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
(55)

Primates
(0)

Invertebrates
(29)

Phages
(0)

SAGE NlaIII
(0)

SAGE RsaI
(0)

SAGE Sau3A
(0)

MPSS
(0)

GeneChip
(0)

Tiling Array
(0)

cDNA Array
(1)

Oligo Array
(21)

Bead Array
(0)

Protein Array
(0)

Antibody
(0)

RT-PCR
(0)

HT-Seq
(7)

Other
(0)

All
(29)

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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	GPL15193	UIUC/Newmark-Smed2 CombiMatrix array	11,584	U of IL / HHMI	2012-02-06	CombiMatrix	Schmidtea mediterranea	Oligo Array	spotted oligonucleotide, UIUC/Newmark-Smed2 CombiMatrix array,
2	GPL15192	UIUC/Newmark-Smed1 CombiMatrix array	11,835	U of IL / HHMI	2012-02-06	CombiMatrix	Schmidtea mediterranea	Oligo Array	spotted oligonucleotide, UIUC/Newmark-Smed1 CombiMatrix array,
3	GPL15157	Stillman Lab Porcelain Crab Array 3	24,748	San Francisco State University	2012-01-24	UCSF Center for Advanced Technology	Petrolisthes cinctipes	cDNA Array	spotted DNA/cDNA, Stillman Lab Porcelain Crab Array 3,
4	GPL15246	NimbleGen P. falciparum 3D7 Whole Genome CGH Array [090317_Plasmodium_3D7_WG_CGH]	385,585	NimbleGen Systems, Inc.	2012-02-16	NimbleGen	Plasmodium falciparum	Oligo Array	in situ oligonucleotide, NimbleGen P. falciparum 3D7 Whole Genome CGH Array [090317_Plasmodium_3D7_WG_CGH], DESIGN_NAME: 090317_Plasmodium_3D7_WG_CGH DESIGN_ID: 9384
5	GPL15364	NimbleGen Honeybee 2.1M array	1,985,432	JHU	2012-03-20	NimbleGen	Apis mellifera	Oligo Array	in situ oligonucleotide, NimbleGen Honeybee 2.1M array, Annotation based on Baylor College of Medicine Human Genome Sequencing Center honeybee genome assembly Oct 2006 (Amel_4.0)
6	GPL15387	NimbleGen Drosophila melanogaster gene expression 12X135K array	16,659	Emory University	2012-03-29	NimbleGen	Drosophila melanogaster	Oligo Array	in situ oligonucleotide, NimbleGen Drosophila melanogaster gene expression 12X135K array, NimbleGen design catalog # 05543762001. The Platform data table is a gene-level representation of the expression array's features. The .ndf and .ngd files are linked below as supplementary files. Native array description file: 100718_Dmel_exp.ndf Native array description file: 100718_Dmel_exp.ngd
7	GPL15352	NimbleGen Drosophila melanogaster 12X135K Gene Expression Array [100718_Dmel_exp, DesignID:535513]	21,051	Emory University	2012-03-14	NimbleGen	Drosophila melanogaster	Oligo Array	in situ oligonucleotide, NimbleGen Drosophila melanogaster 12X135K Gene Expression Array [100718_Dmel_exp, DesignID:535513], Drosophila melanogaster DM5.7 build and having 60 basepair probes with target genes 16637 with 8 probes per gene ( one pair for replicates ) per each array DesignID: 535513 native array description file:100718_Dmel_exp.ngd native array description file:100718_Dmel_exp.ndf
8	GPL15209	Illumina HiSeq 2000 (Taenia multiceps)	0		2012-02-09		Taenia multiceps	HT Sequencing	high-throughput sequencing, Illumina HiSeq 2000 (Taenia multiceps),
9	GPL15118	Illumina HiSeq 2000 (Sterkiella histriomuscorum)	0		2012-01-11		Sterkiella histriomuscorum	HT Sequencing	high-throughput sequencing, Illumina HiSeq 2000 (Sterkiella histriomuscorum),
10	GPL15208	Illumina HiSeq 2000 (Dirofilaria immitis)	0		2012-02-09		Dirofilaria immitis	HT Sequencing	high-throughput sequencing, Illumina HiSeq 2000 (Dirofilaria immitis),
11	GPL15334	Illumina HiSeq 1000 (Drosophila melanogaster)	0		2012-03-08		Drosophila melanogaster	HT Sequencing	high-throughput sequencing, Illumina HiSeq 1000 (Drosophila melanogaster),
12	GPL15247	Illumina Genome Analyzer IIx (Strongylocentrotus purpuratus)	0		2012-02-16		Strongylocentrotus purpuratus	HT Sequencing	high-throughput sequencing, Illumina Genome Analyzer IIx (Strongylocentrotus purpuratus),
13	GPL15222	Illumina Genome Analyzer II (Culex quinquefasciatus)	0		2012-02-13		Culex quinquefasciatus	HT Sequencing	high-throughput sequencing, Illumina Genome Analyzer II (Culex quinquefasciatus),
14	GPL15348	Illumina Genome Analyzer (Giardia intestinalis)	0		2012-03-14		Giardia intestinalis	HT Sequencing	high-throughput sequencing, Illumina Genome Analyzer (Giardia intestinalis),
15	GPL15202	Exiqon Caenorhabditis elegans miRNA array [miRCURY LNA Array V.11, miRBase 14.0]	149	UMDNJ	2012-02-08	Exiqon	Caenorhabditis elegans	Oligo Array	spotted oligonucleotide, Exiqon Caenorhabditis elegans miRNA array [miRCURY LNA Array V.11, miRBase 14.0], miRCURY LNA Array Other species Version 11 annotated to miRBase 14.0
16	GPL15181	Caenorhabditis elegans custom miRNA array	96	University of Cambridge	2012-02-02	Simard Laboratory	Caenorhabditis elegans	Oligo Array	spotted oligonucleotide, Caenorhabditis elegans custom miRNA array, CodeLinkÃ‚Â® Activated Microarray Slides with a TRIDIAÃ¢â€žÂ¢ NHS Coating. Product Code DN01-0025 Ã¢â‚¬â€œ formerly GE Healthcare #300011 (or #256700-00)
17	GPL15131	Agilent_038059 Plasmodium berghei_Mar2011_transcriptome	15,744	Princeton University	2012-01-15	Agilent Technologies	Plasmodium berghei	Oligo Array	in situ oligonucleotide, Agilent_038059 Plasmodium berghei_Mar2011_transcriptome, Arrays of this design have barcodes that begin with 16038059 or 2538059. Orientation: Features are numbered numbered Left-to-Right, Top-to-Bottom as scanned by an Agilent scanner (barcode on the left, DNA on the back surface, scanned through the glass), matching the FeatureNum output from Agilent's Feature Extraction software. The ID column represents the Agilent Feature Extraction feature number. Rows and columns are numbered as scanned by an Axon Scanner (barcode on the bottom, DNA on the front surface). To match data scanned on an Axon scanner, use the RefNumber column contained in the Agilent-provided GAL file as the ID_REF column in sample submissions. The PlasmoDB_IDs are accession numbers for both GeneDB.org and the main community resource PlasmoDB.org
18	GPL15130	Agilent-037237 P.falciparum_Pf3D7v7.1_Transcriptome_apimito	15,744	Princeton University	2012-01-15	Agilent Technologies	Plasmodium falciparum	Oligo Array	in situ oligonucleotide, Agilent-037237 P.falciparum_Pf3D7v7.1_Transcriptome_apimito, DesignID: 037237 Arrays of this design have barcodes that begin with 16037237 or 2537237. Orientation: Features are numbered numbered Left-to-Right, Top-to-Bottom as scanned by an Agilent scanner (barcode on the left, DNA on the back surface, scanned through the glass), matching the FeatureNum output from Agilent's Feature Extraction software. The ID column represents the Agilent Feature Extraction feature number. Rows and columns are numbered as scanned by an Axon Scanner (barcode on the bottom, DNA on the front surface). To match data scanned on an Axon scanner, use the RefNumber column contained in the Agilent-provided GAL file as the ID_REF column in sample submissions.
19	GPL15191	Agilent-034793 Custom Bombyx mori 4x44k designed by Genotypic Technology Pvt. Ltd. (AMADID: 034793)	24,924	Genotypic Technology	2012-02-06	Agilent Technologies	Bombyx mori	Oligo Array	in situ oligonucleotide, Agilent-034793 Custom Bombyx mori 4x44k designed by Genotypic Technology Pvt. Ltd. (AMADID: 034793),
20	GPL15303	Agilent-028465/UniversityPadova Ruditapes decussatus 4x44K v1.0 (Feature Number version)	45,175	University of Padova	2012-03-05	Agilent Technologies	Venerupis decussatus	Oligo Array	in situ oligonucleotide, Agilent-028465/UniversityPadova Ruditapes decussatus 4x44K v1.0 (Feature Number version), Target sequences to be included in the R.decussatus microarray were obtained from the assembly of two sets of libraries (MGE011, 122,471 reads; cDN18 327,209 reads) making a total of 449,680 reads were sequenced using normalized cDNA libraries constructed with a mixture of adult tissues and another containing gonadal tissue and larvaes. The same libraries were been used to obtain 2434 and 2077 ESTs with traditional Sanger sequencing respectively. Assembly perfromed by MIRA3 grouped these seqeunces and reads into 41,119 contigs. The array included all annotated sequences with a blast hit to vertebrates and invertebrates.Probe design started with selection of target sequences to be represented onto the R. philippinarum microarray. All annotated entries (12,479) were included whereas non annotated transcripts were considered only if sequence length was Ã¢â€°Â¥400 bp and average Phred sequence quality was Ã¢â€°Â¥31, yielding 21,900 target sequences. For each contigs two probes with opposite orientation (sense and antisense) were designed. A total of 43,758 out of 43,800 (99.9%) probes were successfully obtained, representing 21,887 R. decussatus transcripts.

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