GEO DataSets

(Submitter supplied) Comparison of ds-cDNA, Indirect and Direct Random Labeling Methods for gene expression analysis on the NimbleGen platform. Expression profiles from artemisinic acid-producing S. cerevisiae strain EPY330 and non-producing strain EPY338 are compared for each labeling method tested. The labeling methods and their comparison are described in detail in Ouellet et al., BMC Biotech 2009. Strains were described in detail previously in Ro et al. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL8435

18 Samples

Download data: PAIR

(Submitter supplied) This study is a quantitative trait linkage mapping study targeted at gene-environment interaction. A family of yeast derived from BY4716 and RM11-1a was grown in two carbon sources (glucose and ethanol) and expression profiled. The analysis revealed how the influence of genetic factors changes in different conditions. Abstract: The effects of genetic variants on phenotypic traits often depend on environmental and physiological conditions, but such gene–environment interactions are poorly understood. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platforms:

GPL884 GPL2883

246 Samples

Download data: TXT

(Submitter supplied) Peripheral blood is an accessible and informative source of transcriptomal information for many human disease and pharmacogenomic studies. While there can be significant advantages to analyzing RNA isolated from whole blood, particularly in clinical studies, the preparation of samples for microarray analysis is complicated by the need to minimize artifacts associated with highly abundant globin RNA transcripts. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL201

24 Samples

Download data: CEL, CHP

(Submitter supplied) see Vodkin et al., BMC Genomics 5:73 (2004) for details of cDNAs represented on the arrays and Thibaud-Nissen et al., Plant Physiol 132:118-136 (2003); Zou et al. Mol Plant Microbe Interat 18:1161-1174 (2005); Zabala and Vodkin, Plant Cell 17: 2619-2632 (2005) for use of cDNA arrays in soybean. Protocol: PCR amplified cDNA inserts printed with Genemachines Omnigrid

Organism:

Glycine max

6 Series

82 Samples

Download data

(Submitter supplied) see Vodkin et al., BMC Genomics 5:73 (2004) for details of cDNAs represented and Thibaud-Nissan, et al., Plant Physiol 132: 118-136 (2003); and Zabala and Vodkin, Plant Cell 17: 2619-2632 (2005) for use of cDNA arrays in soybean Protocol: amplified cDNAs printed with Genemachines Omnigrid

Organism:

Glycine max

12 Series

191 Samples

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

Organism:

Fundulus heteroclitus

Type:

Expression profiling by array

Platforms:

GPL7360 GPL7335

13 Samples

Download data: TXT

(Submitter supplied) Analysis of the relationship between the amount of mRNA and the fluorescent signal from the microarray hybridizations. In addition, we measured expression for differences in RNA labeling and for the day on which RNA is prepared. Keywords: Gene expression

Organism:

Fundulus heteroclitus

Type:

Expression profiling by array

Platform:

GPL7360

8 Samples

Download data: TXT

(Submitter supplied) In the teleost fish Fundulus heteroclitus there is extensive variation in gene expression among individuals within and between populations. Accurate measures of the variation in mRNA expression using microarrays can be confounded by technical variation, which includes variation in RNA isolation procedures, day of hybridization and methods used to amplify and dye label RNA for hybridization. In this manuscript we analyze the relationship between the amount of mRNA and the fluorescent signal from the microarray hybridizations demonstrating that for a wide-range of mRNA concentrations the fluorescent signal is a linear function of the amount of mRNA. more...

Organism:

Fundulus heteroclitus

Type:

Expression profiling by array

Platform:

GPL7335

5 Samples

Download data: TXT

(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

(Submitter supplied) For decades, formalin-fixing and paraffin embedding (FFPE) has been routinely used to preserve tissue samples for histological analysis. Global gene expression analysis of these archival tissues has the potential to greatly advance research attempting to link perturbations in molecular pathways to disease outcome. We investigated 16-year-old FFPE mouse liver samples treated with phenobarbital and created a protocol for their analysis using Agilent gene expression arrays. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL13912

28 Samples

Download data: TXT

(Submitter supplied) Considerable variation in gene expression data from different DNA microarray platforms has been demonstrated. However, no characterization of the source of variation arising from labeling protocols has been performed. To analyze the variation associated with T7-based RNA amplification/labeling methods, aliquots of the Stratagene Human Universal Reference RNA were labeled using 3 eukaryotic target preparation methods and hybridized to a single array type (Affymetrix U95Av2). more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Dataset:

GDS1954

Platform:

GPL8300

20 Samples

Download data: CEL, EXP

Comparison of expression profiles generated using various T7 RNA polymerase-based in vitro transcription (IVT) RNA labeling methods. The length of the IVT reactions ranged from 4 to 16 hours. Results provide evidence for amplification method-dependent biases in gene expression data.

Organism:

Homo sapiens

Type:

Expression profiling by array, count, 3 protocol, 3 time sets

Platform:

GPL8300

Series:

GSE3254

20 Samples

Download data: CEL, EXP

(Submitter supplied) Background:Alternative splicing and isoform level expression profiling is an emerging field of interest within genomics. Splicing sensitive microarrays, with probes targeted to individual exons or exon-junctions, are becoming increasingly popular as a tool capable of both expression profiling and finer scale isoform detection. Despite their intuitive appeal, relatively little is known about the performance of such tools, particularly in comparison with more traditional 3’ targeted microarrays. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platforms:

GPL5175 GPL5188

40 Samples

Download data: CEL

(Submitter supplied) Background:Alternative splicing and isoform level expression profiling is an emerging field of interest within genomics. Splicing sensitive microarrays, with probes targeted to individual exons or exon-junctions, are becoming increasingly popular as a tool capable of both expression profiling and finer scale isoform detection. Despite their intuitive appeal, relatively little is known about the performance of such tools, particularly in comparison with more traditional 3’ targeted microarrays. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL5188

20 Samples

Download data: CEL

(Submitter supplied) Background:Alternative splicing and isoform level expression profiling is an emerging field of interest within genomics. Splicing sensitive microarrays, with probes targeted to individual exons or exon-junctions, are becoming increasingly popular as a tool capable of both expression profiling and finer scale isoform detection. Despite their intuitive appeal, relatively little is known about the performance of such tools, particularly in comparison with more traditional 3’ targeted microarrays. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL5175

20 Samples

Download data: CEL

(Submitter supplied) Background: DNA microarrays provide a powerful method for global analysis of gene expression. The application of this technology to specific cell types and tissues, however, is typically limited by small amounts of available mRNA, thereby necessitating amplification. Here we compare microarray results obtained with two different methods of RNA amplification to profile gene expression in the C. elegans larval nervous system. more...

Organism:

Caenorhabditis elegans

Type:

Expression profiling by array

Platform:

GPL200

8 Samples

Download data: CEL, CHP

(Submitter supplied) Meningococcal strains from different serogroups and different clonal complexes were compared using cGH analyses in a one color experiment.

Organism:

Neisseria meningitidis

Type:

Genome variation profiling by array

Platform:

GPL9218

14 Samples

Download data: TXT

(Submitter supplied) Meningococcal strains from different serogroups and different clonal complexes were compared using cGH analyses

Organism:

Neisseria meningitidis

Type:

Genome variation profiling by array

Platform:

GPL8787

18 Samples

Download data: GPR