Gene Expression Omnibus (GEO) Overview Version：2013-04-06Japanese page
An overview of the GEO entries broken down by the measurement platforms and the features of the measured samples.
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Data Unit : [ DataSet / Sample / Platform ] Show explanation>> <<Hide explanation
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.
The numbers shown in the tabs are the numbers of the data (series, samples or platforms) belonging to the groups.
  Human
(3,705)		   Primates
(37)		   Rodents
(1,748)		   Mammals
(295)		   Vertebrates
(402)		   Invertebrates
(1,004)		   Plants
(2,170)		   Bacteria
(1,636)		   Viruses
(78)		   Phages
(8)		   Unclassified
(399)		   All
(11,528)		  
  SAGE NlaIII
(37)		   SAGE RsaI
(0)		   SAGE Sau3A
(1)		   MPSS
(9)		   GeneChip
(78)		   Tiling Array
(226)		   cDNA Array
(558)		   Oligo Array
(799)		   Bead Array
(0)		   Protein Array
(0)		   Antibody
(0)		   RT-PCR
(0)		   HT-Seq
(432)		   Other
(26)		   All
(2,170)		  
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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 GPL8746 Gang Lab (Agilent)_Z.Officinale/C.Longa_15K array 15,208 The University of Arizona 2009-06-19 Agilent Zingiber officinale,Curcuma longa
Zingiber officinale,Curcuma longa		 Oligo Array spotted oligonucleotide, Gang Lab (Agilent)_Z.Officinale/C.Longa_15K array, Design Format: 8 X 15K (each slide has 8 blocks of 15K array) Number of sequences on each array: 1 (no duplicated spots in each array) Control Grid: IS-15744-8-V1_8x15K_Gx_EQC_V20060608
2 GPL9997 Agilent/WalbotLab Zea mays + Ustilago maydis (dual organism) 4x44K array 45,220 Stanford University 2010-02-01 Agilent Zea mays,Ustilago maydis
Zea mays,Ustilago maydis		 Oligo Array in situ oligonucleotide, Agilent/WalbotLab Zea mays + Ustilago maydis (dual organism) 4x44K array, designed by Walbot Lab
3 GPL8790 NimbleGen Zea Mays 2.1M array 2,124,029 Iowa State University 2009-07-02 NimbleGen Zea mays
Zea mays		 Oligo Array in situ oligonucleotide, NimbleGen Zea Mays 2.1M array, Probe sequences were aligned to Maize pseudomolecules from the Arizona Genome Institure (AGI) released on March, 20th, 2009 to determine their positions in the genome (positions are reflected in the Platform data table). Due to the fact that our array was designed using B73 genomic sequence and the high rate of polymorphism between B73 and Mo17, the CGH data violated the assumption for the regularly used Q-spline normalization to make two channels of hybridization intensities comparable. We used a subset of 840,289 probes that were known to have identical sequence in B73 and Mo17 (based on B73 BAC sequences and Mo17 WGS data) as a control set to obtain a best-fitting cubic spline function (Workman et al., 2002), assuming that most of these probes should have the same hybridization intensities after normalization. The spline function was then globally applied for all probes to normalize the two channels. After within-chip normalization, linear model analyses using LIMMA (Smyth 2004; Smyth 2005) were conducted for the data from all microarrays. The linear model for each probe included effects for dyes and genotypes (B73, Mo17, RIL M0022, and RIL M0023), and p-values were calculated to test for a signal difference between Mo17 and B73 genotypes as part of each linear model analysis. NimbleGen .ndf array description file linked below as supplementary file.
4 GPL13499 NimbleGen 2.1M Maize Methylation Array 2,120,701 University of Minnesota 2011-05-05 NimbleGen Zea mays
Zea mays		 Oligo Array in situ oligonucleotide, NimbleGen 2.1M Maize Methylation Array, Order ID#: OID29684 Native array description file: 100629_Zea_Mays_NS_CGH_HX1.ndf Native array description file: 100629_Zea_Mays_NS_CGH_HX1.pos The sequences of the oligonucleotides are available in the supplementary .ndf file.
5 GPL15621 NimbleGen 3x1.4M Maize Methylation Array 1,400,988 University of Minnesota 2012-05-27 NimbleGen Zea mays
Zea mays		 Oligo Array in situ oligonucleotide, NimbleGen 3x1.4M Maize Methylation Array, Design name: 110325_Zea_mays_NS_CGH Design ID: 550571 Native array description file: 110325_Zea_mays_NS_CGH.ndf Native array description file: 110325_Zea_mays_NS_CGH.pos Coordinates based on the B73 reference genome v2 physical positions (assembly RefGen_v2). Array was designed using probes initially found on the Maize 2.1M array platform (GPL13499). Probes were selected by being single-copy sequences within the maize RefGen_v2 masked genomic sequence. PROBE_ID values from this platform are conserved from their selections from GPL13499, allowing easy cross-comparison between experimental platforms.
6 GPL10846 NimbleGen Zmays 120K CGH array [091006_NS_Zmays_CGH_exp] 119,609 University of Minnesota 2010-08-23 Roche NimbleGen Zea mays
Zea mays		 Oligo Array in situ oligonucleotide, NimbleGen Zmays 120K CGH array [091006_NS_Zmays_CGH_exp], product # OID24389
7 GPL10837 Maize Pioneer Hi-Bred 105K mRNA Microarray 105,072 Pioneer Hi-Bred International 2010-08-18 Agilent Zea mays
Zea mays		 Oligo Array spotted oligonucleotide, Maize Pioneer Hi-Bred 105K mRNA Microarray, The Agilent “105K” microarray chip was designed for maize genomic and transcript sequences in an effort to cover most maize genes with at least one 60-mer oligonucleotide probe. A pool of about 1.4 million public and private ESTs was consulted, derived from diverse tissues and treatments. The majority of the sequences was derived from the B73 genotype, but there were other genotypes represented. A higher quality subset of 1.1 million ESTs was used to generate a transitory transcript assembly of about 66K transcript sequences of average length 1.0 kb. At least one 60-mer oligo was designed for nearly all of these transcripts, but at times more than one oligo was designed per transcript. In an effort to identify other genes, or perhaps parts of genes, not represented in the 66K transcript set, and to fill out the array, various BLAST analyses were conducted against the then (in fall 2006) available public B73 genomic sequences, namely B73 BACs in GenBank and the AZM5 GSS Assembly dataset produced by TIGR. The resulting array design is believed to encompass most maize genes at least once, but there are certainly genes missing, others represented more than once, and sequence errors or genotypic variation in the dataset, or oligos designed to straddling intron-exon junctions, or to chimeric junctions inherent in ESTs and their assemblies, that may deter some oligos from functioning against a B73-specific transcript sample. Subsequent efforts to estimate the number of unique genes in this microarray suggest about 45,000 genes. This “105K” format Agilent microarray consists of 103,685 oligos designed to maize genic sequences. The balance of the space on the “105K” microarray (105,073 total oligos) was reserved for technical and internal hybridization controls.
8 GPL11236 Maize oligo array version 1.4 slide set (slides A and B) 54,492 Washington University 2010-11-22 Maize Oligonucleotide Project, University of Arizona; www.maizearray.org Zea mays
Zea mays		 Oligo Array spotted oligonucleotide, Maize oligo array version 1.4 slide set (slides A and B),
9 GPL6438 Maize oligonucleotide array 46K version 46,128 Maize Oligonucleotide Array Project 2008-01-30 The University of Arizona Zea mays
Zea mays		 Oligo Array spotted oligonucleotide, Maize oligonucleotide array 46K version, Spotted 70-mer oligo array on glass. The maize array set 46K version contains ~46,000 unique probes from maize
10 GPL7209 Zea mays 1x44K Agilent array - designed by Walbot Lab 44,290 Stanford University 2008-08-26 Agilent Zea mays
Zea mays		 Oligo Array in situ oligonucleotide, Zea mays 1x44K Agilent array - designed by Walbot Lab,
11 GPL6460 Universidad Nacional de Rosario Zea Mays 43K 43,451 Universidad Nacional de Rosario 2008-02-05 Agilent Technologies Zea mays
Zea mays		 Oligo Array in situ oligonucleotide, Universidad Nacional de Rosario Zea Mays 43K,
12 GPL7444 Agilent-016047 Walbot Zea mays 4x44K array 43,451 Stanford University 2008-10-08 Agilent Zea mays
Zea mays		 Oligo Array in situ oligonucleotide, Agilent-016047 Walbot Zea mays 4x44K array, designed by Walbot Lab (same probes as 1x44)
13 GPL16089 Agilent-016047 Maize Gene Expression Microarray 4x44K (Probe name version) 42,095 Agilent Technologies 2012-09-21 Agilent Technologies Zea mays
Zea mays		 Oligo Array in situ oligonucleotide, Agilent-016047 Maize Gene Expression Microarray 4x44K (Probe name version), The ID column includes the Agilent Probe Names.
14 GPL14913 Agilent-025271 Zea mays Mais_array_v1 [Probe Name version] 41,838 Heinrich Heine University Duesseldorf 2011-11-22 Agilent Technologies Zea mays
Zea mays		 Oligo Array in situ oligonucleotide, Agilent-025271 Zea mays Mais_array_v1 [Probe Name version], Mais array, v1, basierend auf Design 08/2009 Arrays of this design have barcodes that begin with 16025271 or 2525271. 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.
15 GPL1988 Maize oligo array version 1.1 array A 32,448 The Institute for Genomic Research 2005-04-25 Zea mays
Zea mays		 Oligo Array spotted oligonucleotide, Maize oligo array version 1.1 array A, Spotted oligo array on glass. The whole maize array set 1.1 version contains 55550 unique probes from maize and array A contains 28833 of them. The number of total spots including empty and controls is 32448.
16 GPL1989 Maize oligo array version 1.1 array B 32,448 The Institute for Genomic Research 2005-04-25 Zea mays
Zea mays		 Oligo Array spotted oligonucleotide, Maize oligo array version 1.1 array B, Spotted oligo array on glass. The whole maize array set 1.1 version contains 55550 unique probes from maize and array B contains 27109 of them. The number of total spots including empty and controls is 32448.
17 GPL1990 Maize oligo array version 1.2 array A 32,448 The Institute for Genomic Research 2005-04-25 Zea mays
Zea mays		 Oligo Array spotted oligonucleotide, Maize oligo array version 1.2 array A, Spotted oligo array on glass. The whole maize array set 1.2 version contains 56310 unique probes from maize and array A contains 29132 of them. The number of total spots including empty and controls is 32448.
18 GPL1991 Maize oligo array version 1.2 array B 32,448 The Institute for Genomic Research 2005-04-25 Zea mays
Zea mays		 Oligo Array spotted oligonucleotide, Maize oligo array version 1.2 array B, Spotted oligo array on glass. The whole maize array set 1.2 version contains 56310 unique probes from maize and array B contains 27190 of them. The number of total spots including empty and controls is 32448.
19 GPL1992 Maize oligo array version 1.3 array A 32,448 The Institute for Genomic Research 2005-04-25 Zea mays
Zea mays		 Oligo Array spotted oligonucleotide, Maize oligo array version 1.3 array A, Spotted oligo array on glass. The whole maize array set 1.3 version contains 56310 unique probes from maize and array A contains 29132 of them. The number of total spots including empty and controls is 32448.
20 GPL1993 Maize oligo array version 1.3 array B 32,448 The Institute for Genomic Research 2005-04-25 Zea mays
Zea mays		 Oligo Array spotted oligonucleotide, Maize oligo array version 1.3 array B, Spotted oligo array on glass. The whole maize array set 1.3 version contains 56310 unique probes from maize and array B contains 27190 of them. The number of total spots including empty and controls is 32448.
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