详细内容（前10条）

1. ⭐ GSE339022 小鼠模型中输注前和肿瘤细胞攻击后人CAR-NK细胞的单细胞RNA测序

• ✍️ 作者：未知作者
• 🏷️ 关键词：tumor、sequencing、single-cell
• 📝 描述：Contributors : May Daher ; Nadima Uprety ; Ana Karen Nunez Cortes ; Emily Ensley ; Rejeena Shrestha ; Donghai Xiong ; Francia Reyes Silva ; Elif Gokdemir ; Madison Moore ; Silvia Tiberti ; Huihui Fan ; Andre Nguyen ; Cameron L Gardner ; Elizabeth Wood ; Mayra Shanley ; Sunil Acharya ; Amina Nurmammadova ; Luis Muniz-Feliciano ; Ye Li ; Michael Wang ; Vivian Jiang ; Merve Dede ; Vakul Mohanty ; Pinaki P Banerjee ; Bin Liu ; Enli Liu ; Ken Chen ; Elizabeth J Shpall ; Katayoun Rezvani ; Rafet BasarSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensWe profiled the transcriptomes of human CD5 CAR-NK cells at the single-cell level to compare the pre-infusion state with the post-challenge state.
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2. GSE313582 不同的 SAGA 复合物塑造了弓形虫在宿主响应基因网络和核心基因网络中的转录组 [RNAseq]

• ✍️ 作者：未知作者
• 🏷️ 关键词：RNAseq、transcriptome
• 📝 描述：Contributors : Dominique Cannella ; Belen Pachano ; Martina Shahinas ; Jon deVries ; Charlotte Corrao ; Léa Pounot ; Lucid Belmudes ; Anne-Marie Hesse ; Yohann Couté ; Alexandre Bougdour ; Christopher Swale ; Mohamed-Ali HakimiSeries Type : Expression profiling by high throughput sequencingOrganism : Toxoplasma gondiiGCN5 (General Control Non-repressed protein 5) plays a central role in the regulation of gene expression through its histone acetyltransferase (HAT) activity. Within the SAGA complex (Spt-Ada-Gcn5 acetyltransferase), GCN5 regulates transcription by modifying the chromatin structure and thus influencing the accessibility of gene promoters. Its conservation in all eukaryotes underscores its essential role in cell biology. Remarkably, among invertebrates, Toxoplasma possesses two HAT variants of the GCN5 family. GCN5a plays an important role in parasite gene expression under alkaline conditions, but is not critical for growth. In contrast, GCN5b is essential for parasite survival. Previous pioneering studies have begun to elucidate the unique molecular properties of GCN5b HAT activity, but also its partnership. However, these studies were performed on zoites still expressing the native GCN5b gene, which may lead to potentially misleading or incomplete conclusions. Here, we re-examine the unique interactome associated with the native GCN5b protein and we investigate the transcriptional consequences of depleting the protein using auxin-inducible degron technology. We are also investigating the interplay between GCN5b and its counterpart HDAC3 at the chromatin level as the parasite transitions from the tachyzoite to the merozoite stage. We will analyze their selective engagement as activator, repressor or chromatin insulator using ChIP-seq and try to decipher the ‘histone code’ that ensures precise spatial and temporal regulation of stage-specific genes. We are also comparing the dynamics of the Toxoplasma SAGA complex between the two different zoite populations, focusing on the DNA-targeting AP2 transcription factors, but also on the PHD-containing histone PTM reader identified in the interactome of GCN5b.
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3. GSE313273 不同的 SAGA 复合物塑造了弓形虫在宿主响应基因网络和核心基因网络中的转录组 [ChIP-Seq]

• ✍️ 作者：未知作者
• 🏷️ 关键词：ChIP-seq、transcriptome
• 📝 描述：Contributors : Dominique Cannella ; Belen Pachano ; Martina Shahinas ; Jon deVries ; Charlotte Corrao ; Léa Pounot ; Lucid Belmudes ; Anne-Marie Hesse ; Yohann Couté ; Alexandre Bougdour ; Christopher Swale ; Mohamed-Ali HakimiSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Toxoplasma gondiiGCN5 (General Control Non-repressed protein 5) plays a central role in the regulation of gene expression through its histone acetyltransferase (HAT) activity. Within the SAGA complex (Spt-Ada-Gcn5 acetyltransferase), GCN5 regulates transcription by modifying the chromatin structure and thus influencing the accessibility of gene promoters. Its conservation in all eukaryotes underscores its essential role in cell biology. Remarkably, among invertebrates, Toxoplasma possesses two HAT variants of the GCN5 family. GCN5a plays an important role in parasite gene expression under alkaline conditions, but is not critical for growth. In contrast, GCN5b is essential for parasite survival. Previous pioneering studies have begun to elucidate the unique molecular properties of GCN5b HAT activity, but also its partnership. However, these studies were performed on zoites still expressing the native GCN5b gene, which may lead to potentially misleading or incomplete conclusions. Here, we re-examine the unique interactome associated with the native GCN5b protein and we investigate the transcriptional consequences of depleting the protein using auxin-inducible degron technology. We are also investigating the interplay between GCN5b and its counterpart HDAC3 at the chromatin level as the parasite transitions from the tachyzoite to the merozoite stage. We will analyze their selective engagement as activator, repressor or chromatin insulator using ChIP-seq and try to decipher the ‘histone code’ that ensures precise spatial and temporal regulation of stage-specific genes. We are also comparing the dynamics of the Toxoplasma SAGA complex between the two different zoite populations, focusing on the DNA-targeting AP2 transcription factors, but also on the PHD-containing histone PTM reader identified in the interactome of GCN5b.
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4. GSE289424 IGF2BP3 在未折叠蛋白反应过程中调节 RNA 代谢 [RNA-Seq]

• ✍️ 作者：未知作者
• 🏷️ 关键词：metabolism、RNA-seq
• 📝 描述：Contributors : Aleksandra S Anisimova ; Harald Hornegger ; Irmgard Fischer ; Gijs Versteeg ; Stefan Ameres ; Elif G KaragözSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensAccumulation of misfolded proteins in the endoplasmic reticulum (ER) perturbs cellular homeostasis and leads to pathological conditions termed ER stress. The Unfolded Protein Response (UPR) is a highly conserved signaling cascade that maintains ER homeostasis. While the transcriptional response is paramount for UPR signaling, several mRNAs are regulated at the posttranscriptional level, yet how this is achieved remains poorly understood. Here, we show that a highly conserved RNA-binding protein, IGF2BP3, interacts with transcripts encoding for the UPR target genes and regulates the UPR signaling. During ER stress, IGF2BP3 destabilized most of its targets, including the UPR target RNAs. On the other hand, IGF2BP3 stabilized a subset of mRNAs encoding for transcription regulators through this indirectly regulated transcription of the UPR target genes. This feedback loop allows IGF2BP3 to elevate the levels of stress response genes while leading to the degradation of other transcripts during ER stress. Our results reveal a novel IGF2BP3-driven gene regulatory network contributing to cellular adaptation to ER stress.
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5. GSE327700 空间转录组分析揭示伯氏疏螺旋体感染的 C3H 小鼠的关节炎症特征

• ✍️ 作者：未知作者
• 🏷️ 关键词：inflammation、spatial
• 📝 描述：Contributors : Kaitlyn Gura ; Mollie Hostetter ; Veena Potluri ; Sarah Johnson ; Michael Hill ; Yuelin Zhong ; Eleanor L Astley ; Tanja Petnicki-Ocwieja ; Suba Nookala ; Catherine A Brissette ; Archana DhasarathySeries Type : OtherOrganism : Mus musculusLyme arthritis, a manifestation of Lyme disease, is triggered by the spirochetal bacterium Borrelia burgdorferi (Bb), which is transmitted through the bite of the Ixodes tick. Although multiple studies have been performed on the complex host immune response in Lyme arthritis, the spatial gene expression environment in the joint tissue remains unexplored. Here, we applied spatial transcriptomics to ankle joints of C3H mice infected with B. burgdorferi, profiling tissues at peak inflammation (2 weeks post infection) and after antibiotics (4 weeks post-infection) during inflammation resolution. Analysis revealed spatially restricted signatures: pro-inflammatory responses dominated synovial and fibroblast populations 2 weeks post-infection, with elevated levels of Vimentin and I-Ek related gene and protein expression localized to these regions. In contrast, 4 weeks post-infection during the inflammation resolution phase, levels of Vimentin and I-Ek related gene and protein expression are reduced drastically despite the persistent pathology seen by H&E staining. Notably, fibroblasts and synoviocytes in the medial humeroulnar joint regions adopted immune-like phenotypes during peak inflammation, while the same cell types in the lateral humeroradial joint displayed a more infection-resilient phenotype. Comparison with scRNA-seq synoviocyte cluster revealed little overlap, but concordant genes that were upregulated were involved in ECM remodeling (Col1a1, Col3a1, Mmp2, Timp1), fibroblast activation (Postn, Runx1, Ctnnb1), and inflammation (Saa3, Ccl7, Tnfaip6). By week 4, concordant downregulation of genes coding for ribosomal proteins, mitochondrial complex subunits, and Jun (an immediate-early inflammatory gene) was noted. These spatially resolved maps demonstrate that joint microenvironments play a crucial role in pathogenesis, offering unique insights into Lyme arthritis pathology.
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6. GSE311199 复杂组织中三维基因组结构和基因表达的整合空间分析

• ✍️ 作者：未知作者
• 🏷️ 关键词：spatial、genome
• 📝 描述：Contributors : Pengfei Guo ; Yan Cui ; Yanxiang DengSeries Type : Expression profiling by high throughput sequencing ; Genome binding/occupancy profiling by high throughput sequencing ; OtherOrganism : Homo sapiens ; Mus musculusThree-dimensional genome organization shapes transcriptional regulation, yet measuring its spatial coordination in situ within intact tissues remains challenging. We present Spatial Hi-C-RNA, a multimodal platform that simultaneously maps genome-wide chromatin contacts and transcriptomes from the same tissue section at near single-cell resolution. Across mouse brain, developing embryos, and human melanoma, Spatial Hi-C-RNA generated multimodal maps that aligned with tissue anatomy while revealing complementary chromatin- and RNA-defined spatial patterns. Multiscale features, including A/B compartments, topologically associating domains, and chromatin loops, were associated with region- and cell-type-specific transcriptional programs. In mouse embryos, Spatial Hi-C-RNA resolved coordinated chromatin and transcriptional remodeling during neuronal maturation across developmental stages. In human melanoma, chromatin architecture delineated intratumoral subregions not detected by RNA alone and linked tumor-state transitions to changes in compartments, domain boundaries, and regulatory programs. Spatial Hi-C-RNA thus provides a broadly applicable framework for investigating genome structure–function relationships in development and disease within native tissue environments.
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7. GSE303569 Burkitt淋巴瘤细胞系Ramos和ST14敲除Ramos的RNA测序

• ✍️ 作者：未知作者
• 🏷️ 关键词：lymphoma、RNA-seq
• 📝 描述：Contributors : Yi-Lin Chiu ; Xin-Jie Lu ; Hsing-Fan LaiSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensThis dataset presents RNA sequencing (RNA-seq) data from human Burkitt lymphoma cell lines, Ramos and ST14 knockout Ramos. The study aimed to investigate transcriptomic changes between parental cells and ST14 knockout cells.
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8. GSE330925 PI3K 和 HSP90 的协同抑制增强了肾上腺皮质癌的抗肿瘤疗效

• ✍️ 作者：未知作者
• 🏷️ 关键词：carcinoma
• 📝 描述：Series Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensAdrenocortical cancer (ACC) is a rare and aggressive malignancy with poor survival due to a lack of effective treatments; therefore, it is important to identify therapies that can be readily studied in clinical trials. Quantitative high-throughput drug combination screening identified potent synergy between phosphatidylinositol-3-kinase (PI3K) inhibition and heat shock protein 90 (HSP90) inhibition. This GEO submission contains the 18 bulk RNA-seq samples from NCI-H295R ACC cells that were used in the publication to evaluate transcriptional responses to PI3K and HSP90 inhibitors alone and in combination. The submitted samples include untreated controls and cells treated with STA9090, PIK75, BGT226, STA9090+PIK75, or STA9090+BGT226, with three biological replicates per condition. These RNA-seq data supported the comparison of molecular responses induced by PI3K/HSP90 inhibitor combinations in ACC cells, including distinct responses associated with PIK75+STA9090 and BGT226+STA9090 treatment.
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9. GSE313048 不同的 SAGA 复合物塑造了弓形虫在宿主响应基因网络和核心基因网络中的转录组

• ✍️ 作者：未知作者
• 🏷️ 关键词：transcriptome
• 📝 描述：Contributors : Dominique Cannella ; Belen Pachano ; Martina Shahinas ; Jon deVries ; Charlotte Corrao ; Léa Pounot ; Lucid Belmudes ; Anne-Marie Hesse ; Yohann Couté ; Alexandre Bougdour ; Christopher Swale ; Mohamed-Ali HakimiSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Toxoplasma gondiiHistone acetylation, a fundamental epigenetic mechanism that controls gene activity, is essential for the developmental plasticity and virulence of the parasite Toxoplasma gondii. However, how this parasite organizes and deploys its acetyltransferase machinery has remained unclear. Here, we show that T. gondii rewired this process using a plant-like system built around the acetyltransferase TgGCN5b, which differs from the typical SAGA complex found in other eukaryotes. Proteomic and structural analyses reveal a modular assembly that integrates multiple acetyltransferase (GNAT) enzymes and chromatin-reader proteins carrying PHD and PZP domains and Apetala-related transcription factors, an organization unique to apicomplexan parasites. TgGCN5b catalyzes a selective tri-site acetylation pattern on histone H3 at lysines 9, 14, and 18 that maintains open chromatin and sustains transcription of core metabolic, invasion, and virulence genes. Its conditional depletion disrupts these post-translational modifications, silencing key promoters and decoupling transcription from histone methylation. Genome-wide analyses further show that TgGCN5b functions independently of the MORC/HDAC3 repressive pathway, defining a distinct regulatory circuit that connects chromatin acetylation with gene expression and developmental transitions. These findings reveal that the SAGA complex has been evolutionarily reconfigured in T. gondii into a plant-like, yet featuring divergent and apicomplexan-specific feature, positioning TgGCN5b as a central regulator that links epigenetic control to parasite growth, adaptation, and virulence.
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10. GSE311536 嘌呤能信号轴调控受损导致 STAT3 功能获得性突变中 CD8+ T 细胞功能失调

• ✍️ 作者：未知作者
• 🏷️ 关键词：T cell
• 📝 描述：Contributors : Jose S Campos Duran ; Montana S Knight ; Samir Sayed ; Megan C Dalalo ; Andrea A Mauracher ; Peyton E Conrey ; Aaron B Schultz ; Ceire A Hay ; Robert B Lindell ; Eric D Abrams ; Erica G Schmitt ; Martin A Thelin ; Christian A Howard ; Sara Bluestein ; Christine M Seroogy ; Tamara C Pozos ; Akaluck Thatayatikom ; Ingrid Lundgren ; Amelie Gauthier ; Scott W Canna ; Helen C Su ; Michael D Keller ; Ottavia M Delmonte ; Lisa R Forbes Satter ; Steven M Holland ; Jenna R Bergerson ; Jennifer W Leiding ; Neil Romberg ; Alexandra F Freeman ; Alejandro V Villarino ; Mark S Anderson ; Megan A Cooper ; Tiphanie P Vogel ; Sarah E HenricksonSeries Type : Expression profiling by high throughput sequencing ; OtherOrganism : Homo sapiensGain-of-function (GOF) variants in STAT3 cause a complex disorder characterized by early-onset autoimmunity, lymphoproliferation, recurrent infections, and immune dysregulation. In both primary human and mouse models of STAT3 GOF, CD8+ T cells have been implicated as pathogenic drivers of autoimmunity, though the exact mechanisms remain poorly understood. Here, we found that in patients with STAT3 GOF, CD8+ T cells exist in a phenotypically activated state. Functional assessment revealed that naïve CD8+ T cells have an increased capacity for IFN-g and TNF-a production, with evidence of a Type I/II IFN transcriptional signature. Changes in immunoregulatory pathways revealed dysregulation of the purinergic signaling axis on CD8+ T cells: while CD39 was increased, downstream purinergic family members, CD73 and the adenosine receptor, A2AR, were downregulated, impairing the potential to produce or sense immunosuppressive adenosine. Evaluation of the impact of precision therapy in the form of JAK inhibitors at a cellular and functional level revealed partial normalization of naïve CD8+ T cell dysregulation, including aberrant cytokine production in patients. Our study suggests that a dysregulated purinergic signaling axis plays a key role in CD8+ T cell dysregulation in STAT3 GOF and may have implications for other rare monogenic immune disorders and common inflammatory disorders.
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1. 空间RNA测序揭示T细胞如何识别肿瘤

• ✍️ 作者：未知作者
• 🏷️ 关键词：sequencing、spatial
• 📝 描述：RNA sequencing combined with spatial genotyping mapped where neoantigen-specific T cells interact with tumor cells, revealing organized immune niches that may guide personalized cancer treatments…
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• GSE289482 IGF2BP3 在未折叠蛋白反应期间调节 RNA 代谢 [HCT116]
• GSE289481 IGF2BP3 在未折叠蛋白反应期间调节 RNA 代谢 [IGF2BP3 细胞]
• GSE289480 IGF2BP3 在未折叠蛋白反应期间调节 RNA 代谢 [RKO iCas9 细胞]
• GSE289425 IGF2BP3 在未折叠蛋白反应期间调节 RNA 代谢 [Ribo-Seq]
• GSE289214 IGF2BP3 在未折叠蛋白反应期间调节 RNA 代谢
• GSE289024 IGF2BP3 在未折叠蛋白反应过程中调节 RNA 代谢 [QuantSeq]
• GSE289023 IGF2BP3 在未折叠蛋白反应期间调节 RNA 代谢 [PAR-CLIP]
• GSE277496 克罗恩病患者外周血单核细胞的单细胞多组学研究
• GSE268626 克罗恩病中单核细胞的系统性重编程促进其肠道炎症功能
• GSE339137 研究表明，红豆杉提取物可减轻过敏性气道炎症，其成分紫杉碱可靶向肥大细胞中的IL-17/TNF信号通路。
• GSE272970 辛伐他汀和 2,3,7,8-四氯二苯并二恶英 (TCDD) 共同暴露小鼠的肝脏 RNA 测序
• GSE336233 心肌细胞内在体细胞线粒体DNA突变诱导氧化磷酸化依赖性免疫反应并促进进行性心力衰竭
• GSE318183 棘球绦虫感染患者血清中外泌体microRNA的小RNA测序
• GSE311549 RNA测序用于胃型宫颈内膜腺癌（GAS）、普通型宫颈内膜腺癌（UEA）和小叶型宫颈内膜腺体增生（LEGH）