详细内容（前10条）

1. ⭐ 刚刚发表7.5分生信，聚焦新热点棕榈酰化，单细胞+无监督聚类+百种机器学习+简单验证。非肿瘤生信模板！

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

2. ⭐ 韩雪祥团队Trends in Molecular Medicine综述 | CAR免疫细胞治疗的基因递送之路

• ✍️ 作者：CellPress全科学
• 🏷️ 关键词：免疫、TME、scRNA、scDNA
• 📝 描述：这些进步将共同推动CAR疗法最终惠及更多患者。
• 🔗 查看原文

3. 最新7.5分生信，作者整合自噬+衰老+休眠+线粒体功能+肿瘤干性进行模型构建及验证。这么多热点结合还是第一回见！

• ✍️ 作者：东晓生物
• 🏷️ 关键词：肿瘤、生信
• 🔗 查看原文

4. 王凌华团队新发Cancer Cell，顶刊生信分析和绘图学习

• ✍️ 作者：生信钱同学
• 🏷️ 关键词：cancer、生信
• 📝 描述：王淩华生信大佬的生信文章代码都很好
• 🔗 查看原文

5. 三种方法解决KEGG功能富集总是出现的断网报错：cannot read from connection

• ✍️ 作者：生信技能树
• 🏷️ 关键词：TME、富集
• 📝 描述：最近群里问的比较多的问题如下。
• 🔗 查看原文

6. 浙大陈淑洁团队Trends in Cancer综述 | 重塑T细胞干性对抗肿瘤

• ✍️ 作者：CellPress全科学
• 🏷️ 关键词：肿瘤、cancer
• 📝 描述：该研究有望更系统地揭示Tpex细胞在不同临床背景下的动态变化。
• 🔗 查看原文

7. 单细胞空间外显子–多模态空间组学揭示肺前驱病变进展中肺泡祖细胞与促炎微环境的协同演变

• ✍️ 作者：单细胞空间交响乐
• 🏷️ 关键词：单细胞、空间组学
• 📝 描述：单细胞空间外显子–多模态空间组学揭示肺前驱病变进展中肺泡祖细胞与促炎微环境的协同演变
• 🔗 查看原文

8. 因为半懂不懂所以更好发单细胞数据挖掘文章（ESM1特异性的内皮细胞？）

• ✍️ 作者：单细胞天地
• 🏷️ 关键词：单细胞
• 🔗 查看原文

9. 详解：乙酰辅酶 A（Acetyl-CoA）代谢

• ✍️ 作者：小李代谢
• 🏷️ 关键词：代谢
• 📝 描述：其在肿瘤微环境中的代谢动态，不仅影响着癌细胞自身的增殖和生存，还深刻调控着抗肿瘤免疫反应的强度和方向。
• 🔗 查看原文

10. 基因组可视化细节优化

• ✍️ 作者：老俊俊的生信笔记
• 🏷️ 关键词：基因组
• 🔗 查看原文

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详细内容（全部10条）

1. ⭐ GSE295124 VGLL1 对发育中的滋养层细胞的转录组和表观基因组均有贡献 [ChIP-Seq]

• ✍️ 作者：未知作者
• 🏷️ 关键词：tumor、cancer、TME、cardiac、glioma、resistance、TCGA、DepMap、depmap、RNA-seq、RNAseq、DNA-seq、ChIP-seq、ATAC-seq、scRNA、scDNA、scATAC、genome、genomics、transcriptome、transcriptomics、Seurat、epigenetic、epigenome、histone、enrichment
• 📝 描述：Contributors : Ruben I Calderon ; Nirvay Sah ; Molly Huang ; Ryan H Kittle ; Walee B Shaik ; Jennifer N Chousal ; Sampada Kallol ; Tony Bui ; Robert Morey ; Alexandra Mitre ; Norah M Fogarty ; Claudia Gerri ; Claire Zheng ; Peter DeHoff ; Pratik Home ; Kathy K Niakan ; Heidi Cook-Andersen ; Kathleen M Fisch ; Soumen Paul ; Francesca SoncinSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Homo sapiensThe trophectoderm (TE), the outer layer of the blastocyst, is the first lineage specified during mammalian development. It initiates attachment and implantation into the maternal endometrium and gives rise to trophoblasts, the epithelial cells of the placenta that support development in utero. Animal models have identified key signaling pathways, including BMP, WNT, and HIPPO, that regulate extra-embryonic ectoderm development, but species-specific differences in regulatory networks underlying TE specification and placental development emphasize the need for human-specific models. We were the first to previously identify Vestigial-like Family Member 1 (VGLL1), a coactivator of the TEAD family of transcription factors, as a human-specific placental marker highly expressed in first trimester trophoblast progenitors. The HIPPO signaling pathway effector TEAD4 in complex with YAP1 regulates initial TE specification by acting on key TE transcription factors (TEtra factors): GATA2, GATA3, TFAP2A, and TFAP2C. Pluripotent stem cells (PSCs) represent a unique resource to study species-specific genetic and epigenetic mechanisms of TE and trophoblast development. Here, we use a PSC model in which BMP4 treatment and WNT inhibition (via IWP2) induce TE-like cells. We examined BMP4-dependent chromatin accessibility during the transition from PSC to TE-like cells in relation to gene expression and WNT activation. We found that BMP4 drives chromatin remodeling toward a trophoblast identity and that mesoderm genes are only transiently expressed with canonical WNT activation. Using this model, we determined that, while VGLL1 expression activation is temporally downstream of the TEtra factors, it is necessary for complete trophoblast differentiation by regulating EGFR expression and reinforcing GATA3 activation through positive feedback. We also found that VGLL1 enhanced canonical WNT signaling by directly regulating WNT receptors and effector genes. Furthermore, we identified KDM6B as a direct target of VGLL1. As a chromatin remodeler, KDM6…
• 🔗 查看原文

2. ⭐ GSE295121 VGLL1 对发育中的滋养层细胞的转录组和表观基因组均有贡献 [ATAC-Seq]

• ✍️ 作者：未知作者
• 🏷️ 关键词：tumor、cancer、TME、cardiac、glioma、resistance、TCGA、DepMap、depmap、RNA-seq、RNAseq、DNA-seq、ChIP-seq、ATAC-seq、scRNA、scDNA、scATAC、genome、genomics、transcriptome、transcriptomics、Seurat、epigenetic、epigenome、histone、enrichment
• 📝 描述：Contributors : Ruben I Calderon ; Nirvay Sah ; Molly Huang ; Ryan H Kittle ; Walee B Shaik ; Jennifer N Chousal ; Sampada Kallol ; Tony Bui ; Robert Morey ; Alexandra Mitre ; Norah M Fogarty ; Claudia Gerri ; Claire Zheng ; Peter DeHoff ; Pratik Home ; Kathy K Niakan ; Heidi Cook-Andersen ; Kathleen M Fisch ; Soumen Paul ; Francesca SoncinSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Homo sapiensThe trophectoderm (TE), the outer layer of the blastocyst, is the first lineage specified during mammalian development. It initiates attachment and implantation into the maternal endometrium and gives rise to trophoblasts, the epithelial cells of the placenta that support development in utero. Animal models have identified key signaling pathways, including BMP, WNT, and HIPPO, that regulate extra-embryonic ectoderm development, but species-specific differences in regulatory networks underlying TE specification and placental development emphasize the need for human-specific models. We were the first to previously identify Vestigial-like Family Member 1 (VGLL1), a coactivator of the TEAD family of transcription factors, as a human-specific placental marker highly expressed in first trimester trophoblast progenitors. The HIPPO signaling pathway effector TEAD4 in complex with YAP1 regulates initial TE specification by acting on key TE transcription factors (TEtra factors): GATA2, GATA3, TFAP2A, and TFAP2C. Pluripotent stem cells (PSCs) represent a unique resource to study species-specific genetic and epigenetic mechanisms of TE and trophoblast development. Here, we use a PSC model in which BMP4 treatment and WNT inhibition (via IWP2) induce TE-like cells. We examined BMP4-dependent chromatin accessibility during the transition from PSC to TE-like cells in relation to gene expression and WNT activation. We found that BMP4 drives chromatin remodeling toward a trophoblast identity and that mesoderm genes are only transiently expressed with canonical WNT activation. Using this model, we determined that, while VGLL1 expression activation is temporally downstream of the TEtra factors, it is necessary for complete trophoblast differentiation by regulating EGFR expression and reinforcing GATA3 activation through positive feedback. We also found that VGLL1 enhanced canonical WNT signaling by directly regulating WNT receptors and effector genes. Furthermore, we identified KDM6B as a direct target of VGLL1. As a chromatin remodeler, KDM6…
• 🔗 查看原文

3. ⭐ GSE295126 VGLL1 对发育中的滋养层细胞的转录组和表观基因组均有贡献 [RNA-Seq]

• ✍️ 作者：未知作者
• 🏷️ 关键词：tumor、cancer、TME、cardiac、glioma、TCGA、DepMap、depmap、RNA-seq、RNAseq、DNA-seq、ChIP-seq、ATAC-seq、scRNA、scDNA、scATAC、genome、genomics、transcriptome、transcriptomics、Seurat、epigenetic、epigenome、histone、enrichment
• 📝 描述：Contributors : Ruben I Calderon ; Nirvay Sah ; Molly Huang ; Ryan H Kittle ; Walee B Shaik ; Jennifer N Chousal ; Sampada Kallol ; Tony Bui ; Robert Morey ; Alexandra Mitre ; Norah M Fogarty ; Claudia Gerri ; Claire Zheng ; Peter DeHoff ; Pratik Home ; Kathy K Niakan ; Heidi Cook-Andersen ; Kathleen M Fisch ; Soumen Paul ; Francesca SoncinSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensThe trophectoderm (TE), the outer layer of the blastocyst, is the first lineage specified during mammalian development. It initiates attachment and implantation into the maternal endometrium and gives rise to trophoblasts, the epithelial cells of the placenta that support development in utero. Animal models have identified key signaling pathways, including BMP, WNT, and HIPPO, that regulate extra-embryonic ectoderm development, but species-specific differences in regulatory networks underlying TE specification and placental development emphasize the need for human-specific models. We were the first to previously identify Vestigial-like Family Member 1 (VGLL1), a coactivator of the TEAD family of transcription factors, as a human-specific placental marker highly expressed in first trimester trophoblast progenitors. The HIPPO signaling pathway effector TEAD4 in complex with YAP1 regulates initial TE specification by acting on key TE transcription factors (TEtra factors): GATA2, GATA3, TFAP2A, and TFAP2C. Pluripotent stem cells (PSCs) represent a unique resource to study species-specific genetic and epigenetic mechanisms of TE and trophoblast development. Here, we use a PSC model in which BMP4 treatment and WNT inhibition (via IWP2) induce TE-like cells. We examined BMP4-dependent chromatin accessibility during the transition from PSC to TE-like cells in relation to gene expression and WNT activation. We found that BMP4 drives chromatin remodeling toward a trophoblast identity and that mesoderm genes are only transiently expressed with canonical WNT activation. Using this model, we determined that, while VGLL1 expression activation is temporally downstream of the TEtra factors, it is necessary for complete trophoblast differentiation by regulating EGFR expression and reinforcing GATA3 activation through positive feedback. We also found that VGLL1 enhanced canonical WNT signaling by directly regulating WNT receptors and effector genes. Furthermore, we identified KDM6B as a direct target of VGLL1. As a chromatin remodeler, KDM6B removes the …
• 🔗 查看原文

4. ⭐ GSE295122 VGLL1 对发育中的滋养层细胞的转录组和表观基因组均有贡献 [RNA-Seq 2]

• ✍️ 作者：未知作者
• 🏷️ 关键词：tumor、cancer、TME、cardiac、glioma、TCGA、DepMap、depmap、RNA-seq、RNAseq、DNA-seq、ChIP-seq、ATAC-seq、scRNA、scDNA、scATAC、genome、genomics、transcriptome、transcriptomics、Seurat、epigenetic、epigenome、histone、enrichment
• 📝 描述：Contributors : Ruben I Calderon ; Nirvay Sah ; Molly Huang ; Ryan H Kittle ; Walee B Shaik ; Jennifer N Chousal ; Sampada Kallol ; Tony Bui ; Robert Morey ; Alexandra Mitre ; Norah M Fogarty ; Claudia Gerri ; Claire Zheng ; Peter DeHoff ; Pratik Home ; Kathy K Niakan ; Heidi Cook-Andersen ; Kathleen M Fisch ; Soumen Paul ; Francesca SoncinSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensThe trophectoderm (TE), the outer layer of the blastocyst, is the first lineage specified during mammalian development. It initiates attachment and implantation into the maternal endometrium and gives rise to trophoblasts, the epithelial cells of the placenta that support development in utero. Animal models have identified key signaling pathways, including BMP, WNT, and HIPPO, that regulate extra-embryonic ectoderm development, but species-specific differences in regulatory networks underlying TE specification and placental development emphasize the need for human-specific models. We were the first to previously identify Vestigial-like Family Member 1 (VGLL1), a coactivator of the TEAD family of transcription factors, as a human-specific placental marker highly expressed in first trimester trophoblast progenitors. The HIPPO signaling pathway effector TEAD4 in complex with YAP1 regulates initial TE specification by acting on key TE transcription factors (TEtra factors): GATA2, GATA3, TFAP2A, and TFAP2C. Pluripotent stem cells (PSCs) represent a unique resource to study species-specific genetic and epigenetic mechanisms of TE and trophoblast development. Here, we use a PSC model in which BMP4 treatment and WNT inhibition (via IWP2) induce TE-like cells. We examined BMP4-dependent chromatin accessibility during the transition from PSC to TE-like cells in relation to gene expression and WNT activation. We found that BMP4 drives chromatin remodeling toward a trophoblast identity and that mesoderm genes are only transiently expressed with canonical WNT activation. Using this model, we determined that, while VGLL1 expression activation is temporally downstream of the TEtra factors, it is necessary for complete trophoblast differentiation by regulating EGFR expression and reinforcing GATA3 activation through positive feedback. We also found that VGLL1 enhanced canonical WNT signaling by directly regulating WNT receptors and effector genes. Furthermore, we identified KDM6B as a direct target of VGLL1. As a chromatin remodeler, KDM6B removes the …
• 🔗 查看原文

5. ⭐ GSE298023 位置和病因调节衰竭人类心脏中的成纤维细胞活化

• ✍️ 作者：未知作者
• 🏷️ 关键词：cancer、TME、glioma、TCGA、scRNA、scDNA、scATAC、genome、Seurat
• 📝 描述：Contributors : Mohamad Youness ; Samaneh Ekhteraei-Tousi ; Rosa Doñate Puertas ; Chandan K Nagaraju ; Karin R Sipido ; Hywel L RoderickSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensCardiac fibrosis is a major contributor to heart failure (HF), yet its therapeutic targeting remains limited due to the complexity of fibrosis types and distributions. This study investigates fibroblast heterogeneity and spatial organization in the left ventricle of human hearts from non-failing donors and HF patients with ischemic or dilated cardiomyopathy. Using single-nucleus RNA sequencing and spatial transcriptomics, distinct fibroblast subpopulations were identified, with resident fibroblasts being depleted in HF and replaced by disease-associated states. Differences in activation ligands, transcriptional trajectories, and spatial localization revealed divergent fibroblast transitions between scar and interstitial fibrosis, and between HF subtypes. These results provide insight into fibroblast dynamics and offer potential targets to modulate fibrosis in heart failure.
• 🔗 查看原文

6. ⭐ GSE246179 镍暴露皮肤表皮的单细胞分析

• ✍️ 作者：未知作者
• 🏷️ 关键词：glioma、single.cell、scRNA、scDNA、genome、genomics
• 📝 描述：Contributor : Kelvin YeungSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensIn this study, we investigated the consequences of repetitive nickel challenge at previously nickel-challenged skin sites in allergic participants. Repeated challenge with nickel resulted in progressive worsening allergic skin reactions in nearly all participants (11 out of 12). To investigate the immunopathogenesis of nickel in ACD, clinically cleared epidermal skin taken 21 days after each challenge was analyzed by immunohistochemistry, flow cytometry and single-cell RNA sequencing (scRNA-seq). Correlating with the worsening skin reactions, an expanding pool of epidermal CD4+ and CD8+ tissue-resident memory T (TRM) cells was seen locally in the challenged skin. Using scRNA-seq a broad subset of TRM cells with various effector phenotypes was identified, which included a predominant population of type 2 T helper (TH2) and KIR+CD8+ TRM cells that expanded with repeated challenge. We observed, broad clonal expansion after nickel challenge with interindividual variations, and clonally related clusters of less differentiated cells which may supply more developed effector TRM cells. Furthermore, repetitive challenge resulted in an increasing population of exhausted regulatory T (Treg) cells that showed lesser clonal expansion. Collectively, our data suggests that repeated challenge to nickel leads to aggravation of eczema and is supported by the increased numbers of effector TRM cells, phenotype differentiation, clonal expansion, and exhaustion of Treg cells in the challenged skin.
• 🔗 查看原文

7. ⭐ GSE280244 甘草查尔酮 B 通过靶向 FTO 缓解克罗恩病损伤

• ✍️ 作者：未知作者
• 🏷️ 关键词：cancer、scRNA、scDNA、Seurat
• 📝 描述：Contributors : Duo Ma ; Xinhua Liu ; Yaling Hong ; Xingxing ZhangSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusTo investigate the mechanism of demethylase FTO in Crohn’s disease，We used RNA-seq data from three normal colon samples and three TNBS-induced IBD colon samples of C57 mice for gene expression profiling.
• 🔗 查看原文

8. GSE308590 内含子RNA结构对基因表达的控制

• ✍️ 作者：未知作者
• 🏷️ 关键词：scRNA、Seurat
• 📝 描述：Contributors : Leonard Schärfen ; Pernille Bech ; Paulina Podszywałow-Bartnicka ; Karla M NeugebauerSeries Type : OtherOrganism : Saccharomyces cerevisiaeIntron removal through pre-mRNA splicing is a central step in gene expression across Eukarya. The process initiates with the recognition of intronic sequence elements (splice sites) by highly conserved RNA-protein components of the spliceosome. Intron sequences themselves are not generally conserved beyond the splice sites, yet intronic mutations are often associated with genetic disease. Here we systematically test if and how intron RNA structure formation modulates gene output. We generated intron variant libraries that measure the impact of base pairing at every position across a natural intron. Using a massively parallel reporter assay (MPRA), we find that base pairing involving the splice sites modulates splicing across orders of magnitude. An additional intron region upstream of the branch site was also sensitive to structure, suggesting steric hindrance. Combining thermodynamic structure prediction with libraries designed to sequester splice sites in structures of varying stability, we show that machine learning models can nearly fully explain observed gene output. Informed by this, designed alterations in intron sequence that modulate base pairing are shown to improve inefficient splicing of human β-globin IVS1. Finally, intronic mutations that alter RNA structure emerge rapidly under selection pressure, providing eukaryotes with a simple evolutionary strategy to fine-tune gene output.
• 🔗 查看原文

9. GSE282578 组蛋白变体H2BE在大脑中具有年龄和细胞类型特异性效应

• ✍️ 作者：未知作者
• 🏷️ 关键词：scRNA、histone
• 📝 描述：Series Type : Expression profiling by high throughput sequencing ; Genome binding/occupancy profiling by high throughput sequencingOrganism : Mus musculusThis SuperSeries is composed of the SubSeries listed below.
• 🔗 查看原文

10. GSE190151 蓝绿色鳉鱼尾鳍RNA测序

• ✍️ 作者：未知作者
• 🏷️ 关键词：RNAseq
• 📝 描述：Contributors : David Willemsen ; Jongbeom Park ; Dario R ValenzanoSeries Type : Expression profiling by high throughput sequencingOrganism : Nothobranchius furzeriIn this study we investigated gene expression in tail fins of 12 samples. 3 samples from adult red-tailed male fish (MZCS002), 3 samples from adult yellow-tailed male fish (GRZ-BELL) and 3 samples each of the corresponding region in female fish of the same strain.
• 🔗 查看原文

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