详细内容（前10条）

1. ⭐ GSE290041 单细胞空间分析揭示了 HPV 相关口咽癌中免疫细胞组织和癌细胞异质性的分子机制 [xenium]

• ✍️ 作者：未知作者
• 🏷️ 关键词：cancer、carcinoma、immune、single-cell、spatial
• 📝 描述：Contributors : Cem Sievers ; Clint Allen ; Charalampos FloudasSeries Type : OtherOrganism : Homo sapiensWe combined spatial gene expression profiling with single-cell RNA-sequencing to study cellular organization in HPV-associated oropharyngeal carcinoma. The single-cell spatial gene expression portion of the study is described and provided in this deposition.
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2. ⭐ GSE290040单细胞空间分析揭示了HPV相关口咽癌中免疫细胞组织和癌细胞异质性的分子机制

• ✍️ 作者：未知作者
• 🏷️ 关键词：cancer、carcinoma、immune、single-cell、spatial
• 📝 描述：Contributors : Cem Sievers ; Clint Allen ; Charalampos FloudasSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensWe combined spatial gene expression profiling with single-cell RNA-sequencing to study cellular organization in HPV-associated oropharyngeal carcinoma. The single-cell RNA-sequencing portion of the study is described and provided in this deposition.
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3. ⭐ GSE329692 猕猴外周血单核细胞在T细胞活化或用促炎或抗炎细胞因子处理后等位基因特异性MHC表达的单细胞RNA分析

• ✍️ 作者：未知作者
• 🏷️ 关键词：T cell、MHC、single-cell
• 📝 描述：Contributors : Max C Ertl ; Roger W Wiseman ; Anthony J Veltri ; Julie A Karl ; Miranda R Stauss ; William K Gardner ; Nicholas R Minor ; David H O’ConnorSeries Type : Expression profiling by high throughput sequencing ; OtherOrganism : Macaca fascicularis ; Macaca mulattaWe have employed a single-cell sequencing approach using 10X Genomics 5’scRNAseq to study expression of the Major Histocompatibility Complex (MHC) in peripheral blood mononuclear cells (PBMC) from Mauritian-origin cynomolgus and Indian-origin rhesus macaques. The MHC region has undergone a complex series of duplications in macaques relative to humans. Steady-state RNA levels of macaque MHC class I and class II transcripts vary over several orders of magnitude in whole blood and bulk PBMC. In this study, we compared transcript levels in untreated control PBMC with transcript levels after T cell activation, treatment with pro-inflammatory cytokines, or treatment with anti-inflammatory cytokines. Transcript levels for several minor MHC alleles were preferentially induced in monocytes and dendritic cells after treatment with pro-inflammatory cytokines or T cell activation.
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4. ⭐ GSE296334 NeuID 是一种新型的神经元特异性 lncRNA，可调控阿尔茨海默病中的神经元功能 [ChIP-seq]

• ✍️ 作者：未知作者
• 🏷️ 关键词：Alzheimer、Neuronal、ChIP-seq
• 📝 描述：Contributors : Ranjit Pradhan ; Sadman M Sakib ; Iga Grzadzielewska ; Eren Diniz ; Dennis M Krueger ; Sophie Schroeder ; Susanne Burkhardt ; Anna-Lena Schuetz ; Jelena Radulovic ; Farahnaz Sananbenesi ; André FischerSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Mus musculusNon-coding RNAs are transcripts that do not encode proteins and comprise 98.5% of the human transcriptome. Among these, long non-coding RNAs (lncRNAs) have been implicated in various biological functions, including the control of gene expression and translation. The central nervous system (CNS) harbors a diverse array of lncRNA transcripts, yet the functions of many remain largely unexplored. In this study, we employed FANS with total RNA-sequencing and single-nuclei RNA sequencing approaches using human and mouse brain tissue to identify novel lncRNAs specific to neurons, and potentially associated with neurodegenerative diseases. We discovered a novel brain-specific lncRNA, the we named ‘NeuID’, that is specifically expressed in neuronal cells in the mouse and human brains. NeuID expression was found to be reduced in the brains of Alzheimer’s disease (AD) patients. Knockdown (KD) of NeuID resulted in the downregulation of synaptic plasticity genes. Additionally, NeuID KD led to decreased dendritic spine density and reduced neuronal network activity in MEA recordings. Furthermore, we demonstrate that NeuID interacts with EZH2, a component of the PRC2 complex, and mediates the h3k27me3 levels of Olig2 transcription factor. Notably, CRISPRa mediated overexpression of NeuID resulted in the rescue of functional impairment caused by AD-related pathological Aβ oligomers. Overall, our findings identify a novel brain and neuron-exclusive lncRNA that regulates neuronal function, is dysregulated in AD, and might be a potential therapeutic target against neuronal pathology in AD.
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5. ⭐ GSE296682 支气管肺泡灌洗液单细胞转录组学揭示间质性肺疾病中不同的巨噬细胞亚群和演化轨迹

• ✍️ 作者：未知作者
• 🏷️ 关键词：macrophage、single-cell、transcriptomics
• 📝 描述：Contributors : Lai-Ying Zhang ; Peter C Allen ; Viviana P Lutzky ; Simon H Apte ; Penelope L Groves ; Maxine E Tan ; Tharushi De Silva ; Quan H Nguyen ; Joseph E Powell ; Daniel C Chambers ; Brendan J O’SullivanSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensRATIONALE: Interstitial lung diseases (ILDs) encompass a diverse range of fibrotic conditions and contribute to significant respiratory morbidity and mortality. Assessment of the cellular composition of bronchoalveolar lavage (BAL) fluid is an important diagnostic test in people presenting with ILD, but BAL cellularity remains relatively uncharacterized at single-cell resolution. OBJECTIVE: To characterize immune cell populations in BAL across different ILDs and investigate the impact of shortened peripheral blood leukocyte telomere length on BAL immune profiles. METHODS: Single-cell RNA sequencing and downstream analysis were performed on BAL samples from 25 patients with various ILDs, including idiopathic pulmonary fibrosis (IPF), hypersensitivity pneumonitis, sarcoidosis, and silicosis. Both normal-telomere and short-telomere patients were included. Additionally, we integrated our findings with IPF genome-wide association study (GWAS) data. RESULTS: We identified sixteen distinct cell populations in BAL with notable differences across ILD subtypes. Analysis revealed six monocyte-like macrophage (MLM) subclusters following divergent trajectories: inflammatory CXCL10hi MLMs predominated in hypersensitivity pneumonitis, while pro-fibrotic SPP1hi MLMs were significantly expanded in IPF. Short-telomere patients demonstrated an increased proportion of pro-fibrotic SPP1hi MLMs with enhanced expression of fibrotic genes compared to patients with normal telomere length. Integration with genomic data confirmed that SPP1hi and CCL2hi MLM subclusters harbour cells with the highest IPF disease relevance scores. CONCLUSION: BAL-derived transcriptomics reveals distinct myeloid subpopulations across ILD subtypes, with specific populations associated with disease pathogenesis. These findings provide insight into ILD pathogenesis, motivate the development of more sophisticated diagnostic tests using BAL sampling, and highlight specific myeloid subpopulations as potential therapeutic targets.
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6. GSE318189 孕期和产后母体表观遗传衰老指标的轨迹

• ✍️ 作者：未知作者
• 🏷️ 关键词：aging、epigenetic
• 📝 描述：Contributors : Laura Etzel ; Idan Shalev ; Patricia Garrett-PetersSeries Type : Methylation profiling by genome tiling arrayOrganism : Homo sapiensPregnancy has been proposed as a biological “stress test” that may transiently accelerate maternal biological aging, followed by partial recovery in the postpartum period; however, longitudinal evidence characterizing these trajectories remains limited. This longitudinal study followed 130 women across mid to late pregnancy, early postpartum (6–9 months), and later postpartum (36–43 months) to characterize nonlinear changes in multiple markers of biological aging. Biological aging was assessed using complementary indicators, including telomere length, DNA methylation–based epigenetic aging measures, and pace-of-aging metrics. Genome-wide DNA methylation data were generated from maternal biospecimens using the Illumina Infinium MethylationEPIC v2.0 BeadChip to support derivation of epigenetic aging measures and evaluation of longitudinal methylation dynamics. Generalized additive mixed models were used to examine within-person changes over time. Results indicated relative stability or slowing of biological aging during early postpartum, followed by marker-specific patterns of stabilization or decline during later postpartum. Subsequent pregnancy during the later postpartum period was associated with shorter telomere length and altered recovery trajectories, including accelerated pace of aging among women who became pregnant again. Together, these findings suggest that while partial recovery of biological aging markers may occur following pregnancy, such recovery may be sensitive to additional reproductive demands. The DNA methylation data deposited here support longitudinal analyses of maternal biological aging across pregnancy and postpartum and provide a resource for future studies examining reproductive influences on epigenetic aging processes. Additional study data available via figshare at: https://doi.org/10.6084/m9.figshare.30005287
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7. GSE316424 西妥昔单抗或帕妥昔单抗在体外对结肠癌HCT116或HT29细胞中miRNA表达和潜在信号通路的影响存在差异

• ✍️ 作者：未知作者
• 🏷️ 关键词：cancer、pathway
• 📝 描述：Contributors : laetitia Corset ; Frederic Picou ; Frauke Beilstein ; Sadija Ibrahim ; Romain Chautard ; William RaoulSeries Type : Non-coding RNA profiling by high throughput sequencingOrganism : Homo sapiensAiming to understaned resistance to monocolonal antibodies (Cetuximab, Ctx or Panituximab, Pani) in colon cancer cells, miRNA were studies in both HT29 cells(B-RAF mutated, moderattely-sensitive to Ctx) and HCT116 (K-RAS mutated, highly resistant to Ctx)
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8. GSE299125 HIV-1感染免疫细胞的旁分泌信号重编程宫颈癌通路

• ✍️ 作者：未知作者
• 🏷️ 关键词：cancer、immune
• 📝 描述：Contributors : Charles O Olwal ; Ujjwal Rathore ; Sara Makanani ; Prashant Kaushal ; Immy A Ashley ; Manisha R Ummadi ; Vincent Appiah ; Alexandra L DjomkamZune ; Sophie Blanc ; Declan Winters ; Yennifer Delgado ; Kapten Muthoka ; Jacqueline M Fabius ; Manon Eckhardt ; Robyn M Kaake ; Maureen Su ; Oliver Fregoso ; Judd F Hultquist ; Elkanah O Orang’o ; Danielle L Swaney ; George K Boateng ; Nevan J Krogan ; Peter K Quashie ; Yaw Bediako ; Mehdi BouhaddouSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensPersistent infection with human papillomavirus (HPV) is the primary cause of cervical cancer worldwide. Notably, women co-infected with HPV and human immunodeficiency virus type 1 (HIV-1) have a six-fold higher lifetime risk of developing cervical cancer compared to those without HIV, even when adhering to antiretroviral therapy (ART) and achieving T-cell reconstitution. While chronic HIV-1 infection is known to cause inflammation, how paracrine signals from immune cells alter signaling in cervical cells remain poorly understood. To address this, we conducted global transcriptomics analysis on cervical swabs from Kenyan women with HPV, stratified by HIV-1 and cancer status. Strikingly, women with HIV-1 showed cancer-like gene expression patterns in non-cancerous cervical epithelial cells. Complementary global mass spectrometry (MS) proteomics of cervical cells exposed to the secretome of HIV-1–infected primary CD4+ T-cells revealed altered expression of proteins in MAPK, PI3K-AKT, and β-catenin signaling pathways. Integrative network analyses of transcriptomic and proteomic datasets revealed that HIV-1 altered gene expression in key pathways known to drive cervical cancer, including genes commonly mutated in HIV-1-naïve disease. Notably, IRS-1, a key PI3K-AKT pathway activator, was found to be consistently upregulated in both participant samples and cell culture models, as were interferon-stimulated genes. Phosphoproteomics MS analysis confirmed PI3K-AKT pathway activation in cervical cells exposed to conditioned media from HIV-1-infected T-cells. Together, our findings uncover how HIV-1 reshapes cervical cell signaling via paracrine mechanisms and highlights the PI3K pathway as a potential therapeutic target in HIV-associated cervical cancer.
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9. GSE278193 NuRD复合物在CTCF位点重塑染色质环境和维持基因组结构中的关键作用[mESC ChIP-seq]

• ✍️ 作者：未知作者
• 🏷️ 关键词：ChIP-seq、genome
• 📝 描述：Contributors : Jian Yan ; Xi Wang ; Wenju Sun ; Nan WuSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Mus musculusCCCTC-binding factor (CTCF) is an evolutionarily conserved transcription factor with diverse regulatory roles. Around stable CTCF binding sites, nucleosomes are highly ordered and DNA methylation is reduced, yet the mechanisms establishing and maintaining this epigenetic environment remain unclear. Utilizing an innovative eBioID method, we identified that virtually all subunits of the nucleosome remodeling and deacetylase (NuRD) complex are associated with CTCF in cells. Further analyses revealed that the NuRD complex is necessary for the chromatin binding of CTCF, and emerges as a novel regulator of the genome architecture. Additionally, we discovered that MBD3-NuRD facilitates the recruitment of TET demethylases to CTCF sites, initiating local DNA demethylation essential for the activation of adjacent gene expression. Embryonic stem cells deficient in the NuRD complex showed impaired lineage commitment. In summary, this study elucidates a mechanism illustrating the interplay between CTCF binding and the epigenome including 3D genome organization and DNA methylation, with the NuRD complex serving as an indispensable mediator.
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10. GSE278192 NuRD复合物在CTCF位点重塑染色质环境和维持基因组结构中的关键作用[HEK293T ChIP-seq]

• ✍️ 作者：未知作者
• 🏷️ 关键词：ChIP-seq、genome
• 📝 描述：Contributors : Jian Yan ; Xi Wang ; Wenju Sun ; Nan WuSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Homo sapiensCCCTC-binding factor (CTCF) is an evolutionarily conserved transcription factor with diverse regulatory roles. Around stable CTCF binding sites, nucleosomes are highly ordered and DNA methylation is reduced, yet the mechanisms establishing and maintaining this epigenetic environment remain unclear. Utilizing an innovative eBioID method, we identified that virtually all subunits of the nucleosome remodeling and deacetylase (NuRD) complex are associated with CTCF in cells. Further analyses revealed that the NuRD complex is necessary for the chromatin binding of CTCF, and emerges as a novel regulator of the genome architecture. Additionally, we discovered that MBD3-NuRD facilitates the recruitment of TET demethylases to CTCF sites, initiating local DNA demethylation essential for the activation of adjacent gene expression. Embryonic stem cells deficient in the NuRD complex showed impaired lineage commitment. In summary, this study elucidates a mechanism illustrating the interplay between CTCF binding and the epigenome including 3D genome organization and DNA methylation, with the NuRD complex serving as an indispensable mediator.
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1. 一项基于人工智能的下一代测序血液检测方法正在评估其在急性髓系白血病 (AML) 和骨髓增生异常综合征 (MDS) 患者造血干细胞移植 (HCT) 后复发检测中的应用。

• ✍️ 作者：未知作者
• 🏷️ 关键词：sequencing
• 📝 描述：RNA sequencing and AI-powered blood monitoring may detect relapse earlier after hematopoietic cell transplantation, improving risk prediction in AML and myelodysplastic syndrome patients…
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2. 这种简单的氨基酸补充剂能显著减轻阿尔茨海默病造成的损害。

• ✍️ 作者：未知作者
• 🏷️ 关键词：Alzheimer
• 📝 描述：A new study suggests a surprisingly simple compound could help fight Alzheimer’s disease. Researchers found that arginine—an inexpensive amino acid already considered safe—can reduce the buildup of toxic amyloid proteins in the brain, a hallmark of the disease. In animal models, oral arginine not only lowered harmful protein deposits but also improved behavior and reduced brain inflammation.
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• GSE262036 NuRD复合物在CTCF位点重塑染色质环境和维持基因组结构中的关键作用[BPK25 Hi-C]
• GSE188175 NuRD复合物在CTCF位点重塑染色质环境和维持基因组结构中的关键作用[ChIP-Seq]
• GSE178813 NuRD复合物在CTCF位点重塑染色质环境和维持基因组结构中的关键作用[Hi-C]
• GSE329135 保守的 Notch-Meis1-Pbx 信号通路将分泌祖细胞分化为空间分布多样的肠道 best4+ 细胞
• GSE270920 CDK4 对组蛋白修饰的生酮调控促进白血病发生 [ChIP-seq]
• GSE268071 LCMV 13 克隆感染期间耗竭 CD8 T 细胞亚群的批量 RNA-seq 分析
• GSE243273 骨桥蛋白将获得性抗缺氧诱导抗血管生成药物耐药性与乳腺癌抗 PD-L1 药物耐药性联系起来 [III]
• GSE241539 骨桥蛋白将获得性低氧诱导抗血管生成药物耐药性与乳腺癌抗PD-L1药物耐药性联系起来
• GSE241538 骨桥蛋白将获得性抗缺氧诱导抗血管生成药物耐药性与乳腺癌抗 PD-L1 药物耐药性联系起来 [II]
• GSE241527 骨桥蛋白将获得性抗缺氧诱导抗血管生成药物耐药性与乳腺癌抗 PD-L1 药物耐药性联系起来 [I]
• GSE325158 熊果酸膳食补充剂可维持癌症恶病质小鼠模型的骨骼肌质量和力量 [RNA-seq]
• GSE291816 大细胞胰腺神经内分泌癌中异常的脑型神经元程序
• GSE329725 狒狒子宫内膜异位症诱导后microRNA的差异表达
• GSE310570 转录组和激素调控影响不同大麦基因型对干旱胁迫依赖性镰刀菌穗腐病的易感性
• GSE301844 研究表明，mTOR 抑制可通过抑制 ATF4-MTHFD2 通路增强 RAF 二聚体-MEK 阻断的抗肿瘤疗效。
• GSE297994 人类单核细胞的天然长读长RNA测序揭示了激活诱导的选择性剪接，从而产生功能性异构体
• GSE278195 NuRD复合物在CTCF位点重塑染色质环境和维持基因组结构中的关键作用[mESC亚硫酸氢盐测序]
• GSE278194 NuRD复合物在CTCF位点重塑染色质环境和维持基因组结构中的关键作用[mESC_BPK25_HiC 批次 2]
• GSE253697 NuRD复合物在CTCF位点重塑染色质环境和维持基因组结构中的关键作用[HEK293T_siNURD_TET1_ChIP_Seq]
• GSE253695 NuRD复合物在CTCF位点重塑染色质环境和维持基因组结构中的关键作用[CTCF_MBD2_HT_Me_CAP_SELEX]
• GSE253694 NuRD复合物在CTCF位点重塑染色质环境和维持基因组结构中的关键作用[HEK293T_siNURD_CTCF_ChIP_Seq]
• GSE253693 NuRD复合物在CTCF位点重塑染色质环境和维持基因组结构中的关键作用[mESC_d0246_DMSO_BPK25_IAA_RNA_Seq]
• GSE253692 NuRD复合物在CTCF位点重塑染色质环境和维持基因组结构中的关键作用[mESC_d0246_CTCF_MBD3_ChIP_Seq]
• GSE253691 NuRD复合物在CTCF位点重塑染色质环境和维持基因组结构中的关键作用[mESC_d0246_RNA_Seq]
• GSE215331 NuRD复合物在CTCF位点重塑染色质环境和维持基因组结构中的关键作用[hESC_H9_d049_RNA_Seq]
• GSE215328 NuRD复合物在CTCF位点重塑染色质环境和维持基因组结构中的关键作用[hESC_H9_d049_ChIP_Seq]
• GSE215326 NuRD复合物在CTCF位点重塑染色质环境和维持基因组结构中的关键作用[HEK293T_IAA72h_ChIP_Seq]
• GSE215323 NuRD复合物在CTCF位点重塑染色质环境和维持基因组结构中的关键作用[HEK293T_BPK25_ChIP_Seq]
• GSE215320 NuRD复合物在CTCF位点重塑染色质环境和维持基因组结构中的关键作用[HEK293T_BPK25_BS_Seq]
• GSE215319 NuRD复合物在CTCF位点重塑染色质环境和维持基因组结构中的关键作用[CTCF_Methyl_SELEX_data]
• GSE176248 NuRD复合物在CTCF位点重塑染色质环境和维持基因组结构中的关键作用[BS-seq]
• GSE328562 组蛋白去甲基化酶 KDM6B 促进出生后少突胶质细胞发育和皮质髓鞘形成
• GSE327021 阿尔茨海默病中泛素-蛋白酶体系统失调影响蛋白质丰度
• GSE329643 宿主-灰霉病菌共转录组学揭示了与近缘豆科植物的精细调控相互作用
• GSE329637 NanoString nCounter 小鼠泛癌免疫分析：用 DC 疫苗治疗的 B16F10 肿瘤
• GSE329594 适体-CRBNL PROTAC靶向降解SETDB1作为乳腺癌的新型治疗策略
• GSE329346 轨迹解析的人类肾脏类器官模型揭示了与成人慢性肾脏病相关的OPFR发育毒性
• GSE329299 NOTCH2致病变异体改变小鼠股骨成骨细胞和血管细胞转录组
• GSE329119 糖尿病角膜神经病变中长链非编码RNA的差异表达及其在发病机制中的意义
• GSE313659 人类T细胞中TNFR1和TNFR2表达的单细胞多组学分析
• GSE297755 RNA-seq 数据来自孕妇龈沟液，用于预测妊娠期糖尿病 (GDM)
• GSE297263 研究发现，脱氧雪腐镰刀菌烯醇 (DON) 与猪繁殖与呼吸综合征病毒 (PRRSV) 共同暴露可通过 PERK-ATF4 通路加剧 Marc-145 细胞中的未折叠蛋白反应 (UPR)。
• GSE296433 工程化益生菌通过激活肠道树突状细胞中的 AHR-KLF4-FADS3 信号通路来限制 T 细胞驱动的中枢神经系统自身免疫
• GSE279157 补体因子H通过TRPM7信号通路维持巨噬细胞稳态