GEO DataSets

(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) 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) 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) The probe set printed on the array consists of 380,000 unique oligonucleotide sequences. On this particular platform, all the 380k unique probes were mapped to all the matched loci of the reference genome, thus each unique probe sequence may appear multiple times due to the repeated probe sequence found in the genome. Protocol: The probes were synthesized on the Nimblgen 385K arrays using Nimblegen's proprietary Maskless Array Synthesizer (MAS) technology. more...

Organism:

Porphyromonas gingivalis W83

1 Series

18 Samples

Download data: NDF

(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) 60-mers oligonucleotide probes, in-situ synthesis on 1 Protocol: Sure Print Technology-In situ synthesis

Organism:

Staphylococcus aureus

4 Series

30 Samples

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(Submitter supplied) An oligonucleotide tiling array technology is utilized to measure the entire Escherichia coli transcriptome and its transcriptional changes after induction of the adaptive response by the alkylating agent N-methyl-N'-nitro-N-nitrosoguanidine (MNNG). Keywords: Gene expression during the adaptive response in Escherichia coli

Organism:

Escherichia coli str. K-12 substr. MG1655

Type:

Expression profiling by genome tiling array

Platform:

GPL7714

10 Samples

Download data: CEL, XLS

(Submitter supplied) The transcriptional changes in Escherichia coli upon induction of the SOS response are investigated by utilizing custom designed oligonucleotide microarrays. Keywords: Gene expression during the SOS response in Escherichia coli

Organism:

Escherichia coli str. K-12 substr. MG1655

Type:

Expression profiling by genome tiling array

Platform:

GPL7714

10 Samples

Download data: CEL

(Submitter supplied) Species-specific genes play an important role in defining the phenotype of an organism. However, current gene prediction methods can only efficiently find genes that share features such as sequence similarity or general sequence characteristics with previously known genes. Novel sequencing methods and tiling arrays can be used to find genes without prior information and they have demonstrated that novel genes can still be found from extensively studied model organisms. more...

Organism:

Trichoderma reesei

Type:

Expression profiling by array

Platform:

GPL7331

9 Samples

Download data: PAIR

(Submitter supplied) Quantifying interactions in DNA microarrays is of central importance for a better understanding of their functioning. Hybridization thermodynamics for nucleic acid strands in aqueous solution can be described by the so-called nearest-neighbor model, which estimates the hybridization free energy of a given sequence as a sum of dinucleotide terms. Compared with its solution counterparts, hybridization in DNA microarrays may be hindered due to the presence of a solid surface and of a high density of DNA strands. more...

Organism:

synthetic construct

Type:

Other

4 related Platforms

32 Samples

Download data: TXT

(Submitter supplied) Recently, long oligonucleotide (60-70mer) microarrays for two-color experiments have been developed and are gaining widespread use. In addition, when there is limited availability of mRNA from tissue sources, RNA amplification can and is being used to produce sufficient quantities of cRNA for microarray hybridization. Taking advantage of the selective degradation of RNA under alkaline conditions, we have developed a method to “strip” glass-based oligonucleotide microarrays that use fluorescent RNA in the hybridization, while leaving the DNA oligonucleotide probes intact and usable for a second experiment. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platforms:

GPL1390 GPL887 GPL885

20 Samples

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(Submitter supplied) Transcriptional profiling of bovine in-vitro produced blastocysts at day 7 and granulosa cells collected at day 8 to 11 post-eostrus of lactating cows.

Organism:

Bos taurus

Type:

Expression profiling by array

Platform:

GPL13226

6 Samples

Download data: 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) BACKGROUND: Microarray comparative genomic hybridization (CGH) is currently one of the most powerful techniques to measure DNA copy number in large genomes. In humans, microarray CGH is widely used to assess copy number variants in healthy individuals and copy number aberrations associated with various diseases, syndromes and disease susceptibility. In model organisms such as Caenorhabditis elegans (C. more...

Organism:

Caenorhabditis elegans; Homo sapiens

Type:

Genome variation profiling by genome tiling array

Platforms:

GPL7085 GPL7084

3 Samples

Download data: PAIR

(Submitter supplied) Picky is an optimal microarray design software which designed the NSF Rice 45K Array. A series of microarray experiments using a one-chip version of this array were conducted to validate as well as to develop a calibration method for Picky designed microarrays. Synthesized samples with known content were used in the validation. PICKY designed microarrays were found to be highly reliable. The PICKY predicted closest nontarget information was used to quantitatively calibrate the best microarray hybridization conditions using the same microarrays and synthesized samples. more...

Organism:

Oryza sativa; synthetic construct

Type:

Other

Platform:

GPL8161

165 Samples

Download data: GPR