UMB Data Catalog

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UMB Dataset

Plasmodium vivax Transcriptomes Reveal Stage-specific Chloroquine Response and Differential Regulation of Male and Female Gametocytes

UID: 47
Author(s): Adam Kim, Jean Popovici, Didier Menard, David Serre*
* Corresponding Author
Description
Plasmodium vivax is the most widespread human malaria parasite. However, its biology is little understood for a number of reasons, not the least of which is the inability to continuously propagate it in vitro. Utilizing samples of whole blood taken from 26 Cambodian patients who were determined to be solely infected with the parasite, this research investigated three aspects of P. vivax activity: 1) the statistical contribution of the different developmental stages present in infection using gene expression deconvolution; 2) the regulation of expression of gametocyte genes, and 3) the effect of chloroquine on the P. vivax transcriptome. The primary dataset includes RNA-sequencing reads from the blood of the Cambodian patients as well as reads derived from dissected sporozoites from mosquitoes. Four supplementary data files provide additional details from the study.
Geographic Coverage
Cambodia
Subject of Study
Subject Domain
Gene Expression Profiling
Plasmodium vivax
Keywords
Chloroquine
Gametocytes
Gene Expression Deconvolution
Trophozoites

Access

Restrictions
Unrestricted access
Instructions
Freely available in the NCBI SRA under the BioProject PRJNA378759
Associated Publications
Kim A, Popovici J, Menard D, Serre D. (2019). Plasmodium vivax transcriptomes reveal stage-specific chloroquine response and differential regulation of male and female gametocytes. Nature Communications, 10:371. DOI: 10.1038/s41467-019-08312-z
Data Type
Stranded RNA-sequencing reads
Equipment Used
Illumina HiSeq 2500 System

High throughput DNA and RNA sequencing system

Software Used
CIBERSORT

Implements a method for characterizing cell heterogeneity using RNA mixtures from nearly any tissue

edgeR

Empirical analysis of digital gene expression data in R

TopHat

Spliced read mapper for RNA-Seq

Study Type
Empirical Research
Grant Support
5R01AI103228/National Institute of Allergy and Infectious Diseases
Other Resources
Supplementary Information

PDF with additional graphs and figures

Peer Review File

PDF of reviewers' comments

Description of Additional Supplementary Files

PDF of descriptions of supplementary data files 1, 2, 3, and 4

Supplementary Data 1

Excel file of sequencing and alignment statistics for each infection

Supplementary Data 2

Excel file list of P. vivax genes whose expression levels are correlated with the expression of known gametocyte genes

Supplementary Data 3

Excel file of genes differentially expressed after chloroquine treatment (FDR<0.1)

Supplementary Data 4

Excel file of gene expression signatures of the different developmental stages obtained by gene expression deconvolutoin

Reporting Summary

PDF of completed Nature Research reporting summary document

Custom Code

Code and additional data for P. vivax RNA-Seq studies from patient samples perfomred in the Serre lab