详细内容（前10条）

1. ⭐ 利用ONT纳米孔测序技术对绿水螅（Hydra viridissima）进行全基因组CpG甲基化分析（GSE329152）。

• ✍️ 作者：未知作者
• 🏷️ 关键词：sequencing、genome、methylation
• 📝 描述：Contributors : Alexander Gimelbrant ; Alex BortvinSeries Type : Methylation profiling by high throughput sequencingOrganism : Hydra viridissimaGenome-wide 5-methylcytosine (5mC) profiling at CpG dinucleotides in Hydra viridissima using Oxford Nanopore long-read sequencing with Dorado base modification detection. Five ONT runs (one symbiotic, four aposymbiotic clone 2) were basecalled with Dorado sup,5mCG_5hmCG, aligned to Carnegie v1 genome assembly (JBWVZK000000000), and methylation quantified with modkit. Global CpG methylation is ~9-10%, bimodal (88% unmethylated, 7% fully methylated). Unique genomic regions show higher methylation (12%) than repetitive regions (7.5%).
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2. GSE331452 DICER驱动的脂质代谢和巨噬细胞-脂肪细胞相互作用在部分性脂肪营养不良中的调控

• ✍️ 作者：未知作者
• 🏷️ 关键词：macrophage、metabolism
• 📝 描述：Contributors : Andréa L. Rocha ; Rhaissa Godoi ; Tanes Imamura de Lima ; Diogo de Moraes ; Bruna Brasil Brandao ; Alan Saghatelian ; Marcelo A. MoriSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusPartial lipodystrophy is characterized by abnormal fat distribution, impaired thermogenesis, systemic inflammation, and diminished DICER expression in adipose tissue. Using adipocyte-specific DICER-deficient models to mimic lipodystrophy, we identified early metabolic and inflammatory alterations that coincide with the onset of partial lipodystrophy. DICER deficiency in adipocytes impaired lipid metabolism, leading to increased release of saturated lipids and triglycerides into the medium while reducing the biosynthesis of anti-inflammatory lipids. These changes promoted a pro-inflammatory environment by reprogramming macrophages to release IL-1beta. Lipidomic analyses revealed reduced levels of docosahexaenoic acid (DHA) and other polyunsaturated fatty acids (PUFAs) in DICER-deficient adipocytes, accompanied by increased expression of CYP450 enzymes linked to lipid degradation and reduced DHA biosynthesis. DHA supplementation mitigated the pro-inflammatory response triggered by conditioned media from DICER-deficient adipocytes.
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3. GSE317204 白纹按蚊 lola 基因敲除免疫反应差异转录组：白纹按蚊 lola 基因敲除对免疫刺激蚊子中肠基因表达谱的影响

• ✍️ 作者：未知作者
• 🏷️ 关键词：immune、transcriptome
• 📝 描述：Contributors : Verónica Valverde-Garduño ; Heidi G Espadas-ÁlvarezSeries Type : Expression profiling by high throughput sequencingOrganism : Anopheles albimanusAnopheles mosquitoes are a potential transmitter of viruses and parasites that cause human diseases. An. albimanus is among the main malaria vectors in Mexico and Latin America. Mosquitoes’ ability to transmit pathogens (vectorial competence) is directly related to their genetics and immunity. The innate immunity system is the first line of defense against non-self microbial invaders. The mosquito midgut is a crucial entry point for such microbial invaders and for mosquito immune interactions with them. Here, we provide evidence that the lola gene expression is upregulated by immune challenge in three mosquito tissues and cells: the midgut, fat body, and hemocytes. We applied an efficient method for double-stranded RNA (dsRNA)-mediated silencing of this gene expression in vivo as assessed by RT-qPCR. A transcriptome analysis was conducted to investigate the potential involvement of the Lola transcription factor in regulating gene expression. We combined RNAseq with reverse genetics, and our transcriptome analysis revealed that Lola participates in mosquito defense mechanisms. The knockdown of lola showed that it regulates the expression of genes associated with multiple functions, especially those related to detoxification and immunity. Here, we show for the first time a list of mosquito immunity genes that require Lola expression. These lola-dependent genes include antimicrobial peptides, C-lectins, pattern recognition receptors, Clip-domain serine proteases, ML-domain-containing proteins, enzymes that catalyze the generation and detoxification of reactive oxygen species, and components of the JNK immune signaling pathways in the midgut of An. albimanus. Our studies provide direct evidence of a functional link between JNK signaling and Lola factor in the mosquito midgut. Dysregulation of this pathway may contribute to increased pathogen invasion.
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4. GSE312645 酵母 Rpd3L 组蛋白去乙酰化酶将营养变化与全基因组染色质重编程联系起来

• ✍️ 作者：未知作者
• 🏷️ 关键词：genome、histone
• 📝 描述：Contributors : Saikat Bhattacharya ; Benjamin M Sutter ; Benjamin P TuSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Saccharomyces cerevisiaeAdaptive transcriptional rewiring underlies the metabolic flexibility of Saccharomyces cerevisiae. We demonstrate that the histone deacetylase Rpd3 mediates nutrient-dependent chromatin reprogramming that coordinates transcriptional shutdown and global acetylation balance during metabolic transitions. Genome-wide analyses reveal that Rpd3 complexes drive rapid, reversible histone deacetylation across promoters and gene bodies, fine-tuning transcriptional output. Rpd3, primarily through the large complex (Rpd3L), localizes at promoters of active genes enriched in H3K9ac and the acetyltransferase Gcn5. Upon nutrient shift, Gcn5 disengages while Rpd3-mediated H3K9 deacetylation enforces repression. Loss of Rpd3 or its Rpd3L-specific subunit, Pho23, disrupts this balance, resulting in the aberrant persistence of growth programs upon starvation and defective activation of respiratory genes in the presence of glucose. HDACs thus can act as metabolic gatekeepers, coupling nutrient cues to chromatin reprogramming and ensuring transcriptional fidelity during metabolic transitions, thereby resolving the long-standing paradox of HDAC enrichment at active promoters.
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5. GSE310711 婴儿双歧杆菌和人乳寡糖对无菌小鼠模型的免疫反应和氨基酸代谢具有独立的影响

• ✍️ 作者：未知作者
• 🏷️ 关键词：immune、metabolism
• 📝 描述：Contributors : Bharath K Mulakala ; Michael L Salinas ; Laurie A Davidson ; Selim Romero ; Quentin D Read ; Renne Fox ; Tanya LeRoith ; James J Cai ; Robert S Chapkin ; Sharon M Donovan ; Laxmi YeruvaSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusEarly-life microbial colonization is essential for gut and immune development. Human milk oligosaccharides (HMO) support the growth of Bifidobacterium infantis (BI), a keystone infant species. Herein, we studied the individual and combined effects of BI and HMO on immune and colon transcriptomes, and the serum metabolome. Germ-free mice were randomly assigned to four groups [10-14/group: HMO, BI, BI+HMO and control (no HMO or BI)]. HMO and BI+HMO groups received 5 mg/d each of 2′-fucosyllactose, lacto-N-tetraose and 3′-sialyllactose for 14 d. BI and BI+HMO received B. infantis ATCC 15697 (1x10^9 CFU/d) on days 1, 4, and 9. Mono-colonization with BI increased monocytes, macrophages, B cells, CD4+ T cells, and Treg cells in mesenteric lymph nodes (MLN) relative to control. In the spleen, BI alone increased B cells, dendritic cells, Th17 cells, and ILC3 cells, and enriched serum amino acid metabolism pathways. Additionally, BI influenced colonocyte gene expression, and modulated serum metabolites regulating circadian rhythms. BI+HMO increased MLN Th17 cells and spleen monocytes compared to HMO alone. Collectively, the results of this study highlight the complex interplay between host-microbe-diet interactions and emphasize the importance of considering these interactions when designing strategies to modulate infant health during early life.
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6. GSE332840 用于准确预测病毒和肿瘤抗原的T细胞特异性的生物物理模型

• ✍️ 作者：未知作者
• 🏷️ 关键词：tumor、T cell
• 📝 描述：Contributors : Jeffrey Molldrem ; Xizeng Mao ; Noah Tubo ; Priya Koppikar ; Jason George ; Zahra GhoreyshiSeries Type : Expression profiling by high throughput sequencing ; OtherOrganism : Homo sapiensAccurate predictions of T cell receptor (TCR) specificity remain an important open problem in immunology, with broad implications for vaccine design, optimal immunotherapy, and improved management of autoimmune diseases. However, diversity in peptide antigens and TCR sequences at the level of individual patient repertoires remains a formidable computational challenge. Here, we develop a joint experimental and computational approach for predicting the antigen specificity of clinically-derived TCR sequences. Our model is trained on a combination of experimentally pre-identified and in silico-predicted TCR-pMHC structures using AlphaFold3. We apply our structural model in the clinical setting of hematopoietic stem cell transplant (HSCT) and demonstrate that our model is able to effectively discern the specificity of previously unseen donor and patient-derived TCR sequences against tumor associated and viral antigens. Model performance was further enhanced through the integration of sequence-based clustering and structurally diverse training templates. Our results highlight the predictive capabilities of structurally guided machine learning frameworks, trained on a minority test dataset, for antigen specificity prediction on unseen TCR sequences and their potential impact on a wide range of immunological applications.
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7. GSE328048 单细胞转录组揭示了角质形成细胞亚群在特应性皮炎中导致分化改变和炎症反应的机制

• ✍️ 作者：未知作者
• 🏷️ 关键词：single-cell、transcriptome
• 📝 描述：Contributors : Johann E Gudjonsson ; Lam C TsoiSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensAtopic dermatitis (AD) is a common chronic inflammatory skin disease with complex, poorly understood pathogenesis due to its mechanistic heterogeneity. To investigate underlying mechanisms, we performed single-cell RNA sequencing (scRNA-seq) on lesional (LAD) and non-lesional (NAD) skin from 42 AD patients and skin from 23 healthy controls (HC). Keratinocytes (KCs) were the most abundant cell type identified. In healthy skin, KC differentiation followed a linear trajectory from basal KCs (BKs) through seven differentiated stages (DK1–DK7) to terminal keratinized cells (KK1 and KK2). In LAD, this process was disrupted, showing a reversed transition from KK2 to KK1, mainly driven by DK7. APOD and LYZ were identified as LAD-specific regulators of this aberrant keratinization, linked to IL-13- and IL-22-driven responses involving endoplasmic reticulum (ER) stress and oxidative damage. Mitochondrial and ER dysfunction were specifically enriched in LAD DK6 cells, suggesting this subcluster as a key pathogenic compartment associated with cytokine activation. Further, cell-cell interaction analysis (validated through Xenium spatial transcriptomics and immunohistochemistry) highlighted TWEAK, derived from IL13+ Th2 and cycling T cells acting on FN14+ basal and differentiated KCs, as a key contributor to AD-associated epidermal responses. These findings reveal how disrupted KC differentiation and specific immune pathways contribute to AD pathogenesis, identifying distinct cellular compartments and inflammatory circuits as potential therapeutic targets.
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8. GSE328981 量子分子共振减弱人视网膜色素上皮细胞中氧化应激诱导的嵌合转录组程序，同时保持RNA结构保真度

• ✍️ 作者：未知作者
• 🏷️ 关键词：transcriptome
• 📝 描述：Contributors : Alibrandi Simona ; Mordà Domenico ; Scimone Concetta ; Dascola Angela ; Aliquò Federica ; Abate Giorgia ; Pozzato Gianantonio ; Scalinci Sergio Zaccaria ; D’Angelo Rosalia ; Sidoti Antonina ; Donato LuigiSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensChimeric and fusion-like transcripts are increasingly recognized as dynamic, non-genomic responses to acute environmental stress. Elevated reactive oxygen species (ROS) compromise RNA Polymerase II (RNAPII) termination and splicing fidelity, generating a potentially proteotoxic burden of structurally aberrant RNAs. However, robust quantification of these stress-induced chimeras in non-tumor perturbation models remains technically challenging. We profiled the structural fidelity of the transcriptome across a large-scale RNA-seq cohort (n=72 samples) centered on Quantum Molecular Resonance (QMR) therapy and oxidative stress (H2O2 400 µM) in ARPE-19 human retinal pigment epithelial cells, across four treatment groups (Control, QMR Rescue, Secretome, QMR+Secretome Rescue) at 8h, 24h, and 72h post-challenge. Using a stringently uniform bioinformatic pipeline (CLC Genomics Workbench v25.0.3, Detect and Refine Fusion Genes v1.6; hg38/Ensembl v113), chimeric events were stratified into three escalating confidence tiers: Tier 1 (PASS), Tier 2 (PASS + in-frame CDS), and Tier 3 (high-confidence: PASS + in-frame + spanning reads > 0). Ubiquitous background chimeras constitutively expressed across all conditions (e.g., NBPF14–NOTCH2, FBXL5–ENSG00000305512, RAB27A–PIGBOS1) were explicitly identified and partitioned from the dynamic, treatment-responsive fraction. Oxidative stress significantly exacerbated the global Chimeric Burden at 72 hours, with mean aggregate read support surging to 575.5 (SD 55.1) in the Control-OX group. QMR Rescue and QMR+Secretome treatment profoundly attenuated this structural derailment (525.5 ± 139.3 and 449.0 ± 33.9, respectively). A robust 25-event QMR-Rescued Signature was derived, mapping OX-induced chimeras to four discrete biological modules: (I) Lipid/Steroidogenic pathway integrity (CTDNEP1–ENSG00000262526, HSD17B7P2–HSD17B7); (II) Extracellular matrix structural integrity (COL7A1–UCN2, COP1-DT–PAPPA2); (III) Nuclear architecture and mitochondrial coupling (COX17–POPDC2); and (IV) Zinc-finger transcriptional networks (ZNF721–ABCA11P, ZNF782–ZNF510). Top events were orthogonally validated by Arriba and STAR-Fusion (93.3% con…
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9. GSE328193 人类胚胎干细胞血管内皮细胞分化的多组学分析 [HUVEC RNA-Seq]

• ✍️ 作者：未知作者
• 🏷️ 关键词：RNA-seq
• 📝 描述：Contributors : Andrew J Lee ; Sunwoo Min ; Mei-Yu Qiu ; Gou Young Koh ; Inkyung JungSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensTo investigate gene regulatory dynamics of normal endothelial cell (EC) differentiation at high resolution, an in vitro differentiation system was employed to derive functional vascular ECs from human embryonic stem cells. Human embryonic stem cells, mesodermal cells, and differentiating cells following VEGF-A stimulation at eight time points (1–48 hours), along with internal controls without VEGF-A treatment (referred to as non-ECs), were collected to profile global RNA expression and H3K27ac signals. In addition, in situ Hi-C data were generated for ECs and non-ECs at 24 hours after VEGF-A treatment to characterize global chromatin contact profiles associated with the EC progenitor state.
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10. GSE328192 人类胚胎干细胞血管内皮细胞分化的多组学分析 [Hi-C]

• ✍️ 作者：未知作者
• 🏷️ 关键词：Hi-C
• 📝 描述：Contributors : Andrew J Lee ; Sunwoo Min ; Mei-Yu Qiu ; Gou Young Koh ; Inkyung JungSeries Type : OtherOrganism : Homo sapiensTo investigate gene regulatory dynamics of normal endothelial cell (EC) differentiation at high resolution, an in vitro differentiation system was employed to derive functional vascular ECs from human embryonic stem cells. Human embryonic stem cells, mesodermal cells, and differentiating cells following VEGF-A stimulation at eight time points (1–48 hours), along with internal controls without VEGF-A treatment (referred to as non-ECs), were collected to profile global RNA expression and H3K27ac signals. In addition, in situ Hi-C data were generated for ECs and non-ECs at 24 hours after VEGF-A treatment to characterize global chromatin contact profiles associated with the EC progenitor state.
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详细内容（全部4条）

1. 利用单细胞RNA测序技术推动真菌感染研究

• ✍️ 作者：未知作者
• 🏷️ 关键词：sequencing、single-cell
• 📝 描述：Single-cell RNA sequencing is helping researchers uncover cellular responses to fungal pathogens, providing new insights into host-pathogen interactions, biomarkers, and potential therapeutic targets… The post Empowering fungal infection research with single-cell RNA sequencing appeared first on RNA-Seq Blog.
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2. Blank Bio宣布获得种子轮融资，并与PacBio达成战略合作，以推进RNA基础模型在精准肿瘤学领域的应用。

• ✍️ 作者：未知作者
• 🏷️ 关键词：oncology、regex:onco(logy|logist|gene|genic)
• 📝 描述：The Blank Bio and PacBio collaboration combines long-read RNA sequencing and AI foundation models to improve biomarker discovery, patient stratification, and precision… The post Blank Bio Announces Seed Financing and Strategic Collaboration with PacBio to Advance RNA Foundation Models for Precision Oncology appeared first on RNA-Seq Blog.
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3. USADAE——一种利用深度学习方法解析RNA-seq数据中隐藏协变量的方法

• ✍️ 作者：未知作者
• 🏷️ 关键词：RNA-seq
• 📝 描述：RNA sequencing analysis with the USADAE deep learning framework improves detection of hidden confounders while preserving biological signals for transcriptomics studies… The post USADAE – a deep learning approach to disentangle hidden covariates in RNA-seq data appeared first on RNA-Seq Blog.
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4. 这种常见的氨基酸帮助小鼠在致命的炎症中存活下来。

• ✍️ 作者：未知作者
• 🏷️ 关键词：inflammation
• 📝 描述：A Salk Institute study found that a simple dietary amino acid, methionine, dramatically improved survival in mice facing severe infections and inflammatory conditions. Rather than directly targeting the immune system, methionine boosted kidney filtration, helping the body flush out excess inflammatory molecules that can cause tissue damage, brain dysfunction, wasting, and death.
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• GSE328191 人类胚胎干细胞血管内皮细胞分化的多组学分析 [ChIP-seq]
• GSE328189 人类胚胎干细胞血管内皮细胞分化的多组学分析 [EC diff RNA-Seq]
• GSE297917 青春期相关蛋白 TIMP2 调节健康和老年小鼠的小胶质细胞状态和功能 [批量 RNA 测序]
• GSE333729 ChIP-seq 数据显示，嗜水弧菌（Vibrio natriegens）的固氮酶调控与其他γ-变形菌不同。
• GSE325147 小鼠背根神经节单细胞测序（假性股内接种）
• GSE269002 利用冷冻组织单核RNA测序研究表皮痣对模拟太阳辐射的反应
• GSE254038 在Mtb/SIV共感染的恒河猴模型中，利用单细胞转录组学研究HIV对潜伏性结核感染的影响
• GSE211688 缺陷的角质层衍生信号增强细胞外ATP反应和植物免疫力
• GSE333737 MERFISH 成人胰腺细胞外基质和血管相关细胞群的空间转录组分析
• GSE333588 单细胞图谱描绘了慢性粒细胞白血病 (CML) 患者慢性期和 B 淋巴母细胞危象期样本之间不同的表达特征。
• GSE306625 不同的治疗诱发性神经内分泌前列腺癌亚型可预测预后
• GSE298674 靶向星形胶质细胞CLC2(CLCN2)可通过抑制SPP1/CD44信号通路恢复脑白质病中的髓鞘再生
• GSE279340 番茄红素可减轻电离辐射引起的肠道损伤
• GSE298774 痣向黑色素瘤转变过程中的空间基因表达和微环境变化
• GSE280655 发育中小鼠脑皮层抑制性神经元的单细胞转录组