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
(71)		   Primates
(1)		   Rodents
(53)		   Mammals
(6)		   Vertebrates
(9)		   Invertebrates
(20)		   Plants
(71)		   Bacteria
(29)		   Viruses
(1)		   Phages
(2)		   Unclassified
(1)		   All
(264)		  
  SAGE NlaIII
(0)		   SAGE RsaI
(0)		   SAGE Sau3A
(0)		   MPSS
(0)		   GeneChip
(1)		   Tiling Array
(0)		   cDNA Array
(24)		   Oligo Array
(25)		   Bead Array
(0)		   Protein Array
(0)		   Antibody
(0)		   RT-PCR
(2)		   HT-Seq
(0)		   Other
(1)		   All
(53)		  
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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 GPL2707 Mouse Exons 837,251 University of Toronto 2005-07-31 Agilent Mus musculus
Mus musculus		 Oligo Array in situ oligonucleotide, Mouse Exons,
2 GPL2850 Applied Biosystems TaqMan Gene Expression Assays (mouse) 175,755 Life Technologies 2005-09-15 Applied Biosystems Mus musculus
Mus musculus		 RT-PCR RT-PCR, Applied Biosystems TaqMan Gene Expression Assays (mouse), Pre-designed TaqMan probe and primer sets for quantitative gene expression studies of mouse genes.
3 GPL2847 Applied Biosystems TaqMan Gene Expression Assays (rat) 150,478 Life Technologies 2005-09-14 Applied Biosystems Rattus norvegicus
Rattus norvegicus		 RT-PCR RT-PCR, Applied Biosystems TaqMan Gene Expression Assays (rat), Pre-designed TaqMan probe and primer sets for quantitative gene expression studies of rat genes.
4 GPL2720 ares_ucsc_mouse_59198_affyMouseA 59,198 UC Santa Cruz 2005-08-04 Affymetrix Mus musculus
Mus musculus		 GeneChip in situ oligonucleotide, ares_ucsc_mouse_59198_affyMouseA,
5 GPL2897 GE Healthcare/Amersham Biosciences CodeLinkâ„¢ Mouse Whole Genome Bioarray 45,920 GE Healthcare Life Sciences 2005-09-26 GE Healthcare Mus musculus
Mus musculus		 Oligo Array spotted oligonucleotide, GE Healthcare/Amersham Biosciences CodeLinkâ„¢ Mouse Whole Genome Bioarray, Mice exhibit high similarity to many human biological pathways, making it a key model system for human physiological and toxicological studies in drug discovery applications. The probe sequences, representing well annotated, full length and partial mouse gene sequences, were designed based on sequences selected from the NCBI UniGene build #139, RefSeq database (April 1, 2004 release) and dbEST database (July 31, 2004 release).Well-annotated mRNA or coding sequences were chosen to ensure usefulness for a large range of applications in basic research, biotechnology, and drug development. Each sequence was carefully screened to ensure high-quality, specific probe design, and to reduce redundancy of gene targets. All of the probes designed to these sequences were functionally tested, and over 97% were functionally validated against 14 mouse tissues to ensure best representation of the gene and biologically relevant results. For flexibility and data preservation, CodeLink Mouse Whole Genome Bioarrays are compatible with lower density CodeLink mouse bioarrays. This means that existing data from CodeLink UniSet Mouse 20K Bioarrays can be continuously used in future studies along with newly generated data from CodeLink Mouse Whole Genome Bioarrays. CodeLink users can submit data to GEO by exporting tab-delimited text files from the CodeLink software. The "Feature_id" header will need to be renamed to "ID_REF", and the "Normalized_intensity" header to "VALUE" before uploading the exported tables. In addition, users are encouraged to include additional raw data columns in their data uploads. These additional columns do not need to be renamed.
6 GPL2872 Agilent-012694 Whole Mouse Genome G4122A (Feature Number version) 44,290 Agilent Technologies 2005-09-23 Agilent Technologies Mus musculus
Mus musculus		 Oligo Array in situ oligonucleotide, Agilent-012694 Whole Mouse Genome G4122A (Feature Number version), Designed to truly represent all known genes in the mouse genome and their resulting transcripts, Agilent's Whole Mouse Genome Oligo microarray is comprised of 41,534 60-mer oligonucleotide probes representing over 41,000 mouse genes and transcripts. Content for this microarray was generated from leading public databases, including RefSeq, RIKEN, NIA, Ensembl, RIKEN, UCSC Goldenpath, and Unigene. Arrays of this design have barcodes that begin with 16012694 or 2512694. 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. *** A different version of this platform with the Agilent Probe names in the ID column is assigned accession number GPL7042.
7 GPL2876 Agilent-012799 Mouse Developmental Microarray 44K G2519A Option 002 (Feature Number version) 44,290 Agilent Technologies 2005-09-23 Agilent Technologies Mus musculus
Mus musculus		 Oligo Array in situ oligonucleotide, Agilent-012799 Mouse Developmental Microarray 44K G2519A Option 002 (Feature Number version), The Mouse Development Oligo Microarray 44K array represents the first commercial whole mouse genome microarray based on the NIA (National Institute on Aging) Mouse Gene Index, which is optimized for stem cell and developmental research. Arrays of this design have barcodes that begin with 16012799 or 2512799. 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. *** A different version of this platform with the Agilent Probe names in the ID column is assigned accession number GPL7273.
8 GPL2877 Agilent-013162 Whole Rat Genome Microarray G4131A (Feature Number version) 44,290 Agilent Technologies 2005-09-23 Agilent Technologies Rattus norvegicus
Rattus norvegicus		 Oligo Array in situ oligonucleotide, Agilent-013162 Whole Rat Genome Microarray G4131A (Feature Number version), With a focus on well known rat genes and homologues to human and mouse genes with useful annotation, Agilent's Whole Rat Genome Oligo Microarray provides researchers with a new tool for modeling human biology in the rat model organism. For researchers, this means they now have access to a microarray made up of relevant content that has been empirically validated by Agilent. Arrays of this design have barcodes that begin with 16013162 or 2513162. 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. *** A different version of this platform with the Agilent Probe names in the ID column is assigned accession number GPL7289.
9 GPL2884 Agilent-013490 Mouse Genome CGH Microarray 44A G4414A (Feature Number version) 44,290 Agilent Technologies 2005-09-23 Agilent Technologies Mus musculus
Mus musculus		 Oligo Array in situ oligonucleotide, Agilent-013490 Mouse Genome CGH Microarray 44A G4414A (Feature Number version), Designed and validated for genome-wide profiling of DNA copy number changes, Agilents Mouse Genome CGH Microarray 44A is the only commercial product for high-resolution, genome-wide analyses of chromosomal abnormalities in cancer and other genetics diseases in this critical model organism. The microarray provides comprehensive genome-wide coverage with an emphasis on the most commonly studied genomic regions and cancer-related genes. It consists of over 43,000 60-mer oligonucleotide probes, empirically validated in multiple model systems, that span coding and noncoding sequences with an average spatial resolution of 35kb. Coupled with Agilents optimized assay protocols, this microarray allows researchers to identify and locate genetic alterations in this critical model organism with the highest resolution and precision. Arrays of this design have barcodes that begin with 16013490 or 2513490. 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.
10 GPL2855 MMAC 43,008 Stanford Microarray Database (SMD) 2005-09-16 Stanford Functional Genomics Facility, Stanford School of Medicine Mus musculus
Mus musculus		 cDNA Array spotted DNA/cDNA, MMAC,
11 GPL2608 MMP 42,624 Stanford University 2005-07-08 Joan,,Hebert; SFGF, 2255, CCSR, Stanford, Ca, USA, 94025; 650-736-0075; jhebert@genome.Stanford.edu Mus musculus
Mus musculus		 cDNA Array spotted DNA/cDNA, MMP,
12 GPL2635 MMU 42,624 Stanford Microarray Database (SMD) 2005-07-15 Stanford Functional Genomics Facility, Stanford School of Medicine Mus musculus
Mus musculus		 cDNA Array spotted DNA/cDNA, MMU,
13 GPL2680 MMAB 42,624 Stanford Microarray Database (SMD) 2005-07-27 Stanford Functional Genomics Facility, Stanford School of Medicine Mus musculus
Mus musculus		 cDNA Array spotted DNA/cDNA, MMAB,
14 GPL2698 MMC 42,624 Stanford Microarray Database (SMD) 2005-07-28 Stanford Functional Genomics Facility, Stanford School of Medicine Mus musculus
Mus musculus		 cDNA Array spotted DNA/cDNA, MMC,
15 GPL2727 MML 42,624 Stanford Microarray Database (SMD) 2005-08-05 Stanford Functional Genomics Facility, Stanford School of Medicine Mus musculus
Mus musculus		 cDNA Array spotted DNA/cDNA, MML,
16 GPL2896 GE Healthcare/Amersham Biosciences CodeLinkâ„¢ Rat Whole Genome Bioarray 36,736 GE Healthcare Life Sciences 2005-09-26 GE Healthcare Rattus norvegicus
Rattus norvegicus		 Oligo Array spotted oligonucleotide, GE Healthcare/Amersham Biosciences CodeLinkâ„¢ Rat Whole Genome Bioarray, CodeLink Rat Whole Genome Bioarray is designed to interrogate approximately 34,000 transcripts representing most of the known and predictive genes of the rat genome, as it is described today in the public domain. Each transcript is represented by a 30-mer probe which is designed to conserved exons across the transcripts of targeted genes. The probe sequences, representing well annotated, full length and partial rat gene sequences, were designed based on sequences selected from the NCBI UniGene build #129, RefSeq database (April 1, 2004 release) and dbEST database (March 20, 2004 release). Well-annotated mRNA or coding sequences were chosen to ensure usefulness for a large range of applications in basic research, biotechnology, and drug development. Each sequence was carefully screened to ensure high-quality, specific probe design, and to reduce redundancy of gene targets. All of the probes designed to these sequences were functionally tested, and over 95% were functionally validated against 10 rat tissues to ensure best representation of the gene and biologically relevant results. For flexibility and data preservation, CodeLink Rat Whole Genome Bioarrays are compatible with lower density CodeLink rat bioarrays. This means that existing data from CodeLink UniSetâ„¢ Rat 10K Bioarrays can be continuously used in future studies along with newly generated data from CodeLink Rat Whole Genome Bioarrays. CodeLink users can submit data to GEO by exporting tab-delimited text files from the CodeLink software. The "Feature_id" header will need to be renamed to "ID_REF", and the "Normalized_intensity" header to "VALUE" before uploading the exported tables. In addition, users are encouraged to include additional raw data columns in their data uploads. These additional columns do not need to be renamed.
17 GPL2640 Mouse Genomic Long Oligo Array (AECOM) 33,600 University of California, San Diego, School of Medicine 2005-07-18 Microarray Core Facility of Albert Einstein College of Medicine Mus musculus
Mus musculus		 Oligo Array spotted oligonucleotide, Mouse Genomic Long Oligo Array (AECOM),
18 GPL2594 INSERM Rat Operon Pronto plus Systems 6 Oligoarray 28,800 INSERM U858 2005-07-04 platform Biopuces, Toulouse Genopole Rattus norvegicus
Rattus norvegicus		 Oligo Array spotted oligonucleotide, INSERM Rat Operon Pronto plus Systems 6 Oligoarray, Deposition on each glass slide of the cDNA from one lean with one obese SHHF rats
19 GPL2769 EDGE Liver Microarray version 1 27,648 McArdle Laboratory 2005-08-22 Bradfield Laboratory Mus musculus
Mus musculus		 cDNA Array spotted DNA/cDNA, EDGE Liver Microarray version 1,
20 GPL2894 GE Healthcare/Amersham Biosciences CodeLinkâ„¢ UniSet Mouse 20K I Bioarray 23,572 GE Healthcare Life Sciences 2005-09-26 GE Healthcare Mus musculus
Mus musculus		 Oligo Array spotted oligonucleotide, GE Healthcare/Amersham Biosciences CodeLinkâ„¢ UniSet Mouse 20K I Bioarray, CodeLink UniSet Mouse 20K I Bioarray content is based on the public NCBI, UniGene, and RefSeq databases. Well-annotated mRNA or coding sequences were chosen to ensure usefulness for a large range of applications in basic research, biotechnology, and drug development. Each sequence was carefully screened to ensure high-quality, specific probe design, and to reduce redundancy of gene targets. Every probe was functionally validated against multiple tissues to ensure best representation of the gene so that the results will be biologically relevant. Every bioarray is also functionally validated during production to further ensure quality performance. CodeLink users can submit data to GEO by exporting tab-delimited text files from the CodeLink software. The "Feature_id" header will need to be renamed to "ID_REF", and the "Normalized_intensity" header to "VALUE" before uploading the exported tables. In addition, users are encouraged to include additional raw data columns in their data uploads. These additional columns do not need to be renamed.
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