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
(67)

Rodents
(38)

Viruses
(0)

Phages
(0)

Unclassified
(8)

All
(275)

SAGE NlaIII
(0)

SAGE RsaI
(0)

SAGE Sau3A
(0)

MPSS
(2)

GeneChip
(0)

Tiling Array
(0)

cDNA Array
(18)

Oligo Array
(17)

Bead Array
(0)

Protein Array
(0)

Antibody
(0)

RT-PCR
(0)

HT-Seq
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Other
(1)

All
(38)

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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	GPL4571	MPSS 20bp [DpnII: Mus musculus] signature list	50,727	Harvard Medical School	2006-11-18		Mus musculus	MPSS	MPSS, MPSS 20bp [DpnII: Mus musculus] signature list, MPSS signatures detected in Lynx mouse transcriptome analysis experiment. To generate a complete, annotated mouse signature database, we extracted all the possible signatures (Ã¢â‚¬Å“virtual signaturesÃ¢â‚¬Â) from the mouse genome sequence (NCBI build 33) and the mouse UniGene sequences (UniGene build #145). Each virtual signature is ranked based on its position and orientation in the original sequence. The annotation for that sequence is then assigned to the signature and the resulting signature database is used to annotate the data from the experiments, using our Ã¢â‚¬Å“TopHitÃ¢â‚¬Â algorithm. Virtual Signature Class\| mRNA Orientation\| Poly-Adenelation\| Features\| Position ------------------------------------------------------------------------------------------ 0 Either - Repeat Warning Not applicable Not applicable 1 Forward Strand Poly-A Signal, Poly-A Tail 3' most 2 Forward Strand Poly-A Signal 3' most 3 Forward Strand Poly-A Tail 3' most 4 Forward Strand None 3' most 5 Forward Strand None Not 3' most 6 Forward Strand Internal Poly-A Not 3' most 11 Reverse Strand Poly-A Signal, Poly-A Tail 5' most 12 Reverse Strand Poly-A Signal 5' most 13 Reverse Strand Poly-A Tail 5' most 14 Reverse Strand None 5' most 15 Reverse Strand None Not 5' most 16 Reverse Strand Internal Poly-A Not 3' most 22 Unknown Poly-A Signal Last before signal 23 Unknown Poly-A Tail Last before tail 24 Unknown None Last in sequence 25 Unknown None Not last 26 Unknown Internal Poly-A Not 3' most 1000 Unknown - Derived from Genomic Sequence Not applicable Not applicable
2	GPL4572	MPSS 17bp [DpnII: Mus musculus] signature list	47,450	Harvard Medical School	2006-11-18		Mus musculus	MPSS	MPSS, MPSS 17bp [DpnII: Mus musculus] signature list, MPSS signatures detected in Lynx mouse transcriptome analysis experiment. To generate a complete, annotated mouse signature database, we extracted all the possible signatures (Ã¢â‚¬Å“virtual signaturesÃ¢â‚¬Â) from the mouse genome sequence (NCBI build 33) and the mouse UniGene sequences (UniGene build #145). Each virtual signature is ranked based on its position and orientation in the original sequence. The annotation for that sequence is then assigned to the signature and the resulting signature database is used to annotate the data from the experiments, using our Ã¢â‚¬Å“TopHitÃ¢â‚¬Â algorithm. Virtual Signature Class\| mRNA Orientation\| Poly-Adenelation\| Features\| Position ------------------------------------------------------------------------------------------ 0 Either - Repeat Warning Not applicable Not applicable 1 Forward Strand Poly-A Signal, Poly-A Tail 3' most 2 Forward Strand Poly-A Signal 3' most 3 Forward Strand Poly-A Tail 3' most 4 Forward Strand None 3' most 5 Forward Strand None Not 3' most 6 Forward Strand Internal Poly-A Not 3' most 11 Reverse Strand Poly-A Signal, Poly-A Tail 5' most 12 Reverse Strand Poly-A Signal 5' most 13 Reverse Strand Poly-A Tail 5' most 14 Reverse Strand None 5' most 15 Reverse Strand None Not 5' most 16 Reverse Strand Internal Poly-A Not 3' most 22 Unknown Poly-A Signal Last before signal 23 Unknown Poly-A Tail Last before tail 24 Unknown None Last in sequence 25 Unknown None Not last 26 Unknown Internal Poly-A Not 3' most 1000 Unknown - Derived from Genomic Sequence Not applicable Not applicable
3	GPL4542	MMAF	43,008	Stanford Microarray Database (SMD)	2006-11-08	Stanford Functional Genomics Facility, Stanford School of Medicine	Mus musculus	cDNA Array	spotted DNA/cDNA, MMAF,
4	GPL4378	MMJ	42,624	Stanford Microarray Database (SMD)	2006-10-02	Stanford Functional Genomics Facility, Stanford School of Medicine	Mus musculus	cDNA Array	spotted DNA/cDNA, MMJ,
5	GPL4379	MMP	42,624	Stanford Microarray Database (SMD)	2006-10-02	Stanford Functional Genomics Facility, Stanford School of Medicine	Mus musculus	cDNA Array	spotted DNA/cDNA, MMP,
6	GPL4382	MMO	42,624	Stanford Microarray Database (SMD)	2006-10-03	Stanford Functional Genomics Facility, Stanford School of Medicine	Mus musculus	cDNA Array	spotted DNA/cDNA, MMO,
7	GPL4383	MMS	42,624	Stanford Microarray Database (SMD)	2006-10-03	Stanford Functional Genomics Facility, Stanford School of Medicine	Mus musculus	cDNA Array	spotted DNA/cDNA, MMS,
8	GPL4517	UCT Brombacher lab Mus MEEBO 40K version1	39,200	Institute for Infectious Diseases and Molecular Medicine, University of Cape Town	2006-11-02	Capar Microarray Facility, University of Cape Town, South Africa	Mus musculus	Oligo Array	spotted oligonucleotide, UCT Brombacher lab Mus MEEBO 40K version1, The MEEBO (Mouse Exonic Evidence Based Oligonucleotide) Set contains a collection of oligo probes, largely derived from constitutively expressed exons, allowing interrogation of almost 25,000 mouse genes. The set was designed to enable study of mouse transcription patterns and, as broadly as possible, alternative splicing. An exon-centric design was selected to allow the differentiation of constitutively expressed versus alternatively expressed exons. This design also supports comparative genome hybridization (CGH) analysis. In addition to the exon-centric probes, the set contains an extensive assortment of controls that facilitate accurate evaluation of expression results. The MEEBO Set contains 38,467 70mer oligonucleotide probes with an amino modification on the 5Ã¢â‚¬â„¢ end. Probes are provided at a final yield of 200pmol each, and delivered in 101 384-well microarray print plates (Genetix model X7020). Probes are Tm normalized, and are designed to minimize cross-hybridization and secondary structure.
9	GPL4610	Illumina Mouse 38K Oligo array(MEEBO)	38,784	nih	2006-11-29	NHGRI Microarray Core facility	Mus musculus	Oligo Array	spotted oligonucleotide, Illumina Mouse 38K Oligo array(MEEBO),
10	GPL4468	VUMC MACF Mouse 38K oligo v64	37,632	Vrije Universiteit Medical Center	2006-10-19	VUMC Microarray Core Facility	Mus musculus	Oligo Array	spotted oligonucleotide, VUMC MACF Mouse 38K oligo v64, - oligonucleotides were mapped by using the file MEEBO_track from UCSF
11	GPL4478	GE Healthcare/Amersham Biosciences CodeLinkÃ¢â€žÂ¢ Rat Whole Genome Bioarray	33,994	Texas A&M Health Science Center	2006-10-23	GE Healthcare	Rattus norvegicus	Oligo Array	spotted oligonucleotide, GE Healthcare/Amersham Biosciences CodeLinkÃ¢â€žÂ¢ 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 UniSetÃ¢â€žÂ¢ Rat 10K Bioarrays can be continuously used in future studies along with newly generated data from CodeLink Rat Whole Genome Bioarrays. This platform submission is identical to GPL2896, except that it utilizes the PROBE_NAME for the unique identifier (ID). Additionally, duplicate PROBE_NAME values have been condensed so each probe is only represented once in the platform data table. Finally, the annotations are derived from NCBI UniGene build #144, RefSeq database (August 8, 2005 release) and dbEST database (September 5, 2005 release).
12	GPL4612	Qiagen Mouse V3 31K Oligo array (MV3)	32,640	nih	2006-11-29	NHGRI Microarray Core facility	Mus musculus	Oligo Array	spotted oligonucleotide, Qiagen Mouse V3 31K Oligo array (MV3),
13	GPL4380	Mouse NIA 15K Custom Duplicate Spots	31,200	University of Arizona	2006-10-02	University of Arizona	Mus musculus	cDNA Array	spotted DNA/cDNA, Mouse NIA 15K Custom Duplicate Spots, Custom array including the NIA Mouse 15K Cloneset plus addition unidentified clones printed in duplicate
14	GPL4575	Mus Musculus Mm27k_7M Array	27,974	Albert Einstein College of Medicine	2006-11-20	Aldo Massimi	Mus musculus	cDNA Array	spotted DNA/cDNA, Mus Musculus Mm27k_7M Array, The cDNA microarrays used in this study were obtained from the Albert Einstein College of Medicine Functional Genomics Facility (http://www.aecom.yu.edu/cancer/new/cores/microarray/default.htm). 27400 sequence verified mouse clones were spotted in each array. The clones are from 3 sources: the 8968 clones in the MGEM1.0 plates from Incyte, the 14208 clones in the MNCI-V1 plates from NCI (see http://lgsun.grc.nia.nih.gov/cDNA/15k.html), and the 4224 clones in the MIMP-V1 plates originally from Research Genetics. The spatial arrangement of the M7 series of this array differs from the previous Mm27K arrays.
15	GPL4528	CapitalBio Rat 27k long oligo array	26,962	Medical Systems Biology Research Center	2006-11-08	CapitalBio	Rattus norvegicus	Oligo Array	spotted oligonucleotide, CapitalBio Rat 27k long oligo array, This set includes 27k oligonucleotides, mostly 70-mers, designed based upon the Ensembl Rat Database Version v19.3b.2 and Rat Genome Project.
16	GPL4696	Rosetta/Merck Mouse 25k v1.9 microarray	23,546	Merck & Co.	2006-12-22	Rosetta Inpharmatics / Merck Pharmaceuticals	Mus musculus	Oligo Array	spotted oligonucleotide, Rosetta/Merck Mouse 25k v1.9 microarray, Oligonucleotide array on glass. Contains 60-mer probes (60-mer).
17	GPL4389	NIA Mouse 22.4K cDNA array_Hepatotoxicity	23,040	Central Drug Research Institute	2006-10-05	University Health Network	Mus musculus	cDNA Array	spotted DNA/cDNA, NIA Mouse 22.4K cDNA array_Hepatotoxicity,
18	GPL4527	SRC Mouse Compugen Printed Long Oligonucleotide 22K set Run 54	22,504	Institute for Molecular Bioscience, Uni of Qld	2006-11-08	SRC Microarray Facility	Mus musculus	Oligo Array	spotted oligonucleotide, SRC Mouse Compugen Printed Long Oligonucleotide 22K set Run 54,
19	GPL4555	SRC Mouse Compugen Printed Long Oligonucleotide 22K set version 6	22,504	Institute for Molecular Bioscience, Uni of Qld	2006-11-11	SRC Microarray Facility	Mus musculus	Oligo Array	spotted oligonucleotide, SRC Mouse Compugen Printed Long Oligonucleotide 22K set version 6,
20	GPL4674	AresLabUCSC_Mouse_24K_MuSpliceV1	22,228	UCLA	2006-12-18	UCSC, Manuel Ares Lab	Mus musculus	Oligo Array	spotted oligonucleotide, AresLabUCSC_Mouse_24K_MuSpliceV1,

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