CDS described in the annotated genome sequence of X. fastidiosa strain 9a5c (http://aeg.lbi.ic.unicamp.br/xf). Primers (18-23mers) with equivalent predicted melting temperature were designed with the use of a perl program that ran PRIMER3 (http://www-genome.wi.mit.edu/genome_software/other/primer3.html) for the complete CDS list, automatically testing many parameter settings and also guaranteeing that primers hybridized only to a single genome location. Oligonucleotides were synthesized by MWG and Operon Technologies. Genomic or cosmid DNA, obtained in the X. fastidiosa genome sequencing project (Simpson et al. 2000), were used as template in the first round of PCR amplification, and 200-fold-diluted PCR products were used as templates for PCR reamplification to increase product concentration when necessary. The reactions were done in 96-well plates. The mixture in each well contained 100 ng of DNA, 0.5 U of Biolase Taq polymerase (Bioline), 0.2 mM of each dNTP (Invitrogen), 1.5 mM MgCl2 and the primers at 0.5 uM, in a total volume of 100 ul. A 5min denaturing step at 95oC was applied, followed by 40 cycles of 95oC for 45s, 50oC for 30s, 72oC for 1min and a final step at 72oC for 10min. 4 ul of each PCR reaction were checked for product size and concentration by electrophoresis in 1.2% agarose gels. The amplicons were then purified with 96-well MultiScreen purification plates (Millipore) and an equal volume of dimethyl sulfoxide was added to the purified products (~100 ng/ul final concentration). Generation III DNA spotter (Amersham Biosciences) was used to array the samples onto coated type-7 glass slides (Amersham Biosciences). After deposition, the probes were crosslinked to the slides by applying 50 mJ of UV light and the slides were stored desiccated at ~10% relative humidity at room temperature until use. Keywords = xylella fastidiosa Keywords = genomotyping Keywords = DNA microarray Keywords = comparative genomics
6	GPL2708	Xylella USP microarray v2 (Koide et al. 2004 J.Bact.)	4,608	Universidade de SÃƒÂ£o Paulo	2005-07-31	Instituto de QuÃƒÂmica da Universidade de SÃƒÂ£o Paulo (IQ-USP)	Xylella fastidiosa	cDNA Array	spotted DNA/cDNA, Xylella USP microarray v2 (Koide et al. 2004 J.Bact.),
7	GPL3409	Xylella USP microarray v1 (Koide et al. 2004 J.Bact.)	4,608	Universidade de SÃƒÂ£o Paulo	2006-02-01	Instituto de QuÃƒÂmica da Universidade de SÃƒÂ£o Paulo (IQ-USP)	Xylella fastidiosa	cDNA Array	spotted DNA/cDNA, Xylella USP microarray v1 (Koide et al. 2004 J.Bact.),
8	GPL9024	IQ-USP Xylella fastidiosa 9.2K v2.0.	4,608	Universidade de SÃƒÂ£o Paulo	2009-08-12	IQ-USP microarray facility	Xylella fastidiosa	cDNA Array	spotted DNA/cDNA, IQ-USP Xylella fastidiosa 9.2K v2.0.,
9	GPL4683	Xylella fastidiosa 9a5c Biochip v.2.0	2,688	UFABC - Universidade Federal do ABC	2006-12-19	LaboratÃƒÂ³rio de GenÃƒÂ´mica Estrutural e Funcional - NÃƒÂºcleo Integrado de Biotecnologia - Universidade de Mogi das Cruzes	Xylella fastidiosa	cDNA Array	spotted DNA/cDNA, Xylella fastidiosa 9a5c Biochip v.2.0, Xylella fastidiosa, isolate 9a5c
10	GPL7554	UNESP Xylella fastidiosa array version 1	493	Max-Delbruck Center for Molecular Medicine	2008-11-04	Sao Paulo State University (UNESP) Jaboticabal Campus. Laboratory of Biochemistry of microorganisms and plants (LBMP).	Xylella fastidiosa	cDNA Array	spotted DNA/cDNA, UNESP Xylella fastidiosa array version 1,
11	GPL14720	CapitalBio 4.3K Xcc cDNA array	14,112	institute of microbiology, Chinese academy of sciences	2011-10-12	CapitalBio	Xanthomonas campestris pv. campestris	cDNA Array	spotted DNA/cDNA, CapitalBio 4.3K Xcc cDNA array,
12	GPL3842	XCC 4.3K cDNA array	12,768	CapitalBio Corporation	2006-06-06	CapitalBio	Xanthomonas campestris pv. campestris	cDNA Array	spotted DNA/cDNA, XCC 4.3K cDNA array,
13	GPL7730	Wolbachia pipientis wMel microarray	9,540	Univeristy of Maryland Baltimore	2008-12-03	TIGR	Wolbachia pipientis	cDNA Array	spotted DNA/cDNA, Wolbachia pipientis wMel microarray,
14	GPL1904	VV1_0_1	160	Sogang University	2005-03-14		Vibrio vulnificus	cDNA Array	spotted DNA/cDNA, VV1_0_1, The PCR products were purified using Qiagen PCR purification kit, and printed on Corning GAPS II coated slide in quadriplicate using a DNA arrayer, Affimatrix 427. This set includes 160 genes, DNA fragment spanning about a 700-bp region of the 3Ã‚Â¡Ãƒâ€¡end portion of each gene was prepared by PCR using primers specific to DNA nucleotide sequence of each gene designed based on the genome sequences of V. vulnificus in the GenBank (Accession numbers NC_004459 and NC_004460) Keywords = Vibrio vulnificus, cyclic dipeptide
15	GPL6058	Vibrio parahaemolyticus RIMD2210633 5k microarray	4,866	Osaka University	2007-10-29	Molecular Gene Technics, Department of Genetic Resources Technology, Faculty of Agriculture, Kyushu University, Fukuoka, Japan.	Vibrio parahaemolyticus RIMD 2210633	cDNA Array	spotted DNA/cDNA, Vibrio parahaemolyticus RIMD2210633 5k microarray,
16	GPL8691	Beijing Institute of Microbiology and Epidemiology Vibrio parahaemolyticus 4.7K	4,769	Institute of Microbiology and Epidemiology	2009-06-09	Beijing Institute of Microbiology and Epidemiology	Vibrio parahaemolyticus	cDNA Array	spotted DNA/cDNA, Beijing Institute of Microbiology and Epidemiology Vibrio parahaemolyticus 4.7K,
17	GPL2742	VCholerae_A	5,760	Stanford Microarray Database (SMD)	2005-08-10	Tina,,Boussard; School of Medicine, Department of Genetics, Stanford, CA, United States, 94305; 650-736-0077; boussard@genome.stanford.edu	Vibrio cholerae	cDNA Array	spotted DNA/cDNA, VCholerae_A,
18	GPL8044	SMD Vibrio cholerae Print_356	5,760	Stanford Microarray Database (SMD)	2009-01-09	Stanford Functional Genomics Facility, Stanford School of Medicine	Vibrio cholerae	cDNA Array	spotted DNA/cDNA, SMD Vibrio cholerae Print_356,
19	GPL3052	VC-oligos	4,224	Stanford University	2005-11-07	Stanford, CA	Vibrio cholerae	cDNA Array	spotted DNA/cDNA, VC-oligos,
20	GPL5747	VC-oligos	4,224	Stanford Microarray Database (SMD)	2007-08-15	Stanford	Vibrio cholerae	cDNA Array	spotted DNA/cDNA, VC-oligos,

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