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.
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describe methods we have used and optimised to generate single cell transcriptomes for malaria parasites as well as unpublished data.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 firstname.lastname@example.org
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.
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
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
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.
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 (2019) DOWNLOAD DATA <- This repository contains gene count tables, analysis code and supplementary files associated with this study.
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.
Sanger Institute Contributors
The Parasite Genomics group uses comparative and functional genomics approaches to investigate the biology of helminths and protozoan parasites.
Rodent models of malaria
At the Sanger Institute Oliver Billker's group used experimental genetics in rodent models to study the basic biology of malaria ...
Programmes and Facilities
We are focused on using single-cell approaches: cell atlas technologies and understanding human genetics at the cellular level. The team combines ...
Parasites and Microbes
We use genomics to study important problems in infectious disease, with a strong desire to develop and refine tools for disease ...
Human Cell Atlas
The International Human Cell Atlas initiative aims to create comprehensive reference maps of all human cells—the fundamental units of life— ...