Similar Datasets
Project description:Utilizing next-generation sequencing technology, combined with ChIP (Chromatin Immunoprecipitation) technology to analyze histone modification (acetylation) induced by butyrate and to map the epigenomic landscape of normal histone H3, H4 Cells were treated with 10 mM butyrate for 24 hr, The cells were scraped from the flask and homogenized with ice-cold Dounce homogenizer to release the nuclei. The collected nuclei were resuspended in digestion buffer and enzymatic shearing was performed. ChIP with anti H3, H4 and acetyl-H3 and acetyl-H4.
2014-01-24 | E-GEOD-38973 | biostudies-arrayexpress
Project description:Iridocorneal endothelial (ICE) syndrome is a rare ocular disease affecting the anterior segment, characterized by progressive deterioration leading to significant complications, including corneal endothelial compensation and secondary glaucoma. The unclear etiology of this syndrome limits clinical management to symptomatic interventions. The abnormality of corneal endothelial cells (ICE cells) in patients with ICE syndrome is considered the initial step of this disease. This study endeavors to elucidate the transcriptomic profiles of ICE cells utilizing smart-seq2 single-cell RNA sequencing techniques.
2026-01-12 | GSE256242 | GEO
Project description:Background: The halophyte Mesembryanthemum crystallinum (ice plant) is a model for studying salt tolerance. The morphology, physiology, metabolism, and gene expression of ice plant have been studied for over 40 years. Although the complete genome sequence has not been revealed, large-scale analyses of gene expression profiling have drawn an outline of salt tolerance in ice plant. Despite ample information in the transcriptome, miRNA information has not been documented. Results: We examined responses to a sudden increase in salinity in ice plant seedlings. Using a fluorescent dye to detect Na+, we found that ice plant roots respond to an increased flux of Na+ by either secreting or storing Na+ in specialized cells. High-throughput sequencing was used to identify small RNA profiles in three-day-old seedlings treated with or without 200 mM NaCl. Totally 132 conserved miRNAs belonging to 22 families were found. The hairpin precursor of 19 conserved mcr-miRNAs and 12 novel mcr-miRNAs were identified. Target genes are involved in a broad range of biological processes: transcription factors that regulate growth and development, enzymes that catalyze miRNA biogenesis for the most conserved mcr-miRNA, and proteins that are involved in ion homeostasis and drought-stress responses for some novel mcr-miRNAs. After 6 h of salt stress, the expressions of most mcr-miRNAs were down-regulated, whereas the expressions of their corresponding target genes were up-regulated. Analyses of the functions of target genes revealed that cellular processes, including growth and development, metabolism, and ion transport activity were up-regulated in roots under salt stress. Conclusions: Analyses of small RNA profile of ice plant seedlings identified many conserved miRNA families and several novel miRNAs. The expression of ten conserved miRNAs and three novel miRNAs were reciprocally correlated to predicted targets hourly after salt stress. Based on the expression pattern of miRNA and target genes in combination with the observation of Na+ distribution, we suggest that ice plant roots respond effectively to increased salinity by using Na+ as an osmoticum for cell expansion and guard cell opening. Excessive Na+ could either be secreted through root epidermis or stored in specialized leaf epidermal cells. These responses are partially regulated at the miRNA-mediated post-transcriptional level.
2016-12-31 | GSE83508 | GEO
Project description:<p>Antimicrobial resistance (AMR) is one of the most urgent challenges in public health, and the horizontal transfer of antibiotic resistance genes (ARGs) mediated by mobile genetic elements (MGEs) drives its widespread global dissemination. Although integrative conjugative elements (ICEs) outnumber conjugative plasmids, research on ICE-mediated horizontal gene transfer (HGT) remains largely lacking, especially concerning SXT ICEs, which are highly prevalent, pose significant risks, and are directly related to human health. Cyromazine is a widely used feed additive, with high detection rates in the feces of farmed animals and related environments. It has also been shown to increase the abundance of ARGs, and the potential driving mechanisms urgently require further exploration. Thus, we investigated the impact of cyromazine on SXT ICE-mediated ARGs transfer and elucidated its underlying mechanisms. Our study demonstrates that cyromazine promotes SXT ICE conjugative transfer both intra- and inter-species. This facilitating effect confirmed in mouse intraperitoneal and intestinal conjugation models. The potential mechanisms include cyromazine-induced ROS accumulation and triggering of the SOS response, which could promote SXT ICE excision and activate conjugation-related operons. Furthermore, enhanced energy metabolism and altered lipid metabolism further facilitate SXT ICE transfer. Collectively, our study partially fills the gap in understanding ICE-mediated AMR transmission dynamics, and highlighting that the exacerbated AMR crisis is associated with cyromazine-stimulated high-frequency SXT ICE conjugation in vitro and in vivo.</p>
2025-10-15 | MTBLS13146 | MetaboLights
Project description:Despite its importance during viral or bacterial infections, transcriptional regulation of the interferon-b gene (Ifnb1) in activated macrophages is only partially understood. Here we report that TRIM33 deficiency results in high-sustained expression of Ifnb1 at late stages of toll-like receptor-mediated activation in macrophages but not in fibroblasts. In macrophages, TRIM33 is recruited by PU.1 to a conserved region, Ifnb1 Control Element (ICE), located 15kb upstream of the Ifnb1 transcription start site. ICE constitutively interacts with Ifnb1 through a TRIM33-independent chromatin loop. At late phases of lipopolysaccharide activation of macrophages, TRIM33 is bound to ICE, regulates Ifnb1 enhanceosome loading, controls Ifnb1 chromatin structure, and represses Ifnb1 gene transcription by preventing recruitment of CBP/p300. These results characterize a previously unknown mechanism of macrophage-specific regulation of Ifnb1 transcription whereby TRIM33 is critical for Ifnb1 gene transcription shut down.
2015-11-18 | GSE73322 | GEO
Project description:Cryopreservation of mature oocytes is a critical means for female fertility preservation. Despite clinical advances using vitrification preservation method, the high concentrations of toxic penetrating cryoprotectant agents (CPA, up to 4.3 M) and low throughput (only one every experiment) put forward a challenge. Here, we report a synergetic ice inhibition platform via PVA/Fe3O4/GO nanoparticles (PFG NPs), that achieves sharp ice morphology, ice recrystallization, and devitrification inhibition, thus reducing cryodamage both in cooling and warming stages. Oocyte cryopreservation experiment demonstrates the survival rate can attain 98.6% using 2.5 M penetrating CPA while ensuring the scalability (ten oocytes each cryopreservation procedure). In contrast, recovered oocytes via PFG platform show 85 gene variation compared with fresh oocytes, whereas tradition CPA (TCPA) formulation induces 1396 gene changes. Meanwhile, the PFG-cryopreservation oocytes maintain normal ability of fertilization, development, and birth of offspring.
2025-04-30 | GSE244977 | 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:Sea ice phages
| PRJEB101482 | ENA