Supplementary Materials

The Malaria Cell Atlas: Single parasite transcriptomes across the complete Plasmodium life cycle

Virginia M. Howick, Andrew J. C. Russell, Tallulah Andrews, Haynes Heaton, Adam J. Reid, Kedar Natarajan, Hellen Butungi, Tom Metcalf, Lisa H. Verzier, Julian C. Rayner, Matthew Berriman, Jeremy K. Herren, Oliver Billker, Martin Hemberg, Arthur M. Talman, Mara K. N. Lawniczak

Materials/Methods, Supplementary Text, Tables, Figures, and/or References

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  • Figs. S1 to S20
  • Tables S1 and S2
  • Captions for data S1 to S4
  • References
Data S1
Information from P. berghei Smart-seq2 analyses including summary statistics for each gene, cluster assignment, highly variable genes, marker genes, and unique core assignments (Gene info tab). Additional tabs include the differential expression analyses, gene ontology and motif discovery results.
Data S2
Summary statistics of the down-sampled Smart-seq2 data set. Sixty cells from each stage that were selected for the core unique analysis along with their quality control metrics, the summary statistics for each gene (e.g. total transcript counts), and the mean expression for each gene across each of the 10 stages are reported.
Data S3
One-to-one orthologs across ten Plasmodium species. These orthologs were used for mapping cells across species.
Data S4
Differential expression analysis over IDC development in three species. Slopes and FDR-corrected p-values (qval) for each of the 306 conserved genes across each of the 13 segments. Segments are labelled by their mid-point pseudotime and species are labelled pb (P. berghei), pk (P. knowlesi), and pf (P. falciparum) respectively. In addition, there is a column for each segment indicating if the Pk[Pf] slope was significant and agreed with Pb (1) or not (0). Additional sheets provide slope results for all RNA velocity genes in each species.