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GSE8057
Homo sapiens
51 Downloadable Samples
Affymetrix Human Genome U95 Version 2 Array (hgu95av2)
Description
Time-course and concentration-effect experiments with multiple time points and drug concentrations provide far more valuable information than experiments with just two design-points (treated vs. control), as commonly performed in most microarray studies. Analysis of the data from such complex experiments, however, remains a challenge. Here we present a semi-automated method for fitting time profiles and concentration-effect patterns, simultaneously, to gene expression data. The submodels for time-course included exponential increase and decrease models with parameters such as initial expression level, maximum effect, and rate-constant (or half-time). The submodel for concentration-effect was a 4-parameter Hill model.
Publication Title
Simultaneous modeling of concentration-effect and time-course patterns in gene expression data from microarrays.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 2 Downloadable Samples
- Affymetrix Human Gene 1.0 ST Array (hugene10st)
Description
Prostate cancer C4-2B cells were cultured in docetaxel in a dose-escalation manner. After nine months selection, cells were able to divide freely in 5 nM docetaxel, with a specific sets of genes been deregulated.
Publication Title
Inhibition of ABCB1 expression overcomes acquired docetaxel resistance in prostate cancer.
Sample Metadata Fields
Cell line
View Samples- Mus musculus
- 21 Downloadable Samples
Illumina Genome Analyzer IIx
Description
RNA-seq was performed using the RNA extracted from the bottom half of right lobe of mouse livers. Mice fall into two groups, mutant group which express ectopic hURI and their control littermates which do not express hURI. Two time points were considered in the study, 1-week-old mice, expressing hURI since 1 week (n =3, 4 for control and mutant, respectively) and 8-week-old mice expressing hURI since 8 week (n= 4, 3 for control and mutant, respectively), as hURI is expressed since conception. Overall design: Determination of differentially expressed transcripts over two time points (1 week and 8 weeks) in mouse livers expressing hURI (1 week and 8 weeks).
Publication Title
Inhibition of de novo NAD(+) synthesis by oncogenic URI causes liver tumorigenesis through DNA damage.
Sample Metadata Fields
Specimen part, Subject
View Samples- Homo sapiens
- 21 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
We analyzed transcriptional changes in 4 prostate cancer cell lines following treatment with the BET inhibitor I-BET762 using Affymetrix Human Genome U133 Plus 2.0 Arrays.
Publication Title
Inhibition of BET bromodomain proteins as a therapeutic approach in prostate cancer.
Sample Metadata Fields
Cell line, Time
View Samples- Homo sapiens
- 45 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
Transcriptional changes were analyzed in two colorectal cancer, two pancreatic cancer, and one small cell lung cancer cell line following treatment with the BET inhibitor GSK525762 and/or the MEK inhibitor trametinib using Affymetrix Human Genome U133 Plus 2.0 Arrays.
Publication Title
MEK inhibitors overcome resistance to BET inhibition across a number of solid and hematologic cancers.
Sample Metadata Fields
Cell line, Treatment, Time
View Samples- Homo sapiens
- 8 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
Gene expression changes were analyzed in 2 acute lymphoblastic leukemia cell lines treated with the GSK126 EZH2 inhibitor using Affymetrix Human Genome U133 Plus 2.0 arrays.
Publication Title
A687V EZH2 is a driver of histone H3 lysine 27 (H3K27) hypertrimethylation.
Sample Metadata Fields
Cell line, Treatment, Time
View Samples- Mus musculus
- 6 Downloadable Samples
- Illumina HiSeq 2000, NextSeq 500
Description
Cell proliferation is essential to rapid tissue growth and repair, but is inherently associated with considerable genome damage that cells must efficiently prevent or fix to prevent cell cycle arrest. Here, we implicate the transcription factor Gata6 in regulation of adult mouse hair follicle regeneration where it controls the renewal of the rapidly proliferating epithelial (matrix) progenitors and hence the extent of production of terminally differentiated lineages. We find that Gata6 protects against DNA damage associated with proliferation, thus preventing cell cycle arrest and apoptosis. Furthermore, we show that Gata6 stimulates the Eddarad/NF-kB pathway, important for DNA-damage repair and stress response in general, and for hair follicle growth in particular. Finally, we find Edaradd essential, downstream of Gata6 for cell survival and proliferation. Our data add to recent evidence in embryonic stem and neural progenitor cells, suggesting a model whereby developmentally regulated transcription factors protect from DNA damage associated with proliferation occurring at key stages of rapid tissue growth. Our data may aid in understanding why Gata6 is a frequent target of amplification in cancers. Overall design: Gene expression profiling by mRNA-seq to identify differentially expressed genes in wild type (WT) and Gata6 induced knockout (iKO) mouse epidermal keratinocytes
Publication Title
Gata6 promotes hair follicle progenitor cell renewal by genome maintenance during proliferation.
Sample Metadata Fields
Treatment, Subject
View Samples- Arabidopsis thaliana
- 24 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
Metal oxide engineered nanoparticles, which are widely used in diverse applications, are known to impact terrestrial plants. These nanoparticles have a potential to induce changes in plant tissue transcriptomes, and thereby the productivity. Here we looked at how the two commonly used nanoparticles, nano-titania (TiO2) and nano-ceria (CeO2) can impact the underlying mechanisms associated plant growth at genome level.
Publication Title
Molecular and physiological responses to titanium dioxide and cerium oxide nanoparticles in Arabidopsis.
Sample Metadata Fields
Age, Specimen part
View Samples- Arabidopsis thaliana
- 12 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
Seed germination of a terrestrial plant constitute dynamic changes in various physiological processes related to growth and development. These physiological processes can be affected by various abiotic and biotic stressors. Here we looked at how the two commonly used nanoparticles, nano-titania (TiO2) and nano-ceria (CeO2) can impact the underlying mechanisms associated with germination at genome level.
Publication Title
Phenotypic and genomic responses to titanium dioxide and cerium oxide nanoparticles in Arabidopsis germinants.
Sample Metadata Fields
Age, Specimen part, Treatment
View Samples- Homo sapiens
- 43 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
EZH2 inhibition as a therapeutic strategy for lymphoma with EZH2-activating mutations.
Sample Metadata Fields
Specimen part, Cell line, Treatment
View Samples