GEO DataSets

(Submitter supplied) Serine/arginine-rich protein kinases (SRPK) are cell cycle-regulated serine/threonine protein kinases and are important regulators of splicing factors. In this study, we functionally characterize SRPK1 of the human malaria parasite Plasmodium falciparum (Pf). PfSRPK1 was expressed in asexual blood stages and sexual stage gametocytes. Pfsrpk1¯ parasites formed asexual schizonts that generated far fewer merozoites when compared to wildtype parasites, causing reduced replication rates. more...

Organism:

Plasmodium falciparum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16607

6 Samples

Download data: CSV, TXT

(Submitter supplied) Current transcriptomic methods for mapping 5′-ends of eukaryotic RNA employ only 5′-end enriched samples. The absence of a matched unenriched control limits the ability to distinguish genuine 5′ ends from incomplete cDNAs. We developed a transcriptomic method based on sequencing of cDNA enriched for full-length fragments and an unenriched control. From the mapped sequence reads, enrichment scores are calculated for all transcribed nucleotides and a statistical model of the enrichment constructed. more...

Organism:

Plasmodium falciparum

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL16607 GPL19269

24 Samples

Download data: TXT

(Submitter supplied) The malaria parasite has a complex lifecycle, including several events of differentiation and stage progression, while actively evading immunity in both its mosquito and human hosts. Important parasite gene expression and regulation during these events remain hidden in rare populations of cells. Here, we combine a capillary-based platform for cell isolation with single-cell RNA-sequencing to transcriptionally profile 165 single infected red blood cells (sc.iRBCs) during the intra- erythrocyte developmental cycle (IDC). more...

Organism:

Plasmodium falciparum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16607

208 Samples

Download data: TXT

(Submitter supplied) Background: Human malaria is a major cause of disease and poverty in developing countries being P. falciparum the most deadly of malaria parasites. To successfully develop and adapt within hosts, P. falciparum undergoes drastic switches in chromatin structure and gene expression, but the identity and function of regulatory elements driving these events remain poorly understood. In this work, we performed genome-wide profiling of chromatin accessibility in two culture-adapted subclones and four developmental stages during the intraerythrocytic development by the Assay for Transposase-Accessible Chromatin by sequencing (ATAC-seq). more...

Organism:

Plasmodium falciparum

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL16607

17 Samples

Download data: BED, BEDGRAPH, TXT

(Submitter supplied) P. falciparum H4K8ac ChIP-seq

Organism:

Plasmodium falciparum

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL16607 GPL19269

8 Samples

Download data: TXT

(Submitter supplied) ChIP-seq experiments were performed to profile PfH3.3 (PF3D7_0617900) in the malaria parasite Plasmodium falciparum. Sequencing of ChIP samples showed enrichment of PfH3.3 at GC-rich coding sequences and subtelomeric repetitive regions throughout the intraerythrocytic life cycle and additionally in intergenic regions during trophozoite stages. Also the promoter and the coding sequence of the active and poised var2CSA gene were marked (reference genome Plasmodium falciparum 3D7 from PlasmoDB version 6.1)

Organism:

Plasmodium falciparum

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL16607

12 Samples

Download data: BEDGRAPH

(Submitter supplied) P. falciparum undergoes antigenic variation during its life cycle in the human host. To accomplish this, the malaria parasite has developed mechanisms that ensure the expression of a single member of the var gene family to produce one of the PfEMP1 variant proteins. Here we carry out RNA-seq and ChIP-seq analyses of histone modifications to explore transcriptional and epigenomic changes taking place between the transmissible stages of the parasite i.e. more...

Organism:

Plasmodium falciparum

Type:

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

Platform:

GPL16607

21 Samples

Download data: TXT, WIG

(Submitter supplied) Sexual differentiation of malaria parasites into gametocytes in the vertebrate host and subsequent gamete fertilisation in mosquitoes is essential for the spreading of the disease. The molecular processes orchestrating these transitions are far from fully understood. Here we report the first transcriptome analysis of male and female Plasmodium falciparum gametocytes coupled with a comprehensive proteome analysis. more...

Organism:

Plasmodium falciparum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16607

3 Samples

Download data: BEDGRAPH, TSV

(Submitter supplied) The lack of a comprehensive map of transcription start sites (TSS) across P. falciparum genome has hampered advances in decrypting the molecular mechanisms underlying regulation of gene expression in the malaria parasite. In eukaryotic model organisms, development of genome-wide approaches and next-generation sequencing technologies has contributed to a better understanding of the impact of local nucleotide composition on transcriptional regulation. more...

Organism:

Plasmodium falciparum

Type:

Other

Platform:

GPL16607

12 Samples

Download data: BEDGRAPH

(Submitter supplied) In eukaryotes, the chromatin architecture has a pivotal role in regulating all DNA-related processes. For P. falciparum, the causative agent of human malaria, the nucleosome landscape of the extremely AT-rich intergenic regulatory regions is largely unexplored. With the aid of a highly controlled MNase-seq procedure we reveal how positioning of nucleosomes provides a structural and regulatory framework to the transcriptional unit. more...

Organism:

Plasmodium falciparum

Type:

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

Platform:

GPL16607

20 Samples

Download data: BEDGRAPH, GFF, TSV

(Submitter supplied) The human malaria parasite Plasmodium falciparum has a complex and multi-stage life cycle that requires extensive immune escape, invasion of human liver and blood cells, and transmission through the female Anopholes mosquito. To date, the regulatory elements orchestrating these critical parasite processes remain largely unknown. However, there is mounting evidence across a broad range of species that intergenic long non-coding RNA (lncRNA) and antisense RNA can regulate chromatin state and gene expression. more...

Organism:

Plasmodium falciparum

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL16607

15 Samples

Download data: TXT, XLSX

(Submitter supplied) The description of the transcriptome and proteome datasets of Plasmodium falciparum, the deadliest strain of human malaria, has been a tremendous resource for the understanding of the molecular physiology of this parasite. However, the underlying translational control that links global measurements of steady-state mRNA with protein levels is not well understood. Our work bridges this disconnect by measuring translation on a whole genome scale using ribosome profiling, providing the first measurements of new protein synthesis through the asexual blood phase developmental cycle.

Organism:

Plasmodium falciparum

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL16607

10 Samples

Download data: BED, TXT, WIG