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Mus musculus
8 Downloadable Samples
Illumina MouseWG-6 v2.0 expression beadchip
Description
Despite intense investigation of intrinsic and extrinsic factors that regulate pluripotency, the process of initial fate commitment of embryonic stem (ES) cells is still poorly understood. Here, we used a genome wide shRNA screen in mouse ES cells to identify genes that are essential for initiation of differentiation. Knockdown of the scaffolding protein Mek binding protein 1 (Mp1, also known as Lamtor3, Map2k1ip1) stimulated self-renewal of ES cells, blocked differentiation and promoted proliferation. Fibroblast growth factor 4 (FGF4) signaling is required for initial fate commitment of ES cells. Knockdown of Mp1 inhibited FGF4-induced differentiation but did not alter FGF4 driven proliferation. This uncoupling of differentiation and proliferation was also observed when oncogenic Ras isoforms were over expressed in ES cells. Knockdown of Mp1 redirected FGF4 signaling from differentiation towards pluripotency and upregulated the pluripotency-related genes Esrrb, Rex1, Tcl1 and Sox2.
Publication Title
A genome-wide RNAi screen in mouse embryonic stem cells identifies Mp1 as a key mediator of differentiation.
Sample Metadata Fields
Specimen part, Cell line
View Samples- Homo sapiens
- 1 Downloadable Sample
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
Primary colon CSC cultures were transduced with a Wnt responsive construct (TOP-GFP) and were single cell cloned. 10% highest and lowest TOP-GFP cell fractions were FACS sorted and arrayed.
Publication Title
Wnt activity defines colon cancer stem cells and is regulated by the microenvironment.
Sample Metadata Fields
Specimen part
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
- 4 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
The human cytomegalovirus (HCMV) encodes the chemokine receptor US28 that exhibits constitutive activity. NIH-3T3 cells stably transfected with US28 present a pro-angiogenic and transformed phenotype both in vitro and in vivo.
Publication Title
The human cytomegalovirus-encoded chemokine receptor US28 promotes angiogenesis and tumor formation via cyclooxygenase-2.
Sample Metadata Fields
No sample metadata fields
View Samples
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
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