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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Primates
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Rodents
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Viruses
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Phages
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Unclassified
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All
(104)

SAGE NlaIII
(1)

SAGE RsaI
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SAGE Sau3A
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MPSS
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Bead Array
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Protein Array
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Antibody
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RT-PCR
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HT-Seq
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Other
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All
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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	GPL1465	BCM-NIA15k	16,128	Baylor College of Medicine	2004-09-22		Mus musculus	cDNA Array	spotted DNA/cDNA, BCM-NIA15k, BCM-NIA15k array
2	GPL1450	15k-1/3	5,760	National Institutes of Health	2004-09-15		Mus musculus	cDNA Array	spotted DNA/cDNA, 15k-1/3, NIA mouse 15k cDNA clone set 1 of 3
3	GPL1451	15k-2/3	5,760	National Institutes of Health	2004-09-15		Mus musculus	cDNA Array	spotted DNA/cDNA, 15k-2/3, NIA mouse 15k cDNA clone set 2 of 3
4	GPL1452	15k-3/3	5,760	National Institutes of Health	2004-09-15		Mus musculus	cDNA Array	spotted DNA/cDNA, 15k-3/3, NIA mouse 15k cDNA clone set 3 of 3
5	GPL1440	LUNDNIH_Mouse_37K_1	37,632	Lund University	2004-09-09		Mus musculus	cDNA Array	spotted DNA/cDNA, LUNDNIH_Mouse_37K_1, Mouse cDNA 37K
6	GPL1441	LUNDNIH_Mouse_37K_2	37,632	Lund University	2004-09-09		Mus musculus	cDNA Array	spotted DNA/cDNA, LUNDNIH_Mouse_37K_2, Mouse cDNA 37K
7	GPL1437	Mouse miRNA chip	21,939	Best Institute	2004-09-06		Mus musculus	Tiling Array	spotted DNA/cDNA, Mouse miRNA chip, We describe a method to detect miRNAs using microarrays, in which the miRNAs are directly hybridized to the array. We used this method to analyze miRNA expression across 16 mouse organs and tissues. More than half of the 78 miRNAs detected were expressed in specific adult tissues. By comparing miRNA levels to mRNA levels determined in a parallel microarray analysis of the same tissues, we found that the expression of target mRNAs predicted on the basis of sequence similarity is biased towards the tissues in which the corresponding miRNA is expressed. The data shown here includes data for 361 other ncRNAs as positive controls. Probes were generated by tiling across each transcript, including 100 nucleotides of flanking sequence extracted from genomic sequence. Keywords = miRNA mouse
8	GPL1427	NMC_Rat_15k_cDNA_Ser6	30,000	Norwegian University of Science and Technology	2004-08-31		Rattus norvegicus	cDNA Array	spotted DNA/cDNA, NMC_Rat_15k_cDNA_Ser6, The 15k rat cDNA arrays were prepared from a collection of 14k cDNAs purchased from Research Genetics (Huntsville, AL) (http://www.mikromatrise.no). Plasmids were isolated from overnight bacterial cultures in 96-well plates and cDNA inserts amplified by PCR using M13 primers 5'-ctg caa ggc gat taa gtt ggg taa c and 5'-gtg agc gga taa caa ttt cac aca gga aag a. The PCR products were purified with Montage PCR purification kit (Millipore) and quality and concentration was assessed by agarose gel electrophoresis. The purified PCR products were dissolved in 50% DMSO (about 50-200 ng/ l) and spotted in duplicate onto 25 x 75mm amino-silane coated CMT-GAPS glass slides (Corning, NY) using a MicroGrid II printing robot (BioRobotics; Cambridge, UK). The arrays were spotted with 48 pins and contained 4 x 12 blocks of 25 x 25 spots. The probes were fixed to the slide surface by UV irradiation (200 mJ). The 15k cDNA arrays represent 14018 unique probes, all printed in duplicates. In addition, a few in-house cDNA probes and a set of positive and negative control elements including 10 different PCR products of exogenous DNA from SpotReportÃ¢â€žÂ¢ cDNA Array Validation System (Stratagene, La Jolla, CA) were printed on the arrays. Totally, each array contained 30000 elements including duplicates and controls.
9	GPL1425	Rat 2K Array	4,608	Medical College of Wisconsin	2004-08-30		Rattus norvegicus	GeneChip	spotted DNA/cDNA, Rat 2K Array, The custom microarrays were manufactured by the Department of Physiology at the Medical College of Wisconsin. Microarrays were printed with a GMS 417 robotic arrayer from Affymetrix (made by Genetic Microsystems) that has a printhead with 4 pin-and-ring print tips. Arrays were prepared from the first 18 of 88 plates of a rat cDNA library from Research Genetics. The clone set represents 1631 known genes and 192 ESTs. We included 506 negative control spots and 456 positive control spots. Following amplification, PCR amplicons were distributed into 384-well polypropylene plates (Genetix, 384 micro array), resuspended in 50% DMSO and printed onto poly-L-lysine coated glass slides. Print configuration is 8 blocks in a 2 x 4 arrangement. Positive controls were printed in each block, and included beta-actin and GAPDH. Negative controls were also printed in each block, and included 5 Arabidopsis gene fragments, mouse COT-1, DMSO, poly dA, yeast tRNA, and PCR buffer with and without primers. The microarray spot density is 250 microns (center-to-center). Spot diameters are approximately 120-150 microns. After printing, DNA was cross-linked to the slides by UV irradiation at 65 mJ (Stratalinker UV Crosslinker, Stratagene). The microarrays were post-processed according to the procedures on the Stanford website (http://cmgm.stanford.edu/pbrown/protocols/index.html) and subsequently stored at room temperature in a desiccated chamber until use.
10	GPL1415	Rat 8Kx2 cDNA array	16,128	Johns Hopkins University	2004-08-24		Rattus norvegicus	cDNA Array	spotted DNA/cDNA, Rat 8Kx2 cDNA array, Rat 8Kx2 cDNA microarrays were obtained from the Johns Hopkins Cancer Center Microarray Core (Baltimore, MD). They contain 8000 genes and ESTs, double-printed on-site, from a cDNA set generated by The Institute for Genomic Research (Rockville, MD).
11	GPL1413	GSF mouse array	20,419	GSF - National Research Center	2004-08-23		Mus musculus	cDNA Array	spotted DNA/cDNA, GSF mouse array, cDNA array of commercially available set of 20.400 clones (Mus musculus) and specific mouse genes spotted on aldehyde coated slides.
12	GPL1406	IncyteMouseGEM1	8,734	Cincinnati Children's Hospital Medical Center	2004-08-12		Mus musculus	cDNA Array	spotted DNA/cDNA, IncyteMouseGEM1, IncyteMouseGEM1 (127 cloneID)
13	GPL1397	Compugen Rat 5K - 65nt	4,803	Leiden University Medical Center	2004-08-09	Compugen, Sigma Genosis	Rattus norvegicus	Oligo Array	spotted oligonucleotide, Compugen Rat 5K - 65nt, Compugen 5K rat oligonucleotide library, 5' C6-amino modifier printed on CodeLink Activated Slides
14	GPL1388	Mice microarray for muscular dystrophy analysis (Layout 1).	1,200	INSERM	2004-07-29		Mus musculus	cDNA Array	spotted DNA/cDNA, Mice microarray for muscular dystrophy analysis (Layout 1)., The microarray 1082 different cDNA clones (with 93 non-annotated), issued from four subtractive libraries, previously prepared by suppressive/subtractive hybridizations between control and mdx hindlimb muscles, and between control and mdx DIA muscles of 12 week-old mice.
15	GPL1389	Mice microarray for muscular dystrophy analysis (Layout 2).	1,200	INSERM	2004-07-29		Mus musculus	cDNA Array	spotted DNA/cDNA, Mice microarray for muscular dystrophy analysis (Layout 2)., The microarray 1082 different cDNA clones (with 89 non-annotated), issued from four subtractive libraries, previously prepared by suppressive/subtractive hybridizations between control and mdx hindlimb muscles, and between control and mdx DIA muscles of 12 week-old mice.
16	GPL1371	TESSF393	4,968	TIGEM (Telethon Institute of genetics and Medicine)	2004-07-23		Mus musculus	cDNA Array	spotted DNA/cDNA, TESSF393, TESS library is a collection of genes preferentially expressed in the embryonic telencephalon. cDNA clones of library TESS sequence validated, were amplified by PCR using primers that were complementary to the vector sequence. PCR products were robotically arrayed (PIXISYS) into lysine-coated slides (CMT-GAPSTM Coated Slides, Corning Microarray Technology). A total of 1026 cDNA clones were printed twice on each slides.
17	GPL1374	TESS400-2	4,961	TIGEM (Telethon Institute of genetics and Medicine)	2004-07-23		Mus musculus	cDNA Array	spotted DNA/cDNA, TESS400-2, TESS library is a collection of genes preferentially expressed in the embryonic telencephalon. cDNA clones of library TESS sequence validated, were amplified by PCR using primers that were complementary to the vector sequence. PCR products were robotically arrayed (PIXISYS) into lysine-coated slides (CMT-GAPSTM Coated Slides, Corning Microarray Technology). A total of 1026 cDNA clones were printed twice on each slides.
18	GPL1369	UCSF Gladstone v.2 Oligo Array (6-2002)	14,112	University of California, San Francisco	2004-07-22		Mus musculus	Oligo Array	spotted oligonucleotide, UCSF Gladstone v.2 Oligo Array (6-2002), Spotted long oligonucleotide array on glass. The library used was the Qiagen/Operon v2.0 mouse oligo library, which is composed of oligonucleotides (70mers) representing 16,443 unique mouse genes. Keywords = spotted, long oligonucleotide
19	GPL1368	TESS185	1,077	TIGEM (Telethon Institute of genetics and Medicine)	2004-07-22		Mus musculus	cDNA Array	spotted DNA/cDNA, TESS185, TESS library is a collection of genes preferentially expressed in the embryonic telencephalon. cDNA clones of library TESS sequence validated, were amplified by PCR using primers that were complementary to the vector sequence. PCR products were robotically arrayed (PIXISYS) into lysine-coated slides (CMT-GAPSTM Coated Slides, Corning Microarray Technology). A total of 1026 cDNA clones were printed on each slides.
20	GPL1356	TESS039	1,078	TIGEM (Telethon Institute of genetics and Medicine)	2004-07-21		Mus musculus	cDNA Array	spotted DNA/cDNA, TESS039, TESS library is a collection of genes preferentially expressed in the embryonic telencephalon. cDNA clones of library TESS sequence validated, were amplified by PCR using primers that were complementary to the vector sequence. PCR products were robotically arrayed (PIXISYS) into lysine-coated slides (CMT-GAPSTM Coated Slides, Corning Microarray Technology). A total of 1026 cDNA clones were printed on each slides.

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