GEO 数据集

主题由标题与摘要自动归类；样本量为数据集标注之和，SuperSeries 可能与其 SubSeries 重复计算。

• Spatial genome and transcriptome co-mapping reveals clonal heterogeneity in tumor tissue [DNA-Seq]
  GSE276212Homo sapiens; Mus musculus11 个样本2026-10-31

  Tumor heterogeneity arises from the sequential acquisition of somatic mutations and the selection of fitter clones, leading to distinct genotypes and phenotypes. Joint mapping of genome and transcriptome in the same tumor tissue can directly link clonoal relation to transcriptional state enabling a more in-depth understanding of intrinsic and extrinct tumor heterogeneity in the tissue context. Here, we introduce Spatial-GT-seq, a spatial multi-omic technology capable of genome-wide co-profiling of the genome and transcriptome at near single-cell resolution. We demonstrated in situ identification of tumor subclones in a mouse model of lung metastasis, with parallel transcriptomic profiles indicating that the gene expression profile of the same tumor clone is altered by the tumor microenvironment. Furthermore, analysis of primary and recurrent human pancreatic neuroendocrine tumors reveals both persistent and newly emerging tumor subclones, exhibiting transcriptional changes in both the original and recurrence sites. These findings highlight Spatial-GT-seq as a valuable platform for studying genotype-phenotype-microenvironment associations, providing new insights into cancer evolution and heterogeneity.

  单细胞空间转录组多组学
• Spatial genome and transcriptome co-mapping reveals clonal heterogeneity in tumor tissue [RNA-Seq]
  GSE276211Homo sapiens; Mus musculus11 个样本2026-10-31

  Tumor heterogeneity arises from the sequential acquisition of somatic mutations and the selection of fitter clones, leading to distinct genotypes and phenotypes. Joint mapping of genome and transcriptome in the same tumor tissue can directly link clonoal relation to transcriptional state enabling a more in-depth understanding of intrinsic and extrinct tumor heterogeneity in the tissue context. Here, we introduce Spatial-GT-seq, a spatial multi-omic technology capable of genome-wide co-profiling of the genome and transcriptome at near single-cell resolution. We demonstrated in situ identification of tumor subclones in a mouse model of lung metastasis, with parallel transcriptomic profiles indicating that the gene expression profile of the same tumor clone is altered by the tumor microenvironment. Furthermore, analysis of primary and recurrent human pancreatic neuroendocrine tumors reveals both persistent and newly emerging tumor subclones, exhibiting transcriptional changes in both the original and recurrence sites. These findings highlight Spatial-GT-seq as a valuable platform for studying genotype-phenotype-microenvironment associations, providing new insights into cancer evolution and heterogeneity.

  单细胞空间转录组多组学
• Empowering multiplexed ultra-throughput ribosome profiling with RiboWich
  GSE350000Homo sapiens; Mus musculus33 个样本2026-10-30

  Ribosome profiling has improved the understanding of mRNA translation, enabling single-nucleotide resolution mapping of ribosome positioning along transcripts. However, most ribosome profiling methods remain labor-intensive, inefficient, and low-throughput, limiting scalability and broader adoption. Here, we develop RiboWich (Ribosome sandWich), a streamlined approach that directly ligates adaptors to ribosome-embedded RNA fragments, bypassing the need for ribosome purification and footprint size-selection, tackling two major bottlenecks. Through a dual-step multiplexing strategy, RiboWich supports automated 384-well profiling while retaining sensitivity and capturing condition-specific differences in translation. By enabling scalable, low-input, and automated translatome profiling, RiboWich provides a versatile and accessible platform for ultra-throughput and future single-cell ribosome profiling applications.

  单细胞
• iPSC-derived antigen-presenting cells engineered to express IL12 stimulate tumor-tissue reprogramming and antitumor immunity
  GSE303722Homo sapiens; Mus musculus64 个样本2026-10-30

  Activation of cancer-reactive T cells by dendritic cells (DCs) is important for cancer elimination by host immunity. One type of cancer immunotherapy in which DCs loaded with "cancer antigens" are administered has not been able to achieve stable efficacy due to heterogeneity in cell quality dependent on patient DC status. We constructed IL12-producing antigen-presenting cells from mouse induced pluripotent stem cells (iPSC). These cells can be controlled to proliferate using cytokines, allowing for the mass production of cells with stable performance. When these cells were loaded with a model cancer antigen and administered to cancer-bearing mice, cancer-reactive T cells rapidly acquired effector functions and propagated an interferon (IFN)-stimulated gene signature to cancer tissue distant from the site of administration. This was accompanied by infiltration of effector cells into the cancer tissue, while associated with a decrease in myeloid-derived suppressor cells. These were extremely more potent than immune checkpoint inhibitors (ICIs) and were further amplified in combination with ICIs and correlated with antitumor effects. Based on these observations, we constructed IL12-producing antigen-presenting cells from human iPSCs that express only HLA molecules involved in cancer antigen presentation and exclude other HLA molecules for improved versatility. These human cells, like their mouse counterparts, were capable of cytokine-regulated proliferation and induced antigen-specific activation and IFN-γ production of cancer antigen-specific T cells. Thus, these cells may become an alternative antigen-presenting cell platform for patient DCs to overcome HLA polymorphisms and ensure stable supply and quality.
• An Engineered Tn5 Variant Enhances CUT&Tag Fidelity for Transcription Factors
  GSE351354Homo sapiens; Mus musculus357 个样本2026-10-26

  The CUT&Tag method performs exceptionally well for profiling histone modifications, but mapping sequence-specific transcription factors (TFs) has been more challenging. This is because the Tn5 transposase used in CUT&Tag has an intrinsic affinity for DNA, requiring high-salt washes to suppress non-specific signal at accessible sites, but these stringent ionic conditions can also disrupt TF–chromatin interactions. Here, we develop an improved TF-CUT&Tag strategy to capture these salt-sensitive TF binding sites. We engineered the Tn5 DNA-binding channel by neutralizing positively charged residues and identified the K160A mutation as improving CUT&Tag specificity for GATA2, as measured by enrichment of TF DNA-binding motifs under physiological NaCl and KCl-based DynaTag conditions. Applying this improved assay to the Yamanaka pluripotency TFs in mouse embryonic stem cells increased recovery across their genomic binding landscapes while preserving factor-specific motif architectures. During skeletal muscle differentiation, TF-CUT&Tag revealed strongly motif-enriched MyoG binding and a shift in Pax7 occupancy from CpG-rich promoters in progenitors toward Pax7 motif-enriched sites during differentiation. Together, these results show that TF-CUT&Tag captures distinct modes of TF–chromatin interaction, including motif-directed binding sites and more salt-sensitive sites that may depend on lower-affinity DNA recognition or protein–protein interactions and are difficult to predict from DNA sequence alone.
• SCAF1 driven polyadenylation site usage regulates mRNA isoform expression and neuronal differentiation
  GSE307416Homo sapiens; Mus musculus117 个样本2026-10-26

  This SuperSeries is composed of the SubSeries listed below.

  SuperSeries