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PROVIDER: PRJNA1232920 | 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: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:To investigate a Florida manatee (Trichechus manatus latirostris) mortality event following a red tide bloom in Southwest Florida, a RNA-Seq experiment was conducted. Cell processes such as immune response, cell proliferation and differentiation and apoptosis were among the most affected by red tide. These were involved in potential diseases such as neoplasms, inflammation, and wounds and injuries, among others. There were both up-regulated and down-regulated genes, but the highest fold changes relative to controls were for genes that were down-regulated. Piccolo presynaptic cytomatrix protein (PCLO) gene, the one most down-regulated (fold change -9.93; p-value 0.0009) is associated with neurotransmitter release, cognitive functioning, neuronal loss, and neuronal synapse function. Another gene that has a similar function, ankyrin 2, neuronal, transcript variant 1 (ANK2) was also down-regulated (fold change -8.66; p-value 0.0023). ANK2 is associated with the stability of neuron synapses. Two immune genes, interleukin 6 (interferon, beta 2) (IL6) and zinc finger protein 804B (ZNF804B), were down-regulated (fold change -9.31; p-value 0.000003 and fold change -8.90; p-value 0.0164, respectively). Interleukin 6 encodes proteins involved in acute phase response, inflammation, and autoimmune response. ZNF804B is associated with neuronal chemokine and cytokine regulation, autoimmune response, and immune activation. The family with sequence similarity 186, member A (FAM186A) gene was down-regulated (fold change -8.79; p-value 0.0143). FAM186A gene mutation is associated with tumor metastasis in colorectal cancer tumors. Among the most up-regulated genes, CCAAT/enhancer binding protein (C/EBP) is involved in granulocytic differentiation and also involved with the immune system. Determining the differentially expressed genes associated with red tide enhances our understanding of manatee immune response to red tide toxins and aids in the development of red tide biomarkers. This information will better assist clinicians and researchers in diagnosing and treating future illnesses.
2017-10-01 | GSE86792 | GEO
Project description:A scalable derivative-free optimizer trained through learning to optimize approach to interpret drug response mechanism network
| PRJNA765966 | ENA
Project description:seawater metagenome Raw sequence reads in green tide bloom
| PRJNA893582 | ENA