GEO DataSets

(Submitter supplied) Background: The analysis of oligonucleotide microarray data in pathogen surveillance and discovery assays is a challenging task. Target template concentration, nucleic acid integrity, and host nucleic acid composition can each have a profound effect on signal distribution. Exploratory analysis of fluorescent signal distribution in clinical samples has revealed deviations from normality, suggesting that distribution-free approaches should be applied. more...

Organism:

Chlorocebus aethiops; Human alphaherpesvirus 1; Human adenovirus E4; Zaire ebolavirus; SARS coronavirus Tor2; Vesicular stomatitis Indiana virus; Echovirus E18; Influenza A virus (A/Texas/36/1991(H1N1)); Lassa virus Josiah; Viruses; West Nile virus

Type:

Expression profiling by array

Platform:

GPL10320

11 Samples

Download data: TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Chlorocebus aethiops; Homo sapiens; Human alphaherpesvirus 1; Zaire ebolavirus; SARS coronavirus Tor2; Viruses; West Nile virus; Lassa virus Josiah; Vesicular stomatitis Indiana virus; Human adenovirus E4; Echovirus E18; artificial sequences; Influenza A virus (A/Texas/36/1991(H1N1))

Type:

Expression profiling by array

Platforms:

GPL10320 GPL10319

40 Samples

Download data: TXT

(Submitter supplied) Background: The analysis of oligonucleotide microarray data in pathogen surveillance and discovery assays is a challenging task. Target template concentration, nucleic acid integrity, and host nucleic acid composition can each have a profound effect on signal distribution. Exploratory analysis of fluorescent signal distribution in clinical samples has revealed deviations from normality, suggesting that distribution-free approaches should be applied. more...

Organism:

Homo sapiens; West Nile virus; Viruses; artificial sequences

Type:

Expression profiling by array

Platform:

GPL10319

29 Samples

Download data: TXT

(Submitter supplied) Abstract: BACKGROUND: Obtaining reliable and reproducible two-color microarray gene expression data is critically important for understanding the biological significance of perturbations made on a cellular system. Microarray design, RNA preparation and labeling, hybridization conditions and data acquisition and analysis are variables difficult to simultaneously control. A useful tool for monitoring and controlling intra- and inter-experimental variation is Universal Reference RNA (URR), developed with the goal of providing hybridization signal at each microarray probe location (spot). more...

Organism:

Homo sapiens; Mus musculus

Type:

Expression profiling by array

6 related Platforms

31 Samples

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(Submitter supplied) RNA from 11 individual mouse cell lines were reverse-transcribed to cDNA, labeled with Cy5 and cohybridized with Cy3-labeled UMRR onto 7,500-spot mouse oligo microarrays (UNC). The data was analyzed using GeneTraffic software. 300-1000 spots out of 8,000 were flagged on each microarray and excluded from further analysis. Spots with hybridization signals in Cy5 channel higher than 1000 and with Cy5/Cy3 ratio greater than 2 were collected and the number of spots with these characteristics on only one microarray was determined. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL3304

14 Samples

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(Submitter supplied) Microarray coverage of UHRR was determined by counting the number of spots with intensities exceeding the 1% and 5% false positive rates defined using the yeast negative control spots. Seven microarrays from different print runs were used. In four experiments, the UHRR was labeled with Cy5 and in three experiments with Cy3. Labeled UHRR was co-hybridized with Common Reference RNA (CRF) developed at Stanford University (8) labeled with the alternate dye. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

4 related Platforms

7 Samples

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(Submitter supplied) Total RNA isolated from 10 individual human cell lines were reverse-transcribed to cDNA, labeled with Cy5 and co-hybridized with Cy3-labeled UHRR onto 43,000-spot cDNA microarrays (Stanford University). The data was analyzed using GeneTraffic software. Approximately 6000-8000 spots out of 43,000 (14-18 %) were flagged on each microarray and excluded from further analysis. Spots with hybridization signals in Cy5 channel higher than 1000 and with Cy5/Cy3 ratio greater than 2 were collected and the number of spots with these characteristics in only one cell line was determined. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Dataset:

GDS1835

Platform:

GPL3305

10 Samples

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Analysis of individual cell lines representing different tissues against a Universal Reference RNA (URR). URR prepared from pooled RNA from the individual cell lines. Results indicate the individual cell lines contribute their own unique set of genes, thereby diversifying gene representation in URR.

Organism:

Homo sapiens

Type:

Expression profiling by array, log2 ratio, 10 cell line sets

Platform:

GPL3305

Series:

GSE3972

10 Samples

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(Submitter supplied) In the present study, we were interested in gene expression changes in the pectoralis muscle of juvenile king penguins during the transition from terrestrial to marine life. Strictly terrestrial during their first year after hatching, king penguin chicks must then depart to sea to reach nutritional emancipation and pectoralis muscle is largely involved in penguin adaptation to the marine environment. more...

Organism:

Aptenodytes patagonicus; Gallus gallus

Type:

Expression profiling by array

Platform:

GPL3213

7 Samples

Download data: CEL

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platforms:

GPL4133 GPL9283

27 Samples

Download data: TXT

(Submitter supplied) Peripheral blood mononuclear cells (PBMCs) from 13 vasculitis patients expressed varying gene profiles.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL9283

14 Samples

Download data: TXT

(Submitter supplied) Peripheral blood mononuclear cells (PBMCs) from 13 vasculitis patients expressed varying gene profiles.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL4133

13 Samples

Download data: TXT

(Submitter supplied) The Affymetrix GeneChip® system is a commonly used platform for microarray analysis but the technology is inherently expensive. Unfortunately, changes in experimental planning and execution, such as the unavailability of previously anticipated samples or a shift in research focus, may render significant numbers of pre-purchased GeneChip® microarrays unprocessed before their manufacturer’s expiration dates. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platforms:

GPL96 GPL570

12 Samples

Download data: CEL

(Submitter supplied) Microarray technology has had a profound impact on gene expression research. Some studies have questioned whether similar expression results are obtained when the same RNA samples are analyzed on different platforms. The MicroArray Quality Control (MAQC) project was initiated to address these concerns, as well as other performance and analysis issues. We demonstrate the consistency of results within a platform across test sites as well as the high level of cross-platform concordance in terms of genes identified as differentially expressed. more...

Organism:

Rattus norvegicus; Homo sapiens

Type:

Expression profiling by array; Expression profiling by RT-PCR

19 related Platforms

943 Samples

Download data: CEL, CSV, GPR, LSR, PDF, TXT, ZIP

(Submitter supplied) We present a novel method of using commercial oligonucleotide expression microarrays for aCGH, enabling DNA copy number measurements and expression profiles to be combined using the same platform. This method yields aCGH data from genomic DNA without complexity reduction at a median resolution of approximately 17,500 base pairs. Due to the well-defined nature of oligonucleotide probes, DNA amplification and deletion can be defined at the level of individual genes and can easily be combined with gene expression data. more...

Organism:

Homo sapiens

Type:

Genome variation profiling by array

Platform:

GPL570

8 Samples

Download data: CEL

(Submitter supplied) The publicly available genome sequence information of two rice strains, japonica cultivar Nipponbare and indica cultivar 93-11, opens a great opportunity for investigation of performances DNA genotyping by high-density oligonucleotide arrays. Here, we compare single feature polymorphism (SFP) detection performances between whole genome hybridization and transcript hybridization using Affymetrix Rice Expression Array and the two rice cultivars.

Organism:

Oryza sativa; Oryza sativa Indica Group; Oryza sativa Japonica Group

Type:

Expression profiling by array; Genome variation profiling by array

Platform:

GPL2025

27 Samples

Download data: CEL, CHP

(Submitter supplied) A zebra mussel byssus cDNA microarray was used to identify the differentially expressed genes between attachment and detachment. Keywords: Gene differential expression

Organism:

Dreissena polymorpha

Type:

Expression profiling by array

Platform:

GPL6586

4 Samples

Download data: GPR

(Submitter supplied) 716 E.coli clones were selected from thirty-four 96-well plates and re-arranged into eight new 96-well plates. The overnight cultures from the eight 96-well plates were used to prepare the PCR templates. 10 μl of each bacterial culture was taken to mix with 90 μl sterile double distilled water. Then the mixture was incubated at 100 ℃ for 10 minutes followed by 15 minutes 1200g centrifuge. The supernatant was used as PCR templates. more...

Organism:

Dreissena polymorpha

3 Series

62 Samples

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