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)

HT-Seq
(1,218)

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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	GPL7157	Whitehead/Bartel Schizosaccharomyces pombe 454 sequencing ago1 associated small RNAs	235,351	Whitehead Institute/MIT	2008-08-12	Whitehead, 454	Schizosaccharomyces pombe	HT Sequencing	other, Whitehead/Bartel Schizosaccharomyces pombe 454 sequencing ago1 associated small RNAs, 454 sequencing
2	GPL8024	Combimatrix microarray of 454 derived grape berry transcripts	44,229	University of Verona	2009-01-04	University of Verona - Scientific and Technological Department - Plant Functional Genomics Centre	Vitis vinifera	HT Sequencing	in situ oligonucleotide, Combimatrix microarray of 454 derived grape berry transcripts, Spots size: 25 microns Total number of spots: 94928 Number of spots replicates per oligo: 2
3	GPL8198	SNI_human_MPSS	29,953	Swedish Medical Center	2009-02-17	SOLEXA	Homo sapiens	HT Sequencing	MPSS, SNI_human_MPSS,
4	GPL6924	HMS Drosophila ChIP-seq	0	Harvard Medical School	2008-06-03	Solexa	Drosophila melanogaster	HT Sequencing	other, HMS Drosophila ChIP-seq, Solexa sequencing
5	GPL10350	INRA Melampsora larici-populina whole-genome expression array	17,314	INRA	2010-04-22	Roche-NimbleGen	Melampsora laricis-populina	HT Sequencing	in situ oligonucleotide, INRA Melampsora larici-populina whole-genome expression array, The Melampsora larici-populina custom-exon expression array (4 x 72K) manufactured by Roche NimbleGen Systems Limited (Madison, WI) contains four independent, nonidentical, 60-mer probes per sequence. Included in the oligoarray are 16,599 Joint Genome Institute (JGI)-annotated gene models, 376 user-annotated gene models, 395 additional putative gene models identified by Eugene prediction, and 315 putative gene models identified by using 454 transcripts and 69 repeat elements. In addition, 1,063 random 60-mer control probes and labelling controls are present on the array. For 440 gene models, technical duplicates are included on the array. This is a condensed platform of the full array which has probes designed from gene models taken from the Joint Genome Institute (JGI) Melampsora larici-populina genome sequence version 1.0 (http://genome.jgi-psf.org/Mellp1/Mellp1.home.html ).
6	GPL6314	NCI Human Solexa Platform 14814K	14,814,587	National Cancer Institute	2007-12-20	not applicable	Homo sapiens	HT Sequencing	other, NCI Human Solexa Platform 14814K,
7	GPL7059	Whitehead-Young-Mouse-Solexa (small RNA sequences)	6,901,774	Whitehead Institute	2008-07-16	not applicable	Mus musculus	HT Sequencing	other, Whitehead-Young-Mouse-Solexa (small RNA sequences), Solexa sequencing Data generated at Center for Advanced Genome Technology at Whitehead Institute using Genome Analyzer manufactured by Solexa/Illumina (Sequencing by Synthesis)
8	GPL6300	NCI Human 454 Platform 2795K	2,795,975	National Cancer Institute	2007-12-19	not applicable	Homo sapiens	HT Sequencing	other, NCI Human 454 Platform 2795K,
9	GPL6451	Hannon/CSHL-mouse-Illumina 1G sequencing-oocyte small RNAs	1,673,339	Cold Spring Harbor Laboratory	2008-02-01	not applicable	Mus musculus	HT Sequencing	other, Hannon/CSHL-mouse-Illumina 1G sequencing-oocyte small RNAs, Solexa/Illumina 1G sequencing platform. Illumina Inc. San Diego, CA
10	GPL3968	Arabidopsis thaliana high-throughput small RNA sequencing	340,114	Whitehead Institute for Biomedical Research, MIT Department of Biology	2006-06-30	not applicable	Arabidopsis thaliana	HT Sequencing	other, Arabidopsis thaliana high-throughput small RNA sequencing , High-throughput sequencing of endogenous small RNAs from Arabidopsis thaliana. This dataset contains sequences of genome-matching small RNAs generated from cDNA libraries of wild-type seedling, rosette, flower and silique tissues, and mapping to the Arabidopsis nuclear, chloroplast and/or mitochondrial genomes. For isolation protocol please see Axtell, M.J., Jan, C., Rajagopalan, R., and Bartel, D.P. (2006) A two-hit trigger for siRNA biogensis in plants. Cell 127:565-577.
11	GPL7058	Whitehead-Young-Mouse-Solexa (ChIP-seq)	0	Whitehead Institute	2008-07-16	not applicable	Mus musculus	HT Sequencing	other, Whitehead-Young-Mouse-Solexa (ChIP-seq), Solexa sequencing Data generated at Center for Advanced Genome Technology at Whitehead Institute using Genome Analyzer manufactured by Solexa/Illumina (Sequencing by Synthesis)
12	GPL4647	High-throughput sequenced small RNAs in Arabidopsis thaliana and its RISC complexes	44,003	Cold Spring Harbor Laboratory	2006-12-07	none	Arabidopsis thaliana	HT Sequencing	other, High-throughput sequenced small RNAs in Arabidopsis thaliana and its RISC complexes, This dataset contains Arabidopsis thaliana endogenous small RNA sequences from total extraxts, AGO1 and AGO4 complexes. The sequences were obtained using high-throughput sequencing technology provided by 454. For technical details, see Qi, Y., He, X., Wang, X.J., Kohany, O., Jurka, J., and Hannon, G.J. 2006. Distinct catalytic and non-catalytic roles of ARGONAUTE4 in RNA-directed DNA methylation. Nature 443(7114): 1008-1012.
13	GPL5013	Chlamydomonas reinhardtii small RNA sequences	4,182	National Institute of Biological Sciences, Beijing	2007-03-19	none	Chlamydomonas reinhardtii	HT Sequencing	other, Chlamydomonas reinhardtii small RNA sequences, This dataset contains Chlamydomonas reinhardtii endogenous small RNA sequences from total extraxts. The sequences were obtained using high-throughput sequencing technology provided by 454. For technical details, see Tao Zhao, Guanglin Li, Shijun Mi, Shan Li, Gregory J. Hannon, Xiu-Jie Wang, and Yijun Qi. 2007. A Complex System of Small RNAs in the Unicellular Green Alga Chlamydomonas reinhardtii. Genes & Development
14	GPL8267	HudsonAlpha Illumina Homo sapiens Methyl-seq	90,612	Stanford U	2009-03-09	NIH	Homo sapiens	HT Sequencing	other, HudsonAlpha Illumina Homo sapiens Methyl-seq, 1G Genome Analyzer sequencing machine
15	GPL6966	StanfordGenetics/SherlockLab-Scerevisiae-SolexaRNASeq-PolyA RNA	0	Stanford University	2008-06-16	N/A	Saccharomyces cerevisiae	HT Sequencing	other, StanfordGenetics/SherlockLab-Scerevisiae-SolexaRNASeq-PolyA RNA, Solexa Sequencing Solexa Genome Analyzer (GA1)
16	GPL7003	MPIMG-Human-Solexa sequencing HEK PolIIa ChIP	12,814,371	Max Planck Institute for molecular genetics	2008-06-30	MPIMG	Homo sapiens	HT Sequencing	other, MPIMG-Human-Solexa sequencing HEK PolIIa ChIP, Sequencing was carried out using the 1G Illumina Genome Analyser (Solexa)
17	GPL7004	MPIMG-Human-Solexa sequencing-HEK and B cell RNA	12,004,594	Max Planck Institute for molecular genetics	2008-06-30	MPIMG	Homo sapiens	HT Sequencing	other, MPIMG-Human-Solexa sequencing-HEK and B cell RNA, Sequencing was carried out using the 1G Illumina Genome Analyser (Solexa)
18	GPL8664	LC Sciences Human 454 miRHuman_8.2 [condensed version]	503	"Sapienza" University of Rome	2009-06-05	LC sciences	Homo sapiens	HT Sequencing	in situ oligonucleotide, LC Sciences Human 454 miRHuman_8.2 [condensed version], This array represents a condensed version of full array which is linked as a supplementary file.
19	GPL7238	IMBA Ago-1 and TRIM32-bound small RNAs from E14.5 mouse brain (454 GS FLX system)	118,419	Hubrecht Institute	2008-09-01	Institute of molecular Biology of the Austrian Academy of Sciences (IMBA)	Mus musculus	HT Sequencing	MPSS, IMBA Ago-1 and TRIM32-bound small RNAs from E14.5 mouse brain (454 GS FLX system),
20	GPL10247	44K multiplex chip, Agilent (Tailor-made microarray, condensed version)	21,938	Technische UniversitÃƒÂ¤t MÃƒÂ¼nchen	2010-03-24	imaGenes (Berlin, Germany)	Athelia rolfsii	HT Sequencing	spotted oligonucleotide, 44K multiplex chip, Agilent (Tailor-made microarray, condensed version), Tailor-made microarray (44K multiplex chip, Agilent) was designed by imaGenes (Berlin, Germany) using an in-house developed method for empirical selection of best performing probes for each gene (Pre Selection Strategy). Briefly, up to ten probes were designed for each of the 454 unigenes (60 bp long oligomers). The 244K Agilent test array was hybridized with pooled Cy3-labeled cRNAs gained form EPSmax13 and EPSmin17 cultures and (in average) two of the best performing oligos were selected for each unigene. Full physical array layout file linked as a supplementary file, GPL10247_44K_Design.txt. The oligonucleotide sequences can be found in the GPL10247_44K_Design.txt.gz file.

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