详细内容（前10条）

1. ⭐ GSE309130 人类鼻腔转录组和微生物组的双转录组分析揭示了与有症状呼吸道感染相关的宿主-细菌相互作用 [RNA-Seq]

• ✍️ 作者：未知作者
• 🏷️ 关键词：bacteria、regex:bacter(ia|ial|ium)、RNA-seq、transcriptome
• 📝 描述：Series Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensThe human nasopharynx is colonized by a diverse community of commensal microbiota linked to many respiratory diseases, yet their interactions with the host remain unclear. In this study, we introduced a dual-transcriptomics analysis strategy, which can characterize the host transcriptome and microbiome from nasal samples simultaneously. RNA sequencing reads from human nasal swab samples were pre-processed and aligned to the human genome for host gene expression counting, while unmapped reads were further aligned to microbiota genome. After taxonomic classification, microbial abundance matrix was derived at each taxonomic level for differential and host-microbiota interaction analysis. We applied this workflow to a local SARS-CoV-2 cohort with 76 infected patients, among whom 55 (72.37%) were symptomatic at enrollment. Nasal swabs were collected from all 76 patients at enrollment and from 73 patients at one-week later follow-up. We detected a median of 4.81% reads unmapped from the human genome across all 149 samples, among which around half (median 48.63%) were successfully mapped to microbiome genome. Meta-transcriptomic analysis detected significantly higher SARS-related coronavirus loads in samples from the symptomatic group at enrollment, and both groups showed decreased loads one week later. Compared with benchmarking 16S rRNA sequencing on 53 samples, our computational strategy showed high correlation of relative abundance in all top 20 genus. A total of 685 bacteria species were identified to show a relative abundance >= 0.01% in at least 10% samples. Differential abundance analysis identified 66 species (DASs) from 6 phyla with significantly decreased abundance in samples from the symptomatic group compared to the asymptomatic group at enrollment. Integrating these symptom-associated DASs with host’s gene expression using an expression quantitative trait bacteria (eQTB) model, we found 58 symptom-associated DASs identified at enrollment were significantly associated with one to 16 genes. GSEA showed a series of symptom-associated DASs were significantly correlated with pathways related to the activation of olfactory, keratinocyte differentiation, and DNA methylation. In summary, our dual-transcriptomic analysis strategy effectively characterized host-microbiome interactions, offering insights into microbial contributions to respiratory diseases.
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2. ⭐ GSE290806 空间和单细胞转录组学揭示了小脑小胶质细胞随衰老而发生的重组

• ✍️ 作者：未知作者
• 🏷️ 关键词：aging、single-cell、spatial、transcriptomics
• 📝 描述：Contributors : Andy Tsai ; Douglas Henze ; Eduardo Ramirez Lopez ; James Haberberger ; Chuanpeng Dong ; Nannan Lu ; Micaiah Atkins ; Emma Costa ; Amelia Farinas ; Hamilton Oh ; Patricia Moran-Losada ; Yann Le Guen ; Alina Isakova ; Stephen Quake ; Tony Wyss-CoraySeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusAging induces region-specific functional decline across the brain. The cerebellum, critical for motor coordination and cognitive function, undergoes significant structural and functional changes with age. The molecular mechanisms driving cerebellar aging—particularly the role of cerebellar glia, including microglia—remain poorly understood. Here, we used single-nuclei RNA sequencing (snRNA-seq), microglial bulk RNA-seq, and multiplexed error-robust fluorescence in situ hybridization (MERFISH) to characterize transcriptional changes associated with cellular aging in the mouse cerebellum. We discovered that microglia exhibited the most pronounced age-related changes of all cell types and that their transcriptional signatures pointed to enhanced neuroprotective immune activation and reduced lipid-droplet accumulation compared to hippocampal microglia. Furthermore, cerebellar microglia in aged mice, compared to young mice, were found in closer proximity to granule cells. This relationship was characterized using the newly defined neuron-associated microglia score, which captures proximity-dependent transcriptional changes and suggests a novel microglial responsiveness. These findings underscore the unique adaptations of the cerebellum during aging and its potential resilience to Alzheimer’s disease (AD) related pathology, providing crucial insight into region-specific mechanisms that may shape disease susceptibility.
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3. ⭐ GSE309135 人类鼻腔转录组和微生物组的双转录组分析揭示了与症状性呼吸道感染相关的宿主-细菌相互作用

• ✍️ 作者：未知作者
• 🏷️ 关键词：bacteria、regex:bacter(ia|ial|ium)、transcriptome
• 📝 描述：Series Type : Expression profiling by high throughput sequencing ; OtherOrganism : Homo sapiensThis SuperSeries is composed of the SubSeries listed below.
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4. ⭐ GSE309134 人类鼻腔转录组和微生物组的双转录组分析揭示了与有症状呼吸道感染相关的宿主-细菌相互作用（16S验证）

• ✍️ 作者：未知作者
• 🏷️ 关键词：bacteria、regex:bacter(ia|ial|ium)、transcriptome
• 📝 描述：Series Type : OtherOrganism : Homo sapiensThe human nasopharynx is colonized by a diverse community of commensal microbiota linked to many respiratory diseases, yet their interactions with the host remain unclear. In this study, we introduced a dual-transcriptomics analysis strategy, which can characterize the host transcriptome and microbiome from nasal samples simultaneously. RNA sequencing reads from human nasal swab samples were pre-processed and aligned to the human genome for host gene expression counting, while unmapped reads were further aligned to microbiota genome. After taxonomic classification, microbial abundance matrix was derived at each taxonomic level for differential and host-microbiota interaction analysis. We applied this workflow to a local SARS-CoV-2 cohort with 76 infected patients, among whom 55 (72.37%) were symptomatic at enrollment. Nasal swabs were collected from all 76 patients at enrollment and from 73 patients at one-week later follow-up. We detected a median of 4.81% reads unmapped from the human genome across all 149 samples, among which around half (median 48.63%) were successfully mapped to microbiome genome. Meta-transcriptomic analysis detected significantly higher SARS-related coronavirus loads in samples from the symptomatic group at enrollment, and both groups showed decreased loads one week later. Compared with benchmarking 16S rRNA sequencing on 53 samples, our computational strategy showed high correlation of relative abundance in all top 20 genus. A total of 685 bacteria species were identified to show a relative abundance >= 0.01% in at least 10% samples. Differential abundance analysis identified 66 species (DASs) from 6 phyla with significantly decreased abundance in samples from the symptomatic group compared to the asymptomatic group at enrollment. Integrating these symptom-associated DASs with host’s gene expression using an expression quantitative trait bacteria (eQTB) model, we found 58 symptom-associated DASs identified at enrollment were significantly associated with one to 16 genes. GSEA showed a series of symptom-associated DASs were significantly correlated with pathways related to the activation of olfactory, keratinocyte differentiation, and DNA methylation. In summary, our dual-transcriptomic analysis strategy effectively characterized host-microbiome interactions, offering insights into microbial contributions to respiratory diseases.
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5. ⭐ GSE301079 利用新型irg1敲入报告基因，对斑马鱼胚胎急性肌肉损伤后通过FACS分离的免疫细胞进行单细胞RNA测序分析

• ✍️ 作者：未知作者
• 🏷️ 关键词：immune、RNA-seq、single-cell
• 📝 描述：Contributors : Matthew Hamilton ; Ethan Bedsole ; Celia E ShiauSeries Type : Expression profiling by high throughput sequencingOrganism : Danio rerioThe objective of this experiment was to analyze the single-cell transcriptomes of macrophages for molecular profiling of subtypes that emerge during acute muscle injury in zebrafish. This transcriptomic data was used in conjunction with high-resolution live-cell microscopy, in which individual macrophages were tracked to examine both cellular and population-level dynamics. Comparisons were made between baseline (stage-matched, uninjured controls) and distinct phases of injury: the initial inflammatory response at 24 hours post-amputation (hpa) and the resolution phase beginning at 48 hpa of two genotypes, control/wild-type and chronic inflammation mutant (nlrc3l deletion). Single-cell sequencing revealed significant differences in immune cell transcriptome post injury between control and chronic inflammation nlrc3l mutants, and that most irg1 positive cells were macrophages with a fraction of them being altered neutrophils also expressing irg1 after injury particularly in the mutants.
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6. ⭐ GSE312082：结直肠癌对 5-FU 化疗 16 天动力学反应的翻译组和转录组测序数据

• ✍️ 作者：未知作者
• 🏷️ 关键词：cancer、sequencing、transcriptome
• 📝 描述：Contributors : Mounira Chalabi-Dchar ; Laura Jentschel ; Julie Ripoll ; Anne Vincent ; Rita Khoueiry ; Arnaud Vigneron ; Eric Rivals ; Nicole Dalla Venezia ; Julie Pannequin ; Jean-Jacques DiazSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensResistance to 5-fluorouracil (5-FU) remains a major challenge in colorectal cancer therapy, often resulting in tumor relapse fueled by drug-tolerant persister (DTP) cells. Unexpectedly, instead of suppressing translation under chemotherapeutic stress, 5-FU by integrating ribosomal RNA of persister cells drives a transient surge in protein synthesis, revealing a distinct adaptive state. This translational reprogramming drives a highly plastic subpopulation that supports survival under drug pressure. Integrated translatome profiling uncovered selective translation of mRNAs linked to survival pathways including epigenetic and metabolic changes, apoptosis resistance, cell cycle arrest and a senescence-like phenotype. Together, our findings uncover active translation as an unrecognized hallmark of the DTP state.
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7. GSE312178 PM2.5暴露对乳腺癌亚型恶性进展的影响机制[MDA-MB-231 RNA-seq]

• ✍️ 作者：未知作者
• 🏷️ 关键词：cancer、RNA-seq
• 📝 描述：Series Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensAs a major global health threat to women, breast cancer demonstrates significant molecular subtype-specific variations in response to PM2.5 exposure. While epidemiological evidence has confirmed the association between PM2.5 and breast cancer, the molecular mechanisms by which severe PM2.5 pollution drives subtype heterogeneity remain poorly understood and are difficult to characterize using conventional phenotypic approaches. To address this, we apply integrated transcriptomic sequencing and bioinformatics analysis to investigate molecular response mechanisms in three representative breast cancer cell lines—Luminal A (MCF-7), Luminal B (T-47D), and triple-negative (MDA-MB-231)—following severe PM2.5 exposure. Our results reveal that although all three subtypes share a common response to the stress of metal ions and inorganic substances, each exhibits distinct molecular alterations after PM2.5 exposure: the response mechanisms of MCF-7 cells are primarily involved in extracellular matrix remodeling, neuro-lik differentiation, and inflammatory signaling; T-47D cells show significant enrichment in the synaptic membrane, oxidoreductase metabolism, and ferroptosis pathway; and MDA-MB-231 cells exhibit a core response centered on cell cycle progression and mitosis. Furthermore, we identify subtype-specific hub genes and predict the corresponding targeted drugs: Niclosamide targeting BRCA1 in MCF-7, Menadione targeting NQO1 in T-47D, and PHA-793887 targeting CDK1 in MDA-MB-231. This study establishes a comprehensive research framework spanning environmental exposure, cellular response, clinical validation, and drug prediction. The findings provide important insights into the subtype-specific carcinogenic mechanisms of PM2.5 and support the development of individualized prevention strategies for breast cancer.
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8. GSE312177 PM2.5暴露对乳腺癌亚型恶性进展的影响机制[MCF-7 RNA-seq]

• ✍️ 作者：未知作者
• 🏷️ 关键词：cancer、RNA-seq
• 📝 描述：Series Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensAs a major global health threat to women, breast cancer demonstrates significant molecular subtype-specific variations in response to PM2.5 exposure. While epidemiological evidence has confirmed the association between PM2.5 and breast cancer, the molecular mechanisms by which severe PM2.5 pollution drives subtype heterogeneity remain poorly understood and are difficult to characterize using conventional phenotypic approaches. To address this, we apply integrated transcriptomic sequencing and bioinformatics analysis to investigate molecular response mechanisms in three representative breast cancer cell lines—Luminal A (MCF-7), Luminal B (T-47D), and triple-negative (MDA-MB-231)—following severe PM2.5 exposure. Our results reveal that although all three subtypes share a common response to the stress of metal ions and inorganic substances, each exhibits distinct molecular alterations after PM2.5 exposure: the response mechanisms of MCF-7 cells are primarily involved in extracellular matrix remodeling, neuro-lik differentiation, and inflammatory signaling; T-47D cells show significant enrichment in the synaptic membrane, oxidoreductase metabolism, and ferroptosis pathway; and MDA-MB-231 cells exhibit a core response centered on cell cycle progression and mitosis. Furthermore, we identify subtype-specific hub genes and predict the corresponding targeted drugs: Niclosamide targeting BRCA1 in MCF-7, Menadione targeting NQO1 in T-47D, and PHA-793887 targeting CDK1 in MDA-MB-231. This study establishes a comprehensive research framework spanning environmental exposure, cellular response, clinical validation, and drug prediction. The findings provide important insights into the subtype-specific carcinogenic mechanisms of PM2.5 and support the development of individualized prevention strategies for breast cancer.
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9. GSE253891 单细胞和空间组学揭示种子植物木质部发育复杂性的逐渐丧失

• ✍️ 作者：未知作者
• 🏷️ 关键词：single-cell、spatial
• 📝 描述：Contributors : Peng Shuai ; Jo-Wei A Hsieh ; Chung-Ting Kao ; Chen-Wei Hu ; Ray Wang ; Shang-Che Kuo ; Ming-Ren Yen ; Pin-Chien Liu ; Yi-Chi Ho ; Chia-Chen Chu ; Shuotian Huang ; Jiao Liu ; Lixia Zhang ; Chia-Chen Wu ; Yi-Jyun Luo ; Quanzi Li ; Chuan-Chih Hsu ; Chao-Li Huang ; Jung-Chen Su ; Mei-Chun Tseng ; Ying-Lan Chen ; Te-Lun Mai ; Ying-Chung J LinSeries Type : Expression profiling by high throughput sequencingOrganism : Cunninghamia lanceolataSecondary growth is a key characteristic evolved from seed plants and generates secondary xylem—the most abundant tissue on Earth. Recent studies have uncovered xylem developmental lineages in eudicots and magnoliids of angiosperms. However, xylem development in gymnosperms, the other representative clade of seed plants, remained elusive. We performed single-cell transcriptomics for xylem cells of conifers (Cunninghamia lanceolata), the major clade in gymnosperms. Using Seurat and scVI-based cross-species integration, we reconstructed the xylem differentiation trajectories and revealed that the radial system is conserved across seed plants, while the axial system in C. lanceolata exhibits a composite lineage architecture resembling both eudicots and magnoliids. To validate these trajectories, we established a multi-modal spatial framework incorporating spatial transcriptomics, spatial proteomics, and spatial metabolomics. These three spatial layers provided orthogonal evidence confirming cell-type identities and trajectory inference. Additionally, we identified a xylem cell population unique to gymnosperms, suggesting a lineage-specific specialization. Together, our findings uncover a more complex ancestral xylem architecture in gymnosperms and propose a progressive simplification of axial developmental programs from gymnosperms to angiosperms, highlighting a trajectory of reductive evolution in seed plant vascular development.
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10. GSE298031 综合空间分析揭示卵巢癌前病变的分子图谱

• ✍️ 作者：未知作者
• 🏷️ 关键词：spatial
• 📝 描述：Contributors : Ie-Ming Shih ; Tu-Yung Chang ; Tian-Li WangSeries Type : OtherOrganism : Homo sapiensStudying precancerous lesions is essential for improving early detection and prevention, particularly in aggressive cancers such as ovarian carcinoma. Here, we conducted integrated and spatial analyses of transcriptomes, aneuploidy, and clinicopathological features in 166 ovarian precancerous lesions. Four pre-cancerous transcriptomic subtypes were identified: proliferative, immunoreactive, dormant, and mixed. These subtypes varied in their frequency of germline-BRCA1/2 mutations, aneuploidy, CCNE1/MYC amplification, proliferative activity, immune-regulatory gene expression, and histological features. Notably, the immunoreactive subtype upregulated immune-regulatory genes, exhibited chronic inflammation, and was enriched in cases with germline-BRCA1/2 mutations, deletions of chromosomes 17 (harboring TP53 and BRCA1) and 13 (harboring BRCA2), leading to a double “two-hit” involving TP53 and BRCA1/2. Tumor invasion was associated with the activation of interferon response pathways, epithelial-mesenchymal transition, and extracellular matrix remodeling. In summary, these results elucidate the earliest molecular landscape of ovarian precancerous lesions, serving as the foundation for future risk stratification to identify aggressive pre-cancerous lesions.
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1. CircRNF10 通过直接降解和 miR-1275/DKK3 介导的抑制双重调控回路，在驱动基因阴性肺腺癌中进行封存β-catenin。

• ✍️ 作者：未知作者
• 🏷️ 关键词：通路
• 📝 描述：Secret hovertext: 背景 环状 RNA（环 RNA）通过调节与肿瘤发生或肿瘤抑制相关的通路，在肿瘤生物学中发挥关键调控功能。尽管在阐明其在多种恶性肿瘤中的作用方面取得了显著进展，但环 RNA 对驱动基因阴性肺腺癌（LUAD）发病机制的贡献仍然不明确。LUAD 是一种缺乏可作遗传改变且对现有靶向或免疫治疗策略反应有限的分子亚型。方法：通过环 RNA 微阵列分析和 RT-qPCR 验证，分析了驱动基因阴性 LUAD 中 circRNF10 的表达。在体外和体内进行了一系列功能性测定，以评估 circRNF10 对肿瘤细胞行为的影响，包括增殖（EdU 掺入）、迁移（伤口愈合）和侵入（transwell 检测），以及小鼠模型中的肿瘤生长。为阐明其分子机制，我们结合计算和实验方法，包括基于 AlphaFold3 的结构预测、体外转录、生物素标记 RNA 拉下、RNA 免疫沉淀（RIP）以及双荧光素酶报告测定。结果 在本
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2. 结直肠癌中的细胞外囊泡货物调控：免疫逃避、基质重塑与治疗前沿。

• ✍️ 作者：未知作者
• 🏷️ 关键词：免疫
• 📝 描述：Secret hovertext: 细胞外囊泡（EVs）作为肿瘤微环境（TME）细胞间通讯中的关键“信使”，在结直肠癌（CRC）的起始、进展和治疗反应中发挥多方面的调控作用。本综述重点关注 EV 在 CRC 进展中的作用，包括免疫抑制微环境的创建以及 TME 内其他细胞的调节。此外，本文简要讨论了 EV 在早期诊断和转移预测中的潜在生物标志物价值。此外，本文介绍了多种利用 EV 进行 CRC 治疗的治疗策略，如辅助免疫疗法、干细胞衍生 EV 的使用以及工程化 EVs。在此背景下，我们强调基于胚胎血脉瘤（EV）研究的局限性和挑战，并探讨该领域的未来展望，旨在实现其在 CRC 精确诊断和治疗中的实际应用。
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• GSE283438 基于新型irg1敲入报告基因对分选的斑马鱼巨噬细胞进行批量RNA测序，比较对照组和nlrc3l突变体在基线和损伤条件下的表达情况
• GSE281292 利用超抗体编辑器通过引导超突变恢复中和抗体的效力 [抗体测序]
• GSE281195 利用超抗体编辑器引导超突变恢复中和抗体的效力
• GSE312386 早期生命微生物群影响骨髓造血前体细胞的长期基因表达和表观基因组
• GSE312291 支链脂肪酸iso15:0通过抑制GPCR/PI3K/AKT通路抑制HCC恶性进展的新功能
• GSE306819 双相情感障碍患者死后丘脑和皮质的单核RNA测序
• GSE220632 SETD1A 是维持肠道稳态和预防 DNA 损伤所必需的