详细内容（前10条）

1. ⭐ GSE312144 通过细胞系高通量筛选和转录组学揭示肝细胞癌对 Y-90 微球耐药的分子指标

• ✍️ 作者：未知作者
• 🏷️ 关键词：carcinoma、resistance、transcriptomics
• 📝 描述：Contributors : Alexander Zheleznyak ; Dhanusha Duraiyan ; Jessica Silva-Fisher ; Christopher MaloneSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensMolecular signatures predict prognosis in hepatocellular carcinoma; however, their relevance to Y-90 radioembolization remains unknown. Here, we perform Y-90 microsphere screens in a panel of genetically diverse human HCC cell lines. Ten transcriptomically diverse human HCC cell lines were exposed to 20 MBq of Y-90 glass beads. Normalized AUC values qualified sensitivity. Whole-transcriptome RNA sequencing at baseline and post-treatment underwent differential expression analysis and gene set enrichment analysis. The response of HCC cell lines to Y-90 was heterogeneous, with SK-Hep1 and SNU-449 being the most resistant and PLC/PRF/5 being the most sensitive.
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2. ⭐ GSE312733：结肠炎相关癌症模型中上皮HO-1敲除小鼠和对照小鼠结肠肿瘤的单细胞RNA测序

• ✍️ 作者：未知作者
• 🏷️ 关键词：cancer、RNA-seq、single-cell
• 📝 描述：Contributor : Joseph OnyiahSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusThis dataset contains single-cell RNA sequencing profiles of colonic tumor cells isolated from mice with intestinal epithelial-specific deletion of Hmox1 and littermate controls. Tumors were generated using the azoxymethane-dextran sodium sulfate (AOM-DSS) model of colitis-associated cancer. Following enzymatic dissociation and live cell sorting, single-cell libraries were prepared using the 10x Genomics Chromium platform and sequenced to characterize transcriptional programs within the tumor microenvironment. The dataset was designed to examine genotype-dependent shifts in epithelial transcriptional programs within the tumor microenvironment, with a focus on stress-adaptive responses, iron metabolism, and oxidative stress regulation.
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3. ⭐ GSE310129 鸡和鸭喙的空间转录组测序

• ✍️ 作者：未知作者
• 🏷️ 关键词：sequencing、spatial、transcriptome
• 📝 描述：Series Type : OtherOrganism : Anas platyrhynchos ; Gallus gallusThe power of any genotype-phenotype mapping approach ultimately depends on whether the identified genetic variants correspond to genes with demonstrable roles in the developmental processes that shape the target traits. We generated bulk RNAseq, single cell and spatial transcriptomic data from multiple embryonic stages (HH29, HH30, HH36 and HH38) for beak buds and whole embryos to evaluate whether candidate genes are functionally enriched in the cellular and molecular programs regulating beak morphogenesis.
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4. ⭐ GSE308115 肝脏转录组学揭示 UB-NPs 调控脂质代谢和炎症基因

• ✍️ 作者：未知作者
• 🏷️ 关键词：inflammation、metabolism、transcriptomics
• 📝 描述：Contributors : Chang Liu ; Shangnian Liu ; Chao He ; Tingting Han ; Yajuan Zhao ; Yanjuan Li ; Yijun Lin ; Zimeng Niu ; Dengqun Liao ; Caixia Chen ; Xianen LiSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusThis study utilized RNA-Seq to investigate hepatic gene expression changes in obese mice following intervention with UB-NPs, based on prior evidence indicating the liver as a primary site of UB metabolism. High-quality sequencing data (Q30 > 95.93%, alignment efficiency 90.69–97.47% to GRCm39) revealed 3,387 differentially expressed genes (DEGs) between UB-NPs and high-fat diet (HFD) groups, including 687 overlapping DEGs with the HFD vs. normal diet comparison. Among these, 570 DEGs showed expression reversal patterns, indicating potential key targets of UB-NPs. Functional enrichment analyses (GO, Reactome, KEGG) demonstrated that UB-NPs significantly modulate genes involved in lipid and fatty acid metabolism, mitochondrial beta-oxidation, TCA cycle, inflammatory pathways (e.g., NF-kappa B), and PPAR signaling. UB-NPs upregulated fatty acid oxidation genes (e.g., Ppara, Ehhadh, Cyp4a14) and downregulated pro-inflammatory genes (e.g., Tnf, Traf1). These results suggest UB-NPs ameliorate obesity-related metabolic dysregulation by enhancing lipid catabolism and suppressing inflammation.
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5. GSE306487 DNA甲基化和lncRNA表达控制特定印记基因区域的异步DNA复制[RNA-seq]

• ✍️ 作者：未知作者
• 🏷️ 关键词：RNA-seq、methylation
• 📝 描述：Contributors : Yui Imaizumi ; Pol Arnaud-Romero ; Jean-Christophe Andrau ; Robert FeilSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusBesides genome-wide patterns of replication timing (RT), some genes display allelic replication asynchrony in stem cells, brought about by stochastic events and genetic polymorphisms. Whether epigenetic modifications control asynchronous replication remains unclear. We explored mammalian imprinted domains, where parental DNA methylation imprints mediate allele-specific gene expression. Our genome-wide and locus-specific assays in mono-parental and hybrid mouse ESCs reveal pronounced RT asynchrony—which is parent-of-origin dependent and lost upon neural differentiation—at the Dlk1-Dio3 and Snrpn domains, which both comprise lncRNA polycistrons. Generating a range of mutant lines, we find that asynchronous replication at Dlk1-Dio3 is mediated by differential DNA methylation, and that the lncRNA Meg3 controls early replication across parts of the domain on the maternal chromosome. RT thereby becomes unlinked from 3D chromatin architecture as assayed by Hi-C. The combined replication timing, DNA methylation, 3D chromatin structure and gene expression data highlight how parental methylation imprints and lncRNA expression control replication and can override RT domain organisation.
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6. GSE306486 DNA甲基化和lncRNA表达控制特定印记基因区域的异步DNA复制[Hi-C]

• ✍️ 作者：未知作者
• 🏷️ 关键词：Hi-C、methylation
• 📝 描述：Contributors : Benoit Moindrot ; François Charon ; Daan NoordermeerSeries Type : OtherOrganism : Mus musculusBesides genome-wide patterns of replication timing (RT), some genes display allelic replication asynchrony in stem cells, brought about by stochastic events and genetic polymorphisms. Whether epigenetic modifications control asynchronous replication remains unclear. We explored mammalian imprinted domains, where parental DNA methylation imprints mediate allele-specific gene expression. Our genome-wide and locus-specific assays in mono-parental and hybrid mouse ESCs reveal pronounced RT asynchrony—which is parent-of-origin dependent and lost upon neural differentiation—at the Dlk1-Dio3 and Snrpn domains, which both comprise lncRNA polycistrons. Generating a range of mutant lines, we find that asynchronous replication at Dlk1-Dio3 is mediated by differential DNA methylation, and that the lncRNA Meg3 controls early replication across parts of the domain on the maternal chromosome. RT thereby becomes unlinked from 3D chromatin architecture as assayed by Hi-C. The combined replication timing, DNA methylation, 3D chromatin structure and gene expression data highlight how parental methylation imprints and lncRNA expression control replication and can override RT domain organisation.
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7. GSE289022 DNA甲基化和lncRNA表达控制特定印记基因区域的异步DNA复制[Capture Hi-C]

• ✍️ 作者：未知作者
• 🏷️ 关键词：Hi-C、methylation
• 📝 描述：Contributors : François Charon ; Benoit Moindrot ; Daan NoordermeerSeries Type : OtherOrganism : Mus musculusBesides genome-wide patterns of replication timing (RT), some genes display allelic replication asynchrony in stem cells, brought about by stochastic events and genetic polymorphisms. Whether epigenetic modifications control asynchronous replication remains unclear. We explored mammalian imprinted domains, where parental DNA methylation imprints mediate allele-specific gene expression. Our genome-wide and locus-specific assays in mono-parental and hybrid mouse ESCs reveal pronounced RT asynchrony—which is parent-of-origin dependent and lost upon neural differentiation—at the Dlk1-Dio3 and Snrpn domains, which both comprise lncRNA polycistrons. Generating a range of mutant lines, we find that asynchronous replication at Dlk1-Dio3 is mediated by differential DNA methylation, and that the lncRNA Meg3 controls early replication across parts of the domain on the maternal chromosome. RT thereby becomes unlinked from 3D chromatin architecture as assayed by Hi-C. The combined replication timing, DNA methylation, 3D chromatin structure and gene expression data highlight how parental methylation imprints and lncRNA expression control replication and can override RT domain organisation.
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8. GSE288248 前列腺原位癌自体疫苗注射：利用瘤内病毒模拟物 Poly-ICLC 使冷肿瘤变热

• ✍️ 作者：未知作者
• 🏷️ 关键词：tumor、cancer
• 📝 描述：Contributors : S Nair ; D Chakravaty ; E Davicioni ; A TewariSeries Type : Expression profiling by arrayOrganism : Homo sapiensGene expression study of the poly-ICLC Phase II clinical trial
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9. GSE312932 对早期未经治疗的系统性硬化症皮肤进行空间分析，发现巨噬细胞-成纤维细胞信号传导的促炎血管微环境

• ✍️ 作者：未知作者
• 🏷️ 关键词：macrophage、spatial
• 📝 描述：Contributors : Jarnagin C Helen ; Whitfield L MichaelSeries Type : OtherOrganism : Homo sapiensUncovering the early interactions and spatial distribution of dermal fibroblasts and immune cells in treatment-naïve diffuse cutaneous systemic sclerosis (dcSSc) patients is critical to understanding the initiating events skin fibrosis. We generated an integrated multiomic dataset of early, treatment naïve dcSSc skin. Skin biopsies were analyzed by single-nuclei multiome sequencing (snRNA-seq and snATAC-seq) and two different paired spatial transcriptomic platforms to comprehensively describe the molecular changes in these individuals. We identified a proinflammatory niche within papillary, hypodermis, and vascular niches, that are enriched for activated myeloid cells and proinflammatory fibroblasts characterized by expression of proinflammatory cytokines. Pathway analyses showed significant enrichment of PI3K-AKT-mTOR signaling pathway expression in these cellular niches, driven by profibrotic growth factor signaling networks. Macrophage subclustering showed SSc-specific macrophage activation of IL6-JAK-STAT signaling and the enrichment of oxidative phosphorylation pathways. Ligand-receptor analysis revealed that SSc macrophages secrete PDGF and TGFB to activate the inflammatory SSc-dominant fibroblast subclusters. Spatial transcriptomic analyses showed infiltrating macrophages secreted PDGF and TGFB, modulating fibroblast activation in these niches. Multiomic data integration and spatial transcriptomic neighborhood analysis showed co-localization of fibroblasts, macrophages, and T cells around the vasculature. These data suggest that interactions between activated immune cells and proinflammatory fibroblasts around vascular niches are an early event in scleroderma pathogenesis.
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10. GSE312129 对早期未经治疗的系统性硬化症皮肤进行单核多组学和空间分析，发现巨噬细胞-成纤维细胞信号传导的促炎血管微环境

• ✍️ 作者：未知作者
• 🏷️ 关键词：macrophage、spatial
• 📝 描述：Contributors : Helen C Jarnagin ; Michael L WhitfieldSeries Type : Expression profiling by high throughput sequencing ; Other ; Genome binding/occupancy profiling by high throughput sequencingOrganism : Homo sapiensUncovering the early interactions and spatial distribution of dermal fibroblasts and immune cells in treatment-naïve diffuse cutaneous systemic sclerosis (dcSSc) patients is critical to understanding the initiating events skin fibrosis. We generated an integrated multiomic dataset of early, treatment naïve dcSSc skin. Skin biopsies were analyzed by single-nuclei multiome sequencing (snRNA-seq and snATAC-seq) and two different paired spatial transcriptomic platforms to comprehensively describe the molecular changes in these individuals. We identified a proinflammatory niche within papillary, hypodermis, and vascular niches, that are enriched for activated myeloid cells and proinflammatory fibroblasts characterized by expression of proinflammatory cytokines. Pathway analyses showed significant enrichment of PI3K-AKT-mTOR signaling pathway expression in these cellular niches, driven by profibrotic growth factor signaling networks. Macrophage subclustering showed SSc-specific macrophage activation of IL6-JAK-STAT signaling and the enrichment of oxidative phosphorylation pathways. Ligand-receptor analysis revealed that SSc macrophages secrete PDGF and TGFB to activate the inflammatory SSc-dominant fibroblast subclusters. Spatial transcriptomic analyses showed infiltrating macrophages secreted PDGF and TGFB, modulating fibroblast activation in these niches. Multiomic data integration and spatial transcriptomic neighborhood analysis showed co-localization of fibroblasts, macrophages, and T cells around the vasculature. These data suggest that interactions between activated immune cells and proinflammatory fibroblasts around vascular niches are an early event in scleroderma pathogenesis.
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1. 破坏癌症的秘密枢纽：阻止肿瘤生长的新方法

• ✍️ 作者：未知作者
• 🏷️ 关键词：tumor、cancer
• 📝 描述：Researchers reveal how RNA sequencing uncovers RNA-driven condensates that power an aggressive kidney cancer and demonstrate a molecular switch that dissolves these growth hubs…
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2. RNA测序揭示了气候驱动的北极熊基因变化

• ✍️ 作者：未知作者
• 🏷️ 关键词：sequencing
• 📝 描述：RNA sequencing reveals shifting gene activity in Greenland polar bears, showing how temperature-linked changes in jumping genes may support adaptation to warmer, rapidly transforming Arctic habitats…
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3. 科学家发现黑巧克力中有一种成分可以延缓衰老

• ✍️ 作者：未知作者
• 🏷️ 关键词：aging
• 📝 描述：Scientists have uncovered a surprising link between dark chocolate and slower aging. A natural cocoa compound called theobromine was found in higher levels among people who appeared biologically younger than their real age.
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• GSE313107 AMPK激动剂可优化嵌合抗原受体T细胞的体内激活和抗白血病疗效
• GSE313055 这项研究比较了来自不同种族的前列腺癌细胞系的癌基因和抑癌基因的差异表达模式，这是一项健康差异研究。
• GSE221083 整合蛋白质组学和转录组学鉴定出乙型肝炎病毒感染后肝硬化患者的新型纤维化相关生物标志物
• GSE312998 晚发性家族性脑海绵状血管畸形病例中新型非编码变异的发现和功能表征 [RNA-seq]
• GSE302643 肿瘤相关巨噬细胞 (TAM) 伴或不伴 HRS 敲低 (KD)
• GSE289027 DNA甲基化和lncRNA表达控制特定印记基因区域的异步DNA复制[Capture Repli-seq]
• GSE287263 HepG2-TAF2-V5克隆的ChIP-seq分析
• GSE222754 人类 iPSC 衍生小胶质细胞在不同培养条件下的基因表达谱 [批量 RNA 测序]
• GSE210485 TAF2 和 MYC 协同促进肝细胞癌的发生
• GSE203312 阴阳1在小鼠KMWT1胶质瘤细胞中的作用
• GSE313642 在索拉非尼联合纳武利尤单抗的 II 期临床试验中，肝功能障碍的肝细胞癌患者体内免疫抑制性单核细胞富集
• GSE312912：对暴露于血红素或载体的健康上皮HO-1敲除小鼠和对照小鼠的结肠上皮干细胞衍生类器官进行批量RNA测序。
• GSE307520 人类黏膜组织中免疫细胞的 snATAC-seq 分析
• GSE305622 先天性巨结肠症患者的近端神经节肠段纤维化且僵硬
• GSE305028 皮肤成纤维细胞稳态的改变有助于愈合结果 [批量 RNA 测序]
• GSE244187 黑人和白人女性子宫肌层（正常和高危）及子宫肌瘤组织的转录组分析
• GSE271087 GSDME 控制的细胞焦亡通过协调组织驻留巨噬细胞和纤维脂肪生成祖细胞来促进肌肉修复 [RNA-seq]
• GSE264673 EPOP 通过直接调节酶复合物二聚化限制 PRC2.1 靶向染色质 (RNA-Seq)
• GSE264672 EPOP 通过直接调节酶复合物二聚化限制 PRC2.1 靶向染色质 (ChIP-Seq)
• GSE313178 靶向 cGAS–STING 通路可减轻基因敲入小鼠模型中的亨廷顿病发病机制
• GSE313071 干扰素诱导潜能的单细胞异质性是可遗传的，并受细胞状态 IV 变异的调控
• GSE313068 干扰素诱导潜能的单细胞异质性是可遗传的，并受细胞状态 III 变异的调控
• GSE313067 干扰素诱导潜能的单细胞异质性是可遗传的，并受细胞状态 II 变异的调控
• GSE313066 干扰素诱导潜能的单细胞异质性是可遗传的，并受细胞状态 I 变异的调控
• GSE297610 KMT2C 缺陷通过 H3K27ac 介导的 HIPPO 通路失活促进脑膜瘤进展