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
(21)

Primates
(1)

Rodents
(12)

Mammals
(0)

Vertebrates
(0)

Invertebrates
(10)

Plants
(23)

Bacteria
(21)

Viruses
(0)

Phages
(0)

Unclassified
(1)

All
(90)

SAGE NlaIII
(0)

SAGE RsaI
(0)

SAGE Sau3A
(0)

MPSS
(0)

GeneChip
(0)

Tiling Array
(0)

cDNA Array
(11)

Oligo Array
(5)

Bead Array
(1)

Protein Array
(0)

Antibody
(0)

RT-PCR
(3)

HT-Seq
(0)

Other
(0)

All
(21)

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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	GPL5833	Verrando Homo sapiens 9K cDNA array	9,250	Currently unaffilliated	2007-09-12	P Verrando	Homo sapiens	MIXTURE	spotted DNA/cDNA, Verrando Homo sapiens 9K cDNA array, normalized cDNA library was used to minimize redundancy. All clones on the microarray were sequence-verified and carefully mapped to NCBI's GenBank/UniGene database on 3 April 2000. An update was performed at the end of this work on 12 March 2001 and the list of clones (name, GenBank's accession numbers) was modified accordingly. After amplification, more than 9000 human cDNA clones were deposited on the solid support through optimized key processes. Thirty percent of them were EST as defined by the GenBank release on 12 March 2001. cDNA sizes ranged from 500 to 5000 bp, with an average of 1 kb.
2	GPL11384	USZ/Human Toll-Like Receptor Signaling Pathway PCR Array PAHS-18A	84	University Hospital of Zurich	2011-01-05	SABiosciences	Homo sapiens	RT-PCR	RT-PCR, USZ/Human Toll-Like Receptor Signaling Pathway PCR Array PAHS-18A, see http://www.sabiosciences.com/rt_pcr_product/HTML/PAHS-018A.html
3	GPL2040	UHN Human CpG 12K Array (HCGI12K)	13,056	Friedrich Miescher Institute	2005-05-12	UHN Microarray Centre	Homo sapiens	cDNA Array	spotted DNA/cDNA, UHN Human CpG 12K Array (HCGI12K), This array contains single-spotted clones representing 12,192 CpG-island clones from the Sanger Institute. The CpG Library was originally prepared by Sally Cross in the laboratory of Adrian Bird at The Wellcome Trust Centre for Cell Biology (University of Edinburgh). For information on the preparation of the original library, please see Cross, S.H., et.al., Purification of CpG islands using a methylated DNA binding column. Nature Genetics (1994) 6:236- 244. Individual clones were sequenced by the UHN Microarray Centre.
4	GPL13482	SMD Print_1561 (hoag)	49,152	UniversitÃƒÂ¤tsspital Basel	2011-05-03	Stanford Functional Genomics Facility, Stanford School of Medicine	Homo sapiens	cDNA Array	spotted DNA/cDNA, SMD Print_1561 (hoag),
5	GPL9551	SMD Print_1451 Homo sapiens	49,152	UniversitÃƒÂ¤tsspital Basel	2009-11-09	Stanford Functional Genomics Facility, Stanford School of Medicine	Homo sapiens	cDNA Array	spotted DNA/cDNA, SMD Print_1451 Homo sapiens,
6	GPL9550	SMD Print_1308 Homo sapiens	44,544	UniversitÃƒÂ¤tsspital Basel	2009-11-09	Stanford Functional Genomics Facility, Stanford School of Medicine	Homo sapiens	cDNA Array	spotted DNA/cDNA, SMD Print_1308 Homo sapiens,
7	GPL4990	SHGE	43,008	University Hospital Basel	2007-03-13	Stanford Functional Genomics Facility, Stanford School of Medicine	Homo sapiens	cDNA Array	spotted DNA/cDNA, SHGE,
8	GPL4989	SHFU	41,472	University Hospital Basel	2007-03-13	Stanford Functional Genomics Facility, Stanford School of Medicine	Homo sapiens	cDNA Array	spotted DNA/cDNA, SHFU,
9	GPL3090	Sanger Pilot Study V1	1,433	University of Geneva Medical School	2005-11-16	Illumina, Inc.	Homo sapiens	Bead Array	oligonucleotide beads, Sanger Pilot Study V1, The array contains 630 protein coding genes of all RefSeq genes in the ENCODE regions, all RefSeq genes on human chromosome 21 and all RefSeq and manually curated genes from a 10Mb region at 20q12-13.2. The array is composed of 3 micron features with an average feature redundancy of 30-fold. All features are quality controlled by a sequential hybridization process called array decoding. Each gene represented on the array contains 2 or more unique probes that are fully screened, full-length 50-mers.
10	GPL7142	Print_1186	43,008	Swiss Federal Institute of Technology	2008-08-05	Stanford Functional Genomics Facility, Stanford School of Medicine	Homo sapiens	cDNA Array	spotted DNA/cDNA, Print_1186,
11	GPL7141	Print_1182	43,008	Swiss Federal Institute of Technology	2008-08-05	Stanford Functional Genomics Facility, Stanford School of Medicine	Homo sapiens	cDNA Array	spotted DNA/cDNA, Print_1182,
12	GPL3606	OHU16K (old)	18,432	Currently unaffilliated	2006-03-30	W.M. Keck Foundation Biotechnology Resource Laboratory	Homo sapiens	Oligo Array	spotted oligonucleotide, OHU16K (old), Human OHU16K (old) array is created from the first 16K Operon set - 70 mer oligos. The array is in 32 pin conformation with 24 columns and 22 rows and only 4 spots on the 23rd row.
13	GPL6650	Novachip human 34.5k	34,592	UniversitÃƒÂ¤tsspital Basel	2008-03-26	Novartis	Homo sapiens	Oligo Array	spotted oligonucleotide, Novachip human 34.5k, Novachip is an evanescent resonator microarray platform. The approach takes advantage of a phenomenon that has been attributed as abnormal reflection. Excitation photons incident on the chip under resonance conditions couple into a thin corrugated metal oxide surface at the site of incidence. As a result of the transducer geometry, the energy is locally confined into the thin corrugated layer of high refractive index material. Consequently, strong electromagnetic fields are generated at the surface of the chip. The effect has been attributed as evanescent resonance and leads to increased fluorescence intensity of chromophores close to the surface. The effective field strength can be increased up to 100-fold by the confinement of the available excitation energy, depending on the optical properties of the used optical detection system. The Novachips used for the experiments described in the present paper have a resonance angle of 2Ã‚Â° with respect to normal for TE polarized light of 633 nm wavelength. The observed increase of fluorescence intensity with the used Agilent microarray laser scanner was about 5-fold compared to glass slides processed under identical conditions. The slides were cleaned and the AROS human v3 oligonucleotide set from Operon Inc. was arrayed with a Microgrid printer at 23Ã‚Â°C and 55-60% relative humidity (total approx. 37K features, print buffer 4x SSC / 0.001% Sarcosyl). Scatter light scans (Tecan Laser Scanner) were used to assess the quality of the printed slides ("salt images"). Slides were stored sealed until use.
14	GPL7751	NimbleGen Homo sapiens 386K HG18 RefSeq promoter 2006-07-18	386,230	Friedrich Miescher Institute for Biomedical Research (FMI)	2008-12-08	Nimblegen	Homo sapiens	Oligo Array	in situ oligonucleotide, NimbleGen Homo sapiens 386K HG18 RefSeq promoter 2006-07-18,
15	GPL7430	MCI Human HEEBOChip 42k oligo array	41,964	Currently unaffilliated	2008-10-06	This array was assembled by/for researchers at the Mitchell Cancer Institute (MCI) of the University of South Alabama.	Homo sapiens	Oligo Array	spotted oligonucleotide, MCI Human HEEBOChip 42k oligo array, Human Exonic Evidence-Based Oligonucleotide Chip (HEEBOChip), 70mer oligos.
16	GPL6803	Low Density Microvascular Differentiation Array (LD-MDA) version 2.0	96	ETH Zurich	2008-04-30	Applied Biosystems	Homo sapiens	RT-PCR	RT-PCR, Low Density Microvascular Differentiation Array (LD-MDA) version 2.0, Microfluidic 384-well TaqManÃ¢â€žÂ¢ real time RT-PCR platform
17	GPL6802	Low Density Microvascular Differentiation Array (LD-MDA) version 1.0	192	ETH Zurich	2008-04-30	Applied Biosystems	Homo sapiens	RT-PCR	RT-PCR, Low Density Microvascular Differentiation Array (LD-MDA) version 1.0, Microfluidic 384-well TaqManÃ¢â€žÂ¢ real time RT-PCR platform
18	GPL1213	Human Transporter OligoChip	3,024	ISREC	2004-05-04		Homo sapiens	Oligo Array	spotted oligonucleotide, Human Transporter OligoChip, Custom array chip focusing on transporters and ion channels. Genes are represented by 70 mers.
19	GPL1935	Human Skeletal Muscle Array	231	University of Bern	2005-03-29		Homo sapiens	cDNA Array	spotted DNA/cDNA, Human Skeletal Muscle Array, Nylon, custom-designed human cDNA array produced by Clontech, BD Biosciences. The cDNA fragments (200-600 bp) are PCR-amplified using gene-specific primers, and are selected so that they lack repetitive elements and have minimal homology with other genes on the array.
20	GPL2746	human 10K E	11,552	ISREC	2005-08-11	DAFL - UNIL -CH	Homo sapiens	cDNA Array	spotted DNA/cDNA, human 10K E ,

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