R code and downstream analysis objects for the scRNA-seq atlas of normal and tumorigenic human breast tissueMAMMARY glandsCELL populationsBREAST cancerCARCINOGENESISGENE expressionBREASTBreast cancer is a common
while adjacent resected tumor material is used to establish the BT21 tumor cell line. TCR reactivity data are then integrated with scRNA + VDJ-seq data to train the predicTCR classifier, which is later tested on externally generated
To further investigate whether the observed differences were maintained across different models and tissues, we expanded the benchmarking and analyzed a large and diverse set of public 10x Genomics scRNA-seq datasets. Specifically, we used data from human healthy intestine53, healthy lung and pulmonary...
对每个CAFs样本的scRNA-seq文库进行建库,使用Smart-seq2方法并且在细胞裂解液中加入ERCC来质控。经过滤后得到10835个内源性基因和53个质控基因用于进一步下游分析。每个细胞含有平均大约4600不同基因的转录本(图1c)。为了研究这一群分离出的CAFs细胞是否能够代表不同细胞亚群,研究人员用不同方法进行了降维,通过t-SNE...
Single-cell RNA sequencing (scRNA-seq) has revolutionized the transcriptomics field by advancing analyses from tissue-level to cell-level resolution. Despite the great advances in the development of computational methods for various steps of scRNA-seq an
1利用优化的转录组参考序列恢复缺失的scRNA-seq数据 Recovery of missing single-cell RNA-sequencing data with optimized transcriptomic references Nature Methods; IF:48.000; DOI: 10.1038/s41592-023-02003-w 内容概要:通过恢复错误的基因间reads,实施杂交的mRNA前体(pre-mRNA)图分析策略和解决基因重叠,表明可以通...
(G and H) UMAP of scRNA-seq data from 9,053 fresh and 5,620 INs-seq fixed human blood PBMC (CD45+ immune cells) (G). The color code for cell type assignment is indicated in the plot, with (H) the fraction of the different cell types in each sample. See also Figures S1 and ...
BMC Genomics (2024) 25:393 https://doi.org/10.1186/s12864-024-10319-w BMC Genomics RESEARCH Open Access scGAL: unmask tumor clonal substructure by jointly analyzing independent single-cell copy number and scRNA-seq data Ruixiang Li1, Fangyuan Shi1,2, Lijuan Song1,2 and ...
Single-cell RNA sequencing (scRNA-seq) has revolutionized the transcriptomics field by advancing analyses from tissue-level to cell-level resolution. Despite the great advances in the development of computational methods for various steps of scRNA-seq an
Somatic copy number alterations (CNAs) are major mutations that contribute to the development and progression of various cancers. Despite a few computational methods proposed to detect CNAs from single-cell transcriptomic data, the technical sparsity of