Cell type-specific immunological hallmarks in dengue children

We profiled the viral and host transcriptomes in PBMCs derived from 19 DENV-infected children and 4 healthy controls using an optimized viscRNA-Seq 2 approach.

We computed the abundance, gene expression and communication network of multiple distinct cell types across disease categories and validated key observations by single-cell proteomics and functional assays in patient-derived samples.

Our findings reveal DENV target cells in the human blood and point to key molecular mechanisms preceding SD progression.

Folder structure

• dengue_children: this folder contains the code used for the analysis

  • modules: this folder contains functions for pilots
  • pilots: old scripts for data analysis
  • paper_figures: this folder contains the code used for the analysis
    • pilots: old scripts for data analysis
    • .ipynb files: code for reference
    • final: this folder contains the code used for the analysis
      • Enrichr: some files obtained by GSEA ananlysis
      • all samples: this folder contains the code used for the analysis with patient 1_075_01
      • modules: this folder contains functions for data analysis
      • references: this folder contains files for reference
      • YK_figure5_cell_cell_communication: this folder contains the jupyter note book files for cell-cell communication analysis without patient 1_075_01
      • .ipynb & .py files: this folder contains the jupyter note book files for the analysis without patient 1_075_01

• data: this folder contains some Excel/TSV files after analyzing the data and associated figures

  • paper_figure: this folder contains the cell-cell communication panels for the dengue children paper

  • tables: this folder contains useful cell-cell communication tables for the dengue children paper, e.g., differential gene expression, differential interactions

  • Yike's code: this folder contains old scripts for data analysis

  • Zhiyuan_code: this folder contais code of the co-first author Dr Zhiyuan Yao