GEO DataSets

(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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