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describe methods we have used and optimised to generate single cell transcriptomes for malaria parasites as well as unpublished data.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 datahttps://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 datahttps://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

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.

Contact

If you need help or have any queries, please contact us using the details below.

For comments and questions, please contact us at malariacellatlas@sanger.ac.uk


Sanger Institute Contributors

Photo of Dr Sunil Kumar Dogga

Dr Sunil Kumar Dogga

Postdoctoral Fellow

Photo of Dr Mara Lawniczak

Dr Mara Lawniczak

Senior Group Leader

Previous contributors

Photo of Tallulah S. Andrews

Tallulah S. Andrews

Postdoctoral Fellow

Photo of Dr Matt Berriman

Dr Matt Berriman

Former Senior Group Leader

Photo of Dr Oliver Billker

Dr Oliver Billker

Former Senior Group Leader

Photo of Dr Martin Hemberg

Dr Martin Hemberg

Former CDF Group Leader

Photo of Dr Virginia Muriel Howick

Dr Virginia Muriel Howick

Postdoctoral Fellow

Photo of Dr Adam James Reid

Dr Adam James Reid

Senior Staff Scientist

Photo of Dr Arthur M Talman

Dr Arthur M Talman

Postdoctoral Fellow

External Contributors

Photo of Prof Abdoulaye Djimdé

Prof Abdoulaye Djimdé

CAMES Professor of Parasitology and Mycology and Honorary Faculty at the Wellcome Sanger Institute

Photo of Dr Julian C Rayner

Dr Julian C Rayner

Honorary Faculty (formerly Senior Group Leader at the Sanger Institute) and Director of Wellcome Connecting Science

Photo of Jake Baum

Jake Baum

Professor

Photo of Haynes Heaton

Haynes Heaton

Former PhD student

 
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Publications

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