详细内容（前10条）

1. ⭐ GSE269377 成年健康小鼠和突变型 FUS 小鼠脊髓转录组的空间特征分析 [空间转录组学]

• ✍️ 作者：未知作者
• 🏷️ 关键词：spatial、spatial transcriptomics、transcriptome、transcriptomics
• 📝 描述：Contributors : Diana Piol ; Theo Killian ; Gabriele Partel ; Nikolai Hecker ; Sam Kint ; Katy Vandereyken ; Thierry Voet ; Kristofer Davie ; Stein Aerts ; Alejandro Sifrim ; Sandrine Da CruzSeries Type : OtherOrganism : Mus musculusHere we investigated the spatial transcriptome of the aged mouse spinal cord using 10X Genomics Visium platform. We produced local transcriptomes of the full spinal cord with a resolution of 100 um, characterizing ventral and dorsal horn regions, in addition to grey and white matter regions. With these spatial data, it is possible to explore the spatial transcriptome of the aged mouse spinal cord, extrapolating information on the cellular composition of this tissue.
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2. ⭐ GSE309894 ALK阳性非小细胞肺癌早期对阿来替尼耐药的临床特征和空间转录组分析：一项回顾性OLCSG研究

• ✍️ 作者：未知作者
• 🏷️ 关键词：cancer、resistance、spatial、transcriptome
• 📝 描述：Contributors : Tadahiro Kuribayashi ; Go Makimoto ; Kadoaki Ohashi ; Shuta TomidaSeries Type : OtherOrganism : Homo sapiensIn anaplastic lymphoma kinase (ALK) gene rearrangements positive lung cancer, alectinib has shown good efficacy and is used as a first-line drug. However, some cases show early resistance within 3 months, but the characteristics of these cases have not been established. We analyzed patients with unresectable stage III/IV without indications for radical radiotherapy and recurrent ALK-positive lung cancer who received alectinib for primary ALK-TKI. Spatial transcriptome analysis and immunohistochemical staining revealed upregulation of Annexin A1 (ANXA1) in the early resistant group.
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3. ⭐ GSE306114 前列腺癌等位基因特异性表达图谱揭示了 AR 信号传导和耐药通路中反复出现的、阶段特异性的事件 [ChIP-Seq]

• ✍️ 作者：未知作者
• 🏷️ 关键词：cancer、resistance、ChIP-seq
• 📝 描述：Contributors : Margaret Tsui ; Rebecca ChenSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Homo sapiensThe effects of cis-regulatory alterations in prostate cancer (PCa) are insufficiently characterized, presenting an opportunity to discover driver genes and therapeutic targets. To comprehensively study these effects, we identify genes undergoing allele-specific expression (ASE) in localized PCa and metastatic castration-resistant PCa (mCRPC) samples. By defining recurrent ASE events across prostate tissue and tumor-enriched ASE, we develop CASEDI, a computational framework for prioritizing cancer drivers by integrating ASE and clinical data. CASEDI reveals genes showing recurrent ASE and altered expression in PCa, including AR-regulated and oncogenic ACSM1. mCRPC samples show enrichment of ASE in DNA repair, resistance pathways, and oncogenes and increased frequency of monoallelic expression (MAE) compared to localized tumors. We define an mCRPC gene signature based on MAE status that identifies a subgroup of localized patients with worse prognosis. Using ASE analysis, we expand the landscape of cis-regulatory events in PCa to inform the identification of additional therapeutic targets.
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4. ⭐ GSE306113 前列腺癌等位基因特异性表达图谱揭示了 AR 信号传导和耐药通路中反复出现的、阶段特异性的事件 [RNA-Seq 2]

• ✍️ 作者：未知作者
• 🏷️ 关键词：cancer、resistance、RNA-seq
• 📝 描述：Contributors : Margaret Tsui ; Rebecca ChenSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensThe effects of cis-regulatory alterations in prostate cancer (PCa) are insufficiently characterized, presenting an opportunity to discover driver genes and therapeutic targets. To comprehensively study these effects, we identify genes undergoing allele-specific expression (ASE) in localized PCa and metastatic castration-resistant PCa (mCRPC) samples. By defining recurrent ASE events across prostate tissue and tumor-enriched ASE, we develop CASEDI, a computational framework for prioritizing cancer drivers by integrating ASE and clinical data. CASEDI reveals genes showing recurrent ASE and altered expression in PCa, including AR-regulated and oncogenic ACSM1. mCRPC samples show enrichment of ASE in DNA repair, resistance pathways, and oncogenes and increased frequency of monoallelic expression (MAE) compared to localized tumors. We define an mCRPC gene signature based on MAE status that identifies a subgroup of localized patients with worse prognosis. Using ASE analysis, we expand the landscape of cis-regulatory events in PCa to inform the identification of additional therapeutic targets.
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5. ⭐ GSE306112 前列腺癌等位基因特异性表达图谱揭示了 AR 信号传导和耐药通路中反复出现的、阶段特异性的事件 [RNA-Seq 1]

• ✍️ 作者：未知作者
• 🏷️ 关键词：cancer、resistance、RNA-seq
• 📝 描述：Contributors : Margaret Tsui ; Lorraine NunizSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensThe effects of cis-regulatory alterations in prostate cancer (PCa) are insufficiently characterized, presenting an opportunity to discover driver genes and therapeutic targets. To comprehensively study these effects, we identify genes undergoing allele-specific expression (ASE) in localized PCa and metastatic castration-resistant PCa (mCRPC) samples. By defining recurrent ASE events across prostate tissue and tumor-enriched ASE, we develop CASEDI, a computational framework for prioritizing cancer drivers by integrating ASE and clinical data. CASEDI reveals genes showing recurrent ASE and altered expression in PCa, including AR-regulated and oncogenic ACSM1. mCRPC samples show enrichment of ASE in DNA repair, resistance pathways, and oncogenes and increased frequency of monoallelic expression (MAE) compared to localized tumors. We define an mCRPC gene signature based on MAE status that identifies a subgroup of localized patients with worse prognosis. Using ASE analysis, we expand the landscape of cis-regulatory events in PCa to inform the identification of additional therapeutic targets.
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6. ⭐ GSE299441 戊糖磷酸途径的糖酵解旁路是神经系统感觉稳态和轴突再生的代谢检查点

• ✍️ 作者：未知作者
• 🏷️ 关键词：metabolic、nervous、pathway
• 📝 描述：Contributors : Yayue Song ; Simone Di GiovanniSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusHomeostasis and repair in the nervous system are thought to rely on distinct molecular programs. Here, we uncover an unexpected role for the pentose phosphate pathway (PPP) in peripheral sensory axons, where it supports both homeostatic mechanosensation and injury-induced axonal regeneration. We show that the PPP is enriched and active in sciatic nerve axoplasms, where it maintains redox balance via NADPH production, enabling normal mechanical sensation. Following sciatic nerve injury, the PPP is required for regeneration by fueling ribonucleotide synthesis through ribose-5-phosphate production. In contrast, this pathway remains inactive after spinal cord injury (SCI), contributing to regenerative failure. Reactivation of the PPP, through neuronal transketolase overexpression or oral ribose supplementation, promotes metabolic reprogramming, restores sensory and motor axonal growth, and improves neurological recovery after SCI. These findings reveal a dual role for the PPP as metabolic rheostat in sensory neuron physiology and regeneration and highlight its therapeutic potential for central nervous system repair.
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7. GSE313593 犬和人骨肉瘤的大规模比较分析揭示了保守的临床相关肿瘤微环境亚型

• ✍️ 作者：未知作者
• 🏷️ 关键词：tumor、tumor microenvironment
• 📝 描述：Contributors : Sushant Patkar ; Joshua Mannheimer ; Stephanie A Harmon ; Christina J Ramirez ; Christina N Mazcko ; Peter L Choyke ; Gregory T Brown ; Baris Turkbey ; Amy K LeBlanc ; Jessica A BeckSeries Type : Expression profiling by arrayOrganism : Canis lupus familiarisAnalyze clinically annotated bulk tumor transcriptomic datasets of canine and patients with human osteosarcoma to identify potentially conserved patterns of disease progression
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8. GSE293013 单细胞外显子缺失分析揭示了影响基因表达和细胞状态动态的剪接事件 [scRNA-seq]

• ✍️ 作者：未知作者
• 🏷️ 关键词：single-cell、scRNA
• 📝 描述：Contributors : Bandana Kumari ; Arun P Damodaran ; Wilfried Guiblet ; Mei-Sheng Xiao ; Amit K Behera ; Tyler On ; Carl Mcintosh ; Maxwell Teszler ; Chelsee Holloway ; Sandra Le ; Nikhil Parab ; Yongmei Zhao ; Michael Aregger ; Thomas Gonatopoulos-PournatzisSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensAlternative splicing is a pervasive gene regulatory mechanism critical for diversifying the human proteome. To systematically investigate its role in cell fate determination, we developed scCHyMErA-Seq, a scalable CRISPR-based exon deletion screening platform integrated with 10x Genomics single-cell transcriptomic readouts. This tool enables efficient exon deletion while simultaneously capturing Cas9/Cas12a guides and polyadenylated transcripts at single-cell resolution. Applying scCHyMErA-Seq to high-throughput profiling of alternative cassette exons, we identified numerous exons with strong regulatory effects on gene expression. Analysis of NRF1 alternative exon-7 revealed that this exon modulates NRF1 transcriptional activity by regulating its recruitment to the promoters of target genes. Importantly, gene expression profiles generated using scCHyMErA-Seq accurately recapitulate findings from traditional, labor-intensive orthogonal methods, while offering enhanced scalability and efficiency. Overall, scCHyMErA-Seq represents a robust and versatile platform for systematically unraveling the functional impact of alternative splicing by directly linking specific splicing variants to transcriptional phenotypes.
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9. GSE292984 单细胞外显子缺失分析揭示了影响基因表达和细胞状态动态的剪接事件 [ChIP-Seq]

• ✍️ 作者：未知作者
• 🏷️ 关键词：ChIP-seq、single-cell
• 📝 描述：Contributors : Bandana Kumari ; Arun P Damodaran ; Wilfried Guiblet ; Mei-Sheng Xiao ; Amit K Behera ; Tyler On ; Carl Mcintosh ; Maxwell Teszler ; Chelsee Holloway ; Sandra Le ; Nikhil Parab ; Yongmei Zhao ; Michael Aregger ; Thomas Gonatopoulos-PournatzisSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Homo sapiensAlternative splicing is a pervasive gene regulatory mechanism critical for diversifying the human proteome. To systematically investigate its role in cell fate determination, we developed scCHyMErA-Seq, a scalable CRISPR-based exon deletion screening platform integrated with 10x Genomics single-cell transcriptomic readouts. This tool enables efficient exon deletion while simultaneously capturing Cas9/Cas12a guides and polyadenylated transcripts at single-cell resolution. Applying scCHyMErA-Seq to high-throughput profiling of alternative cassette exons, we identified numerous exons with strong regulatory effects on gene expression. Analysis of NRF1 alternative exon-7 revealed that this exon modulates NRF1 transcriptional activity by regulating its recruitment to the promoters of target genes. Importantly, gene expression profiles generated using scCHyMErA-Seq accurately recapitulate findings from traditional, labor-intensive orthogonal methods, while offering enhanced scalability and efficiency. Overall, scCHyMErA-Seq represents a robust and versatile platform for systematically unraveling the functional impact of alternative splicing by directly linking specific splicing variants to transcriptional phenotypes.
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10. GSE269707 成年健康小鼠和突变型FUS小鼠运动和非运动体细胞及轴突转录组的空间特征分析

• ✍️ 作者：未知作者
• 🏷️ 关键词：spatial、transcriptome
• 📝 描述：Contributors : Diana Piol ; Theo Killian ; Maria Georgopoulou ; Alejandro Sifrim ; Sandrine Da CruzSeries Type : OtherOrganism : Mus musculusHere we investigated the transcriptome of motor and non-motor axons and cell bodies in the context of mutant FUS-related amyotrophic lateral sclerosis (ALS). We applied Nanostring GeoMX Digital Spatial Profiler platform to profile the transcriptome of subcellular compartments in the lower motor circuitry of a mouse model ricapitulating ALS motor symptoms. This work sheds light for the first time on the transcriptomic alterations in axons and in somas which may contribute to axonal degeneration and neuromuscular junction denervation, early features of ALS.
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1. MD安德森癌症中心和SOPHiA GENETICS宣布建立战略合作关系，以加速人工智能驱动的精准肿瘤学发展。

• ✍️ 作者：未知作者
• 🏷️ 关键词：oncology、regex:onco(logy|logist|gene|genic)
• 📝 描述：MD Anderson and SOPHiA GENETICS are combining AI analytics with RNA sequencing to accelerate precision oncology by translating complex genomic and multimodal data into actionable clinical insights…
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2. 癌症研究人员可申请单细胞研究资助

• ✍️ 作者：未知作者
• 🏷️ 关键词：cancer
• 📝 描述：Join this online info session on January 15 at 8:00 AM Pacific to learn how Parse Biosciences’ combinatorial barcoding enables cancer research, what the grant includes, and how to apply…
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3. ASPEN——单细胞RNA测序中等位基因动态的稳健检测

• ✍️ 作者：未知作者
• 🏷️ 关键词：RNA-seq
• 📝 描述：ASPEN enhances RNA sequencing analyses to detect allelic imbalance and variance in single cells, revealing regulatory control differences in essential, neurodevelopmental, and immune genes…
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• GSE262252 APOBEC3A、APOBEC3B 和 APOBEC3H 单倍型 I 在乳腺癌小鼠异种移植模型中对肿瘤进展的不同影响
• GSE315576 核仁扩张驱动癌症中的三维基因组重组和转录抑制
• GSE304507 赖氨酸乳酸化调节犬血管肉瘤在葡萄糖饥饿条件下的 ATF4 介导的应激反应 [RNAseq]
• GSE298402 RNA-Seq 分析 Trim28 缺失的 NPp53 小鼠前列腺组织
• GSE292988 单细胞外显子缺失分析揭示了影响基因表达和细胞状态动态的剪接事件 [RNA-seq_Rescue_exp]
• GSE292986 单细胞外显子缺失分析揭示了影响基因表达和细胞状态动态的剪接事件 [RNA-seq_BaseEditor]
• GSE283548 吞噬过程中 Notch 的抑制可阻止巨噬细胞的炎症极化 [RNA-seq.小鼠]
• GSE283547 吞噬过程中 Notch 的抑制可阻止巨噬细胞的炎症极化 [RNA-seq.HumanMouse]
• GSE272501 生殖细胞配子发生过程中基因组组织的全局性重塑
• GSE245135 钠肌醇共转运蛋白-1 (SMIT1) 促进压力超负荷小鼠心脏的心肌肥大和纤维化
• GSE307045 小鼠黑素细胞的特征分析揭示了内耳功能的超微结构和免疫学见解 [RNA-Seq]
• GSE300400 干扰素γ在猪早期妊娠期间对子宫内膜免疫微环境的编程
• GSE271977 猪间充质干细胞克隆的批量RNA测序，这些克隆具有高或低的脂肪生成能力
• GSE269749 通过内切和外切偶联模式高效处理广泛存在的R环可防止基因组不稳定
• GSE253653 DRIP-seq 揭示 REXO4 和 RNaseH1 共同作用，处理基因组同一基因组区域中的 R 环。
• GSE315982 DAXX 控制小鼠精子发生过程中 LINE1 的沉默 [RNA-seq]
• GSE309333 单核转录组学揭示了小鼠前神经胶质瘤进展过程中细胞周期控制和突触通路失调。
• GSE302146 诱导多能干细胞来源的蜕膜自然杀伤细胞的单细胞RNA测序
• GSE299592 APEX-seq 绘制活细胞中转录组范围的亚细胞 RNA 定位图谱
• GSE291215 利用SARS-CoV-2感染老年和成年小鼠肺细胞进行单细胞基因表达分析
• GSE236762 奥希替尼诱导小鼠心脏功能障碍的单核转录组分析