Then, for the same Fore/Midbrain cells under subtree 9, 10, and 12, we compute their linear dimensionality reduction using PCA. Then, on the first 50 PCs, we computed pairwise Euclidean distances between pairs of single cells and grouped them based on their clone IDs. The results (Fig. ...
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...
We discarded genes that had low counts, that had low mean expression across the subclusters making up the cells of each cell type, and that were characterized by severe batch effects. We used ZINB-WaVE81 to compute gene and cell-specific observational weights that can be used to unlock DE...
We then annotated day 5 ancestors by their day 10 fates (Figure 5C). Day 5 ancestors fated to give rise exclusively to T cells and day 5 ancestors fated to give rise to multiple cell types were distributed diffusely in gene expression space throughout the MPP/HSC population (Figure 5C)....
For both images, we transform to polar coordinates, take their Fourier transforms, and then compute their cross-correlation. The point of maximum activation of the cross-correlogram in polar coordinates corresponds to the re-alignment angle. We perform the same process on the reflection of the ...
The potential ligand/receptor (L/R) interactions among all cells, especially the interactions between PCs and tumor cells, were calculated and analyzed based on the functions "computeCommunProb", "computeCommunProbPathway", and "aggregateNet" using standard parameters. Risk model construction based ...
Table S3. A summary of cell cluster information, multiome gene expression (GEX) and TF motif enrichment, peaks enrichment, and gene activity differential expression in multiome scATAC-seq from TRM-like versus re-circulating CD8 + TILs sorted from 4 HGSOCs, related to Figure 3 Table S4. A ...
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...
The state of a component will decay (back to control state 1) if its regulators can no longer maintained their active state. Given this transition rules and a specific initial state of the system, we can compute a series of “state-changes” for each component along discrete time steps, ...
Natural Killer cells are innate lymphocytes with central roles in immunosurveillance and are implicated in autoimmune pathogenesis. The degree to which regulatory variants affect Natural Killer cell gene expression is poorly understood. Here we perform e