We proceeded to integrate the data using other two models conditioned on the covariates that showed association with the first PC of the embedding space (experiment and cohort). Additionally, we trained a model with a dummy batch covariate, which was equal for all cells. In this case, scPoli...
In the lab we can determine the maximum dosage of a stress (a combination of time of exposure to and concentration of the agent used) that will give rise to no death [119], [120], [121]. Hydrogen peroxide (H2O2) is a commonly used agent to induce apoptosis and is an excellent ...
Seurat Satija et al., 2015 http://satijalab.org/seurat/old-get-started/ GO (DAVID) Huang et al., 2009a, Huang et al., 2009b https://david.ncifcrf.gov/home.jsp ARACNe-AP software Lachmann et al., 2016 N/A ssmarina package Lefebvre et al., 2010 http://dx.doi.org/10.6084/m9...
CellRank probabilities for acquiring the terminal delta cell fate. Cells are colored by the probability of reaching the delta state. Inset, group of cells likely to become delta, showing differentiation path predicted by CellRank. Fev+
All analyses of the scRNA profiles were conducted following the standard workflow provided by the Seurat package (version 4.1.0, https://satijalab.org/seurat/) in R (version 4.0.4). The data were filtered according to the following thresholds: <200 or >2,500 as unique expressed genes (n...
The fact that PCLS support biliary epithelial cell and portal fibroblast proliferation will make this model very useful for the study of the mechanisms involved in portal fibrosis. 展开 关键词: Animals Rats Rats, Wistar Bile Ducts, Intrahepatic Liver Fibroblasts Epithelial Cells Taurocholic Acid ...
Millefy - [R] - An R package and a Docker image with JupyterLab for visualizing read coverage of scRNA-seq datasets in genomic contexts. By dynamically and automatically reorder single cells based on 'locus-specific' pseudotime, Millefy highlights cell-to-cell heterogeneity in read coverage of...
The final library concentration and profile were assessed using a Quant-iT Picogreen dsDNA assay kit (Thermo Fisher Scientific) and High sensitivity (HS) DNA assay on the Caliper LabChip Gx (PerkinElmer Inc.), respectively. Quantitative PCR was performed on the final libraries using a KAPA ...
(Chemistry–Biology Interface Training Program). We acknowledge Ethan Yang from the Bruker Imaging Demo Apps Team for help on SCiLS Lab. L.L. would like to acknowledge a Pancreas Cancer Pilot grant from the University of Wisconsin Carbone Cancer Center (233-AAI9632), a Diabetes Research Center...
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