详细内容（前10条）

1. GSE315346 大鼠心肌梗死后心脏胸椎背根神经节多聚RNA测序数据

• ✍️ 作者：未知作者
• 🏷️ 关键词：cardiac、RNAseq
• 📝 描述：Contributors : Hanjun Wang ; Samuel GillmanSeries Type : Expression profiling by high throughput sequencingOrganism : RattusThe overall goal is to detect any signficant changes in the rat thoracic DRG mRNA expressions post myocardial infarction.
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2. GSE310588 铜对在甲烷或甲醇培养基中生长的甲基嗜菌OB3b的生理和转录组的影响

• ✍️ 作者：未知作者
• 🏷️ 关键词：transcriptome
• 📝 描述：Contributors : Peng Peng ; Jeremy D SemrauSeries Type : Expression profiling by high throughput sequencingOrganism : Methylosinus trichosporium OB3bThis study investigates the combined effects of copper availability and carbon source (methane versus methanol) on the physiology and transcriptome of Methylosinus trichosporium OB3b, a model Type II methanotroph. Methanotrophs oxidize methane to carbon dioxide through intermediates such as methanol, formaldehyde, and formate, using two forms of methane monooxygenase (MMO): the copper-dependent particulate MMO (pMMO) and the soluble MMO (sMMO). Although Msn. trichosporium OB3b can utilize both methane and methanol as sole carbon sources, growth on methanol is significantly affected by copper. In the presence of copper, methanol-grown cells exhibited impaired growth, formate accumulation, and decreased pH, while buffering with MOPS restored growth. NADH/NAD ratios increased nearly tenfold in methanol-grown cultures with copper, indicating redox imbalance. Transmission electron microscopy revealed disrupted intracytoplasmic membranes under these conditions. Transcriptomic analysis showed that genes involved in methanol oxidation were differentially expressed in response to copper and carbon source, and two siderophore biosynthetic gene clusters were repressed during methanol growth with copper. Overall, the findings suggest that Msn. trichosporium OB3b modulates metallophore expression and carbon metabolism to manage oxidative and redox stress under methanol growth conditions. Understanding these regulatory mechanisms is critical for optimizing methanotroph-based biotechnological applications, including methanol-driven biosynthesis of valuable compounds such as methanobactin.
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3. GSE315372 纤溶酶原脂质货物驱动巨噬细胞 TLR2 激活，且该过程独立于蛋白酶活性。

• ✍️ 作者：未知作者
• 🏷️ 关键词：macrophage
• 📝 描述：Contributors : Danielle L. Michell ; Kasey C. VickersSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusPlasminogen (Plg) is a highly abundant, liver-secreted plasma protein and zymogen precursor of plasmin, a key serine-protease in fibrinolysis. Zymogen Plg (Glu-Plg) has been reported to transport extracellular RNA, cholesterol, and oxidized phospholipids (oxPL) cargo which likely defines the biological functions of non-enzymatic Plg particles, including immunogenicity towards innate immune cells. Here, we demonstrate that native Plg dose-dependently activates NF-kB transactivity, pro-inflammatory gene expression and cytokine secretion in primary macrophages through toll-like receptors, i.e., toll-like receptor 2 (TLR2), as identified through a TLR screen. Plg stimulation of macrophages and NF-kB transactivity reporter cells were sensitive to small molecule inhibitors of TLR2, and Tlr2 and Myd88 genetic-deficiency. Plg treatments were found to stimulate both mouse and human primary macrophages but failed to activate microglial cells and vascular smooth muscle cells. Both C29, and its derivative ortho-vanillin, were found to inhibit macrophage TLR2 signaling and cytokine secretion in vitro, as profiled by proximity extension assays (PEA). Plg activation of TLR2 was observed to be independent of Plg’s conversion to plasmin or down-stream plasmin protease activity, as Plg stimulation of TLR2 were not affected by active-site mutagenesis, lysine analogues ε-aminocaproic acid and tranexamic acid, VPLCK peptide inhibitor, α2-anti-plasmin, α2-macroglobin, or urokinase plasminogen activator (uPA, Plau-/-) and tissue plasminogen activator (tPA, Plat-/-) macrophage deficiency. Mass spectrometry-based untargeted lipidomics demonstrated the full profile of bioactive lipids covalently bound or loosely associated with human Plg particles. Plg’s immunogenicity towards macrophages was found to be dependent, in part, through lipid cargo, as lipid removal with lipases and organic lipid extractions were found to reduce Plg’s capacity to activate macrophages. Plg-deficiency in hypercholesterolemic mice were observed to be associated with reduced atherosclerosis and intravenous injections of ortho-vanillin were found to significantly reduce lesion area and alter macrophage sub-phenotypes in mouse lesions, as per single cell RNA sequencing. Results from these studies support that Glu-Plg’s lipid cargo and TLR2 may be viable drug targets to re…
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4. GSE315229 RNA-seq 分析 Huh7 细胞中 QRICH1 敲低的情况

• ✍️ 作者：未知作者
• 🏷️ 关键词：RNA-seq
• 📝 描述：Contributor : Su-Yeon ParkSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensThis study investigates the transcriptomic changes following QRICH1 knockdown in Huh7 hepatocellular carcinoma cells using RNA sequencing.
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5. GSE308970 多组织转录组衰老图谱揭示了鳉鱼的预测性衰老生物标志物

• ✍️ 作者：未知作者
• 🏷️ 关键词：aging
• 📝 描述：Contributors : Emma K Costa ; Jingxun Chen ; Ian H Guldner ; Man-Ru Wu ; Param P Singh ; Anne Brunet ; Tony Wyss-CoraySeries Type : Expression profiling by high throughput sequencingOrganism : Nothobranchius furzeriAging is associated with progressive tissue dysfunction, leading to frailty and mortality. Characterizing aging features, such as changes in gene expression and dynamics, shared across tissues or specific to each tissue, is crucial for understanding systemic and local factors contributing to the aging process. We performed RNA-sequencing on 13 tissues at 6 different ages in the African turquoise killifish, the shortest-lived vertebrate that can be raised in captivity. This comprehensive, sex-balanced ‘atlas’ dataset reveals the varying strength of sex-age interactions across killifish tissues and identifies age-altered biological pathways that are evolutionarily conserved. Demonstrating the utility of this resource, we discovered that the killifish head kidney exhibits a myeloid bias during aging, a phenomenon more pronounced in females than in males. In addition, we developed tissue-specific ’transcriptomic clocks’ and identified biomarkers predictive of chronological age. We show the importance of sex-specific clocks for selected tissues and use the tissue clocks to evaluate a dietary intervention in the killifish. Our work provides a comprehensive resource for studying aging dynamics across tissues in the killifish, a powerful vertebrate aging model.
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6. GSE308317 肿瘤细胞外囊泡 lncOSLMT 通过 m6A 依赖的 hnRNPA2B1/COX-2 轴驱动骨肉瘤肺部炎症转移前微环境的形成。

• ✍️ 作者：未知作者
• 🏷️ 关键词：tumor
• 📝 描述：Contributors : Xianbiao Xie ; Hongbo Li ; Zehao GuoSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusTumor-derived extracellular vesicles (EVs) play critical roles in premetastatic niche (PMN) formation. Here, we demonstrated that EVs from highly metastatic osteosarcoma cell lines preferentially localized to lung fibroblasts and induce inflammatory PMN formation. High-throughput profiling of EVs-derived long noncoding RNAs (lncRNAs) identified lncOSLMT as a candidate enriched in EVs and markedly upregulated in patient tumor and serum, with elevated levels correlating with poor prognosis. Mechanistically, in EVs, lncOSLMT directly bound the RNA-binding protein hnRNPA2B1. Following internalization by recipient lung fibroblasts, hnRNPA2B1 bound to N⁶-methyladenosine (m⁶A) -modified sites in the 3’UTR of PTGS2 mRNA, leading to transcript stabilization and increased COX-2 expression. For therapeutic intervention, we developed lactoferrin-resveratrol (LF-RES) nanoparticles, which loaded siRNA against lncOSLMT. Intravenous administration of LF-RES-siRNA in mice reduced EVs-induced lung inflammation and suppressed lung metastasis. Combination with EP2/EP4 antagonists produced enhanced anti-metastatic effects. These findings establish EVs-derived lncOSLMT as a key regulator of inflammatory PMN formation in the lung and highlight the potential of LF-RES-siRNA nanoparticles as a targeted anti-metastatic therapy in osteosarcoma.
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7. GSE308154 肿瘤细胞外囊泡 lncOSLMT 通过 m6A 依赖性 hnRNPA2B1/COX-2 轴驱动骨肉瘤肺部炎症转移前微环境的形成 [ncRNA-Seq]

• ✍️ 作者：未知作者
• 🏷️ 关键词：tumor
• 📝 描述：Contributors : Xianbiao Xie ; Hongbo Li ; Zehao GuoSeries Type : Non-coding RNA profiling by high throughput sequencingOrganism : Homo sapiensTumor-derived extracellular vesicles (EVs) play critical roles in premetastatic niche (PMN) formation. Here, we demonstrated that EVs from highly metastatic osteosarcoma cell lines preferentially localized to lung fibroblasts and induce inflammatory PMN formation. High-throughput profiling of EVs-derived long noncoding RNAs (lncRNAs) identified lncOSLMT as a candidate enriched in EVs and markedly upregulated in patient tumor and serum, with elevated levels correlating with poor prognosis. Mechanistically, in EVs, lncOSLMT directly bound the RNA-binding protein hnRNPA2B1. Following internalization by recipient lung fibroblasts, hnRNPA2B1 bound to N⁶-methyladenosine (m⁶A) -modified sites in the 3’UTR of PTGS2 mRNA, leading to transcript stabilization and increased COX-2 expression. For therapeutic intervention, we developed lactoferrin-resveratrol (LF-RES) nanoparticles, which loaded siRNA against lncOSLMT. Intravenous administration of LF-RES-siRNA in mice reduced EVs-induced lung inflammation and suppressed lung metastasis. Combination with EP2/EP4 antagonists produced enhanced anti-metastatic effects. These findings establish EVs-derived lncOSLMT as a key regulator of inflammatory PMN formation in the lung and highlight the potential of LF-RES-siRNA nanoparticles as a targeted anti-metastatic therapy in osteosarcoma.
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8. GSE308128 肿瘤细胞外囊泡 lncOSLMT 通过 m6A 依赖性 hnRNPA2B1/COX-2 轴驱动骨肉瘤肺部炎症转移前微环境的形成

• ✍️ 作者：未知作者
• 🏷️ 关键词：tumor
• 📝 描述：Contributors : Xianbiao Xie ; Hongbo Li ; Zehao GuoSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensTumor-derived extracellular vesicles (EVs) play critical roles in premetastatic niche (PMN) formation. Here, we demonstrated that EVs from highly metastatic osteosarcoma cell lines preferentially localized to lung fibroblasts and induce inflammatory PMN formation. High-throughput profiling of EVs-derived long noncoding RNAs (lncRNAs) identified lncOSLMT as a candidate enriched in EVs and markedly upregulated in patient tumor and serum, with elevated levels correlating with poor prognosis. Mechanistically, in EVs, lncOSLMT directly bound the RNA-binding protein hnRNPA2B1. Following internalization by recipient lung fibroblasts, hnRNPA2B1 bound to N⁶-methyladenosine (m⁶A) -modified sites in the 3’UTR of PTGS2 mRNA, leading to transcript stabilization and increased COX-2 expression. For therapeutic intervention, we developed lactoferrin-resveratrol (LF-RES) nanoparticles, which loaded siRNA against lncOSLMT. Intravenous administration of LF-RES-siRNA in mice reduced EVs-induced lung inflammation and suppressed lung metastasis. Combination with EP2/EP4 antagonists produced enhanced anti-metastatic effects. These findings establish EVs-derived lncOSLMT as a key regulator of inflammatory PMN formation in the lung and highlight the potential of LF-RES-siRNA nanoparticles as a targeted anti-metastatic therapy in osteosarcoma.
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9. GSE303866 对照组和同型半胱氨酸处理组鸡胚35体节尾部单细胞RNA测序

• ✍️ 作者：未知作者
• 🏷️ 关键词：RNAseq
• 📝 描述：Contributors : Stephanie Maupetit-Mehouas ; Felipe Maurelia ; Nicolas Allègre ; Yoan Renaud ; Pouria Hosseinna ; Jonas Cruzel ; Claire Chazaud ; Charlène GuillotSeries Type : Expression profiling by high throughput sequencingOrganism : Gallus gallus35 somites tail single cell RNAseq in control and homocysteine treated chicken embryo
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10. GSE285866 RNA-Seq 分析 Stylosanthes guianensis 的根系对锰毒性的响应

• ✍️ 作者：未知作者
• 🏷️ 关键词：RNA-seq
• 📝 描述：Contributor : Zhijian ChenSeries Type : Expression profiling by high throughput sequencingOrganism : Stylosanthes guianensisStylo (Stylosanthes guianensis) is an important tropical legume with superior tolerance to manganese (Mn) toxicity, which severely constrains plant growth especially in tropical acid soils. However, the underlying mechanisms of Mn tolerance in stylo remain largely unknown. SgUBC2, an ubiquitin-conjugating enzyme, has been documented to involved in Mn tolerance in stylo. RNA-seq analysis showed that overexpression of SgUBC2 resulted in changes in a variety of Mn-responsive gene expressions, including genes associated with antioxidant defense response, ion transporter and organic acid metabolism.
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1. Running Around：一个用于分析 Garmin 跑步数据的 R 包

• ✍️ 作者：未知作者
• 🏷️ 关键词：R package
• 📝 描述：In my previous post, I shared my annual running stats which were generated in R using summary data from Garmin Connect. The code I use to generate these summaries was beginning to get a bit unwieldy, so I have now rebased it into a package. GarminCSVr – is an R package … Continue reading: Running Around: an R package to analyse Garmin running data
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1. 科学家找到了一种帮助老年人肠道自我修复的方法。

• ✍️ 作者：未知作者
• 🏷️ 关键词：aging
• 📝 描述：Researchers have discovered a way to help aging intestines heal themselves using CAR T-cell therapy. By targeting senescent cells that build up over time, the treatment boosted gut regeneration, reduced inflammation, and improved nutrient absorption in mice. It even helped protect the intestine from radiation damage, with benefits lasting up to a year. Early results in human intestinal cells suggest the approach could one day improve gut health in older adults and cancer patients.
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• 对从CNC-SMC-Cre;Smad4flox/flox;R26-tdT基因型成年小鼠中分离的主动脉细胞进行GSE285521 scRNA-seq分析