Cells constantly face environmental challenges and deal with them by changing their gene expression patterns. They make decisions regarding which genes to express and which genes not to express based on intra-cellular and environmental cues. These decisions are often made by regulating the process of...
To remove cells of poor quality, we used scater [103] to compute QC metrics. For each barcode, we assessed the total UMI counts, total number of genes detected, and the proportion of counts mapping to mitochondrial genes (Additional file 1: Fig. S2A). We removed any barcodes that deviat...
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Gene set enrichment analysis In each RNA-seq profile from the lungs of treated and non-treated tumor-bearing mice, we ranked genes in descending order based on their log-fold change in expression compared to non-tumor-bearing control mice. We tested the enrichment of selected pathways using the...
gene expression52. We applied our NE scoring method across all cancer lineages (pan-cancer analysis) to compute NE scores and assess their relationship with immune phenotypes. In pediatric (Therapeutically Applicable Research to Generate Effective Treatments—TARGET) and adult (The Cancer Genome Atlas...
As stated in the Results, no significant DE genes are found, indicating that lineage information is not reflected in the gene expression profiles under different clones. Then, for the same Fore/Midbrain cells under subtree 9, 10, and 12, we compute their linear dimensionality reduction using ...
Gene therapy using replication competent viral vectors could deliver their effects in two ways: 1) viral vectors can kill the tumor cells by infecting them and replicating inside cells (oncolysis); or 2) viral vectors can be used to insert therapeutic or suicidal genes, which can be targeted ...
Next, we performed principal component analysis (PCA) of the single-cell protein dataset using all 2844 quantified proteins by pSCoPE (Fig.2e). To compute the PCA, missing values were imputed usingk-nearest neighbor imputation. The PCA of single cells analyzed by pSCoPE identified three distinct...
3A). Longitudinal measurement of tumor size across different SSTR2+ tumors revealed that the level of SSTR2 expression had no significant effect on the growth of Jurkat T cell tumors. We tested our ability to detect SSTR2 positive T cells within tumors when both their tumor density and ...
(D) Ki67-positive beta cells maintain Ucn3 expression, indicating that proliferating beta cells and Ucn3-negative beta cells are not the same. (E) Image analysis to detect the islet outline and center of mass to compute the position of all cells relative to the center and nearest edge. (...