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1. ⭐ 5月最新6+生信，单细胞+空转分析MMP1+ 肿瘤细胞对肿瘤-免疫相互作用的影响，识别某基因阳性的细胞亚群是目前流行的发文思路！

• ✍️ 作者：生信小课堂
• 🏷️ 关键词：肿瘤、免疫、单细胞、生信
• 📝 描述：点击查看详情
• 🔗 查看原文

2. ⭐ 最新8+生信，结合单细胞+空转+ 18 种程序性细胞死，着重于对预后和免疫治疗疗效的预测及基因功能验证！

• ✍️ 作者：生信小课堂
• 🏷️ 关键词：免疫、单细胞、生信
• 📝 描述：点击查看详情
• 🔗 查看原文

3. ⭐ 7+生信，基于单细胞和空转识别生态位特异性转录和细胞组成特征，识别关键基因并进行验证。思路新颖！

• ✍️ 作者：生信小课堂
• 🏷️ 关键词：单细胞、转录组、生信
• 📝 描述：点击查看详情
• 🔗 查看原文

4. ⭐ 免疫逃逸新型驱动因素！南方医科大学南方医院：克服肿瘤免疫耐药性的精确治疗策略

• ✍️ 作者：转化医学网
• 🏷️ 关键词：肿瘤、免疫、耐药
• 📝 描述：靶向 MCUB-PRKN 相互作用可能是一种精确的治疗策略，以克服免疫耐药性，同时对正常组织的毒性最小。
• 🔗 查看原文

5. 8.3分肠脑轴创新点速看！暨南&北医大【肠道菌群-代谢物-炎症通路】这套思路直接用！

• ✍️ 作者：神经岛
• 🏷️ 关键词：代谢、通路
• 🔗 查看原文

6. 最新10分生信，单细胞+空转识别ECM 重塑相关成纤维细胞，并确定关键基因进行实验验证，干湿结合值得借鉴！

• ✍️ 作者：生信小课堂
• 🏷️ 关键词：单细胞、生信
• 📝 描述：点击查看详情
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7. 11月26-27日合肥！蛋白表达与工程化改造、基因编辑与功能组学、AI+合成生物学、生物催化与细胞工厂、代谢与发酵工程…

• ✍️ 作者：闲谈 Immunology
• 🏷️ 关键词：代谢、基因组
• 📝 描述：60+生物制造专家齐聚，800+行业同仁与会，期待与会~
• 🔗 查看原文

8. Nature重磅！解析癌症免疫中的树突状细胞

• ✍️ 作者：生信人
• 🏷️ 关键词：癌症、免疫
• 📝 描述：树突状细胞是连接innate 免疫（先天免疫）和adaptive 免疫（适应性免疫）的关键枢纽，在肿瘤免疫中既
• 🔗 查看原文

9. Cancer Cell突破综述：破译肿瘤转移新路径

• ✍️ 作者：生信人
• 🏷️ 关键词：肿瘤、cancer
• 📝 描述：循环肿瘤细胞（CTCs）作为癌症转移的"种子"，其捕获技术与生物学解析对突破晚期治疗瓶颈、开发精准干预策略具有
• 🔗 查看原文

10. 《Cancer Cell》重磅：跨15种组织癌种，首度揭秘两类抗原呈递癌症成纤维细胞空间分布图！

• ✍️ 作者：生信人
• 🏷️ 关键词：癌症、cancer
• 📝 描述：近日，美国德克萨斯大学教授Huocong Huang及其小组的最新研究提出单细胞分辨率下抗原呈递癌症相关成纤维
• 🔗 查看原文

💡 该来源还有 17 条内容，详见 文末

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1. ⭐ GSE308792 基于单细胞RNA测序的宫颈癌免疫细胞亚群及功能特征分析

• ✍️ 作者：未知作者
• 🏷️ 关键词：cancer、immune、sequencing
• 📝 描述：Series Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensA comprehensive characterization of immune cells within the tumor microenvironment (TME) of cervical squamous cell carcinoma (CSCC) is essential to advance understanding of tumor biology and guide immunotherapy development. Using single-cell RNA sequencing, we analyzed 14,441 immune cells isolated from tumor tissues and paratumor tissues of three CSCC patients. This analysis identified nine major immune cell subsets, including CD8+ T cells, regulatory T cells (Tregs), natural killer/T cells (NK/T cells), B cells, plasmacytoid dendritic cells (pDCs), and macrophages. Notably, elevated CCR7 expression in exhausted CD8+ T cells was associated with improved prognosis, suggesting it as a preliminary candidate for an immunoregulatory target that warrants further investigation. Additionally, CCL5 levels were elevated in Tregs, indicating a possible involvement in their recruitment to the tumor site that requires further validation. By integrating data on tumor suppressors, oncogenic factors, cytokines, and chemokines, we performed differential gene expression analyses across immune populations, identifying candidate genes for further mechanistic investigation. This systematic comparison of the TME between tumor and paratumor tissues reveals dynamic changes in the immune landscape, providing insights and suggesting potential targets for further study to enhance understanding and treatment of CSCC.
• 🔗 查看原文

2. ⭐ GSE292993 COPD 的实质、气道和血管空间转录组学特征

• ✍️ 作者：未知作者
• 🏷️ 关键词：spatial、spatial transcriptomics、transcriptomics
• 📝 描述：Contributors : Joselyn J Rojas-Quintero ; Scott A Ochsner ; Francesca PolverinoSeries Type : OtherOrganism : Homo sapiens ; synthetic constructSpace Profiling for WTA RNA transcriptomics in lung parenchymal, airway, and vessel of COPD and control patients.
• 🔗 查看原文

3. ⭐ GSE274738 胃癌干细胞和非胃癌干细胞的全转录组测序

• ✍️ 作者：未知作者
• 🏷️ 关键词：cancer、sequencing、transcriptome
• 📝 描述：Contributors : Xiaowei Chen ; Qiong Li ; Yanan Wang ; Ai Chen ; Xiaobing ShenSeries Type : Expression profiling by high throughput sequencing ; Non-coding RNA profiling by high throughput sequencingOrganism : Homo sapiensAs a subpopulation of tumor cells with stemness characteristics such as self-renewal ability and high oncogenicity, gastric cancer stem cells (GCSCs) are considered to be tumor-initiating cells and are the root cause of cancer recurrence and chemoresistance. Therefore, an in-depth study of the stemness characteristics and maintenance mechanism of GCSCs is of great significance for the treatment of gastric cancer (GC). In this study, GCSCs and non-gastric cancer stem cells (Non-GCSCs) derived from tumor tissues of GC patients were used for whole transcriptome sequencing. The goal of identifying key differentially expressed circRNAs, lncRNAs, miRNAs and mRNAs associated with GCSCs. In conclusion, we mapped the molecular feathers at RNA level closely related to GCSCs and revealed certain ncRNAs with great research potentia based on the whole transcriptome sequencing.
• 🔗 查看原文

4. ⭐ GSE273375 最大化癌症纳米疫苗的疗效以及免疫疗法应答者和非应答者中的免疫细胞图谱

• ✍️ 作者：未知作者
• 🏷️ 关键词：cancer、immune、regex:immuno(logy|therapy|suppression)
• 📝 描述：Contributors : Xiangxiang Xu ; Lu Diao ; Ao Zhu ; Jin Wang ; Yuhan Liu ; Xianlan Chen ; Yan Zheng ; Jun Zhao ; Mi LiuSeries Type : OtherOrganism : Mus musculusThe therapeutic efficacy of cancer vaccines can be optimized from 3 aspects: adjuvants, vaccine formulation, and processing of tumor antigens. Herein, various different adjuvants, such as toll like receptors and STING agonists etc., and their combinations were compared in cancer nanovaccines loaded with whole tumor antigens were illustrated. By comparing different sized nanovaccines and micronvaccines, 200nm-400nm and 2.5μm were discovered to be optimal sizes of nanovaccines and micronvaccines. Rapid freezing, fixation, heating, salting-out, ethanol precipitate can affect the immunogenicity of tumor antigens and efficacy of cancer vaccines. The optimal cancer vaccine can cure all or most tumor-bearing body in melanoma mouse model, lung cancer mouse model, subcutaneous pancreatic cancer model, orthotopic pancreatic cancer model, melanoma lung metastasis model. In addition, the immune cell profiles were systematically investigated using single-cell sequencing, in blood, splenocytes and draining lymph nodes of healthy mice, PBS treated tumor-bearing mice, vaccine-treated non-cured mice and cured mice after different time. By comparing 21 samples, some featured clusters and markers, such as S100A4, KLRG1, SIPR5, CXCR3, IL2Ra, IKZF2, CX3CR1, S100A8, and S100A9 etc., were identified to distinguish responders and non-responders to immunotherapy. These biomarkers were verified and confirmed the feasibility of predicting therapeutic efficacy in mouse cancer model and cancer patients. In summary, this study presented a method to optimize cancer nanovacines from different aspects, systematically investigated immune cell profiles in non-responders and responders to immunotherapy, and discovered some featured biomarkers for predicting or distinguishing responders and non-responders to immunotherapy.
• 🔗 查看原文

5. ⭐ GSE309938 EBV+ 与 EBV- 胃癌中地西他滨治疗后通路激活的转录组分析 [RNA-Seq]

• ✍️ 作者：未知作者
• 🏷️ 关键词：cancer、RNA-seq、pathway
• 📝 描述：Contributors : Yin Wang ; Benjamin E GewurzSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensEpstein-Barr virus associated gastric cancer (EBVaGC) accounts for ∼9–10% of gastric cancers worldwide and is defined by a distinctive molecular profile, including extreme hypermethylation of the DNA. Targeting this aberrant methylation may be a potential therapeutic strategy. EBV ⁺ gastric cancer cell lines (YCCEL1, SNU719) and EBV ⁻ lines (AGS, SNU16, HGC27) were treated with a DNA methyl-transferase inhibitor (DNMT), decitabine (DCB), for three days followed by RNA sequencing to identify EBV-specific responses.
• 🔗 查看原文

6. GSE307857 BRG1 缺失在肺癌中很常见，并通过转录和表观遗传重编程改变肺上皮细胞。

• ✍️ 作者：未知作者
• 🏷️ 关键词：cancer、epigenetic
• 📝 描述：Contributors : Mathewos Tessema ; Christin M Yingling ; Loryn M Phillips ; Kieu Do ; Maria A Picchi ; Randy Willink ; Steven A BelinskySeries Type : Methylation profiling by genome tiling arrayOrganism : Homo sapiensBackground/Objectives: BRG1 loss-of-function (LOF) mutation is found in ~10% non-small cell lung cancer (NSCLC) but its role in lung tumorigenesis is unclear and investigated in this study. Methods: BRG1-knockout (KO) lines were generated from various non-malignant, pre-malignant, and malignant human lung epithelia-derived cell lines using CRISPR. Effects of BRG1-KO on cell growth, transcriptome, methylome, and epigenetic therapy were compared with wild-type (BRG1-WT) isogenic controls using standard in vitro and in vivo assays. Results: BRG1 protein was expressed in all non/pre-malignant lung epithelial cells but lost in 47% (14/30) of NSCLC cell lines. BRG1-KO and cigarette smoke (CS) exposure individually transformed human bronchial epithelial cell lines (HBECs) as evident by anchorage-independent growth. BRG1-KO and CS produced additive to synergistic effects on sensitivity to transformation that differed across HBECs. RNA-seq analysis revealed BRG1-KO significantly changed expression of over 8,500 genes on average impacting lung development, function, damage repair and cancer pathways including axonal guidance, pulmonary wound healing, and epithelial-to-mesenchymal transition (EMT). BRG1-KO also led to hypermethylation of >47,000 promoter CpGs within ~9,500 genes on average in different HBECs that included silencing of epithelial genes involved in EMT and tumor suppressor genes. BRG1-KO also moderately increased the in vitro and in vivo sensitivity of NSCLC cells to some epigenetic drugs. Conclusion: BRG1-LOF is frequent in NSCLC, can drive transformation of lung epithelial cells to acquire properties of premalignant cells indicating a potential role in lung cancer initiation, and sensitizes lung tumors to epigenetic therapy.
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7. GSE305006 用于模拟心脏损伤和疾病中免疫动力学的人类多器官类器官平台

• ✍️ 作者：未知作者
• 🏷️ 关键词：immune、cardiac
• 📝 描述：Contributors : Jasmeet S Reyat ; Yuqi Shen ; Gowishan Poologasundarampillai ; Amirpasha Moetazedian ; Julie Rayes ; Abdullah O KhanSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensWe devised a microphysiological system (MPS) coupling comBOs (combined bone and bone marrow organoids) and VCOs (vascularised cardiac organoids), enabling the recruitment of immune cells to VCOs follwing ischemic injury. Ischemia was modelled by exposing VCOs to hypoxic culture conditions (1% O2 for 24 hrs) before co-culture in our MPS. single nuclear RNA-sequencing was used to assess fibrosis and immune cell infiltration after cardiac injury.
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8. GSE301405 DNA甲基化紊乱导致ATRT中可靶向转录可塑性[RNA-seq]

• ✍️ 作者：未知作者
• 🏷️ 关键词：RNA-seq、methylation
• 📝 描述：Contributors : Michael A. Koldobskiy ; Ashley R. TetensSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensAtypical teratoid rhabdoid tumor (ATRT) is a highly aggressive but genetically simple pediatric central nervous system tumor, defined by biallelic inactivation of the chromatin regulator SMARCB1 with remarkably few other cooperating mutations. Despite its genetic homogeneity, ATRT exhibits profound clinical and epigenetic heterogeneity, with three major subgroups (ATRT-TYR, ATRT-MYC, and ATRT-SHH) defined by DNA methylation and transcriptional signatures. Beyond these subgroup-defining features, we aimed to investigate epigenetic variability within tumors by applying whole-genome bisulfite sequencing and probabilistic modeling to quantify stochastic DNA methylation in primary ATRT samples encompassing all three subgroups. We show that ATRT exhibits a destabilized and increasingly stochastic methylome. While ATRT global methylation patterns diverge according to subgroup, some methylation perturbations, such as hypermethylation and increased methylation entropy over bivalent promoters, are consistent across subgroups. We find that methylation stochasticity alterations map onto potential drivers of ATRT, such as LIN28a, the HOXD cluster for ATRT-MYC, and OTX2 for ATRT-TYR, and identify actionable targets, such as hypermethylation of the tumor suppressor CDKN2a across all subgroups. We investigate the sensitivity of the aberrant DNA methylation landscape of ATRT to pharmacologic DNA methyltransferase inhibition and histone deacetylase inhibition (HDACi). We show that decitabine leads to profound demethylation of patient-derived ATRT cell lines, including reversal of hypermethylation at bivalent promoters and the CDKN2a locus. The addition of HDACi leads to dramatic gene expression changes, including upregulation of innate immune signaling pathways, such as STING/interferon signaling, genes under the regulation of bivalent promoters, and reactivation of the tumor suppressor CDKN2A. The combination of DNMTi and HDACi synergistically reduces cell viability. Taken together, we show that ATRT has a highly stochastic methylome sensitive to epigenetic manipulation.
• 🔗 查看原文

9. GSE298745 基于血清外泌体microRNA的人工智能诊断模型可高精度检测肝细胞癌[RNA-seq]

• ✍️ 作者：未知作者
• 🏷️ 关键词：carcinoma、RNA-seq
• 📝 描述：Contributors : Dae-Soo Kim ; Sugi Lee ; Tae-Su HanSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusRNA sequencing was performed on mouse liver tissue samples from four groups: ND+oil (normal), WD+oil (NASH), ND+CCl₄ (cirrhosis), and WD+CCl₄ (HCC).
• 🔗 查看原文

10. GSE295777 转录因子 Yin-Yang 1 调控心脏代谢重编程以应对运动或病理应激

• ✍️ 作者：未知作者
• 🏷️ 关键词：metabolic、cardiac
• 📝 描述：Contributors : Manling Zhang ; Zishan Peng ; Haiqing Ping ; Zoe Li ; Jia-Jun Liu ; Silvia Liu ; Ning FengSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusThe pleiotropic transcription factor Yin Yang 1 (YY1) regulates cellular metabolism in a stage- and tissue-dependent manner. However, its role in cardiac energetic regulation remains unclear. We found that cardiac-specific YY1 knockout (cYY1 KO) mice exhibited cardiac dysfunction after two weeks of swimming exercise, suggesting an impaired adaptive cardiac response. Further analysis revealed that exercise-induced upregulation of transcription factor networks controlling cardiac metabolism, including peroxisome proliferator-activated receptor gamma coactivator 1 alpha (PGC-1α), was blunted in cYY1 KO mice. Consistently, citrate synthase activity, an indicator of mitochondrial content, was reduced in these mice. In response to transaortic constriction (TAC), cYY1 KO mice developed significantly exacerbated heart failure. RNA sequencing showed downregulation of metabolic genes and pathways, including PGC-1α, in TAC cYY1 KO mice hearts. Additionally, mitochondrial complex protein levels and complex I activity were reduced, consistent with suppressed metabolic gene transcription. Previously, we observed increased YY1 expression in hearts subjected to both exercise and TAC. However, while cardiac metabolism was enhanced with exercise, it was impaired with TAC. We found that p300 binding to YY1 increased during exercise, whereas histone deacetylase 3 (HDAC3) binding to YY1 increased in TAC hearts. These findings suggest that YY1-mediated transcriptional regulation of metabolic genes is modulated by the epigenetic regulators p300 and HDAC3.
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1. 新英格兰生物实验室®推出NEBNext®甲型流感病毒集成索引引物模块，以推进甲型流感病毒的监测和测序。

• ✍️ 作者：未知作者
• 🏷️ 关键词：sequencing
• 📝 描述：A new integrated indexing workflow accelerates high-throughput Influenza A sequencing, enabling rapid RNA sequencing for global…
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• 张泽民院士团队Cancer Cell 新作，重塑肿瘤免疫新机制
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• GSE282803 KMT2D 通过暂时激活神经元转录因子基因来控制小脑颗粒细胞分化 [RNA-seq]
• GSE262167 s-腺苷甲硫氨酸 (SAM) 饮食决定后代表观遗传修饰和代际免疫反应。
• GSE261489 单细胞测序揭示大鼠皮下筋膜中一种新型间充质细胞簇
• GSE208307 通过靶向 HCC 中的癌症 USP14 实现 CD8+ T 细胞依赖性杀伤作用 [scRNA-seq]
• GSE309844 两栖植物水藤的单细胞转录组数据集
• GSE307412 有丝分裂期间 SOX2 磷酸化限制基因组损伤 [ChIP-Seq 2]
• GSE298268 Atg5 敲除下调 erastin2 处理的原代 PTEC 中的 KEGG 通路“氧化磷酸化”
• GSE277316 有丝分裂期间 SOX2 磷酸化限制基因组损伤 [ChIP-Seq]
• GSE276865 有丝分裂期间 SOX2 磷酸化限制基因组损伤 [ATAC-Seq]
• GSE276848 有丝分裂期间 SOX2 磷酸化限制基因组损伤 [RNA-Seq]
• GSE309926 不同条件下小鼠骨髓培养产生的常规树突状细胞的RNA测序
• GSE309882 多重预处理白血病中Menin抑制剂的直接耐药性
• GSE307589转录组学揭示了南方比目鱼（Paralichthys lethostigma）幼体和幼鱼发育及变态的调控机制
• GSE307180 转录组分析和实验验证揭示了 PI3K/AKT 信号通路参与高海拔认知功能障碍 [6_OHG]
• GSE304295 腺病毒E1A对奥沙利铂敏感和耐药的人结直肠癌HCT116细胞奥沙利铂反应的影响
• GSE301412 DNA甲基化紊乱导致ATRT中可靶向转录可塑性[WGBS]
• GSE301410 DNA甲基化紊乱导致ATRT[WGBS细胞系]中可靶向的转录可塑性
• GSE299994 对对照组小鼠或长期阿魏酸处理小鼠的造血干细胞进行 RNA 测序
• GSE298588 基于血清外泌体microRNA的人工智能诊断模型可高精度检测肝细胞癌
• GSE296150 抑制室旁核中的 Ephrin 受体信号传导可通过调节突触可塑性和免疫稳态来减轻银屑病
• GSE290640 CCDC137 敲低对膀胱癌细胞 T24 基因表达的影响。
• GSE290435 环境相关铅暴露影响SH-SY5Y细胞神经元分化过程中的基因表达
• GSE287381 SF3A3通过增强c-FOS表达驱动子宫内膜癌的肿瘤发生，并代表一个潜在的治疗靶点
• GSE287111 人类免疫肺类器官模型用于研究 SARS-CoV-2 感染后巨噬细胞介导的肺细胞衰老 [scRNA-seq]
• GSE286888 顺铂或CX-5461处理下高级别浆液性卵巢癌细胞的基因表达谱比较
• GSE286045 疫苗接种和年龄对水痘-带状疱疹病毒gE抗原特异性T细胞进行单细胞测序
• GSE284266 胆固醇25-羟化酶增强结直肠癌中髓源性抑制细胞的免疫抑制功能
• GSE282804 KMT2D 通过时间性激活神经元转录因子基因来控制小脑颗粒细胞分化
• GSE282802 KMT2D 通过暂时激活神经元转录因子基因来控制小脑颗粒细胞分化 [CUT&RUN]
• 利用 GS​​E281987 RNA-seq 确定 Ctrl-EVs 和 M. bovis NX2-EVs 的 miRNA 表达谱。
• GSE281311 地塞米松诱导发育中骨骼骨毒性的机制：单细胞视角
• GSE281279 miRNA26b 敲除对血管钙化的影响 [RNA-seq]
• GSE281028 miRNA26b 敲除对血管钙化的影响 [scRNA-seq]
• GSE280807 具有自体组织驻留巨噬细胞免疫微环境的自组织人类心脏类器官
• GSE279534 PTEN 是静脉性腿部溃疡难愈合表型的主要驱动因素，它抑制免疫反应、血管生成和淋巴管生成。
• GSE275955 人类乳腺癌 FFPT 组织的 BulkRNA 序列；TLS 缺乏和 TLS 丰富的
• GSE267761 肿瘤外泌体加剧心肌缺血/再灌注损伤中的线粒体损伤
• GSE228833 A549细胞中flag（ETV4）的全基因组靶向
• GSE208308 通过靶向肝细胞癌中的癌症 USP14 实现 CD8+ T 细胞依赖性杀伤作用
• GSE208306 通过靶向 HCC 中的癌症 USP14 实现 CD8+ T 细胞依赖性致死性 [CRISPR 筛选]
• GSE302553 扩张型心肌病中肌肉特异性核糖体的致病机制（AC16 RNA-seq）
• GSE293958 单核 RNA 测序揭示小肠切除术引起的肝损伤中独特的肝细胞群
• GSE309843 RNA测序数据包括：喂食高脂饮食4个月的野生型（WT）和AKO小鼠，喂食高脂饮食4个月后注射载体和三苯氧胺的条件性人胰淀素表达小鼠，以及喂食高脂饮食2个月的野生型（WT）小鼠的前额皮质RNA测序数据。
• GSE304980 利用 CUT&Tag 技术在 NIH/3T3 细胞中对 Xap5 和 Nono 结合位点进行全基因组定位
• GSE297252 circ72039 过表达对胰腺癌细胞系中吉西他滨敏感性相关基因表达的影响
• GSE282008 曲马多通过 ATF4 诱导乳腺癌细胞发生副凋亡
• GSE279782 多发性骨髓瘤细胞中FOXM1表达的全基因组筛选