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.

Plants
(2,239)

Bacteria
(1,690)

Viruses
(78)

SAGE RsaI
(0)

Bead Array
(0)

Protein Array
(0)

Antibody
(0)

RT-PCR
(0)

HT-Seq
(473)

Other
(26)

All
(2,239)

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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	GPL6705	Illumina Arabidopsis thaliana SBS inflorescence (polyA RNA)	7,109,274	Delaware Biotechnology Institute	2008-04-08		Arabidopsis thaliana	Other	other, Illumina Arabidopsis thaliana SBS inflorescence (polyA RNA),
2	GPL7071	Small RNA SBS signatures indentified from maize using Illumina's SBS technnology	5,386,553	University of Delaware	2008-07-19		Zea mays	Other	other, Small RNA SBS signatures indentified from maize using Illumina's SBS technnology,
3	GPL6708	Illumina Arabidopsis thaliana SBS inflorescence (small RNA)	3,589,785	Delaware Biotechnology Institute	2008-04-08		Arabidopsis thaliana	Other	other, Illumina Arabidopsis thaliana SBS inflorescence (small RNA),
4	GPL3886	Physcomitrella patens high-throughput small RNA sequencing	214,996	Pennsylvania State University	2006-06-19		Physcomitrella patens	Other	other, Physcomitrella patens high-throughput small RNA sequencing, Endogenous small RNAs from Physcomitrella patens were sequenced using pyrosequencing as described in Axtell et al. (2006) A two-hit trigger for siRNA biogenesis in plants. Cell 127: 565-577. UPDATED JULY 9, 2007 TO INCLUDE SEQUENCED RNAS THAT DO NOT HAVE AN EXACT MATCH IN THE GENOME
5	GPL5014	Sequenced small RNAs from the lycopod Selaginella moellendorffii	36,582	Pennsylvania State University	2007-03-20		Selaginella moellendorffii	Other	other, Sequenced small RNAs from the lycopod Selaginella moellendorffii, Pyrosequencing of small RNAs from the lycopod Selaginella moellendorffii.
6	GPL973	UMAS:MboI/FokI:Saccharomyces cerevisiae	32,097	Agilix Corporation	2004-02-04		Saccharomyces cerevisiae	Other	other, UMAS:MboI/FokI:Saccharomyces cerevisiae, This is a virtual platform for UMAS libraries generated for Saccharomyces cerevisiae using MboI/FokI as an anchor enzyme. Platform_anchor: MboI/FokI
7	GPL10695	SMD Print_1478 yeast protoarray YA104704	19,200	Stanford University	2010-07-16	Stanford Functional Genomics Facility, Stanford School of Medicine	Saccharomyces cerevisiae	Other	spotted peptide or protein, SMD Print_1478 yeast protoarray YA104704,
8	GPL7736	JHMI/Zhu_YEAST_14K_v1.0	13,632	Johns Hopkins	2008-12-04	Zhu lab	Saccharomyces cerevisiae	Other	spotted peptide or protein, JHMI/Zhu_YEAST_14K_v1.0,
9	GPL3234	Invitrogen Yeast Protoarray	12,288	University of Colorado School of Medicine	2005-12-05	Invitrogen	Saccharomyces cerevisiae	Other	spotted peptide or protein, Invitrogen Yeast Protoarray, The Yeast ProtoArrayÃ¢â€žÂ¢ high-density functional protein microarray is the first microarray product that enables rapid elucidation of proteinprotein interactions on a proteome scale. The Yeast ProtoArrayÃ¢â€žÂ¢ contains 4,088 S. cerevisiae open reading frames (ORFs) expressed as 5'-GST fusions, purified and spotted in duplicate on a 1 inch x 3 inch nitrocellulose-coated slide (Figure 1).With the Yeast ProtoArrayÃ¢â€žÂ¢ PPI Kit, you can identify novel protein interactions in a single day, instead of the several weeks required using alternatives such as yeast two-hybrid systems. In addition, protein interactions can be easily assayed under different conditions to better understand interaction dynamics.
10	GPL9404	Yeast Protoarray 082004_YeastProtoArrayKSP	12,288	Duke University	2009-10-08	Invitrogen	Saccharomyces cerevisiae	Other	spotted peptide or protein, Yeast Protoarray 082004_YeastProtoArrayKSP,
11	GPL9445	Yeast Protoarray YA103104 gal file	12,288	Duke University	2009-10-14	Invitrogen	Saccharomyces cerevisiae	Other	spotted peptide or protein, Yeast Protoarray YA103104 gal file,
12	GPL10696	SMD Print_1531 yeast protoarray YPROT2	11,520	Stanford University	2010-07-16	Stanford Functional Genomics Facility, Stanford School of Medicine	Saccharomyces cerevisiae	Other	spotted peptide or protein, SMD Print_1531 yeast protoarray YPROT2,
13	GPL14990	Pleiss Lab_S.cerevisiae_Q-PCR Screen Library	5,760	Cornell University	2011-12-09	Pleiss Lab	Saccharomyces cerevisiae	Other	other, Pleiss Lab_S.cerevisiae_Q-PCR Screen Library,
14	GPL4992	Quantitative proteomics of anaerobic and aerobic yeast cultures	892	Delft University of Technology	2007-03-14		Saccharomyces cerevisiae	Other	MS, Quantitative proteomics of anaerobic and aerobic yeast cultures, Proteins identified in quantitative analysis of anaerobic and aerobic yeast cultures
15	GPL2543	18O Isotopic Labeling of Plasma Membrane	658	University of Wisconsin	2005-06-14		Arabidopsis thaliana	Other	MS, 18O Isotopic Labeling of Plasma Membrane, An isotopic labeling experiment designed to identifiy plasma membrane proteins. Fractions from a two-phase partitioning experiment are labeled using natural abundance or 18O enriched water to compare the PM enriched fraction to the PM-depleted microsomal fraction.
16	GPL6919	Identification of targets of the protein disulfide reductase thioredoxin	210	Technical University of Denmark	2008-06-03		Hordeum vulgare	Other	MS, Identification of targets of the protein disulfide reductase thioredoxin,
17	GPL7033	Proteins from vacuoles of Cyanidioschyzon merolae strain 10D	46	Rikkyo (St. Paul's) University	2008-07-08		Cyanidioschyzon merolae strain 10D	Other	MS, Proteins from vacuoles of Cyanidioschyzon merolae strain 10D, The vacuoles of Cyanidioschyzon merolae strain 10D (Eukaryota; Rhodophyta; Bangiophyceae; Cyanidiales; Cyanidiaceae) synchronized at interphase. The vacuoles of C. merolae synchronized at interphase were isolated by differential and iodixanol-gradient ultracentrifugation. The supernatant (5 ug of protein) were subjected to SDS-PAGE, cut into 69 slices without staining, and subjected to automatic sample preparation for MALDI-TOF-MS by a robot Xcise (Shimadzu). Alternatively, the vacuolar fraction protein (15.8 ug) was alkylated with 5% (w/v) acrylamide, subjected to SDS-PAGE, and stained with Imperial Protein Stain (Pierce). The gel slices of 58 visible bands were destained and digested as described previously (PMID: 11507753). After the digestion, the peptide fragments were extracted from the gel pieces with 5% (v/v) formic acid in 50% (v/v) CH3CN. Extracts were dried in a vacuum concentrator. The dried peptides were dissolved in 0.1% (v/v) trichloroacetic acid (TFA), desalted using uC18-Zip Tip microcolumns (Millipore) and spotted onto a 384-well plate (KRATOS Analytical). After completely drying the samples, 0.5% (w/v) alpha-cyano-4-hydroxycinnamic acid in 50% (v/v) CH3CN and 0.1% (v/v) TFA were spotted on the peptide spots and allowed to dry. The samples were analyzed by peptide mass fingerprinting (PMF) using a mass spectrometer (AXIMA-TOF2; Shimadzu) in the reflectron mode. When samples could not be identified by PMF, several peptide peaks were further analyzed by post source decay (PSD)-MS/MS. Database searches were performed using the software program MASCOT v2.2.01 (Matrix Science) running on a local database built from the FASTA files of 5014 open reading frames in the C. merolae genome database (http://merolae.biol.s.u-tokyo.ac.jp/). The peptide tolerance was set to 0.1-0.2 Da. Cysteine carbamidomethylation (for samples prepared by Xcise) or propionamidation (for manually prepared samples) was included as a fixed modification and methionine oxidation was included as a variable modification. The identification threshold was set to p < 0.05. As a result, 46 proteins were identified.
18	GPL10138	SAGE:22:BfaI:Arabidopsis thaliana	0		2010-03-05		Arabidopsis thaliana	Other	other, SAGE:22:BfaI:Arabidopsis thaliana, This is a virtual platform for SAGE libraries generated for Arabidopsis thaliana using BfaI as an anchor enzyme.
19	GPL10299	SAGE:16:DpnII:Schizophyllum commune	0		2010-04-08		Schizophyllum commune	Other	other, SAGE:16:DpnII:Schizophyllum commune, This is a virtual platform for SAGE libraries generated for Schizophyllum commune using DpnII as an anchor enzyme.
20	GPL6641	SalkGAL-Arabidopsis-IlluminaGA-epigenome - bisulphite sequencing	0	Salk-Institute	2008-03-21		Arabidopsis thaliana	Other	other, SalkGAL-Arabidopsis-IlluminaGA-epigenome - bisulphite sequencing, Genetic Analyzer, Illumina, San Diego, CA.

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