Then, we developed a T cell marker gene signature (TCMGS) and evaluated its prognostic potential for STAD using bulk RNA-seq data. We looked into the relationship between the TCMGS's prediction power and the immune therapy response in 3 separate cohorts from the GEO collection. Materials and...
Drawing on single cell profiles from GSE148071, we extracted gene expression matrix encompassing 60,288 cells derived from 42 original LUAD samples, subsequently subjecting them to further scrutiny (Fig.1A). The harmony method facilitated dimensionality reduction, revealing 17 distinct cell clusters—in...
scRNA-seq, single-cell RNA sequencing; TME, tumor immune environment; PDAC, pancreatic ductal adenocarcinoma; UMAP, uniform manifold approximation and projection; GSEA, gene set enrichment analysis; TMGs, T cell marker genes; TCGA; The Cancer Genome Atlas; TMGS, T cell marker genes score; Tcm...
故而,咱们可以看到TCellSI软件的实现过程中有一个样本间基因表达值矫正的过程,从而使不同数据集的样本具有可比性,如下原图所示。文章没有使用现有的单细胞数据批次矫正的方法,而是利用比较经典的思路,借助Housekeeping gene的表达值来矫正不同数据集的基因表达值。
基于gene_list以及0.8阈值的umap图进行细胞亚群注释 ###注释 pdf("dotplot_DimPlot.pdf",10,6) DimPlot(sce_T,reduction = "umap",label = T)+ DotPlot(sce_T,features = genes_to_check)+coord_flip() dev.off() celltype=data.frame(ClusterID=0:6, cell...
基于实验的方法通常成本较高,此外来源于相同样本的细胞形成的doublet无法被检测(cell hashing) 而目前已有的计算方法有以下问题: 1. 基本上基于marker gene,导致homotypic doublets无法检测 2. 只检测doublets,而无法检测multiplets 3. 基于单模态 创新点
marker gene的选择:All other parameters were kept as the default values. After clustering, limma (version 3.42.2) was used for detecting differentially expressed genes. For each cluster, cells were compared with cells from all other clusters. Genes withlog2 fold change larger than a specified thr...
通过CellMarker 2.0对细胞类型的注释表明,PBMC包含多种血细胞类型,包括T细胞、NK细胞、单核细胞、B细胞、巨噬细胞和中性粒细胞,而TIL包含大量的肿瘤细胞、成纤维细胞和非肿瘤上皮细胞,这些细胞可能共存于Percoll液的中间淋巴细胞层(图1D...
T cell marker metagene predicts a favourable prognosis in estrogen receptor negative and Her2 positive breast cancers. 喜欢 0 阅读量: 17 作者:Rody,A,Ruckhaeberle,E,Holtrich,U,Gaetje,R,Engels,K DOI: 10.1158/0008-5472.sabcs-1048 被引量: 1 ...
FIG. 4: Inhibitory potential of regulatory T cells. Conventional CD4+ T cells are stimulated with allogene PBMCs alone or in combination with different concentrations of Treg cells. T cell proliferation was measured by BrdU incorporation.FIG. 5: Sorting strategy for CD4+CD25high vs. CD4+CD25...