Ontology highlight
ABSTRACT:
PROVIDER: PRJNA736338 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Lettuce is one of most consumed vegetables globally. This crop is susceptible to abiotic stresses. To understand the molecular mechanisms of stress response in lettuce, global transcriptome analysis was conducted. This analysis revealed distinctive temporal expression patterns among the stress-regulated genes in lettuce plants exposed to abiotic stresses
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Project description:Raw RNAseq data of hydroponically grown crops (cai xin, lettuce, and spinach) subjected under 31 different conditions. Comparative analysis of gene expression across species and stress conditions were carried out.
2024-04-30 | E-MTAB-14018 | biostudies-arrayexpress
Project description:Heat-evolved Symbiodiniaceae can improve the physiological performances of their coral host under heat stress, but their gene expression responses to heat remained unknown. We explore here the transcriptomic basis of differential thermal stress responses between in hospite wild-type and heat-evolved Cladocopium proliferum strains and their coral host Platygyra daedealea.
2024-03-01 | GSE256269 | GEO
Project description:Chitin soil amendment is known to improve soil quality, plant growth and plant stress resilience, but the underlying mechanisms are not well understood. In this study, we monitored chitin’s effect on lettuce physiology every two weeks through an eight-week growth period, analyzed the early transcriptional reprogramming and related metabolomic changes of lettuce, in response to crab chitin treatment in peat-based potting soil. In commercial growth conditions, chitin amendment still promoted lettuce growth, increased chlorophyll content, the number of leaves and crop head weight from week six. The flavonoid content in lettuce leaves was altered as well, showing an increase at week two but a decrease from week six. Transcriptomic analysis showed that over 300 genes in lettuce root were significant differentially expressed after chitin soil treatment. Gene Ontology-term (GO) enrichment analysis revealed statistical overrepresentation of GO terms linked to photosynthesis, pigment metabolic process and phenylpropanoid metabolic process. Further analysis of the differentially expressed genes (DEGs) showed that the flavonoid pathway is mostly upregulated whereas the bifurcation of upstream phenylpropanoid pathway towards lignin biosynthesis is mostly downregulated. Metabolomic analysis revealed the upregulation of salicylic acid, chlorogenic acid, ferulic acid, and p-coumaric acid in chitin treated lettuce seedlings. These phenolic compounds mainly influence the phenylpropanoid biosynthesis pathway and may play important roles in plant defense reactions. Our results suggest that chitin soil amendments might activate induced resistance by priming lettuce plants and promote lettuce growth via transcriptional changes.
2023-03-28 | GSE224725 | GEO
Project description:A heat and drought tolerant rice cultivar (N22) was grown in the field under control and drought conditions during the dry season in 2013. Drought was applied during early grain filling and resulted in simultaneous heat stress, leading to reduced grain yield and quality. Total RNA was extracted from developing seeds under stress and control (fully flooded) conditions and RNA-seq analysis was performed. These samples are a part of a bigger experiment analysing the responses of three contrasting rice cultivars (N22, Dular, Anjali) to combined heat and drought stress including different organs (developing seeds, flag leaves, flowering spikelets) and developmental stages (early grain filling, flowering) at the transcriptomic level.
2020-11-04 | GSE153030 | GEO
Project description:Korean peninsular weather is rapidly becoming subtropical due to global warming. In summer 2018, South Korea experienced the highest temperatures since the meteorological observations recorded in 1907. Heat stress has a negative effect on Holstein cows, the most popular breed of dairy cattle in South Korea, which is susceptible to heat. To examine physiological changes in dairy cows under heat stress conditions, we analyzed the profiles circulating microRNAs isolated from whole blood samples collected under heat stress and non-heat stress conditions using small RNA sequencing. We compared the expression profiles in lactating cows under heat stress and non-heat stress conditions to understand the regulation of biological processes in heat-stressed cows. Moreover, we measured several heat stress indicators, such as rectal temperature, milk yield, average daily gain, and progesterone concentration. All these assessments showed that pregnant cows were more susceptible to heat stress than non-pregnant cows. Particularly, progesterone concentrations known to have maternal warming effects were at similar levels in non-pregnant cows but significantly increased in pregnant cows under heat stress conditions. The differentially expressed miRNAs and their putative target genes were analyzed in pregnant cows. Interestingly, we found that differentially expressed miRNAs (bta-miR-146b, bta-miR-20b, bta-miR-29d-3p, bta-miR-1246) specifically targeted progesterone biosynthesis (StAR) and the function of corpus luteum-related genes (CCL11, XCL), suggesting that pregnant cows with elevated progesterone concentrations are more susceptible to heat stress. In addition, we found the differential expression of 11 miRNAs (bta-miR-19a, bta-miR-19b, bta-miR-30a-5p, and several from the bta-miR-2284 family) in both pregnant and non-pregnant cows under heat stress conditions. In target gene prediction and gene set enrichment analysis, these miRNAs were found to be associated with the cytoskeleton, cell junction, vasculogenesis, cell proliferation, ATP synthesis, oxidative stress, and immune responses involved in heat response. These miRNAs can be used as potential biomarkers for heat stress.
2020-05-21 | GSE150912 | GEO
Project description:Rainbow trout (Oncorhynchus mykiss) is highly sensitive to high-temperature stress as an important economic cold-water fish. While previous research has concentrated on the transcriptomic to acute heat stress in rainbow trout, there remains a gap in knowledge regarding the overarching regulatory mechanisms at the translation level. In our research, we utilized a combination of transcriptomic and translatomic analyses to investigate the intricate molecular response mechanisms in the liver of rainbow trout when subjected to heat stress. Through comprehensive multi-omics analysis, we revealed the dynamic translational pattern of rainbow trout liver under heat stress for the first time. Comparative analysis of ribosome analysis data with RNA-seq data showed that the fold changes of gene expression at the transcriptional level were highly correlated (R2 = 0.83) with those at the translational level globally. In total, 2,203 genes exhibited significant alterations exclusively within the translational level. However, the limited overlap in response genes between transcription and translation under heat stress suggests that these two processes may independently modulate the cellular response to thermal challenges. Significant changes in the translation efficiency of 809 genes were observed under heat stress. Further analysis indicated that the translation efficiency of genes were strongly influenced by sequence characteristics such as GC content, coding sequence length and NMFE. Moreover, 3,468 putative uORFs were identified in 2,676 genes, which potentially modulating translation efficiency of mORFs. These findings provide a novel perspective for understanding the physiological adaptations of rainbow trout in response to changes in ambient temperature.
2024-04-16 | GSE263547 | GEO
Project description:Rainbow trout (Oncorhynchus mykiss) is highly sensitive to high-temperature stress as an important economic cold-water fish. While previous research has concentrated on the transcriptomic to acute heat stress in rainbow trout, there remains a gap in knowledge regarding the overarching regulatory mechanisms at the translation level. In our research, we utilized a combination of transcriptomic and translatomic analyses to investigate the intricate molecular response mechanisms in the liver of rainbow trout when subjected to heat stress. Through comprehensive multi-omics analysis, we revealed the dynamic translational pattern of rainbow trout liver under heat stress for the first time. Comparative analysis of ribosome analysis data with RNA-seq data showed that the fold changes of gene expression at the transcriptional level were highly correlated (R2 = 0.83) with those at the translational level globally. In total, 2,203 genes exhibited significant alterations exclusively within the translational level. However, the limited overlap in response genes between transcription and translation under heat stress suggests that these two processes may independently modulate the cellular response to thermal challenges. Significant changes in the translation efficiency of 809 genes were observed under heat stress. Further analysis indicated that the translation efficiency of genes were strongly influenced by sequence characteristics such as GC content, coding sequence length and NMFE. Moreover, 3,468 putative uORFs were identified in 2,676 genes, which potentially modulating translation efficiency of mORFs. These findings provide a novel perspective for understanding the physiological adaptations of rainbow trout in response to changes in ambient temperature.
2024-04-01 | GSE262612 | GEO
Project description:Xylose-utilizing yeasts with tolerances to fermentation inhibitors (such as weak organic acids) and high temperature are needed for cost-effective simultaneous saccharification and co-fermentation (SSCF) of lignocellulosic materials. We constructed a novel xylose-assimilating Saccharomyces cerevisiae strain with improved fermentation performance under heat and acid co-stress using the genome shuffling technique. Two xylose-utilizing diploid yeasts with different genetic backgrounds were used as the parental strains for genome shuffling. The hybrid strain Hyb-8 showed significantly higher xylose fermentation ability than both parental strains (Sun049T-Z and Sun224T-K) under co-stress conditions of heat and acids. To screen for genes that might be important for fermentation under heat and acid co-stress, a transcriptomic analysis of hybrid strain Hyb-8 and its parental strains was performed.
2017-07-25 | GSE101786 | GEO