The role of the interaction between the SARS-CoV-2 Spike protein and the renin-angiotensin pathway, in particular human ACE2 in pulmonary blood pressure regulation
The Interferon-lambda (IFNL) map describes the action of the drug candidate IFNL on intra- and intercellular signal transduction under SARS-CoV-2.
Here, we describe the index file generation of the mm10 genome, the genome alignment with kallisto, and quantification with bustools to obtain the used spliced / unspliced transcript input.
Here is the detailed R script to generate the input needed by scSynO for synthetic cell generation and classification model training.
The code that can be embedded into any other Seurat data processing workflow is:
Single nuclei transcriptomics data as .csv files from the Allen Brain atlas data set of mus musculus (https://celltypes.brain-map.org/) have been utilized as an input for scSynO. The underlying analysis is part of the manuscript entitled "Automated annotation of rare-cell types from single-cell RNA-sequencing data through synthetic oversampling". Data anaylsis and visalizations were mainly generated with the Seurat R package (https://satijalab.org/seurat/archive/v3.2/spatial_vignette.html)
Model derived from P2011.1.2 in which the steady state assumptions for the Evening complex in P2011 were eliminated. After eliminating these assumptions the model was fitted to the original dynamics of P2011.1.2 for the networks WT, lhycca1, prr79, toc1, gi, ztl. In particular for the lhycca1 double mutant only the repressive "arms" (edges) for cL were set to zero. The parameter values or cP and for COP1 variables were fixed as these have been fitted before in Pokhilko et al 2012 Mol Sys Bio.