详细内容（前10条）

1. ⭐ GSE303036 圆锥角膜的眼锥空间转录组学

• ✍️ 作者：未知作者
• 🏷️ 关键词：spatial、spatial transcriptomics、transcriptomics
• 📝 描述：Contributors : Alicja Wysocka ; Katarzyna Jaskiewicz-Rajewicz ; Jakub Wozniak ; Malgorzata Rydzanicz ; Rafal Ploski ; Monika Udziela ; Jacek Szaflik ; Marzena GajeckaSeries Type : OtherOrganism : Homo sapiensThe cornea is a transparent, avascular eye tissue composed of five layers: epithelium, Bowman’s layer, stroma, Descemet’s membrane, and endothelium, each of which, if affected by keratoconus (KTCN), may exhibit specific morphological changes. Due to the complexity of the tissue, the studies preserving the spatial location should be applied to identify the layer-specific molecular changes in KTCN, for further understanding of the mechanistic aspects of its cone formation.
• 🔗 查看原文

2. ⭐ GSE301378 输卵管及其匹配的卵巢癌样本中组织驻留记忆T细胞的单细胞RNA测序和TCR谱分析

• ✍️ 作者：未知作者
• 🏷️ 关键词：cancer、RNA-seq、single-cell
• 📝 描述：Contributors : Luyao Wang ; Breeshey Roskams-Hieter ; Nancy Zaarour ; Ahmed AhmedSeries Type : Expression profiling by high throughput sequencing ; OtherOrganism : Homo sapiensThis study investigates the immune characteristics of tissue-resident memory T cells in the human fallopian tube in high-grade serous ovarian cancer (HGSOC). Single-cell RNA sequencing (scRNA-seq) and paired T-cell receptor sequencing (scTCR-seq) were performed on samples from non-cancerous fallopian tube tissue, metastatic omental tumors, and peripheral blood from HGSOC patients.The dataset enables analysis of tissue-resident T cell populations, clonal relationships across tissues, and immune features associated with tumor progression. These data provide a resource for studying tissue-resident T cell heterogeneity, clonal expansion, and tumor-associated immune responses in ovarian cancer.
• 🔗 查看原文

3. GSE281482 移植后间充质细胞的单细胞多组学分析揭示了肺纤维化的分子特征和调节因子（单细胞多组测序）

• ✍️ 作者：未知作者
• 🏷️ 关键词：sequencing、single-cell
• 📝 描述：Contributors : Lu Lu ; Aidan P McLinden ; Natalie M Walker ; Ragini Vittal ; Michael P Combs ; Joshua D Welch ; Vibha N LamaSeries Type : Genome binding/occupancy profiling by high throughput sequencing ; Expression profiling by high throughput sequencingOrganism : Homo sapiensChronic lung allograft dysfunction (CLAD) is a critical challenge in lung transplantation. Dysregulated gene expression and epigenomic states in lung mesenchymal cells (MCs) play a key role in these conditions. We performed single-cell multi-omic profiling on MCs isolated from human bronchoalveolar lavage samples of lung transplant recipients with CLAD, compared with time-matched controls. Our results provide deeper insights into the transcriptomic and epigenomic changes in post-transplant MCs, nominating biomarkers and disease-associated factors with implications for future therapeutic efforts.
• 🔗 查看原文

4. GSE326997 行为灵活性和肠道微生物群作为口服羟考酮自我给药的潜在预测因子

• ✍️ 作者：未知作者
• 🏷️ 关键词：gut、regex:gut(-?microbiome)?
• 📝 描述：Contributors : Claire M Corbett ; Alexis E O’Shall ; Mark Niedringhaus ; Elizabeth A WestSeries Type : OtherOrganism : feces metagenomePrescription opioids such as oxycodone have been widely used in the United States and have contributed to the ongoing opioid epidemic. While many individuals limit use to prescribed contexts, a subset transitions to misuse and, in some cases, to illicit opioid use. Identifying behavioral and biological factors that predict this vulnerability is critical for improving prevention and intervention strategies. Here, we investigated whether individual differences in behavioral flexibility and gut microbiome composition are associated with future oxycodone intake using a translationally relevant model of oral oxycodone self-administration in male and female Long-Evans rats. We established a model in which distinct intake phenotypes emerged, characterized by animals with high versus low oxycodone consumption. Behavioral flexibility, assessed using a contingency degradation task, was associated with oxycodone intake, identifying it as a potential behavioral biomarker of vulnerability. In parallel, oral oxycodone exposure altered gut microbiome composition, and microbiome features were associated with both behavioral flexibility and drug-taking behavior. These findings support a framework in which individual differences in opioid intake arise from the interaction of pre-existing behavioral traits and biological states, including gut microbiome composition which provides a foundation for identifying predictive biomarkers and developing individualized strategies to mitigate risk for opioid misuse.
• 🔗 查看原文

5. GSE326400 高效稳健地生成功能性嵌合抗原受体工程化小鼠巨噬细胞，可缓解心脏纤维化

• ✍️ 作者：未知作者
• 🏷️ 关键词：antigen、cardiac
• 📝 描述：Contributors : Hengxing Lu ; Jishou Zhang ; Hailing ZhangSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusTo investigate the therapeutic potential of chimeric antigen receptor engineered macrophages (CAR-Ms), studies in immunocompetent mouse models are essential. However, due to the low editing efficiency and limited proliferative capacity of primary murine macrophages, efficient generation of functional CAR-Ms remains a technical challenge, hampering the advancement of this promising immunotherapeutic approach. Here, we established immortalized mouse monocytes using the DHFR-HOXB8 system, in which the presence of overexpressed HOXB8 protein is controlled by trimethoprim (TMP), allowing for conditional immortalization and subsequent macrophage differentiation. Transcriptomic and functional analyses confirmed that DHFR-HOXB8-derived cells retain bona fide monocyte and macrophage identity, closely resembling primary cells. Using this platform, we achieved CAR editing efficiencies exceeding 95% in monocytes/macrophages and showed that CAR expression conferred potent phagocytic and cytotoxic activity upon DHFR-HOXB8-derived macrophages against target cells. Adoptive transfer of FAP-targeted CAR-Ms in mouse models of myocardial infarction (MI) and transverse aortic constriction (TAC) attenuated cardiac fibrosis and improved cardiac function, demonstrating their in vivo activity and underscoring their therapeutic potential across diverse cardiac pathologies. This study thus provides a potent platform for generating genetically engineered macrophages suitable for preclinical murine studies.
• 🔗 查看原文

6. GSE326394 全基因组鉴定维生素 D 受体调控的增强子 RNA 揭示了 CYP24A1 转录的表观遗传调控

• ✍️ 作者：未知作者
• 🏷️ 关键词：genome、epigenetic
• 📝 描述：Contributors : Takahiro Sawada ; Koki Nojiri ; Yoshiak Kanemoto ; Thi-Ngoc T Nguyen ; Yusuke Hakozaki ; Tomoyuki Kurokawa ; Shigeaki KatoSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensVitamin D (VD) exerts diverse physiological and pathological effects primarily through the vitamin D receptor (VDR), a ligand-dependent transcription factor. However, the limited number of known VDR target genes does not fully explain the broad spectrum of VD actions. In this study, we performed a comprehensive genome-wide analysis to identify enhancer RNAs (eRNAs) involved in VD-dependent gene regulation. Using integrated ChIP-seq, RNA-seq, and NET-CAGE analyses in human HCT116 and HaCaT cells, we mapped VDR binding sites and identified VD-responsive transcripts. VDR binding was strongly dependent on vitaminD and predominantly localized to enhancer regions marked by H3K27ac, indicating association with active chromatin. Through stepwise filtering, we identified a limited number of high-confidence eRNA candidates associated with VDR-bound regulatory regions. Among these, eRNAs located at the CYP24A1 locus were robustly induced by VD and correlated with strong transcriptional activation of the gene. Functional analyses using BET inhibition and LNA-mediated knockdown demonstrated that these eRNAs contribute to VD-dependent transcription. Furthermore, CRISPR/dCas9-mediated induction of specific eRNAs enhanced CYP24A1 expression, supporting a direct regulatory role. In contrast, newly identified target genes such as DLX2 and SYT8 exhibited modest, cell type–dependent responses to VD. Our findings reveal that VDR-mediated gene regulation involves a limited but functionally significant set of eRNAs, particularly at super-enhancer regions, and highlight a unique epigenetic mechanism underlying VD action.
• 🔗 查看原文

7. GSE313813 单核细胞趋化因子增强细菌性肾脏感染后动脉粥样硬化斑块坏死

• ✍️ 作者：未知作者
• 🏷️ 关键词：monocyte、regex:bacter(ia|ial|ium)
• 📝 描述：Contributors : Lena Possenriede ; Peyman Falahat ; Marie Foerster ; Georg W Sendtner ; Julia Miranda ; Leonie Richard-Strophal ; Uta Scheidt ; Christian Kurts ; Florian Wagenlehner ; Ekaterina K Koltsova ; Sibylle von VietinghoffSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusUrinary tract infections (UTI) are frequent and highly inflammatory. Using a pyelonephritis mouse model, we investigated the impact of pyelonephritis on the development of atherosclerosis. Bulk RNA sequencing analysis of kidneys and aortas harvested four weeks post-infection was performed to identify key molecular markers and delineate differentially regulated inflammatory pathways in both organs. Our results show an upregulation of inflammatory mediators in kidney and aorta, providing a possible mechanistic link between pyelonephritis and atherosclerosis.
• 🔗 查看原文

8. GSE326913 光遗传受体酪氨酸激酶信号传导诱导发育启发式出芽形态发生

• ✍️ 作者：未知作者
• 🏷️ 关键词：kinase
• 📝 描述：Contributors : Alex Hughes ; Louis Prahl ; Ronald Canlla ; Sandra ShefterSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensThe mammalian kidney relies on a branched network of collecting ducts for fluid transport and homeostasis. Replicating this network in vitro would parallelize function in synthetic replacement kidneys, yet current organoids have limited branching capacity. Here, we establish a developmentally-informed strategy to control organoid budding through optogenetic control of a receptor tyrosine kinase, RET. We first show pharmacological manipulation of RET signaling controls the extent of branching in mouse embryonic kidneys and human stem cell-derived kidney organoids. Next, we develop an optogenetic RET receptor (optoRET) that signals in a ligand-independent manner via blue light-mediated clustering. Epithelial cells expressing optoRET reproduce stereotyped RET signaling, scattering, and symmetry breaking in response to blue light. Human kidney organoids undergo budding with controllable orientation in response to spatially patterned optoRET stimulation. Our results establish ligand-free optogenetic control of branching and inspire new synthetic biology strategies for epithelial organoid design.
• 🔗 查看原文

9. GSE310111 BAY 11-7082 通过抑制经典 NF-κB 信号通路发挥抗病毒和抗炎双重作用，抑制 SARS-CoV-2 感染

• ✍️ 作者：未知作者
• 🏷️ 关键词：pathway
• 📝 描述：Contributors : Chin-Mao Hung ; Po-Chih Wu ; Meng-Chang Lee ; Ming-Sian Wu ; Chun-Hsi Tso ; Jia-Chuan Hsu ; Der-Yuan Wang ; Hao-Ai Shui ; Chi-Tun Tang ; Chia-Wen ShihSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensThe continued emergence of SARS-CoV-2 variants and persistent inflammatory complications of COVID-19 highlight the urgent need for therapeutics with both antiviral and anti-inflammatory properties. Despite intensive global efforts, no approved antiviral therapy with these dual functions has yet been developed, representing a significant gap in current COVID-19 treatment strategies. In this study, we identify BAY 11-7082 (BAY) as a dual–action compound that inhibits SARS-CoV-2 replication and the production of virus-induced proinflammatory cytokines and chemokines, including IL-6, IL-8, CXCL1, and CXCL2. BAY predominantly exerts its antiviral activity at the post-entry stage of the viral life cycle. Mechanistically, BAY potentially interacts with SARS-CoV-2 NSP14 and inhibits virus-induced phosphorylation and degradation of IκBα, suppressing NF-κB activation through the IKK-IκBα signaling axis. Furthermore, BAY exhibits potent antiviral activity against multiple SARS-CoV-2 variants of concern (VOCs). Collectively, these findings support the potential of BAY as a dual-action therapeutic candidate, combining antiviral and anti-inflammatory effects, against SARS-CoV-2 and its emerging variants.
• 🔗 查看原文

10. GSE316584 微RNA-224调控BMP通路，并代表肺动脉高压的新治疗靶点

• ✍️ 作者：未知作者
• 🏷️ 关键词：pathway
• 📝 描述：Contributors : Yassine Sassi ; Aymen Halouani ; Yifei Sun ; Martin Walsh ; Lahouaria HadriSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusMice were maintained under hypoxic conditions for 3 weeks with weekly Sugen injections and were then randomized to receive an intratracheal injection of a chemically modified antisense oligonucleotide targeting miR-224 (LNA-224) or a control antimiR (LNA-Ctrl; 5 mg/kg each) at week 3. A separate group of mice was maintained under normoxic conditions and received an intratracheal injection of LNA-Ctrl at week 3 (Nox). All mice were sacrificed at week 6, and scRNA-seq analyses were performed.
• 🔗 查看原文

💡 该来源还有 9 条内容，详见 文末

详细内容（全部2条）

1. 深度学习改进了单细胞RNA测序数据的分析。

• ✍️ 作者：未知作者
• 🏷️ 关键词：sequencing
• 📝 描述：RNA sequencing combined with deep learning improves identification of cell populations and key genes, enabling more accurate analysis of complex single cell datasets…
• 🔗 查看原文

2. SPTEdU-seq——无需光学器件的并行新生儿细胞追踪和空间总转录动态

• ✍️ 作者：未知作者
• 🏷️ 关键词：spatial
• 📝 描述：RNA sequencing combined with spatial profiling tracks gene expression and cell proliferation, revealing dynamic cellular interactions and uncovering new insights into development…
• 🔗 查看原文

• GSE314390 烟酰胺核苷通过增强 NAD⁺ 水平激活 SLIT2/ROBO1 信号通路来减弱银屑病中的 Th17 炎症
• GSE296612 KLF2-KLF3 调控的细胞定位对耗竭 T 细胞分化的影响 [scMultiome-seq]
• GSE296608 KLF2-KLF3 调控的细胞定位对耗竭 T 细胞分化的影响 [CUT&Tag]
• GSE176376 特异性 Hnrnpa2b1 过表达的 iWAT 中 RNA 的转录组分析
• GSE326530 比较昼夜节律转录组分析揭示日晒皮肤的节律减弱和相位提前
• GSE326484 多巴胺受体抑制和放射疗法联合靶向间皮瘤起始细胞并提高间皮瘤小鼠模型的生存率[scRNA-Seq]
• GSE326337 梭杆菌FadA通过与TFRC结合促进食管鳞状细胞癌的进展
• GSE293902 Deltex-1 (Dtx1) 对生发中心 B 细胞稳态的调控 [scRNA]
• GSE326179 Beckwith-Wiedemann 谱显示由全基因组父系单亲异二体引起的 46,XY 核型