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GSE34378
Mus musculus
90 Downloadable Samples
Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
Lifelong murine gene expression profiles in relation to chronological and biological aging in multiple organs
Publication Title
Life spanning murine gene expression profiles in relation to chronological and pathological aging in multiple organs.
Sample Metadata Fields
Age, Specimen part
View Samples- Arabidopsis thaliana
- 36 Downloadable Samples
- Arabidopsis Gene 1.1 ST Array (aragene11st)
Description
Short periods of heat (>37°C) are extremely damaging to non-acclimated plants and their capacity to acclimate to and recover from heat stress is a key parameter for their survival and longevity. To acclimate, the Heat Shock transcription Factor A1 (HSFA1) subfamily activates a transcriptional response that resolves the heat stress-induced protein damage. Importantly, HSFA1 activity is also critical for Arabidopsis to withstand sustained warmer periods of 28°C, a non-detrimental condition that triggers a thermomorphogenesis response. We find that SUMO, a protein modification whose adduct levels increase as a result of acute heat stress in eukaryotes, is also critical for plant longevity during warmer periods, in particular for shoot meristem development. The known E3 and E4 SUMO ligases (SIZ1, HPY1/MMS21, PIAL1/2) were not essential to endure these warmer periods, alone or in combination. Thermo-lethality was also not seen when plants lacked certain SUMO proteases (ESD4, OTS1/OTS2, SPF1/SPF2 combined) or when SUMO chain formation was blocked. Furthermore, SUMO thermo-resilience is not connected to the autoimmune phenotype found in the corresponding SUMO knockdown and a SIZ1 loss-of-function mutant. As acquired thermotolerance was normal in the SUMO knockdown mutant, we thus conclude that the role of SUMO in heat acclimation differs from that of HSFA1 and SIZ1. Combined, this study reveals that SUMO appears to be critical for shoot meristem integrity during warmer periods.
Publication Title
No associated publication
Sample Metadata Fields
No sample metadata fields
View Samples- Arabidopsis thaliana
- 27 Downloadable Samples
- Arabidopsis Gene 1.1 ST Array (aragene11st)
Description
Increased ambient temperature is widely considered to be inhibitory to basal and effector-triggered plant immunity. For example, SNC1-dependent auto-immunity in Arabidopsis results in enhanced basal resistance at 22C, which is fully suppressed at 28C. The sumoylation mutant siz1 also displays auto-immunity at 22C. We find that its auto-immunity is sustained at 28C while still requiring PAD4/EDS1 and SNC1 function. Moreover, its rosette size does not fully recover at 28C, which is normally seen for SNC1 gain-of-function mutants. Related, thermomorphogenesis is also compromised in the SUMO mutants. This role of SIZ1 in growth regulation does not depend on PAD4 or SNC1. In corroboration, SUMO mutants show a global delay in their transcriptional profile for thermosensitive growth regulators and these differentially expressed genes show an overrepresentation for PIF4 genomic targets. This transcription factor (TF) PIF4 is the central regulator of thermomorphogenesis, while also inhibiting plant immunity at 28C. Our findings thus reveal that SUMO conjugation has a central role in PIF4 regulation prioritizing growth over immunity at elevated temperatures. Such molecular understanding of how temperature affects growth over immunity is important to mitigate the effects of climate change on agriculture
Publication Title
No associated publication
Sample Metadata Fields
Specimen part, Time
View Samples- Saccharomyces cerevisiae
- 27 Downloadable Samples
- Affymetrix Yeast Genome S98 Array (ygs98)
Description
Whole-genome transcriptional response of S. cerevisiae to an increase in temperature from 28C to 41C under well-controlled conditions.
Publication Title
No associated publication
Sample Metadata Fields
Time
View Samples- Arabidopsis thaliana
- 22 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
Comparison of expression differences between Col-0 Arabidopsis thaliana and transgenic plants in the same background carrying three different Fusarium oxysporum effector genes
Publication Title
No associated publication
Sample Metadata Fields
Specimen part
View Samples- Arabidopsis thaliana
- 18 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
Plants are known to be responsive to volatiles, but knowledge about the molecular players involved in transducing their perception remain scarce.
Publication Title
WRKY40 and WRKY6 act downstream of the green leaf volatile E-2-hexenal in Arabidopsis.
Sample Metadata Fields
Treatment
View Samples- Homo sapiens
- 5 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
The three-dimensional (3D) folding of the chromosomal fibre in the human interphase nucleus is an important, but poorly understood aspect of gene regulation. Especially basic principles of 3D chromatin and chromosome organisation are still elusive. In this paper, we quantitatively analyse the 3D structure of large parts of chromosomes 1 and 11 in the G1 nucleus of human cells and relate it to the human transcriptome map (HTM). Despite a considerable cell-to-cell variation, our results show that subchromosomal domains, which are highly expressed, are more decondensed, have a more irregular shape and are located in the nuclear interior compared to clusters of low expressed genes. These aspects of chromosome structure are shared by six different cell lines and therefore are independent of cell type specific differences in gene expression within the investigated domains. Systematic measurements show that there is little to no intermingling of chromatin from different parts of the same chromosome, indicating that the chromosomal fibre itself is a compact structure. Together, our results reveal several basic aspects of 3D chromosome architecture, which are related to genome function.
Publication Title
The three-dimensional structure of human interphase chromosomes is related to the transcriptome map.
Sample Metadata Fields
No sample metadata fields
View Samples- Rattus norvegicus
- 49 Downloadable Samples
- Affymetrix Rat Genome 230 2.0 Array (rat2302)
Description
REACH, the EU regulation on chemicals and their safe use, stipulates that about 30,000 chemical substances are to be assessed on their possible risks. Toxicological evaluation of these compounds will at least partly be based on animal testing. Especially reproductive toxicity is one of the most complicated, time-consuming and expensive in vivo endpoints. Introducing microarray-based endpoints can potentially refine in vivo toxicity testing. If compounds from a distinct chemical class induce reproducible gene-expression responses with a recognizable overlap, these gene-expression signatures may indicate intrinsic features of certain compounds, including toxicity. In the present study, we investigated this theory for the reproductive toxicity of phthalates.
Publication Title
No associated publication
Sample Metadata Fields
Sex, Age, Specimen part, Compound
View Samples- Mus musculus
- 15 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
Canonical Wnt signalling regulates the self-renewal of most if not all stem cell systems. In the blood system, the role of Wnt signalling has been subject of much debate, with positive and negative roles of Wnt signalling proposed for hematopoietic stem cells (HSC). As we have shown previously, this controversy can be largely explained by the effects of different dosages of Wnt signalling. What remained unclear however, was why high Wnt signals would lead to loss of reconstituting capacity. To better understand this phenomenon, we have taken advantage of a series of hypomorphic mutant Apc alleles resulting in a broad range of Wnt dosages in HSCs, purified those HSCs and performed whole genome gene expression analyses. Gene expression profiling and functional studies show that HSCs with APC mutations lead to high Wnt levels , enhanced differentiation and diminished proliferation, but have no effect on apoptosis, collectively leading to loss of stemness. Thus, we provide mechanistic insight into the role of APC mutations and Wnt signalling in HSC biology. As Wnt signals are explored in various in vivo and ex vivo expansion protocols for HSCs, our findings also have clinical ramifications.
Publication Title
High Levels of Canonical Wnt Signaling Lead to Loss of Stemness and Increased Differentiation in Hematopoietic Stem Cells.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 10 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
Cortical tubers in patients with tuberous sclerosis complex (TSC) are associated with cognitive disability and intractable epilepsy. While these developmental malformations are believed to result from the effects of TSC1 or TSC2 Gene mutations, the molecular mechanisms leading to tuber formation during brain development as well as the onset of seizures remain largely unknown. We used the Affymetrix Gene Chip platform as a genome-wide strategy to define the Gene expression profile of cortical tubers resected during epilepsy surgery compared to histologically normal perituberal tissue (adjacent to the cortical tuber) from the same patients or autopsy control tissue.
Publication Title
Gene expression analysis of tuberous sclerosis complex cortical tubers reveals increased expression of adhesion and inflammatory factors.
Sample Metadata Fields
Specimen part, Disease, Subject
View Samples