Published September 15, 2022 | Version v1
Dataset Open

A spatiotemporally resolved single cell atlas of the Plasmodium liver stage

Creators

  • 1. Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
  • 2. Instituto de Medicina Molecular, João Lobo Antunes, Faculdade de Medicina Universidade de Lisboa, Lisbon, Portugal
  • 3. Department of Systems Immunology, Weizmann Institute of Science, Rehovot 7610001, Israel

Description

This code is associated with the paper "A spatiotemporally resolved single cell atlas of the Plasmodium liver stage"

Data generated in this study have been deposited in Gene Expression Omnibus with the accession code GSE181725. The code used to process the raw data to a Scanpy/Seurat structure used for analysis is available at https://github.com/AmichayAfriat/SpatioTemporal_malaria_liver_stage_atlas/.

In this repository, you will find processed scRNAseq data and the codes used for further analysis and data visualization. Codes written in R (4.0.2; packages include seurat, dplyr, tidyr, ggpubr, stats, and EnhancedVolcano) and MATLAB (2019a).

Folder: Additional data

  • Metadata used in the analysis
  • NZ_data.txt - Zonation data extracted from smFISH images using the 'analyze_neighborhood_intensity.m' function 

Folder: Figures_source_data

  • Data underlying the graphical representations used in figures
  • Each file contains clearly labeled sheets for distinct subplots

Folder: functions

  • Functions used in Matlab scripts

Folder: GSEA_OUTPUT

  • Gene Set Enrichment Analysis (GSEA, v3.0) output.
  • Curated KEGG and HALLMARK annotations were used
  • Filtered for minimum 15 genes in set and maximum 500. Default setting of 1,000 permutation was used to establish significance. For abortive cells DGE stricter thresholds were used - relative expression > 10-4, and minimum 30 genes in set

 

Files

Afriat_2022_codes_and_source_data.zip

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