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Screening of differentially expressed genes in three Plasmodium falciparum parasite lines [expression]

ABSTRACT: We performed Agilent chip analysis with synchronized 0-6h ring stage parasites of three P.falciparum lines within their third life cycle, to study the change of expression profiling when knocking down PfSWIB .

ORGANISM(S): Plasmodium falciparum

PROVIDER: GSE141404 | GEO | 2020/02/18

REPOSITORIES: GEO

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Screening of differentially expressed genes in three Plasmodium falciparum parasite lines [RNA-seq]

Project description:We performed RNA-Seq analysis with synchronized 0-6h ring stage parasites of three P.falciparum lines within their third life cycle, to study the change of expression profiling when knocking down PfSWIB. The comparison analysis on screening of differentially expressed genes was done in parasite lines including 3D7(wild type: blank control), PfSWIB (wild type: self-control) and PfSWIB∆ (PfSWIB knockdown). Approximately 10.8% of the transcripts showed up-regulation between the PfSWIB-KD and two WT parasite, whereas 11.9% showed down-regulation (Fold change>1.5, P<0.05). Hierarchical clustering of differentially expressed genes uncovered several transcription factors such as PfApiAP2 family and PfSir2B, as well as certain histone modification enzymes, which proved to be involved in regulating on var gene transcription. We further screened out a number of var genes which exhibited differential expression among different lines, and performed qPCR on 44 diﬀerentially expressed vars in the PfSWIB vs PfSWIB∆ comparison group based on the RNA-seq results, to study the transcription patterns of upsA-, upsB- and upsC-subtype var genes. We found that most upsA- and upsC- type vars were significant down-regulated in PfSWIB∆ line. In contrast, the expression pattern of partial upsB vars presented a distinct change in PfSWIB∆ line. The RNA-seq and qPCR analysis provide a better understanding of the mechanism and function of PfSWIB on regulating the expression switching and clonal variation of var gene family contributing to the pathogenesis in malaria parasites.

2020-02-18 | GSE141155 | GEO

Transcriptional profiling of growth perturbations of the human malaria parasite Plasmodium falciparum

Project description:The microarray experiments were carried out using a long oligonucleotide DNA microarray that represent all 5363 P. falciparum genes with one oligonucleotide per 1.9kb of coding sequence on average (Hu et al. 2007). Total 247 microarray experiments were carried out including 29-drug treatment time courses with 20 compounds and corresponding untreated controls from different drug or inhibitor treatment. Data of each drug/inhibitor experiment were normalized using a linear normalization and background filtering as implemented by the NOMAD database (http://derisilab.ucsf.edu). Time-series sampling and experiments with synchronized ex vivo culturing parasites. Each experiment has treatment and controls, and starts at a specific time of post invasion. For an example of quinine treatment, the treatments start from late ring stage through trophozoite stage of the parasites. First, IC50 is determined by drug assay with synchronized parasites (5% parasiteomia and 2% RBC). Second, synchronized parasite cultures are splitted into 12 flasks (75ml culture/flask) for a 6 time-point time-series experiment. 6 flasks are treated with quinine (final concentration is IC50) and 6 flasks are negative controls. 1,2,4,6,8 and 10 hrs after the treatment, parasites in each flask were harvested for total RNA isolation and microarray hybridizaiton.

2010-05-18 | E-GEOD-19468 | biostudies-arrayexpress

The high resolution transcriptome of Plasmodium falciparum gametocytes

Project description:The gametocyte transcriptomes were generated in P.falciparum parasites of 3D7 strain after PfHP1 depletion aming to determin the transriptional profiles of sexual stages during the parasites gametocyte development.

2018-12-10 | GSE121505 | GEO

Interactions of PfETRAMP14.1 with PfEMP1 and EXP-2 at the parasitophorous vacuolar membrane (PVM) of human malaria parasite Plasmodium falciparum [HIGH PARASITEMIA ANALYSIS]

Project description:In our global differential gene expression analyses,ETRAMP14.1, an ETRAMP family member was found to be highly transcribed in vivo in severe Malaria patients from highly endemic Indian region. This study for the first time reports the interaction of ETRAMP14.1 with PfEMP1, EXP2 and Hsp70-1. Therefore, we propose that ETRAMP14.1 facilitate PfEMP1 to cross the PVM via transcolon machinery component EXP2. Peripheral blood samples containing ring forms of the P.falciparum from mild and severe malaria patients were used for RNA extraction, CDNA synthesis and hybridization on Affymetrix microarrays. In vitro ring stage P.falciparum cultures were used for normalization.

2015-08-28 | E-GEOD-72446 | biostudies-arrayexpress

Interactions of PfETRAMP14.1 with PfEMP1 and EXP-2 at the parasitophorous vacuolar membrane (PVM) of human malaria parasite Plasmodium falciparum [LOW PARASITEMIA ANALYSIS]

2015-08-28 | E-GEOD-72447 | biostudies-arrayexpress

Plasmodium falciparum: hyperoxic vs normoxic conditions

Project description:Transcriptional profiling of P. falciparum comparing parasites exposed to 5% and 21% oxygen environmental conditions in the late ring stage.

2009-10-30 | GSE18831 | GEO

Plasmodium falciparum: hyperoxic vs normoxic conditions

Project description:Transcriptional profiling of P. falciparum comparing parasites exposed to 5% and 21% oxygen environmental conditions in the late ring stage. Two experimental conditions: 5% vs 21%. Biological replicates: 3 normoxia and 3 hyperoxia replicates

2010-06-20 | E-GEOD-18831 | biostudies-arrayexpress

Small molecule transcriptional responses in Plasmodium falciparum

Project description:Comparison of whole genome gene expression profiles for Plasmodium falciparum parasites perturbed with small molecules with diverse mechanisms of action. Perturbations were performed by treating each synchronized parasite culture with a given small molecule at 24 hrs post-eryhrocyte invasion and RNA collected 2 hrs post-exposure

2015-12-01 | GSE67127 | GEO

RNA-seq of the malaria parasite Plasmodium falciparum 3D7 during its intraerythrocytic development cycle

Project description:The parasite Plasmodium falciparum is responsible for severe malaria, which is still one of the major causes of death in developing countries. To provide a new RNA-seq reference dataset for its blood-stage transcriptome according to current guidelines and best practices, we performed a time course experiment with three independent biological replicates of synchronized P. falciparum 3D7 cells, that were cultivated at a haematocrit of 5% in human O+ erythrocytes. RNA-seq samples were taken at 8 developmental stages including young ring stage (8 hpi), late ring stage/early trophozoite (16 hpi), mid-age trophozoite (24 hpi), late trophozoite (32 hpi), early schizont (40 hpi), schizont (44 hpi), late schizont (48 hpi) and purified merozoites (0 hpi). Red blood cell pellets were lysed with Trizol and total RNA was purified using column-based purification (PureLink RNA Kit) including DNase treatment on the column and controlling for absence of genomic DNA contamination using qPCR. Whole blood total RNA samples were depleted of human globin mRNA using magnetic bead isolation technology (GLOBINclear kit). After RNA sample quality control and optimized cDNA libraries preparation for AT-biased genomes for Illumina sequencing, RNA-seq was performed at BGI Genomics (Shenzhen, China) on HiSeq 4000 to generate 100 bp paired-end sequencing reads.

2019-07-02 | E-MTAB-7731 | biostudies-arrayexpress

Impact of sickle cell trait hemoglobin on the intraerythrocytic transcriptional program of Plasmodium falciparum

Project description:Purpose: The goals of this study are to compare parasite transcriptomes in sickle cell trait infected red blood cells during the intraerythrocytic developmental cycle (IDC) from in vitro time series and in vivo blood samples to identify new therapeutic targets in the treatment of malaria Methods: In vitro time series: Parasites were synchronized to early ring-stage parasites and sampled every three hours for 48 hours to capture every stage of the IDC, generating 16 RNA-seq libraries per replicate (128 total). In vivo blood samples: Samples were collected in an observational study of malaria in children in Kenieroba, Mali (ClinicalTrials.gov Identifier: NCT02645604). From children presenting with uncomplicated falciparum malaria, we selected all available samples from children with HbAS and matched each of these to a sample from a child with HbAA on: month of episode, parasite density, ethnic background, and, if possible, ABO blood type.

2021-05-26 | GSE163144 | GEO

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