GEO DataSets

(Submitter supplied) Global transcription of the malaria parasite, Plasmodium falciparum, is finely regulated, yet the genome encodes for a limited number of sequence-specific transcription factors (TFs) to coordinate this pattern. A subset of these TFs bind overlapping DNA motifs (i.e., CACACA and GTGCAC); however, mechanisms of binding site selection and redundancy have not yet been investigated in P. falciparum. Therefore, we integrated a variety of approaches from new and published work such as high-throughput in vitro and in vivo binding assays, DNA shape predictions, epigenetic post translational modification mapping, and genome-wide chromatin accessibility mapping to comprehensively interrogate the impact of DNA sequence context and the chromatin landscape on TF binding in P. more...

Organism:

Plasmodium falciparum

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL21078 GPL32020

8 Samples

Download data: BED, BIGWIG

(Submitter supplied) Purpose: In malaria parasites, the regulation of mRNA translation, storage and degradation is a critical aspect of gene expression, especially during the life stage transition. Since the DEAD-box helicases are involved in RNA metabolism, we wanted to determine whether pfdozi disruption led to altered mRNA abundance in P. falciparum. Methods: In this study, we functionally characterized the DEAD-box RNA helicase PfDOZI in the human malaria parasite Plasmodium falciparum and discovered its functions on mRNA metabolism during development. more...

Organism:

Plasmodium falciparum

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL21078 GPL19269

44 Samples

Download data: FASTA, XLSX

(Submitter supplied) Genome-wide ChIP-sequencing analysis of PfMCM6 was carried out in trophozoite stage parasites using PfMCM6 antibodies. We have observed that PfMCM6 is highly enriched at the exon regions. Moreover, PfMCM6 was also found in promoter-TSS, transcription termination site (TTS), and intergenic regions in minimal proportion. This study shed some light on PfMCM6 binding sites in Plasmodium falciparum genome.

Organism:

Plasmodium falciparum

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL21078

2 Samples

Download data: BROADPEAK

(Submitter supplied) Purpose: this study is to analyze the change of RNA splicing events 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 by RNAseq.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). more...

Organism:

Plasmodium falciparum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21078

8 Samples

Download data: FASTA, XLSX

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Plasmodium falciparum

Type:

Expression profiling by high throughput sequencing; Expression profiling by array

Platforms:

GPL21379 GPL26920 GPL21078

68 Samples

Download data: XLSX

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Plasmodium falciparum

Type:

Expression profiling by array; Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL21078 GPL26985

43 Samples

Download data: BEDGRAPH, NARROWPEAK, TXT

(Submitter supplied) The survival of malaria parasites in the changing human blood environment largely depends on their ability to alter gene expression by epigenetic mechanisms. The active state of Plasmodium falciparum clonally variant genes is associated with euchromatin characterized by the histone mark H3K9ac, whereas the silenced state is characterized by H3K9me3-based heterochromatin. However, the localization of the euchromatin-heterochromatin transitions associated with expression switches in different clonally variant genes has not been characterized. more...

Organism:

Plasmodium falciparum

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL21078

25 Samples

Download data: BEDGRAPH, NARROWPEAK

(Submitter supplied) Plasmodium parasites are reliant on the Apicomplexan AP2 (ApiAP2) transcription factor family to regulate gene expression programs. AP2 DNA binding domains have no homologs in the human or mosquito host genomes, making them potential antimalarial drug targets. Using an in-silico screen to dock thousands of small molecules into the crystal structure of the AP2-EXP (Pf3D7_1466400) AP2 domain (PDB:3IGM), we identified compounds that interact with this domain. more...

Organism:

Plasmodium falciparum

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL21078 GPL26920

8 Samples

Download data: BIGWIG, NARROWPEAK

(Submitter supplied) Plasmodium falciparum parasites alternate between two different obligate hosts during their life cycle: humans and Anopheles mosquitoes. During the blood stage in the human host they proliferate asexually inside erythrocytes. A small proportion of parasites develops into male and female gametocytes, which enter the sexual part of the life cycle once taken up by a mosquito. The production of male and female gametocytes is therefore critical for malaria transmission. more...

Organism:

Plasmodium falciparum

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL27825 GPL21078

54 Samples

Download data: BW

(Submitter supplied) In the human host, Plasmodium falciparum parasites propagate asexually in erythrocytes causing the symptoms of malaria. However, in every asexual cycle, a small proportion of the parasites commits to sexual differentiation, which is critical for transmission. During a period of about 10 days, the sexually committed parasites either develop into male or female gametocytes. In this study, gametocytes carrying an endogenously GFP tagged version of the female specifically expressed ABCG2 gene were FACS sorted to separate male (GFP low) and female (GFP high) gametocyte populations at different days of development. more...

Organism:

Plasmodium falciparum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21078

19 Samples

Download data: TXT

(Submitter supplied) Clonally variant genes (CVGs) play fundamental roles in the adaptation of Plasmodium falciparum parasites to the fluctuating conditions of the human host, but their expression patterns under the natural conditions of the blood circulation have been characterized in detail only for a few specific gene families. Here we provide a detailed characterization of the full P. falciparum transcriptome across the full intraerythrocytic development cycle (IDC) at the onset of a blood infection in non-immune human volunteers. more...

Organism:

Plasmodium falciparum

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL21078

4 Samples

Download data: BED, NARROWPEAK

(Submitter supplied) Plasmodium falciparum is a deadly human pathogen responsible for the devastating disease called malaria. In this study, we measured the differential accumulation of RNA secondary structures in coding and noncoding transcripts from the asexual developmental cycle in P. falciparum in human red blood cells. Our comprehensive analysis that combined high-throughput nuclease mapping of RNA structures by duplex RNA-seq, SHAPE-directed RNA structure validation, immunoaffinity purification and characterization of antisense RNAs collectively measured differentially base-paired RNA regions throughout the parasite’s development. more...

Organism:

Plasmodium falciparum

Type:

Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL21078 GPL21298

6 Samples

Download data: TXT

(Submitter supplied) Purpose: In malaria parasite, PfGCN5, a histone acetyltansferase (HAT),forms a unique complex including a PHD domain containing protein named PfPHD1. To understand the function of this complex, the BrD in PfGCN5 and PHD in PfPHD1 were deleted. The transcritional changes after domain deletions were measured by RNA-seq. Methods: The mRNA profiles of parasite lines : 3D7 (WT), PfGCN5-ΔBrD and PfPHD1-ΔPHD, were generated by deep sequencing, in triplicate, using Illumina HiSeq 2500 in Rapid Run mode using 100nt single read sequencing. more...

Organism:

Plasmodium falciparum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21078

36 Samples

Download data: XLSX

(Submitter supplied) RNAPII ChIP seq was carried out with various phospho antibodies and compared and correlated with the RNA -seq expression data from the same stage sample

Organism:

Plasmodium falciparum

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL19269 GPL21078

30 Samples

Download data: BED, BEDGRAPH, BW, NARROWPEAK, TXT, XLS

(Submitter supplied) The aim of this study was to identify transcriptonal responses during sexual commitment of P. falciparum mutants unable to form gametocytes.

Organism:

Plasmodium falciparum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21078

21 Samples

Download data: CSV, XLS

(Submitter supplied) The dry season is a major challenge for Plasmodium falciparum parasites in many malaria endemic regions, where water availability limits mosquitoes to only part of the year. How P. falciparum bridges two transmission seasons months apart, without being cleared by the host or compromising host survival is poorly understood. Here we show that low levels of P. falciparum parasites persist in the blood of asymptomatic Malian individuals during the 5- to 6-month dry season, rarely causing symptoms and minimally affecting the host immune response. more...

Organism:

Plasmodium falciparum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21078

24 Samples

Download data: TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Plasmodium falciparum

Type:

Expression profiling by array; Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL21078 GPL26985

20 Samples

Download data: TXT

(Submitter supplied) Malaria transmission requires the conversion of some asexual parasites into sexual forms termed gametocytes. The initial stages of sexual development, including sexually-committed schizonts and sexual rings, remain poorly characterized, in part because only a subset of parasites undergo sexual development and they are morphologically identical to their asexual counterparts. Here we present a system based on conditional expression of PfAP2-G, the master regulator of sexual conversion, for controlled sexual induction. more...

Organism:

Plasmodium falciparum

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL21078

8 Samples

Download data: BED, BEDGRAPH, FASTA

(Submitter supplied) The blood-stage infection of the malaria parasite, Plasmodium falciparum, exhibits a 48-hour developmental cycle that culminates in the synchronous release of parasites from red blood cells, triggering 48-hour fever cycles in the host. This cycle could be driven extrinsically by host circadian processes, or by a parasite-intrinsic oscillator. To distinguish between hypotheses, we examined the P. falciparum cycle in an in vitro culture system that lacks extrinsic cues from the host and show that P. more...

Organism:

Plasmodium falciparum

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL21078 GPL27825

91 Samples

Download data: TXT

(Submitter supplied) P. falciparum chromatin is highly structured at the three-dimensional (3D) level, and this structure provides an epigenetic mechanism for gene expression regulation. To investigate how parasite nuclear architecture is being maintained and regulated, we undertook complementary computational and experimental approaches to identify and characterize chromatin-associated proteins (CAPs) in P. falciparum.

Organism:

Plasmodium falciparum

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL21078

3 Samples

Download data: TDF