A spatiotemporally resolved single cell atlas of the Plasmodium liver stage
DOI10.5281/zenodo.7081863Zenodo7081863MaRDI QIDQ6725301FDOQ6725301
Dataset published at Zenodo repository.
Ido Amit, Maria Manuel Mota, Vanessa Zuzarte-Luís, Keren Bahar Halpern, Sofia Marques, Lisa Buchauer, Shalev Itzkovitz, Ângelo Ferreira Chora, Aparajita Lahree, Amichay Afriat
Publication date: 15 September 2022
Copyright license: Creative Commons Attribution 4.0 International
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 athttps://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 inR (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
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