详细内容（前10条）

1. ⭐ GSE304727 小鼠和人类肿瘤相关树突状细胞的泛癌单细胞图谱

• ✍️ 作者：未知作者
• 🏷️ 关键词：tumor、cancer、single-cell
• 📝 描述：Contributors : Daliya Kancheva ; Caro Aarushi ; Laoui DamyaSeries Type : Other ; Expression profiling by high throughput sequencingOrganism : Mus musculusDendritic cells (DCs) are critical inducers of anti-tumor immunity. Yet, a comprehensive mapping of mouse and human DC subsets and states in a cancer context is lacking. Aiming to address this knowledge gap, we have generated pan-cancer mouse and human tumor-associated DC (TADC) scRNA-seq atlases, encompassing 15 mouse tumor models and 10 human cancer types, within which we identified several lineage-defined DC subsets along with functional states. We show that TADCs acquire an inflammatory profile with tumor progression and that tumor-mediated reprogramming occurs within the DCs from lymph nodes of tumor-bearing mice. Importantly, we demonstrate that TADCs are conserved across mice and human, and that gene signatures of different TADC subsets/states correlate with patient outcomes. Overall, we provide an in-depth characterization of the TADC compartment in mouse and human cancers, which can improve our understanding of the tumor microenvironment and contribute to the development of new anti-cancer therapies.
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2. GSE319599 通过分析循环 miRNA 和整体 DNA 甲基化，研究职业性接触挥发性麻醉剂的兽医的表观遗传学特征

• ✍️ 作者：未知作者
• 🏷️ 关键词：epigenetic、methylation
• 📝 描述：Contributors : Tony Fernando Grassi ; Mariane Aparecida Pereira Silva ; Maria Vitória Destro ; Iael Weissberg Minutentag ; Patrícia Pintor dos Reis ; Bruno Spinosa De Martinis ; Mónica Cappetta ; Leandro Gobbo Braz ; Mariana Gobbo BrazSeries Type : Non-coding RNA profiling by arrayOrganism : Homo sapiensOccupational exposure to waste anesthetic gases (WAGs) in veterinary operating rooms represents a potential health concern due to limited environmental monitoring. In this study, plasma samples from veterinarians chronically exposed to isoflurane and sevoflurane and from matched unexposed controls were analyzed to investigate molecular alterations associated with WAG exposure. Circulating microRNA expression was profiled using the NanoString nCounter® Human v3 miRNA Expression Assay. Differential expression analysis was performed to identify miRNAs associated with occupational exposure. Additional bioinformatic analyses were conducted to explore the potential biological pathways related to the identified miRNAs.
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3. GSE311002 绘制原始巨噬细胞胞外囊泡的 miRNA 图谱，突显其在工程化人类心脏组织中的促血管生成作用

• ✍️ 作者：未知作者
• 🏷️ 关键词：macrophage、cardiac
• 📝 描述：Contributors : Karl T Wagner ; Shira Landau ; Gregory M Kent ; David F Bodenstein ; Milica RadisicSeries Type : Non-coding RNA profiling by high throughput sequencingOrganism : Homo sapiensResident cardiac macrophages, derived from primitive yolk sac precursors during embryogenesis, have increasingly been recognized for their distinct phenotype and functions in regulating homeostasis of the human heart. However, the profile of their extracellular vesicles (EVs) in cardiac signalling and regulation remains uncharted. Here, we employ differentiation of human pluripotent stem cell (hPSC)-derived primitive macrophages (Mac) for isolation of their secreted EVs and in-depth characterization of EV-miRNA cargo. Primitive macrophages secreted nanoscale EVs that expressed canonical EV markers, and miRNA sequencing highlighted a diverse and unique profile of miRNAs when compared to EVs sourced from other principal cardiac cell lineages and published data from monocyte-derived cells. In particular, we noted the abundance and enrichment of vascular-modulatory let-7 miRNAs and miR-126-3p. Functional screening of Mac-EVs in a 3D model of in vitro cardiac vasculogenesis confirmed enhanced early endothelial cell organization and branching. Establishing a reference for the human Mac-EV miRNome enables further hypothesis-driven mechanistic tests of Mac-EV miRNAs in mediating cardiac physiology and disease, opening the door to identification of therapeutic targets and modalities for cardiac repair.
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4. GSE320160 Optineurin 调节 mTORC2/AKT/STAT3 信号通路以控制 MHC II 表达和针对 HSV-1 的适应性免疫

• ✍️ 作者：未知作者
• 🏷️ 关键词：immunity、MHC
• 📝 描述：Contributors : Rashmi Kadam ; Deepak Shukla ; Leonid Feferman ; Mark Maienschein-Cline ; George ChlipalaSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusHerpes simplex virus 1 (HSV-1) infection contributes to immunopathogenic diseases and lacks an effective vaccine. Improving antigen presentation is key to better vaccine strategies and more robust immune responses. Here, we show that OPTN, an autophagy receptor traditionally involved in protein recycling, unexpectedly stabilizes RICTOR (mTORC2), a crucial step in enhancing MHC-II surface expression in dendritic cells. OPTN regulates the AKT/mTOR/STAT3 pathway, with AKT2 isoform playing a central role. Using scRNA-seq and transgenic mouse models, we identify the mechanistic details of this pathway. Dysregulation impairs antigen presentation, weakening immunity and vaccine efficacy. Our findings uncover a novel function for OPTN and highlight its role in coordinating innate and adaptive immune defenses, with implications for vaccine development and immune response modulation in HSV-1 and other viral and bacterial diseases.
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5. GSE286038 BRD8 是克服 HR+/HER2+ 乳腺癌对 ER/HER2 双重阻断疗法耐药性的治疗靶点

• ✍️ 作者：未知作者
• 🏷️ 关键词：cancer、resistance
• 📝 描述：Contributors : Ang Gao ; Parth H Khatri ; Huy Q Dinh ; Wei XuSeries Type : Genome binding/occupancy profiling by high throughput sequencing ; Expression profiling by high throughput sequencingOrganism : Homo sapiensHormone receptor (HR)-positive, HER2-positive breast cancers often develop resistance to endocrine and anti-HER2 therapies due to the heterogeneous expression of estrogen receptor (ER) and HER2 and the crosstalk of these growth-promoting pathways. However, how anti-HER2 agents activate ER and other growth-promoting pathways remains unknown. Single-cell RNA sequencing of BT474 breast cancer cells identified Bromodomain Containing Protein 8 (BRD8), an acetyl-lysine reader protein in the histone acetylase EP400 complex, as a pivotal mediator to activate ER in response to neratinib treatment. BRD8 expression was rapidly induced by various anti-HER2 agents (neratinib, lapatinib, and trastuzumab), and its depletion disrupted the crosstalk between ER and HER2 signaling pathways and rendered HR+/HER2+ cells and tumor organoids more sensitive to anti-HER2 agents. BRD8, ER, and ER target genes are co-induced by neratinib in single-nucleus (sn) RNA sequencing of a patient-derived xenograft (PDX). Concomitantly, SnATAC-seq reveals that the activated genes share open chromatin regions enriched in transcription factors (TF) binding motifs of ER, forkhead box (FOX), and ETS family. Since EP400 enhances H2AZ deposition and acetylation on chromatin, we performed H2AZ and H2AZac ChIP-sequencing in the presence or absence of BRD8 and neratinib treatment. Upon neratinib treatment, BRD8 activates ER, FOX, and ETS target genes through modulating H2AZac deposition and chromatin decompaction. This finding coincides with RNA-sequencing, where BRD8 promotes cell growth in an ER-dependent and independent manner. In line with these findings, patients who responded poorly to the anti-HER2 therapies exhibited higher BRD8 gene signatures. Furthermore, BRD8 knockdown ablates the ER and HER2 signaling crosstalk and re-sensitizes neratinib-resistant HR+/HER2+ cells to neratinib. Together, this work not only explains why ER signaling is activated upon anti-HER2 therapies but also identifies BRD8 as a druggable vulnerability in HR+/HER2+ breast cancer.
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6. GSE283036 BRD8 是克服 HR+/HER2+ 乳腺癌对 ER/HER2 双重阻断疗法耐药性的治疗靶点

• ✍️ 作者：未知作者
• 🏷️ 关键词：cancer、resistance
• 📝 描述：Series Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Homo sapiensHormone receptor (HR)-positive, HER2-positive breast cancers often develop resistance to endocrine and anti-HER2 therapies due to the heterogeneous expression of estrogen receptor (ER) and HER2 and the crosstalk of these growth-promoting pathways. However, how anti-HER2 agents activate ER and other growth-promoting pathways remains unknown. Single-cell RNA sequencing of BT474 breast cancer cells identified Bromodomain Containing Protein 8 (BRD8), an acetyl-lysine reader protein in the histone acetylase EP400 complex, as a pivotal mediator to activate ER in response to neratinib treatment. Since EP400 enhances H2AZ deposition and acetylation on chromatin, we performed H2AZ and H2AZac ChIP-sequencing in the presence or absence of BRD8 and neratinib treatment. This will help us address how BRD8 regulates ER as well as other growth factors.
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7. GSE230328 BRD8 是克服 HR+/HER2+ 乳腺癌对 ER/HER2 双重阻断疗法耐药性的治疗靶点

• ✍️ 作者：未知作者
• 🏷️ 关键词：cancer、resistance
• 📝 描述：Series Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensThis SuperSeries is composed of the SubSeries listed below.
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8. GSE321682 miR-99b-5p抑制驱动三阴性乳腺癌细胞凋亡和肿瘤缩小：基于AGO2-RIP-seq的功能表征和机制研究

• ✍️ 作者：未知作者
• 🏷️ 关键词：tumor、cancer
• 📝 描述：Contributors : Senem Noyan ; Kubra N Kaplan-Ilhan ; Muge O Demirtas ; Begum Dalli ; Bora Ergin ; Rabia Sen ; Hakan Gurdal ; Bala G DedeogluSeries Type : OtherOrganism : Homo sapiensBackground: Dysregulated microRNAs (miRNAs) are critical contributors to breast cancer biology, yet the functional roles of many remain incompletely understood. miR-99b-5p has been widely characterized as a tumor-suppressive miRNA in numerous cancer types, where its expression is consistently reduced in tumors compared with normal tissues. In contrast, our analyses of breast cancer datasets revealed a unique expression pattern: miR-99b-5p is significantly upregulated in breast tumors, suggesting a context-dependent oncogenic function. In this study, we identified miR-99b-5p as an oncogenic driver in triple-negative breast cancer (TNBC). Methods and Results: TCGA-based expression profiling confirmed its elevated levels in breast tumors. Functional assays demonstrated that downregulation of miR-99b-5p in TNBC cells inhibits proliferation and induces apoptosis, indicating a critical role in sustaining tumor cell survival. To elucidate the molecular mechanisms underlying this activity, we performed AGO2-RNA immunoprecipitation followed by high-throughput sequencing (AGO2-RIP-Seq), enabling unbiased identification of miR-99b-5p-associated transcripts. Pathway enrichment analyses revealed that its direct targets converge on apoptotic regulation, cell-cycle control, and ubiquitin-mediated protein degradation. Mechanistic validation through qRT-PCR, Western blotting, and luciferase assays confirmed that miR-99b-5p modulates the TRAIL-R signaling pathway via DR5 and BAK, attenuating apoptotic signaling. In vivo studies using xenograft models established with MDA-MB-231 cells stably expressing miR-99b-5p knockdown showed marked tumor regression, further supporting its oncogenic role. Conclusion: Collectively, these findings establish miR-99b-5p as a context-specific oncogenic miRNA in breast cancer and a promising therapeutic target, particularly for TNBC, where targeted treatment options remain limited.
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9. GSE312007 新一代测序促进了对 Ddx21 在造血干细胞中的作用进行定量分析 [RNA-seq]

• ✍️ 作者：未知作者
• 🏷️ 关键词：sequencing、RNA-seq
• 📝 描述：Contributors : Yalan Xiao ; Zhigang Li ; Yu HouSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusHematopoietic stem cell (HSC) homeostasis is critically dependent on precisely regulated protein synthesis, with the nucleolus serving as the principal orchestrator of ribosome biogenesis and cellular stress sensing. DDX21, a nucleolus-localized DEAD-box RNA helicase, serves as a master regulator in ribosomal DNA (rDNA) transcription and ribosome assembly. Nevertheless, its precise function in adult hematopoiesis remains incompletely understood. Here, we reveal that conditional knockout of Ddx21 in the murine hematopoietic system triggers collapse of HSC homeostasis, characterized by loss of quiescence, impaired self-renewal capacity, and raised apoptosis. Mechanistically, we demonstrate that DDX21 physically associates with both rDNA loci and promoters of ribosomal protein genes. Its loss disrupts ribosome production, causes nucleolar stress, culminates in p53-mediated cell cycle arrest and apoptosis in HSPCs. Taken together, our study establishes DDX21 as a master regulator in HSCs, integrating ribosome biogenesis with nucleolar stress induction and hematopoietic homeostasis.
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10. GSE325364 PAF1 N 端延伸产生的 PAF1c-SKIP-CDKB 模块调控植物界的植物特异性细胞周期 [RNA-seq]

• ✍️ 作者：未知作者
• 🏷️ 关键词：RNA-seq
• 📝 描述：Contributors : Yan Li ; Renshen YuanSeries Type : Expression profiling by high throughput sequencingOrganism : Chlamydomonas reinhardtiiThrough systematic biochemical analyses, we identified a novel protein-protein interaction between PAF1 and SKIP in Chlamydomonas reinhardtii. To investigate the functional significance of this interaction, we generated targeted mutants using CRISPR-Cas9 genome editing technology. Phenotypic characterization revealed that both PAF1 and SKIP mutants exhibit coordinated regulation of the cell cycle progression. To elucidate the molecular mechanism underlying PAF1-SKIP mediated cell cycle regulation, we employed an integrated multi-omics approach. RNA sequencing (RNA-seq) analysis was performed to identify differentially expressed genes, while chromatin immunoprecipitation sequencing (ChIP-seq) was utilized to map the genomic loci directly bound by the PAF1-SKIP protein complex. This comprehensive strategy enabled us to delineate the transcriptional network governed by the PAF1-SKIP regulatory module.
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1. 牙龈疾病细菌与乳腺癌的生长和扩散有关

• ✍️ 作者：未知作者
• 🏷️ 关键词：cancer、regex:bacter(ia|ial|ium)
• 📝 描述：A common oral bacterium tied to gum disease may help spark and fuel breast cancer, according to new research. Scientists discovered it can travel through the bloodstream to breast tissue, where it causes DNA damage and speeds tumor growth and spread. It also appears to make cancer cells more aggressive and resistant to therapy. The effect is even stronger in people with BRCA1 mutations, raising new questions about the role of oral health in cancer risk.
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2. 利用基于测序的分析方法绘制突变驱动的RNA药物相互作用图谱

• ✍️ 作者：未知作者
• 🏷️ 关键词：sequencing
• 📝 描述：RNA sequencing reveals how single mutations alter RNA structure and small molecule binding, enabling detection of variant-specific interactions that may guide development of…
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• GSE324486 CapMux：一个用于将拆分池单细胞RNA测序数据早期解复用为样本解析输出的Snakemake流程
• GSE308833 PRSS22 缺失对 HCT116 结直肠癌细胞基因表达的影响
• GSE305349 IDHwt胶质母细胞瘤的表观遗传演化
• GSE295863 翻译组分析揭示急性和慢性疼痛中脊髓星形胶质细胞代谢的改变
• GSE288233 Caspase-8抑制由持续性TNF-α驱动的、不依赖于细胞死亡的组成型免疫激活
• GSE266019 通过 tRNA 测序对 HEK293T 细胞中的转移 RNA 进行定量分析
• GSE312657 小鼠小脑中Tox3依赖性基因表达的单核RNA测序分析
• GSE312655 RNA测序分析小鼠小脑中Tox3依赖性基因的表达
• GSE300399 CNS1 在塑造 CD4+ T 细胞和 Treg 对流感的反应中的作用
• GSE283815 WRI1 和 DGAT1 过表达对菥蓂胚胎发育过程中脂质代谢的影响
• GSE324926 GLS1 通过谷氨酸代谢调控血管平滑肌细胞表型转换和主动脉夹层
• GSE323969 RNA 结合蛋白 TRA2B 通过调节 Dicer 依赖的 miRNA 生物合成促进结肠癌进展。
• GSE322740 动力蛋白相关蛋白 AoVps1 与 AoMdv1 形成复合物介导线粒体分裂，这对于寡孢节丛孢菌的线粒体形态、线粒体自噬、分生孢子形成、陷阱形成和能量代谢至关重要。
• GSE316200 Nrf1 协调蛋白酶体和自噬以维持心脏蛋白质稳态
• GSE314077 B细胞受体-mTOR信号通路限制流感感染后肺组织驻留记忆B细胞的积累
• GSE310426 对照和DDX21缺陷造血干细胞染色质状态的全基因组图谱[CUT&Tag]
• GSE292573 线粒体-溶酶体偶联导致溶酶体酸化和衰老
• GSE266265 子宫内膜异位症洞察：通过单细胞分析和人工智能预测揭示子宫内膜异位症
• GSE262992 慢性应激通过抑制 Ascl1 表达诱导海马神经干细胞静止 [RNA-seq]
• GSE262365 ZNF638 通过 HUSH 复合物表观遗传沉默抑制 HBV 共价闭合环状 DNA 转录
• GSE228457 IL-7 介导的免疫调节反馈回路促进低炎症单核细胞抑制免疫效应功能。
• GSE228456 IL-7R 信号传导对感染利什曼原虫的 C57BL/6J 小鼠耳内单核细胞的细胞内在效应 [bulk RNA-seq]
• GSE228455 利什曼原虫感染后 3 周从 C57BL/6J 小鼠耳组织中分选的单核细胞的单细胞水平基因表达谱 [scRNA-seq]
• GSE194141 线粒体RNA结合蛋白组图谱
• GSE194140 线粒体 RNA 结合蛋白组图谱 [RNAseq_siDHX30_siTFam]
• GSE194139 线粒体 RNA 结合蛋白组的图谱 [Par_clip]
• GSE194138 线粒体 RNA 结合蛋白组图谱 [mitoRICK]
• GSE300605 微管锚定及CD20与RhoA/Rock1通路偶联
• GSE293050 RNA-seq结果显示，在补充或不补充丝氨酸的禁食条件下，雄性肝细胞特异性GAPDH敲除小鼠的肝脏中，RNA-seq结果存在差异。
• GSE287612 p53 保护人类体细胞化学重编程为多能性 [批量 RNA 测序]
• GSE287611 p53 保护人类体细胞化学重编程为多能性 [scRNA-seq]