Gene expression differences under freezing and ice encasement stress in between temporal populations
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PROVIDER: PRJEB83884 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:The experiment was aimed at studying gene expression differences between three temporal populations of two timothy cultivars; Engmo (Early=1988, Mid=2003 & Current=2020) and Noreng (Early=1998, Mid=2010 & Current=2020), under freezing stress and Ice encasement stress. The idea is when the temporally separated populations; the ancestor and its descendant populations, were subjected to similar stress conditions the gene expression differences between populations could be due to plasticity or adaptation and the non-random changes in gene expression could be indicative of adaptative responses. The cold acclimated samples were used as controls in both freezing and ice encasement comparisons
2025-09-01 | E-MTAB-14732 | biostudies-arrayexpress
Project description:The predicted increase in frequency and duration of winter warming episodes (WWEs) at the higher northern latitudes is expected to negatively impact the forage production in this region. The formation of non-permeable ice cover due to WWEs could subject the plants to hypoxic or anoxic conditions leading to severe winter damages. Knowledge about molecular mechanisms underlaying various winter stress is crucial to develop cultivars with better winter survival under changing climatic conditions. In the current study, we aimed at identifying genes involved in ice encasement stress responses in a perennial forage grass timothy and study gene expression differentiation due to field survival using timothy cultivars from diverse genetic backgrounds. The LD50 (the number of days under ice that kill 50% of the plants) varied across cultivars and origin. The expression of many genes involved in hypoxia and freezing stress responses were highly upregulated under ice encasement conditions. Functional analysis of DEGs revealed that the upregulated genes were linked to glycolysis, pyruvate metabolism, carbon metabolism, biosynthesis of amino acids while downregulated genes were related to photosynthesis, phenylpropanoid biosynthesis and flavonoid biosynthesis pathways. The results from a current study indicate a substantial overlap of ice encasement stress responses with those of hypoxic and freezing stresses. In addition, the potential strategies leading to higher ice encasement tolerance of timothy are outlined. Furthermore, differences in gene expression between field survivors and original material and the differences between ice encasement responses of northern adapted cultivar and southern adapted cultivar are briefly discussed.
2024-02-29 | E-MTAB-13705 | biostudies-arrayexpress
Project description:This study investigates the impact of cryopreservation and freezing media on RNA quality and gene expression profiles of peripheral blood mononuclear cells (PBMC). No significant difference in cell viability or RNA quality was observed between freshly isolated and cryopreserved cells, even after two freeze-thaw cycles. Transcriptome analysis revealed no significant differences in alignment rates or read counts across various conditions. Differential gene expression analysis identified changes between fresh and thawed samples, with a consistent downward trend of mRNA abundance in the frozen samples, but minimal changes were observed between the first and second freeze-thaw cycles. Gene set enrichment analysis showed only minor significant differences, and stress-related gene sets were not upregulated. Freezing medium appears to be the safer option compared to freezing in trizol. These results confirm that cryopreservation and thawing processes do not compromise RNA integrity or sequencing reliability in PBMC, supporting the use of cryopreserved samples for gene expression studies.
2025-06-19 | GSE299980 | GEO
Project description:Glacier ice algae of the streptophyte genus Ancylonema live on glaciers globally, including the Greenland Ice Sheet. Each summer these algae bloom despite freezing temperatures, low nutrient availability, and very high light intensities. These algae also survive continual darkness during polar night. However, little is known about the cellular mechanisms underpinning glacier ice algae resistance and adaptation to high light or how they survive during dark periods. To address this knowledge gap, we evaluated the response of Ancylonema-dominated samples from the Greenland Ice Sheet to light and dark conditions over a 12-day incubation experiment using combined multi-omics analyses: amplicon sequencing, metatranscriptomics, and metaproteomics.
2025-09-29 | PXD058696 | Pride
Project description:Transcriptomic differences in bovine blastocysts following vitrification and slow freezing at morula stage
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Project description:Greenland Ice Sheet - A sequence based temporal-spatial study
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Project description:Improvement of freezing tolerance of red clover (Trifolium pratense L.) would increase its persistence under cold climate. In this study, we assessed the freezing tolerance and compared the proteome composition of non-acclimated and cold-acclimated plants of two initial cultivars of red clover: Endure (E-TF0) and Christie (C-TF0) and of populations issued from these cultivars after three (TF3) and four (TF4) cycles of phenotypic recurrent selection for superior freezing tolerance. Through this approach, we wanted to identify proteins that are associated with the improvement of freezing tolerance in red clover. Recurrent selection performed indoor is an effective approach to improve the freezing tolerance of red clover. Significant improvement of freezing tolerance by recurrent selection was associated with differential accumulation of a small number of cold-regulated proteins that may play an important role in the determination of the level of freezing tolerance.
2016-03-15 | PXD003689 | Pride
Project description:Arabidopsis sfr mutants are deficient in cold acclimation during exposure to coolnon-freezing temperatures. Although not visibly affected by the cold they have lost the ability to survive subsequent freezing. We plan to investigate how the sfr2 and sfr6 mutants respond to low temperature on the gene expression level. Wild type plants that have undergone identical treatments in parallel are necessary controls. The cold treatment of plants in the rosette stage (soil grown in a 8/16 hours day/night cycle) will be carried out in a cooled growth chamber at 4 degrees for 24 hours (same light regimetreatment starting/ending at the 4th hour of light). The aerial parts of the treated and untreated plants will be collected and frozen immediately in liquid nitrogen for RNA extraction. Comparison of the cold response of thousands of Arabidopsis genes in the wild type to the situation in our freezing sensitive mutants will enhance our understanding of the cold response itself and illuminate the effect of the mutations on the cold acclimation process. Experimenter name = Irene Bramke Experimenter phone = 01784 44 3770 Experimenter fax = 01784 43 4326 Experimenter address = Royal Holloway Experimenter address = University of London Experimenter address = School of Biological Sciences Experimenter address = Bourne Building Experimenter address = Laboratory 406 Experimenter zip/postal_code = TW20 OEX Experimenter country = UK Keywords: growth_condition_design; genetic_modification_design
2007-01-08 | GSE5711 | GEO
Project description:Freezing causes physiological changes even in a hardy, cold-acclimated wild type. During recovery from freezing, gene expression will reflect the induction of damage-repair processes distinct from the damage-prevention associated with cold acclimation. This will be detected by observing the wild-type transcriptome at two time points during recovery from a freezing episode. The appropriate control is the unfrozen, cold-acclimated wild type. Experimenter name = Glenn Thorlby Experimenter phone = 01874 443770 Experimenter address = School of biological Sciences Experimenter address = Bourne Building Experimenter address = Royal Holloway Experimenter address = Egham Experimenter zip/postal_code = TW20 0EX Keywords: growth_condition_design;
2006-08-15 | GSE5524 | GEO