Filters
Technology
Platform
Homo sapiens
4 Downloadable Samples
Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
Coordinated regulation of the ubiquitin-proteasome system is crucial for the cell to adjust its protein degradation capacity to changing proteolytic requirements. The transcription factor TCF11 has been identified as a regulator for 26S-proteasome formation in human cells to compensate for reduced proteolytic activity. To expand the current knowledge of other UPS-related TCF11 target genes in response to epoxomicin, we performed microarray analyses of cells exposed to epoxomicin and with or without depletion of TCF11.
Publication Title
Proteasomal degradation is transcriptionally controlled by TCF11 via an ERAD-dependent feedback loop.
Sample Metadata Fields
Specimen part
View Samples- Homo sapiens
- 8 Downloadable Samples
- Affymetrix Human Genome U133A Array (hgu133a)
Description
Comparison of gene and protein expression in the large airway epithelium of never and current smokers.
Publication Title
Comparison of proteomic and transcriptomic profiles in the bronchial airway epithelium of current and never smokers.
Sample Metadata Fields
Sex, Age, Specimen part, Race, Subject
View Samples- Homo sapiens
- 17 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
Molecular mechanisms of cell cycle exit are poorly understood. A group of genes required for cell cycle exit and maintenance of cell quiescence in human fibroblasts following serum deprivation has been recently identified. Studies on lymphocytes following growth factor deprivation-induced cell cycle exit have predominantly focused on the initiation of apoptosis. A set of genes involved in lymphocyte quiescence have also been identified among genes highly expressed in resting lymphocytes and down-regulated after cell activation. In our study, proliferating IL-2-dependent human T cells were forced to exit cell cycle by growth factor withdrawal, and their gene expression profiles were examined.
Publication Title
Molecular signature of cell cycle exit induced in human T lymphoblasts by IL-2 withdrawal.
Sample Metadata Fields
No sample metadata fields
View Samples- Caenorhabditis elegans
- 18 Downloadable Samples
Illumina HiSeq 2500
Description
Organisms respond to mitochondrial stress through the upregulation of an array of protective genes, often perpetuating an early response to metabolic dysfunction across a lifetime. We find that mitochondrial stress causes widespread changes in chromatin structure through histone H3K9 di-methylation marks traditionally associated with gene silencing. Mitochondrial stress response activation requires the di-methylation of histone H3K9 through the activity of the histone methyltransferase met-2 and the nuclear co-factor lin-65. While globally the chromatin becomes silenced by these marks, remaining portions of the chromatin open up, at which point the binding of canonical stress responsive factors such as DVE-1 occurs. Thus, a metabolic stress response is established and propagated into adulthood of animals through specific epigenetic modifications that allow for selective gene expression and lifespan extension. Overall design: comparison of gene expression changes in response to cco-1 RNAi treatment in N2, lin-65(n3441) and met-2(ok2307) populations of C. elegans L4 animals
Publication Title
Mitochondrial Stress Induces Chromatin Reorganization to Promote Longevity and UPR(mt).
Sample Metadata Fields
Specimen part, Subject
View Samples- Hordeum vulgare
- 15 Downloadable Samples
- Affymetrix Barley Genome Array (barley1)
Description
FN044, FN211, FN242 and FN303 are the fast neutron generated mutants in cv. Steptoe background. These 4 mutants have lesion mimic phenotype and increase disease resistance to stem rust. ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor, ling zhang. The equivalent experiment is BB54 at PLEXdb.]
Publication Title
A cation/proton-exchanging protein is a candidate for the barley NecS1 gene controlling necrosis and enhanced defense response to stem rust.
Sample Metadata Fields
Specimen part
View Samples- Zea mays
- 4 Downloadable Samples
- Illumina Genome Analyzer IIx
Description
Endosperm is a product of double fertilization, and provides nutrients and signals to the embryo during seed development in flowering plants. Early stages of endosperm development are critical for the development of its storage capacity through synthesis and accumulation of starch and storage proteins. Here we report on the isolation and sequencing of mRNAs from the central portion of the starchy endosperm of Zea mays (maize) B73 at 6 days after pollination. We detected high correlation among the four biological replicates of RNAs isolated using laser-capture microdissection of the cell type. Because the assayed stage of development precedes the synthesis and accumulation of the major storage proteins and starch in the endosperm, our dataset likely include mRNAs for genes that are involved in control and establishment of these developmental programs. Overall design: Four replicates of mRNAs from the central portion of starchy endopserm were isolated using laser-capture microdissection and sequenced using the Illumina GAIIx platform.
Publication Title
RNA-Seq analysis of laser-capture microdissected cells of the developing central starchy endosperm of maize.
Sample Metadata Fields
Age, Specimen part, Cell line, Subject
View Samples
GSE30762- Mus musculus
- 6 Downloadable Samples
- Affymetrix Mouse Gene 1.0 ST Array (mogene10st)
Description
Comparison between APPPS1-FVB and APPPS1-FVBxABCC1ko mice
Publication Title
Cerebral amyloid-β proteostasis is regulated by the membrane transport protein ABCC1 in mice.
Sample Metadata Fields
Specimen part
View Samples- Mus musculus
- 18 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
Regeneration of differentiated tissue in mammals is rare. In an effort to identify genes that affect the healing process, we screened G3 mice containing germline point mutations for closure of an ear punch wound. One particular line was identified with a heritable hole closure phenotype containing differentiated tissue. Mapping and sequencing efforts revealed that the mutant mice harbor a R244Q point mutation coded by the TGFBR1 gene which leads to enhanced signaling activity in a reporter gene assay. Although there was no obvious effect on the immune system, bone marrow stromal cells from the mutant mice revealed accelerated chondrogenesis, mimicking the in vivo development of cartilage islands in the regenerated ears. This genetically well-defined mouse model should help to further dissect the role of TGF-beta signaling in vertebrate healing and regeneration.
Publication Title
Regenerative phenotype in mice with a point mutation in transforming growth factor beta type I receptor (TGFBR1).
Sample Metadata Fields
No sample metadata fields
View Samples- Rattus norvegicus
- 10 Downloadable Samples
- Affymetrix Rat Genome 230 2.0 Array (rat2302)
Description
Multiple sclerosis is a chronic, inflammatory, demyelinating disease of the central nervous system in which macrophages and microglia play a central role. During active multiple sclerosis foamy macrophages and microglia, containing degenerated myelin, are abundantly found in demyelinated areas. Recent studies have described an altered macrophage phenotype after myelin internalization. However, by which mechanisms myelin affects the phenotype of macrophages and how this phenotype can influence lesion progression is unclear.
Publication Title
Myelin-derived lipids modulate macrophage activity by liver X receptor activation.
Sample Metadata Fields
Specimen part, Treatment
View Samples- Arabidopsis thaliana
- 192 Downloadable Samples
- Illumina HiSeq 2000
Description
In this study, we describe the impact of genetic variation on transcript abundance in an F2 population of Arabidopsis thaliana. The RNA-seq resource generated by this study is suitable for expression quantitative trait locus (eQTL) mapping. From the aligned RNA-seq reads, and available genomic data for each of the parents of the cross, we imputed the genomes of each F2 individual (to allow genetic mapping of RNA abundance traits; briefly, genetic differences in aligned RNA-seq reads were used to impute each F2 genome). Our results show that heritable differences on gene expression can be detected using F2 populations (that is, single F2 plants), and shed light on the control of expression differences among strains of this reference plant. Overall design: 183 samples consisting of single F2 plants of a cross between Arabidopsis thaliana accessions 8230 and 6195 were generated. For each sample, RNA was collected from the aerial shoot at the 9th true leaf stage, and Illumina mRNA-seq libraries were constructed. Using these libraries, 50 bp single end RNA-seq Illumina reads were generated for each sample, and used to quantify gene expresison in each individual. The resulting expression phenotypes are suitable for genetic mapping of the control of gene expression differences in the species.
Publication Title
Epistatic and allelic interactions control expression of ribosomal RNA gene clusters in Arabidopsis thaliana.
Sample Metadata Fields
Specimen part, Subject
View Samples