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Homo sapiens
42 Downloadable Samples
Affymetrix Human Genome U133B Array (hgu133b), Affymetrix Human Genome U133A Array (hgu133a)
Description
Comparatative gene expression analysis for CD4 T cell subsets isolated from peripheral blood and palatine tonsils
Publication Title
A methodology for global validation of microarray experiments.
Sample Metadata Fields
Specimen part
View Samples- Mus musculus
- 30 Downloadable Samples
- Affymetrix Murine Genome U74A Version 2 Array (mgu74av2)
Description
DNA microarrays are popular tools for measuring gene expression of biological samples. This ever increasing popularity is ensuring that a large number of microarray studies are conducted, many of which with data publicly available for mining by other investigators. Under most circumstances, validation of differential expression of genes is performed on a gene to gene basis. Thus, it is not possible to generalize validation results to the remaining majority of non-validated genes or to evaluate the overall quality of these studies. <br></br> We have devised an approach for the global validation of DNA microarray experiments that will allow researchers to evaluate the general quality of their experiment and to extrapolate validation results of a subset of genes to the remaining non-validated genes. We applied this method to a microarray experiment validated with quantitative real time polymerase chain reaction. The experiment consists of three biological replicate treatments of mouse 3T3-L1 preadipocytes with the steroid hormone dexamethasone for 3 hours. Total RNA was extracted from each of our three treatment and three control samples, and we labeled and hybridized five aliquots of each sample to Affymetrix MGU74Av2 microarrays, for a total of 30 microarrays.<br></br> We illustrate why the popular strategy of selecting only the most differentially expressed genes for validation generally fails as a global validation strategy and propose random-stratified sampling as a better gene selection method. We also illustrate shortcomings of often-used validation indices such as overlap of significant effects and the correlation coefficient and recommend the concordance correlation coefficient (CCC) as an alternative.
Publication Title
A methodology for global validation of microarray experiments.
Sample Metadata Fields
Cell line, Subject, Compound
View Samples- Mus musculus
- 140 Downloadable Samples
NextSeq 550
Description
DNA is strictly compartmentalised within the nucleus to prevent autoimmunity despite this cGAS, a cytosolic sensor of dsDNA, is activated in autoinflammatory disorders and by DNA damage. Precisely how cellular DNA gains access to the cytoplasm remains to be determined. Here, we report that cGAS localises to micronuclei arising from genome instability in a model of monogenic autoinflammation, after exogenous DNA damage and spontaneously in human cancer cells. These micronuclei occur after mis-segregation of DNA during cell division and consist of chromatin surrounded by their own nuclear membrane. Breakdown of the micronuclear envelope, a process associated with chromothripsis, leads to rapid accumulation of cGAS, providing a mechanism by which self-DNA becomes exposed to the cytosol. cGAS binds to and is activated by chromatin and consistent with a mitotic origin, micronuclei formation and the proinflammatory response following DNA-damage are cell-cycle dependent. Furthermore, by combining live-cell laser microdissection with single cell transcriptomics, we establish that induction of interferon stimulated gene expression occurs in micronucleated cells. We therefore conclude that micronuclei represent an important source of immunostimulatory DNA. As micronuclei formed from lagging chromosomes also activate this pathway, cGAS recognition of micronuclei may act as a cell-intrinsic immune surveillance mechanism detecting a range of neoplasia-inducing processes. Overall design: RNA-seq of 35 individual mouse embryonic fibroblasts 48 h after 1 Gy irradiation: 21 test (with micronuclei) and 14 controls (without micronuclei).
Publication Title
cGAS surveillance of micronuclei links genome instability to innate immunity.
Sample Metadata Fields
Specimen part, Cell line, Treatment, Subject
View Samples- Homo sapiens
- 10 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
Exposure to Polychlorobiphenyls (PCBs) is known to cause serious health effects in human but the gene expression profiles leading to development of differnet diseases and disorders are not fully understood. The knowledge of global gene expression will help us to devlop early disease or disorder biomarkers for PCB induced health effects.
Publication Title
Transcriptional profiling and biological pathway analysis of human equivalence PCB exposure in vitro: indicator of disease and disorder development in humans.
Sample Metadata Fields
Sex, Age, Specimen part, Treatment
View Samples- Homo sapiens
- 30 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Discovery of drug mode of action and drug repositioning from transcriptional responses.
Sample Metadata Fields
Specimen part, Cell line, Treatment
View Samples
GSE19638- Homo sapiens
- 14 Downloadable Samples
Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
The effects of several compounds on the MCF7 human adenocarcinoma mammary cell line were analysed by gene expression profiling.
Publication Title
Discovery of drug mode of action and drug repositioning from transcriptional responses.
Sample Metadata Fields
Specimen part, Cell line, Treatment
View Samples- Homo sapiens
- 6 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
The effects of the CDK inhibitors PHA-848125 and PHA-690509 on the A2780 cell line were analysed by gene expression profiling.
Publication Title
Discovery of drug mode of action and drug repositioning from transcriptional responses.
Sample Metadata Fields
Specimen part, Cell line, Treatment
View Samples- Homo sapiens
- 4 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
The effects of the CDK inhibitor PHA-793887 on the A2780 human adenocarcinoma ovary cell line were analysed by gene expression profiling.
Publication Title
Discovery of drug mode of action and drug repositioning from transcriptional responses.
Sample Metadata Fields
Specimen part, Cell line, Treatment
View Samples- Homo sapiens
- 3 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
The effects of the CDK inhibitor PHA-848125 (referred to as CDK-125) on the MCF7 human adenocarcinoma mammary cell line were analysed by gene expression profiling.
Publication Title
Discovery of drug mode of action and drug repositioning from transcriptional responses.
Sample Metadata Fields
Specimen part, Cell line, Treatment
View Samples GSE18504- Homo sapiens
- 3 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
The effects of the CDK inhibitor Flavopiridol on the A2780 human adenocarcinoma ovary cell line were analysed by gene expression profiling.
Publication Title
Discovery of drug mode of action and drug repositioning from transcriptional responses.
Sample Metadata Fields
Specimen part, Cell line, Treatment
View Samples