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GSE6351
Homo sapiens
15 Downloadable Samples
Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
Characterization of the underlying genetic defects in patients with a rare and peculiar phenotype is challenging. Here we have utilized whole genome expression profiling, and identified a homozygous germline mutation in the DDB2 gene in a patient with several facial tumors. The feasibility of using blood derived RNA, diminishing costs of the technology, and the limited number of samples needed provide this approach a powerful new tool that may substantially aid in such gene identification efforts.
Publication Title
Blood-derived gene-expression profiling in unravelling susceptibility to recessive disease.
Sample Metadata Fields
No sample metadata fields
View Samples- Oryza sativa
- 34 Downloadable Samples
- Affymetrix Rice Genome Array (rice)
Description
Plant hormones interact with each other and regulate gene expression to control plant growth and development. To understand the complex network, accumulation of comprehensive and integrative data of gene expression and hormone concentration is important. Using microarray, global gene expression profile was analyzed to compare with plant hormone concentration in 14 parts of rice at reproductive stage.
Publication Title
UniVIO: a multiple omics database with hormonome and transcriptome data from rice.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 4 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
The epiblast (foremost embryonic ectoderm) generates all three germ layers and therefore has crucial roles in the formation of all mammalian body cells. Regulation of epiblast gene expression is poorly understood due to the difficulty of manipulating epiblast tissues in vivo. In the present study, using the self-organizing properties of embryonic stem cells (ESCs), we generated and characterized epiblast-like tissue in three-dimensional (3D) culture. We identified significant genome-wide expression changes in this epiblast-like tissue. Additionally, we identified the significance of the Fgf/Erk and ectoderm formation pathways, using the bioinformatics resource IPA and DAVID. We first focused on Fgf5, which ranked in the top 10 among discovered genes. Toward functional analysis of Fgf5, we developed efficient methods of genome engineering (CRISPR/Cas9) and RNA interference (RNAi). Notably, we show one-step generation of an Fgf5 reporter line, null and in/del mutants. Furthermore, mutation types correlated well with CRISPR/Cas9 activity. For time- and dose-dependent depletion of Fgf5 over the course of development, we generated an ESC line harboring a drug-inducible short hairpin RNA cassette integrated by the Tol2 transposon system (pRNAi). Our methods provide a framework for a broad array of applications in the areas of mammalian genetics and molecular biology to understand development and to improve future therapeutics.
Publication Title
Establishment of Functional Genomics Pipeline in Mouse Epiblast-Like Tissue by Combining Transcriptomic Analysis and Gene Knockdown/Knockin/Knockout, Using RNA Interference and CRISPR/Cas9.
Sample Metadata Fields
Specimen part
View Samples- Homo sapiens
- 40 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
The unfolded protein response (UPR) is a cellular defense mechanism against glucose deprivation, a cell condition that occurs in solid tumors.
Publication Title
Chemical genomics identifies the unfolded protein response as a target for selective cancer cell killing during glucose deprivation.
Sample Metadata Fields
No sample metadata fields
View Samples- Rattus norvegicus
- 8 Downloadable Samples
- Affymetrix Rat Genome 230 2.0 Array (rat2302)
Description
We used microarrays to detail transcriptional changes in the rat heart in response to doxorubicin, a chemotherapeutic drug known to induce cardiac disfunction/heart failure
Publication Title
Early effects of doxorubicin in perfused heart: transcriptional profiling reveals inhibition of cellular stress response genes.
Sample Metadata Fields
No sample metadata fields
View Samples- Arabidopsis thaliana
- 30 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
Nitrogen (N) is a key nutrient that is often the limiting factor in plant growth. However, the molecular mechanisms underlying transcriptional regulation of N-starvation-responses remain largely unknown.
Publication Title
A NIGT1-centred transcriptional cascade regulates nitrate signalling and incorporates phosphorus starvation signals in Arabidopsis.
Sample Metadata Fields
Specimen part
View Samples- Homo sapiens
- 108 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
Patients who cleared HCV viremia early during therapy tended to show favorable outcomes, whereas patients who needed a longer period to clear HCV had poorer outcomes. We explored the mechanisms of treatment resistance by comparing hepatic gene expression before and during treatment
Publication Title
Differential interferon signaling in liver lobule and portal area cells under treatment for chronic hepatitis C.
Sample Metadata Fields
Specimen part, Time
View Samples- Homo sapiens
- 18 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
Genes related to sleep and wakefulness were evaluated by RNA microarray in patients, including CKD,HD patients and control subjects.
Publication Title
Messenger RNA expression profile of sleep-related genes in peripheral blood cells in patients with chronic kidney disease.
Sample Metadata Fields
Sex, Specimen part
View Samples- Homo sapiens
- 10 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
Induction of germline-competent pluripotent stem cells from mouse fibroblasts has been achieved by the ectopic expression of four genes (Oct3/4, Sox2, c-Myc and Klf4). If this method can be applied to humans for the generation of personalized human pluripotent stem cells, it would greatly facilitate the therapeutic application of stem cells by avoiding the problem of immune rejection by the recipient associated with allograft transplants. Here we show that the ectopic expression of the same four genes in human neonatal skin derived cells is sufficient to induce pluripotent stem cells indistinguishable from human embryonic stem cells in morphology, gene expression, DNA methylation, teratoma formation and long term self-renewal ability. Extensive analysis of colonies generated by ectopic expression of these four genes indicates the presence of considerable heterogeneity in the induced colonies. These results provide a new finding to generate human induced pluripotent stem cells from postnatal somatic tissues.
Publication Title
Heterogeneity of pluripotent marker gene expression in colonies generated in human iPS cell induction culture.
Sample Metadata Fields
No sample metadata fields
View Samples- Saccharomyces cerevisiae
- 20 Downloadable Samples
Illumina HiSeq 1500
Description
The PAT-seq approach was utilised to determine the gene expression changes over the cell-cycle of wildtype and delta-set1 yeast strains. The cell were synchronised by alpha-factor arrest and cell-cycle release Overall design: Analysis gene expresson across the S. cerevisiae cell cycle.
Publication Title
Coordination of Cell Cycle Progression and Mitotic Spindle Assembly Involves Histone H3 Lysine 4 Methylation by Set1/COMPASS.
Sample Metadata Fields
Cell line, Subject, Time
View Samples