详细内容（前10条）

1. ⭐ GSE307447 韩国家犬血液样本的哺乳动物甲基化芯片分析及其在表观遗传衰老研究中的应用

• ✍️ 作者：未知作者
• 🏷️ 关键词：aging、epigenetic、methylation
• 📝 描述：Contributors : Subin Jang ; Seong Jun KimSeries Type : Methylation profiling by genome tiling arrayOrganism : Canis lupus familiaris ; Homo sapiens ; Mus musculus ; Rattus norvegicusGenome-wide DNA methylation profiles were generated from whole blood of Korean companion dogs (n = 84) using the Illumina HorvathMammalMethylChip40 array. Samples cover a broad age range (0.58–14 years), both sexes, and multiple breeds. The dataset provides a resource for investigating age-associated CpG variation and epigenetic aging markers in domestic dogs.
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2. ⭐ GSE295173 多模态单细胞测序揭示循环单核细胞中的网络转变与创伤患者的更快恢复相一致，并有利于对 M-CSF 的反应 [scRNA-Seq]

• ✍️ 作者：未知作者
• 🏷️ 关键词：sequencing、single-cell、scRNA
• 📝 描述：Contributors : Chen Tianmeng ; Hughes Julia ; Cornoy Julia ; Billiar TimothySeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensPrevious transcriptomic studies to characterize the changes in circulating immune cells after major trauma in humans have demonstrated a dramatic early upregulation of inflammatory features and simultaneous downregulation of MHCII and IFN signaling pathways in monocytes; changes that gradually return to baseline. The magnitude and duration of these changes is associated with post-injury complications. To determine if unique immune cell subsets or features emerging in the subacute time frame associated with patient outcomes after severe injury, we applied DOGMA-seq (single-cell RNA + ATAC + ADT sequencing) on peripheral blood mononuclear cells isolated at day 3 after injury. Patients were segregated into slow or fast recovery from critical illness (8 patients/ group) and compared to age and sex matched healthy controls. An analysis that integrated all three single cell modes identified a subset of CD172a hi/MHCII hi, CD14+ monocytes overrepresented in patients that recovered faster and distinct from baseline monocytes. This monocyte subset appeared prior to recovery and increased over time and was associated with changes in several key gene co-expression networks (referred to as a red-to-green network transition). A green-shifted pattern (associated with chemotaxis and cell adhesion) was overrepresented in fast recovery patients, continuously deviated from baseline, and specifically associated with increased accessibility of AP1 family motifs. In contrast, the red-shifted pattern (mainly pro-inflammatory genes) was associated with slow recovery, increased accessibility of CEBPB, less accessibility of IRF motifs, and gradually returned to baseline. Subsequent in vitro cell culture demonstrated that, compared to red-shifted cells, green shifted cells favored higher response to M-CSF-stimulated macrophage differentiation that included the upregulation of the genes involved in cell motility, while not obviously influenced the response to GM-CSF stimulation. Our findings add a new information layer to the current human paradigm for the immune response to injury, that includes the trauma-inducible features augmented along recovery leading to post-traumatic monocytes continuously different from baseline. The changes in circulating monocytes may have a wide influence on peripheral tissues via differentiat…
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3. ⭐ GSE335518 CDK7 抑制可抑制 Hippo-YAP 信号传导，从而逆转激素受体阳性乳腺癌中的 CDK4/6 抑制剂耐药性 [ChIP-seq]

• ✍️ 作者：未知作者
• 🏷️ 关键词：cancer、resistance、ChIP-seq
• 📝 描述：Contributors : Chung-Jen Yu ; Chih-Yi Lin ; Yong-Ji Zhuang ; Yi-Ru Tseng ; Chun-Yu Liu ; Yi-Fang Tsai ; Chi-Cheng Huang ; Ling-Ming Tseng ; Ta-Chung Chao ; Jiun-I LaiSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Homo sapiensHormone receptor-positive (HR+) breast cancer is the most prevalent breast cancer subtype, and cyclin-dependent kinase 4/6 inhibitors (CDK4/6i) are the mainstay of treatment for metastatic disease. Amplification or overexpression of CDK6 is an established driver of CDK4/6i resistance, for which no targeted strategy exists. Through a kinase-inhibitor screen for compounds that suppress CDK6, we identified PIK-75 as an agent that downregulates CDK6 and reverses CDK4/6i resistance in HR+ breast cancer. We found that PIK-75 acts as an inhibitor of CDK7, abolishing phosphorylation of serine 5 on the RNA polymerase II (Pol II) carboxy-terminal domain. The structurally distinct CDK7 inhibitor THZ1 and shRNA-mediated CDK7 depletion both phenocopied the suppression of yes-associated protein (YAP) and CDK6, establishing the effect as CDK7-dependent. Chromatin immunoprecipitation demonstrated that CDK7 inhibition reduced Pol II-serine 5 occupancy at the YAP1 promoter, downregulating YAP1 transcription and YAP-TEAD output. Genome-wide, PIK-75 induced promoter-proximal Pol II pausing that was more pronounced at oncogenic-pathway genes, and transcriptomic and proteomic profiling confirmed a bona fide CDK7-inhibition signature, accompanied by widespread intron retention, rather than a phosphoinositide 3-kinase-dominated response. In CDK6-overexpressing xenografts, PIK-75 combined with abemaciclib reversed resistance and suppressed YAP and CDK6 in vivo. These findings define a transcriptional axis linking CDK7 and Pol II-serine 5 phosphorylation to Hippo-YAP signaling and CDK6, and establish CDK7 inhibition as a rational strategy for CDK4/6i-resistant HR+ breast cancer, supporting evaluation of clinical-stage CDK7 inhibitors in combination with continued CDK4/6 inhibition.
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4. ⭐ GSE314549 化疗诱导单链 DNA 积累可增强三阴性乳腺癌对免疫疗法的敏感性 [RNA-Seq]

• ✍️ 作者：未知作者
• 🏷️ 关键词：cancer、regex:immuno(logy|therapy|suppression)、RNA-seq
• 📝 描述：Contributors : Yong Du ; Shiaw-Yih LinSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensDespite the widespread adoption of chemo-immunotherapy in triple-negative breast cancer (TNBC), how cytotoxic chemotherapy engages antitumor immunity remains poorly defined. Here, we identify cytosolic single-stranded DNA (ssDNA) accumulation as the mechanistic bridge linking genotoxic stress to immune activation. By integrating in vivo TREX1-deficiency transcriptional signatures, we show that ssDNA-driven immunostimulatory programs—rather than TREX1 expression—robustly predict clinical response to chemo-immunotherapy across independent TNBC cohorts. Through a chemotherapeutic screen, we identify LP-184, an acylfulvene-derived alkylating agent in clinical development, as a potent pharmacologic inducer of cytosolic ssDNA and type I interferon signaling. LP-184 enhances antigen presentation, reduces M2-like tumor-suppressive macrophages, and promotes CD8⁺ T-cell priming, thereby synergizing with anti-PD-1 therapy in vivo. These findings redefine the interface between DNA damage and immune activation, establishing ssDNA-driven immune programs as both a predictive biomarker and a therapeutic axis for next-generation chemo-immunotherapy design.
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5. ⭐ GSE311488 化疗诱导单链 DNA 积累可增强三阴性乳腺癌对免疫疗法的敏感性 [scRNA-seq]

• ✍️ 作者：未知作者
• 🏷️ 关键词：cancer、regex:immuno(logy|therapy|suppression)、scRNA
• 📝 描述：Contributors : Yong Du ; Shiaw-Yih LinSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusDespite the widespread adoption of chemo-immunotherapy in triple-negative breast cancer (TNBC), how cytotoxic chemotherapy engages antitumor immunity remains poorly defined. Here, we identify cytosolic single-stranded DNA (ssDNA) accumulation as the mechanistic bridge linking genotoxic stress to immune activation. By integrating in vivo TREX1-deficiency transcriptional signatures, we show that ssDNA-driven immunostimulatory programs—rather than TREX1 expression—robustly predict clinical response to chemo-immunotherapy across independent TNBC cohorts. Through a chemotherapeutic screen, we identify LP-184, an acylfulvene-derived alkylating agent in clinical development, as a potent pharmacologic inducer of cytosolic ssDNA and type I interferon signaling. LP-184 enhances antigen presentation, reduces M2-like tumor-suppressive macrophages, and promotes CD8⁺ T-cell priming, thereby synergizing with anti-PD-1 therapy in vivo. These findings redefine the interface between DNA damage and immune activation, establishing ssDNA-driven immune programs as both a predictive biomarker and a therapeutic axis for next-generation chemo-immunotherapy design.
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6. ⭐ GSE271232 利用 ChIP-exo 和 RNA-seq 数据集重建细菌转录调控网络的优化方法 [RNA-seq]

• ✍️ 作者：未知作者
• 🏷️ 关键词：bacteria、regex:bacter(ia|ial|ium)、RNA-seq
• 📝 描述：Contributors : Minchang Jang ; Joon Y Park ; Donghyuk KimSeries Type : Expression profiling by high throughput sequencingOrganism : Escherichia coli K-12We propose an optimized protocol to reconstruct bacterial transcriptional regulatory networks (TRNs) using ChIP-exo and RNA-seq datasets. For the reconstruction of TRNs, the omics datasets were targeted to RpoS and generated in Escherichia coli K-12 MG1655 cultured at mid-exponential phase in M9 glucose media.
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7. ⭐ GSE271231 利用 ChIP-exo 和 RNA-seq 数据集重建细菌转录调控网络的优化方法 [ChIP-exo]

• ✍️ 作者：未知作者
• 🏷️ 关键词：bacteria、regex:bacter(ia|ial|ium)、RNA-seq
• 📝 描述：Contributors : Minchang Jang ; Joon Y Park ; Donghyuk KimSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Escherichia coli K-12We propose an optimized protocol to reconstruct bacterial transcriptional regulatory networks (TRNs) using ChIP-exo and RNA-seq datasets. For the reconstruction of TRNs, the omics datasets were targeted to RpoS and generated in Escherichia coli K-12 MG1655 cultured at mid-exponential phase in M9 glucose media.
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8. GSE273368 雌性小鼠体内LPS诱导炎症反应中心脏内皮细胞的共翻译谱分析：概念验证方法

• ✍️ 作者：未知作者
• 🏷️ 关键词：inflammation、cardiac
• 📝 描述：Contributors : Chad M Warren ; Bhairavi Swaminathan ; Paulina Langa ; Stephanie R Villa ; Walter C Thompson ; Magdalena Chrzanowska ; Jan K Kitajewski ; R. John Solaro ; Beata M Wolska ; Paul H GoldspinkSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusProducing functional proteins involves multiple steps during mRNA translation on the ribosomes. However, co-translational regulatory mechanisms remain poorly characterized in intact mammalian systems. As a proof-of-concept, we developed a multi-omics approach to investigate endothelial-specific, co-translational regulation by modifying the translating ribosome affinity purification (TRAP) in vivo. We simultaneously co-immunoprecipitated (IP) polysome-associated mRNAs and proteins from the hearts of hemagglutinin-tagged ribosomal protein L22 mice (RiboTag) crossed with inducible endothelial-specific Cdh5CreERT2 mice (RiboTagEC). To perturb endothelial function, female mice were injected with E. coli lipopolysaccharide (LPS) (6 mg/Kg, i.p., 12 h). Hearts were homogenized, with ~ 10% used for input RNA-Seq and proteomics controls, and the remainder for IP of ribosome-bound polyadenylated mRNA and proteins. Endothelial cell transcripts (pecam1, cdh5) were enriched > 5-fold, while markers characteristic of other cell types were significantly depleted ( 1250 overlapping terms) to identify pathways associated with concordant and discordant co-translational regulation. LPS was identified as the upstream regulator of the co-translational dataset that was concordantly regulated. Upregulated mRNAs but not proteins related to glycolysis were discordantly regulated. These findings validate our proof-of-concept multi-omics approach as a predictive platform for identifying disease-relevant pathways regulated at the co-translational level in vivo.
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9. GSE335773 汇总的 CRISPR/Cas9 筛选鉴定出介导 HepG2 肝细胞癌细胞索拉非尼耐药性的染色质调控基因

• ✍️ 作者：未知作者
• 🏷️ 关键词：carcinoma、resistance
• 📝 描述：Contributors : Jackie Brinkman ; Jesse R RaabSeries Type : OtherOrganism : Homo sapiensFocused pooled CRISPR/Cas9 screen in HepG2 HCC cells. ~6,000 sgRNAs targeting ~750 chromatin/TF genes (~800 non-targeting controls). 4 conditions: T0, DMSO, sorafenib 2.5 µM IC10, sorafenib 4 µM IC50; 3 replicates each. MAGeCK identified ARID1B among top sorafenib-resistance hits. Preprint: https://doi.org/10.64898/2026.06.11.731725
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10. GSE335770 ARID1B 缺失重塑染色质结构，促进肝细胞癌对索拉非尼的耐药性

• ✍️ 作者：未知作者
• 🏷️ 关键词：carcinoma、resistance
• 📝 描述：Contributors : Jacqueline A Brinkman ; Jesse RaabSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Homo sapiensCUT&RUN in HepG2 and HLF HCC cell lines mapping H3K27ac, H3K4me3, ARID1B, FOXA1, FOXA2 occupancy under sorafenib treatment and ARID1B-KO conditions. 2x2 factorial (genotype x treatment), 2 biological replicates per condition. Identifies cBAF-pioneer factor chromatin axis mediating sorafenib sensitivity. Preprint: https://doi.org/10.64898/2026.06.11.731725
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1. DIVINE：一个用于处理真实世界 COVID-19 临床队列的全新 R 包

• ✍️ 作者：未知作者
• 🏷️ 关键词：R package
• 📝 描述：Clinical data are rarely as clean, compact or convenient as the examples we often use when teaching statistics or R. Real hospital datasets are usually distributed across several tables, include missing values, contain repeated structures, and require careful documentation before they can be reused. The new R package DIVINE is … Continue reading: DIVINE: a new R package for working with a real-world COVID-19 clinical cohort
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1. ⭐ 膀胱癌空间分布图揭示了隐藏的肿瘤微环境，并为精准治疗开辟了新途径

• ✍️ 作者：未知作者
• 🏷️ 关键词：tumor、cancer、spatial
• 📝 描述：RNA sequencing and spatial transcriptomics mapped distinct bladder cancer cell states, immune environments, and treatment vulnerabilities, supporting more precise therapy selection… The post Spatial map of bladder cancer reveals hidden tumor environments and new paths toward precision therapy appeared first on RNA-Seq Blog.
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2. Alithea Genomics 启动 MERCURIUS™ 1536 DRUG-seq 的早期使用计划，将转录组学应用于化合物筛选规模化应用。

• ✍️ 作者：未知作者
• 🏷️ 关键词：genomics、transcriptomics
• 📝 描述：MERCURIUS™ 1536 DRUG-seq brings RNA sequencing to large-scale compound screening, enabling efficient gene expression profiling… The post Alithea Genomics launches early access program for MERCURIUS™ 1536 DRUG-seq, bringing transcriptomics to compound screening scale appeared first on RNA-Seq Blog.
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3. 科学家对大脑免疫细胞进行重新编程，以对抗阿尔茨海默病。

• ✍️ 作者：未知作者
• 🏷️ 关键词：immune、Alzheimer
• 📝 描述：A newly identified molecule called OLE helped restore the brain’s immune cells to a more protective state in Alzheimer’s models. The treatment reduced toxic plaque buildup and improved memory, raising hopes for a new therapeutic approach.
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4. segSHAPE：基于纳米孔直接RNA测序的RNA二级结构预测

• ✍️ 作者：未知作者
• 🏷️ 关键词：sequencing
• 📝 描述：segSHAPE improves RNA sequencing signal alignment and modification detection, enabling more accurate secondary structure predictions from individual RNA molecules across multiple chemical probes… The post segSHAPE: RNA secondary structure prediction from nanopore direct RNA sequencing appeared first on RNA-Seq Blog.
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• GSE335769 ARID1B缺失通过转录重编程驱动肝细胞癌中的索拉非尼耐药性
• GSE322556 朗格汉斯细胞通过调节早期真皮淋巴发育来调节成年期的免疫力
• GSE295174 多模态单细胞测序揭示循环单核细胞网络转变，这与创伤患者的更快康复相一致，并有利于对 M-CSF 的反应。
• GSE335537 T细胞微环境通过调节细胞骨架和TCR-抗原相互作用来调控免疫功能
• GSE335516 CDK7抑制剂抑制Hippo-YAP信号通路，从而逆转激素受体阳性乳腺癌中CDK4/6抑制剂的耐药性
• GSE235320 LMO2在肿瘤血管生成和乳腺癌转移中的转录调控图谱
• GSE311343 化疗诱导单链DNA积累可增强三阴性乳腺癌对免疫疗法的敏感性
• GSE327307 DOT1L 通过调控 ncPRC1 靶基因的抑制来维持 DLBCL 的细胞特性 [RNA-Seq]
• GSE330657 放射性药物治疗前激活肿瘤特异性CD8+ T细胞可增强抗肿瘤反应
• GSE326354 长读长 RNA 测序和多聚核糖体分析框架揭示了胶质母细胞瘤中转座元件驱动的转录多样性和翻译重编程 [多聚核糖体]
• GSE326349 长读长 RNA 测序和多聚核糖体分析框架揭示了胶质母细胞瘤中转座元件驱动的转录多样性和翻译重编程 [LR]
• GSE270134 丙酮酸激酶M2调节光感受器神经保护
• GSE335562 谷氨酸离子型红藻氨酸受体作为恩扎卢胺耐药和神经内分泌性前列腺癌的治疗靶点
• GSE335535 通过超高通量 3D 球体筛选进行药物再利用，用于罕见癌症治疗
• GSE335431 HCT116 细胞中的 H4R3me2a ChIP-seq
• GSE333456 KANSL1 缺陷小鼠和对照小鼠的 Lgr5-GFP+ ISC 的 RNA-seq。
• GSE331545 IGF2BP3 通过调节 FASN 表达促进上皮性卵巢癌的进展
• GSE329738 GLP-1R激动剂索玛鲁肽保护发育中的人类前脑类器官免受胆固醇诱导的神经毒性——scRNA序列
• GSE325745 CLN7抑制通过mTOR调控和分子伴侣介导的自噬诱导髓系白血病细胞凋亡
• GSE300407 单核 RNA 测序揭示肥胖驱动的子宫内膜样腺癌雌激素信号重编程