Data for investigation of cell-type-specific expression and regulation in Setbp1 (p.S858R) atypical SGS male mice

Author ORCID

Jordan H. Whitlock 0000-0002-9336-545X

Tabea M. Soelter 0000-0003-1654-4240

Vishal H. Oza 0000-0001-6990-0267

Elizabeth J. Wilk 0000-0002-7078-1215

Timothy C. Howton 0000-0002-9423-0135

Brittany N. Lasseigne 0000-0002-1642-8904

Publication Date

7-27-2023

Abstract

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

Repository

Zenodo

Distribution License

The MIT License

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