详细内容（前10条）

1. ⭐ GSE316782 多模态单细胞和空间分析揭示侵袭性非小细胞肺癌患者非转移性淋巴结中 T 细胞介导的免疫和 B 细胞滤泡结构的改变

• ✍️ 作者：未知作者
• 🏷️ 关键词：cancer、immunity、lymph、T cell、regex:lymph(o|atic)?、single-cell、spatial
• 📝 描述：Contributors : Zhan Hao Xi ; Yusuke Koga ; Sarah A Mazzilli ; Kei Suzuki ; Joshua D CampbellSeries Type : Expression profiling by high throughput sequencing ; OtherOrganism : Homo sapiensRegional lymph nodes (LNs) in the thoracic cavity serve as essential immunological hubs that coordinate humoral and cell-mediated responses against the development and progression of non-small cell lung cancer (NSCLC). To investigate immune dysregulation in the non-metastatic regional LNs of patients with aggressive NSCLC, we performed multimodal profiling on 36 LNs from 11 patients undergoing curative-intent resection including CITE-seq, scRNA-seq, and Imaging Mass Cytometry (IMC). Regional N1 LNs from patients with more aggressive disease (stage IB–IIIA) exhibited a significant enrichment of dysfunctional CD8⁺ T cells and regulatory T cells (Tregs) compared to N2 LNs and LNs from patients with less aggressive disease (stage IA). These immune subsets were spatially co-localized with mature regulatory dendritic cells (mregDCs; CD1c⁺, TIM3⁺, LAMP3⁺), forming an immunosuppressive niche uniquely enriched in the N1 LNs of higher-stage patients. Concurrently, higher-stage N1 LNs contained larger number of “decorticated” B-cell follicles characterized by decreased encapsulation of the mantle zone layer surrounding the germinal centers. This mantle zone disorganization was associated with increased spatial niches involving Tregs, CD68⁺ CD163⁺ TIM3⁺ Macrophages, CD163⁺ TIM3dim Monocytic-Myeloid Derived Suppressor Cells (M-MDSC), plasma B cells, and a decrease in spatial niches involving CD4⁺ T helper cells and fibroblastic reticular cells (FRCs). Together, our findings reveal parallel alterations in humoral and cell-mediated immunity within the regional LNs of patients with aggressive NSCLC.
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2. ⭐ GSE316608 通过原位多聚腺苷酸化和空间 RNA 测序对微生物组-宿主相互作用进行高分辨率空间映射 [空间转录组学]

• ✍️ 作者：未知作者
• 🏷️ 关键词：sequencing、spatial、spatial transcriptomics、transcriptomics
• 📝 描述：Contributors : Ioannis Ntekas ; David W McKellar ; Lena Takayasu ; Iwijn De VlaminckSeries Type : OtherOrganism : Mus musculusInter-microbial and host-microbial interactions are critical for the functioning of the gut microbiome, but few tools are available to measure these interactions in situ. Here, we report a method for broad spatial sampling of microbiome-host interactions in the gut at high resolution (1 µm). This method combines enzymatic in situ polyadenylation of both bacterial and host RNA with spatial RNA-sequencing to increase bacterial RNA recovery and enable transcriptomic analysis of low-abundance and spatially restricted microbial taxa. We benchmark the method against existing spatial transcriptomic workflows, demonstrating improved sensitivity and resolution. Application of this method in a mouse model of intestinal neoplasia revealed the biogeography of the mouse gut microbiome as function of location in the intestine, frequent strong inter-microbial interactions at short length scales, and tumor-associated changes in the architecture of the host-microbiome interface. This method is compatible with widely available commercial platforms for spatial RNA-sequencing and can therefore be readily adopted to study the role of short-range, bidirectional host-microbe interactions in microbiome health and disease.
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3. ⭐ GSE294120 类维生素A对紫外线诱导的皮肤光老化的影响研究[空间转录组学]

• ✍️ 作者：未知作者
• 🏷️ 关键词：spatial、spatial transcriptomics、transcriptomics
• 📝 描述：Contributors : Fan Hu ; Qijiang Zhao ; Chengzhi Zheng ; Ye Zhong ; Jian Shen ; Ruian Qiu ; Hao Zhu ; Tongquan Wu ; Rui Ye ; Le Du ; Daqing Ma ; Yicheng XieSeries Type : OtherOrganism : Mus musculusPhotoaging contributes to up to 80% of visible facial aging signs, making it a major dermatological concern. While retinoids such as retinol and all-trans retinoic acid (ATRA) promote extracellular matrix (ECM) regeneration, their side effects limit widespread use. We propose that hydroxypinacolone 9-cis retinoate (9-cis HPR), a derivative of 9-cis retinoic acid, activates both retinoic acid receptor (RAR) and retinoid X receptor (RXR), enhancing efficacy while minimizing irritation. However, its in vivo anti-photoaging effects remain underexplored. This study evaluates 9-cis HPR in the UVR-damaged SKH-1 mouse model, investigating its role in inflammation control, ECM regeneration, and melanogenesis suppression.
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4. ⭐ GSE316918 巨噬细胞-成纤维细胞相互作用的时空分子谱分析定义了协调炎症发生和消退的检查点 [RNA-seq]

• ✍️ 作者：未知作者
• 🏷️ 关键词：macrophage、inflammation、RNA-seq
• 📝 描述：Contributors : Katharina Weishaupt ; David Chambers ; Maria Dzamukova ; Ivana Androšević ; Jean-Philippe Auger ; Darleen Hüser ; Sébastien Trzebanski ; Andreas Ramming ; Anika Grüneboom ; Georg Schett ; Steffen Jung ; Markus H Hoffmann ; Gerhard KrönkeSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusThe molecular details of macrophage-fibroblast crosstalk during the onset and resolution of inflammatory disease remain incompletely understood. Here, we apply a scRNAseq-, scATACseq- and bulk RNAseq-based bioinformatic modelling approach to map heterocellular signaling circuits of synovial macrophage and synovial fibroblast (SF) subsets during various stages of inflammatory arthritis. While SFs function as key pacemakers of synovial inflammation, individual subsets of synovial macrophages support both the perpetuation and the resolution of arthritis. While pro-inflammatory Il1b+ macrophages dominate the early stages of inflammation, these cells also retain a substantial intrinsic plasticity that is characterized by chromatin remodeling and an eventual differentiation into Spp1+ macrophages. These cells display a terminally-differentiated phenotype, suppresses activation of pro-inflammatory SFs, and initiates the resolution of arthritis by secretion of regulatory mediators including osteopontin. Our data highlight the dichotomous character of macrophage-fibroblast crosstalk and define the cellular and molecular checkpoints that control the onset and resolution of immune-mediated inflammatory diseases.
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5. ⭐ GSE316869 通过原位多聚腺苷酸化和空间 RNA 测序对微生物组-宿主相互作用进行高分辨率空间映射 [bulk RNA-Seq]

• ✍️ 作者：未知作者
• 🏷️ 关键词：sequencing、RNA-seq、spatial
• 📝 描述：Contributors : Ioannis Ntekas ; David W McKellar ; Lena Takayasu ; Iwijn De VlaminckSeries Type : Expression profiling by high throughput sequencingOrganism : mouse gut metagenomeInter-microbial and host–microbial interactions are thought to be critical for the functioning of the gut microbiome, but few substantive tools are available to measure these interactions. Here, we report a method for unbiased spatial sampling of microbiome-host interactions in the gut at high spatial resolution. This method combines enzymatic in situ polyadenylation of both bacterial and host transcripts with spatial RNA-sequencing. Application of this method revealed the biogeography of the mouse gut microbiome as function of location in the intestine, short-range intermicrobial interaction, local shaping of the microbiome by the host, and tumor-associated changes in the architecture of the host-microbiome interface. This method is compatible with broadly available commercial platforms for spatial RNA-sequencing, and can therefore be readily adopted to broadly study the role of short-range, bidirectional host-microbe interactions in microbiome health and disease.
• 🔗 查看原文

6. ⭐ GSE316833 巨噬细胞-成纤维细胞相互作用的时空分子谱分析定义了协调炎症发生和消退的检查点 [scRNA-seq]

• ✍️ 作者：未知作者
• 🏷️ 关键词：macrophage、inflammation、scRNA
• 📝 描述：Contributors : Katharina Weishaupt ; David Chambers ; Maria Dzamukova ; Ivana Androšević ; Jean-Philippe Auger ; Darleen Hüser ; Sébastien Trzebanski ; Andreas Ramming ; Anika Grüneboom ; Georg Schett ; Steffen Jung ; Markus H Hoffmann ; Gerhard KrönkeSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusThe molecular details of macrophage-fibroblast crosstalk during the onset and resolution of inflammatory disease remain incompletely understood. Here, we apply a scRNAseq-, scATACseq- and bulk RNAseq-based bioinformatic modelling approach to map heterocellular signaling circuits of synovial macrophage and synovial fibroblast (SF) subsets during various stages of inflammatory arthritis. While SFs function as key pacemakers of synovial inflammation, individual subsets of synovial macrophages support both the perpetuation and the resolution of arthritis. While pro-inflammatory Il1b+ macrophages dominate the early stages of inflammation, these cells also retain a substantial intrinsic plasticity that is characterized by chromatin remodeling and an eventual differentiation into Spp1+ macrophages. These cells display a terminally-differentiated phenotype, suppresses activation of pro-inflammatory SFs, and initiates the resolution of arthritis by secretion of regulatory mediators including osteopontin. Our data highlight the dichotomous character of macrophage-fibroblast crosstalk and define the cellular and molecular checkpoints that control the onset and resolution of immune-mediated inflammatory diseases.
• 🔗 查看原文

7. ⭐ GSE316802 巨噬细胞-成纤维细胞相互作用的时空分子谱分析定义了协调炎症发生和消退的检查点 [scATAC-Seq]

• ✍️ 作者：未知作者
• 🏷️ 关键词：macrophage、inflammation、scATAC
• 📝 描述：Contributors : Katharina Weishaupt ; David Chambers ; Maria Dzamukova ; Ivana Androšević ; Jean-Philippe Auger ; Darleen Hüser ; Sébastien Trzebanski ; Andreas Ramming ; Anika Grüneboom ; Georg Schett ; Steffen Jung ; Markus H Hoffmann ; Gerhard KrönkeSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Mus musculusThe molecular details of macrophage-fibroblast crosstalk during the onset and resolution of inflammatory disease remain incompletely understood. Here, we apply a scRNAseq-, scATACseq- and bulk RNAseq-based bioinformatic modelling approach to map heterocellular signaling circuits of synovial macrophage and synovial fibroblast (SF) subsets during various stages of inflammatory arthritis. While SFs function as key pacemakers of synovial inflammation, individual subsets of synovial macrophages support both the perpetuation and the resolution of arthritis. While pro-inflammatory Il1b+ macrophages dominate the early stages of inflammation, these cells also retain a substantial intrinsic plasticity that is characterized by chromatin remodeling and an eventual differentiation into Spp1+ macrophages. These cells display a terminally-differentiated phenotype, suppresses activation of pro-inflammatory SFs, and initiates the resolution of arthritis by secretion of regulatory mediators including osteopontin. Our data highlight the dichotomous character of macrophage-fibroblast crosstalk and define the cellular and molecular checkpoints that control the onset and resolution of immune-mediated inflammatory diseases.
• 🔗 查看原文

8. ⭐ GSE316470 SLC6A3 多巴胺能信号传导破坏剪接体保真度以促进透明细胞肾细胞癌的免疫检查点抑制剂耐药性[2]

• ✍️ 作者：未知作者
• 🏷️ 关键词：carcinoma、immune、resistance
• 📝 描述：Contributor : Junhui SuSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusClear cell renal cell carcinoma (ccRCC) remains refractory to immune checkpoint inhibitors (ICIs) despite its high tumor mutational burden, highlighting an urgent need to elucidate tumor-intrinsic mechanisms of immune escape. Here, leveraging lineage tracing and single-cell multi-omic profiling in immunocompetent models, we identify a pre-existing SLC6A3-positive tumor subpopulation that persists following anti-PD-1 therapy and orchestrates immune evasion by exploiting renal dopamine uptake. SLC6A3 overexpression is robustly associated with diminished infiltration of cytotoxic CD8⁺ T cells and myeloid dendritic cells, establishing it as a biomarker of ICI resistance in ccRCC. Mechanistically, SLC6A3-mediated dopamine import disrupts the MHC-I antigen presentation pathway through direct sequestration of the spliceosomal regulator USP39, resulting in aberrant splicing of B2m and Tap1/2 pre-mRNAs and consequent loss of antigenicity. This disconnects high mutational burden from effective immune surveillance, enabling sustained immune escape. Critically, both genetic and pharmacologic inhibition of SLC6A3 restore antigen presentation competency, potentiate CD8⁺ T cell cytotoxicity, and synergize with anti-PD-1 treatment to achieve durable tumor regression in vivo. Our findings redefine dopamine as a tumor-intrinsic immunosuppressant in ccRCC and nominate the SLC6A3-USP39 axis as a tractable target for reversing antigen presentation defects and overcoming microenvironment-driven ICI resistance.
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9. ⭐ GSE316468 SLC6A3 多巴胺能信号传导破坏剪接体保真度以促进透明细胞肾细胞癌的免疫检查点抑制剂耐药性[1]

• ✍️ 作者：未知作者
• 🏷️ 关键词：carcinoma、immune、resistance
• 📝 描述：Contributor : Junhui SuSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusClear cell renal cell carcinoma (ccRCC) remains refractory to immune checkpoint inhibitors (ICIs) despite its high tumor mutational burden, highlighting an urgent need to elucidate tumor-intrinsic mechanisms of immune escape. Here, leveraging lineage tracing and single-cell multi-omic profiling in immunocompetent models, we identify a pre-existing SLC6A3-positive tumor subpopulation that persists following anti-PD-1 therapy and orchestrates immune evasion by exploiting renal dopamine uptake. SLC6A3 overexpression is robustly associated with diminished infiltration of cytotoxic CD8⁺ T cells and myeloid dendritic cells, establishing it as a biomarker of ICI resistance in ccRCC. Mechanistically, SLC6A3-mediated dopamine import disrupts the MHC-I antigen presentation pathway through direct sequestration of the spliceosomal regulator USP39, resulting in aberrant splicing of B2m and Tap1/2 pre-mRNAs and consequent loss of antigenicity. This disconnects high mutational burden from effective immune surveillance, enabling sustained immune escape. Critically, both genetic and pharmacologic inhibition of SLC6A3 restore antigen presentation competency, potentiate CD8⁺ T cell cytotoxicity, and synergize with anti-PD-1 treatment to achieve durable tumor regression in vivo. Our findings redefine dopamine as a tumor-intrinsic immunosuppressant in ccRCC and nominate the SLC6A3-USP39 axis as a tractable target for reversing antigen presentation defects and overcoming microenvironment-driven ICI resistance.
• 🔗 查看原文

10. GSE308009 抑制 Gerozyme 15-前列腺素脱氢酶可促进损伤或衰老引起的骨关节炎的关节软骨再生 [scRNA-Seq]

• ✍️ 作者：未知作者
• 🏷️ 关键词：aging、scRNA
• 📝 描述：Contributors : Mamta Singla ; Yu X Wang ; Elena Monti ; Yudhishtar S Bedi ; Pranay Agarwal ; Shiqi Su ; Sara Ancel ; Maiko Hermsmeier ; Nitya Devisetti ; Akshay Pandey ; Mohsen A Bakooshli ; Adelaida R Palla ; Stuart Goodman ; Helen M Blau ; Nidhi BhutaniSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusAging or injury to the joints can lead to cartilage degeneration osteoarthritis (OA), for which there are limited effective treatments. We found that expression of the gerozyme 15-Prostaglandin Dehydrogenase (15-PGDH) was increased in the articular cartilage of aged or injured mice. Both systemic and local inhibition of 15-PGDH with a small molecule inhibitor (PGDHi) led to regeneration of articular cartilage and reduction in OA-associated pain. We used single cell RNA-sequencing and multiplexed immunofluorescence imaging of cartilage), to identify the major chondrocyte subpopulationsInhibition of 15-PGDH decreased hypertrophic-like chondrocytes expressing 15-PGDH and fibro-chondrocytes towards hyaline matrix-synthesizing articular chondrocytes. Regeneration of joint cartilage appears to occur through changes in pre-existing chondrocytes, not stem or progenitor cell proliferation.Gerozyme inhibition could be a potential identifying a disease-modifying and regenerative approach with potential utility for the treatment of osteoarthritis.
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1. 一种用于纳米孔直接RNA测序的新方法突破了长转录本鉴定和异构体分辨率的极限

• ✍️ 作者：未知作者
• 🏷️ 关键词：RNA-seq
• 📝 描述：Direct RNA sequencing (DRS) on nanopore platforms promises something short-read methods cannot: native RNA molecules read end-to-end, with isoforms, long transcripts, and RNA modifications preserved. In practice, however, many labs find that conventional DRS workflows underdeliver on that promise—especially for transcripts longer than a few kilobases. This article outlines a recent benchmarking study that …
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2. 科学家在人类精子中发现隐藏的RNA“衰老时钟”

• ✍️ 作者：未知作者
• 🏷️ 关键词：aging
• 📝 描述：Advanced RNA sequencing reveals age-related shifts in sperm RNA that may influence metabolism and offspring health, highlighting a conserved molecular clock in male reproduction…
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3. 以单分子分辨率全面发现人类转录组中的m6A位点

• ✍️ 作者：未知作者
• 🏷️ 关键词：transcriptome
• 📝 描述：Deep learning paired with Nanopore RNA sequencing enables near-perfect detection of m6A and reveals unexpected complexity in human RNA modification patterns…
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• GSE301729 多发性骨髓瘤中甲基化变异性和 LINE-1 激活 [RNA-seq]
• GSE300881 果蝇环状腺单细胞转录组学研究发现 SoxN–Vvl 复合物是保幼激素生物合成的关键调控因子
• GSE293360 T1期非小细胞肺癌N2淋巴结转移的机制和治疗策略
• GSE282125 WT 和 mdig/mina53 KO MDA-MB 231 乳腺癌细胞的基因表达谱 [RNA-Seq]
• GSE309200 单细胞 RNA 测序揭示矢状缝间充质的细胞异质性
• GSE306974 肠类器官血清淀粉样蛋白A (SAA) 转录组测序
• GSE299258 单细胞RNA测序揭示IL-23抑制在银屑病和系统性红斑狼疮并发中的分子改善
• GSE290660 T细胞内在VISTA缺陷通过限制TCR库多样性和肿瘤特异性CD8+细胞毒性T细胞的效应功能，降低CTLA4阻断的疗效
• GSE316957 单细胞 RNA 测序揭示了类固醇诱导的股骨头坏死与酒精诱导的股骨头坏死和髋关节骨关节炎相比，具有独特的细胞和分子特征
• GSE316823 细胞因子处理的人胰腺导管细胞产生的细胞外囊泡增强β细胞中HLA I类分子的表达
• GSE316812：对髓系特异性S1pr1功能获得和功能丧失小鼠的硫代乙醇酸盐诱导的腹膜细胞进行单细胞RNA测序
• GSE316771 RNA-seq 分析：用 CIr2 处理 24 小时的 MDA-MB-231 三阴性乳腺癌细胞
• GSE316568 miR-424-5p 通过激活 PI3K/AKT 信号通路在 Hep3B 细胞中发挥癌基因的作用
• GSE316297 Fbxw11 调控巨噬细胞极化并增强抗白血病活性
• GSE308507 通过原位多聚腺苷酸化和空间 RNA 测序 (Stereoseq) 对微生物组-宿主相互作用进行高分辨率空间映射
• GSE287635 巨噬细胞 Lyn 激酶是蛛网膜下腔出血后神经炎症的性别特异性调节因子
• GSE284997 基因治疗载体与宿主细胞基因组之间的相互作用 [Capture Hi-C]
• GSE284996 基因治疗载体与宿主细胞基因组之间的相互作用 [ATAC-Seq]
• GSE277197 通过原位多聚腺苷酸化和空间 RNA 测序对微生物组-宿主相互作用进行高分辨率空间映射 [回肠，采用原位多聚腺苷酸化]
• GSE277196 通过原位多聚腺苷酸化和空间 RNA 测序对微生物组-宿主相互作用进行高分辨率空间映射 [回肠，未进行原位多聚腺苷酸化]
• GSE276866 通过原位多聚腺苷酸化和空间RNA测序对微生物组-宿主相互作用进行高分辨率空间定位
• GSE305039 吸烟通过 CKAP2L/STAT3/AREG/EGFR 轴促进结直肠癌的进展
• GSE305020 吸烟通过 CKAP2L/STAT3/AREG/EGFR 轴促进结直肠癌进展
• GSE301728 多发性骨髓瘤中的甲基化变异性和 LINE-1 激活 [WGBS]
• GSE299954 MeCP2 基因剂量依赖性神经发育限制性缺陷是由 SWI/SNF 介导的细胞命运决定二价基因的异常激活引起的 [RNA-Seq]
• GSE299820 受控人类流感病毒感染后的先天免疫表观基因组图谱
• GSE291014 TL1A 激活的 T 细胞作为克罗恩病患者直肠肛周瘘管疾病相关变化的上游调节因子 [RNA-seq]
• GSE290220 TL1A 激活的 T 细胞作为克罗恩病患者直肠肛周瘘管疾病相关变化的上游调节因子 [scRNA-seq]
• GSE287824 两种获得性癫痫大鼠模型中基因表达和甲基化变化的共性
• GSE286518 整合脑脊液分析可识别软脑膜疾病中的疾病特异性免疫反应
• GSE282126 野生型和mdig/mina53敲除MDA-MB 231乳腺癌细胞单细胞水平的基因表达谱
• GSE261216 Paneth细胞SIRT1调节肠道组织稳态
• GSE220633 RecQ 功能障碍导致小鼠出现社交和抑郁样行为以及醛缩酶活性改变 [代谢]
• GSE316353 多步骤免疫功能基因小鼠模型揭示葡萄膜黑色素瘤的表型可塑性
• GSE312348 细胞周期分辨的Hi-C揭示了A/B区室在间期出乎意料的可塑性
• GSE311351 CD9 调控肥胖症中巨噬细胞介导的脂肪组织重塑
• GSE296765 蛋氨酸代谢和NOP2甲基转移酶对MYC驱动的肝脏肿瘤发生至关重要
• GSE316967 基于纳米二氧化硅的褪黑素输送系统优化了盐碱地大豆的光合碳代谢和产量形成
• GSE311223 肝移植结果中组织和液体活检中小RNA的比较分析[灌注液小RNA测序]
• GSE311219 肝移植结果中组织和液体活检中小RNA的比较分析[组织小RNA测序]
• GSE294121 类维生素A对紫外线诱导的皮肤光老化的影响研究[RNA-seq]
• GSE294119 类维生素A对紫外线诱导的皮肤光老化的影响研究[scRNA-seq]
• GSE294110 新生儿皮肤中共生髓系细胞的相互作用调节皮肤17型炎症
• GSE279551 利用基于NanoString技术的尿液检测方法对犬侵袭性尿路上皮癌的基因表达进行表征
• GSE316962 以接近细胞分辨率绘制总转录组图谱
• GSE316795 TCER-1-siRNA调控轴抑制秀丽隐杆线虫的先天免疫
• GSE316510 研究发现，NCKX4 介导的钙清除率随年龄增长而下降，加速主动脉重塑并导致血管早期老化。
• GSE316455 缺氧诱导的富含CD147的迁移体通过PI3K/AKT/TWIST1信号通路诱导血管生成拟态，从而促进HCC对索拉非尼的耐药性
• GSE294073 斑马鱼心脏再生过程中纤连蛋白-2的作用
• GSE287653 独特的分子 Sox9 动力学表征了肠道类器官模型中的分化状态和 Sox9 过表达诱导的形态变化。
• GSE284998 基因治疗载体与宿主细胞基因组之间的相互作用