GEO DataSets

(Submitter supplied) cDNA array of commercially available set of 20.400 clones (Mus musculus) and specific mouse genes spotted on aldehyde coated slides.

Organism:

Mus musculus

3 Series

31 Samples

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(Submitter supplied) cDNA array of commercially available set of 20k clones (Mus musculus) spotted on aldehyde coated slides.

Organism:

Mus musculus

6 Series

69 Samples

Download data: GAL

(Submitter supplied) This series represents a set of experiments preformed using RNA isolated from human mammary epithelial cells, human MDA-MB-436 cells and HCC1954 cells. Keywords: parallel sample

Organism:

Homo sapiens

Type:

Expression profiling by array

Datasets:

GDS817 GDS820 GDS823 GDS825

4 related Platforms

22 Samples

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Expression profiling of breast cancer cell lines HCC 1954 and MDA-MB-436 in reference to mammary epithelial cells. Results used to validate a method of comparing data generated from cDNA arrays to that from Affymetrix arrays. The method uses DNA sequence to match probes between platforms.

Organism:

Homo sapiens

Type:

Expression profiling by array, log ratio, 2 cell line sets

Platform:

GPL875

Series:

GSE1299

4 Samples

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Expression profiling of breast cancer cell lines HCC 1954 and MDA-MB-436 in reference to mammary epithelial cells. Results used to validate a method of comparing data generated from Affymetrix arrays to that from cDNA arrays. The method uses DNA sequence to match probes between platforms.

Organism:

Homo sapiens

Type:

Expression profiling by array, transformed count, 3 cell line, 2 disease state sets

Platform:

GPL97

Series:

GSE1299

6 Samples

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Expression profiling of breast cancer cell lines HCC 1954 and MDA-MB-436 in reference to mammary epithelial cells. Results used to validate a method of comparing data generated from Affymetrix arrays to that from cDNA arrays. The method uses DNA sequence to match probes between platforms.

Organism:

Homo sapiens

Type:

Expression profiling by array, transformed count, 3 cell line, 2 disease state sets

Platform:

GPL96

Series:

GSE1299

6 Samples

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Expression profiling of breast cancer cell lines HCC 1954 and MDA-MB-436 in reference to mammary epithelial cells. Results used to validate a method of comparing data generated from Affymetrix arrays to that from cDNA arrays. The method uses DNA sequence to match probes between platforms.

Organism:

Homo sapiens

Type:

Expression profiling by array, transformed count, 3 cell line, 2 disease state sets

Platform:

GPL8300

Series:

GSE1299

6 Samples

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(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) DNA microarray technology is a powerful tool for getting the overview of gene expression in biological samples. Although the successful application of microarray-based expression analysis was demonstrated in a number of applications, the main problem with this approach is the fact that expression levels deduced from hybridization experiments do not necessarily correlate with RNA concentrations. Moreover, oligonucleotide probes corresponding to the same gene can give different hybridization signals. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL4746

6 Samples

Download data: TXT

(Submitter supplied) The LNA capture probes are intelligently designed and Tm-normalized ensuring all miRNA targets hybridize to the array with equal affinity under high stringency hybridization conditions.

Organism:

Mus musculus

2 Series

1 Related Platform

13 Samples

Download data: TXT

(Submitter supplied) miChip v8.0 annotation was done for human. miChip v8.0 contains capture probe matching several mouse and rat microRNAs that were not validated in human (miRbase v 8.0) miChip array are spotted on CodeLink, GE Life Science, cat. no. 30001100). Codelink glass slides are coated with N-hydroxysuccinimide Protocol: LNA-modified oligonucleotide (Exiqon) capture probes are designed to have a close to uniform Tm of 72 Celsius against their complementary targets. more...

Organism:

Homo sapiens

3 Series

50 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 report the design, fabrication, and validation of a microarray covering the majority of the Schistosoma japonicum and Schistosoma mansoni transcriptomes. The oligonucleotide microarray contains 12,166 S. mansoni and 7055 S. japonicum target sequences. A confidence threshold of 0.001 (P value) was used in all analyses. The cross hybridization potential of the microarray was representative of 10,362 probes detected in both channels, while 12,052 probes hybridised to S. more...

Organism:

Schistosoma mansoni; Schistosoma japonicum

Type:

Expression profiling by array

Platform:

GPL3821

4 Samples

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(Submitter supplied) DNA sequences for the 3163 C. thermocellum ATCC 27405 predicted protein-encoding genes were obtained from The Joint Genome Institute using sequence assembled in November 2003. Oligonucleotide probes that represented the whole genome of C. thermocellum were designed using the CommOligo software and were commercially synthesized without modification (MWG Biotech, High Point, NC) in 96-well plates. The concentration of the probes was adjusted to 100 pmol/JlL, transferred to 384-well printing plates in a final concentration of 50% dimethyl sulfoxide using a BioMek FX liquid handling robot (Beckman-Coulter, Fullerton, CA) and then spotted onto UltraGAPS glass slides (Corning Life Sciences, Corning, NY) using a BioRobotics Microgrid II microarrayer (Genomic Solutions, Ann Arbor, MI) in a dust-free clean room maintained at 21°C and 50% relative humidity. more...

Organism:

Acetivibrio thermocellus ATCC 27405

1 Series

39 Samples

Download data: TXT

(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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