详细内容（前10条）

1. ⭐ GSE297388 B6-mdx 和 D2-mdx 小鼠腓肠肌的空间转录组学和单细胞 RNA 测序

• ✍️ 作者：未知作者
• 🏷️ 关键词：sequencing、scRNA、spatial、spatial transcriptomics、transcriptomics
• 📝 描述：Contributors : Caroline E Brun ; Fabien Le Grand ; Bénédicte ChazaudSeries Type : Other ; Expression profiling by high throughput sequencingOrganism : Mus musculusWe investigated the cell-type composition of muscle domains that associate with muscle degeneration severity in two mouse models of human DMD, namely the B6.mdx and D2.mdx. We first combined immunofluorescence-based histological analysis and spatial transcriptomics to highlight specific muscle tissue clusters that display dystrophic features with necrotic fibers, inflammatory cell infiltration and increased fibrosis. Using single-cell RNA-sequencing reference and spatial deconvolution, we profiled cell types and states within each dystrophic domain, thereby identifying the enrichment for specific cell subpopulations in these spatial clusters.
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2. ⭐ GSE330658 抗PD-L1/VEGF疗法在EGFR-TKI初治的EGFR突变型肺癌（肿瘤微环境无炎症）中免疫介导疗效有限

• ✍️ 作者：未知作者
• 🏷️ 关键词：tumor、cancer、immune、tumor microenvironment
• 📝 描述：Contributors : Atsuko Hirabae ; Kadoaki Ohashi ; Shuta TomidaSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusPatients with EGFR-mutated lung cancer show limited response to immune checkpoint inhibitors. In this study, we found that anti-PD-L1/VEGF combination therapy failed to activate tumor immunity in a syngeneic Egfr-mutant lung cancer mouse model. Unlike the combination of paclitaxel (PTX) and anti-PD-L1, the combination of PTX and anti-VEGF enhanced anti-tumor effects and altered the tumor microenvironment (TME), showing potential to activate anti-tumor immunity. To investigate these mechanisms, we profiled the transcriptomes of tumors treated with PTX and/or anti-VEGF. The data suggested a potential trend where the combination of PTX and anti-VEGF therapy might be associated with a modest increase in natural killer (NK) cell populations within the TME.
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3. ⭐ GSE329033 谷氨酸-半胱氨酸连接酶的代谢抑制增强黑色素瘤中树突状细胞介导的抗肿瘤免疫

• ✍️ 作者：未知作者
• 🏷️ 关键词：tumor、immunity、dendritic cell、metabolic
• 📝 描述：Contributors : Sophie M Dieckmann ; Patrizia Stoitzner ; Irene Rigato ; Francesca FinotelloSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusMetabolic competition and nutrient restriction in the tumor microenvironment (TME) shape the immune infiltrate in tumors and subsequently tumor immunity. In this study we used the transgenic melanoma mouse model tg(Grm1)EPv, which spontaneously develops melanoma due to the ectopic expression of the metabotropic glutamate receptor 1 (Grm1) in melanocytes to investigate if aberrant glutamate metabolism drives tumor formation, and affects immune cell function. LC-MS/MS-based metabolomic analyses and RNA sequencing revealed changes in glutaminolysis, a glycolytic shift (Warburg effect), and reduced ATP levels in advanced tumors compared with tumor free tissue, suggesting respiratory chain dysfunction. These metabolic changes in the TME are advantageous for the tumor cells and unfavorable for immune cells, such as dendritic cells (DC). Indeed, flow cytometry analysis of myeloid subsets during tumor progression showed a decline in tumor-infiltrating conventional type 2 dendritic cell (cDC2) and macrophages, alongside an increase in neutrophil and monocyte populations in advanced lesions. Interference with glutaminolysis using L-buthionine sulfoximine (BSO), an inhibitor of the glutamylcysteine synthetase depleting cellular glutathione levels, induced immunogenic cell death, namely ferroptosis, in an tg(Grm1)EPv -derived cell line in vitro. Therefore, we evaluated the combination of this inhibitor with immunotherapy as a promising new approach for the treatment of tumors in the tg(Grm1)EPv mouse model. We observed that tumor growth could be delayed in vivo when BSO was combined with a therapy regimen boosting DC numbers and activation. This knowledge can drive the design of novel therapeutic strategies for cancer patients involving potential modification of tumor glutamate metabolism.
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4. ⭐ GSE313035 METIMMOX：结直肠癌转移——奥沙利铂塑造抗肿瘤免疫

• ✍️ 作者：未知作者
• 🏷️ 关键词：tumor、cancer、immunity
• 📝 描述：Contributors : Paula Anna Bousquet ; Kjersti Flatma ; Anne Hansen Ree ; Sebastian MeltzerSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensThis study aims to determine the efficacy, safety, and tolerability of the sequential addition of immune-modulating therapy to standard-of-care therapy of microsatellite-stable (MSS)/mismatch repair-proficient (pMMR) metastatic colorectal cancer (mCRC).Patients with MSS/pMMR-mCRC harbor tumor that can be transformed into an immunogenic disease by short-course oxaliplatin-based therapy, and may thereby benefit from the addition of immune-modulating therapy to improve outcome of the current oxaliplatin-based standard-of-care. Primary objective: To determine progression-free survival (PFS), in terms of failure of treatment strategy, of sequential treatment with the Nordic FLOX (5-Fluorouracil, oxaliplatin and leucovorin) regimen and nivolumab compared with the standard-of-care Nordic FLOX regimen in previously untreated MSS/pMMR-mCRC. Secondary objectives: To determine safety and tolerability of sequential treatment with the Nordic FLOX regimen and nivolumab compared with the standard-of-care Nordic FLOX regimen. To monitor and compare quality-of-life (QoL) alterations during therapy courses.
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5. ⭐ GSE287472 LUAD 空间转录组学

• ✍️ 作者：未知作者
• 🏷️ 关键词：spatial、spatial transcriptomics、transcriptomics
• 📝 描述：Contributors : Damien Chua ; Shumin Liao ; Liang LiSeries Type : OtherOrganism : Homo sapiensIn this study, we performed spatial transcriptomics and bulk transcriptomics to profile LUAD patient samples. Next we constructed lung tumoroid from the patient and performed bulk transcriptome profiling to demonstrate its relevancy, and drug sensitivity assays
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6. GSE337162 人类线粒体基因组单细胞变异图谱揭示了细胞类型特异性和疾病相关的变化

• ✍️ 作者：未知作者
• 🏷️ 关键词：single-cell、genome
• 📝 描述：Contributors : Chunjie Liu ; Ting Peng ; Zimu Cen ; Peiran Lu ; Prasanth Potluri ; Po Hu ; Shiping Zhang ; Marie Lott ; Gabrielle Widjaja ; Douglas C Wallace ; Yi Xing ; Liming PeiSeries Type : Expression profiling by high throughput sequencing ; OtherOrganism : Homo sapiensMitochondria generate over 90% of the cellular energy and are central to health and disease. Mitochondrial DNA (mtDNA) heteroplasmy represents a significant source of cellular genetic diversity and has been shown to cause impaired mitochondrial function and even mitochondrial diseases. However, mitochondrial genetic heterogeneity across different human cell types at the population level is poorly understood. Here we present scMOCHA, a scalable computational framework that resolves high-confidence, single-cell resolution mtDNA heteroplasmy directly from standard single-cell RNA sequencing (scRNA-seq) data. Applying scMOCHA to all publicly available human peripheral blood mononuclear cells (PBMC) and bone marrow (BM) scRNA-seq datasets comprising 5.5 million cells, we uncover the single-cell landscape of mtDNA single-nucleotide variants (SNVs) and heteroplasmy levels in the human hematopoietic system across ages and cell types, including previously unreported SNVs and recurrent somatic hotspot SNVs in unrelated individuals. PBMCs and BM share many inherited homoplasmic and highly heteroplasmic SNVs but few somatic SNVs. Somatic SNVs are tissue- and cell type-specific and distributed across the mtDNA genome, suggesting that they arise in a largely random fashion. Although mtDNA replication error is the most likely dominant force shaping homoplasmic variants, oxidative stress may drive a significant portion of heteroplasmic and somatic mutations in the mtDNA genome. Importantly, we discover cell type-specific and human disease-associated mtDNA SNVs. By coupling mtDNA genotypes with matched single-cell nuclear transcriptomes and structural modeling, we uncover potential molecular mechanisms of how these disease-associated mtDNA SNVs impact cellular function such as inflammation and contribute to disease. Together, these findings define the single-cell variant landscape of the human mitochondrial genome and reveal previously unrecognized lineage- and disease-associated patterns of mtDNA variation in the human hematopoietic system.
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7. GSE329941 单细胞转录组学鉴定麦角硫因作为线粒体保护剂，可预防 AKI 向 CKD 进展。

• ✍️ 作者：未知作者
• 🏷️ 关键词：single-cell、transcriptomics
• 📝 描述：Contributors : Jiaxin Peng ; Ling Chen ; Jing Chen ; Zhipu Qian ; Mingzhang HanSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusThis study investigates the role and mechanism of ergothioneine (EGT) in mitigating the progression of acute kidney injury (AKI) to chronic kidney disease (CKD). Using a cisplatin-induced mouse model of the AKI-to-CKD transition with EGT intervention, we combined histopathological examination, biochemical assays, and single-cell RNA sequencing (scRNA-seq) to demonstrate that EGT may significantly improve renal function parameters and attenuate renal injury and fibrosis. scRNA-seq analysis revealed that EGT may restore the expression of mitochondrial function-related genes in renal tubular epithelial cells, enhance oxidative phosphorylation and electron transport chain activity, thereby potentially promoting mitochondrial homeostasis. Furthermore, our in vitro experiments confirmed the protective effects of EGT on mitochondria in injured renal tubular epithelial cells, including reducing reactive oxygen species (ROS) generation, restoring diminished mitochondrial membrane potential, and increasing ATP production. These findings elucidate a mechanism by which EGT might delay AKI-to-CKD progression through multi-cellular coordination aimed at improving mitochondrial function, offering a promising therapeutic strategy for kidney diseases.
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8. GSE329924 炎症性单核细胞抑制 YAP 诱导的细胞增殖 [scRNA-seq 免疫]

• ✍️ 作者：未知作者
• 🏷️ 关键词：immune、scRNA
• 📝 描述：Contributors : Serrena Singh ; Nareh Tahmasian ; Jia-Jun Liu ; Wenjia Wang ; Lucas Haas ; Yingdong Zhu ; Magdalena M Griswold ; Nina N Brodsky ; Silvia Liu ; Brian T Kalish ; Dean YimlamaiSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusYAP and its paralog, TAZ are transcriptional co-activators of the Hippo pathway that regulate cell growth. Their structural distinctiveness suggests important independent functional differences. To investigate this further, we generated YAP- and TAZ-predominant clones in the liver and followed their long-term behavior. YAP clones rapidly de-differentiate cells into a stem cell-like state with inflammatory immune cell recruitment followed by their clearance. In contrast, TAZ clones promote an anti-inflammatory immune environment resulting in their long-term maintenance, massive organ growth and increased mortality. YAP clones recruit inflammatory blood-derived monocytes, which if inhibited permits YAP clonal growth. Consistent with these results, YAPHigh colorectal cancer (CRC) patients had a 67% 5-year survival rate, while TAZHigh CRC patients did not survive to 5 years. Similar trends were seen in hepatocellular carcinoma patients. These findings underscore the importance of understanding the intrinsic differences in YAP and TAZ biology as independent drivers of disease.
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9. GSE328097 SP11治疗的DLA淋巴瘤小鼠模型的单细胞转录组分析

• ✍️ 作者：未知作者
• 🏷️ 关键词：lymphoma、single-cell
• 📝 描述：Contributors : Shahana MV ; Yash Chindarkar ; Bibha ChoudharySeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusWe used single-cell RNA sequencing with the 10x Genomics platform to study the effect of SP11 treatment in a DLA lymphoma mouse model. The goal was to examine tumor heterogeneity, identify potential treatment-resistant cell populations, and assess changes in the tumor microenvironment and immune cell infiltration. This dataset provides an overview of how SP11 impacts tumor biology at single-cell resolution.
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10. GSE327394 RNA测序数据来自不同年龄组的果蝇肠道干细胞，其中E374A（ADAR突变体）过表达，Zn72d和ADAR基因敲低。

• ✍️ 作者：未知作者
• 🏷️ 关键词：sequencing、regex:intestin(e|al)
• 📝 描述：Series Type : Expression profiling by high throughput sequencingOrganism : Drosophila melanogasterMaintaining tissue homeostasis necessitates the presence of stem cells capable of self-renewal and differentiation. However, stem cell functionality is known to deteriorate with age, although the precise mechanisms involved remain elusive. In this study, we reveal that adenosine deaminase acting on RNA (ADAR) curbs intestinal stem cell (ISC) proliferation via an RNA editing mechanism during gut regeneration and aging in Drosophila, mice, and humans. Notably, the absence of ADAR in Drosophila ISCs elicits an elevation in Insulin-MAPK signaling activities, ultimately resulting in ISC over-proliferation. Our further findings reveal that this ADAR activity is mediated by zinc-finger protein at 72D (Zn72D), an RNA-binding protein known to govern ADAR editing in vivo. This investigation provides valuable insights into the role of ADAR-mediated editing in the regulation of stem cell function during tissue regeneration and aging. Moreover, it underscores the importance of appropriate editing regulation in delaying the onset of natural aging processes.
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1. ⭐ HistoMap 从批量 RNA 测序数据中重建单细胞空间分布图谱。

• ✍️ 作者：未知作者
• 🏷️ 关键词：sequencing、single-cell、spatial
• 📝 描述：RNA sequencing combined with artificial intelligence reconstructed single-cell spatial organization from bulk data, revealing immune barriers that may influence colorectal cancer… The post HistoMap reconstructs single-cell spatial profiles from bulk RNA sequencing appeared first on RNA-Seq Blog.
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2. 为什么多学科团队在转化转录组学中至关重要

• ✍️ 作者：未知作者
• 🏷️ 关键词：transcriptomics
• 📝 描述：RNA sequencing delivers its greatest clinical value when multidisciplinary teams integrate laboratory, computational, and clinical expertise to ensure findings are accurate, interpretable, and relevant for patient care… The post Why Multidisciplinary Teams Matter in Translational Transcriptomics appeared first on RNA-Seq Blog.
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3. RNA测序在患者护理中的应用：从样本采集到临床解读

• ✍️ 作者：未知作者
• 🏷️ 关键词：RNA-seq
• 📝 描述：RNA sequencing supports clinical decision making when specimen quality, analysis, and interpretation remain aligned from sample collection through patient-focused reporting… The post RNA-Seq in Patient Care: From Sample Collection to Clinical Interpretation appeared first on RNA-Seq Blog.
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4. 验证RNA测序在可靠检测植物病毒和类病毒方面的应用

• ✍️ 作者：未知作者
• 🏷️ 关键词：sequencing
• 📝 描述：A validated RNA sequencing workflow demonstrates reliable detection of plant viruses and viroids, supporting accurate, comprehensive diagnostics for symptomatic crop samples… The post Validating RNA sequencing for reliable detection of plant viruses and viroids appeared first on RNA-Seq Blog.
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• GSE324929 RNA-seq 分析了常氧和低氧条件下 FDX2 诱导敲除 (FDX2-iKO) ES2 卵巢癌细胞的表达情况
• 对稳定转染了 PON1 过表达慢病毒 (PON1-OE) 及其阴性对照 (PON1-NC) 的 HCCLM3 细胞进行了 RNA-seq 转录组分析（GSE322594）。
• GSE319665 RNA-seq 来自接受 FPC（5-FU、抗 PD-1 抗体和抗 CTLA-4 抗体）、mRNA-LNP 和 KDM5B 抑制剂治疗的小鼠的肿瘤。
• GSE319374 缺氧后头颈癌细胞系的 RNA-seq 分析
• GSE318861 利用 ChIP-seq 和 RNA-seq 对 Tat 依赖性和宿主驱动的 HIV 转录进行定量分析
• GSE316941 Bcl11a 通过调节多能祖细胞命运决定来协调衰老造血过程中的多系完整性 [ATAC-seq]
• GSE314969 主动脉单细胞转录组分析揭示 ApoE 同工型在血管疾病调控中的特异性作用
• GSE313027 转录组学鉴定出轻度高温处理的肿瘤上清液是 HepG2 细胞成熟的诱导剂
• GSE312456 塑料添加剂对MCF-7乳腺癌细胞转录组的影响存在差异
• GSE311385 ATRX 失活破坏整体染色质状态和拓扑结构，从而扰乱神经胶质瘤起源细胞的神经发育途径 [Hi-C]
• GSE309141 广泛的 H3K9me3 结构域和染色质折叠的破坏调节 ATRX 缺陷型胶质瘤中的致癌转录环境 [ChIP-seq]
• GSE307744 人类膀胱视觉空间基因表达
• GSE295454 大规模高分辨率质谱蛋白质组学分析定义了鼻咽癌的分子亚型，可用于治疗靶向。
• GSE294033 MC38小鼠肿瘤的单细胞RNA测序揭示了LMO7在调控肿瘤微环境中的多种功能
• GSE287471 LUAD肿瘤、正常邻近组织和肿瘤样组织转录组学
• GSE224372 组蛋白甲基转移酶 NSD3 增强癌症中的 rDNA 转录
• GSE330733 EZH1/2抑制通过MHC II类分子去抑制和中性粒细胞重编程改善免疫治疗反应
• GSE271348 以单细胞分辨率绘制血根草诱导的免疫调节图谱
• GSE337189 通过ChIP-seq分析MCF7细胞在雌二醇存在和不存在的情况下TOP2A和TOP2B的占位情况
• GSE335941 利用人类结肠类器官模拟肠聚集性大肠杆菌感染的单细胞反应的个体宿主差异
• GSE330821 THBS1 通过激活 TGF-β/Smad 通路诱导多囊卵巢综合征患者卵巢颗粒细胞功能障碍
• GSE328525 SP11 处理的 MOLT4 细胞系和未处理的对照的单细胞转录组分析。
• GSE328288 迈向更具转化性的肿瘤模型：基于乳腺 dECM 的 3D 系统捕获天然微环境信号
• GSE327405 USP22 通过稳定 SFRP1 启动子处 KAT2A 介导的组蛋白乙酰化来抑制先兆子痫中的滋养层细胞坏死
• GSE324519 阿霉素在荷瘤小鼠和非荷瘤小鼠中诱导的差异基因表达
• GSE324345 野生型和转录因子敲除 HCT116 细胞中内质网应激诱导的三维增强子网络分析 [RNA-Seq]
• GSE324344 野生型和转录因子敲除 HCT116 细胞中内质网应激诱导的三维增强子网络分析 [Hi-C]
• GSE324343 野生型和转录因子敲除 HCT116 细胞中内质网应激诱导的三维增强子网络分析 [ChIP-Seq]
• GSE324342 野生型和转录因子敲除 HCT116 细胞中内质网应激诱导的三维增强子网络分析 [ATAC-Seq]
• GSE319664 RNA-seq 分析来自异种移植模型的肿瘤，该模型使用 KDM5B 抑制剂 JB-157 或 JB-161 进行治疗。
• GSE319663 ChIP-seq 分析了用 KDM5B 抑制剂 JB-157 或 JB-161 处理的 HT-29 细胞
• GSE317839 PMR4胼胝质合成酶的缺失赋予拟南芥和甘蓝型油菜对根肿病的茉莉酸依赖性抗性
• GSE317231 Bcl11a通过调控多能祖细胞命运决定，在衰老造血过程中协调多谱系完整性
• GSE316942 Bcl11a 通过调节多能祖细胞命运决定来协调衰老造血过程中的多系完整性 [CUT&Tag]
• GSE315025 急性心脏移植排斥反应患者的纤维化过程激活：一种新型的非侵入性诊断方法
• GSE314321 炎症性单核细胞抑制 YAP 诱导的细胞增殖 [批量 RNA 测序]
• GSE314267：对阿霉素治疗有反应或部分反应的肿瘤内皮细胞进行单细胞RNA测序
• GSE314159 曲唑酮用于治疗阿尔茨海默病，通过调节可溶性ST2水平来缓解阿尔茨海默病理
• GSE311885 血浆来源的 miRNA 作为液体生物标志物区分阿尔茨海默病和额颞叶痴呆
• GSE311784 肿瘤内皮细胞转录组学对阿霉素治疗的反应。
• GSE311556 BMX-001 是一种选择性放射防护剂，目前处于 II 期临床试验阶段，在放射治疗后三周给予该药可逆转放射引起的纤维化 [RNA-seq]
• GSE310259 ATRX失活破坏了胶质瘤细胞的整体染色质状态和拓扑结构，从而导致神经发育通路失调
• GSE310029 研究发现，使用acalabrutinib靶向布鲁顿酪氨酸激酶可减轻小鼠硬皮病慢性移植物抗宿主病。
• GSE309142 ATRX 失活破坏整体染色质状态和拓扑结构，从而扰乱神经胶质瘤起源细胞的神经发育通路 [CTCF CUT&TAG]
• GSE307521 CEACAM 1 缺失不影响视网膜和脉络膜形态或转录组
• GSE304246 氟西汀通过激活SREBP2干扰内皮细胞中的胆固醇代谢
• GSE303892 光子照射5天、7天和11天甲状腺类器官的RNA测序分析
• GSE303108 与肝细胞癌相关的差异甲基化假定印记控制区域的组[亚硫酸氢盐测序]
• GSE291958 ORCA介导的多梳抑制复合物稳定化维持3D基因组结构并控制复制时间[TSA-seq]
• GSE275551 葡萄糖-Chi3l1相互作用调节库普弗细胞代谢失衡并改善代谢功能障碍相关的脂肪肝
• GSE261982 miP-PSTPIP2 过表达对内皮细胞在稳态和炎症中基因表达的影响。[ext501]
• GSE248834 AMPK 调控小 RNA 通路的普遍性，从而介导体细胞与生殖细胞之间的通讯并建立生殖细胞干细胞的静止状态
• GSE154509 LncRNA-NFYB轴通过正反馈驱动免疫抑制，促进肝细胞癌进展
• GSE336973 Col1a1 敲低抑制口腔鳞状细胞癌的 EMT、迁移和侵袭，无论是在体外还是在体内。
• GSE314068 利用单细胞多组学绘制认知障碍中的ISR图谱
• GSE311401：质粒脂质体转染或病毒样颗粒转导后CFF-16HBEge细胞的批量RNA测序
• GSE307620 哺乳动物组织的空间染色质结构和可及性共分析
• GSE336861 ID2 通过拮抗多效性 Zeb2 增强子上的 E 蛋白来确保 cDC1 的特化 [scRNA-seq]
• GSE336821 阴茎鳞状细胞癌患者来源的体外和体内模型的建立和表征
• GSE309674 STING 缺陷并不能挽救 TERC 或 TERT 端粒酶缺陷小鼠中由端粒缩短介导的衰老表型和寿命问题
• GSE301483 HT-29细胞暴露于铅离子的转录组分析
• GSE189489 RNA测序数据，用于分析小鼠B16-F10黑色素瘤细胞系在siEzh2敲低、GSK126甲基转移酶抑制剂或DZNep处理后的情况。
• GSE300504 ScRNA-Seq 分析揭示了新型损伤模型中内耳毛细胞自发再生过程中 dlx5a 的关键作用