详细内容（前10条）

1. ⭐ GSE329527 抗原限制性稳态白色念珠菌 Th17 细胞连接口腔-肠道免疫并适应肠道炎症

• ✍️ 作者：未知作者
• 🏷️ 关键词：immunity、antigen、inflammation、gut、regex:gut(-?microbiome)?、regex:intestin(e|al)
• 📝 描述：Contributors : Gabriela Rios Martini ; Philipp Hofmann ; Ann K Kamps ; Amos Weichberger ; Ekaterina Tikhonova ; Aidan Conroy ; Xiangyu Pan ; Diana M Namuch ; Laura Rathjens ; Arne Bergfeld ; Susanna Nikolaus ; Jeanette Riffert ; Florian Tran ; Konrad Aden ; Maria Witte ; Clemens Schafmayer ; Dora Stölzl ; Stephan Weidinger ; Markus M Heimesaat ; Miriam Cyris ; Ann K Härdter ; Christof Dörfer ; Robert Zarnowski ; David Andes ; Sascha Brunke ; Bernhard Hube ; Alexander Scheffold ; Iliyan D Iliev ; Stefan Schreiber ; Petra BacherSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensThe commensal yeast Candida albicans is a major inducer of human Th17 cells. How C. albicans drives Th17 responses at homeostasis, and whether such responses contribute to inflammatory diseases, remains poorly understood. Here, we show that C. albicans-reactive Th17 cells exhibit a surprisingly narrow antigen-specificity, targeting a limited set of proteins enriched in fungal extracellular vesicles. At homeostasis, these cells predominantly reside in the oral mucosa. T cell receptor profiling reveals shared clonotypes across oral and gut tissues with C. albicans emerging as the major driver of this repertoire overlap. In Crohn’s disease (CD), C. albicans-specific Th17 cells with features of oral priming are enriched in intestinal tissues where they retain specificity for the same protein targets but acquire pathogenic Th17 traits. Together, our results reveal a stable, antigen-restricted C. albicans Th17 response shared across mucosal sites that undergoes functional adaptation in the inflamed intestine, thus representing a novel target for immune modulation in CD.
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2. ⭐ GSE290480 匹配的单细胞染色质、转录组和表面标志物分析捕获乳腺基底细胞向腔细胞转变过程中的体内表观基因组重编程 [ChIP-seq]

• ✍️ 作者：未知作者
• 🏷️ 关键词：ChIP-seq、single-cell、transcriptome
• 📝 描述：Contributors : Eve Moutaux ; Anna Schwager ; Adeline Durand ; Mélanie Miranda ; Louisa Hadj ; Simon Dumas ; Mathias Schwartz ; Marthe Laisné ; Justine Marsolier ; Manuel Guthmann ; Délia Dupré ; Grégoire Jouault ; Mélissa Saichi ; Déborah Bourc’his ; Elisabetta Marangoni ; Nicolas Servant ; Leïla Perié ; Céline VallotSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Homo sapiensSingle-cell multi-omics methods enable simultaneous mapping of chromatin states and transcriptomes, offering deep insights into gene regulation. Yet, the full potential of these approaches remains untapped for rare cell populations, as most methods require thousands of cells and are limited in their ability to capture multiple molecular layers comprehensively within the same cell. Here, we introduce OneCell CUT&Tag a user-friendly method that provides matched high-resolution epigenome, full-transcriptome, and surface marker quantification from every cell, with input as low as one cell. Using this approach, we uncovered epigenomic priming of basal cells in the mammary gland and captured the dynamics of basal-to-luminal transdifferentiation. We identified a transitional cell population with intermediate epigenomic profiles—absent in reference populations—and demonstrated a continuous epigenomic progression from basal to luminal states, while transcriptomes exhibited a binary switch. Adaptable to diverse samples and tissues, this method also revealed the role of H3K27me3 in shaping zygotic expression programs. By matching multiple layers of molecular information at single-cell resolution, OneCell CUT&Tag dissects the complementary roles of each omics layer in shaping cellular identity and function, opening new avenues to study rare and complex biological systems.
• 🔗 查看原文

3. ⭐ GSE302187 MRSA诱导肾损伤的小鼠模型（空间转录组学）

• ✍️ 作者：未知作者
• 🏷️ 关键词：spatial、spatial transcriptomics、transcriptomics
• 📝 描述：Contributor : Hato TakashiSeries Type : OtherOrganism : Mus musculus ; Staphylococcus aureusSpatial transcriptomics was performed on mouse kidneys 2 datys and 4 days after systemic MRSA infection. Two consecutive slides were prepared for each time point.
• 🔗 查看原文

4. ⭐ GSE301718 Mezigdomide 通过降解 Aiolos/Ikaros 和重新激活细胞因子产生途径来逆转 T 细胞耗竭 [Hi-C]

• ✍️ 作者：未知作者
• 🏷️ 关键词：T cell、cytokine、Hi-C
• 📝 描述：Contributors : Junfei Zhao ; Hsiling Chiu ; Patrick HagnerSeries Type : OtherOrganism : Homo sapiensGiven the well-established notion that T cells undergo significant changes in their nuclear architecture and chromatin accessibility between different stages of differentiation or phenotypic stage such as activation and exhaustion, we aimed to investigate the chromatin binding patterns of the Ikaros transcription factor, which plays a crucial role in T cell biology and gene regulation, including development, differentiation and activation in response to TCR stimulation. However, a thorough genome-wide analysis of its occupancy and transcriptional regulatory activity between T cell activation and exhaustion has not been performed. To address this, we conducted an integrated epigenomic investigation utilizing Hi-C, ATAC-seq, RNA-seq and ChIP-seq, focusing on Ikaros and histone modifications, including H3K27ac, H3K4me1, and H3K4me3. This approach allows us to understand Ikaros-specific regulation of transcription by characterizing the epigenome in Tact versus Tex cells.
• 🔗 查看原文

5. ⭐ GSE301717 Mezigdomide 通过降解 Aiolos/Ikaros 和重新激活细胞因子产生途径逆转 T 细胞耗竭 [scRNA-seq]

• ✍️ 作者：未知作者
• 🏷️ 关键词：T cell、cytokine、scRNA
• 📝 描述：Contributors : Junfei Zhao ; Hsiling Chiu ; Patrick HagnerSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensGiven the well-established notion that T cells undergo significant changes in their nuclear architecture and chromatin accessibility between different stages of differentiation or phenotypic stage such as activation and exhaustion, we aimed to investigate the chromatin binding patterns of the Ikaros transcription factor, which plays a crucial role in T cell biology and gene regulation, including development, differentiation and activation in response to TCR stimulation. However, a thorough genome-wide analysis of its occupancy and transcriptional regulatory activity between T cell activation and exhaustion has not been performed. To address this, we conducted an integrated epigenomic investigation utilizing Hi-C, ATAC-seq, RNA-seq and ChIP-seq, focusing on Ikaros and histone modifications, including H3K27ac, H3K4me1, and H3K4me3. This approach allows us to understand Ikaros-specific regulation of transcription by characterizing the epigenome in Tact versus Tex cells.
• 🔗 查看原文

6. ⭐ GSE301716 Mezigdomide 通过降解 Aiolos/Ikaros 和重新激活细胞因子产生途径逆转 T 细胞耗竭 [RNA-seq]

• ✍️ 作者：未知作者
• 🏷️ 关键词：T cell、cytokine、RNA-seq
• 📝 描述：Contributors : Junfei Zhao ; Hsiling Chiu ; Patrick HagnerSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensGiven the well-established notion that T cells undergo significant changes in their nuclear architecture and chromatin accessibility between different stages of differentiation or phenotypic stage such as activation and exhaustion, we aimed to investigate the chromatin binding patterns of the Ikaros transcription factor, which plays a crucial role in T cell biology and gene regulation, including development, differentiation and activation in response to TCR stimulation. However, a thorough genome-wide analysis of its occupancy and transcriptional regulatory activity between T cell activation and exhaustion has not been performed. To address this, we conducted an integrated epigenomic investigation utilizing Hi-C, ATAC-seq, RNA-seq and ChIP-seq, focusing on Ikaros and histone modifications, including H3K27ac, H3K4me1, and H3K4me3. This approach allows us to understand Ikaros-specific regulation of transcription by characterizing the epigenome in Tact versus Tex cells.
• 🔗 查看原文

7. ⭐ GSE301715 Mezigdomide 通过降解 Aiolos/Ikaros 和重新激活细胞因子产生途径逆转 T 细胞耗竭 [ChIP-seq]

• ✍️ 作者：未知作者
• 🏷️ 关键词：T cell、cytokine、ChIP-seq
• 📝 描述：Contributors : Junfei Zhao ; Hsiling Chiu ; Patrick HagnerSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Homo sapiensGiven the well-established notion that T cells undergo significant changes in their nuclear architecture and chromatin accessibility between different stages of differentiation or phenotypic stage such as activation and exhaustion, we aimed to investigate the chromatin binding patterns of the Ikaros transcription factor, which plays a crucial role in T cell biology and gene regulation, including development, differentiation and activation in response to TCR stimulation. However, a thorough genome-wide analysis of its occupancy and transcriptional regulatory activity between T cell activation and exhaustion has not been performed. To address this, we conducted an integrated epigenomic investigation utilizing Hi-C, ATAC-seq, RNA-seq and ChIP-seq, focusing on Ikaros and histone modifications, including H3K27ac, H3K4me1, and H3K4me3. This approach allows us to understand Ikaros-specific regulation of transcription by characterizing the epigenome in Tact versus Tex cells.
• 🔗 查看原文

8. ⭐ GSE301714 Mezigdomide 通过降解 Aiolos/Ikaros 和重新激活细胞因子产生途径逆转 T 细胞耗竭 [scATAC-seq]

• ✍️ 作者：未知作者
• 🏷️ 关键词：T cell、cytokine、scATAC
• 📝 描述：Contributors : Junfei Zhao ; Hsiling Chiu ; Patrick HagnerSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Homo sapiensGiven the well-established notion that T cells undergo significant changes in their nuclear architecture and chromatin accessibility between different stages of differentiation or phenotypic stage such as activation and exhaustion, we aimed to investigate the chromatin binding patterns of the Ikaros transcription factor, which plays a crucial role in T cell biology and gene regulation, including development, differentiation and activation in response to TCR stimulation. However, a thorough genome-wide analysis of its occupancy and transcriptional regulatory activity between T cell activation and exhaustion has not been performed. To address this, we conducted an integrated epigenomic investigation utilizing Hi-C, ATAC-seq, RNA-seq and ChIP-seq, focusing on Ikaros and histone modifications, including H3K27ac, H3K4me1, and H3K4me3. This approach allows us to understand Ikaros-specific regulation of transcription by characterizing the epigenome in Tact versus Tex cells.
• 🔗 查看原文

9. ⭐ GSE301713 Mezigdomide 通过降解 Aiolos/Ikaros 和重新激活细胞因子产生途径逆转 T 细胞耗竭 [ATAC-seq]

• ✍️ 作者：未知作者
• 🏷️ 关键词：T cell、cytokine、ATAC-seq
• 📝 描述：Contributors : Junfei Zhao ; Hsiling Chiu ; Patrick HagnerSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Homo sapiensGiven the well-established notion that T cells undergo significant changes in their nuclear architecture and chromatin accessibility between different stages of differentiation or phenotypic stage such as activation and exhaustion, we aimed to investigate the chromatin binding patterns of the Ikaros transcription factor, which plays a crucial role in T cell biology and gene regulation, including development, differentiation and activation in response to TCR stimulation. However, a thorough genome-wide analysis of its occupancy and transcriptional regulatory activity between T cell activation and exhaustion has not been performed. To address this, we conducted an integrated epigenomic investigation utilizing Hi-C, ATAC-seq, RNA-seq and ChIP-seq, focusing on Ikaros and histone modifications, including H3K27ac, H3K4me1, and H3K4me3. This approach allows us to understand Ikaros-specific regulation of transcription by characterizing the epigenome in Tact versus Tex cells.
• 🔗 查看原文

10. GSE334481 匹配的单细胞染色质、转录组和表面标志物分析捕获了乳腺基底细胞向腔细胞转变过程中的体内表观基因组重编程 [mouse_mammary_gland_multiome]

• ✍️ 作者：未知作者
• 🏷️ 关键词：single-cell、transcriptome
• 📝 描述：Contributors : Anna Schwager ; Eve Moutaux ; Adeline Durand ; Mélanie Miranda ; Louisa Hadj ; Simon Dumas ; Mathias Schwartz ; Marthe Laisné ; Justine Marsolier ; Manuel Guthmann ; Délia Dupré ; Grégoire Jouault ; Mélissa Saichi ; Déborah Bourc’his ; Elisabetta Marangoni ; Nicolas Servant ; Leïla Perié ; Céline VallotSeries Type : Genome binding/occupancy profiling by high throughput sequencing ; Expression profiling by high throughput sequencingOrganism : Mus musculusSingle-cell multi-omics methods enable simultaneous mapping of chromatin states and transcriptomes, offering deep insights into gene regulation. Yet, the full potential of these approaches remains untapped for rare cell populations, as most methods require thousands of cells and are limited in their ability to capture multiple molecular layers comprehensively within the same cell. Here, we introduce OneCell CUT&Tag a user-friendly method that provides matched high-resolution epigenome, full-transcriptome, and surface marker quantification from every cell, with input as low as one cell. Using this approach, we uncovered epigenomic priming of basal cells in the mammary gland and captured the dynamics of basal-to-luminal transdifferentiation. We identified a transitional cell population with intermediate epigenomic profiles—absent in reference populations—and demonstrated a continuous epigenomic progression from basal to luminal states, while transcriptomes exhibited a binary switch. Adaptable to diverse samples and tissues, this method also revealed the role of H3K27me3 in shaping zygotic expression programs. By matching multiple layers of molecular information at single-cell resolution, OneCell CUT&Tag dissects the complementary roles of each omics layer in shaping cellular identity and function, opening new avenues to study rare and complex biological systems.
• 🔗 查看原文

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1. 重新思考空间机器学习的验证：演讲要点

• ✍️ 作者：未知作者
• 🏷️ 关键词：spatial
• 📝 描述：Title slide of the talk Keynote slides: https://jakubnowosad.com/ml4eo2026/ Workshop materials: https://jakubnowosad.com/ml4eo2026workshop/ Machine learning is now deeply embedded1 in Earth observation workflows, from mapping current enviro… Continue reading: Rethinking Validation for Spatial Machine Learning: Takeaways from the Talk
• 🔗 查看原文

• GSE333887 匹配的单细胞染色质、转录组和表面标志物分析捕获了乳腺基底细胞向腔细胞转变过程中的体内表观基因组重编程 [移植_单细胞_多组]
• GSE333817 匹配的单细胞染色质、转录组和表面标志物分析捕获了乳腺基底细胞向腔细胞转变过程中的体内表观基因组重编程 [mm468_OneCell_multiome]
• GSE319066 小鼠短暂性大脑中动脉闭塞后脑内Ms4a3谱系髓系细胞的单细胞RNA测序
• GSE318800：Ms4a3特异性Htr2b条件性敲除小鼠缺血性卒中后脑髓系细胞的单细胞RNA测序分析
• GSE290516 匹配的单细胞染色质、转录组和表面标志物分析捕获乳腺基底细胞向腔细胞转变过程中的体内表观基因组重编程 [scChIC]
• GSE290513 匹配的单细胞染色质、转录组和表面标志物分析捕获了乳腺基底细胞向腔细胞转变过程中的体内表观基因组重编程 [zygotes_bulkCUT&RUN]
• GSE290512 匹配的单细胞染色质、转录组和表面标志物分析捕获了乳腺基底细胞向腔细胞转变过程中的体内表观基因组重编程 [zygotes_OneCell_multiome]
• GSE290486 匹配的单细胞染色质、转录组和表面标志物分析揭示了乳腺基底细胞向腔细胞转变过程中体内表观基因组的重编程。
• GSE290484 匹配的单细胞染色质、转录组和表面标志物分析捕获了乳腺基底细胞向腔细胞转变过程中的体内表观基因组重编程 [frozen_pdx_OneCell_CUT&Tag]
• GSE290481 匹配的单细胞染色质、转录组和表面标志物分析捕获乳腺基底细胞向腔细胞转变过程中的体内表观基因组重编程 [scCUT&Tag]
• GSE285319 肿瘤巨噬细胞中siglec10的高表达可能促进结直肠癌的进展
• GSE271176 142 株癌细胞系的全基因组染色质状态图谱
• GSE271175 142 株癌细胞系染色质状态的全基因组图谱 [患者]
• GSE142751 142 株癌细胞系染色质状态的全基因组图谱 [细胞系]
• GSE333915 单细胞多组学分析揭示 MeCP2 磷酸化调节作用的神经元偏向性
• GSE336950 Epstein-Barr病毒诱导的B细胞甲硫氨酸依赖性是一种可靶向的代谢脆弱性
• GSE313792 多形螺旋线虫分泌产物抑制树突状细胞中Toll样受体信号传导和细胞因子产生
• GSE302057 利用 ChIP-seq 分析研究黑色素瘤中 KMT2D 缺失的表观遗传学后果
• GSE301779 利用 ChIP-seq 分析研究黑色素瘤中 KMT2D 缺失的表观遗传后果 [CUT&Run]
• GSE301719 Mezigdomide 通过降解 Aiolos/Ikaros 和重新激活细胞因子产生途径来逆转 T 细胞耗竭
• GSE272950 tRNA m1A 修饰通过 TGF-β 通路的翻译调控促进良性前列腺增生 [RNA-seq]
• GSE236737 环状RNA（circRNA）测序在伴有和不伴有微血管侵犯（MVI）的肝细胞癌（HCC）患者中
• GSE236736 野生型和 circpTK2 沉默的 HCCLM3 细胞系的转录组测序
• GSE328813 RNA-seq 分析 5-HT2B 受体激动剂 BW723C86 对外周血单核细胞的影响
• GSE328636 RNA-seq 分析 5-HT2B 受体激动剂 BW723C86 在 OGD 诱导的 HT22 细胞与 BMDM 的 Transwell 共培养系统中的作用
• GSE327186 GNPs-pIL-4 重编程巨噬细胞极化并激活 OSM/GSNOR/ENG 轴以改善小鼠缺血肢体的血管生成和组织修复
• GSE337004 野生型和恶性转化小鼠乳腺上皮细胞球状体培养物中 PM2.5 反应的比较 RNA-seq 分析
• GSE336959：脊髓损伤和卵巢切除相关骨质疏松性脊髓损伤小鼠模型脊髓组织的RNA测序分析
• GSE301821 长链非编码RNA TTN-AS1促进脓毒症急性肝损伤：一种新的潜在监测和治疗靶点[RNA-Seq]
• GSE272951 tRNA m1A 修饰通过 TGF-β 通路的翻译调控促进良性前列腺增生 [tRNA-seq]
• GSE272949 tRNA m1A 修饰通过 TGF-β 通路的翻译调控促进良性前列腺增生 [Ribo-seq]
• GSE272948 tRNA m1A 修饰通过 TGF-β 通路的翻译调控促进良性前列腺增生 [m1A-MAP-seq]
• GSE236514 小鼠长链非编码RNA（lncRNA）心脏组织分析
• GSE232589 小肠上皮细胞分化中的亚型转换
• GSE337487 miRNA测序分析了经胫骨皮质横向运输治疗的糖尿病足大鼠血浆sEVs。