processed.tar.gz, contains all files from the data directory associated with this projects and includes the following: setbp1_targets.csv : list of human SETP1 gene targets from ChIP-seq experiments converted to mouse and enriched for additional interactions from literature references (https://pubmed.ncbi.nlm.nih.gov/35685777/ and https://www.nature.com/articles/s41467-018-04462-8, seurat_objects/ kidney_integrated_celltypes.Rdata : filtered and preprocessed seurat object with cell type assignments for input to SoupX processing kidney_integrated_celltypes_postSoup.Rdata : preprocessed and quality controlled seurat object with final cell type assignments after SoupX processing setbp1_cerebralintcelltypes.Rdata : preprocessed and quality controlled seurat object with final cell type assignments decoupleR_CollecTRI/ mouse_prior_tri.csv : accessed May 2023, it is unclear how versioning or accessions are used so we provided the Mouse CollecTRI (https://github.com/saezlab/CollecTRI) used in this study to calculate cell-type-specific TF activity motif_inputs/ Mus_motif_all.txt : TF-motif PANDA input for mm10 reference genome enriched for expression_inputs/ : expression matrices for all cell types for both tissues and conditions (n = 50) used to construct cell-type-specific PANDA networks The below files are from the data/results directory of this associated project and include the following: alpaca.tar.gz : directory containing differential community analysis outputs from ALPACA seurat.tar.gz : directory containing SoupX intermediates, as well as the