As part of the model building, calibration, and validation effort, various heterogeneous data are generated. As new publications appear, a brief description with appropriate links will be included here.
- Time series characterization of Aspergillus infected mice.
To characterize the dynamics of cytokine production, as well as cell recruitment into the lung, we measured CXCL2, IL6 protein levels (ELISAs), and performed flow cytometry to characterize neutrophil and monocyte recruitment into the lung 12 hours post infection, 1dpi, 2dpi, 3dpi. This data was utilized to validate the main computational model presented in https://doi.org/10.1101/2021.06.08.447590, and the processed data can be found here. Details of methodology can be found in https://doi.org/10.1101/2021.06.08.447590.
- RNA sequencing data of macrophages exposed to A. fumigatus
To characterize the transcriptional response to A.fumigatus, we performed RNA sequencing of human monocyte derived macrophages exposed to A. fumigatus conidia in a time series fashion after 0 hours, 2 hours, 4 hours, 6 hours, and 8 hours of co-culture (See https://www.biorxiv.org/content/10.1101/2022.01.24.477648v1 for details). This data was utilized to create an intracellular network model of the altered iron-handling phenotype of macrophages in response to A. fumigatus. The gene count matrix, as well as all scripts utilized to preprocess sequencing data and mathematical model can be found here.
The workflow to generate the model is summarized below.