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1. ⭐ GSE310042 A2780 模型的全面转录组和表观基因组分析揭示了顺铂、紫杉醇和双重耐药性的独特程序 [RNA-seq]

• ✍️ 作者：未知作者
• 🏷️ 关键词：resistance、RNA-seq、transcriptome、epigenome
• 📝 描述：Contributors : Won-Young Choi ; Rachel Perkins ; Wenjing ZhangSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensOvarian cancer is the most lethal gynecologic cancer, largely because most patients eventually relapse after initially responding to platinum- and taxane-based chemotherapy. To understand how cancer cells adapt to these drugs, we generated cisplatin-resistant (CpR), paclitaxel-resistant (TxR), and dual-resistant (TxCpR) derivatives from the parental A2780 cell line and profiled their transcriptomes and chromatin landscapes using RNA-seq and ATAC-seq. The three resistant lines displayed distinct cellular morphologies, gene expression profiles, and chromatin accessibility patterns. Notably, the dual-resistant state was not simply a combination of the cisplatin- and paclitaxel-resistant states but instead represented a unique regulatory configuration. Integrative analysis of RNA-seq and ATAC-seq identified potential regulators associated with specific drug-resistance of A2780. Furthermore, we suggested resistance-specific distal regulatory regions highly related with transcription factors either directly or indirectly involved in cancer progression, cell plasticity and chemotherapy resistance. Our paired RNA-seq and ATAC-seq datasets provide valuable and comprehensive resources for exploring how enhancer–transcription factor interactions drive chemotherapy resistance and for identifying new therapeutic targets in ovarian cancer.
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2. ⭐ GSE313244 子宫平滑肌肉瘤的多维单细胞转录组分析鉴定出具有不同治疗脆弱性的分子亚型 [空间转录组学]

• ✍️ 作者：未知作者
• 🏷️ 关键词：single-cell、spatial、spatial transcriptomics、transcriptomics
• 📝 描述：Contributors : Maria Korah ; James Agolia ; Daniel DelittoSeries Type : OtherOrganism : Homo sapiensUterine leiomyosarcoma (ULMS) is an orphan disease that frequently recurs and metastasizes, with patients undergoing multiple lines of chemotherapy due to lack of effective therapeutic targets. To address this gap, we used single-cell RNA sequencing and spatial transcriptomic analysis to comprehensively profile ULMS. We uncovered eight subtypes of tumor cells, including stem cell-like hormone receptor-positive cells, tumor cells with mesenchyme-like features, ischemic tumor cells defined by a MYC program, and inflammatory tumor cells with active interferon signaling. The spatial correlates of these tumor cell subtypes demonstrated unique localization patterns. By correlating these signatures to bulk RNA sequencing data, we demonstrate the scalability of these findings to clinical outcomes. Finally, using the single-cell integration and drug response prediction algorithm, we derive previously undescribed drug predictions targeting specific tumor subtypes that may be more efficacious than existing adjuvant regimens. Our findings highlight new individualized and multifaceted therapeutic avenues to treat ULMS.
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3. ⭐ GSE310043 对 A2780 模型进行全面的转录组和表观基因组分析，揭示了顺铂、紫杉醇和双重耐药的不同耐药机制。

• ✍️ 作者：未知作者
• 🏷️ 关键词：resistance、transcriptome、epigenome
• 📝 描述：Contributors : Choi Won-Young ; Perkins Rachel ; Zhang WenjingSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Homo sapiensOvarian cancer is the most lethal gynecologic cancer, largely because most patients eventually relapse after initially responding to platinum- and taxane-based chemotherapy. To understand how cancer cells adapt to these drugs, we generated cisplatin-resistant (CpR), paclitaxel-resistant (TxR), and dual-resistant (TxCpR) derivatives from the parental A2780 cell line and profiled their transcriptomes and chromatin landscapes using RNA-seq and ATAC-seq. The three resistant lines displayed distinct cellular morphologies, gene expression profiles, and chromatin accessibility patterns. Notably, the dual-resistant state was not simply a combination of the cisplatin- and paclitaxel-resistant states but instead represented a unique regulatory configuration. Integrative analysis of RNA-seq and ATAC-seq identified potential regulators associated with specific drug-resistance of A2780. Furthermore, we suggested resistance-specific distal regulatory regions highly related with transcription factors either directly or indirectly involved in cancer progression, cell plasticity and chemotherapy resistance. Our paired RNA-seq and ATAC-seq datasets provide valuable and comprehensive resources for exploring how enhancer–transcription factor interactions drive chemotherapy resistance and for identifying new therapeutic targets in ovarian cancer.
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4. ⭐ GSE271370 空间转录组学揭示致命性 COVID-19 患者肺部的原位细胞和分子特征

• ✍️ 作者：未知作者
• 🏷️ 关键词：spatial、spatial transcriptomics、transcriptomics
• 📝 描述：Contributors : Carlos A Garcia-Prieto ; Eva Musulen ; Veronica Davalos ; Manel EstellerSeries Type : OtherOrganism : Homo sapiensSevere Coronavirus disease 2019 (COVID-19) induces heterogeneous and progressive diffuse alveolar damage (DAD) highly disrupting lung tissue architecture and homeostasis, hampering disease management leading to fatal outcomes. Characterizing DAD pathophysiology across disease progression is of ultimate importance to better understand the molecular and cellular features driving different DAD patterns and to optimize treatment strategies. To contextualize the interplay between cell types and assess their distribution, spatial transcriptomics (ST) techniques have emerged, allowing unprecedented resolution to investigate spatial architecture of tissues. To this end, post-mortem lung tissue provides valuable insights into cellular composition and their spatial relationships at the time of death. Here, we have leveraged VisumST technology in post-mortem COVID-19 induced acute and proliferative DAD lungs including control samples with normal morphological appearance, to unravel the immunopathological mechanisms underlying DAD, providing novel insights into cellular and molecular communication events driving DAD progression in fatal COVID-19. We report a progressive loss of endothelial cell types, pneumocytes type I and natural killer cells coupled with a continuous increase of myeloid and stromal cells, mostly peribronchial fibroblasts, over disease progression. Spatial organization analysis identified variable cellular compartments, ranging from major compartments defined by cell type lineages in control lungs to increased and more specific compartmentalization including immune-specific clusters across DAD spectrum. Importantly, spatially informed ligand-receptor interaction (LRI) analysis revealed an intercellular communication signature defining COVID-19 induced DAD lungs. Transcription factor (TF) activity enrichment analysis identified TGF-B pathway as DAD driver, highlighting SMAD3 and SMAD7 TFs activity role during lung fibrosis. Integration of deregulated LRIs and TFs activity allowed us to propose a downstream intracellular signaling pathway in peribronchial fibroblasts, suggesting potential novel therapeutic targets. Finally, spatio-temporal trajectories analysis provided insights into the alveolar epithelium regeneration program, characterizing markers of pneumocytes type II differentiation towards pneumocytes type I. In conc…
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5. ⭐ GSE343161 GM-CSF驱动的骨髓来源单核细胞/树突状细胞培养物中Hspa1a敲低的批量RNA测序

• ✍️ 作者：未知作者
• 🏷️ 关键词：dendritic cell、monocyte、sequencing
• 📝 描述：Contributors : Zeping Gui ; Neda Feizi ; Berkay Demirors ; Canxiang Lin ; Hehua Dai ; Mouhamad Al Moussawy ; Andrew Friday ; Steven M Sanders ; Latha Halesha ; Amanda L Williams ; Faruk Sacirbegovic ; Parmjeet S Randhawa ; Khodor I Abou-Daya ; Martin H OberbarnscheidtSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusWe performed bulk RNA sequencing of granulocyte-macrophage colony-stimulating factor (GM-CSF)-driven bone marrow-derived monocyte/dendritic cell cultures treated with Hspa1a-targeting shRNA or non-targeting control shRNA (sh-NC). The dataset was generated to identify Hspa1a-dependent transcriptional changes during monocyte-to-dendritic cell differentiation.
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6. GSE342942 口服递送载有R-spondin1的小细胞外囊泡可激活WNT信号通路，加速肠道损伤修复并逆转衰老

• ✍️ 作者：未知作者
• 🏷️ 关键词：pathway、regex:intestin(e|al)
• 📝 描述：Contributors : Shixiang Wang ; Lingyan YangSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusThe intestine plays a crucial role in regulating metabolism and immunity, with functional decline occurring during injury and ageing. Stimulating the neogenesis of intestinal stem cells (ISCs) by activating the WNT/β-catenin signalling pathway represents a promising approach for intestinal tissue regeneration and injury repair. However, effective oral delivery of functional WNT signalling agonists to the gut remains challenging. Herein, we report a potent WNT/β-catenin signalling-inducing small extracellular vesicles (sEV) that can be administered orally and present remarkable therapeutic efficacy. We demonstrate that active R-spondin1 (RSPO1) protein can be loaded onto the surface of sEV via heparan sulfate proteoglycans. Notably, sEV-delivered RSPO1 (evRSPO1) effectively induces WNT/β-catenin signalling-inducing activity, enhances ISCs proliferation, and supports intestinal organoid growth in vitro. Importantly, oral administration of evRSPO1 activates the WNT/β-catenin signalling pathway in the cryptic stem cell niche, thereby accelerating tissue repair and regeneration in a radiation-induced intestinal injury model. Furthermore, evRSPO1 treatment induces ISCs proliferation and reverses the intestinal senescence phenotype in aged mice. Collectively, this study establishes evRSPO1 as a potential first-in-class, orally deliverable therapeutic that overcomes biological barriers to activate ISCs, enabling efficient intestinal tissue repair and rejuvenation.
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7. GSE339043 一种经过基因工程改造的溶瘤副痘病毒可诱导免疫原性肿瘤细胞死亡，并通过增强T细胞反应展现抗肿瘤功效

• ✍️ 作者：未知作者
• 🏷️ 关键词：tumor、T cell
• 📝 描述：Contributors : Qi Li ; Jing Lin ; Fei Gao ; Xinyue Wang ; Ying Ma ; Chengyi Zhang ; Haizhu Wu ; Fanglin Zhao ; Yinghao Song ; Mengshi Xu ; Wenqi He ; Kui Zhao ; Guowen Liu ; Jiyu GuanSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusBy harnessing B16-derived immunologically ‘cold’ tumor models, we assessed therapeutic effects of ORFV recombinants .
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8. GSE313239 子宫平滑肌肉瘤的多维单细胞转录组分析鉴定出具有不同治疗脆弱性的分子亚型 [scRNA-seq]

• ✍️ 作者：未知作者
• 🏷️ 关键词：single-cell、scRNA
• 📝 描述：Contributors : Maria Korah ; James Agolia ; Daniel DelittoSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensUterine leiomyosarcoma (ULMS) is an orphan disease that frequently recurs and metastasizes, with patients undergoing multiple lines of chemotherapy due to lack of effective therapeutic targets. To address this gap, we used single-cell RNA sequencing and spatial transcriptomic analysis to comprehensively profile ULMS. We uncovered eight subtypes of tumor cells, including stem cell-like hormone receptor-positive cells, tumor cells with mesenchyme-like features, ischemic tumor cells defined by a MYC program, and inflammatory tumor cells with active interferon signaling. The spatial correlates of these tumor cell subtypes demonstrated unique localization patterns. By correlating these signatures to bulk RNA sequencing data, we demonstrate the scalability of these findings to clinical outcomes. Finally, using the single-cell integration and drug response prediction algorithm, we derive previously undescribed drug predictions targeting specific tumor subtypes that may be more efficacious than existing adjuvant regimens. Our findings highlight new individualized and multifaceted therapeutic avenues to treat ULMS.
• 🔗 查看原文

9. GSE338923 STK11缺陷型和亲代Lacun3小鼠肺腺癌细胞的批量RNA测序

• ✍️ 作者：未知作者
• 🏷️ 关键词：sequencing
• 📝 描述：Contributors : Daniel Ajona ; Ruben PioSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusSTK11 mutations are associated with primary resistance to immune checkpoint inhibitors in lung adenocarcinoma, but the tumor cell-intrinsic mechanisms underlying this phenotype remain incompletely understood. To investigate transcriptional changes induced by STK11 loss independently of the tumor microenvironment, bulk RNA sequencing was performed on parental Lacun3 murine lung adenocarcinoma cells and CRISPR-generated Stk11-deficient Lacun3 cells cultured in vitro. Differential gene expression analysis identified increased expression of several mediators associated with complement activation and neutrophil extracellular trap (NET) formation, supporting a tumor cell-intrinsic transcriptional program that promotes a pro-NETotic tumor microenvironment.
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10. GSE334888 E11.5 鳃弓 RNA-seq 和 CUT&RUN

• ✍️ 作者：未知作者
• 🏷️ 关键词：RNA-seq
• 📝 描述：Series Type : Expression profiling by high throughput sequencing ; Genome binding/occupancy profiling by high throughput sequencingOrganism : Mus musculusThis SuperSeries is composed of the SubSeries listed below.
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1. NextLongIso——一个用于多维长读长RNA测序分析的综合性Nextflow流程

• ✍️ 作者：未知作者
• 🏷️ 关键词：RNA-seq
• 📝 描述：NextLongIso provides a unified RNA sequencing pipeline for analyzing transcript isoforms, alternative splicing, promoter usage, and…
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• GSE333517 石珊瑚 Galaxea fascicularis 无性出芽的高分辨率单细胞转录组图谱
• GSE331354 瞬时上皮可塑性状态定义了子宫腺体发育的窗口 [空间]
• GSE318813 E11.5 鳃弓 RNA-seq 来自对照组和 Ehmt1/2 神经嵴敲除组
• GSE300153 自噬在炎症期间维持 HEV 的特性和功能。
• GSE337369 NIH COVID-19 尸检唾液腺全转录组分析
• GSE328701 真菌病原体耳念珠菌暴露几丁质以触发 IFNγ 并在毛囊中持续存在 [scRNA-seq EDM_exp2]
• GSE319837 人类眼表双潜能基底上皮细胞的微环境驱动可塑性 [RNA-Seq]
• GSE319836 人类眼表双潜能基底上皮细胞的微环境驱动可塑性 [scRNA-seq]
• GSE306536 利用 CRISPR/Cas9 技术敲除 MOLM-13、MV4-11 和 K-562 人类白血病细胞系中的 PTBP1、PTBP2 或两者对基因表达和 RNA 剪接的影响
• GSE306460 人类急性髓系白血病细胞系 MOLM-13 中 PTBP1 与转录本结合的评估
• GSE342935 人类纹状体中与年龄相关的改变发现 PPP1R15B-miR-196a 节点是亨廷顿病表型的修饰因子 [RNA-Seq]
• GSE342934 CD146敲低/过表达后的RNA测序
• GSE342858 用 TGF-β1 处理的原代小鼠肺成纤维细胞的 RNA 测序
• GSE342855 二甲双胍通过促进巨噬细胞的稳态，以依赖于环境的方式调节胶质母细胞瘤中肿瘤相关巨噬细胞的表型
• GSE342848 SETDB2 通过调节剪接因子 U2AF1 的表达来抑制甲状腺癌的进展
• GSE342728 内皮细胞 VEGFR2 不足促进淋巴转录程序向造血转录程序的转变 [Vegfr2_ecko_48h_skin]
• GSE342725 内皮细胞 VEGFR2 不足促进淋巴转录程序向造血转录程序的转变 [Vegfr2_siRNA_mLEC]
• GSE342723 内皮细胞 VEGFR2 不足促进淋巴转录程序向造血转录程序的转变 [Vegfr2_lecko_P21skin]
• GSE342716 内皮细胞 VEGFR2 不足促进淋巴转录程序向造血转录程序的转变 [Vegfr2_ecko_P21skin]
• GSE342290 炎症小体过度激活通过 NLRP3-IL-18-TNFa 轴破坏气体交换表面的构建 [scRNA-seq]
• GSE275073 嵌合癌蛋白通过相分离的细胞质凝聚体增强天然激酶活性以驱动肿瘤发生
• GSE273922 双相情感障碍患者中脑类器官的单细胞转录组分析揭示了锂反应机制
• GSE343154 通过整合 RNA 相互作用组和可解释机器学习揭示功能性细菌 sRNA–mRNA 相互作用的分子决定因素 [Hfq-CLASH]
• GSE342672 通过整合 RNA 互作组和可解释机器学习揭示功能性细菌 sRNA-mRNA 相互作用的分子决定因素
• GSE320532 经典 PRC1 的冷冻电镜结构、酶活性和基因组靶向性
• GSE309078 超声增强外泌体分泌和无抗体SERS分析用于检测APOE基因型依赖性特征
• GSE254314 m6A RNA甲基化缺陷促进ZBP1介导的细胞死亡