Filters
Technology
Platform
GSE25070
Homo sapiens
52 Downloadable Samples
Illumina HumanRef-8 v3.0 expression beadchip
Description
We performed gene expression profiling of 26 colorectal tumors and matched histologically normal adjacent colonic tissue samples using the Illumina Ref-8 whole-genome expression BeadChip. We performed an integrated analysis of promoter DNA methylation and gene expression data to investigate the effects of DNA hypermethylation on gene expression.
Publication Title
Genome-scale analysis of aberrant DNA methylation in colorectal cancer.
Sample Metadata Fields
Sex, Disease, Disease stage
View Samples- Mus musculus
- 40 Downloadable Samples
- Illumina MouseRef-8 v2.0 expression beadchip
Description
This study investigates how 17-estradiol (E2) both stimulates and inhibits Runx2 in a locus-specific manner. We compare the effects of E2 to those of the Selective Estrogen Receptor Modulators (SERMs) raloxifene (ral) and lasofoxifen (las) and the phytoestrogen peurarin
Publication Title
No associated publication
Sample Metadata Fields
Sex, Age, Specimen part
View Samples- Homo sapiens
- 24 Downloadable Samples
- Illumina HumanHT-12 V4.0 expression beadchip
Description
Comparative analysis of RUNX1 and RUNX2 responsiveness in the presence or absence of E2
Publication Title
RUNX1 prevents oestrogen-mediated AXIN1 suppression and β-catenin activation in ER-positive breast cancer.
Sample Metadata Fields
Cell line, Treatment
View Samples- Drosophila melanogaster
- 20 Downloadable Samples
- Affymetrix Drosophila Genome Array (drosgenome1)
Description
Profiled the transcriptional response to over-expression Manganese-SOD (MnSOD) in adult Drosophila. A doxycycline-regulated system was employed to induce MnSOD over-expression, resulting in mean and maximal lifespan increases of ~ 20%. Examination of the genome-wide response to this lifespan intervention provided key insights into the molecular basis of aging.
Publication Title
No associated publication
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 18 Downloadable Samples
- Affymetrix Human Genome U133A 2.0 Array (hgu133a2)
Description
In an acute skin wound, newly released serum growth factors in the wound bed drive lateral migration of human keratinocytes (HKs) to re-epithelialize the wound. However, profiling the migration signal-specific genes has long been challenged by pleiotropic effects of a given growth factor, including proliferation, migration and factor-specific responses. To overcome these technical problems, we 1) took advantage of a unique response of HKs to transforming growth factor-beta (TGFbeta) to selectively suppress growth signal-responding genes and identify motility-specific genes and 2) employed dual stimulation of HKs with TGFalpha and insulin to identify the common genes and eliminate factor-specific genes. Under these conditions, DNA microarray analyses were utilized to study the profiles of both TGFalpha-regualted and insulin-regulated immediate early (IE, 30 min), early (E, 60 min) and delayed early (DE, 120 min) genes.
Publication Title
Profiling motility signal-specific genes in primary human keratinocytes.
Sample Metadata Fields
No sample metadata fields
View Samples- Drosophila melanogaster
- 17 Downloadable Samples
- Affymetrix Drosophila Genome Array (drosgenome1)
Description
The experimental spike-in studies of microarray hybridization conducted by Affymetrix demonstrate a nonlinear response of fluorescence intensity signal to target concentration. It was shown that the Langmuir adsorption isotherm recapitulates a general trend of signal response to concentration. However, this model fails to explain some key properties of the observed signal. In particular, according to the simple Langmuir isotherm, all probes should saturate at the same intensity level. However, this effect was not observed in the publicly available Affymetrix spike-in datasets. In our experimental study, we attempt to account for the unexplained variation in the observed probe intensities using customized fluidics scripts. We explore experimentally the effect of the stringent wash, target concentration, and hybridization time on the final microarray signal.
Publication Title
No associated publication
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 3 Downloadable Samples
- Illumina HumanHT-12 V4.0 expression beadchip
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
SNF5 is an essential executor of epigenetic regulation during differentiation.
Sample Metadata Fields
Specimen part, Cell line
View Samples- Mus musculus
- 12 Downloadable Samples
- Affymetrix Mouse Gene 1.0 ST Array (mogene10st)
Description
The requirements for self-renewal differ between EpiSCs and ES cells and the underlying mechanism is largely unknown. Here we show that mouse EpiSCs can be efficiently derived and robustly propagated even from single cells, using two small-molecule inhibitors: CHIR99021 and XAV939.
Publication Title
No associated publication
Sample Metadata Fields
Specimen part, Treatment
View Samples- Homo sapiens
- 12 Downloadable Samples
- Illumina HumanHT-12 V4.0 expression beadchip
Description
Effect of RUNX1 depletion in the presence or absence of Estradiol
Publication Title
RUNX1 prevents oestrogen-mediated AXIN1 suppression and β-catenin activation in ER-positive breast cancer.
Sample Metadata Fields
Cell line, Treatment
View Samples- Homo sapiens
- 3 Downloadable Samples
- Illumina HumanHT-12 V4.0 expression beadchip
Description
Analysis of global gene expression by SNF5 level change in human pluripotent and differentiated cells. The core subunit of BAF complex SNF5 is at the nexus of the link between chromatin remodeling and tumor suppression. We demonstrated a role for the remodeler SNF5 as a key executor in regulating pluripotency gene networks during differentiation by using loss and gain of function experiments followed by gene-expression arrays.
Publication Title
SNF5 is an essential executor of epigenetic regulation during differentiation.
Sample Metadata Fields
Specimen part, Cell line
View Samples