title: Whole transcriptome expression analysis and comparison of two different strains of Plasmodium falciparum using RNA-Seq.
abstract: The emergence and distribution of drug resistance in malaria are serious public health concerns in tropical and subtropical regions of the world. However, the molecular mechanism of drug resistance remains unclear. In the present study, we performed a high-throughput RNA-Seq to identify and characterize the differentially expressed genes between the chloroquine (CQ) sensitive (3D7) and resistant (Dd2) strains of Plasmodium falciparum. The parasite cells were cultured in the presence and absence of CQ by in vitro method. Total RNA was isolated from the harvested parasite cells using TRIzol, and RNA-Seq was conducted using an Illumina HiSeq 2500 sequencing platform with paired-end reads and annotated using Tophat. The transcriptome analysis of P. falciparum revealed the expression of ~ 5000 genes, in which ~ 60% of the genes have unknown function. Cuffdiff program was used to identify the differentially expressed genes between the CQ-sensitive and resistant strains. Here, we furnish a detailed description of the experimental design, procedure, and analysis of the transcriptome sequencing data, that have been deposited in the National Center for Biotechnology Information (accession nos. PRJNA308455 and GSE77499).
authors.affiliation: Department of Microbiology, Jawaharlal Institute of Postgraduate Medical Education and Research (JIPMER), Puducherry 605006, India.
authors.forename: Hiasindh Ashmi
authors.initials: HA
authors.lastname: Antony
authors.affiliation: Department of Haematogenetics, National Institute of Immunohaematology (NII), Mumbai, Maharashtra 400012, India.
authors.forename: Vrushali
authors.initials: V
authors.lastname: Pathak
authors.affiliation: Department of Microbiology, Jawaharlal Institute of Postgraduate Medical Education and Research (JIPMER), Puducherry 605006, India.
authors.forename: Subhash Chandra
authors.initials: SC
authors.lastname: Parija
authors.affiliation: Surat Raktadan Kendra & Research Centre, Surat, Gujarat 395002, India.
authors.forename: Kanjaksha
authors.initials: K
authors.lastname: Ghosh
authors.affiliation: SciGenom Labs Pvt. Ltd., Cochin, Kerala 682037, India.
authors.forename: Amrita
authors.initials: A
authors.lastname: Bhattacherjee
keywords: Chloroquine resistance; Malaria; Next generation sequencing; Plasmodium falciparum; Transcriptomics