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GSE44655
Arabidopsis thaliana
16 Downloadable Samples
Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
HSFA1s are a gene family of HSFA1 with four members, HSFA1a, HSFA1b, HSFA1d, and HSFA1e. HSFA1s are the master regulators of heat shock response. As a part of the heat shock response, HSFA2 can prolong the heat shock response and amplify the heat shock response in response to repeat heat shock. To identify the heat-shock-responsive genes differentially regulated by HSFA1s and HSFA2, we compared the transcriptomic differences of plants containing only constitutively expressed HSFA1s or HSFA2 after heat stress.
Publication Title
Common and distinct functions of Arabidopsis class A1 and A2 heat shock factors in diverse abiotic stress responses and development.
Alternate Accession IDs
Sample Metadata Fields
Age, Specimen part
View Samples- Homo sapiens
- 104 Downloadable Samples
- Affymetrix Human Genome U133A Array (hgu133a)
Description
We used microarrays to detail the global transcriptional response mediated by ERalpha or ERbeta to the phytoestrogen genistein in the MCF-7 human breast cancer cell model.
Publication Title
Estrogen Receptors alpha and beta as determinants of gene expression: influence of ligand, dose, and chromatin binding.
Alternate Accession IDs
Sample Metadata Fields
No sample metadata fields
View Samples- Arabidopsis thaliana
- 12 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
In order to study the importance of HSFA1 in thermotolerance in Arabidopsis, we generated the HSFA1a, b, d and e quadruple mutant (QK). QK is very sensitive to heat. Therefore, we used microarray to study how many genes regulated by HSFA1 after heat shock.
Publication Title
The role of class A1 heat shock factors (HSFA1s) in response to heat and other stresses in Arabidopsis.
Alternate Accession IDs
Sample Metadata Fields
Age, Specimen part, Treatment
View Samples- Homo sapiens
- 24 Downloadable Samples
- Affymetrix Human Genome U133A Array (hgu133a)
Description
The nuclear receptor, estrogen receptor alpha (ER), controls the expression of hundreds of genes responsible for target cell phenotypic properties, but the relative importance of direct vs. tethering mechanisms of DNA binding has not been established. In this first report, we examine the genome-wide chromatin localization of an altered-specificity mutant ER with a DNA-binding domain deficient in binding to estrogen response element (ERE)-containing DNA (DBDmut ER) vs. wild type ER. Using high-throughput sequencing of ER chromatin immunoprecipitations (ChIP-Seq) and mRNA transcriptional profiling, we show that direct ERE binding is required for most (75%) estrogen-dependent gene regulation and 90% of hormone-dependent recruitment of ER to genomic binding sites. De novo motif analysis of the chromatin binding regions in MDA-MB-231 human breast cancer cells defined unique transcription factor profiles responsible for genes regulated through tethering vs. direct DNA (ERE) binding, with Runx motifs enriched in ER-tethered sites. We confirmed a role for Runx1 in mediating ERa genomic recruitment and regulation of tethering genes. Our findings delineate the contributions of ERE binding vs. binding through response elements for other transcription factors in chromatin localization and ER-dependent gene regulation, paradigms likely to underlie the gene regulatory actions of other nuclear receptors as well.
Publication Title
Genome-wide analysis of estrogen receptor alpha DNA binding and tethering mechanisms identifies Runx1 as a novel tethering factor in receptor-mediated transcriptional activation.
Alternate Accession IDs
Sample Metadata Fields
Specimen part, Time
View Samples- Homo sapiens
- 24 Downloadable Samples
- Affymetrix Human Genome U133A Array (hgu133a)
Description
Estradiol Timecourse of MDA-MB-231ER+ cells containing a WT-ER and DBDmut-ER
Publication Title
Genome-wide analysis of estrogen receptor alpha DNA binding and tethering mechanisms identifies Runx1 as a novel tethering factor in receptor-mediated transcriptional activation.
Alternate Accession IDs
Sample Metadata Fields
Time
View Samples- Arabidopsis thaliana
- 8 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
Several lipocalin genes from higher plants were shown to be responsive to both high and low temperature stresses and have been named as temperature-induced lipocalin (Til). In this study, a reverse genetic approach was taken to elucidate the role of Arabidopsis Til1 (At5g58070) in thermotolerance. We showed that Til1 proteins was constitutively expressed and increased significantly after heat shock treatment. A T-DNA knockout line of Til1, designated as til1-1, could not produce Til1 and showed severe defects in basal and acquired thermotolerance. Introducing a wild type copy of Til1 gene into til1-1 complemented the mutant phenotype. Over-expression of Til1 in the wild type plant did not enhance thermotolerance. Til1 is peripherally associated with plasma membrane, suggesting a regulatory or protective role of this protein in membrane function. Transcriptomic analysis showed that the heat shock response in til1-1 was not altered as compared to the wild type plants. The temperature threshold for heat shock protein induction was not affected by the level of Til1. Ion leakage analysis revealed no significant difference in membrane stability between the wild type and til1-1 seedlings. These results suggested that Til1 is not involved in regulating membrane fluidity or stability. Nevertheless, the level of malondialdehyde was significantly higher in til1-1 than in the wild type after severe heat treatment. The mutant plants were also more sensitive than the wild type to tert-butyl hydroperoxide, a reagent that induces lipid peroxidation. Taken together, our data indicate that Til1 is an essential component for thermotolerance probably by acting against lipid peroxidation induced by severe heat stress.
Publication Title
Temperature-induced lipocalin is required for basal and acquired thermotolerance in Arabidopsis.
Alternate Accession IDs
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 4 Downloadable Samples
- Affymetrix Human Genome U133A 2.0 Array (hgu133a2)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Integrative genomics of gene and metabolic regulation by estrogen receptors α and β, and their coregulators.
Alternate Accession IDs
Sample Metadata Fields
Specimen part, Cell line
View Samples- Homo sapiens
- 4 Downloadable Samples
- Affymetrix Human Genome U133A 2.0 Array (hgu133a2)
Description
The closely related transcription factors (TFs), estrogen receptors ER and ER, regulate divergent gene expression programs and proliferative outcomes in breast cancer. Utilizing MCF-7 breast cancer cells with ER, ER, or both receptors as a model system to define the basis of differing response specification by related TFs, we show that these TFs and their key coregulators, SRC3 and RIP140, generate overlapping as well as unique chromatin-binding and transcription-regulating modules.
Publication Title
Integrative genomics of gene and metabolic regulation by estrogen receptors α and β, and their coregulators.
Alternate Accession IDs
Sample Metadata Fields
Specimen part, Cell line
View Samples- Mus musculus
- 4 Downloadable Samples
- Affymetrix Murine Genome U74A Version 2 Array (mgu74av2)
Description
A murine model that mimic the decidualization and regression observed in human was used to investigate the molecular mechanisms underlying the dynamic processes in endometrium. Ovariectomized mice were treated sequentially with steroid hormones and then, to induce decidualization, oil was injected into the uterine lumen. A process similar to menstruation was induced by hormone-withdrawal. The uterine tissues were collected at 4 time-points after the induction of decidualization.
Publication Title
Quantitative cellular and molecular analysis of the effect of progesterone withdrawal in a murine model of decidualization.
Alternate Accession IDs
Sample Metadata Fields
Sex, Specimen part
View Samples- Mus musculus
- 58 Downloadable Samples
- Affymetrix Mouse Gene 1.1 ST Array (mogene11st)
Description
Delaying first childbirth is associated with a range of pregnancy complications, but the mechanisms underlying this are unclear. We have hypothesized that prolonged, cyclical, pre-pregnancy exposure to estrogen and progesterone contributes to age-related deterioration of uterine function. We conducted a series of studies in virgin mice of varying age and exposure to hormonal manipulations. We compared the myometrial transcript profile from young (10-12 weeks, n=7) and old (28-30 weeks, n=7) mice. We validated this list using a second experiment of young versus old mice housed in a different animal facility and comparing animals of 10-12 (n=8) and 38-40 (n=7) weeks of age. The pattern of change in these transcripts was very similar. We determined whether removal of the ovaries in early life (8-10 weeks of age) prevented age-related changes. When we compared old animals (38-40 weeks) which had early ovariectomy (n=7) with sham operated controls of the same age (n=7), we found that the transcripts which had been down-regulated by age were upregulated in old animals that had an early ovariectomy. The converse was observed for genes which had been downregulated by age. Hence, early ovariectomy prevented changes in myometrial gene expression associated with aging. We then studied the effect of prolonged, continuous exposure to progesterone between 8 and 36 weeks of age. When we compared old animals (38-40 weeks) that received progesterone implants from 8 to 36-38 weeks (n=10) with old animals receiving implants containing only vehicle (n=5), transcripts which had been down-regulated by age were upregulated by prolonged exposure to progesterone. The converse was observed for genes which had been downregulated by age. Hence, prolonged exposure to progesterone also ameliorated changes in myometrial gene expression associated with aging.
Publication Title
Age-related changes in murine myometrial transcript profile are mediated by exposure to the female sex hormones.
Alternate Accession IDs
Sample Metadata Fields
Specimen part
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