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	GPL8620	Penn State Physcomitrella SOLiD sequencing	2,784,945	Pennsylvania State University	2009-06-01		Physcomitrella patens	HT Sequencing	MPSS, Penn State Physcomitrella SOLiD sequencing, Processed degradome signatures representing the 5' ends of uncapped, polyA+ mRNAs. AB SOLiD System 2.0
2	GPL6670	CSIRO-PI Oryza Sativa small RNA sequences 2007 (Solexa sequenced)	2,683,656	CSIRO Plant Industry	2008-04-01		Oryza sativa	HT Sequencing	other, CSIRO-PI Oryza Sativa small RNA sequences 2007 (Solexa sequenced), Small RNAs from Oryza Sativa were sequenced from 1-5 days-after-fertilisation grains and 6-10 days-after-fertilisation grains, using the Solexa sequencing technology. This is the unique list of trimmed sequences obtained from these experiments
3	GPL6684	Axtell_Arabidopsis_Degradome_v1 (Solexa/Illumina sequenced)	2,010,253	Pennsylvania State University	2008-04-04		Arabidopsis thaliana	HT Sequencing	other, Axtell_Arabidopsis_Degradome_v1 (Solexa/Illumina sequenced), Unique tags of 20 or 21nt length obtained from Col-0 wild-type A. thaliana.
4	GPL7174	Axtell_Physco_WT_Linker1 (Solexa sequencing)	617,860	Pennsylvania State University	2008-08-17		Physcomitrella patens	HT Sequencing	other, Axtell_Physco_WT_Linker1 (Solexa sequencing), Small RNAs were sequenced using a Solexa GA. Three different linkers were used for different samples and mixed prior to sequencing. Raw data was filtered to identify small RNAs associated with each linker and the linkers removed. Subsequently, small RNAs were filtered to remove rRNA fragments. The remainder were mapped to the Physcomitrella patens draft genome version 1.2 (using oligomap) and filtered to retain only those with one or more perfect match. This platform is all retained small RNA sequences from two technical replicates from 10 day old Wild-Type. See Cho et al. for details.
5	GPL6331	NIBS-Arabidopsis-solexa-AGO sRNAs	586,511	National Institute Of Biological Sciences, Beijing (NIBS)	2007-12-27		Arabidopsis thaliana	HT Sequencing	other, NIBS-Arabidopsis-solexa-AGO sRNAs, Solexa, CSHL
6	GPL7176	Axtell_Physco_rdr6_Linker3 (Solexa sequencing)	582,688	Pennsylvania State University	2008-08-17		Physcomitrella patens	HT Sequencing	other, Axtell_Physco_rdr6_Linker3 (Solexa sequencing), Small RNAs were sequenced using a Solexa GA. Three different linkers were used for different samples and mixed prior to sequencing. Raw data was filtered to identify small RNAs associated with each linker. Subsequently, small RNAs were filtered to remove rRNA fragments. The remainder were mapped to the Physcomitrella patens draft genome version 1.2 (using oligomap) and filtered to retain only those with one or more perfect match. This platform is all small RNA sequences from two technical replicates from 10 day old rdr6-19 plants. See Cho et al. for details.
7	GPL7175	Axtell_Physco_dcl3_Linker2 (Solexa sequencing)	522,668	Pennsylvania State University	2008-08-17		Physcomitrella patens	HT Sequencing	other, Axtell_Physco_dcl3_Linker2 (Solexa sequencing), Small RNAs were sequenced using a Solexa GA. Three different linkers were used for different samples and mixed prior to sequencing. Raw data was filtered to identify small RNAs associated with each linker. Subsequently, small RNAs were filtered to remove rRNA fragments. The remainder were mapped to the Physcomitrella patens draft genome version 1.2 (using oligomap) and filtered to retain only those with one or more perfect match. This platform is all small RNA sequences from 10 day old dcl3 samples (line 5 and 10). See Cho et al. for details.
8	GPL7029	Carrington-Arabidopsis-Illumina-miRNA-AGO-high-throughput sequencing	515,462	Donald Danforth Plant Science Center	2008-07-08	Center for Genome Research and Biocomputing, Oregon State University	Arabidopsis thaliana	HT Sequencing	other, Carrington-Arabidopsis-Illumina-miRNA-AGO-high-throughput sequencing, Sequencing-by-synthesis technology was used to sequence small RNA from input and co-immunoprecipitation fractions from cell lysates of inflorescence tissue from Arabidopsis plants transformed with HA epitope-tagged AGO2 or AGO7 constructs. Meaningful intepretation requires comparison between the input and co-immunoprecipitation datasets. Small RNA sequences were parsed from Illumina sequencing data files through identification of adaptor boundaries. Only sequences that mapped to the Arabidopsis thaliana Col-0 genome were included in the analysis.
9	GPL7470	Monsanto-rice-454-smallRNAs-high throughput sequencing	386,608	Monsanto	2008-10-10		Oryza sativa	HT Sequencing	in situ oligonucleotide, Monsanto-rice-454-smallRNAs-high throughput sequencing, intrument model: 454 GS FLX
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	GPL7043	High-throughput pyrosequencing of small RNAs in Tomato fruits and leaves	312,719	University of East Anglia	2008-07-11		Solanum lycopersicum	HT Sequencing	other, High-throughput pyrosequencing of small RNAs in Tomato fruits and leaves, The dataset contains Lycopersicon esculentum cv. MicroTom endogenous small RNA sequences in the range 16-30 nucleotides. High-throughput sequencing was carried out at 454 Life Sciences. Please see www.454.com for details of the technology. Total RNA was extracted from tomato leaf, bud before flower blooming and different developmental stages of whole fruits.Small RNA sequences that did not match tRNA or rRNA sequences (obtained from RFAM), The Genomic tRNA Database and EMBL were mapped to bacs version 175 of the Solanum lycopersicum cv. Heinz 1706-BG genome. The number of matches to the unfinished genome, if any, is recorded in the table.
12	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
13	GPL4732	Arabidopsis thaliana small RNAs sequences identified using high-throughput 454 sequencing technology	218,575	Donald Danforth Plant Science Center	2007-01-08		Arabidopsis thaliana	HT Sequencing	other, Arabidopsis thaliana small RNAs sequences identified using high-throughput 454 sequencing technology, The dataset contains unique, 20-25 nucleotide small RNA sequences identified using high-throughput 454 sequencing of samples prepared from Arabidopsis thaliana. Each sequence has a minimum of one genomic locus. Small RNAs were sequenced from inflorescence tissue (containing stage 1-12 flowers) of wildtype Col-0 plants, mutants with defects in each DCL gene (dcl1-7, dcl2-1, dcl3-1, dcl4-2), mutants with defects in each RDR gene for which a function has been established (rdr1-1, rdr2-1, rdr6-15), and whole seedling tissue (3 day post-germinations) of Col-0 and rdr6-15 plants. Small RNA preparations from leaf samples of Col-O that were either uninoculated or inoculated by Pseudomonas syringae pv tomato (DC3000hrcC) for 1 hr and 3 hr were also sequenced.
14	GPL7123	Small RNAs from 4-week old seedling of Oryza sativa	162,943	Washington University in St. Louis	2008-08-03		Oryza sativa	HT Sequencing	other, Small RNAs from 4-week old seedling of Oryza sativa, Small RNAs were sequenced with 454 high-throughput pyro-sequencing platform at 454 Life Sciences
15	GPL6669	CSIRO-PI Oryza Sativa small RNA sequences 2007 (454 sequenced)	99,654	CSIRO Plant Industry	2008-04-01		Oryza sativa	HT Sequencing	other, CSIRO-PI Oryza Sativa small RNA sequences 2007 (454 sequenced), Small RNAs from Oryza Sativa were sequenced from 1-5 days-after-fertilisation grains, 6-10 days-after-fertilisation grains, and from roots and shoots, using the 454 sequencing technology. This is the unique list of trimmed sequences obtained from these experiments.
16	GPL8587	Preliminary exploration of Oryza sativa small RNAs - Run 1 and 2	99,647	University of California Davis	2009-05-22	454 Life Sciences	Oryza sativa	HT Sequencing	other, Preliminary exploration of Oryza sativa small RNAs - Run 1 and 2, The datasets contain Oryza sativa var Nipponbar endogenous small RNA sequences in the size range 18 to 34 nt. High-throughput sequencing was performed at 454 Life Sciences using the 454 pyrosequencing method (Margulies et al., 2005) using 5' and 3' adapter oligonucleotides. Plants were grown in a Conviron Environmental Chamber at high light intensity using both high pressure sodium and metal halide lamps for 10.5 hr at 28 degrees C and for 13.5 hr at 26 degrees C in the dark. RNA was extracted from rice tissues at various stages of development and under different abiotic and biotic stresses. The small RNAs presented here were all mapped to the rice genome TIGR version 5. The total number of distinct mapped sequences are 12879 for Run 1 and 88508 for Run 2. The total number of sequence reads were respectively 70406 and 191682.
17	GPL6375	High-throughput pyrosequencing of small RNAs in Arabidopsis thaliana	96,443	University of East Anglia	2008-01-15		Arabidopsis thaliana	HT Sequencing	other, High-throughput pyrosequencing of small RNAs in Arabidopsis thaliana, The dataset contains Arabidopsis thaliana endogenous small RNA sequences in the range 16 to 31 nucleotides. High-throughput sequencing was carried out at 454 Life Sciences. Please see www.454.com for details of the technology. Total RNA was extracted from mixed-stage flower buds grown under 16h light.
18	GPL4011	Small RNAs identified using 454 sequencing	49,402	University of Delaware	2006-07-18		Arabidopsis thaliana	HT Sequencing	other, Small RNAs identified using 454 sequencing,
19	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
20	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.

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