Malaria Cell Atlas

The Malaria Cell Atlas is an active project led by the Lawniczak lab to provide an interactive data resource of single cell transcriptomic data across the full lifecycle of malaria parasites.

All data can be found here: malariacellatlas.org

Overview of MCA

Nearly half of the world’s population remains at risk for malaria with 228 million reported cases in 2018 and over 400,000 deaths. Understanding transcriptional diversity across the lifecycle under different disease settings will help in the fight to eliminate and eventually eradicate this disease.

The MCA includes data from multiple collaborative projects (more details below), and more are in the works. Currently, it includes data from our eLife, SCIENCE, NatureComms and bioRxiv papers, which describe methods we have used and optimised to generate single cell transcriptomes for malaria parasites as well as unpublished data. Our Atlas includes single cell RNA-sequencing data covering all stages of the life cycle in both Anopheles vector and mammalian host tissues, spans both cell sorting and droplet-based scRNAseq and includes five Plasmodium species, including four human pathogens. It also includes the first single cell data from parasites isolated directly from clinical samples.

In the MCA, users can explore how genes are expressed over thousands of individual parasites from several different Plasmodium species and across all life stages. We aim for this tool to be beneficial to all malaria researchers, from those focused on particular gene families, to those developing novel drugs and vaccines.

If you have suggestions for improvement, please get in touch at malariacellatlas@sanger.ac.uk

Papers, collaborators, data summaries, and raw data are linked to for the MCA instalments below.

Papers & Datasets

MCA bioRxiv (2023): Collaborators on this instalment of the atlas, which includes 10x data examining the asexual and sexual life cycle stages of P. falciparum of laboratory strains as well as the first transcriptomes of parasites from a natural infection, were Sunil Kumar Dogga, Jesse Rop, Juliana Cudini, Elias Farr, Antoine Dara, Dinkorma Ouologuem, Arthur Talman, and Abdoulaye A. Djimde.

Raw data: https://www.ebi.ac.uk/ena/browser/view/PRJEB58790 and https://www.ebi.ac.uk/ena/browser/view/PRJEB55754

MCA NatureComms (2021): Collaborators on this instalment of the atlas, which includes SmartSeq2 data for all P. falciparum stages were Eliana Real, Virginia Howick, Farah Dahalan, Kathrin Witmer, Juliana Cudini, Clare Andradi-Brown, Mira Davidson, Sunil Kumar Dogga, and Jake Baum

Raw data:  https://www.ebi.ac.uk/ena/browser/view/PRJEB40487

MCA Science (2019): Collaborators on this instalment of the atlas, which includes SmartSeq2 data examining the full life cycle stages of P. berghei as well as 10x studies on the asexual stages of P. falciparum, P. knowlesi, and P. berghei were Virginia Howick, Andrew Russell, Tallulah Andrews, Haynes Heaton, Adam Reid, Kedar Natarajan, Hellen Butungi, Tom Metcalf, Lisa Verzier, Julian Rayner, Matthew Berriman, Jeremy Herren, Oliver Billker, Martin Hemberg, and Arthur Talman

Raw data:  https://www.ebi.ac.uk/ena/browser/view/PRJEB28169

MCA eLife (2018): Collaborators on the original installment of the MCA were Adam Reid, Arthur Talman, Hayley Bennett, Ana Gomes, Christopher Illingworth, Oliver Billker, and Matthew Berriman. This presented SmartSeq2 data on P. berghei and P. falciparum blood stages.

Raw data:  https://www.ebi.ac.uk/ena/browser/view/PRJEB19245

Downloads

MCA – VISUALISE DATA <- explore how genes are expressed over thousands of individual Plasmodium parasites from across the life cycle.

eLife (2018) <- Further information about this study.

eLife (2018) RAW DATA <- European Nucleotide Archive accession PRJEB19245

SCIENCE (2019) paper <- Further information about this study.

SCIENCE (2019) RAW DATA <-  European Nucleotide Archive accession PRJEB28169

SCIENCE (2019) DOWNLOAD DATA <- Our Github contains gene count tables for the scRNAseq data from this study.

NatureComms (2021) MCA paper <- Further information about this study.

NatureComms (2021) MCA RAW DATA <-  European Nucleotide Archive accession PRJEB40487

bioRxiv (2023) MCA paper <- Further information about this study.

bioRxiv (2023) MCA RAW DATA <-  European Nucleotide Archive accession PRJEB55754 and PRJEB58790

bioRxiv (2019) DOWNLOAD DATA <- This repository contains gene count tables, analysis code and supplementary files associated with this study.

Further information

Learn and support

The Malaria Cell Atlas is supported by Wellcome (WT098051) and by a Medical Research Council Career Development Award (G1100339) to Mara Lawniczak. The authors would like to thank the staff of the Illumina Bespoke Sequencing and Core Cytometry teams at the Wellcome Sanger Institute for their contribution.