GEO DataSets

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) 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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(Submitter supplied) To facilitate collaborative research efforts between multi-investigator teams using DNA microarrays, we identified sources of error and data variability between laboratories and across microarray platforms and methods to accommodate this variability. RNA expression data were generated in seven laboratories, comparing two standard RNA samples using twelve microarray platforms. At least two standard microarray types (one spotted, one commercial) were used by all laboratories. more...

Organism:

Mus musculus

Type:

Expression profiling by array

12 related Platforms

215 Samples

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(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:

GPL570 GPL96

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) Transcriptional profiling of two A. nidulans strains, aiming to compare the control strain CV125 (pabaA1) with the transgenic strain NA1363 (pabaA1) harbouring a gpdAp-lacZ-trpCt.riboB construct integrated in chromosome VIII. This construct, carried out in a derivative of the pBR322 vector, contained the E. coli lacZ sequence (encoding ß-galactosidase) fused to the A. nidulans trpC terminator and placed under the control of the strong and constitutive promoter of the A. more...

Organism:

Aspergillus nidulans

Type:

Expression profiling by array

Platform:

GPL21331

16 Samples

Download data: TXT

(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:

Homo sapiens; Mus musculus; unidentified

Type:

Expression profiling by array

Platforms:

GPL8300 GPL96 GPL1857

15 Samples

Download data: CEL, EXP

(Submitter supplied) Microarray technology provides a powerful tool for defining gene expression profiles of airway epithelium that lend insight into the pathogenesis of human airway disorders. The focus of this study was to establish rigorous quality control parameters to ensure that microarray assessment of the airway epithelium is not confounded by experimental artifact. Samples (total n=223) of trachea, large and small airway epithelium were collected by fiberoptic bronchoscopy of 144 individuals (42 healthy non-smokers, 49 healthy smokers, 11 symptomatic smokers, 22 smokers with lone emphysema with normal spirometry, and 20 smokers with COPD) were processed and hybridized to Affymetrix HG-U133 2.0 Plus microarrays. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

223 Samples

Download data: CEL, CHP

(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) In three different ts-LT keratinocyte lines, TP53 was downregulated in four different ways. The vector constructs used for p53 abrogation were pWZL-p53DN-hygro (encoding the human p53 dominant-negative mutant Arg(175)His, pRS-p53shRNA-puro (containing a short hairpin RNA specific for p53), LZRS-E6-GFP (containing the HPV16-E6 oncogene) and the pRetrosuper miR-372. (containing the MicroRNA 372). Cells were transduced at 32°C as described above and checked for transduction efficiency by using an LZRS-GFP control. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL4133

32 Samples

Download data: TXT

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

Organism:

Homo sapiens

Type:

Expression profiling by array

Platforms:

GPL7473 GPL570

3248 Samples

Download data: CEL

(Submitter supplied) An International Multi-Center Study to Define the Clinical Utility of Microarray–Based Gene Expression Profiling in the Diagnosis and Sub-classification of Leukemia (MILE Study) Established in 2005, the MILE (Microarray Innovations in LEukemia) study research program included 11 participating centers in three continents. This cohort of n=1,152 samples represents data on the retrospective whole-genome analysis phase. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL7473

1152 Samples

Download data: CEL

(Submitter supplied) An International Multi-Center Study to Define the Clinical Utility of Microarray–Based Gene Expression Profiling in the Diagnosis and Sub-classification of Leukemia (MILE Study) Established in 2005, the MILE (Microarray Innovations in LEukemia) study research program included 11 participating centers in three continents. This cohort of n=2,096 samples represents data on the retrospective whole-genome analysis phase. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

2096 Samples

Download data: CEL

(Submitter supplied) An international standardization program towards the application of gene expression profiling in routine leukaemia diagnostics: The MILE study pre-phase. A total of 11 laboratories from three continents performed 204 analyses using a whole-genome expression microarray. In an effort to standardize the microarray procedure, each participating centre was equipped with identical hardware, software, and reagents. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

204 Samples

Download data: CEL

(Submitter supplied) Several technical parameters are now being optimized for microRNA expression profiling experiments, but the finite amount of total RNA available continues to bottleneck clinical investigations. We used microarrays to determine the influence of the labeling reagent on total RNA requirements and data quality.

Organism:

synthetic construct; Homo sapiens

Type:

Non-coding RNA profiling by array

Platform:

GPL8786

44 Samples

Download data: CEL

(Submitter supplied) We carried out a parallel nested experiment performed simultaneously on RNA-Seq and microarrays that systematically split variation into four stages (treatment, biological variation, library preparation, and chip/lane noise), allowing a separation and comparison of the sources of variation in a well-controlled cellular system, Saccharomyces cerevisiae.

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL11382

16 Samples

Download data: TXT