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.

Invertebrates
(1,027)

Plants
(2,220)

Bacteria
(1,678)

SAGE RsaI
(0)

SAGE Sau3A
(0)

Oligo Array
(381)

Protein Array
(0)

Antibody
(0)

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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.
81	GPL7221	NimbleGene-P.tetrauerlia-variousSETs-50mer-v1	387,837	Laboratoire BiomÃƒÂ©trie et Biologie Evolutive	2008-08-28	NimbleGen	Paramecium tetraurelia	Oligo Array	in situ oligonucleotide, NimbleGene-P.tetrauerlia-variousSETs-50mer-v1, The grid of features is 768x1024 (X, Y). It consists of 11 different SETs as described below. SET01 : Probes that match annotated transcripts. Each transcript has 6 probes (3 on the forward strand and 3 on the reverse strand). SET02 : Probes for complete tilling of 4 scaffolds : SCAFFOLD_106, SCAFFOLD_142, SCAFFOLD_164, SCAFFOLD_96. The probes cover both strands of the 4 scaffolds with a 25 nucleotides overlap. SET03 : Probes designed specifically to distinguish spliced and unspliced transcripts from the 4 scaffolds described in SET02. For each annotated intron, one probe covers the genomic sequence, centered on the middle of the intron (since introns in P. tetraurelia are between 20 and 30 nt length these probes contain the full sequence of the intron and a few bases from the surronding exons) while an other probe covers the spliced version of the transcript, centered on the exon-exon junction site. SET04 : Probes that match 219 annotated tRNAs. Each tRNAs has 4 probes (2 on the forward and 2 on the reverse strand). SET05 : Probes that match 3 non-codgin RNAs of particular interrest : AB059619, MS2B and PTU45433. Each ncRNA is fully tilled by the probes on both strands. SET06 : Probes that match the rDNA. SET07 : Probes designed specifically to study retention and expression of known IESs in paramecium (see Duret & al. Genome Res. 2008; 18(4):585-96 for more informations about IESs). SET08 : Probes that match 74 known transposons. Each transposons is fully coverd by tilling on both strands. SET09 : Tilling of both strands for 51Gmic gene. SET10 : Probes that match the mitochondrial genome (both strands) SET11 : Probes designed to distinguish spliced and unspliced transcripts from 6137 annotated genes confirmed by EST alignment. The protocol is the same than described for SET03. RANDOM : random probes.
82	GPL4573	NimbleGen/UW-Madison_Drosophila_whole_genome_v1	13,450	Clemson University	2006-11-19	NimbleGen Systems, Inc	Drosophila melanogaster	Oligo Array	in situ oligonucleotide, NimbleGen/UW-Madison_Drosophila_whole_genome_v1,
83	GPL4568	NimbleGen/UW-Madison Drosophila wing validation array	1,387	Clemson University	2006-11-16	NimbleGen Systems, Inc	Drosophila melanogaster	Oligo Array	in situ oligonucleotide, NimbleGen/UW-Madison Drosophila wing validation array,
84	GPL17034	NimbleGen Trypanosoma brucei Strain 927 Oligonucleotide Expression Array [120828_Tbrucei927_RS_exp]	8,078	University of Toronto	2013-04-17	NimbleGen	Trypanosoma brucei TREU927	Oligo Array	in situ oligonucleotide, NimbleGen Trypanosoma brucei Strain 927 Oligonucleotide Expression Array [120828_Tbrucei927_RS_exp], DESIGN_NAME: 120828_Tbrucei927_RS_exp DESIGN_ID: 574071 The Platform data table reflects a condensed representation of the array's replicate features. The full array layout representing all of the individual features (and probe sequences) is linked as a supplementary file at the foot of this record.
85	GPL10781	Nimblegen T. cruzi 290K version 1.0	35,010	University of Georgia	2010-08-11	NimbleGen	Trypanosoma cruzi	Oligo Array	in situ oligonucleotide, Nimblegen T. cruzi 290K version 1.0, Trypanosoma cruzi CL-Brener strain
86	GPL10466	NimbleGen Schistosoma mansoni 385K v1	389,211	Universidade de Sao Paulo	2010-05-28	NimbleGen	Schistosoma mansoni	Oligo Array	in situ oligonucleotide, NimbleGen Schistosoma mansoni 385K v1, The annotations provided are the results from mapping to version f of the S. mansoni genome assembly at GeneDB.org. As the annotations are continually evolving, if re-mapped to the current version, newer annotations may be available.
87	GPL10125	Nimblegen Rhipicephalus microplus 385K microarray	385,770	DEEDI	2010-03-03	NimbleGen Systems Inc.	Rhipicephalus microplus	Oligo Array	in situ oligonucleotide, Nimblegen Rhipicephalus microplus 385K microarray,
88	GPL13355	NimbleGen Pfalciparum 720K 1.0	355,803	University of Notre Dame	2011-03-31	NimbleGen	Plasmodium falciparum	Oligo Array	in situ oligonucleotide, NimbleGen Pfalciparum 720K 1.0, PlasmoDB v5.5 P.falciparum genome
89	GPL15768	NimbleGen P. falciparum 72K array [100712_Pfal_3D7_JM_exp_72K]	5,367	Pennsylvania State University	2012-07-05	NimbleGen	Plasmodium falciparum 3D7	Oligo Array	in situ oligonucleotide, NimbleGen P. falciparum 72K array [100712_Pfal_3D7_JM_exp_72K], NimbleGen design name 100712_Pfal_3D7_exp, NimbleGen design ID 05327954001. A 35809 45-60mer probes were selected with two replicates on final array for a total of 71618 probes. For transcripts between 1-299bp, 3 probes were selected per transcript. For transcripts between 300-3999bp, 6 probes were selected per transcript. For transcripts >4000bp, 11 probes were selected per transcript. No 3' bias was used during probe selection. Tm weighting parameter (500) was used when selecting the final probes (Tm distribution between 60.90 and 77.80). It was design for 5367 genes from Plasmodium falciparum 3D7. The probes were designed based on the NCBI genomic sequence (July 2010), and these genomic sequence accession numbers are NC_004314 -004318, NC_004325-004331, NC_002375, NC_000910, NC_000521, X95276. The Platform data table reflects a condensed representation of the expression array's replicate (SEQ_ID) features. The .ndf and .ngd files are linked below as supplementary files. native array description file: 100712_Pfal_3D7_JM_exp.ndf native array description file: 100712_Pfal_3D7_JM_exp.ngd DesignID: 539063
90	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
91	GPL10359	Nimblegen Naegleria gruberi 385K array, v1.0	33,260	UC Berkeley	2010-04-26	NimbleGen	Naegleria gruberi	Oligo Array	in situ oligonucleotide, Nimblegen Naegleria gruberi 385K array, v1.0, NimbleGen design name 080519_N_gruberi_UCBerk_LFL_expr, NimbleGen design ID 2451. Array consists of 182,813 probes corresponding to 15,777 gene models predicted on the N.gruberi genome sequence version 1.0 (http://genome.jgi-psf.org/Naegr1/Naegr1.home.html), and an additional 963 orfs identified in intergenic regions (these orf ids can also be accessed via http://genome.jgi-psf.org/Naegr1/Naegr1.home.html). Each gene is represented by 11 60-mer probes, and each probe set is replicated twice on the array. The design includes control probes. Oligonucleotide sequences are available in the supplementary 'GPL10350_080519_N_gruberi_UCBerk_LFL_expr.ndf' file.
92	GPL13212	NimbleGen Matzkin Drosophila mojavensis 70K array v2.0.	71,998	University of Alabama in Huntsville	2011-02-21	NimbleGen	Drosophila mojavensis	Oligo Array	in situ oligonucleotide, NimbleGen Matzkin Drosophila mojavensis 70K array v2.0.,
93	GPL8596	NimbleGen Matzkin Drosophila mojavensis 70K array v1.0.	69,997	University of Alabama in Huntsville	2009-05-26	NimbleGen	Drosophila mojavensis	Oligo Array	in situ oligonucleotide, NimbleGen Matzkin Drosophila mojavensis 70K array v1.0.,
94	GPL10446	NimbleGen Leishmania infantum JPCM5 8k Expression Array	8,178	Seattle Biomedical Research Institute	2010-05-20	NimbleGen	Leishmania infantum JPCM5	Oligo Array	in situ oligonucleotide, NimbleGen Leishmania infantum JPCM5 8k Expression Array, 60mer probes were designed to known coding regions of Leishmania infantum strain JPCM5. Approximately 10 probes were designed to each protein coding gene, 3 probes to each RNA genes and the remaining probes were evenly distributed through the genome. Probe sequences can be found in the ndf file. NimbleGen array description files are linked below as supplementary files: 2006-12-20_PM_LINF_expr.ndf 2006-12-20_PM_LINF_expr.ngd
95	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)
96	GPL16433	NimbleGen Gibbs Drosophila mojavensis 135K 12-plex Array	14,528	University of Nevada	2012-12-31	NimbleGen Systems Inc.	Drosophila mojavensis	Oligo Array	in situ oligonucleotide, NimbleGen Gibbs Drosophila mojavensis 135K 12-plex Array, The probe selection was based on the sequences from ftp://flybase.net/genomes/Drosophila_mojavensis/current/fasta/dmoj-all-transcript-r1.3.fasta.gzÃ‚Â downloaded onÃ‚Â 4/14/2009. Nine probes per transcript were selected. The report.txt file will give you the details of how many probes were chosen for each transcript. There is a total ofÃ‚Â 130705 probesÃ‚Â (12-plex design holdÃ‚Â 135K probes. The empty spaces were filled with random (negative) probes.) OID21283_rank9.select is a tab-delimited file containing each probes' sequence as well as other information about the probe (score, tm, etc.) Report.txt tells you the number of probes we were able to select for each id. No_probes.txt contains a list of what we weren't able to select a probe for. Exemplars.txt will let you know if one probe set represents multiple ids (for ex. When doing the selection,Ã‚Â FBtr0160978 and FBtr0160979Ã‚Â shared the same probes, soÃ‚Â FBtr0160979 was filtered out of the probe set). Finally,Ã‚Â annotation.txt is the annotation file we were able to pull together based onÃ‚Â the file we downloaded.
97	GPL4634	Nimblegen Dyak expression custom array/2005-06-03_D_yakuba_50mer	391,015	NIDDK, NIH	2006-12-05	NimbleGen Systems Inc.	Drosophila yakuba	Oligo Array	in situ oligonucleotide, Nimblegen Dyak expression custom array/2005-06-03_D_yakuba_50mer, Nimblegen custom design array for Drosophila species expression: An average of 10 array element probes per predicted genes was selected without-bias vis-a-vis position within the gene model. Sources of gene predictions include EIS (Annotations from Eisen lab v.1.0, Feb. 2005), GID (ab-initio GeneID predictions on draft assembly), and GBK (EST sequence from GeneBank). Probes have been remapped to final genome assemblies (Comparative Assembly Freeze 1 CAF1, http://rana.lbl.gov/drosophila/caf1.html) and genome annotation (GLEANR set, http://rana.lbl.gov/~venky/AAA/freeze_20061030/protein_coding_gene/GLEANR/annotation). Arrays are described in detail on http://intramural.niddk.nih.gov/research/multifly/multifly.htm.
98	GPL4633	Nimblegen Dvir expression custom array/2005-06-03_D_virilis_50mer	391,015	NIDDK, NIH	2006-12-05	NimbleGen Systems Inc.	Drosophila virilis	Oligo Array	in situ oligonucleotide, Nimblegen Dvir expression custom array/2005-06-03_D_virilis_50mer, Nimblegen custom design array for Drosophila species expression: An average of 10 array element probes per predicted genes was selected without-bias vis-a-vis position within the gene model. Sources of gene predictions include EIS (Annotations from Eisen lab v.1.0, Feb. 2005), GID (ab-initio GeneID predictions on draft assembly), and GBK (EST sequence from GeneBank). Probes have been remapped to final genome assemblies (Comparative Assembly Freeze 1 CAF1, http://rana.lbl.gov/drosophila/caf1.html) and genome annotation (GLEANR set, http://rana.lbl.gov/~venky/AAA/freeze_20061030/protein_coding_gene/GLEANR/annotation). Arrays are described in detail on http://intramural.niddk.nih.gov/research/multifly/multifly.htm.
99	GPL4632	Nimblegen Dsim expression custom array/2005-06-03_D_simulans_50mer	390,209	NIDDK, NIH	2006-12-05	NimbleGen Systems Inc.	Drosophila simulans	Oligo Array	in situ oligonucleotide, Nimblegen Dsim expression custom array/2005-06-03_D_simulans_50mer, Nimblegen custom design array for Drosophila species expression: An average of 10 array element probes per predicted genes was selected without-bias vis-a-vis position within the gene model. Sources of gene predictions include EIS (Annotations from Eisen lab v.1.0, Feb. 2005), GID (ab-initio GeneID predictions on draft assembly), and GBK (EST sequence from GeneBank). Probes have been remapped to final genome assemblies (Comparative Assembly Freeze 1 CAF1, http://rana.lbl.gov/drosophila/caf1.html) and genome annotation (GLEANR set, http://rana.lbl.gov/~venky/AAA/freeze_20061030/protein_coding_gene/GLEANR/annotation). Arrays are described in detail on http://intramural.niddk.nih.gov/research/multifly/multifly.htm.
100	GPL13351	Nimblegen Drosophila melanogaster r5.25 Expression Array (12x135k)	133,713	Indiana University	2011-03-30	NimbleGen	Drosophila melanogaster	Oligo Array	in situ oligonucleotide, Nimblegen Drosophila melanogaster r5.25 Expression Array (12x135k), This is a whole fruitfuly genome exon and transcript expression array in 12-plex format provided by Roche Nimblegen. See manufacturer's website at http://www.nimblegen.com/.

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