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Comparison of developmental stage transcripts in the K1 strain

ABSTRACT: To identify the developmentally regulated genes, which could confound identification of PN and CQ drug responsive genes, RNA samples from drug-free synchronized cultures from ring, trophozoite, and schizont stages were individually labelled and hybridized with a pooled sample from the three stages. The data from this experiment were used to compare the developmental profile of the K1 strain with the data from other P. falciparum strains.

ORGANISM(S): Plasmodium falciparum

PROVIDER: GSE30869 | GEO | 2011/08/02

SECONDARY ACCESSION(S): PRJNA154595

REPOSITORIES: GEO

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Comparison of developmental stage transcripts in the K1 strain

Project description:To identify the developmentally regulated genes, which could confound identification of PN and CQ drug responsive genes, RNA samples from drug-free synchronized cultures from ring, trophozoite, and schizont stages were individually labelled and hybridized with a pooled sample from the three stages. The data from this experiment were used to compare the developmental profile of the K1 strain with the data from other P. falciparum strains. 9 samples were obtained from three developmental stages of parasite development (3 each from ring, trophozoite and schizont synchronized parasites). Three independent cultures were obtained, synchronized on different days.

2011-08-01 | E-GEOD-30869 | biostudies-arrayexpress

Pyronaridine and chloroquine responses in the K1 strain

Project description:Pyronaridine (PN) and chloroquine (CQ) are structurally related anti-malarial drugs with primarily the same mode of action. However, PN is effective against several multidrug-resistant lines of Plasmodium falciparum, including CQ-resistant lines, suggestive of important operational differences between the two drugs. Synchronized trophozoite-stage cultures of P. falciparum strain K1 (CQ resistant) were exposed to 50% inhibitory concentrations (IC50) of PN and CQ, and parasites were harvested from culture after 4 and 24 hours exposure. Global transcriptional changes effected by drug treatment were investigated using DNA microarrays. Plasmodium falciparum in vitro cultures were synchronized to trophozoite stage (22-24h post infection) and exposed to either CQ or PN at IC50 concentrations. 18 sample pairs (drug treated/untreated) were analyzed; 9 for CQ and 9 for PN. All drug-treated samples were labelled with Cy5 and untreated controls were labelled with Cy3.

2011-08-01 | E-GEOD-30867 | biostudies-arrayexpress

Pyronaridine and chloroquine responses in the K1 strain

2011-08-02 | GSE30867 | GEO

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Project description:Effects of PfAP2-EXP2 knockdown on gene expression at the ring, trophozoite, and schizont stages

2022-02-02 | GSE180436 | GEO

Dynamics of H3K64 trimethylation on histone core regulates the schizont specific expression of exported proteins in Plasmodium falciparum

Project description:We identified unconventional histone lysine trimethylation mark in the nucleosome core at H3K64 position in human malaria parasite Plasmodium falciparum. Global ChIP analysis was performed using anti-H3K64me3 specific antibody for three major blood stages, i.e. ring, trophozoite and schizont stages to identify the genomic position of the H3K64me3. The sheared chromatin was prepared from highly synchronous P. falciparum culture and subjected for ChIP followed by library preparation from the ChIP DNA and were subjected to sequencing using the HiSeq Illumina platform. H3K64me3 binding sites were determined after sequence alignment and normalization with input sequence. Interestingly, there was a significant reduction in the number of peaks on different chromosomes during multinucleated schizont stage as compared to ring and trophozoite stage. Collectively, this is first study to show that H3K64me3 function as repressor methyl mark during ring and trophozoite stages to regulate the expression of schizont specific export family of proteins in P. falciparum.

2020-07-18 | GSE154651 | GEO

Next Generation Sequencing of transfected NC K1 cells and transfected si-NEAT1_2 K1 cells

Project description:Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of transfected NC K1 cells and transfected si-NEAT1_2 K1 cells. The goals of this study are to analysis the different mRNA expression between transfected NC K1 cells and transfected si-NEAT1_2 K1 cells. Quantitative reverse transcription polymerase chain reaction (qRT–PCR) methods and to evaluate protocols for optimal high-throughput data analysis. We performed mRNA-seq in the NEAT1_2 knockdown group and NC group in the K1 cell line. We found that after knockdown of NEAT1_2, 615 mRNAs were upregulated and 2364 mRNAs were downregulated.

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Transcriptional alteration in malaria parasite after disruption of PfPRMT5 [Array]

Project description:Purpose: this study is to analyze the change of overall transctiption after disruption of Protein Arginine Methyltranferase 5 (PRMT5) in Plasmodium falciparum. Methods: In this study, the transcriptomes of a PfPRMT5 gene knockout (KO) parasite line with its wildtype control were analyzed a custom-desinged Agilent microarray.Total RNA were harvested from the asexual parasites at four stages (ring, early trophozoite, late trophozoite, and schizont)(12h, 24h, 36h, and 46h post-invasion) using the Quick-RNA MiniPrep kit (Zymo Research).

2023-06-28 | GSE199419 | 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

IP pTKL - Plasmodium pseudo-Tyrosine Kinase-like binds PP1 and SERA5 and is exported to host erythrocytes

Project description:PbpTKL-AID-HA was immunoprecipitated from iRBC ghosts at trophozoite stages and from parasite + PV fractions at schizont stages. Total lysis of P. berghei pG230 strain trophozoites was also performed and anti-HA immunoprecipitation assays were performed on lysates as for ghosts to generate WT samples. After checking by WB for the presence of PbpTKL-AID-HA in ghost and schizont samples, as well as its absence from WT samples, 3 biological replicates were analyzed by Mass Spectrometry for each sample.

2019-06-05 | PXD011986 | Pride

circRNA maps in AhR antagonist treated K1 cells

Project description:High-throughput data analysis was performed to identify the differentially expressed circRNAs in K1 control cell and AhR antagonist treated K1 cells. In total, 45 differentially expressed circRNAs were found.

2021-11-30 | GSE188657 | GEO

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