{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Isabelle Henshall"],"organism":["Plasmodium falciparum"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-15427"],"description":["Plasmodium falciparum malaria remains a global health challenge and causes a significant number of deaths in tropical and subtropical countries annually. Merozoite surface proteins, located of the surface of the invasive stage of the parasite, are targets of immunity and have been explored as vaccine candidates. Here we removed the highly abundant surface protein MSP2 by CRISPR Cas9 to study the role of this protein. RNA samples were taken of schizonts stage parasites to examine any changes at the transcriptome level as a consequence of MSP2 KO. P. falciparum cultures were centirfuged before resuspension in Trizol and RNA purification performed using chloroform in combination with RNeasy Kit (Qiagen). DNAseing was performed to ensure absence of genomic DNA. RNA sequencing of the schizont stage transcriptome of Pf3D7 MSP2 KO and Pf3D7 WT was performed using the Illumina total RNA with Ribo Zero plus for library preparation and sequenced on the NovaSeq 6000 platform with 2×150 bp paired end reads."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sample Collection - Cultures were tightly synchronised and harvested at late schizont. Cultures were pelleted, resuspended in TriZol (Invitrogen) and incubated for 5 minutes at 37°C before either immediate RNA extraction or freezing at -80°C.","Library Construction - Library construction and sequencing was performed by Victorian Clinical Genetics Services (VCGS) Australia. Library was prepared using llumina stranded total RNA kit with Ribo -Zero Plus. QC was performed after libary prepration and prior to sequencing.","Sequencing - Library sequencing was performed on NovaSeq 6000 using 2x150 bp PE reads.","Nucleic Acid Extraction - Chloroform (Sigma Aldrich) was added, mixed and then spun at 12,000g for 30 minutes at 4°C. Supernatant was collected and mixed with an equal volume of 70% Ethanol and processed using the RNeasy Kit (Qiagen) to extract purified RNA. RNA was DNAse l (Qiagen) treated for 30 mins at room temperature and cleaned up on RNeasy columns according to the manufacturers protocol. Absence of gDNA was checked by qPCR of gDNA and DNAse I treatment repeated if necessary."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","MAGE-TAB Files"],"omics_type":["Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina NovaSeq 6000"],"study_type":["RNA-seq of total RNA"],"species":["Plasmodium falciparum"],"pubmed_title":["An abundant merozoite surface protein of Plasmodium falciparum modulates susceptibility to inhibitory antibodies"],"pubmed_authors":["Isabelle G Henshall, Jill Chmielewski, Dimuthu Angage, Ornella Romeo, Keng Heng Lai, Kaitlin R Turland, Nicki Badii, Michael Foley, Robin F Anders, James Beeson and Danny W Wilson","Isabelle Henshall","Danny Wilson"],"additional_accession":[]},"is_claimable":false,"name":"RNASeq of Plasmodium falciparum 3D7 WT compared to MSP2 KO","description":"Plasmodium falciparum malaria remains a global health challenge and causes a significant number of deaths in tropical and subtropical countries annually. Merozoite surface proteins, located of the surface of the invasive stage of the parasite, are targets of immunity and have been explored as vaccine candidates. Here we removed the highly abundant surface protein MSP2 by CRISPR Cas9 to study the role of this protein. RNA samples were taken of schizonts stage parasites to examine any changes at the transcriptome level as a consequence of MSP2 KO. P. falciparum cultures were centirfuged before resuspension in Trizol and RNA purification performed using chloroform in combination with RNeasy Kit (Qiagen). DNAseing was performed to ensure absence of genomic DNA. RNA sequencing of the schizont stage transcriptome of Pf3D7 MSP2 KO and Pf3D7 WT was performed using the Illumina total RNA with Ribo Zero plus for library preparation and sequenced on the NovaSeq 6000 platform with 2×150 bp paired end reads.","dates":{"release":"2026-01-01T00:00:00Z","modification":"2026-01-02T02:02:39.529Z","creation":"2025-07-31T22:21:05.506Z"},"accession":"E-MTAB-15427","cross_references":{"ENA":["ERP177674"],"EFO":["EFO_0002944","EFO_0004170","EFO_0009653","EFO_0005518","EFO_0004184"],"doi":["10.7554/eLife.107603"]}}