Gene Expression Omnibus (GEO) Overview

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.

All
(11,528)

SAGE NlaIII
(83)

SAGE RsaI
(1)

RT-PCR
(144)

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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	GPL1624	PorkChip 2,600 cDNA array	12,288	University of Minneosta	2004-10-29		Sus scrofa	RT-PCR	spotted DNA/cDNA, PorkChip 2,600 cDNA array, Spotted cDNA array on glass. This set includes approximately 2,600 cDNA clones, selected from a PeyerÃ¢â‚¬â„¢s patch subtracted library and other sources. The PorkChip2 cDNA microarray contains 2,423 ESTs from the subtracted jejunal PeyerÃ¢â‚¬â„¢s patch library (UMNMPM3), 10 ESTs from the normal jejunal PeyerÃ¢â‚¬â„¢s patch library (UMNMPM1), and 26 ESTs from the immune-stimulated jejunal PeyerÃ¢â‚¬â„¢s patch library (UMNMPM2), which were cloned using the GeneTrapper cDNA Positive Selection System and pCMVSport6 vector (Invitrogen Corporation, Carlsbad, CA) (2). Each array also contains 86 ESTs identified by differential display RT-PCR (DD-RT-PCR) of PRRSV-infected macrophages (Library: PRRSV DD-RT-PCR)(5), 19 ESTs identified by DD-RT-PCR of influenza-infected porcine epithelial PK-15 cells (Library: UMNMPM4), 40 porcine genes, which were the result of directed cloning efforts (Library: Sus scrofa gene), and 7 porcine reproductive and respiratory syndrome virus strain VR-2332 sequences (Library: PRRSV) positive and negative controls (Library: Control). Positive controls included 8 Ambion ArrayControl sequences. The plasmid inserts were amplified by two rounds of nested PCR using vector-specific primers. The products from the second round PCR were cleaned by the Montage PCR(96) kit (Millipore, Billerica, MA) and were run on 0.8% agarose gels to quantify the amount of DNA by comparison to standards run on each gel. The dried PCR products were resuspended in phosphate buffer (150 mM sodium phosphate and 1 mM EDTA (pH 8.5)) at a final concentration of 100-300 ng/microliter and transferred to 384 well plates. A BioRobotics MicroGrid II (BioRobotics Ltd., Haslingfield, Cambridge, UK) arrayed the DNA on slides coated with poly-L-lysine (Sigma, St. Louis, MO)(3). Elements were arranged in 48 subarrays of 16 X 16, for a total of 12,288 spots per microarray, with each clone represented in by 4 spots. The slides were baked for 15 min at 80 C, UV irradiated (65 mJ), and chemically blocked with 1-methyl-2-pyrrolidinone and succinic anhydride (4) and were stored at room temperature under vacuum until use. The quality of each printing run was verified by staining one slide with SYBR Gold (Molecular Probes, Eugene, OR) and scanning at 488/530 nm (Excitation/ Emission) (1). Platform_references: 1. Battaglia C, Salani G, Consolandi C, Bernardi LR, and De Bellis G. Analysis of DNA microarrays by non-destructive fluorescent staining using SYBR green II. Biotechniques 29: 78-81, 2000. 2. Dvorak CMT, Hyland KA, Machado JG, Zhang Y, Fahrenkrug SC, and Murtaugh MP. Gene discovery and expression profiling in porcine Peyer's patch. Vet Immunol Immunopathol, submitted, 2004. 3. Eisen MB and Brown O. DNA arrays for analysis of gene expression. Methods Enzymol 303: 179-205, 1999. 4. Shalon D, Smith SJ, and Brown PO. A DNA microarray system for analyzing complex DNA samples using two-color fluorescent probe hybridization. Genome Res 6: 639-645, 1996. 5. Zhang X, Shin J, Molitor TW, Schook LB, and Rutherford MS. Molecular responses of macrophages to porcine reproductive and respiratory syndrome virus infection. Virology 262: 152-162, 1999. Keywords = small intestine, cDNA, pig
2	GPL10963	PFGRC Staphylococcus_aureus_full_genome_RT-PCR	2,647	J Craig Venter Institute	2010-09-23		Staphylococcus aureus	RT-PCR	RT-PCR, PFGRC Staphylococcus_aureus_full_genome_RT-PCR, Full genome Staphylococcus aureus qRT-PCR
3	GPL10974	Francisella tularensis full genome qRT-PCR	1,068	J Craig Venter Institute	2010-09-24		Francisella tularensis	RT-PCR	RT-PCR, Francisella tularensis full genome qRT-PCR, Francisella tularensis full genome qRT-PCR
4	GPL4097	TaqMan Human MAQC (TAQ)	1,044	NCTR/FDA	2006-08-15		Homo sapiens	RT-PCR	RT-PCR, TaqMan Human MAQC (TAQ),
5	GPL7701	CNRS Mouse 432 GPCR1 v1.0	432	MGX - Montpellier GenomiX	2008-11-26		Mus musculus	RT-PCR	RT-PCR, CNRS Mouse 432 GPCR1 v1.0,
6	GPL11636	TaqManÃ‚Â® Rodent miRNA card A v2.0	384	Stanford University School of Medicine	2011-01-20		Mus musculus,Rattus norvegicus	RT-PCR	RT-PCR, TaqManÃ‚Â® Rodent miRNA card A v2.0, A Card Content: MicroRNAs of demonstrated interest to the research community (these tend to be functionally defined, broadly expressed and/or highly expressed).
7	GPL11637	TaqManÃ‚Â® Rodent miRNA Card B v2.0	384	Stanford University School of Medicine	2011-01-20		Mus musculus,Rattus norvegicus	RT-PCR	RT-PCR, TaqManÃ‚Â® Rodent miRNA Card B v2.0, B Card Content: MicroRNAs less extensively studied (these tend to have less defined functions, be narrowly expressed, and/or be expressed at a low level).
8	GPL13987	Taqman Array Human MicroRNA A Card v2.0	384	Tokyo Medical University	2011-07-28		Homo sapiens	RT-PCR	RT-PCR, Taqman Array Human MicroRNA A Card v2.0, Format: 384-well plate Manufacturer: Applied Biosystems See manufacturer's website (http://www.appliedbiosystems.com/).
9	GPL5073	Applied Biosystems Customized TaqMan Low Density Array (Mouse) _ In vivo T cell gene expression	384	University of Birmingham	2007-04-09		Mus musculus	RT-PCR	RT-PCR, Applied Biosystems Customized TaqMan Low Density Array (Mouse) _ In vivo T cell gene expression, To probe T cell responses in vivo, naÃƒÂ¯ve OVA-specific transgenic CD4 T (OTII) cells were transferred into normal mice and the chimeras were then immunized with specific forms of OVA driving either a Th1 or a Th2 type of immune responses. This was achieved respectively by following the response in the draining lymph node after immunizing subcutaneously, either with live attenuated Salmonella typhimurium engineered to express an OVA transgene, or alum-precipitated OVA. Virtual platform listing 384 in vivo T cell polarization-related candidate genes investigated using RT-PCR.
10	GPL11111	Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S 0.3K	288	J Craig Venter Institute	2010-10-25		Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S	RT-PCR	RT-PCR, Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S 0.3K,
11	GPL9019	TaqMan MicroRNA Assays Human Panel Early Access Kit (Applied Biosystems)	157	University of Modena and Reggio Emilia	2009-08-11		Homo sapiens	RT-PCR	RT-PCR, TaqMan MicroRNA Assays Human Panel Early Access Kit (Applied Biosystems), The original platform is composed of two 96-well plates (Plate A and Plate B) whose content is here merged into one single platform. Applied Biosystems Catalog Number: 4365409. Currently no more available for sale.
12	GPL1793	Rainbow trout sex differentiation cascade-related genes investigated using RT-PCR	102	Institut National de la Recherche Agronomique-INRA	2005-01-12		Oncorhynchus mykiss	RT-PCR	RT-PCR, Rainbow trout sex differentiation cascade-related genes investigated using RT-PCR, Virtual platform listing sex differentiation cascade-related candidate genes investigated using RT-PCR.
13	GPL5174	Applied Biosystems TaqMan mouse B cell_low density array	96	University of Birmingham	2007-05-18		Mus musculus	RT-PCR	RT-PCR, Applied Biosystems TaqMan mouse B cell_low density array, A custom designed low density TaqMan array.
14	GPL6926	Superarray DNA damage signaling APHS-029B	96	University of Illinois	2008-06-03		Homo sapiens	RT-PCR	RT-PCR, Superarray DNA damage signaling APHS-029B, The Human DNA Damage Signaling RTÃ‚Â² ProfilerÃ¢â€žÂ¢ PCR Array profiles the expression of 84 genes involved in DNA damage signaling pathways. The genes featured are those associated with the ATR/ATM signaling network and transcriptional targets of DNA damage response. DNA damage can result in cell cycle arrest, apoptosis, and the stabilization and repair of the cellular genome.
15	GPL6933	Superarray Signal Transduction PathwayFinder PCR Array APHS-014b	96	University of Illinois	2008-06-04		Homo sapiens	RT-PCR	RT-PCR, Superarray Signal Transduction PathwayFinder PCR Array APHS-014b, The Human Signal Transduction PathwayFinderÃ¢â€žÂ¢ RTÃ‚Â²ProfilerÃ¢â€žÂ¢ PCR Array profiles the expression of 84 key genes representative of 18 different signal transduction pathways listed below. Using real-time PCR, you can easily and reliably analyze the expression of a focused panel of genes related to any of the 18 signal transduction pathways that may be involved in your favorite biological response.
16	GPL7726	SuperArray Mouse Th-17 pathway PCR Array	96	University of Southern California	2008-12-02		Mus musculus	RT-PCR	RT-PCR, SuperArray Mouse Th-17 pathway PCR Array, The Mouse Th17 for Autoimmunity & Inflammation RTÃ‚Â²ProfilerÃ¢â€žÂ¢ PCR Array profiles the expression of 84 genes related to the Th17 Regulatory Network. Th17 is a newly defined subset of CD4(+) T cells that is distinct from the traditional Th1, Th2 and Treg. Th17 is highly proinflammatory and induces severe autoimmunity. This array contains surface molecules, cytokines and receptors, chemokines, matrix metalloproteinases, cell signaling molecules and transcriptional factors. Using real-time PCR, you can easily and reliably analyze expression of a focused panel of genes related to the Th17 regulatory network with this array.
17	GPL7747	SuperArray Mouse Th1-Th2-Th3 PCR Array PCR Array	96	University of Southern California	2008-12-05		Mus musculus	RT-PCR	RT-PCR, SuperArray Mouse Th1-Th2-Th3 PCR Array PCR Array, The Mouse Th1-Th2-Th3 RTÃ‚Â² ProfilerÃ¢â€žÂ¢ PCR Array profiles the expression of 84 genes related to the three classes of helper T cells (CD4+ T lymphocytes): Th1, Th2, and Th3. This array includes cytokine genes representative of Th1, Th2 and Th3 cells. The array also contains genes encoding transcriptional factors that regulate the expression of these cytokines as well as other markers of CD4+ T lymphocytes. Genes involved in immune cell activation, in the Th1 and Th2 type immune responses, and genes involved in the antimicrobial humoral response are included on this array as well as other immune response-related genes. Using real-time PCR, you can easily and reliably analyze expression of a focused panel of genes related to helper T cells with this array.
18	GPL8370	Human Stress & Toxicity PathwayFinder PCR Array PAHS-003A	96	University of Illinois at Urbana-Champaign	2009-03-31		Homo sapiens	RT-PCR	RT-PCR, Human Stress & Toxicity PathwayFinder PCR Array PAHS-003A, From manufacturer SA biosciences (former superarray) website: The Human Stress and Toxicity PathwayFinderÃ¢â€žÂ¢ RTÃ‚Â²ProfilerÃ¢â€žÂ¢ PCR Array profiles the expression of 84 genes whose expression level is indicative of stress and toxicity. The array includes genes that are directly up-regulated by oxidative or metabolic stress and by heat shock. The array also includes genes representative of pathways activated by prolonged stress, which range from cell death by apoptosis or necrosis to growth arrest and senescence to proliferation and carcinogenesis. This kit is also designed to include only those genes that have been reported in the literature to respond to a toxic compound at the transcriptional level. Using real-time PCR, you can easily and reliably analyze expression of a focused panel of genes related to Stress & Toxicity Pathway with this array.
19	GPL9850	DNA Damage Signaling Pathway PCR Array Human PAHS-029	96	University of Illinois at Urbana-Champaign	2009-12-31		Homo sapiens	RT-PCR	RT-PCR, DNA Damage Signaling Pathway PCR Array Human PAHS-029, The Human DNA Damage Signaling RTÃ‚Â² ProfilerÃ¢â€žÂ¢ PCR Array profiles the expression of 84 genes involved in DNA damage signaling pathways. The genes featured are those associated with the ATR/ATM signaling network and transcriptional targets of DNA damage response. DNA damage can result in cell cycle arrest, apoptosis, and the stabilization and repair of the cellular genome. Using real-time PCR, you can easily and reliably analyze expression of a focused panel of genes related to DNA Damage Signaling with this array.
20	GPL5152	RT^2 Profiler PCR Array Mouse Angiogenesis (PAMM-024A)	90	Lab of Bioeffects of Nanosized Materials, Institute of High Energy Physics	2007-05-09		Mus musculus	RT-PCR	RT-PCR, RT^2 Profiler PCR Array Mouse Angiogenesis (PAMM-024A), We synthesize a novel nanoparticle with functional surface coating, which inhibits tumor growth without detectable cytotoxicities by suppress angiogenesis in the tumor mass. Quantitative counting RTPCR-array analysis was used to evalute the pro-angiogenic factor(s) on mRNA level.

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