详细内容（前10条）

1. ⭐ GSE344364 单细胞和空间转录组图谱揭示了胡萝卜主根次生生长和特化代谢的遗传调控[空间转录组学]

• ✍️ 作者：未知作者
• 🏷️ 关键词：metabolism、single-cell、spatial、spatial transcriptomics、transcriptomics
• 📝 描述：Contributors : Xiaoyu Han ; Ye Chen ; Xinyue Zhan ; Song Yang ; Pinli Hu ; Siqi Liang ; Bao Nie ; Xing Liu ; Feiyun Zhuang ; Haojing Shao ; Cheng Li ; Li WangSeries Type : OtherOrganism : Daucus carotaCarrot (Daucus carota) is an economically important vegetable, accumulating a wealth of bioactive secondary metabolites (SMs), and is a promising model species for investigating storage root development. However, the regulatory mechanisms governing root thickening and cell-type-specific SM biosynthesis remain largely elusive. Here, we combined single-cell RNA sequencing and Stereo-seq spatial transcriptomics to construct a high-resolution spatiotemporal transcriptomic atlas of carrot taproots during secondary growth. We resolved the cell fate trajectory of major vascular tissues and revealed that sequential expression of NAC transcription factors (TFs) drove xylem differentiation prior to phloem development. Spatiotemporal screening further identified DcERF1 as a critical positive regulator of the biosynthesis of falcarindiol, a vital anti-cancer SM. This study elucidates the regulatory mechanisms underlying carrot taproot secondary development and specialized metabolism, providing a valuable resource for improving the yield and nutritional quality of storage root crops.
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2. ⭐ GSE343114 挖掘微生物转录组以在肠道驻留拟杆菌科中构建基于细胞的细菌生物传感器 [DSS RNAseq]

• ✍️ 作者：未知作者
• 🏷️ 关键词：regex:micro(b|be|bial|organism)、regex:bacter(ia|ial|ium)、RNAseq、gut、regex:gut(-?microbiome)?
• 📝 描述：Contributors : Joshua Glazier ; Mark MimeeSeries Type : Expression profiling by high throughput sequencingOrganism : Bacteroides thetaiotaomicron ; mouse gut metagenomeThe gastrointestinal tract is rich in metabolic, immune, and microbiome-derived signals that can inform the design of live biotherapeutics and diagnosis of intestinal disorders. Engineered cell-based biosensors can tap into this molecular information and report on their environment, yet their development in gut-resident symbionts has been limited by a lack of validated sensor systems. Here, we present a generalizable pipeline that leverages bacterial transcriptional profiling to identify environment-responsive systems for biosensor engineering. Candidate Sensors Systems (CSSs) mined from healthy, disease, and in vitro transcriptomes were assembled into a barcoded library in Bacteroidaceae chassis and screened in high-throughput in vivo to identify responsive promoters. A unique Bacteroidales ECF-type sigma factor operon with ties to sphingolipid metabolism and flux was highly responsive in chemically-induced colitis models. The biosensor responded robustly to disease and returned to baseline upon recovery, establishing an in vivo-driven strategy for discovering functional biosensors in non-model gut-resident bacteria.
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3. ⭐ GSE344363 单细胞和空间转录组图谱揭示了胡萝卜主根次生生长和特化代谢的遗传调控 [scRNA-seq]

• ✍️ 作者：未知作者
• 🏷️ 关键词：metabolism、single-cell、scRNA、spatial
• 📝 描述：Contributors : Xiaoyu Han ; Ye Chen ; Song Yang ; Xinyue Zhan ; Pinli Hu ; Siqi Liang ; Bao Nie ; Xing Liu ; Feiyun Zhuang ; Haojing Shao ; Cheng Li ; Li WangSeries Type : Expression profiling by high throughput sequencingOrganism : Daucus carotaCarrot (Daucus carota) is an economically important vegetable, accumulating a wealth of bioactive secondary metabolites (SMs), and is a promising model species for investigating storage root development. However, the regulatory mechanisms governing root thickening and cell-type-specific SM biosynthesis remain largely elusive. Here, we combined single-cell RNA sequencing and Stereo-seq spatial transcriptomics to construct a high-resolution spatiotemporal transcriptomic atlas of carrot taproots during secondary growth. We resolved the cell fate trajectory of major vascular tissues and revealed that sequential expression of NAC transcription factors (TFs) drove xylem differentiation prior to phloem development. Spatiotemporal screening further identified DcERF1 as a critical positive regulator of the biosynthesis of falcarindiol, a vital anti-cancer SM. This study elucidates the regulatory mechanisms underlying carrot taproot secondary development and specialized metabolism, providing a valuable resource for improving the yield and nutritional quality of storage root crops.
• 🔗 查看原文

4. ⭐ GSE343117 挖掘微生物转录组以在肠道驻留拟杆菌科中构建基于细胞的细菌生物传感器 [BCSeq]

• ✍️ 作者：未知作者
• 🏷️ 关键词：regex:micro(b|be|bial|organism)、regex:bacter(ia|ial|ium)、gut、regex:gut(-?microbiome)?
• 📝 描述：Contributors : Joshua Glazier ; Mark MimeeSeries Type : OtherOrganism : mouse gut metagenomeThe gastrointestinal tract is rich in metabolic, immune, and microbiome-derived signals that can inform the design of live biotherapeutics and diagnosis of intestinal disorders. Engineered cell-based biosensors can tap into this molecular information and report on their environment, yet their development in gut-resident symbionts has been limited by a lack of validated sensor systems. Here, we present a generalizable pipeline that leverages bacterial transcriptional profiling to identify environment-responsive systems for biosensor engineering. Candidate Sensors Systems (CSSs) mined from healthy, disease, and in vitro transcriptomes were assembled into a barcoded library in Bacteroidaceae chassis and screened in high-throughput in vivo to identify responsive promoters. A unique Bacteroidales ECF-type sigma factor operon with ties to sphingolipid metabolism and flux was highly responsive in chemically-induced colitis models. The biosensor responded robustly to disease and returned to baseline upon recovery, establishing an in vivo-driven strategy for discovering functional biosensors in non-model gut-resident bacteria.
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5. ⭐ GSE314531 高分辨率空间转录组学研究：Ep-FH 处理的受照射小鼠颌下腺

• ✍️ 作者：未知作者
• 🏷️ 关键词：spatial、spatial transcriptomics、transcriptomics
• 📝 描述：Contributors : Kihoon Nam ; Mark Maienschein-Cline ; Rodrigo A Osorio ; Harim Tavares dos Santos ; Frank M Maslow ; Stelios T Andreadis ; Olga J BakerSeries Type : OtherOrganism : Mus musculusOur previous studies developed a novel scaffold by chemically conjugating laminin-1 peptides (A99 and YIGSR) and growth factors, FGF-7 and FGF-10, to fibrin hydrogels (Ep-FH). The resulting hydrogel, Ep-FH applied via a single intraglandular injection to irradiated mouse submandibular gland (SMG), enhanced epithelial tissue organization while promoted secretory function after 60 days of treatment. Together these results suggest a remarkable potential for clinical applications; however, before applying Ep-FH in a clinical setting, it is necessary to understand how the treatment affects different cell populations within SMG. Therefore, the goal of this study was to perform high-resolution spatial transcriptomics (Xenium 10 Genomics) to characterize how treatment with Ep-FH alters irradiated mouse SMG cell populations as well as relevant signaling mechanisms.
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6. ⭐ GSE344216 单核转录组学揭示重度抑郁症患者背外侧前额叶皮层中神经元、免疫细胞和胶质细胞的协同失调

• ✍️ 作者：未知作者
• 🏷️ 关键词：immune、Neuronal、transcriptomics
• 📝 描述：Contributors : Yogesh Dwivedi ; Aleena FrancisSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensWe used single-nucleus RNA sequencing to define cell-type-specific molecular alterations in the dorsolateral prefrontal cortex (dlPFC) of individuals with MDD. We assessed cell-type composition, differential expression, pathway enrichment, oligodendrocyte-lineage pseudotime, ligand-receptor communication, transcription-factor regulon activity, and overlap with MDD-linked genetic variants. The integrated atlas resolved excitatory and inhibitory neuronal subclasses, oligodendrocyte-lineage cells, astrocytes, microglia/perivascular macrophages, endothelial cells, and vascular-associated populations.
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7. ⭐ GSE344166 整合空间和单细胞分析表明，CCL21+淋巴内皮细胞是肢端黑色素瘤中有利免疫环境的驱动因素

• ✍️ 作者：未知作者
• 🏷️ 关键词：immune、regex:lymph(o|atic)?、spatial
• 📝 描述：Contributors : Larissa Anastacio Da Costa Carvalho ; Y. Ann Chen ; Keiran S.M. SmalleySeries Type : OtherOrganism : Homo sapiensAcral melanoma (AM) is a rare type of melanoma that responds poorly to immunotherapy. In the current study we undertook integrated single cell RNA-Seq, spatial transcriptomics and multiplexed immunofluorescence to identify potential regulators of the immune environment. Our analyses identified distinct immune habitats at the invasive front, intratumoral regions and areas of distant inflammation across the AM samples. Two distinct subclasses of endothelial cells were identified, one with an immune-regulating profile (CCL21, IGF1, IL-7, PDPN) that were characteristic of lymphatic endothelial cells (LECs) and a population of vascular endothelial cells (VECs) (SPARCL1, PVLAP, ADGRL4). Cell-cell interaction and correlation analysis showed the CCL21+ LECs to be a strong regulator of the immune microenvironment through communication with dendritic cells (DCs) and CD4+ T cells. These LEC-dendritic cell interactions were mediated through CCL21-CCR7 and were strongly correlated in both the single cell and spatial data. By contrast, the VECs were predicted to interact with fibroblasts and macrophages. Validation by multiplexed immunofluorescence identified LECs in the majority of AM samples and demonstrated that only those staining positively for CCL21 were spatially associated with DCs, B-cells and CD4+ T-cells. Expression of CCL21 and CCR7 showed a significant correlation and were associated with increased survival in melanoma patient cohorts. Together these data identify the presence of CCL21+ LECs in acral melanoma that positively regulate the immune microenvironment.
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8. ⭐ GSE337500 8 个三阴性乳腺癌细胞系的 RNA-seq 和 ATAC-seq 处理数据 [ATAC-Seq]

• ✍️ 作者：未知作者
• 🏷️ 关键词：cancer、RNA-seq、ATAC-seq
• 📝 描述：Contributors : Johan Staaf ; Deborah F NacerSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Homo sapiensMultiomics data were generated from triple-negative breast cancer (TNBC) cell lines to compare patterns first observed in TNBC tumors, as well as to inform possible gene regulation occurring specifically in tumor cells.
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9. ⭐ GSE337499 8 个三阴性乳腺癌细胞系的 RNA-seq 和 ATAC-seq 处理数据 [RNA-Seq]

• ✍️ 作者：未知作者
• 🏷️ 关键词：cancer、RNA-seq、ATAC-seq
• 📝 描述：Contributors : Johan Staaf ; Deborah F NacerSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensMultiomics data were generated from triple-negative breast cancer (TNBC) cell lines to compare patterns first observed in TNBC tumors, as well as to inform possible gene regulation occurring specifically in tumor cells.
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10. GSE342688 鼻窦和颅底腺样囊性癌肿瘤内异质性和微环境的单细胞解剖

• ✍️ 作者：未知作者
• 🏷️ 关键词：carcinoma、single-cell
• 📝 描述：Contributors : Yan Fang ; Weihong JiangSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensWe profiled 8 patients with sinonasal-skull base adenoid cystic carcinoma by single-cell RNA sequencing (10x Genomics) to characterize intratumoral heterogeneity and the immune landscape.
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1. 一种主要的阿尔茨海默病风险基因可能在症状出现前数年就导致脑细胞萎缩。

• ✍️ 作者：未知作者
• 🏷️ 关键词：Alzheimer
• 📝 描述：Researchers have uncovered a possible reason why the Alzheimer’s risk gene APOE4 can disrupt the brain long before memory problems begin. In mice, APOE4 increased a protein called Nell2, shrinking neurons and making memory circuits unusually active. That early hyperactivity predicted worse memory later in life. Reducing Nell2 in adult mice reversed the abnormal changes, raising hopes for a new way to intervene before Alzheimer’s progresses.
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• GSE342687 鼻窦和颅底腺样囊性癌肿瘤内异质性和微环境的空间转录组学解析
• GSE339482 利用单细胞多组学[scRNA-Seq]解码胶质母细胞瘤的可塑性调节因子和转变轨迹
• GSE336321 利用单细胞多组学解码胶质母细胞瘤的可塑性调节因子和转变轨迹 [ATAC-seq]
• GSE294939 利用单细胞多组学[RNA-seq]解码胶质母细胞瘤的可塑性调节因子和转变轨迹
• GSE262408 单细胞转录组学揭示高脂饮食对下丘脑（ARC）和后脑（DVC）葡萄糖感知的影响[实验诱导普通饲料喂养小鼠高血糖]
• GSE262407 单细胞转录组学揭示高脂饮食对下丘脑（ARC）和后脑（DVC）葡萄糖感知的影响[饮食诱导肥胖小鼠实验性高血糖]
• GSE339230 白细胞介素-1介导胰岛中的先天免疫信号传导和抗病毒防御
• GSE307398 帕博利珠单抗联合卡培他滨和贝伐珠单抗治疗微卫星稳定/错配修复功能正常的转移性结直肠癌的II期研究
• GSE344487 Paneth细胞来源的Notch配体DLL1和DLL4对肠隐窝基底干细胞至关重要
• GSE344336 lncRNA uc.123 和 uc.382 通过染色质水平表观遗传重编程和改变转录动力学将早期生活压力与抑郁症易感性联系起来 [ChIRP-Seq ELS]
• GSE344329 lncRNA uc.123 和 uc.382 通过染色质水平表观遗传重编程和改变转录动力学将早期生活压力与抑郁症易感性联系起来 [ChIRP-Seq]
• GSE344273 CACNA1C 基因变异通过不同的途径对神经元网络产生不同的影响
• GSE320374 协同靶向MET和mTOR可克服胶质母细胞瘤的适应性耐药性
• GSE309737 小鼠野生型和 Uhrf1-/- E9.5 胚胎干细胞 (ESC) 的 RNAseq 分析
• GSE309704 小鼠野生型和 Uhrf1-/- E9.5 胚胎的 RNA 测序分析
• GSE309154 不同的细胞毒性和免疫调节免疫程序将麻疹样药物疹与 SDRIFE 区分开来
• GSE309152 不同的细胞毒性和免疫调节免疫程序将麻疹样药物疹与 SDRIFE 区分开来
• GSE308697 不同的细胞毒性和免疫调节免疫程序区分了麻疹样药物疹和 SDRIFE
• GSE306224 GNAQ p.R183Q 内皮细胞无法响应层流剪切应力而排列，并表现出 MAPK、炎症和细胞黏附基因表达增加。
• GSE294940 利用单细胞多组学解码胶质母细胞瘤中的可塑性调节因子和转变轨迹
• GSE294518 利用单细胞多组学解码胶质母细胞瘤的可塑性调节因子和转变轨迹 [CUT&RUN]
• GSE344586 通过比较患者和小鼠相应原位异种移植瘤，揭示胶质母细胞瘤侵袭的代谢和转录组特征
• GSE331021 肌母细胞和横纹肌肉瘤细胞系中 DEGS1 过表达的批量 RNA 测序。
• GSE330085 性别差异的骨骼肌重塑在癌症恶病质早期出现