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ABSTRACT:
PROVIDER: PRJNA431124 | ENA |
REPOSITORIES: ENA
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Project description:The variability of the marine intertidal environment poses unique challenges for sessile species. Diurnal, tidal, and seasonal cycles introduce drastic variations in temperature, salinity, availability of nutrients and water. The California ribbed mussel Mytilus californianus is a filter feeder that dominates a middle range of the intertidal of many wave-swept rocky shores. The bivalve attaches to the substrate by several byssal threads. This sessile lifestyle allows us to accurately document the thermal history of an individual. We have profiled gene expression in M. californianus during a natural tidal cycle using a cDNA microarray composed of genes from mussels exposed to various stressors. Over three days, mussels were sampled from two sites differing in emersion exposure and average temperature. At each time point, three mussels were cut open in the field and frozen immediately on dry ice and stored at -80 degrees C until the gill, hepatopancreas, and adductor muscle were excised and processed for RNA extraction, reverse transcription, and hybridization to our microarrays. The resulting expression profile showed that genes involved in the cell cycle were diurnally regulated, heat shock proteins increased with temperature, and expression of several hundred other genes varied across the tidal cycle. Tide series (times and tide height): 26th July, low tide 0052, 0.8 ft; high tide 0705, 3.1 ft; low tide 1113, 2.4 ft; high tide 1810, 5.9ft. 27th July, low tide 0154, 0.1 ft; high tide 0837, 3.3 ft; low tide 1216, 2.7ft; high tide 1903, 6.2 ft. 28th July, low tide 0249, -0.6ft; high tide 0943, 3.5 ft; low tide 1323, 2.8ft; high tide 1903, 6.2ft. 15th Aug, low tide 0530, 0.26 ft; high tide 1200, 4.08 ft, low tide 0432, 2.65 ft; high tide 1036, 5.84 ft.
2007-07-30 | E-TABM-287 | biostudies-arrayexpress
Project description:To identify the effect of high-salt diet on immune cells of brain tissues, we isolated immune cells of brain from mice fed with control diet or high-salt diet.
2022-08-24 | GSE199459 | GEO
Project description:Beach and tide pools meiofaunal sequences Raw sequence reads
| PRJNA974547 | ENA
Project description:To identify the effect of high-salt diet on immune cells of brain tumor microenvironment, we isolated immune cells of brain from mice fed with control diet or high-salt diet.
2022-09-10 | GSE200533 | GEO
Project description:Molecular subtyping is expected to enable bladder cancer (BC) precise treatment. However, reliable subtyping strategies for clinical application remains defective and controversial. Given the significance of tumor immune dysfunction and exclusion (TIDE) in tumor immune escape and immunotherapy, we aimed to develop a novel TIDE-based subtyping method to facilitate personalized management. Transcriptome data of BC was used to evaluate the heterogeneity and the status of TIDE patterns. We identified 69 TIDE biomarker genes and classified BC samples into three subtypes using consensus clustering. Subtype I showed the lowest TIDE status and malignancy with the best prognosis and highest sensitivity to immune checkpoint blockade (ICB) treatment, which was enriched of metabolic related signaling pathways. Subtype III represented the highest TIDE status and malignancy with the poorest prognosis and resistance to ICB treatment, resulting from its inhibitory immune microenvironment and T cell terminal exhaustion. Subtype II was in a transitional state with intermediate TIDE level, malignancy, and prognosis. We further confirmed the existence and characteristics of our novel TIDE subtypes using real-world BC samples. This subtyping method was proved to be more efficient than previous known methods in identifying non-responders to immunotherapy. We also propose that combining our TIDE subtypes with known biomarkers can potentially improve the sensitivity and specificity of these biomarkers. Moreover, besides guiding ICB treatment, this classification approach can assist in selecting the frontline or recommended drugs. Finally, we confirmed that the TIDE subtypes are conserved across the pan-tumors. In conclusion, our novel TIDE-based subtyping method can serve as a powerful clinical tool for BC and pan-cancer patients, and potentially guiding personalized therapy decisions for selecting potential beneficiaries and excluding resistant patients of ICB therapy.
2024-04-19 | GSE248167 | GEO
Project description:84 coral samples were taken form Waiopae tide pools in Kapoho Hawaii.
2018-04-17 | MSV000082281 | GNPS
Project description:We performed an in-depth proteome analysis of the haloarchaeal model organism Haloferax volcanii under standard, low and high salt and low and high temperature conditions using label-free mass spectrometry. Qualitative analysis of protein identification data from high pH/reversed phase fractionated samples indicated 61.1% proteome coverage (2,509 proteins), which is close to the maximum recorded values in archaea. Identified proteins matched to the predicted proteome in their physicochemical protein properties, with only a small bias against low molecular wright and membrane-associated proteins. Cells grown under low and high salt stress as well as low and high temperature stress were quantitatively compared to standard cultures by SWATH mass spectrometry. 2,244 proteins, or 54.7% of the predicted proteome, were quantified across all conditions at high reproducibility which allowed for global analysis of protein expression changes under these stresses. Pathway enrichment analysis by KEGG annotation showed that most major cellular pathways are part of H. volcanii’s universal stress response. In addition, specific pathways were found to be selectively affected by either salt or temperature stress.
2019-09-04 | PXD011056 | Pride
Project description:We perfomred sc RNA seq of intetinal immun cell and PBMCs to figure out the roles of intestine in development of salt-sensitive hypertension. We fed a high salt diet(4% NaCl) or a normal salt diet(0.2% NaCl) to Dahl-salt senstive rats for 4 weeks. We isolated immune cells from small instesinal lamin propria and blood.
2025-07-23 | GSE293074 | GEO
Project description:Seaweeds in the upper intertidal zone experience extreme desiccation during low tide, followed by rapid rehydration during high tide. Porphyra sensu lato are typical upper intertidal seaweeds. Thus, it is valuable to investigate the adaptive conditions and mechanisms of seaweed to desiccation-rehydration stress.
2022-03-02 | PXD030324 | Pride
Project description:Transcriptional profiling of Haloferax mediterranei DF50 and M-NM-^TdeoR2 with induction by fructose comparing with the strains without this induction. Goal was to explore the effect of induction by fructose on Haloferax mediterranei. Total RNA from the Haloferax mediterranei DF50 and M-NM-^TdeoR2 with or without induction by fructose were used to generate target cDNA, and then hybridized to Haloferax mediterranei genome array genechips, representing about 3800 genes.
2013-12-18 | E-GEOD-41134 | biostudies-arrayexpress