title: R2.3D7lowLPC
organism: Plasmodium falciparum 3D7
description: Protocols: P. falciparum cell culture was performed as described previously (Brancucci, 2015; Trager, 1976). RPMI-1640 culture media were supplemented with 25 mM HEPES, 100 μM hypoxanthine, 24 mM sodium bicarbonate, and gentamicin (all from Sigma-Aldrich). Media containing serum were generated by additional supplementation of 10% O+ human serum (Zurich bloodbank). Minimal fatty acid (mFA) media were generated by additional supplementation of 0.39% fatty acid-free BSA, 30 μM oleic acid, and 30 μM palmitic acid (all from Sigma-Aldrich). To generate serum-free media supplemented with 20 μM LysoPC, LysoPC (Avanti Polar Lipids) was dissolved in methanol. Cells were exposed either to serum, 20µM LPC, 2.5µM LPC, mFA or 1 hour pulse 50nM of DHA (Dihydroartemisinin) prior to mFA.  All cell cultures were maintained in a 5% CO2, 1% O2 and 94 % N2 gas mixture (Med-Tech Gases). Experiments used a clone of the Pf2004/164TdTomato P. falciparum line17, which requires addition of 4 nM WR99210 (Jacobus Pharmaceuticals) to select for stable maintenance of episomes. Additional experiments were performed with strain Dd2, which is a clone derived from W2-MEF which itself is derived from W2'82 (Indochina III/CDC) (Oduola, 1988; Wellems, 1990) and 3D7/3xHAGDV1 ( Filarsky, Science. 2018). Dd2 KO_ben was maintained with or without 1.5µM DSM1. Per time point 1mL PCV at ~3% parasitaemia were treated has fallow. Parasites were isolate by saponin treatment (0.01%). RNA extraction was performed with RNeasy plus kit from   Qiagen, parasite pellets were resuspended in 350 ¬µl of lysis buffer and stored at -80 degrees C utile extraction. Up to 10 µg of RNA was treated with DNAse Turbo kit (Ambion) prior reverse transcription or RNA seq. RNA quality was check with the Agilent bioanalyzer. 150 ng total RNA of each sample was used for library preparation. RNA quality was check with the Agilent bioanalyzer. Stranded libraries were prepared by using TruSeq Stranded mRNA kit (Illumina) using manufacturer instructions with 13 cycles of PCR. Library quantification was conducted by Qubit measurements using the HS DNA Kit.
attributes.tag: ENA first public
attributes.value: 2025-08-31
attributes.tag: INSDC center name
attributes.value: SII, MVLS, University of Glasgow
attributes.tag: INSDC status
attributes.value: public
attributes.tag: Submitter Id
attributes.value: E-MTAB-15236:R2.3D7lowLPC
attributes.tag: broker name
attributes.value: ArrayExpress
attributes.tag: cell line
attributes.value: 3D7
attributes.tag: collection date
attributes.value: not collected
attributes.tag: common name
attributes.value: malaria parasite P. falciparum
attributes.tag: developmental stage
attributes.value: 40-44 hpi
attributes.tag: disease
attributes.value: Plasmodium falciparum malaria
attributes.tag: genotype
attributes.value: DD2 ∆ben G5
attributes.tag: geographic location (country and/or sea)
attributes.value: not collected
attributes.tag: growth condition
attributes.value: lowLPC
attributes.tag: isolate
attributes.value: not applicable
attributes.tag: sample name
attributes.value: E-MTAB-15236:R2.3D7lowLPC
attributes.tag: scientific_name
attributes.value: Plasmodium falciparum
attributes.tag: isolate
attributes.value: 3D7