详细内容（前10条）

1. ⭐ GSE342215 单细胞空间转录组学揭示 Prph2C213Y 小鼠外节破坏后 RPE 和 Muller 胶质细胞向感光细胞的信号通路重连

• ✍️ 作者：未知作者
• 🏷️ 关键词：single-cell、spatial、spatial transcriptomics、transcriptomics
• 📝 描述：Contributors : Haoxin Guo ; Linfei Wei ; Binghan Chen ; Juan Huang ; Meijiao Zhu ; Xieyichang Li ; Ruiyi Yan ; Xufeng Zhao ; Xiaoxu Han ; Weihong YuSeries Type : OtherOrganism : Mus musculusPRPH2 mutations cause inherited retinal dystrophies (IRDs), but how photoreceptor outer segment (OS) disruption reshapes the surrounding retina remains unclear. Using a heterozygous Prph2C213Y/+ mouse model generated by CRISPR/Cas9, we characterized age-related retinal pathology and responses of retinal pigment epithelium (RPE) and Muller glia. Independent age- and sex-matched cohorts were examined at 1, 3, and 6 months by electroretinography, optical coherence tomography, and fundus autofluorescence. Mutant mice showed rod dysfunction from 1 month, RPE dysfunction from 3 months, and cone dysfunction by 6 months, accompanied by progressive outer retinal thinning and hyperautofluorescent deposits. Histological and ultrastructural analyses revealed OS disorganization, shortened RPE microvilli, RPE monolayer remodeling, increased RPE autofluorescence, and reactive Muller gliosis. Single-cell spatial transcriptomics of wild-type and mutant retinas at 6 months resolved nine cell populations and identified RPE cells and Muller glia as prominently perturbed non-photoreceptor populations. RPE cells showed an epithelial-mesenchymal transition-related remodeling state linked to a candidate Nfib-Fstl1 module, whereas Muller glia showed activation of activator protein 1 (AP-1) regulons, including Fos, Fosl2, and Junb, with predicted targets Osmr, A2m, and Stat3. Cell-cell communication analyses indicated coordinated changes in neuroprotective, inflammatory, and matrix-related signaling from RPE cells and Muller glia toward photoreceptors. These findings indicate that PRPH2-associated retinal dystrophy is a multicellular process in which OS disruption drives coordinated RPE and Muller glial remodeling with potentially protective or pro-degenerative effects, and nominate the RPE Nfib-Fstl1 program, Muller glial AP-1 responses with predicted STAT3 involvement, and support-cell-derived growth factor signaling as candidate mutation-independent therapeutic targets.
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2. GSE333704 肺炎克雷伯菌相关脓毒症中单细胞宿主免疫谱和病原体基因组特征的平行分析：一项初步研究

• ✍️ 作者：未知作者
• 🏷️ 关键词：immune、single-cell
• 📝 描述：Contributors : Claudia Rotondo ; Alberto Rossi ; Michele Properzi ; Giovanni Chillemi ; Daniele Pietrucci ; Ludovica Picarone ; Lucrezia Pierfederici ; Giulia Capecchi ; Germana Grassi ; Laura Loiacono ; Eleonora Cimini ; Simona Nanni ; Carla Fontana ; Francesco Messina ; Maria Grazia BocciSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensThis study employed a single-cell RNA sequencing approach using 10x Genomics scRNA-seq to investigate peripheral blood immune responses in sepsis. Peripheral blood mononuclear cells (PBMCs) were collected from adult patients with sepsis associated with Enterobacterales bloodstream infection and from healthy controls. The study was designed to characterize the single-cell immune profile of sepsis and to compare PBMC transcriptional profiles between septic patients and healthy subjects. Processed Cell Ranger raw/unfiltered and filtered feature-barcode matrices are provided for each sample.
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3. GSE326604 Inv(16)癌基因CBFB::MYH11是白血病细胞在血液和脾脏中存活所必需的，但在骨髓中则不然

• ✍️ 作者：未知作者
• 🏷️ 关键词：leukemia、regex:onco(logy|logist|gene|genic)
• 📝 描述：Contributors : Sipra Panda ; Peng Xiao ; Yiqian Wang ; Rahul Dogiparthi ; Michelle Becker ; Arjun Dhir ; Calvin Lam ; Cecilia Rivas ; Lemlem Alemu ; Lisa Garrett ; Sanantha Swenson ; Kyle Hewitt ; Katherine HydeSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusInversion of chromosome 16 [inv(16)] generates the fusion gene CBFB::MYH11 (CM) and is one of the most common chromosomal rearrangements in Acute Myeloid Leukemia (AML). Expression of CM is required for leukemia initiation. Patients with inv(16) at diagnosis invariably have the rearrangement at relapse, leading to the assumption that CM is also required after leukemic transformation. However, a role for CM in leukemia maintenance has yet to be shown experimentally. To address this, we used an inducible CM knockdown (KD) mouse model and found that decreased CM eliminated leukemia cells from the peripheral blood and spleen, but not the bone marrow, despite all populations exhibiting significantly decreased CM mRNA and protein. The surviving CM KD cells in the bone marrow showed decreased apoptosis and proliferation, and increased expression of autophagy related genes. Surprisingly, with prolonged KD of CM, ~40% of mice re-established disease despite maintaining decreased CM. Our work indicates that CM is required for leukemia survival in the spleen and peripheral blood, but in the bone marrow CM KD leukemia cells can survive and re-establish disease independent of the fusion protein. These findings imply that targeting CM alone has potential to reduce leukemic burden but not cure the disease.
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4. GSE326257 Inv(16)癌基因CBFB::MYH11是白血病细胞在血液和脾脏中存活所必需的，但在骨髓中则不然

• ✍️ 作者：未知作者
• 🏷️ 关键词：leukemia、regex:onco(logy|logist|gene|genic)
• 📝 描述：Contributors : Sipra Panda ; Yiqian Wang ; Venkatasai Rahul Dogiparthi ; Michelle Becker ; Arjun Dhir ; Calvin Lam ; Cecilia Rivas ; Lemlem Alemu ; Lisa Garrett ; Peng Xiao ; Sanantha Swenson ; Kyle Hewitt ; Katherine HydeSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusInversion of chromosome 16 [inv(16)] generates the fusion gene CBFB::MYH11 (CM) and is one of the most common chromosomal rearrangements in Acute Myeloid Leukemia (AML). Expression of CM is required for leukemia initiation. Patients with inv(16) at diagnosis invariably have the rearrangement at relapse, leading to the assumption that CM is also required after leukemic transformation. However, a role for CM in leukemia maintenance has yet to be shown experimentally. To address this, we used an inducible CM knockdown (KD) mouse model and found that decreased CM eliminated leukemia cells from the peripheral blood and spleen, but not the bone marrow, despite all populations exhibiting significantly decreased CM mRNA and protein. The surviving CM KD cells in the bone marrow showed decreased apoptosis and proliferation, and increased expression of autophagy related genes. Surprisingly, with prolonged KD of CM, ~40% of mice re-established disease despite maintaining decreased CM. Our work indicates that CM is required for leukemia survival in the spleen and peripheral blood, but in the bone marrow CM KD leukemia cells can survive and re-establish disease independent of the fusion protein. These findings imply that targeting CM alone has potential to reduce leukemic burden but not cure the disease.
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5. GSE343104 单细胞转录组学揭示斑马鱼固有淋巴细胞的异质性图谱

• ✍️ 作者：未知作者
• 🏷️ 关键词：single-cell、transcriptomics
• 📝 描述：Contributors : Kefan Cheng ; Thi Huong Trinh ; Ying Cao ; Shachuan Feng ; Jiaxin Liang ; Shizheng Zhao ; Jiaxu Yin ; Tao Dong ; Zilong WenSeries Type : Expression profiling by high throughput sequencingOrganism : Danio rerioInnate lymphoid cells (ILCs) are a class of lymphocytes whose activation is independent of antigen receptors. They constitute a major lymphocyte compartment and likely play a prominent role in lower vertebrates, though their precise composition and functions remain poorly characterized. Here, using scRNA-seq, we identify a broad spectrum of distinct ILC subsets, including both conventional subsets resembling their mammalian counterparts and unconventional ILC-like populations with unique features and distinct tissue distributions. We demonstrate that the complete ILC repertoire emerges early in development, independent of hematopoietic stem cells (HSCs), yet is maintained into adulthood via an HSC-dependent mechanism. Our work defines the landscape and ontogeny of zebrafish ILCs, revealing their underappreciated diversity and providing key insights into vertebrate innate immunity evolution.
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6. GSE305345 LINE-1 ORF1p 是癌症中一种共享的免疫原性抗原

• ✍️ 作者：未知作者
• 🏷️ 关键词：cancer、antigen
• 📝 描述：Contributor : Diao LiyangSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensIn this study, we identify and characterize LINE-1 ORF1p as a shared and immunogenic cancer antigen. LINE-1 elements are normally repressed genomic sequences that can be reactivated in cancer. We demonstrate that ORF1p, a protein encoded by LINE-1, is selectively expressed in tumors and its peptides are presented on MHC class I molecules across diverse tumor types. Using public and newly generated immunopeptidomics datasets, we detect ORF1p-derived peptides in a tumor-specific manner. Functional assays confirm that these peptides can elicit IFN-γ responses from CD4+ and CD8+ T cells in vitro. These findings highlight ORF1p as a promising candidate for a broadly applicable cancer vaccine.
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7. GSE275871 对严重皮肤药物不良反应患者的皮肤和水疱液进行多组学单细胞测序。

• ✍️ 作者：未知作者
• 🏷️ 关键词：sequencing、single-cell
• 📝 描述：Contributors : Andrew Gibson ; Elizabeth PhillipsSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensSevere cutaneous adverse reactions (SCAR) are rare but life-threatening drug reactions mediated by human leukocyte antigen (HLA) class I-restricted CD8+ T-cells. To obtain an unbiased assessment of SCAR cellular immunopathogenesis, we performed single-cell (sc) transcriptome, surface proteome, and TCR sequencing (5’ scRNA-TCR-CITE-seq, 10x Genomics) on unaffected skin, affected skin, and blister fluid from diverse SCAR patients.
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8. GSE343701 代谢重编程通过 GLS1 调节慢性肾脏病中的心肌细胞肥大

• ✍️ 作者：未知作者
• 🏷️ 关键词：metabolic
• 📝 描述：Contributors : Linnan Bai ; Yi Wang ; Junnan WuSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusLeft ventricular hypertrophy (LVH) is critical in chronic kidney disease (CKD), but its mechanisms remain unclear. This study employed multi-omics approaches, including RNA-seq and integrated metabolomics, to characterize metabolic alterations in cardiomyocytes (CM) of CKD mice, revealing enhanced glutaminolysis and impaired oxidative phosphorylation. We identified that glutaminase 1 (GLS1), the rate-limiting enzyme of glutaminolysis, is significantly upregulated and enzymatically activated in CM under CKD conditions. A multi-center cohort study confirmed that serum-induced GLS1 activity was associated with LV hypertrophic remodeling. Cardiomyocyte-specific deletion or pharmacological inhibition of GLS1 attenuated CKD-induced cardiac hypertrophy. Proteomic analysis revealed that multiple circulating proteins in the serum of CKD patients are associated with GLS1 enzymatic activity. Furthermore, phosphate (Pi), a representative uremic toxin, functions as a critical modulator of GLS1 activity and expression, compromising mitochondrial bioenergetics by promoting ammonia production and reducing mitochondrially encoded respiratory chain proteins. These integrated metabolic effects underscore the pivotal role of GLS1 in orchestrating myocardial energy reprogramming, thereby contributing to CKD-induced LVH.
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9. GSE339109 3D高级别浆液性卵巢癌模型揭示独特的基因表达和增殖动态

• ✍️ 作者：未知作者
• 🏷️ 关键词：cancer
• 📝 描述：Contributors : Kokondoska Grgič Vesna ; Pavlič Renata ; Janev Aleksandar ; Erdani Kreft Mateja ; Kološa Katja ; Černigoj Lana ; Levatić Jurica ; Džeroski Sašo ; Sinreih Maša ; Lanišnik Rižner Tea ; Jovčevska IvanaSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensHigh-grade serous ovarian cancer (HGSOC) is the most lethal gynaecological malignancy, largely due late diagnosis and tumor heterogeneity. Accurate preclinical modelling of HGSOC biological complexity is essential to improve translational research outcomes and therapeutic development; however, traditional 2D models have limited translational relevance. We therefore compared the morphological, proliferative, and molecular characteristics of four HGSOC cell lines (OVCAR-4, OVSAHO, COV362, and Kuramochi) in 2D versus 3D culture environments. To support systematic interrogation of 3D models, we developed reproducible protocols for 3D spheroid generation and optimized a dissociation method for downstream analysis. We observed significant differences in cellular behaviour, morphology, cell cycle regulation, and gene expression. Kuramochi cells showed upregulated EMT markers WNT11B and VIM, suggesting an increased invasive phenotype, i.e., enhanced epithelial–mesenchymal transition and signalling pathways. In OVSAHO cells, MMP2 was significantly downregulated while VEGFA was upregulated, highlighting alterations in matrix remodelling and angiogenesis, characterizing this cell line as proliferative rather than invasive. COV362 cells showed an initial decrease followed by an increase in KI67 expression. Downregulation of BRCA1 and KI67 indicates reduced cell proliferation in 3D environments. Proliferation kinetics were also altered in 3D environments: Kuramochi and OVCAR-4 adopted a more quiescent phenotype, while COV362 remained more proliferative with significant KI67 overexpression. These proliferation dynamics were confirmed with immunocytochemistry. Alignment of expression data showed that different cell types align with distinct HGSOC subtypes: OVASHO with immunoreactive, OVCAR4 with mesenchymal and differentiated, COV362 with differentiated and proliferative, and Kuramochi with proliferative subtype. The described 3D models can serve as high-throughput platforms for drug testing and functional studies, as well as for studying the complex molecular dynamics of ovarian cancer. Moreover, co-culturing systems can enhance their translational potential for the developme…
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10. GSE335386 靶向 FKBP5 通过 CaMKKβ/AMPK 通路维持线粒体稳态，从而减轻脓毒症引起的急性肺损伤

• ✍️ 作者：未知作者
• 🏷️ 关键词：pathway
• 📝 描述：Contributors : Xinyue Tian ; Yanan LiSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensBackground: Sepsis-induced acute lung injury (ALI) remains a leading cause of mortality in critically ill patients, with endothelial barrier disruption and mitochondrial dysfunction serving as central pathological events. FK506-binding protein 5 (FKBP5) has been implicated in various inflammatory disorders, yet its specific role and underlying mechanism in septic ALI remain elusive.
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1. MitoClipSplice——机器学习改进线粒体RNA加工的RNA测序分析

• ✍️ 作者：未知作者
• 🏷️ 关键词：sequencing
• 📝 描述：RNA sequencing combined with machine learning identifies mitochondrial RNA cleavage sites from soft-clipped reads, providing a new approach for investigating mitochondrial RNA…
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2. 转录组衰老时钟揭示阿片类药物依赖中与年龄相关的分子模式

• ✍️ 作者：未知作者
• 🏷️ 关键词：aging
• 📝 描述：RNA sequencing reveals age-dependent gene expression patterns in opioid dependence, highlighting links among neuroinflammation, neuronal signaling, and molecular processes associated with brain aging…
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• GSE333838 Argonaute-2 切割 Rtl1 促进骨骼肌发育和出生后存活 [RNA-Seq]
• GSE329762 野生型木薯和表达靶向甲基转移酶的转基因木薯的 ChIP-seq 数据
• GSE320554 人类对多种 COVID-19 疫苗免疫的比较多组学图谱
• GSE309991：两种 CDK8 抑制剂处理后 TEX 细胞系的转录组
• GSE296588 IL-1β/IRAK4轴促进间皮损伤部位的卵巢肿瘤发展
• GSE343689 多重单细胞转录组学优化小鼠胚胎干细胞的中胚层模式形成和造血内皮细胞输出
• GSE343653 金黄色葡萄球菌引起的慢性细菌感染不会促进高脂血症小鼠的动脉粥样硬化进展
• GSE316849 青少年特发性脊柱侧弯风险变异的大规模并行表征 [RNA-Seq]
• GSE343718：TGF-β1诱导的巨噬细胞-肾小管上皮细胞共培养模型中血红素处理的骨髓来源巨噬细胞的转录组分析
• GSE342879 小鼠新皮层第2/3层皮层投射神经元的转录组
• GSE330631 mTORC1抑制可上调CD20并增强抗CD20抗体在B细胞急性淋巴细胞白血病（B-ALL）中的疗效
• GSE314119 IL1A 促进炎症反应，同时保护上皮基底细胞的特性和屏障功能
• GSE312606 肺结核疾病中 CD4-CD8-细胞毒性 Vδ1/3 T 细胞的富集
• GSE305507 纳米吸管电穿孔法用于从活体二维和三维细胞培养系统中进行时间RNA取样 - RNA测序数据
• GSE218230 RNA-seq 分析了 shRNA 介导的 DCPS 敲低的胶质母细胞瘤干细胞。
• CuCl₂处理后Ishikawa和KLE细胞的GSE342605 RNA测序
• GSE333845 脑血管周围巨噬细胞通过 cMAF 依赖性转录程序调节小鼠和人类内皮细胞功能 [RNA-seq BEC]
• GSE333844 脑血管周围巨噬细胞通过 cMAF 依赖性转录程序调节小鼠和人类内皮细胞功能 [scRNA-seq APOE4]
• GSE316309：早期非小细胞肺癌DNA甲基化模式的特征分析
• GSE313124 靶向 DKC1 介导的假尿苷化与 PARPi 联合治疗可诱导 HR 功能正常的肿瘤发生合成致死 [RNA-Seq]
• GSE312874 靶向 DKC1 介导的假尿苷化与 PARPi 联合治疗可诱导 HR 功能正常的肿瘤发生合成致死 [ATAC-seq]
• GSE298939 脑血管周围巨噬细胞通过 cMAF 依赖性转录程序调节小鼠和人类内皮细胞功能 [RNA-seq 主动脉]
• GSE289369 脑血管周围巨噬细胞通过 cMAF 依赖性转录程序调节小鼠和人类内皮细胞功能 [scRNA-seq 脑巨噬细胞]
• GSE289367 脑血管周围巨噬细胞通过 cMAF 依赖性转录程序调节小鼠和人类内皮细胞功能 [scRNA-seq 脑血管细胞]
• GSE289366 脑血管周围巨噬细胞通过 cMAF 依赖性转录程序调节小鼠和人类内皮细胞功能 [ChIP-Seq]
• GSE289365 脑血管周围巨噬细胞通过 cMAF 依赖性转录程序调节小鼠和人类内皮细胞功能 [RNA-seq BMDM]