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GSE23036
Homo sapiens
65 Downloadable Samples
Affymetrix Human Genome U133A 2.0 Array (hgu133a2)
Description
The purpose of our study was to identify expression signatures and molecular markers associated with tumor recurrence and survival in patients with locally advanced head and neck squamous cell carcinoma (HNSCC).
Publication Title
Gene expression signatures and molecular markers associated with clinical outcome in locally advanced head and neck carcinoma.
Sample Metadata Fields
Sex, Specimen part
View Samples- Hordeum vulgare
- 12 Downloadable Samples
- Affymetrix Barley Genome Array (barley1)
Description
Caryopses of barley (Hordeum vulgare), like all other cereal seeds, are complex sink organs optimized for storage starch accumulation and embryo development. Their development from early stages after pollination to late stages of seed ripening has been studied in great detail. However, information on the caryopses diurnal adaptation to changes in light, temperature and alterations in phloem-supplied carbon and nitrogen remained unknown.
Publication Title
Significance of light, sugar, and amino acid supply for diurnal gene regulation in developing barley caryopses.
Sample Metadata Fields
Age, Specimen part
View Samples- Hordeum vulgare
- 12 Downloadable Samples
- Affymetrix Barley Genome Array (barley1)
Description
High temperature stress, like any abiotic stress, impairs the physiology and development of plants, including the stages of seed setting and ripening.
Publication Title
Transcriptome analysis of high-temperature stress in developing barley caryopses: early stress responses and effects on storage compound biosynthesis.
Sample Metadata Fields
Age, Specimen part
View Samples- Homo sapiens
- 15 Downloadable Samples
- Affymetrix Human Genome U133A Array (hgu133a)
Description
Background: Glioblastoma multiforme (GBM) is the most aggressive and most lethal primary malignant brain tumor, correlated with survival rates of less than one year from the time of diagnosis. Current surgical procedure attempts to remove the bulk of the tumor mass, whereas GBM frequently recurs within 1-3cm from the primary tumor resection site. Molecular mechanisms involved in the recurrence of the tumor are still poorly understood. The aim of the study was to define the molecular signature of GBM surrounding white matter (WM) in order to better understand the molecular mechanisms involved with tumor relapse.
Publication Title
Gene expression profile of glioblastoma peritumoral tissue: an ex vivo study.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 86 Downloadable Samples
- Affymetrix Mouse Gene 2.0 ST Array (mogene20st)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Diurnal regulation of RNA polymerase III transcription is under the control of both the feeding-fasting response and the circadian clock.
Sample Metadata Fields
Specimen part
View Samples- Mus musculus
- 86 Downloadable Samples
- Affymetrix Mouse Gene 2.0 ST Array (mogene20st)
Description
RNA polymerase III (pol III) synthesizes short non-coding RNAs, many of which, including tRNAs, Rpph1 RNA, Rn5s rRNA, and Rmrp RNA, are essential for translation. Accordingly, pol III activity is tightly regulated with cell growth and proliferation by factors such as MYC, RB1, TRP53, and MAF1. MAF1 is a repressor of pol III transcription whose activity is controlled by phosphorylation; in particular, it is inactivated through phosphorylation by mTORC1 kinase, a sensor of nutrient availability. Pol III regulation is thus sensitive to environmental cues, yet a diurnal profile of pol III transcription activity is so far lacking. Here we document pol III occupancy of its target genes in mouse liver during the diurnal cycle and show that pol III occupancy rises before the onset of the night, stays high during the night, when mice normally ingest food and when translation is increased, and decreases in daytime. By comparing diurnal pol III occupancy in wild-type mice, arrhythmic mice owing to inactivation of the Arntl gene, mice fed at regular intervals during both night and day, and mice lacking the Maf1 gene, we show that whereas higher pol III occupancy during the night reflects a MAF1-dependent response to feeding, the rise of pol III occupancy before the onset of the night reflects a circadian clock-dependent response. Thus, pol III transcription during the diurnal cycle is regulated both in response to nutrients and by the circadian clock, which allows anticipatory pol III transcription.
Publication Title
Diurnal regulation of RNA polymerase III transcription is under the control of both the feeding-fasting response and the circadian clock.
Sample Metadata Fields
Specimen part
View Samples- Homo sapiens
- 27 Downloadable Samples
- Affymetrix Human Genome U133A Array (hgu133a)
Description
Left ventricular mass (LVM) and cardiac gene expression are complex traits regulated by factors both intrinsic and extrinsic to the heart. To dissect the major determinants of LVM, we combined expression quantitative trait locus1 and quantitative trait transcript (QTT) analyses of the cardiac transcriptome in the rat. Using these methods and in vitro functional assays, we identified osteoglycin (Ogn) as a major candidate regulator of rat LVM, with increased Ogn protein expression associated with elevated LVM. We also applied genome-wide QTT analysis to the human heart and observed that, out of 22,000 transcripts, OGN transcript abundance had the highest correlation with LVM. We further confirmed a role for Ogn in the in vivo regulation of LVM in Ogn knockout mice. Taken together, these data implicate Ogn as a key regulator of LVM in rats, mice and humans, and suggest that Ogn modifies the hypertrophic response to extrinsic factors such as hypertension and aortic stenosis.
Publication Title
Integrated genomic approaches implicate osteoglycin (Ogn) in the regulation of left ventricular mass.
Sample Metadata Fields
Sex, Age, Specimen part
View Samples- Arabidopsis thaliana
- 12 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
The Arabidopsis thaliana transcription factor LATERAL ORGAN BOUNDARIES (LOB) is expressed in the boundary between the shoot apical meristem and initiating lateral organs. To identify genes regulated by LOB activity, we used an inducible 35S:LOB-GR line. This analysis identified genes that are differentially expressed in response to ectopic LOB activity.
Publication Title
Arabidopsis lateral organ boundaries negatively regulates brassinosteroid accumulation to limit growth in organ boundaries.
Sample Metadata Fields
Age, Specimen part, Treatment
View Samples- Homo sapiens
- 11 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
p63 mutations have been associated with several human hereditary disorders characterized by ectodermal dysplasia such as EEC syndrome, ADULT syndrome and AEC syndrome . The location and functional effects of the mutations that underlie these syndromes reveal a striking genotype-phenotype correlation. Unlike EEC and ADULT that result from missense mutations in the DNA-binding domain of p63, AEC is solely caused by missense mutations in the SAM domain of p63. We report a study on the TAp63a isoform, the first to be expressed during development of the embryonic epithelia, and on its naturally occurring Q540L mutant derived from an AEC patient. To assess the effects of the Q540L mutation, we generated stable cell lines expressing TAp63a wt, DeltaNp63 alpha or the TAp63 alpha-Q540L mutant protein and used them to systematically compare the cell growth regulatory activity of the mutant and wt p63 proteins and to generate, by microarray analysis, a comprehensive profile of differential gene expression. We found that the Q540L substitution impairs the transcriptional activity of TAp63a and causes misregulation of genes involved in the control of cell growth and epidermal differentiation.
Publication Title
The Hay Wells syndrome-derived TAp63alphaQ540L mutant has impaired transcriptional and cell growth regulatory activity.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 6 Downloadable Samples
- Affymetrix Mouse Genome 430A 2.0 Array (mouse430a2)
Description
Mouse FGF15 and human FGF19 are orthologous proteins that regulate bile acid metabolism. However, other hepatic functions of FGF15/19 are not well characterized.
Publication Title
FGF15/19 regulates hepatic glucose metabolism by inhibiting the CREB-PGC-1α pathway.
Sample Metadata Fields
Sex, Specimen part
View Samples