详细内容（前10条）

1. ⭐ GSE319481 钠通道亚型多样性是心腔特异性兴奋性的基础 [空间转录组学]

• ✍️ 作者：未知作者
• 🏷️ 关键词：cardiac、spatial、spatial transcriptomics、transcriptomics
• 📝 描述：Contributors : Christian Anderson ; Omar Rabab’h ; Jared McLendonSeries Type : OtherOrganism : Mus musculusSodium channels are essential for cardiac conduction and excitability. The sodium current is primarily carried by the voltage gated sodium channel isoform NaV1.5. Using a novel NaV1.5 chimeric construct, our study reveals a unique chamber-specific distribution of non-NaV1.5 sodium channel isoforms, and we performed spatial sequencing of murine hearts to assess the transcriptional changes associated with our chimeric channel.
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2. ⭐ GSE296145 SPEN 缺失导致滤泡外弥漫性大 B 细胞淋巴瘤，该淋巴瘤具有女性特异性致死性和 TLR 通路治疗脆弱性。

• ✍️ 作者：未知作者
• 🏷️ 关键词：lymphoma、B cell、TLR、pathway
• 📝 描述：Contributors : Benedikt Pelzer ; Matt Teater ; Cem Meydan ; Ari M MelnickSeries Type : Expression profiling by high throughput sequencing ; Genome binding/occupancy profiling by high throughput sequencing ; OtherOrganism : Mus musculusIn this study, we explore the interplay between SPEN and NOTCH2 truncating mutations, identifying an alternative, extra-follicular, trajectory of diffuse large B cell lymphomas (DLBCL) transformation. Our findings challenge the traditional germinal centre-centric model of lymphomagenesis, showing that marginal zone B cells (MZB) can give rise to aggressive lymphomas with autoimmune/aged B cells (AiBC)-like features, under the influence of these compound mutations. At a mechanistic level, we found that SPEN loss re-routes NOTCH2-driven transcriptional programs, promoting a ZEB2-driven cell fate that blocks plasmacytic differentiation and skews B cell identity toward a MZB/AiBC mixed phenotype. We further show that SPENTRUNC/NOTCH2TRUNC-mutant lymphomas are associated with reduced overall survival of female DLBCL patients, due to X-chromosomal transcriptional perturbations. By characterizing their unique molecular dependencies, we identify actionable features in this aggressive DLBCL subset, paving the way for new precision medicine strategies that address the disease’s heterogeneity.
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3. ⭐ GSE327372 小鼠正常乳腺成纤维细胞 (mNFs) 和 MMTV-PyMT 癌相关成纤维细胞 (mCAF1) 的表观遗传分析 (H3K27ac ChIP-seq)

• ✍️ 作者：未知作者
• 🏷️ 关键词：cancer、ChIP-seq、epigenetic
• 📝 描述：Contributors : Miguel Juliá ; Fernando CalvoSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Mus musculusIn comparison with normal tissue fibroblast (normal fibroblasts, NFs), cancer-associated fibroblasts (CAFs) have pathologically activated phenotypes that impact in a wide variety of tumoral processes including cancer cell growth and invasion, extracellular matrix (ECM) remodelling, angiogenesis and immune suppression. These phenotypes result from the establishment of altered gene expression programs that may be further sustained through epigenetic alterations. However, how epigenetic rearrangements influence CAF behaviour is not well delineated. Here, we identify aspartoacylase (ASPA) as a metabolic enzyme consistently repressed in tumour stroma and CAFs. We report a reciprocal crosstalk between ASPA and Transforming Growth Factor Beta (TGFβ) signalling that influences fibroblast behaviour. TGFβ suppresses ASPA expression in fibroblasts, whereas ASPA restrains TGFβ-dependent myofibroblast conversion, ECM remodelling, angiogenesis and pro-tumoral macrophage phenotypes. TGFβ/SMAD3-dependent transcriptional repression may require the activity of histone deacetylases (HDACs), which participate in epigenetic rearrangements modulating gene expression. Epigenomic analysis of the 3’ regulatory regions at the Aspa locus in murine MMTV-PyMT-derived breast cancer CAFs (mCAF1) as compared to normal murine mammary gland fibroblasts (mNFs), revealed a selective loss of H3K27Ac, an epigenetic mark of active enhancers. As expected, bona fide CAF marker genes such as Acta2, Fap, Lrrc15 and others presented increased H3K27Ac signal at regulatory regions in mCAF1, whereas peaks at NF marker genes (Cxcl1 and Pi16) were decreased. Our findings unveil ASPA expression in fibroblasts as a previously unknown gatekeeper of TGFβ responses and activation in cancer progression.
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4. ⭐ GSE308260 小鼠胸腔内粘连的空间转录组学研究

• ✍️ 作者：未知作者
• 🏷️ 关键词：spatial、spatial transcriptomics、transcriptomics
• 📝 描述：Contributors : Tomohisa Sakaue ; Yu Mori ; Hironori IzutaniSeries Type : OtherOrganism : Mus musculusIntrathoracic adhesions (IAs) complicate thoracic surgery, causing risks such as bleeding, prolonged operative time, and postoperative air leakage. Severe adhesions (>10% pleura) often necessitate conversion from VATS to open thoracotomy due to dissection difficulties and pleural damage. Given the increasing role of lung segmentectomy and re-lobectomy for small or recurrent NSCLC, reoperations with IA are expected to rise, highlighting the need for effective IA prevention. This study aimed to establish such a murine IA model, evaluate pathological and gene expression changes, and identify targets to prevent lung–chest wall adhesions.
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5. GSE327170 皮肤驻留朗格汉斯细胞通过趋化因子依赖性神经元-免疫通讯驱动神经性疼痛

• ✍️ 作者：未知作者
• 🏷️ 关键词：immune、chemokine
• 📝 描述：Contributors : Pacifico Paola ; George Dale S. ; Jayaraj Nirupa D. ; Ren Dongjun ; Coy-Dibley James S ; Veronesi Sofia ; Baldamani Abdelhak ; Andelic Mirna ; Cartelli Daniele ; Devigili Grazia ; Lombardi Raffaella ; Lauria Giuseppe P ; Paller Amy S ; Miller Richard J ; Menichella Daniela MSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusSingle-cell RNA sequencing of paw epidermis from male and female C57BL/6J mice fed regular diet (RD) or high-fat diet (HFD) for 10 weeks, to investigate the role of Langerhans cells in painful diabetic neuropathy.
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6. GSE319426 钠通道亚型多样性是心腔特异性兴奋性的基础 [批量 RNA 测序]

• ✍️ 作者：未知作者
• 🏷️ 关键词：cardiac、RNA-seq
• 📝 描述：Contributors : Christian Anderson ; Jared M McLendonSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusSodium channels are essential for cardiac conduction and excitability. The sodium current is primarily carried by the voltage gated sodium channel isoform NaV1.5. Using a novel NaV1.5 chimeric construct (NaV1.5-GX), our study reveals a unique chamber-specific distribution of non-NaV1.5 sodium channel isoforms, and we performed bulk RNA sequencing of murine ventricles to assess if acute NaV1.5 inhibition changed the trascriptional profile of the ventricular myocytes.
• 🔗 查看原文

7. GSE300843 解析病毒感染过程中显性抗性基因的细胞类型特异性作用 [scRNA-Seq]

• ✍️ 作者：未知作者
• 🏷️ 关键词：resistance、scRNA
• 📝 描述：Contributors : Yuhong Zhang ; Shan Bu ; Luyou Wang ; Jiayi Liu ; Junchen Xu ; Jiejun Peng ; Fei Yan ; Jian WuSeries Type : Expression profiling by high throughput sequencingOrganism : Solanum lycopersicumPlant viruses cause widespread crop epidemics, with resistance (R) genes playing key roles in plant defense by triggering responses that limit viral replication and spread. However, given the diversity of plant cell types and their developmental paths, the specific roles of R genes in distinct cell types remain unclear. Using tomato brown rugose fruit virus (ToBRFV), which partially overcomes the tobamovirus resistance gene Tm-22, this study employed single-cell RNA sequencing to explore infection dynamics and Tm-22-mediated responses at the cellular level. Results indicated that upon ToBRFV infection, the Tm-22 gene and the tm-2 allele, which carries a recessive form of Tm-22, differentially regulate the composition of cell types in tomato leaves. Tm-22 does not fully inhibit viral entry or movement during the early stages but selectively restricts viral replication or accumulation in certain cell types. ToBRFV differentially modulates signaling pathways depending on cell type and genotype, including Tm-22 and tm-2 homozygotes. Pseudotime analysis revealed that during mesophyll cell development in Tm-22 plants, ToBRFV reverses expression of BR positive regulators, but not negative ones; silencing these BR positive regulators increased infection in Tm-22 plants while suppressing it in tm-2 plants, linking BR signaling to Tm-22-dependent resistance. This study offers the first cell-type-specific insight into R gene function, showing how Tm-22 restrains ToBRFV accumulation through BR signaling pathways. It provides a valuable framework for future single-cell investigations of resistance genes, enhancing our understanding of plant-virus interactions.
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8. GSE299489 LY6D 鉴定出驱动胰腺肿瘤发生的持续性肿瘤起始细胞 [ATAC-seq]

• ✍️ 作者：未知作者
• 🏷️ 关键词：tumor、ATAC-seq
• 📝 描述：Contributors : Juanjuan Shi ; Jing XueSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Mus musculusPancreatic ductal adenocarcinoma (PDAC) is a highly aggressive malignancy driven by oncogenic KRAS and inflammation-induced cellular heterogeneity, yet the mechanisms underlying tumor-initiating cells (TICs) emergence and maintenance remain unclear. Our study establishes LY6D as a marker of persistent TICs that orchestrate pancreatic cancer progression across all disease stages. Single-cell RNA sequencing of inflammation-driven PDAC models reveals that LY6D+ TICs specifically originate from KRAS-mutant acinar-to-ductal metaplasia (ADM) lesions under inflammatory conditions, maintaining conserved stemness properties and exhibiting a distinctive oxidative phosphorylation (OXPHOS) dependency throughout tumor evolution. Moreover, genetic ablation of Ly6d in KrasG12D pancreata delays tumorigenesis, while forced Ly6d expression enhances tumorigenic potential and metastatic capability. Mechanistically, LY6D-despite lacking intracellular domains-scaffolds lipid raft-associated kinase networks and FOSL1-dependent epigenetic reprogramming to establish a stable pro-tumorigenic state. Clinically, LY6D+ cells are enriched in human PDAC and exhibit conserved stemness and epithelial-mesenchymal transition (EMT) properties. Strikingly, LY6D expression levels demonstrate PDAC-restricted prognostic power. Our work defines LY6D as pan-stage TICs marker linking cellular plasticity to PDAC initiation and progression, offering new avenues for early detection and interception of this lethal malignancy.
• 🔗 查看原文

9. GSE299488 LY6D 鉴定出驱动胰腺肿瘤发生的持续性肿瘤起始细胞 [RNA-seq]

• ✍️ 作者：未知作者
• 🏷️ 关键词：tumor、RNA-seq
• 📝 描述：Contributors : Juanjuan Shi ; Jing XueSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusPancreatic ductal adenocarcinoma (PDAC) is a highly aggressive malignancy driven by oncogenic KRAS and inflammation-induced cellular heterogeneity, yet the mechanisms underlying tumor-initiating cells (TICs) emergence and maintenance remain unclear. Our study establishes LY6D as a marker of persistent TICs that orchestrate pancreatic cancer progression across all disease stages. Single-cell RNA sequencing of inflammation-driven PDAC models reveals that LY6D+ TICs specifically originate from KRAS-mutant acinar-to-ductal metaplasia (ADM) lesions under inflammatory conditions, maintaining conserved stemness properties and exhibiting a distinctive oxidative phosphorylation (OXPHOS) dependency throughout tumor evolution. Moreover, genetic ablation of Ly6d in KrasG12D pancreata delays tumorigenesis, while forced Ly6d expression enhances tumorigenic potential and metastatic capability. Mechanistically, LY6D-despite lacking intracellular domains-scaffolds lipid raft-associated kinase networks and FOSL1-dependent epigenetic reprogramming to establish a stable pro-tumorigenic state. Clinically, LY6D+ cells are enriched in human PDAC and exhibit conserved stemness and epithelial-mesenchymal transition (EMT) properties. Strikingly, LY6D expression levels demonstrate PDAC-restricted prognostic power. Our work defines LY6D as pan-stage TICs marker linking cellular plasticity to PDAC initiation and progression, offering new avenues for early detection and interception of this lethal malignancy.
• 🔗 查看原文

10. GSE299487 LY6D 鉴定出驱动胰腺肿瘤发生的持续性肿瘤起始细胞 [scRNA-seq]

• ✍️ 作者：未知作者
• 🏷️ 关键词：tumor、scRNA
• 📝 描述：Contributors : Juanjuan Shi ; Jing XueSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusPancreatic ductal adenocarcinoma (PDAC) is a highly aggressive malignancy driven by oncogenic KRAS and inflammation-induced cellular heterogeneity, yet the mechanisms underlying tumor-initiating cells (TICs) emergence and maintenance remain unclear. Our study establishes LY6D as a marker of persistent TICs that orchestrate pancreatic cancer progression across all disease stages. Single-cell RNA sequencing of inflammation-driven PDAC models reveals that LY6D+ TICs specifically originate from KRAS-mutant acinar-to-ductal metaplasia (ADM) lesions under inflammatory conditions, maintaining conserved stemness properties and exhibiting a distinctive oxidative phosphorylation (OXPHOS) dependency throughout tumor evolution. Moreover, genetic ablation of Ly6d in KrasG12D pancreata delays tumorigenesis, while forced Ly6d expression enhances tumorigenic potential and metastatic capability. Mechanistically, LY6D-despite lacking intracellular domains-scaffolds lipid raft-associated kinase networks and FOSL1-dependent epigenetic reprogramming to establish a stable pro-tumorigenic state. Clinically, LY6D+ cells are enriched in human PDAC and exhibit conserved stemness and epithelial-mesenchymal transition (EMT) properties. Strikingly, LY6D expression levels demonstrate PDAC-restricted prognostic power. Our work defines LY6D as pan-stage TICs marker linking cellular plasticity to PDAC initiation and progression, offering new avenues for early detection and interception of this lethal malignancy.
• 🔗 查看原文

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1. 开发者互动和生物导体

• ✍️ 作者：未知作者
• 🏷️ 关键词：Bioconductor
• 📝 描述：Introduction During the Chan Zuckerberg Institute’s Essential Open Source Software for Science cycle 6 funding round, the Bioconductor Community Manager, Maria Doyle, secured a grant to fund a developer engagement position for Bioconductor, and… Continue reading: Developer Engagement and Bioconductor
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2. Bioconductor 和 R-universe 在通用基础设施开发方面开展合作

• ✍️ 作者：未知作者
• 🏷️ 关键词：Bioconductor
• 📝 描述：This article is cross-posted on rOpenSci and R-Consortium blogs. For more than two decades, the Bioconductor project has been a cornerstone of the R ecosystem, providing high-quality, peer-reviewed tools for bioinformatics and computational biol… Continue reading: Collaborating between Bioconductor and R-universe on Development of Common Infrastructure
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1. ⭐ Caris Life Sciences宣布推出Caris ChromoSeq，这是全球首个针对髓系恶性肿瘤的全基因组和全转录组肿瘤分析检测方法。

• ✍️ 作者：未知作者
• 🏷️ 关键词：tumor、genome、transcriptome
• 📝 描述：Integrating RNA sequencing with whole genome analysis, Caris ChromoSeq delivers…
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2. 哪些人错过了癌症领域的下一代测序技术？

• ✍️ 作者：未知作者
• 🏷️ 关键词：cancer、sequencing
• 📝 描述：RNA sequencing and genomic profiling adoption is rising across cancers, yet disparities in access and delayed testing continue to limit timely precision oncology treatment decisions…
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• GSE315051 纳米孔直接RNA测序和Illumina RNA-seq分析成年小鼠皮层和背根神经节中TRP离子通道的表达
• GSE294391 聚ICLC疫苗佐剂对前列腺癌患者外周血单核细胞的影响
• GSE293124 CRC中KRAS抑制剂的遗传和非遗传耐药机制并存
• GSE327455 DYRK1A 通过 mTORC1 激活增强 1 型常规树突状细胞的抗肿瘤免疫力 [肿瘤浸润 1 型常规树突状细胞]
• GSE293065 侵袭性骨肉瘤的空间转录组图谱揭示了共同的基因表面表达和免疫图谱。
• GSE327332 JAX 研究 13 - 雄性 KOLF2.2J hiPSC 衍生内胚层和中胚层（十种不同转录因子的纯合缺失）的 RNA 测序
• GSE314392 吉非替尼治疗下肺癌细胞系 PC9 中 AGR2 的基因调控。
• GSE304511 组织和发育过程中DNA甲基化变异的遗传基础
• GSE301134 精神分裂症风险基因 XPO7 的缺失通过改变人类神经元中的 Na+ 通道动力学来破坏神经元兴奋性和网络规律性
• GSE299263 雌激素影响NOD2依赖的肠道稳态调节
• GSE326465 PI-5-P 连接 Hippo 通路和 PI5P4K 信号传导 [PIP4K2A/B shRNA]
• GSE313842 妊娠第17.5天FNDC5缺陷型和野生型小鼠胎盘的RNA测序
• GSE313383 LY6D 鉴定出驱动胰腺肿瘤发生的持续性肿瘤起始细胞
• GSE308503 幼稚或 CpG 刺激的 Rfx7 缺陷小鼠滤泡 B 细胞和 RFX7 转染的淋巴瘤人细胞系 U-2932 的转录组谱
• GSE305160 STAT4 驱动炎症性 ILC2 中 I 型干扰素通路的最佳扩增和转录抑制
• GSE304072 利用Arraystar微阵列技术分析弥漫性大B细胞淋巴瘤患者血浆外泌体环状RNA谱
• GSE301297 UTY 和 UTX 在调控多能性相关转录因子定位方面的功能冗余 [RNA-seq]
• GSE301296 UTY 和 UTX 在调控多能性相关转录因子定位方面的功能冗余 [ATAC-seq]
• GSE301294 UTY 和 UTX 在调控多能性相关转录因子定位方面的功能冗余 [ChIP-seq]
• GSE299913 SNCA 三倍体破坏人类中脑类器官神经退行性变之前的蛋白质稳态和细胞外结构 [RNA-seq]
• GSE298270 基于 CRISPR/Cas 的 PPARGC1A 激活可增强内源性线粒体功能，并改善心肌梗死后的心脏功能和恢复情况
• GSE297827 阻断脱嘌呤/脱嘧啶核酸内切酶与DNA二级结构G-四链体的相互作用可抑制三阴性乳腺癌转移
• GSE290491 脂联素受体激动剂 AdipoRON 对乳腺癌细胞系的影响
• GSE285558 人类腹侧脊髓类器官的单细胞RNA测序（由hESCs生成）
• GSE273442 3T3-L1脂肪细胞与MCF7乳腺肿瘤细胞共培养的影响。
• GSE269435 MyD88抑制剂对IL-33诱导的小鼠过敏性气道炎症的影响
• GSE268003 AML-PDX 加速 KMT2A 重排急性髓系白血病新型药物组合的开发
• GSE327108 Tet 调控肠道干细胞发育和稳态所需的转录程序
• GSE327000 RNA-seq 基因表达数据，用于研究 WH8102 型聚球藻在实验室 EFB 实验中连续高、中、低磷处理下的基因表达情况。
• GSE300596 一个拮抗性多效基因调控脊椎动物的生长、成熟和衰老
• GSE294305 抑制果糖转运蛋白 Glut5 通过扰乱小鼠睾丸间质细胞的代谢来促进雄激素的产生
• GSE293833 SOGA1缺陷对卵巢癌细胞基因表达的影响
• GSE243728 跨平台 Hi-C 荟萃分析鉴定出能够主动阻断增强子-启动子相互作用的功能性绝缘子。