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
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Plants
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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	GPL3618	Maize CornChip0 8.5K GeneChip	8,475	Iowa State University	2006-04-03	Affymetrix	Zea mays	GeneChip	in situ oligonucleotide, Maize CornChip0 8.5K GeneChip, The Maize CornChip0 comprises 8,403 probesets, each represented by a set of 30 PM and 30 MM probes. Probe sets were designed from B73 (4,050) or from a contig consensus of mixed maize line DNA sequences (4,353), and were based on EST singletons (2,811), EST clusters (4,295) and other non-EST derived cDNA sequences (1,297).
2	GPL3681	[mpiUstilagoa] MPI UstilagoA	6,795	University of Karlsruhe	2006-04-19	Affymetrix	Ustilago maydis	GeneChip	in situ oligonucleotide, [mpiUstilagoa] MPI UstilagoA, Whole genome Affymetrix array, based on a map based assembly supplied by BayerCropScience. Information available at http://mips.gsf.de/genre/proj/ustilago/
3	GPL3802	[wheat] Affymetrix Wheat Genome Array	61,290	Affymetrix, Inc.	2006-05-24	Affymetrix	Triticum aestivum	GeneChip	in situ oligonucleotide, [wheat] Affymetrix Wheat Genome Array, Affymetrix submissions are typically submitted to GEO using the GEOarchive method described at http://www.ncbi.nlm.nih.gov/projects/geo/info/geo_affy.html This array contains 61,127 probe sets representing 55,052 transcripts for all 42 chromosomes in the wheat genome. Sequence information for the GeneChip Wheat Genome Array includes public content from Triticum aestivum UniGene Build #38 (build date April 24, 2004). Also included are ESTs from the wheat species T. monococcum, T. turgidum, and Aegilops tauschii, and GenBank full-length mRNAs from all species through May 18, 2004.
4	GPL3816	MVGE_TRI_RUB1	11,232	State Key Lab of Virus Gene Engineering	2006-05-26	State Key Laboratory For Molecular Virology and Genetics EngineeringÃ¯Â¼Å’Beijing	Trichophyton rubrum	cDNA Array	spotted DNA/cDNA, MVGE_TRI_RUB1, In this chip there were two fields named A and B, they described the upper and lower part(location) of the chip.Each field contains 11,232 spots.The spots in field A are same with those in field B.
5	GPL3838	Potato 10k cDNA array version 4	32,448	Plant Genomics	2006-06-05	The Institute for Genomic Research	Solanum tuberosum	cDNA Array	spotted DNA/cDNA, Potato 10k cDNA array version 4, Spotted PCR amplified cDNA array on glass. This version 4 set includes PCR products amplified from 15264 potato EST clones. Each PCR product is duplicated on the slide. The number of total spots including empty and controls is 32448.
6	GPL3832	tomato cDNA array (Ye lab)	10,368	Boyce Thompson Institute	2006-05-31	Ye lab	Solanum lycopersicum	cDNA Array	spotted DNA/cDNA, tomato cDNA array (Ye lab),
7	GPL3847	Affymetrix S. pombe Tiling 1.0FR Array	125,552	The University of Tokyo	2006-06-08	Affymetrix	Schizosaccharomyces pombe	Tiling Array	in situ oligonucleotide, Affymetrix S. pombe Tiling 1.0FR Array, The S. pombe tiling Array consists of 6 million probe pairs tiled through the complete Schizosaccharomyces pombe genome. Probes are tiled for both strands of the genome at an average of 20 base pair resolution, as measured from the central position of adjacent 25-mer oligos, creating an overlap of approximately 5 base pairs on adjacent probes. The information of oligo probes on the arrays (sequence and location on the chip) is available from Affymetrix.
8	GPL3844	[Sugar_Cane] Affymetrix Sugar Cane Genome Array	8,387	Affymetrix, Inc.	2006-06-06	Affymetrix	Saccharum officinarum	GeneChip	in situ oligonucleotide, [Sugar_Cane] Affymetrix Sugar Cane Genome Array, Affymetrix submissions are typically submitted to GEO using the GEOarchive method described at http://www.ncbi.nlm.nih.gov/projects/geo/info/geo_affy.html The GeneChip Sugar Cane Genome Array contains 8,236 S. officinarum probe sets to monitor gene expression for approximately 6,024 distinct S. officinarum genes (including both UniGene and non-UniGene gene clusters). The sequence information for this array was created in collaboration with leading sugar cane researchers through the GeneChipÃ‚Â® Consortia Program and was designed based on content from Saccharum officinarum UniGene Build 5 from August 27th, 2004 and GenBankÃ‚Â® mRNAs up to November 2, 2004. The array contains 11 probe pairs per probe set and is a 169-format, 11-micron array design.
9	GPL3799	SUCAST Sugarcane 2208 v1.0	4,608	Universidade de SÃƒÂ£o Paulo - USP	2006-05-24	CAGE - USP	Saccharum officinarum	cDNA Array	spotted DNA/cDNA, SUCAST Sugarcane 2208 v1.0, Six 384-well plates representing 1830 unique SUCAST SAS were rearrayed for spotting
10	GPL3723	Shirahige S.cerevisiae Tiling1.0F Array	227,850	The University of Tokyo	2006-05-03	Affymetrix	Saccharomyces cerevisiae	GeneChip	in situ oligonucleotide, Shirahige S.cerevisiae Tiling1.0F Array,
11	GPL3724	Shirahige S.cerevisiae Tiling1.0R Array	227,850	The University of Tokyo	2006-05-03	Affymetrix	Saccharomyces cerevisiae	GeneChip	in situ oligonucleotide, Shirahige S.cerevisiae Tiling1.0R Array,
12	GPL3737	Agilent-012713 Yeast Whole Genome ChIP-on-chip Microarray (G4486A)	44,290	Agilent Technologies	2006-05-09	Agilent Technologies	Saccharomyces cerevisiae	Oligo Array	in situ oligonucleotide, Agilent-012713 Yeast Whole Genome ChIP-on-chip Microarray (G4486A), The Yeast Whole Genome ChIP-on-chip microarray is a high-resolution, high performance 60-mer oligonucleotide that allows the location analysis of DNA binding proteins over 85% (the non-repetitive portion) of 12MB of the yeast genome on a single chip. This chip offers genome-wide coverage and consists of 41,441 oligos (60mer); 14,256 from intergenic pathway, 27,175 from ORF pathway with an average prob spacing of approximately every 266 bp. Arrays with this part number have a design ID 12713. Arrays of this design have barcodes that begin with 16012713 or 2512713. Orientation: Features are numbered numbered Left-to-Right, Top-to-Bottom as scanned by an Agilent scanner (barcode on the left, DNA on the back surface, scanned through the glass), matching the FeatureNum output from Agilent's Feature Extraction software. The ID column represents the Agilent Feature Extraction feature number. Rows and columns are numbered as scanned by an Axon Scanner (barcode on the bottom, DNA on the front surface). To match data scanned on an Axon scanner, use the RefNumber column contained in the Agilent-provided GAL file as the ID_REF column in sample submissions.
13	GPL3703	Lieb Lab at UNC-CH_Yeast Oligo Tiling Array from (RandoLab_Harvard)	24,960	UNC-Chapel Hill	2006-04-25	Center for Genomics Research, Harvard University	Saccharomyces cerevisiae	Tiling Array	spotted oligonucleotide, Lieb Lab at UNC-CH_Yeast Oligo Tiling Array from (RandoLab_Harvard), The sequence from S. cerevisiae chromosome III was fragmented into 50-mers overlapping every 20 base pairs. Potentially cross-hybridizing probes were filtered by BLASTing these sequences against the entire genome and eliminating sequences from chromosome III that included 5 or more contiguous probes with perfect BLAST matches, leaving 30 contigs covering 278,960 base pairs. Oligonucleotides were also tiled over one kilobase of 230 promoters on other chromosomes, starting at -900 from the start codon and extending to +100.
14	GPL3690	KI/Eurogentec S. cerevisiae 12.8K array (E150C)	12,800	Karolinska Institute	2006-04-20	Eurogentec	Saccharomyces cerevisiae	cDNA Array	spotted DNA/cDNA, KI/Eurogentec S. cerevisiae 12.8K array (E150C), The cDNA array contains probe sets that detect entire open reading frame (ORF) of Saccharomyces cerevisiae. Each transcript is double spotted adjacent to each other.
15	GPL3774	IBMMPMC_Scerevisiae_12.8k_EGT_D290C	12,800	UniversitÃƒÂ© Libre de Bruxelles	2006-05-17	Eurogentec	Saccharomyces cerevisiae	cDNA Array	spotted DNA/cDNA, IBMMPMC_Scerevisiae_12.8k_EGT_D290C,
16	GPL3775	IBMMPMC_Scerevisiae_12.8k_EGT_G250E	12,800	UniversitÃƒÂ© Libre de Bruxelles	2006-05-17	Eurogentec	Saccharomyces cerevisiae	cDNA Array	spotted DNA/cDNA, IBMMPMC_Scerevisiae_12.8k_EGT_G250E,
17	GPL3704	Lieb Lab at UNC-CH_Yeast Whole-genome Array (PCR-based)_for Lee CK et al.	12,202	UNC-Chapel Hill	2006-04-25	Lieb Lab at UNC-CH	Saccharomyces cerevisiae	cDNA Array	spotted DNA/cDNA, Lieb Lab at UNC-CH_Yeast Whole-genome Array (PCR-based)_for Lee CK et al., Whole-genome microarrays with PCR-amplified products represent ORFs, intergenic regions, and other noncoding regions (rDNA, tRNA, transposons, transposon long terminal repeats, telomeres, centromeres, and introns). Generally, each ORF was represented from start codon to stop codon. The intergenic regions consisted of the DNA between annotated ORFs divided such that PCR products were not longer than 1.5 kb, with a few exceptions. The noncoding regions conform to boundaries as annotated by the Saccharomyces Genome Database (SGD) as of the year 2000. Mitochondrial segments did not necessarily conform to annotated functional boundaries. This platform covers several print runs, in which print plates were arranged in different orders.
18	GPL3700	Lieb Lab at UNC-CH_Yeast Whole-genome Array (PCR-based)	11,826	UNC-Chapel Hill	2006-04-24	Lieb Lab at UNC-CH	Saccharomyces cerevisiae	cDNA Array	spotted DNA/cDNA, Lieb Lab at UNC-CH_Yeast Whole-genome Array (PCR-based), Whole-genome microarrays with PCR-amplified products represent ORFs, intergenic regions, and other noncoding regions (rDNA, tRNA, transposons, transposon long terminal repeats, telomeres, centromeres, and introns). Generally, each ORF was represented from start codon to stop codon. The intergenic regions consisted of the DNA between annotated ORFs divided such that PCR products were not longer than 1.5 kb, with a few exceptions. The noncoding regions conform to boundaries as annotated by the Saccharomyces Genome Database (SGD) as of the year 2000. Mitochondrial segments did not necessarily conform to annotated functional boundaries. This platform covers several print runs, in which print plates were arranged in different orders.
19	GPL3795	y10	8,064	Stanford Microarray Database (SMD)	2006-05-22	Stanford	Saccharomyces cerevisiae	cDNA Array	spotted DNA/cDNA, y10,
20	GPL3756	UCSF Madhani S. cerevisiae ORFarray v2	6,540	UCSF	2006-05-13	Madhani Lab, UCSF	Saccharomyces cerevisiae	cDNA Array	spotted DNA/cDNA, UCSF Madhani S. cerevisiae ORFarray v2,

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