详细内容（前10条）

1. ⭐ GSE309220 ECTV C15 表达对腘窝淋巴结早期免疫反应的影响（scRNA-seq）

• ✍️ 作者：未知作者
• 🏷️ 关键词：immune、lymph、regex:lymph(o|atic)?、scRNA
• 📝 描述：Contributors : Stephen D Carro ; Laurence C EisenlohrSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusOrthopoxviruses, such as variola and Mpox, encode a myriad of immunomodulatory proteins to promote pathogenesis. One notable family is the B22 family of proteins, which are highly conserved surface glycoproteins that potently inhibit T cell activation in vitro and ex vivo. Using the model poxvirus, ectromelia (ECTV), our lab has demonstrated that its B22 protein, C15, is capable of inhibiting both CD4+ and CD8+ T cells both in vitro and ex vivo, similar to other B22 proteins. Furthermore, we have also identified an additional function of C15: antagonism of NK cells during early infection. Specifically, C15 antagonizes the engagement of NK cells with infected cells in the popliteal lymph node during the innate immune response to infection. This inhibition by C15 promotes viral dissemination and replication, such that in the absence of C15, viral replication is significantly stunted. To date, there has not been any work investigating the mechanisms underlying this NK cell inhibition. To broadly explore the cell type-specific changes occurring during this critical window, we performed single cell RNA-seq on popliteal lymph nodes at 24 and 48 hours post-infection.
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2. ⭐ GSE309219 ECTV C15 表达对腘窝淋巴结早期免疫反应的影响（批量 RNA 测序）

• ✍️ 作者：未知作者
• 🏷️ 关键词：immune、lymph、regex:lymph(o|atic)?、RNA-seq
• 📝 描述：Contributors : Stephen D Carro ; Laurence C EisenlohrSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusOrthopoxviruses, such as variola and Mpox, encode a myriad of immunomodulatory proteins to promote pathogenesis. One notable family is the B22 family of proteins, which are highly conserved surface glycoproteins that potently inhibit T cell activation in vitro and ex vivo. Using the model poxvirus, ectromelia (ECTV), our lab has demonstrated that its B22 protein, C15, is capable of inhibiting both CD4+ and CD8+ T cells both in vitro and ex vivo, similar to other B22 proteins. Furthermore, we have also identified an additional function of C15: antagonism of NK cells during early infection. Specifically, C15 antagonizes the engagement of NK cells with infected cells in the popliteal lymph node during the innate immune response to infection. This inhibition by C15 promotes viral dissemination and replication, such that in the absence of C15, viral replication is significantly stunted. To date, there has not been any work investigating the mechanisms underlying this NK cell inhibition. To broadly explore the transcriptional changes occurring during this critical window, we performed bulk RNA-seq on popliteal lymph nodes at 48 hours post-infection.
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3. ⭐ GSE314735 全基因组甲基化分析揭示了健康、特应性和哮喘年轻供体中人类ILC2的表观遗传差异

• ✍️ 作者：未知作者
• 🏷️ 关键词：genome、epigenetic、methylation
• 📝 描述：Contributors : Stefan Floess ; Matthias Lochner ; Ayush Jain ; Elia C Diem ; Matthias Steglich ; Ruth Grychtol ; Anna-Maria DittrichSeries Type : Methylation profiling by high throughput sequencingOrganism : Homo sapiensDNA methylation of CpG motifs represents a stable epigenetic mark that critically influences the differentiation, stability and function of immune cell populations. Identifying differentially methylated regions within immune cell lineages contributes to their phenotypic and functional characterization, leading to a better understanding of lineage-specific transcriptional regulation. In this study, we performed a genome-wide methylation analysis of type 2 innate lymphoid cells (ILC2) from healthy (HE), atopic (AT) and asthmatic (AS) young individuals, to investigate inflammation-driven epigenetic changes during human development.
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4. ⭐ GSE313891 全基因组甲基化分析定义了人类固有淋巴细胞的表观遗传特征

• ✍️ 作者：未知作者
• 🏷️ 关键词：genome、epigenetic、methylation
• 📝 描述：Contributors : Stefan Floess ; Matthias Lochner ; Ayush Jain ; Chiawen Lu ; Elia C Diem ; Matthias SteglichSeries Type : Methylation profiling by high throughput sequencingOrganism : Homo sapiensDNA methylation of CpG motifs represents a stable epigenetic mark that critically influences the differentiation, stability and function of immune cell populations. Identifying differentially methylated regions within immune cell lineages contributes to their phenotypic and functional characterization, leading to a better understanding of lineage-specific transcriptional regulation. Here, we performed a genome-wide methylation analysis of human innate lymphoid cells (ILCs) isolated from tonsils and blood samples of healthy donors, which allowed us to define specific epigenetic marker regions for ILC1, ILC2 and ILC3.
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5. ⭐ GSE296426 染色质结构重编程揭示乳腺癌中新的表观遗传依赖性 [scRNA-seq]

• ✍️ 作者：未知作者
• 🏷️ 关键词：cancer、scRNA、epigenetic
• 📝 描述：Contributors : Liliana Garcia-Martinez ; Mengsheng Zha ; Rodrigo L Borges ; Tong Liu ; Gretter González-Blanco ; Hao Zhu ; Zheng Wang ; Lluis MoreySeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensChromatin architecture plays a key role in development and cancer, yet most studies lack mechanistic depth due to widespread epigenomic remodeling. To address this, we tracked chromatin structure dynamics during the progression of endocrine resistance in ER+ breast cancer using Hi-C, chromatin accessibility, epigenomic, and transcriptomic profiling. We uncovered a critical role for H3K9 methylation and the demethylase KDM4C in driving proliferation of cells fated to become resistant through a non-genomic estrogen-mediated mechanism. These findings highlight the mechanistic contribution of chromatin regulation in therapy resistance and offer a blueprint for studying similar processes in cancer, development, and cell fate decisions.
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6. ⭐ GSE296421 染色质结构重编程揭示乳腺癌中新的表观遗传依赖性 [ATAC-seq]

• ✍️ 作者：未知作者
• 🏷️ 关键词：cancer、ATAC-seq、epigenetic
• 📝 描述：Contributors : Liliana Garcia-Martinez ; Mengsheng Zha ; Rodrigo L Borges ; Tong Liu ; Gretter González-Blanco ; Hao Zhu ; Zheng Wang ; Lluis MoreySeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Homo sapiensChromatin architecture plays a key role in development and cancer, yet most studies lack mechanistic depth due to widespread epigenomic remodeling. To address this, we tracked chromatin structure dynamics during the progression of endocrine resistance in ER+ breast cancer using Hi-C, chromatin accessibility, epigenomic, and transcriptomic profiling. We uncovered a critical role for H3K9 methylation and the demethylase KDM4C in driving proliferation of cells fated to become resistant through a non-genomic estrogen-mediated mechanism. These findings highlight the mechanistic contribution of chromatin regulation in therapy resistance and offer a blueprint for studying similar processes in cancer, development, and cell fate decisions.
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7. ⭐ GSE324240 代谢辅因子辅酶 A 通过 MyD88 连接信号增强巨噬细胞的替代活化 [ATAC-seq]

• ✍️ 作者：未知作者
• 🏷️ 关键词：macrophage、metabolic、ATAC-seq
• 📝 描述：Contributors : Anthony E Jones ; Ajit S DivakaruniSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Mus musculusMetabolites and metabolic co-factors can shape the innate immune response, though the pathways by which these molecules adjust inflammation remain incompletely understood. Here we show that the metabolic cofactor Coenzyme A (CoA) enhances IL-4 driven alternative macrophage activation [M(IL-4)] in vitro and in vivo. Unexpectedly, we found that perturbations in intracellular CoA metabolism did not influence M(IL-4) differentiation. Rather, we discovered that exogenous CoA is a weak TLR4 agonist which primes macrophages for increased receptivity to IL-4 signals and resolution of inflammation via MyD88. Mechanistic studies revealed MyD88- linked signals enhance IL-4 responsiveness, in part, by reshaping chromatin accessibility to enhance transcription of IL-4-linked genes. The results identify CoA as a host metabolic co-factor that influences macrophage function through an extrinsic TLR4-dependent mechanism and suggest that damage-associated molecular patterns (DAMPs) can prime macrophages for alternative activation and resolution of inflammation.
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8. ⭐ GSE324239 代谢辅因子辅酶 A 通过 MyD88 连接信号增强巨噬细胞的替代活化 [RNA-seq]

• ✍️ 作者：未知作者
• 🏷️ 关键词：macrophage、metabolic、RNA-seq
• 📝 描述：Contributors : Anthony E Jones ; Ajit S DivakaruniSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusMetabolites and metabolic co-factors can shape the innate immune response, though the pathways by which these molecules adjust inflammation remain incompletely understood. Here we show that the metabolic cofactor Coenzyme A (CoA) enhances IL-4 driven alternative macrophage activation [M(IL-4)] in vitro and in vivo. Unexpectedly, we found that perturbations in intracellular CoA metabolism did not influence M(IL-4) differentiation. Rather, we discovered that exogenous CoA is a weak TLR4 agonist which primes macrophages for increased receptivity to IL-4 signals and resolution of inflammation via MyD88. Mechanistic studies revealed MyD88- linked signals enhance IL-4 responsiveness, in part, by reshaping chromatin accessibility to enhance transcription of IL-4-linked genes. The results identify CoA as a host metabolic co-factor that influences macrophage function through an extrinsic TLR4-dependent mechanism and suggest that damage-associated molecular patterns (DAMPs) can prime macrophages for alternative activation and resolution of inflammation.
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9. ⭐ GSE291920 多组学分析脑转移瘤揭示肥胖诱导的前列腺素在肿瘤微环境中的相互作用抑制 CD8T 细胞扩增（RNA-seq）

• ✍️ 作者：未知作者
• 🏷️ 关键词：tumor、tumor microenvironment、RNA-seq
• 📝 描述：Contributors : Zhanao Xu ; Yuekun WangSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensBrain metastasis (BrM) is one of the most crucial complications in tumor patients. Obesity contributes to the metabolic remodeling of tumor cells, yet the how obesity impact tumor microenvironment still remains unclear. We utilized RNA-seq on 115 tumor or peritumor samples in 81 patients to investigate obesity’s effect on BrM.
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10. GSE317174 RPSA-PPP1CA-AR-V7轴驱动前列腺癌去势抵抗和骨转移

• ✍️ 作者：未知作者
• 🏷️ 关键词：cancer、resistance
• 📝 描述：Contributors : Wenshuo Liu ; Wei Liu ; Jing Wan ; Xiaobei Zhou ; Wensu LiuSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensAndrogen is important in the formation, development and progress of prostate cancer, and deprivation of androgen, which is also named castration, is an effective way in prostate cancer therapies. For patients undergoing castration therapies, castration was gradually becoming ineffective in prostate cancer treatment and therefore resulting in castration-resistance for prostate cancer. Co-IP mass spectrometry, Ribo-seq, RNA-seq and system biology methods were applied to detect castration resistance drivers. Ribosomal drivers were found to be highly expressed and promoting invasion and migration in castration resistant prostate cancer cells and also in bone metastasis prostate cancer cells. Within these ribosomal drivers, RPSA played central roles in promoting castration resistance in assistance of RPL28, RPL4X, RPL11 and RPL23A. RPSA promotes castration resistance through interacting with PPP1CA and AR-V7 to form RPSA-PPP1CA-AR-V7 axis. This axis is bind by RPL23A and RPL28 and assisted by RPL4X. IGF-1 is also engaged in the process of promoting castration resistance and bone metastasis by RPSA-PPP1CA-AR-V7 axis. RPSA inhibitors plus PPP1CA inhibitors have also been proven to significantly restore castration resistance and bone metastasis for prostate cancer. This effect can be reversed by IGF-1 and retinoid acid. For these reasons, we propose that RPSA-PPP1CA-AR-V7 axis drives castration resistance and bone metastasis for prostate cancer.
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1. 特殊k：聚类中寻找最优k值的科学（或艺术）

• ✍️ 作者：未知作者
• 🏷️ 关键词：clustering
• 📝 描述：Download slides Cluster analysis is a statistical procedure for grouping observations using an observation-centered approach as compared to variable-centered approaches (e.g. PCA, factor analysis). As an unsupervised method true cluster mem… Continue reading: Special k: The Science (or Art) of Finding the Optimal k in Clustering
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1. 新型“超级抗生素”可在不破坏肠道菌群的情况下阻止致命的肠道感染

• ✍️ 作者：未知作者
• 🏷️ 关键词：gut、regex:gut(-?microbiome)?
• 📝 描述：A newly developed antibiotic called EVG7 could offer a powerful new way to stop Clostridioides difficile, a dangerous gut bacterium that often returns after treatment. In mouse studies, researchers found that even a very small dose of EVG7 was highly effective at clearing the infection and preventing it from coming back. Unlike many current antibiotics, which wipe out large portions of the gut microbiome, EVG7 appears to spare beneficial bacteria that naturally help keep C. difficile in check.
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2. 细菌无需螺旋桨即可传播的惊人新方式

• ✍️ 作者：未知作者
• 🏷️ 关键词：bacteria、regex:bacter(ia|ial|ium)
• 📝 描述：Scientists at Arizona State University have uncovered surprising new ways bacteria move, even without their usual whip-like propellers called flagella. In one study, E. coli and salmonella were found to spread across moist surfaces by fermenting sugars and creating tiny fluid currents that carry them forward — a newly identified behavior researchers call “swashing.” In another study, a different group of bacteria was shown to control its movement using a microscopic molecular “gearbox” that can reverse direction like a biological snowmobile.
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3. RNA测序技术的进步正在改进细胞谱系追踪和细胞命运决定重建。

• ✍️ 作者：未知作者
• 🏷️ 关键词：sequencing
• 📝 描述：Advances in lineage tracing combine experimental labeling with RNA sequencing and computational modeling to reconstruct cell fate decisions and developmental trajectories in complex tissues and disease systems…
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4. 一种令人惊讶的血液蛋白模式可能揭示阿尔茨海默病

• ✍️ 作者：未知作者
• 🏷️ 关键词：Alzheimer
• 📝 描述：A new study suggests Alzheimer’s disease may be detectable through subtle shape changes in proteins found in the blood. Researchers discovered that structural differences in three blood proteins closely track the progression of the disease. By analyzing these changes in more than 500 people, the team was able to distinguish healthy individuals from those with mild cognitive impairment or Alzheimer’s with impressive accuracy. The approach could help move diagnosis and treatment to earlier stages.
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5. 科学家将脑细胞转化为阿尔茨海默病斑块清除剂

• ✍️ 作者：未知作者
• 🏷️ 关键词：Alzheimer
• 📝 描述：Scientists have developed a promising new approach to treating Alzheimer’s disease by turning ordinary brain cells into powerful plaque-clearing machines. Instead of requiring frequent antibody infusions like current therapies, the experimental treatment uses genetically engineered astrocytes — abundant support cells in the brain — that are equipped with a CAR “homing device” similar to those used in cancer immunotherapy.
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6. 一种“镜像”分子可以在不损害健康细胞的情况下，使癌细胞营养匮乏。

• ✍️ 作者：未知作者
• 🏷️ 关键词：cancer
• 📝 描述：Scientists have discovered that a rare “mirror-image” version of the amino acid cysteine can dramatically slow the growth of certain cancers while leaving healthy cells largely untouched. Unlike most anticancer treatments that harm normal tissues, this molecule—called D-cysteine—is taken up mainly by some cancer cells through a specific transporter on their surface. Once inside, it shuts down a crucial mitochondrial enzyme that cancer cells rely on to produce energy and maintain DNA, effectively halting their growth.
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• GSE305437 DNTTIP1 通过 HDAC1 依赖的表观遗传沉默 BMF 驱动白血病发生 [RNA-Seq, 2]
• GSE305435 DNTTIP1 通过 HDAC1 依赖的表观遗传沉默 BMF 驱动白血病发生 [RNA-Seq, 1]
• GSE305428 DNTTIP1 通过 HDAC1 依赖的表观遗传沉默 BMF 驱动白血病发生 [ATAC-Seq]
• GSE303809 人类早期嗅觉发育的单细胞和空间图谱
• GSE300229 肥胖通过DNA甲基化影响CD4 T细胞，从而加剧免疫失调
• GSE300116 Ly6Ghigh 中性粒细胞亚群占据早期转移微环境，并通过抗菌肽诱导的 CD8+ T 细胞死亡决定乳腺癌肺转移_CD8+ T 细胞
• GSE300115 Ly6Ghigh 中性粒细胞亚群占据早期转移微环境，通过抗菌肽诱导的 CD8+ T 细胞死亡决定乳腺癌肺转移_中性粒细胞
• GSE313046 Galt基因编辑小鼠肝组织的单细胞RNA测序
• GSE292514 通过不同的免疫微环境形成实现肿瘤休眠的机制和鼠模型[D2A1]
• GSE292496 通过独特的免疫微环境形成实现肿瘤休眠的机制和鼠模型
• GSE324242 RNA 结合蛋白 Pcbp1 和 Pcbp2 对 B 细胞发育至关重要 [scRNA-seq ko]
• GSE324241 RNA结合蛋白Pcbp1和Pcbp2对B细胞发育至关重要[scRNA-seq]
• GSE324183 乳酸化将 ABHD6 转化为线粒体调节因子，从而驱动肝细胞癌的乐伐替尼耐药性
• GSE313190 无细胞 RNA 揭示了宿主和微生物与 HIV 广谱中和抗体产生相关的机制
• GSE291921 将阿尔茨海默病中脑血管重塑和功能障碍的轨迹与跨物种脑血管转录组联系起来
• GSE305431 DNTTIP1 通过 HDAC1 依赖的表观遗传沉默 BMF 驱动白血病发生 [Cut & Tag, RS4;11 , HA-DNTTIP1]
• GSE305430 DNTTIP1 通过 HDAC1 依赖的表观遗传沉默 BMF 驱动白血病发生 [Cut & Tag, RS4;11]
• GSE304300 主动脉瓣狭窄患者（包括透析患者和非透析患者）主动脉瓣的 RNA 测序
• GSE279616 宫内生长受限对发育中胰腺免疫系统的影响
• GSE318341 肠道拟杆菌驱动的阿拉伯木聚糖发酵可减轻炎症和代谢功能障碍
• GSE311812 先天性恰加斯病的免疫和修复机制
• GSE281852 小鼠胚胎成纤维细胞 (MEF) 复制性衰老中 m6A 修饰的转录组范围分析
• GSE281708 RNA G-四链体动力学通过DHX36介导的调控控制基因表达和基因组稳定性
• GSE264050 帕金森病（PD）在前额叶皮层成对半球样本神经元核中的遗传不对称性
• GSE244679 银屑病皮损及邻近正常皮肤组织的全转录组分析
• GSE228033 单细胞图谱揭示健康和患病人类胸腺的细胞异质性
• GSE324243 研究表明，在断奶羔羊的ST36穴位植入黄芪甲苷IV-甘草酸药物缓释缝线可通过调节Treg/Th17平衡来增强其免疫功能。
• GSE324175 产前发情信号程序在斑胸草雀胚胎脑中的DNA甲基化
• GSE291982 代谢相关性肝病（MASLD）中的酒精摄入
• GSE291097 肌动蛋白解聚加速多能性退出，增强干细胞衍生的胰岛分化 [scRNA-Seq]
• GSE314837 EHMT2介导的染色质重编程在5-氟尿嘧啶（5-FU）耐药性结直肠癌中的作用