Transcriptome profiling reveals functional variation in Plasmodium falciparum parasites from controlled human malaria infection studies
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ABSTRACT:
ORGANISM(S): Plasmodium falciparum 3D7 Plasmodium falciparum NF54 Plasmodium falciparum
PROVIDER: GSE136076 | GEO | 2019/08/21
REPOSITORIES: GEO
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Project description:The parasite Plasmodium falciparum is responsible for severe malaria, which remains a major cause of death, particularly in sub-Saharan Africa. The reference strain NF54 (or its subclone 3D7) is commonly used for controlled human malaria infection (CHMI), but recently strains with a different geographic and genomic background have become available for CHMI, including 7G8, which was subcloned from the Brazilian isolate IMTM22 in 1984 (Burkot TR et al. 1984. Infectivity to mosquitoes of Plasmodium falciparum clones grown in vitro from the same isolate. Trans R Soc Trop Med Hyg 78 (3):339-41. doi: 10.1016/0035-9203(84)90114-7). To provide the first RNA-seq reference dataset for 7G8 ring stage parasites and validate our qPCR primer set targeting all var gene variants above 6 kb encoded in the 7G8 genome according to current guidelines and best practices, we thawed an aliquot from the Sanaria 7G8 parasite working cell bank (Lot: SAN03-021214 dated 20. February 2014) thawed and cultured for 13 parasite generations at a hematocrit of 5% in human O+ erythrocytes. Parasites were kept synchronous by regular sorbitol treatment. Ring-stage infected erythrocytes were lysed with Trizol, and total RNA was purified using column-based purification (Qiagen RNeasy Mini Mit), including DNase treatment on the column and control for absence of genomic DNA contamination by qPCR. Total RNA samples were cleared of human globin mRNA using magnetic bead isolation technology (GLOBINclear kit). After quality control of RNA samples and optimized preparation of cDNA libraries for AT-rich genomes for Illumina sequencing, RNA-seq was performed at BGI Genomics (Shenzhen, China) on the HiSeq 4000 to generate 100 bp paired-end sequencing reads.
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