GEO DataSets

(Submitter supplied) HiSpOD is a new efficient functional microarrays probe design algorithm especially dedicated for the microbial ecology and environmental studies. It was used to design 3392 probes targeting 21 genes involved in chlorinated solvent biodegradation pathways and synthesized on a nimblegen microarray. In order to test the probe specificity, the microarray was firstly hybridized to 6 µg of labelled aRNA from sheep rumen content (background aRNA). more...

Organism:

synthetic construct; uncultured organism

Type:

Expression profiling by array

Platform:

GPL10353

3 Samples

Download data: PAIR

(Submitter supplied) Studying eight enzymes involved in the degradation of polycyclic aromatic hydrocarbons from the model strain Sphingomonas paucimobilis sp. EPA505 using a designed microarray of 8,048 probes. During the biodegradation kinetics with phenanthrene, fluoranthene or a mix of both pollutants, we identified the targeted set of genes induced by these pollutants, compared to basal expression detected with glucose. more...

Organism:

uncultured organism; Sphingomonas paucimobilis

Type:

Expression profiling by array

Platform:

GPL10343

17 Samples

Download data: PAIR

(Submitter supplied) See Talla et al. 2003 (PMID : 14499002)

Organism:

Saccharomyces cerevisiae

1 Series

22 Samples

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(Submitter supplied) See Talla et al. 2003 (PMID : 14499002)

Organism:

Saccharomyces cerevisiae

1 Series

18 Samples

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(Submitter supplied) The yeast 5803 ORFs MicroArray is composed of 32 subgrids, which follow a pattern of 8 metarows and 4 metacolumns. Each subgrid contains 20 columns and 20 rows with a dot spacing of 200 µm. Probes are spotted as closed duplicates. In order to provide a friendly environment, the first subgrid row on each array metarow contains all the normalization controls, which include the controls with serial dilution of the Renilla LuxA cDNA PCR product. more...

Organism:

Saccharomyces cerevisiae

3 Series

16 Samples

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(Submitter supplied) The yeast 5803 ORFs MicroArray is composed of 32 subgrids, which follow a pattern of 8 metarows and 4 metacolumns. Each subgrid contains 20 columns and 20 rows with a dot spacing of 200 µm. Probes are spotted as closed duplicates. In order to provide a friendly environment, the first subgrid row on each array metarow contains all the normalization controls, which include the controls with serial dilution of the Renilla LuxA cDNA PCR product. more...

Organism:

Saccharomyces cerevisiae

1 Series

6 Samples

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(Submitter supplied) This array is a Listeria monocytogenes pan-genome tiling array covering the full genomes of 20 L. monocytogenes strains. Each probe on the array may target multiple strains. Each probe may contain either zero or one mismatch to its intended genomic targets. The whole genomes of all 20 strains are tiled at an average depth of coverage of 2.65x, and the 50-mer probes are offset on average 21 bp from one another. more...

Organism:

Listeria monocytogenes; Listeria monocytogenes EGD-e; Listeria monocytogenes serotype 4b str. F2365; Listeria monocytogenes serotype 1/2a str. F6854; Listeria monocytogenes serotype 4b str. H7858; Listeria monocytogenes FSL F2-515; Listeria monocytogenes FSL J1-194; Listeria monocytogenes FSL J1-175; Listeria monocytogenes FSL J1-208; Listeria monocytogenes FSL J2-003; Listeria monocytogenes FSL J2-071; Listeria monocytogenes FSL J2-064; Listeria monocytogenes FSL N1-017; Listeria monocytogenes FSL N3-165; Listeria monocytogenes FSL R2-503; Listeria monocytogenes F6900; Listeria monocytogenes J0161; Listeria monocytogenes J2818; Listeria monocytogenes LO28; Listeria monocytogenes 10403S; Listeria monocytogenes HPB2262

1 Series

18 Samples

Download data: NDF, POS, TXT

(Submitter supplied) Whole genome gene expression data (baseline and following GR-stimulation with 1.5 mg dexamethasone p.o.) were analysed to identify glucocorticoid receptor (GR)-mediated changes in gene expression.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platforms:

GPL10558 GPL6947

594 Samples

Download data: TXT

(Submitter supplied) Oligonucleotides were selected using the program OligoRankPick, described in Guangan Hu, Manuel Llinás, Jingguang Li, Peter Rainer Preiser & Zbynek Bozdech: Selection of long oligonucleotides for gene expression microarrays using weighted rank-sum strategy. BMC Bioinformatics 2007, 8:350. The 70-bp oligonucleotides were spotted onto poly-L-lysine-coated microscopic slides as described in Zbynek Bozdech, Jingchun Zhu, Marcin P Joachimiak, Fred E Cohen, Brian Pulliam & Joseph L DeRisi: Expression profiling of the schizont and trophozoite stages of Plasmodium falciparum with a long-oligonucleotide microarray. more...

Organism:

Plasmodium falciparum

8 Series

30 Samples

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(Submitter supplied) Oligonucleotides were selected using the program OligoRankPick, described in Guangan Hu, Manuel Llinás, Jingguang Li, Peter Rainer Preiser & Zbynek Bozdech: Selection of long oligonucleotides for gene expression microarrays using weighted rank-sum strategy. BMC Bioinformatics 2007, 8:350. The 70-bp oligonucleotides were spotted onto poly-L-lysine-coated microscopic slides as described in Zbynek Bozdech, Jingchun Zhu, Marcin P Joachimiak, Fred E Cohen, Brian Pulliam & Joseph L DeRisi: Expression profiling of the schizont and trophozoite stages of Plasmodium falciparum with a long-oligonucleotide microarray. more...

Organism:

Plasmodium falciparum

2 Series

6 Samples

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(Submitter supplied) Long oligonucleotides were selected using the program OligoRankPick, described in Guangan Hu, Manuel Llinás, Jingguang Li, Peter Rainer Preiser & Zbynek Bozdech: Selection of long oligonucleotides for gene expression microarrays using weighted rank-sum strategy. BMC Bioinformatics 2007, 8:350. The 70/50-bp oligonucleotides were spotted onto poly-L-lysine-coated microscopic slides as described in Zbynek Bozdech, Jingchun Zhu, Marcin P Joachimiak, Fred E Cohen, Brian Pulliam & Joseph L DeRisi: Expression profiling of the schizont and trophozoite stages of Plasmodium falciparum with a long-oligonucleotide microarray. more...

Organism:

Plasmodium falciparum

12 Series

370 Samples

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(Submitter supplied) Long oligonucleotides were selected using the program OligoRankPick, described in Guangan Hu, Manuel Llinás, Jingguang Li, Peter Rainer Preiser & Zbynek Bozdech: Selection of long oligonucleotides for gene expression microarrays using weighted rank-sum strategy. BMC Bioinformatics 2007, 8:350. The 70-bp oligonucleotides were spotted onto poly-L-lysine-coated microscopic slides as described in Zbynek Bozdech, Jingchun Zhu, Marcin P Joachimiak, Fred E Cohen, Brian Pulliam & Joseph L DeRisi: Expression profiling of the schizont and trophozoite stages of Plasmodium falciparum with a long-oligonucleotide microarray. more...

Organism:

Plasmodium falciparum

26 Series

1 Related Platform

672 Samples

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(Submitter supplied) Long oligonucleotides were selected using the program OligoRankPick, described in Guangan Hu, Manuel Llinás, Jingguang Li, Peter Rainer Preiser & Zbynek Bozdech: Selection of long oligonucleotides for gene expression microarrays using weighted rank-sum strategy. BMC Bioinformatics 2007, 8:350. The 70-bp oligonucleotides were spotted onto poly-L-lysine-coated microscopic slides as described in Zbynek Bozdech, Jingchun Zhu, Marcin P Joachimiak, Fred E Cohen, Brian Pulliam & Joseph L DeRisi: Expression profiling of the schizont and trophozoite stages of Plasmodium falciparum with a long-oligonucleotide microarray. more...

Organism:

Plasmodium falciparum

3 Series

299 Samples

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(Submitter supplied) A original high throughput tool to provide significative information for the microbial community structure, composition and potential metabolic capacity, has been widely used to analyze microbial community from various habitats Protocol: see manufacturer's web site

Organism:

Bacteria; Archaea; Eukaryota; Viruses

2 Series

24 Samples

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(Submitter supplied) We perform a self hybridisation comprative genomic hybridization (CGH) in order to validate the probe tiling design we done on Trichoderma reesei. This hybridization was done using QM6a wild type strain.

Organism:

Trichoderma reesei

Type:

Other

Platform:

GPL9076

1 Sample

Download data: GPR

(Submitter supplied) Affymetrix U133 Plus 2.0 arrays were hybridized with varying amounts of starting material to determine whether different measurements of gene expression were observed. Keywords: Affymetrix starting material study

Organism:

Homo sapiens

Type:

Expression profiling by array

Dataset:

GDS2204

Platform:

GPL570

12 Samples

Download data: CEL

(Submitter supplied) Stratagene universal human RNA hybridized to both U133 Plus 2.0 and U133 A arrays. Keywords: Affymetrix platform comparison

Organism:

Homo sapiens

Type:

Expression profiling by array

Platforms:

GPL96 GPL570

10 Samples

Download data: CEL

Analysis of 1, 2, 5 or 10 ug of Stratagene universal human reference RNA as starting material. Results provide insight into the influence of starting RNA quantity on the subsequent gene expression signal measured from a microarray.

Organism:

Homo sapiens

Type:

Expression profiling by array, count, 4 protocol sets

Platform:

GPL570

Series:

GSE3062

12 Samples

Download data: CEL

(Submitter supplied) Microarrays are useful tools for detecting and quantifying specific functional and phylogenetic genes in natural microbial communities. In order to track uncultivated microbial genotypes and their close relatives in an environmental context, we designed and implemented a “genome proxy” microarray that targets microbial genome fragments recovered directly from the environment. Fragments consisted of sequenced clones from large-insert genomic libraries from microbial communities in Monterey Bay, the Hawaii Ocean Time-series station ALOHA, and Antarctic coastal waters. more...

Organism:

uncultured crenarchaeote 4B7; Prochlorococcus marinus subsp. pastoris str. CCMP1986; Prochlorococcus marinus str. MIT 9312; uncultured marine gamma proteobacterium EBAC31A08; uncultured marine bacterium EB0_41B09; uncultured proteobacterium 60D04; Prochlorococcus marinus str. MIT 9313; Prochlorococcus marinus str. MIT 9515; uncultured marine bacterium 577; uncultured gamma proteobacterium eBACHOT4E07; uncultured marine alpha proteobacterium; uncultured Pseudomonadota bacterium; uncultured crenarchaeote 74A4; uncultured proteobacterium 65D09; uncultured marine group II euryarchaeote EF100_57A08; uncultured marine bacterium EB000_55B11; uncultured marine group II euryarchaeote 37F11; uncultured marine bacterium 440; uncultured marine bacterium 583; marine metagenome

Type:

Other

Platform:

GPL6012

28 Samples

Download data: GPR

(Submitter supplied) A functional biodiversity microarray (EcoChip) prototype has been developed to facilitate the analysis of fungal communities in environmental samples with broad functional and phylogenetic coverage and to enable the incorporation of nucleic acid sequence data as they become available from large-scale (next generation) sequencing projects. A dual probe set (DPS) was designed to detect a) functional enzyme transcripts at conserved protein sites and b) phylogenetic barcoding transcripts at ITS regions present in precursor rRNA. more...

Organism:

soil metagenome

Type:

Expression profiling by array

Platform:

GPL13295

8 Samples

Download data: TXT