详细内容（前10条）

1. ⭐ GSE308952 外周神经胶质细胞构成促修复微环境，触发皮肤伤口愈合 [空间转录组学]

• ✍️ 作者：未知作者
• 🏷️ 关键词：spatial、spatial transcriptomics、transcriptomics
• 📝 描述：Contributors : Lukas Sommer ; Salome Stierli ; Adrian Salas-BastosSeries Type : OtherOrganism : Mus musculusSkin repair is a complex, dynamic process involving multiple cell types. Using multiplex imaging, spatial transcriptomics, and single-cell RNA sequencing, we show that peripheral nerves —containing repair glia— form a pro-reparative niche closely interacting with macrophages and proliferating fibroblasts in acute skin wounds. Repair glia function as critical early-stage regulators of wound healing by initiating the inflammatory response throughsecretion of monocyte chemoattractant proteins, such as CCL2, which recruit monocyte derived macrophages. Accordingly, depletion of repair glia as well as glia-specific deletion of CCL2 reduces the number of macrophages, leading to impaired fibroblast proliferation and diminished fibroblast to myofibroblast transition. These findings position repair glia as a central component of the pro-reparative niche, coordinating the early immune response and orchestrating the temporal progression of wound healing.
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2. ⭐ GSE310753 神经元活动抑制 NEUROD 依赖性转录和基因组组织 [RNA-Seq]

• ✍️ 作者：未知作者
• 🏷️ 关键词：Neuronal、RNA-seq、genome
• 📝 描述：Contributors : Pamela Valnegri ; Tomoko Yamada ; Yue YangSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusNeuronal activity induces gene expression programs associated with plasticity in the brain, but it also transiently suppresses gene expression through poorly understood mechanisms. Here, we report that neuronal activity downregulates NEUROD-dependent gene expression in cerebellar granule neurons in adult mice. Using NEUROD1/2 double conditional knockout mice of both sexes, we show that NEUROD binds and activates its target gene enhancers and establishes a three-dimensional genome architecture that facilitates transcription when neuronal activity is low. Moreover, NEUROD antagonizes activity-dependent gene expression programs, including those regulated by MEF2. However, when granule neurons are activated, NEUROD-dependent transcriptional and genome organizing functions are disrupted. Together, these findings reveal NEUROD as a key regulator of transcriptional programs associated with inactive neurons. Our study provides new insights into how neuronal activity reshapes gene transcription and genome architecture in the brain.
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3. ⭐ GSE310752 神经元活动抑制 NEUROD 依赖性转录和基因组组织 [Hi-C]

• ✍️ 作者：未知作者
• 🏷️ 关键词：Neuronal、Hi-C、genome
• 📝 描述：Contributors : Pamela Valnegri ; Tomoko Yamada ; Yue YangSeries Type : OtherOrganism : Mus musculusNeuronal activity induces gene expression programs associated with plasticity in the brain, but it also transiently suppresses gene expression through poorly understood mechanisms. Here, we report that neuronal activity downregulates NEUROD-dependent gene expression in cerebellar granule neurons in adult mice. Using NEUROD1/2 double conditional knockout mice of both sexes, we show that NEUROD binds and activates its target gene enhancers and establishes a three-dimensional genome architecture that facilitates transcription when neuronal activity is low. Moreover, NEUROD antagonizes activity-dependent gene expression programs, including those regulated by MEF2. However, when granule neurons are activated, NEUROD-dependent transcriptional and genome organizing functions are disrupted. Together, these findings reveal NEUROD as a key regulator of transcriptional programs associated with inactive neurons. Our study provides new insights into how neuronal activity reshapes gene transcription and genome architecture in the brain.
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4. ⭐ GSE310749 神经元活动抑制 NEUROD 依赖性转录和基因组组织 [ChIP-Seq]

• ✍️ 作者：未知作者
• 🏷️ 关键词：Neuronal、ChIP-seq、genome
• 📝 描述：Contributors : Pamela Valnegri ; Tomoko Yamada ; Yue YangSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Mus musculusNeuronal activity induces gene expression programs associated with plasticity in the brain, but it also transiently suppresses gene expression through poorly understood mechanisms. Here, we report that neuronal activity downregulates NEUROD-dependent gene expression in cerebellar granule neurons in adult mice. Using NEUROD1/2 double conditional knockout mice of both sexes, we show that NEUROD binds and activates its target gene enhancers and establishes a three-dimensional genome architecture that facilitates transcription when neuronal activity is low. Moreover, NEUROD antagonizes activity-dependent gene expression programs, including those regulated by MEF2. However, when granule neurons are activated, NEUROD-dependent transcriptional and genome organizing functions are disrupted. Together, these findings reveal NEUROD as a key regulator of transcriptional programs associated with inactive neurons. Our study provides new insights into how neuronal activity reshapes gene transcription and genome architecture in the brain.
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5. ⭐ GSE294749 小鼠胰腺肿瘤 (KPC) 和慢性胰腺炎 (KC) 的单细胞 RNA 测序

• ✍️ 作者：未知作者
• 🏷️ 关键词：tumor、RNAseq、single-cell
• 📝 描述：Contributors : Youngkyu Park ; Sandeep Nadella ; Mojdeh Shakiba ; Jennifer Thalapillil ; Giuseppina Caligiuri ; Juliene Hinds ; Jonathan Preall ; David TuvesonSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusPancreatic ductal adenocarcinoma (PDA) is characterized by a desmoplastic extracellular matrix (ECM) that is produced and remodeled by myofibroblastic cancer-associated fibroblasts (myCAFs), thus promoting tumor progression and resistance to therapy. Thus, identification of the regulatory pathways that drive desmoplasia is a pressing clinical need. Transcriptional profiling of tumor resident fibroblasts across PDA progression identified a CAF subset, termed WNT-sensing myCAFs, in both mouse and human PDA. These surround WNT7A/B+ cancer cells and express genes associated with ECM deposition and remodeling. Pharmacological inhibition of ligand-dependent WNT signaling or genetic ablation of Wnt7b in PDA cells depleted the number of WNT-sensing CAFs subpopulation and reduced collagen deposition in vivo, while ectopic Wnt7b expression enhanced desmoplasia. WNT7B overexpression also led to increased metastasis, resulting in a metastatic niche presenting similar WNT-sensing myCAF architecture. Our findings establish WNT7 as a critical regulator of myCAF function and offer a targetable axis to reduce tumor desmoplasia.
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6. ⭐ GSE315650 空间基因组组织与线虫程序性DNA消除相关[Hi-C Parascaris univalens]

• ✍️ 作者：未知作者
• 🏷️ 关键词：Hi-C、spatial、genome
• 📝 描述：Contributors : James R Simmons ; Jianbin WangSeries Type : OtherOrganism : Parascaris univalensProgrammed DNA elimination (PDE) is a notable exception to genome integrity, characterized by significant DNA loss during development. In many nematodes, PDE is initiated by DNA double-strand breaks (DSBs), which lead to chromosome fragmentation and subsequent DNA loss. However, the mechanism of nematode programmed DNA breakage remains largely unclear. Interestingly, in the human and pig parasitic nematode Ascaris, no conserved motif or sequence structures are present at chromosomal breakage regions (CBRs), suggesting the recognition of CBRs may be sequence-independent. Using Hi-C, we revealed that Ascaris CBRs engage in three-dimensional (3D) interactions before PDE, indicating that physical contacts between break regions may contribute to the PDE process. The 3D interactions are established in both Ascaris male and female germlines, demonstrating inherent genome organization associated with the CBRs and to-be-eliminated sequences. In contrast, in the unichromosomal horse parasite Parascaris univalens, transient pairwise interactions between neighboring CBRs that will form the ends of future somatic chromosomes were observed only during PDE. Intriguingly, we found that Ascaris PDE, which converts 24 germline chromosomes into 36 somatic ones, induces specific compartmentalization changes. Remarkably, Parascaris PDE generates the same set of 36 somatic chromosomes, and the 3D compartment changes following PDE are consistent between the two species. Overall, our findings suggest that CBRs spatially demarcate the retained and eliminated DNA and may contribute to their spatial organization during Ascaris PDE. We also demonstrated that the 3D genome reorganization of the somatic chromosomes in these nematodes following PDE is evolutionary and developmentally conserved.
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7. GSE300602：在Matriel或I型胶原蛋白中培养的人类肠道类器官的单细胞RNA测序分析

• ✍️ 作者：未知作者
• 🏷️ 关键词：single-cell、regex:intestin(e|al)
• 📝 描述：Contributors : Sakura Kirino ; Kensuke Miyake ; Fumiya Uefune ; Shiro YuiSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensIntestinal epithelial regeneration depends on cellular plasticity under inflammatory conditions. Two major forms of plasticity have been described: spatial plasticity, in which mature cells dedifferentiate into crypt base columnar (CBC) stem cells, and fetal reversion, where cells adopt a fetal-like transcriptional state. To investigate the cellular mechanisms underlying these processes, we performed single-cell RNA sequencing on human intestinal epithelial organoids cultured in either Matrigel or collagen-based matrices. This dataset provides a high-resolution atlas of epithelial stem cell states and plasticity transitions, facilitating further investigation of regenerative hierarchies in the human intestine.
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8. GSE300601：在Matriel或I型胶原蛋白中培养的小鼠肠道类器官的单细胞RNA测序分析

• ✍️ 作者：未知作者
• 🏷️ 关键词：single-cell、regex:intestin(e|al)
• 📝 描述：Contributors : Sakura Kirino ; Kensuke Miyake ; Fumiya Uefune ; Shiro YuiSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusIntestinal epithelial regeneration depends on cellular plasticity under inflammatory conditions. Two major forms of plasticity have been described: spatial plasticity, in which mature cells dedifferentiate into crypt base columnar (CBC) stem cells, and fetal reversion, where cells adopt a fetal-like transcriptional state. To investigate the cellular mechanisms underlying these processes, we performed single-cell RNA sequencing on mouse intestinal epithelial organoids cultured in either Matrigel or collagen-based matrices. Combined single-cell transcriptomic and functional analyses revealed bidirectional interconversion between CBCs and revival stem cells (revSCs), as well as the reprogramming of absorptive enterocytes toward revSC-like states. This dataset provides a high-resolution atlas of epithelial stem cell states and plasticity transitions, facilitating further investigation of regenerative hierarchies in the mouse intestine.
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9. GSE280340 肝脏昼夜节律转录组的糖皮质激素依赖性和独立性 [ChIP-seq]

• ✍️ 作者：未知作者
• 🏷️ 关键词：ChIP-seq、transcriptome
• 📝 描述：Contributors : Robert J Maidstone ; Louise Hunter ; Mudassar Iqbal ; Nicola Begley ; David A Bechtold ; Matthew Baxter ; Andrew Loudon ; Magnus Rattray ; David W RaySeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Mus musculusThe liver, a critical metabolic organ, shows clear day-night variation in patterns of gene and protein expression, and in metabolic pathway activity. Liver cells possess molecular circadian clocks, but systemic factors also contribute to the circadian rhythmicity of liver gene expression. Here, we examine the role of glucocorticoid signalling. Glucocorticoids are essential hormones, with a strong circadian oscillation, which control multiple cellular processes via their action on the glucocorticoid receptor (GR). We first compare clock factor and GR binding at promoters and enhancers linked to rhythmic genes, and find increased clock factor binding at those elements where GR is also present. We find that genes with GR binding at the promoter are more likely to show rhythmic expression. We go to test the role of GR more directly, by examining circadian rhythms of gene expression in mice with and without hepatocyte-targeted GR deletion. Notably, we observe only a small effect of GR deletion, with the vast majority of rhythmic genes showing unchanged rhythmic expression, despite evidence for GR binding in the vicinity of these genes. We do find a small number of genes to show lost or gained rhythmicity with GR deletion, and genes which lose rhythmicity do associate with GR binding sites. However, GR appears redundant for conveying timing information to most of the rhythmic liver transcriptome, a conclusion which is supported by our re-analysis of an independent published dataset.
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10. GSE315608 幼稚 CD4+ T 细胞群的异质性和可塑性 [批量 RNA 测序]

• ✍️ 作者：未知作者
• 🏷️ 关键词：T cell、RNAseq
• 📝 描述：Contributors : Alia Sajani ; Evelien Schaafsma ; Walburga Croteau ; Mohamed ElTanbouly ; Elizabeth C Nowak ; Chao Cheng ; Christopher M Burns ; Mary Jo Turk ; Randolph J Noelle ; Louise J LinesSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusWhile naive CD4+ T cells have historically been considered a homogenous population, recent studies provide evidence that functional heterogeneity exists. Using scRNAseq, we identified five transcriptionally distinct naive CD4+ T cell subsets that emerge within the single positive stage in the thymus: a quiescence cluster (TQ), a memory-like cluster (TMEM), a TCR-reactive cluster (TTCR), an IFN-responsive cluster (TIFN), and an undifferentiated cluster (TUND). Elevated expression of transcription factors KLF2, Mx1, and Nur77 within the TQ, TIFN, and TTCR clusters, respectively, enabled enrichment of these subsets for functional validation. Sorted subsets displayed distinctive functional responses upon stimulation. Furthermore, treatment of mice with inflammatory stimuli reduced cytokine production of naive T cells ex vivo. In SLE patients, IFN-induced gene expression was markedly elevated within the TIFN cluster. Our data demonstrate that naive T cells are shaped by their host environment, with functional biases manifesting upon activation. These findings highlight the importance of understanding how naive T cell heterogeneity may be distorted in cancer, autoimmunity, and infectious diseases.
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1. 通过绘制1000万个免疫细胞图谱来解码疾病机制，新的图谱和人工智能模型为精准免疫疗法铺平了道路。

• ✍️ 作者：未知作者
• 🏷️ 关键词：immune、regex:immuno(logy|therapy|suppression)
• 📝 描述：Large-scale RNA sequencing and multi-omics profiling map over 10 million immune cells, revealing how genetics, age, and sex shape immune regulation and disease risk…
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2. 科学家找到增强免疫系统对抗癌症的方法

• ✍️ 作者：未知作者
• 🏷️ 关键词：cancer、immune
• 📝 描述：Researchers have developed a new class of antibodies that amplify the immune system’s ability to fight cancer. By clustering immune receptors that normally receive weak signals from tumors, these four-pronged antibodies push T cells into full attack mode. In early studies, they outperformed conventional antibodies at activating cancer-killing immune cells. The work opens the door to more effective immunotherapy treatments.
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3. 嗜酸性粒细胞在不同组织中的时空分化图谱

• ✍️ 作者：未知作者
• 🏷️ 关键词：spatial
• 📝 描述：High-resolution RNA sequencing reveals how tissue residence time drives eosinophil specialization across organs, shaping their roles in health and immune function…
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4. 新冠后遗症可能由炎症和微小血栓引起。

• ✍️ 作者：未知作者
• 🏷️ 关键词：inflammation
• 📝 描述：Long COVID affects an estimated 65 million people worldwide and can damage the brain, heart, blood vessels, and immune system long after infection. Researchers now link symptoms to lingering virus, inflammation, micro-clots, and disrupted energy metabolism. While structured rehab and pacing can improve quality of life, a growing list of experimental treatments—from antivirals and metformin to microbiome therapies and biologics—shows early promise. Clear answers, however, are still limited by small studies and the lack of large, definitive trials.
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5. 研究表明，年轻血液可以延缓小鼠阿尔茨海默病的发展。

• ✍️ 作者：未知作者
• 🏷️ 关键词：Alzheimer
• 📝 描述：New research shows that aging blood can accelerate Alzheimer’s-like changes in the brain, while younger blood may offer protection. In mouse experiments, older blood worsened memory performance and increased toxic protein buildup linked to the disease. The study also uncovered widespread changes in brain proteins tied to communication and signaling. The findings point to the blood as a powerful influencer of brain health—and a promising new therapeutic target.
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6. 一个隐藏的循环正在驱动致命的胰腺癌

• ✍️ 作者：未知作者
• 🏷️ 关键词：cancer
• 📝 描述：Pancreatic cancer is notoriously hard to treat, often resisting therapies that target its most common mutations. Researchers have now uncovered a hidden three-part loop that fuels tumor growth, involving the cancer drivers SRSF1, AURKA, and MYC. By targeting just one part of this loop with a specially designed molecule, they were able to shut down all three at once. The result was a dramatic loss of tumor cell survival, offering new hope for smarter, more effective treatments.
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• GSE310933 神经元活动抑制 NEUROD 依赖性转录和基因组组织
• GSE312633 激活细胞代谢可纠正新冠后记忆性T细胞对社区获得性病原体的反应受损
• GSE286327 SOX4 调控 STAT6 以调节 MTHFD2 表达并影响肝细胞癌的耐药性
• GSE314334 ACSL5介导对富含棕榈酸的肺微环境的适应，从而增强转移性乳腺癌细胞的存活和肺转移
• GSE310408 人类肠道类器官在胶原/Matrigel培养和5-氟尿嘧啶处理下的基因表达谱
• GSE300603 胎儿从不同谱系逆转维持肠道干细胞库并赋予应激适应能力。
• GSE299792 激活和抑制性 FOX 家族蛋白通过表观遗传调节因子调控 HSV-1 染色质和裂解-潜伏平衡
• GSE298094 EZH2 PROTACs 无法消除 EZH2 激活功能，但可通过快速诱导衰老来抑制某些前列腺癌。
• GSE280339 肝脏昼夜节律转录组的糖皮质激素依赖性和非依赖性
• GSE270817 染色质组织对 I 型干扰素反应的调控（HoxB8-FL pDC 激活的 RNA-seq）
• GSE230051 人类多能干细胞来源的胎肝类器官中高度异质性肝造血谱系的单细胞转录组
• GSE316072 人类 ID3 基因中一种常见的疾病相关 SNP 调节 E 蛋白活性和细胞增殖 [VMSC RNA-Seq]
• GSE316070 人类 ID3 基因中一种常见的疾病相关 SNP 调节 E 蛋白活性和细胞增殖 [HEK293T RNA-Seq]
• GSE315877 代谢手术通过抑制mTORC1/JAK–STAT信号通路减轻肥胖糖尿病青少年早期肾损伤
• GSE315686 初始 CD4+ T 细胞群的异质性和可塑性
• GSE315610 幼稚 CD4+ T 细胞群的异质性和可塑性 [小鼠 CITEseq]
• GSE315609 幼稚 CD4+ T 细胞群的异质性和可塑性 [人类 CITEseq]
• GSE315225 盐皮质激素受体拮抗剂可减少心脏手术后房性心律失常并减弱心脏停搏引起的房性应激反应
• GSE310722 TDP-43 功能障碍导致 iPSC 衍生神经元和 ALS/FTD 患者组织中隐蔽转座元件衍生外显子的积累 [i3N RNAseq]
• GSE280480 基因表达谱分析揭示了两种具有不同靶向生物学特征的间变性大细胞淋巴瘤主要类型：一项 LLMPP 研究
• GSE315579 NKG2D 上调增强 T 细胞和 NK 细胞的细胞毒性，使肿瘤对 αPD1 和 αVEGF 联合疗法更敏感，并有助于预防前庭神经鞘瘤模型中的听力损失
• GSE314711 感觉神经来源的CGRP通过限制巨噬细胞的生物能量来控制骨修复中的破骨细胞生成
• GSE278068 纳米抗体锚定转座用于染色质可及性和DNA甲基化的双重分析
• GSE223337 赖氨酸特异性组蛋白去甲基化酶 1A (KDM1A/LSD1) 抑制剂可减弱 DNA 双链断裂修复并增强替莫唑胺在胶质母细胞瘤 II 中的疗效
• GSE223335 赖氨酸特异性组蛋白去甲基化酶 1A (KDM1A/LSD1) 抑制剂可减弱 DNA 双链断裂修复并增强替莫唑胺在胶质母细胞瘤中的疗效
• GSE143870 肝​​细胞癌中PPT1的下游基因和通路