GEO DataSets

(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: 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) 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) We tested the performance of three methods for amplifying single-cell amounts of RNA under ideal conditions: T7-based in vitro transcription; switching mechanism at 5' end of RNA template (SMART) PCR amplification; and global PCR amplification. All methods introduced amplification-dependent noise when mRNA was amplified 108-fold, compared with data from unamplified cDNA. PCR-amplified cDNA demonstrated the smallest number of differences between two parallel replicate samples and the best correlation between independent amplifications from the same cell type, with SMART outperforming global PCR amplification. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL2584

56 Samples

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(Submitter supplied) Experiment 1: U133A arrays (2) hybridized to duplicate sscDNA samples prepared from 20 ng Clontech UHR RNA Experiment 2: Mu6500A arrays (6) hybridized to triplicate sscDNA samples prepared from 3 x 5 ng mouse liver RNA and 3 x 100 ng mouse liver RNA Experiment 3: U95Av2 arrays (6) hybridized to triplicate sscDNA samples prepared from 3 x 10 ng K562 RNA and 3 x 10 ng Stratagene UHR RNA Experiment 4: U95Av2 array (1) hybridized to sscDNA sample prepared from template minus reaction (negative control) Keywords: parallel sample

Organism:

Mus musculus; unidentified; Homo sapiens

Type:

Expression profiling by array

Platforms:

GPL8300 GPL96 GPL1857

15 Samples

Download data: CEL, EXP

(Submitter supplied) We have demonstrated in vitro transcription (IVT) of cDNA sequences from purified Jurkat T-cell mRNA immobilization on microfluidic packed beads down to single-cell quantities. The microfluidic amplified aRNA was nearly identical in length and quantity compared with benchtop reactions using the same starting sample quantities. Microarrays were used to characterize the number and population of genes in each sample, allowing comparison of the microfluidic and benchtop processes. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6098

36 Samples

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(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) 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) 25x75 mm in dimension. Protocol: 21K 60-mer oligo probes were designed from the MaizeGDB EST contigs and synthesized in situ by an ink-jet printing method employing standard phosphoramidite chemistry on glass slides.

Organism:

Zea mays

1 Series

24 Samples

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(Submitter supplied) Gene expression comparison of Wilms tumor RNA versus Stratagene Universal reference RNA Keywords: repeat sample

Organism:

Homo sapiens

Type:

Expression profiling by array

Dataset:

GDS1791

Platform:

GPL96

4 Samples

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Expression profiling of Wilms' tumor tissue after pre-operative chemotherapy. Stratagene Universal Reference RNA also examined. Results are part of a cross-platform evaluation and compared to data generated from Serial Analysis of Gene Expression.

Organism:

Homo sapiens

Type:

Expression profiling by array, count, 2 other sets

Platform:

GPL96

Series:

GSE1158

4 Samples

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(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) Construction and Preparation of Synechocystis Spotted Microarrays: 3168 genes or putative ORFs of Synechocystis sp. PCC6803 were PCR amplified in two stages. Primary amplification was achieved using gene-specific up-stream and down-stream primers modified with adaptamer sequences and genomic DNA template. Secondary amplification was achieved using adaptamer primers and individual primary PCR product templates. more...

Organism:

Synechocystis sp. PCC 6803

1 Series

16 Samples

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