Consistent with SMC loss in TAAD, cell senescence and death-related pathways were significantly upregulated in SMCs, such as "oxidative stress-induced senescence" and "TP53 regulates tran- scription of cell death genes" (Fig. 3a; GSEA false discovery rate (FDR) <0.05). Oxidative stress-...
Integration and expression reconstruction of single-cell sequencing data.ADISCERN transfers the style of a high-quality (hq) dataset to a related low-quality (lq) dataset, enabling gene expression reconstruction that results in improved clustering, cell type identification, marker gene detection, and ...
Cells subjected to elevated stress such as treatment with anti-cancer therapies can react in two ways: either die or remain suspended in between life and death, a condition known as cellular senescence1,2,3,4. Cellular senescence is a stable cell growth arrest that occurs in tumor cells subje...
Currently, multiple morphological and immunofluorescence markers are required for senescent cell identification. "However, emerging scRNA-seq datasets have enabled increased understanding of the heterogeneity of senescence. "Here we present SenPred, a machine-learning pipeline which can identify senescence ...
By binding with chemokine receptors or regulating protein kinase (Fig. 2C-E). In addition, the results of KEGG [27–29] enrichment analysis showed that they were mainly involved in cell cycle, cellular senescence, and P53 signal pathways, among others (Fig. 2F)....
Regenerative medicine and tissue engineering aim to promote functional rebuilding of damaged tissue. Comprehensively profiling cell identity, function and interaction in healthy tissues, as well as understanding how these change upon tissue disruption, such as that caused by injury, ageing or infection, ...
To perform unbiased identification of cell types in filtered sample datasets and the combined dataset, we used the R package SingleR (v1.4.1), a computational framework that references bulk transcriptomes and helps annotate cell types for each cluster. The built-in Mouse RNAseq Data (MRD) in ...
Previous analyses of gene expression during reprogramming were based on populations of cells, impeding single-cell level identification of reprogramming events. We utilized two gene expression technologies to profile 48 genes in single cells at various stages during the reprogramming process. Analysis of ...
In single-cell studies, cells can be characterized with multiple sources of heterogeneity (SOH) such as cell type, developmental stage, cell cycle phase, activation state, and so on. In some studies, many nuisance SOH are of no interest, but may confound the identification of the SOH of ...
Here we present scGHOST, a single-cell subcompartment annotation method using graph embedding with constrained random walk sampling. Applications of scGHOST to scHi-C data and contact maps derived from single-cell 3D genome imaging demonstrate reliable identification of single-cell subcompartments, ...