详细内容（前10条）

1. ⭐ GSE327441 蓝斑核中黑皮质素通路基因的细胞特征 [空间转录组学]

• ✍️ 作者：未知作者
• 🏷️ 关键词：spatial、spatial transcriptomics、transcriptomics、pathway
• 📝 描述：Contributors : Alisha Basak ; Fahrünisa Meryem Betül Erol ; Maria Caterina De Rosa ; Zhangji Dong ; Victor Ogbolu ; Hannah J Glover ; Rick Rausch ; Gunnar Hargus ; Jordi Creus-Muncunill ; Heather Buchanan ; Yu Bai ; Qi Su ; Betty Chang ; Christina Adler ; Delaney Flaherty ; Benjamin Ciener ; Harrison Xiao ; Hasini Reddy ; Pascaline Aime-Wilson ; Christiane Reitz ; Mark W Sleeman ; Judith Y Altarejos ; Rudolph L Leibel ; Liang Oscar Qiang ; Andrew F Teich ; Claudia A DoegeSeries Type : OtherOrganism : Homo sapiensObesity and Alzheimer’s disease (AD) are epidemiologically associated. The locus coeruleus (LC) – the brain’s primary and most significant source of norepinephrine – is one of the earliest sites of neurodegeneration in AD. The LC participates in feeding behavior through connections with the hypothalamus. The cellular composition of the LC has been characterized at single-cell resolution. However, the constituent cellular signatures of genes related to energy homeostasis – such as the melanocortin pathway genes – in the LC are unclear. We performed single-nucleus RNA sequencing and spatial transcriptomics (Visium) in the human LC, and HiPlex RNAscope in the LC of mice. The melanocortin pathway gene MRAP2 was expressed in the majority of DBH neurons across the LC. Mrap2 was also co-expressed with AD-associated genes such as App, Psen1, Psen2, and Sorl1. More than 20% of Dbh neurons in the LC were positive for Mrap2, App, Psen1, and Psen2. Mrap2 is expressed in the central nervous system and modulates the trafficking and signaling of all five G-protein coupled receptors (GPCRs) of the melanocortin receptor family: Mc1r, Mc2r, Mc3r, Mc4r, and Mc5r. In mice, among the melanocortin receptors, Mc5r showed the highest co-expression with Mrap2, accounting for 17.9% of Mrap2-positive cells, followed by Mc2r with 10.9% of Mrap2-positive cells. Mc1r, Mc3r, and Mc4r showed very limited co-expression with Mrap2. Our study reveals that many Mrap2-positive cells do not express any melanocortin receptor genes, warranting future studies into metabolically relevant GPCRs downstream of MRAP2 in the LC. In summary, our study characterizes melanocortin molecular substrates in the human and mouse LC and highlights MRAP2 as a potential link between pathways of energy homeostasis and neurodegeneration.
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2. ⭐ GSE314875 H3K9二甲基化动态是小鼠次要合子基因组激活的基础[mESC的ChIP-seq]

• ✍️ 作者：未知作者
• 🏷️ 关键词：ChIP-seq、genome、methylation
• 📝 描述：Contributors : Ryo Maeda ; Makoto TachibanaSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Mus musculusMinor zygotic genome activation (ZGA) is crucial for early development and totipotency acquisition, yet the regulatory mechanisms driving minor ZGA genes remain elusive. Here we show that dynamic regulation of H3K9me2 is essential for minor ZGA. H3K9me2 levels at minor ZGA gene loci are reduced at early 2-cell and are re-established by morula. Maternal depletion of the H3K9 demethylases KDM3A and KDM3B leads to increased H3K9me2 and impaired minor ZGA in early 2-cell, followed by developmental arrest at 2- to 4-cell. In mESCs, H3K9 at minor ZGA loci is highly di-methylated; combined loss of the H3K9 methyltransferases G9a and SETDB1 leads to synergistic de-repression of minor ZGA genes. Mechanistically, SETDB1 specifically targets Dux, while G9a broadly represses minor ZGA genes through H3K9 di-methylation linked to lamina-associated heterochromatin formation. These findings establish H3K9me2 dynamics as a key regulator for minor ZGA, highlighting the indispensable role of epigenetic control in early embryogenesis.
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3. ⭐ GSE297574 H3K9二甲基化动态是小鼠次要合子基因组激活的基础[mESC的spike-in ChIP-seq]

• ✍️ 作者：未知作者
• 🏷️ 关键词：ChIP-seq、genome、methylation
• 📝 描述：Contributors : Ryo Maeda ; Makoto TachibanaSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Mus musculusMinor zygotic genome activation (ZGA) is crucial for early development and totipotency acquisition, yet the regulatory mechanisms driving minor ZGA genes remain elusive. Here we show that dynamic regulation of H3K9me2 is essential for minor ZGA. H3K9me2 levels at minor ZGA gene loci are reduced at early 2-cell and are re-established by morula. Maternal depletion of the H3K9 demethylases KDM3A and KDM3B leads to increased H3K9me2 and impaired minor ZGA in early 2-cell, followed by developmental arrest at 2- to 4-cell. In mESCs, H3K9 at minor ZGA loci is highly di-methylated; combined loss of the H3K9 methyltransferases G9a and SETDB1 leads to synergistic de-repression of minor ZGA genes. Mechanistically, SETDB1 specifically targets Dux, while G9a broadly represses minor ZGA genes through H3K9 di-methylation linked to lamina-associated heterochromatin formation. These findings establish H3K9me2 dynamics as a key regulator for minor ZGA, highlighting the indispensable role of epigenetic control in early embryogenesis.
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4. ⭐ GSE296993 H3K9二甲基化动态是小鼠次要合子基因组激活的基础[mESC的RNA测序]

• ✍️ 作者：未知作者
• 🏷️ 关键词：RNA-seq、genome、methylation
• 📝 描述：Contributors : Ryo Maeda ; Makoto TachibanaSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusMinor zygotic genome activation (ZGA) is crucial for early development and totipotency acquisition, yet the regulatory mechanisms driving minor ZGA genes remain elusive. Here we show that dynamic regulation of H3K9me2 is essential for minor ZGA. H3K9me2 levels at minor ZGA gene loci are reduced at early 2-cell and are re-established by morula. Maternal depletion of the H3K9 demethylases KDM3A and KDM3B leads to increased H3K9me2 and impaired minor ZGA in early 2-cell, followed by developmental arrest at 2- to 4-cell. In mESCs, H3K9 at minor ZGA loci is highly di-methylated; combined loss of the H3K9 methyltransferases G9a and SETDB1 leads to synergistic de-repression of minor ZGA genes. Mechanistically, SETDB1 specifically targets Dux, while G9a broadly represses minor ZGA genes through H3K9 di-methylation linked to lamina-associated heterochromatin formation. These findings establish H3K9me2 dynamics as a key regulator for minor ZGA, highlighting the indispensable role of epigenetic control in early embryogenesis.
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5. ⭐ GSE296992 H3K9二甲基化动态是小鼠次要合子基因组激活的基础[早期胚胎RNA测序]

• ✍️ 作者：未知作者
• 🏷️ 关键词：RNA-seq、genome、methylation
• 📝 描述：Contributors : Ryo Maeda ; Shunsuke Kuroki ; Azusa Inoue ; Makoto TachibanaSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusMinor zygotic genome activation (ZGA) is crucial for early development and totipotency acquisition, yet the regulatory mechanisms driving minor ZGA genes remain elusive. Here we show that dynamic regulation of H3K9me2 is essential for minor ZGA. H3K9me2 levels at minor ZGA gene loci are reduced at early 2-cell and are re-established by morula. Maternal depletion of the H3K9 demethylases KDM3A and KDM3B leads to increased H3K9me2 and impaired minor ZGA in early 2-cell, followed by developmental arrest at 2- to 4-cell. In mESCs, H3K9 at minor ZGA loci is highly di-methylated; combined loss of the H3K9 methyltransferases G9a and SETDB1 leads to synergistic de-repression of minor ZGA genes. Mechanistically, SETDB1 specifically targets Dux, while G9a broadly represses minor ZGA genes through H3K9 di-methylation linked to lamina-associated heterochromatin formation. These findings establish H3K9me2 dynamics as a key regulator for minor ZGA, highlighting the indispensable role of epigenetic control in early embryogenesis.
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6. ⭐ GSE296375 经典恐惧条件反射后小脑基因表达的区域和细胞类型特异性变化 [空间转录组学]

• ✍️ 作者：未知作者
• 🏷️ 关键词：spatial、spatial transcriptomics、transcriptomics
• 📝 描述：Contributors : Jungeun Ji ; Jinhee Baek ; Kyoung-Doo Hwang ; Seunghwan Choi ; Junko Kasuya ; Ted Abel ; Joon-Yong An ; Yong-Seok LeeSeries Type : OtherOrganism : Mus musculusThe cerebellum has recently been recognized for its role in non-motor functions, including classical fear conditioning. However, the molecular mechanisms underlying non-motor learning and memory remain largely unknown. Here, we investigate the transcriptional changes in the cerebellum associated with auditory fear conditioning. Spatial transcriptomic analysis revealed that in the deep cerebellar nuclei (DCN), an output region of the cerebellum, the expression of immediate early genes increased following fear learning and retrieval, suggesting that DCN may contribute to fear memory processing. As for the cerebellar cortex, robust and region-specific transcriptional changes were observed, with distinct expression patterns emerging across the Purkinje cell layer of vermis region. To further elucidate transcriptional changes in specific DCN cell types involved in fear processing, we performed single-nucleus RNA sequencing and identified prominent gene expression changes in Kit+ inhibitory neurons. Collectively, our findings highlight region- and cell-type-specific molecular adaptations in the cerebellum, providing insights into its contribution to non-motor learning.
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7. GSE296994 H3K9二甲基化动态是小鼠次要合子基因组激活的基础

• ✍️ 作者：未知作者
• 🏷️ 关键词：genome、methylation
• 📝 描述：Series Type : Expression profiling by high throughput sequencing ; Genome binding/occupancy profiling by high throughput sequencingOrganism : Mus musculusThis SuperSeries is composed of the SubSeries listed below.
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8. GSE296991 H3K9二甲基化动态是小鼠次要合子基因组激活的基础[早期胚胎的CATCH-seq]

• ✍️ 作者：未知作者
• 🏷️ 关键词：genome、methylation
• 📝 描述：Contributors : Ryo Maeda ; Shunsuke Kuroki ; Masahiro Matsuwaka ; Azusa Inoue ; Makoto TachibanaSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Mus musculusMinor zygotic genome activation (ZGA) is crucial for early development and totipotency acquisition, yet the regulatory mechanisms driving minor ZGA genes remain elusive. Here we show that dynamic regulation of H3K9me2 is essential for minor ZGA. H3K9me2 levels at minor ZGA gene loci are reduced at early 2-cell and are re-established by morula. Maternal depletion of the H3K9 demethylases KDM3A and KDM3B leads to increased H3K9me2 and impaired minor ZGA in early 2-cell, followed by developmental arrest at 2- to 4-cell. In mESCs, H3K9 at minor ZGA loci is highly di-methylated; combined loss of the H3K9 methyltransferases G9a and SETDB1 leads to synergistic de-repression of minor ZGA genes. Mechanistically, SETDB1 specifically targets Dux, while G9a broadly represses minor ZGA genes through H3K9 di-methylation linked to lamina-associated heterochromatin formation. These findings establish H3K9me2 dynamics as a key regulator for minor ZGA, highlighting the indispensable role of epigenetic control in early embryogenesis.
• 🔗 查看原文

9. GSE328250 左心房结扎后心脏神经嵴细胞的单细胞RNA测序

• ✍️ 作者：未知作者
• 🏷️ 关键词：cardiac、scRNA
• 📝 描述：Contributors : Stephanie E Lindsey ; Robert Porter ; Aining FanSeries Type : Expression profiling by high throughput sequencingOrganism : Gallus gallusWe have employed a single cell sequencing approach using 10x Genomics scRNAseq to study the affect of altered hemodynamic patterning on cardac neural crest cells (CNCCs). CNCCs play an important role in tunica media formation of the great vessels, cardiac septation, and contribute to cardiomyocytes of he ventricle.
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10. GSE328112 非肌层浸润性膀胱癌 (NMIBC) 肿瘤的 RNA-seq 分析

• ✍️ 作者：未知作者
• 🏷️ 关键词：cancer、RNA-seq
• 📝 描述：Contributors : Robert T Lawrence ; Joseph D DekkerSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensBulk RNA-seq was performed on fresh-frozen non-muscle invasive bladder cancer (NMIBC) tumor biopsies obtained from commercial biobanks (BioIVT and Proteogenex). These data were generated to characterize the transcriptomic landscape of NMIBC tumors and support preclinical studies of integrin beta-6 (ITGB6)-targeted therapies. RNA was extracted from 25 untreated surgical specimens and sequenced using paired-end Illumina sequencing by Azenta Life Sciences.
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💡 该来源还有 22 条内容，详见 文末

• GSE327509 研究发现，白屈菜素通过与 STING 结合并抑制 STING/NFκB 介导的炎症反应，减轻血管紧张素 II 诱导的病理性心脏肥大。
• GSE325517 Cg12712415 位点的甲基化抑制 TAK1 表达，从而介导重症肺炎中的免疫麻痹
• GSE325391 健康衰老、阿尔茨海默病和认知韧性中成年人未成熟神经元的独特转录谱
• GSE318514 系统性自身免疫中的器官损伤是由源自引流淋巴结的干细胞样CD8 T细胞介导的
• GSE275308 血流调节后斑马鱼胚胎和人主动脉内皮细胞的单细胞RNA测序（scRNA-seq）
• GSE325126 CD5L 促进吞噬细胞清除淀粉样β寡聚体，并改善阿尔茨海默病小鼠模型的认知功能 [RNA-Seq]
• GSE309251 研究发现，西方饮食诱导的 PWK/PhJ 小鼠发生 MASH 后，氨基酸和鞘脂代谢紊乱，导致心脏功能障碍。
• GSE324772 黑岩鱼（Sebastes schlegelii）卵巢间质在不同生殖状态下的单细胞图谱
• GSE328169 CRISP 能够比较十个器官中基于图像的空间转录组分割质量
• GSE327675 利用ChIP-seq分析HBV DNA上XRCC5/6的分布
• GSE327442 蓝斑中黑皮质素通路基因的细胞特征 [snRNA-seq]
• GSE311311 UBA1-CDK16：一种在进化过程中出现并参与免疫调节的女性特异性嵌合RNA
• GSE294444 果蝇 16S rDNA 扩增子测序与年龄依赖性睡眠片段化相关
• GSE294309 果蝇头部和身体的 RNA-seq 与年龄依赖性睡眠碎片化相关
• GSE294159 果蝇头部 RNA-seq 数据揭示了位置偏好的差异
• GSE324992 CD5L促进吞噬细胞清除淀粉样β寡聚体，并改善阿尔茨海默病小鼠模型的认知功能
• GSE322787 皮肤-下丘脑轴将热应激和代谢功能障碍联系起来
• GSE311757 巴伐宁抑制口腔鳞状细胞癌的生长和转移
• GSE311226 正常血糖、糖尿病前期和 2 型糖尿病患者全血 DNA 的基线和随访甲基化谱分析
• GSE306599 DNA-PK 介导的 CRTC2 磷酸化促进 CRTC2 从转录到修复复合物的转移，增强 NHEJ 并抑制远隔效应 [RNA-Seq]
• GSE294511 结直肠癌肝转移瘤类器官的基因表达谱分析。
• GSE282001 D4-MASLD 和 D5-MASLD 饮食对大鼠的影响：与人类 MASLD 相似的通路改变