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1. ⭐ GSE318507 利用空间转录组学评估杜氏肌营养不良症中枢神经系统中的外显子跳跃

• ✍️ 作者：未知作者
• 🏷️ 关键词：nervous、spatial、spatial transcriptomics、transcriptomics
• 📝 描述：Contributors : Qirong Mao ; Alireza Ahmadi ; Sharon de Vries ; Laura G Heezen ; Ophélie Vacca ; Mathilde Doisy ; Annemieke Aartsma-Rus ; Maaike van Putten ; Aurélie Goyenvalle ; Ahmed Mahfouz ; Pietro SpitaliSeries Type : OtherOrganism : Mus musculusDuchenne muscular dystrophy (DMD) causes progressive muscle degeneration due to dystrophin deficiency. Dystrophin is also expressed in the brain during development and postnatally, yet a characterization of dystrophin isoform expression across brain cells and regions is lacking, limiting our understanding of the cognitive impairment affecting one-third of the patients and hampering development of dystrophin-restoring drugs in the central nervous system (CNS). Here, we applied spatial transcriptomics to map Dmd isoforms across mouse brain regions and cell types. Mdx52 mice received exon 51-skipping therapies restoring the Dp427-sized isoform at transcript and protein level. We observed distinct spatial patterns: full-length isoforms localized to deeper cortical layers and CA1, while shorter isoforms were enriched in cortical layer 1 and dentate gyrus. We present evidence of isoform restoration, immune activation following treatment, and a framework to evaluate exon skipping therapies in the CNS using spatial transcriptomics.
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2. GSE337281 利用RNA测序对尿道下裂大鼠模型阴茎组织进行转录组分析

• ✍️ 作者：未知作者
• 🏷️ 关键词：sequencing、transcriptome
• 📝 描述：Contributors : Jingmin Zhang ; Shan Wang ; Xianghui XieSeries Type : Expression profiling by high throughput sequencingOrganism : Rattus norvegicusGene expression dysregulation plays an important role in the pathogenesis of congenital malformations, including hypospadias. To characterize transcriptomic alterations associated with hypospadias, RNA sequencing (RNA-seq) was performed on penile tissues collected from normal rats and a rat model of hypospadias. These datasets provide comprehensive gene expression profiles that facilitate the investigation of molecular mechanisms and signaling pathways involved in the development of hypospadias.
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3. GSE337280 大鼠尿道下裂模型阴茎组织转录组范围内的m6A甲基化谱分析

• ✍️ 作者：未知作者
• 🏷️ 关键词：transcriptome、methylation
• 📝 描述：Contributors : Jingmin Zhang ; Shan Wang ; Xianghui XieSeries Type : OtherOrganism : Rattus norvegicusRNA modifications are an important component of epigenetic regulation and play essential roles in embryonic development. Among these modifications, N6-methyladenosine (m6A), the most abundant internal modification in eukaryotic messenger RNA, regulates diverse physiological and pathological processes. Increasing evidence suggests that dysregulated m6A methylation contributes to congenital malformations and reproductive system disorders. In this study, methylated RNA immunoprecipitation sequencing (MeRIP-seq) was performed on penile tissues collected from normal rats and a rat model of hypospadias to characterize the transcriptome-wide m6A methylation landscape associated with hypospadias. These data provide a resource for investigating the potential role of m6A RNA methylation in the molecular mechanisms underlying hypospadias.
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4. GSE337276 DNMT1 介导的 DNA 甲基化维持对人类滋养层干细胞稳态和分化至关重要 [RNA-seq]

• ✍️ 作者：未知作者
• 🏷️ 关键词：RNA-seq、methylation
• 📝 描述：Contributors : Sanam Kavari ; YuJin Jang ; Jonghwan Kim ; Winifred Mak ; Jennifer KalishSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensProliferation of cytotrophoblasts (CTBs) and their differentiation into invasive extravillous trophoblasts (EVTs) are critical processes in early placental development. Defects in these processes are associated with adverse pregnancy outcomes, including recurrent pregnancy loss (RPL). There is evidence that reduced expression of the maintenance DNA methyltransferase DNMT1 in the placenta occurs in pregnancy loss and that RPL is associated with aberrant DNA methylation patterns. Therefore, we investigated the role of DNMT1 in human trophoblast growth and differentiation. Using human trophoblast stem cells (hTSCs), an in vitro analog to CTBs, we found that shRNA-mediated knockdown of DNMT1 led to decreased hTSC proliferation, genome-wide reductions in methylation, broad changes in gene expression, and impaired EVT differentiation. Transcriptome profiling of DNMT1-deficient hTSCs and hTSC-derived EVTs highlighted aberrant cytokine expression, drawing a connection to prior reports of immunological dysfunction in RPL. Finally, using a catalytic DNMT1 chemical inhibitor, we demonstrate the canonical methyltransferase activity of DNMT1 is essential for EVT differentiation and invasion. This study identifies new roles for DNMT1 in trophoblasts and addresses the molecular basis of the associations between DNMT1 expression, altered DNA methylation profiles, and RPL.
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5. GSE301966 通过单细胞RNA测序在小鼠糖尿病肾病模型中绘制肾皮质中新的细胞亚群

• ✍️ 作者：未知作者
• 🏷️ 关键词：sequencing、single-cell
• 📝 描述：Contributors : Ruiyuan Chen ; Jiayue Wan ; Shi BaiSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusType 1 Diabetes Mellitus (T1DM) is a prevalent autoimmune disorder character ized by the destruction of insulin-producing cells, often leading to diabetic kidney disease (DKD). Despite extensive research, the cellular mechanisms underpinning DKD remain poorly understood. This study aims to elucidate the cellular het erogeneity and specific cell populations involved in the renal cortex of diabetic mice using single-cell RNA sequencing. Kidney cortex cells from streptozotocin (STZ)-induced diabetic mice and healthy controls were isolated and subjected to single-cell RNA sequencing. Statistical analyses were performed to identify distinct cellular subsets and evaluate changes in cell population dynamics. Immunohistochemistry and renal function evalua tions via Masson and Hematoxylin and Eosin staining were employed to validate the sequencing data. We first identified 11 distinct cellular subsets within the renal cortex. Diabetic mice exhibited a significant increase in distal convoluted tubule cells compared to controls. Additionally, a marked decrease in immune-related cells, including T and Blymphocytes, neutrophils, and macrophages, was observed. Cell communication analysis highlighted the role of the VISFATIN signaling pathway, particularly the Nampt-Insr gene interaction, in the diabetic renal cortex. Our findings reveal a unique cellular and molecular landscape in the renal cortex of diabetic mice, emphasizing altered cell populations and signaling path ways critical in DKD progression. This study enhances our understanding of T1DM-induced renal alterations and suggests potential targets for therapeutic intervention to mitigate kidney complications in diabetes.
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6. GSE337289 鸡和斑胸草雀 HH28 性腺培养物的单细胞转录组分析和斑胸草雀 HH28 性腺培养物的批量时间序列 mRNA 分析

• ✍️ 作者：未知作者
• 🏷️ 关键词：single-cell
• 📝 描述：Contributors : Matthew T Biegler ; Eli Harter ; Asha V Sidhu ; Christina Szialta ; Paul Collier ; Ji-Dung Luo ; Wei Wang ; Anna L Keyte ; Erich D JarvisSeries Type : Expression profiling by high throughput sequencingOrganism : Gallus gallus ; Taeniopygia guttataPrimordial germ cells (PGCs) are reproductive stem cells that are valuable for avian biobanking and germline transmission. However, their long-term culture remains a challenge beyond a few poultry species. Here, we compare the transcriptomic impact and reproductive viability between short- and long-term chicken and zebra finch gonadal PGC culture protocols. Using single-cell transcriptomics, we identified rapid germline differentiation in zebra finch gonadal cultures compared to stable PGC identity in chicken, highlighting divergent signaling pathway responses to in vitro germline culture between species. These differentiation profiles were similarly found in low-serum zebra finch blood PGC cultures. Nonetheless, injections of these short-term zebra finch gonadal PGC cultures demonstrated sufficient gonadal reconstitution of host embryos to produce zebra finch germline chimeras and donor-derived offspring. This study demonstrates the minimal viability of short-term songbird gonadal cultures, and offers a roadmap to improve the longevity and self-renewal of non-poultry avian PGC cultures.
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7. GSE337277 DNMT1 维持 DNA 甲基化对于人类滋养层干细胞的稳态和分化至关重要 [RRBS]

• ✍️ 作者：未知作者
• 🏷️ 关键词：methylation
• 📝 描述：Contributors : Sanam Kavari ; YuJin Jang ; Jonghwan Kim ; Winifred Mak ; Jennifer KalishSeries Type : Methylation profiling by high throughput sequencingOrganism : Homo sapiensProliferation of cytotrophoblasts (CTBs) and their differentiation into invasive extravillous trophoblasts (EVTs) are critical processes in early placental development. Defects in these processes are associated with adverse pregnancy outcomes, including recurrent pregnancy loss (RPL). There is evidence that reduced expression of the maintenance DNA methyltransferase DNMT1 in the placenta occurs in pregnancy loss and that RPL is associated with aberrant DNA methylation patterns. Therefore, we investigated the role of DNMT1 in human trophoblast growth and differentiation. Using human trophoblast stem cells (hTSCs), an in vitro analog to CTBs, we found that shRNA-mediated knockdown of DNMT1 led to decreased hTSC proliferation, genome-wide reductions in methylation, broad changes in gene expression, and impaired EVT differentiation. Transcriptome profiling of DNMT1-deficient hTSCs and hTSC-derived EVTs highlighted aberrant cytokine expression, drawing a connection to prior reports of immunological dysfunction in RPL. Finally, using a catalytic DNMT1 chemical inhibitor, we demonstrate the canonical methyltransferase activity of DNMT1 is essential for EVT differentiation and invasion. This study identifies new roles for DNMT1 in trophoblasts and addresses the molecular basis of the associations between DNMT1 expression, altered DNA methylation profiles, and RPL.
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8. GSE337275 先锋转录因子 TAL1 重塑染色质结构以指导红系细胞命运决定 [ATAC-Seq 2]

• ✍️ 作者：未知作者
• 🏷️ 关键词：ATAC-seq
• 📝 描述：Contributors : Lixiang Chen ; Ying Cheng ; Lei Sun ; Hengchao Zhang ; Xiuyun WuSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Homo sapiensPioneer transcription factors critically regulate chromatin organization and hematopoietic cell lineage commitment. During erythropoiesis, hematopoietic stem cells undergo dynamic transcriptional and chromatin remodeling to differentiate into erythrocytes. Functionally validated pioneer factors capable of orchestrating erythropoiesis through dynamic chromatin remodeling remain limited, leaving their regulatory mechanisms incompletely resolved. Here, we identify T-cell acute lymphocytic leukemia 1(TAL1) as a pioneer factor that remodels chromatin to drive transcriptional reprogramming during erythropoiesis. By recruiting SWI/SNF complex, TAL1 drives erythroid fate specification while suppressing alternative lineages through lineage-restricted chromatin compartment reorganization. As a pioneer factor, TAL1 recruits chromatin remodelers BPTF and KMT2A to establish erythroid-specific genomic architecture. These complexes collectively execute TAL1 directed differentiation programs by transcriptionally activating erythroid regulators while repressing non-erythroid determinants. Our work establishes a generalizable chromatin accessibility-directed pioneer factor screening strategy, we identify TAL1 as a master pioneer factor and resolve its mechanism in driving erythroid commitment through 3D epigenome restructuring.
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9. GSE337265 果蝇和甲虫的跨物种单细胞转录组学揭示了脑神经母细胞分化的遗传核心

• ✍️ 作者：未知作者
• 🏷️ 关键词：transcriptomics
• 📝 描述：Contributors : Noel Cabañas ; Gregor BucherSeries Type : Expression profiling by high throughput sequencingOrganism : Tribolium castaneumThis work defines the conserved core of TFs involved in insect brain NB specification by cross-species comparison of single-cell transcriptomics of NBs from, the red flour beetle, Tribolium castaneum, and the vinegar fly, Drosophila melanogaster. In Tribolium, we established a Gal4 enhancer trap screen system to generate a line that marks NBs. Using the 10x genomics technology, we sequenced 37,137 Tribolium NBs. We also sequenced 32,112 single nuclei of Drosophila NBs. Cross-species comparison followed by in situ hybridization led to the identification brain-specific TFs of insects. This brain NB-specific gene set confirms fundamentally different spatial patterning compared to the well-studied ventral nerve cord.
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10. GSE337186​​ IFNg 和 IFNg 模拟物通过调节铁代谢和脂质过氧化来预防 IFN-I 介导的结核病易感性。

• ✍️ 作者：未知作者
• 🏷️ 关键词：metabolism
• 📝 描述：Contributors : Prasanna Babu Araveti ; Shivraj M Yabaji ; Muhammad Zainul Arifin ; Suruchi Lata ; Yuriy O Alekseyev ; Alexander A Gimelbrant ; William R Bishai ; Vadim Zhernovkov ; Oleksii S Rukhlenko ; Boris N Kholodenko ; Igor KramnikSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusType I interferons (IFN-I) and IFNγ exert divergent effects during tuberculosis, but the mechanisms that determine whether macrophage activation promotes host defense or inflammatory pathology remain incompletely understood. Here, we dissect the interplay between IFN-I and IFNγ in macrophage activation using genetically susceptible B6.Sst1S macrophages. We show that, during tumor necrosis factor (TNF) stimulation, susceptible macrophages enter a persistent pathological activation state (pPAS) characterized by sustained lipid peroxidation and super-induction of IFN-I responses. This pathological state is maintained by autocrine IFN-I signaling. In contrast, IFNγ priming prevents pPAS development by enhancing macrophage resilience to oxidative stress, in part through regulation of iron metabolism and induction of ferritin expression. Computational cell state transition assessment and regulation (cSTAR) analysis identified pathways and small molecules predicted to promote the transition of susceptible macrophages toward an IFNγ-induced, Mtb-resistant state. Consistent with these predictions, the CDK4/6 inhibitor trilaciclib reduced lipid peroxidation by regulating iron metabolism, whereas retinoic acid signaling enhanced GPX4 expression and lipid biosynthesis programs. Combined CDK4/6 inhibition and retinoic acid receptor activation efficiently prevented the pathological activation state. Together, these findings delineate a mechanism of IFN-I/IFNγ crosstalk during macrophage activation and identify pharmacologic strategies to prevent IFN-I-dominant, lipid peroxidation-driven macrophage pathology.
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1. 科学家或许终于发现了阿尔茨海默病如何杀死脑细胞的机制。

• ✍️ 作者：未知作者
• 🏷️ 关键词：Alzheimer
• 📝 描述：Researchers have identified a previously overlooked mechanism of brain cell death that appears to play a major role in Alzheimer’s disease and frontotemporal dementia. The finding could lead to new treatments aimed at slowing neuron loss by interrupting the process before cells are destroyed.
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• GSE333820 对服用额外七味汤相关化合物的老年小鼠卵巢进行转录组分析
• GSE327389 Gata3 在胚胎干细胞中原始内胚层和滋养外胚层分化中的剂量依赖性作用 [scRNA-Seq]
• GSE325341 BHLHE40 协调 TL1A 驱动的 ILC3 效应程序和 RORγt⁺ APC 介导的耐受性 [ATAC-Seq]
• GSE325198 BHLHE40 协调 TL1A 驱动的 ILC3 效应程序和 RORγt⁺ APC 介导的耐受性 [scRNA-seq]
• GSE320527 靶向Nicastrin N-聚糖的甘露糖基化可减弱γ-分泌酶活性和Notch依赖性白血病进展
• GSE319303：年轻造血干细胞 (HSC) 和 Selp 高表达与 Selp 低表达 HSC 的批量 ATAC-seq 分析（小鼠衰老前）
• GSE319049：年轻造血干细胞 (HSC) 和 Selp 高表达与 Selp 低表达 HSC 在衰老小鼠中的批量 RNA 测序
• GSE306025 Gata3 在胚胎干细胞中原始内胚层和滋养外胚层分化中的剂量依赖性作用 [ChIP-seq]
• GSE306024 Gata3 在胚胎干细胞中原始内胚层和滋养外胚层分化中的剂量依赖性作用 [RNA-seq]
• GSE302447 一种靶向能量和脂质代谢的多功能口服小分子药物，可用于治疗饮食诱导的肥胖症
• GSE302445 一种靶向能量和脂质代谢的多功能口服小分子药物，用于治疗饮食引起的肥胖症[实验 5]
• GSE302444 一种靶向能量和脂质代谢的多功能口服小分子药物，用于治疗饮食引起的肥胖症[实验 4]
• GSE302442 一种靶向能量和脂质代谢的多功能口服小分子药物，用于治疗饮食引起的肥胖症[实验 3]
• GSE302441 一种靶向能量和脂质代谢的多功能口服小分子药物，用于治疗饮食引起的肥胖症[实验 2]
• GSE302440 一种靶向能量和脂质代谢的多功能口服小分子药物，用于治疗饮食引起的肥胖症[实验 1]
• GSE301853 通过合成的IL-2呈递细胞恢复冷冻保存后NK细胞的细胞毒性
• GSE301384 小鼠肾移植抗体介导排斥模型中的纳米串基因表达谱分析
• GSE314562 转录共抑制因子 Panky 和 ​​Panky-like 通过调节神经节苷脂代谢，对视网膜锥体感光细胞的完整性和存活至关重要。
• GSE313106 神经支配的人类心肌模型揭示了KCNH2相关心律失常的交感神经驱动因素