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.

Mammals
(312)

Vertebrates
(411)

Invertebrates
(1,032)

SAGE RsaI
(0)

MPSS
(0)

Protein Array
(0)

Antibody
(0)

RT-PCR
(2)

HT-Seq
(82)

Other
(3)

All
(312)

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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	GPL16726	Illumina HiSeq 2000 (Atelerix albiventris)	0		2013-02-26		Atelerix albiventris	HT Sequencing	high-throughput sequencing, Illumina HiSeq 2000 (Atelerix albiventris),
2	GPL14802	Illumina HiSeq 2000 (Bos grunniens)	0		2011-10-27		Bos grunniens	HT Sequencing	high-throughput sequencing, Illumina HiSeq 2000 (Bos grunniens),
3	GPL11314	NimbleGen Bos taurus UMD3.0 2.1M WG HD CGH	2,166,464	United States Department of Agriculture	2010-12-14	NimbleGen Systems, Inc.	Bos taurus	Oligo Array	in situ oligonucleotide, NimbleGen Bos taurus UMD3.0 2.1M WG HD CGH, This array was designed based on Btau_UMD3.0. The Btau_UMD3.1 assembly is identical in almost all respects to UMD3.0. All chromosomes are unchanged. For additional information, see http://www.cbcb.umd.edu/research/bos_taurus_assembly.shtml . The supplementary file 'GPL11314_Btau_4.0.txt' contains the results of LIFTOVER (default setting) to convert the positions of probes from UMD3.0 to Btau_4.0. About 95% (~2,066,000) of the probes were converted successfully.
4	GPL9220	NimbleGen Agrsci Bovine 6.3M v1, Design 2	2,144,401	Aarhus University, Faculty of Agricultural Sciences	2009-09-17	NimbleGen	Bos taurus	Tiling Array	in situ oligonucleotide, NimbleGen Agrsci Bovine 6.3M v1, Design 2, High density, custom Nimblegen HD2 CGH tiling arrays were planned in 3 designs. Each design covers a specific set of chromosomes with 2.1M probes, which yields 420 bp of average probe spacing (301 bp median probe spacing). Design_ID: 8026 Design_name: 080804_Btau4_design2_CGH_03 Description: HX1 CGH for Bos taurus release 4.0, chr 1,4,6,7,9,13,15,20,22,26,27,M; selection at i300w50. Annotation in this array is based on the bovine genome assembly, version 4.0 (Btau_4.0). Probe sequences are available in the 'PROBE_SEQUENCE' column of the 'GPL9220_080804_Btau4_design2_CGH_HX1.ndf' supplementary file.
5	GPL9219	NimbleGen Agrsci Bovine 6.3M v1, Design 1	2,128,916	Aarhus University, Faculty of Agricultural Sciences	2009-09-17	NimbleGen	Bos taurus	Tiling Array	in situ oligonucleotide, NimbleGen Agrsci Bovine 6.3M v1, Design 1, High density, custom Nimblegen HD2 CGH tiling arrays were planned in 3 designs. Each design covers a specific set of chromosomes with 2.1M probes, which yields 420 bp of average probe spacing (301 bp median probe spacing). Design_ID: 8023 Design_name: 080804_Btau4_design1_CGH_03 Description: HX1 CGH for Bos taurus release 4.0, chr 8,12,18,19,21,28,29,U,X; chrU is all chrUn scaffolds concatenated with 10-base run of N's as separator; selection at i200w50. Annotation in this array is based on the bovine genome assembly, version 4.0 (Btau_4.0). Probe sequences are available in the 'PROBE_SEQUENCE' column of the 'GPL9219_080804_Btau4_design1_CGH_HX1.ndf' supplementary file.
6	GPL9221	NimbleGen Agrsci Bovine 6.3M v1, Design 3	2,121,777	Aarhus University, Faculty of Agricultural Sciences	2009-09-17	NimbleGen	Bos taurus	Tiling Array	in situ oligonucleotide, NimbleGen Agrsci Bovine 6.3M v1, Design 3, High density, custom Nimblegen HD2 CGH tiling arrays were planned in 3 designs. Each design covers a specific set of chromosomes with 2.1M probes, which yields 420 bp of average probe spacing (301 bp median probe spacing). Design_ID: 8029 Design_name: 080804_Btau4_design3_CGH_03 Description: HX1 CGH for Bos taurus release 4.0, chr 2,3,5,10,11,14,16,17,23,24,25; selection at i300w50. Annotation in this array is based on the bovine genome assembly, version 4.0 (Btau_4.0). Probe sequences are available in the 'PROBE_SEQUENCE' column of the 'GPL9221_080804_Btau4_design3_CGH_HX1.ndf' supplementary file.
7	GPL16181	Agilent-024881 Bovine Whole Genome Array 400K 7-31	420,288	Texas A&M University	2012-10-16	Agilent Technologies	Bos taurus	Oligo Array	in situ oligonucleotide, Agilent-024881 Bovine Whole Genome Array 400K 7-31, Array design based on the bosTau4.0 (Baylor 4.0) assembly. Arrays of this design have barcodes that begin with 16024881 or 2524881. 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.
8	GPL16182	Agilent-025320 Bovine Whole Genome Array 400K 9-8-09	420,288	Texas A&M University	2012-10-16	Agilent Technologies	Bos taurus	Oligo Array	in situ oligonucleotide, Agilent-025320 Bovine Whole Genome Array 400K 9-8-09, Array design based on the bosTau4.0 (Baylor 4.0) assembly. Arrays of this design have barcodes that begin with 16025320 or 2525320. 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.
9	GPL16183	Agilent-027266 Bovine CNV Dense Tiling Array V1 2-10-2010	420,288	Texas A&M University	2012-10-16	Agilent Technologies	Bos taurus	Tiling Array	in situ oligonucleotide, Agilent-027266 Bovine CNV Dense Tiling Array V1 2-10-2010, Array design based on the bosTau4.0 (Baylor 4.0) assembly. Arrays of this design have barcodes that begin with 16027266 or 2527266. 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.
10	GPL16270	Agilent-027994 DNZ/UoA_Bovine_~415k_v1	418,408	DairyNZ Ltd	2012-11-12	Agilent	Bos taurus	Oligo Array	in situ oligonucleotide, Agilent-027994 DNZ/UoA_Bovine_~415k_v1,
11	GPL15186	Bos taurus QTL of female fertility region Tiling Array 385K Nimblegen	392,936	INRA	2012-02-03	Nimblegen Systems Inc.	Bos taurus	Tiling Array	in situ oligonucleotide, Bos taurus QTL of female fertility region Tiling Array 385K Nimblegen, The 385k Fertility Tiling Array was designed in both orientations to cover one of female fertility QTL on chr3. Target regions was gotten from UCSC database on Oct 2007 release (bosTau4). The 385k Fertility Tiling Array contains 171581 forward experimental probes, 171581 reverse experimental probes and 45961 randomly generated probes.
12	GPL9865	NimbleGen Bos taurus Btau31 WG CGH	385,048	United States Department of Agriculture	2010-01-08	NimbleGen Systems, Inc.	Bos taurus	Oligo Array	in situ oligonucleotide, NimbleGen Bos taurus Btau31 WG CGH,
13	GPL9866	NimbleGen Bos taurus Btau40 WG CGH	384,025	United States Department of Agriculture	2010-01-08	NimbleGen Systems, Inc.	Bos taurus	Oligo Array	in situ oligonucleotide, NimbleGen Bos taurus Btau40 WG CGH,
14	GPL10990	NimbleGen Bos taurus Whole-genome CGH 385k Array (Btau_4.0 version)	378,977	University of Bologna	2010-09-28	NimbleGen	Bos taurus	Tiling Array	in situ oligonucleotide, NimbleGen Bos taurus Whole-genome CGH 385k Array (Btau_4.0 version), A cattle genome array for cross species experiment (Goat, Sheep). Custom tiling arrays designed on the bovine (Bos taurus) genome, Btau_4.0 version, including a fraction of BTA13 of the University of Maryland (UMD) Bos taurus v. 2.0 assembly (ftp://ftp.cbcb.umd.edu/pub/data/Bos_taurus/Bos_taurus_UMD_2.0/). Arrays contained ~385,000 probes on a single slide to provide an evenly distributed coverage with an average interval of ~6 kb for the Btau_4.0 genome. The BTA13 of the UMD v. 2.0 assembly was included from nucleotide position 48 M bp to nucleotide position 78 M bp (4,673 oligonucleotides and average spacing of ~6 kb). This chromosome region was analysed as internal control because it contains the ASIP gene, not assembled in the BTA13 of the Btau_4.0 version.
15	GPL10155	Agilent-025242 SurePrint G3 Bovine CGH Microarray 4x180K (Feature Number version)	180,880	Agilent Technologies	2010-03-09	Agilent Technologies	Bos taurus	Oligo Array	in situ oligonucleotide, Agilent-025242 SurePrint G3 Bovine CGH Microarray 4x180K (Feature Number version), Bovine (bosTau4) CGH Whole Genome Microarray 4x180K Arrays of this design have barcodes that begin with 16025242 or 2525242. Data table annotations based on build bosTau4:Btau_4.0:Oct2007. 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.
16	GPL223	SAGE:10:NlaIII:Bos taurus	115,184		2002-12-04		Bos taurus	SAGE NlaIII	SAGE NlaIII, SAGE:10:NlaIII:Bos taurus,
17	GPL3711	USDA Bovine 60mer 344k Array (oligo layout)	85,235	USDA	2006-05-01	NimbleGen	Bos taurus	Oligo Array	in situ oligonucleotide, USDA Bovine 60mer 344k Array (oligo layout), There are 85235 distinct 60mer oligonucleotides on the array representing ~45383 unique bovine sequences/genes (4 identical spots/features for each 60 oligo).
18	GPL9862	University of Alberta Bovine 24K long oligo array	49,152	National Institute of Agrobiological Sciences	2010-01-08	Oligo design: Bovine Oligo Microarray Consortium; Array preparation: University of Alberta, Agricultural Genomics and Proteomics Unit	Bos taurus	Oligo Array	spotted oligonucleotide, University of Alberta Bovine 24K long oligo array, UniGene ID of sequence used to design oligonucleotide probe, Gene symbol, GenBank accession number and gene description were annotated in the GeneSifter based on the UniGene ID. The oligonucleotide sequences are provided as a supplementary file.
19	GPL3301	USDA Bovine 60mer 344k Array (gene layout)	46,490	USDA	2006-01-04	NimbleGen	Bos taurus	Oligo Array	in situ oligonucleotide, USDA Bovine 60mer 344k Array (gene layout), There are ~ 340,000 features on the array. The 86,191 disinct 60mer oligonucleotides on the array, each represented by 4 features (spots), represent 45,383 unique bovine sequences including 40808 Tentative Consensus sequneces from the TIGR Bos taurus Gene Index (BTGI, release 11.0) and 4,575 singletons from pooled mammary gland and gut library.
20	GPL11648	Agilent-023647 B. taurus (Bovine) Oligo Microarray v2 (Feature Number version)	45,220	Agilent Technologies	2011-01-24	Agilent Technologies	Bos taurus	Oligo Array	in situ oligonucleotide, Agilent-023647 B. taurus (Bovine) Oligo Microarray v2 (Feature Number version), B. taurus (Bovine) Oligo Microarray v2 Arrays of this design have barcodes that begin with 16023647 or 2523647. 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. *** A different version of this platform with the Agilent Probe names in the ID column is assigned accession number GPL11649.

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