GEO DataSets

(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 NF54; Plasmodium falciparum

Type:

Expression profiling by array

Platform:

GPL26985

24 Samples

Download data: TXT, XLSX

(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) 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) 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:

Expression profiling by array

Platform:

GPL26985

18 Samples

Download data: TXT

(Submitter supplied) Heterochromatin is a tightly packaged form of DNA that leads to permanent or temporal gene silencing. In P. falciparum heterochromatin is formed after trimethylation of lysine 9 on histone H3 and consequent binding of heterochromatin protein 1 (HP1). Genome-wide profiling studies established that in P. falciparum blood stage schizonts heterochromatin is formed at subtelomeres and some intra-chromosomal islands. more...

Organism:

Plasmodium chabaudi; Plasmodium yoelii; Plasmodium berghei; Plasmodium vivax; Plasmodium falciparum; Plasmodium knowlesi

Type:

Genome binding/occupancy profiling by high throughput sequencing

6 related Platforms

26 Samples

Download data: BEDGRAPH

(Submitter supplied) Background: The cytoadherence of Plasmodium falciparum is thought to be mediated by variant surface antigens (VSA), encoded by var, rif, stevor and pfmc-2tm genes. The last three families have rarely been studied in the context of cytoadherence. As most VSA genes are unique, the variability among sequences has impeded the functional study of VSA across different P. falciparum strains. However, many P. more...

Organism:

Plasmodium falciparum

Type:

Expression profiling by array

Platform:

GPL11250

12 Samples

Download data: GPR

(Submitter supplied) The malaria parasite Plasmodium falciparum relies on clonally variant gene expression in order to escape immune recognition and secure continuous proliferation during blood stage infection. Here, we studied the role of heterochromatin protein 1 (HP1), an evolutionary conserved regulator of heritable gene silencing, in the biology of P. falciparum blood stage parasites. We demonstrate that conditional PfHP1 depletion de-represses hundreds of heterochromatic virulence genes and disrupts the elusive mechanism underlying mutually exclusive expression and antigenic variation of PfEMP1. more...

Organism:

Plasmodium falciparum; Plasmodium falciparum 3D7

Type:

Expression profiling by array

Platform:

GPL11248

22 Samples

Download data: GPR

(Submitter supplied) In temperate and sub-tropical regions of Latin America, complicated malaria manifested as hepatic dysfunction or renal dysfunction is seen in all age groups. There has been a concerted focus on understanding the patho-physiological and molecular basis of complicated malaria in children, much less is known about it in adults. This can be attributed to many factors: one of which is the expression of clonally variant families of adhesion proteins: PfEMP1 on the iRBC surface. more...

Organism:

Plasmodium falciparum

Type:

Expression profiling by array

Platform:

GPL18192

12 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) Quantitative studies of the P. falciparum transcriptome have shown that the tightly controlled progression of the parasite through the intraerythrocytic developmental cycle (IDC) is accompanied by a continuous gene expression cascade where most expressed genes exhibit a single transcriptional peak. Since proteins represent the decisive business end of gene expression, understanding the correlation between mRNA and protein levels is crucial for inferring biological activity from transcriptional gene expression data. more...

Organism:

Plasmodium falciparum

Type:

Expression profiling by array

Platform:

GPL10991

24 Samples

Download data: GPR

(Submitter supplied) The P. falciparum genome is equipped with several subtelomeric gene families that are implicated in parasite virulence and immune evasion. The members of these gene families are uniformly positioned within heterochromatic domains of the genome and are thus subject to variegated expression. The best-studied example is that of the var gene family encoding the major parasite virulence factor P. falciparum erythrocyte membrane protein 1 (PfEMP1). more...

Organism:

Plasmodium falciparum

Type:

Expression profiling by array

Platform:

GPL11248

36 Samples

Download data: GPR

(Submitter supplied) The diversity of human immune responses to P. falciparum is unknown and yet immune decision-making likely dictates outcome of infection We infected 15 malaria-naïve human volunteers with P. falciparum and used longitudinal whole blood transcriptional profiling to independently analyse the immune response in every volunteer

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL17586

120 Samples

Download data: CEL

(Submitter supplied) The three-dimensional (3D) genome structure of human malaria parasite Plasmodium falciparum is highly organized and plays important roles in regulating coordinated expression patterns of specific genes such as virulence genes which are involved in antigenic variation and immune escape. However, the molecular mechanisms that control 3D genome of the parasite remain elusive. Here by analyzing genome organization in P. more...

Organism:

Plasmodium falciparum 3D7

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL31231

4 Samples

Download data: BW

(Submitter supplied) The three-dimensional (3D) genome structure of human malaria parasite Plasmodium falciparum is highly organized and plays important roles in regulating coordinated expression patterns of specific genes such as virulence genes which are involved in antigenic variation and immune escape. However, the molecular mechanisms that control 3D genome of the parasite remain elusive. Here by analyzing genome organization in P. more...

Organism:

Plasmodium falciparum 3D7

Type:

Other

Platform:

GPL29863

4 Samples

Download data: MATRIX

(Submitter supplied) Transient regulation of Plasmodium numbers below the density that induces fever has been observed in chronic malaria infections in humans and this species transcending control cannot be explained by immunity alone. Using an in vitro system we have observed density dependent regulation of malaria parasitemia as a mechanism to possibly explain these in vivo observations. P. falciparum blood stages from a high but not low-density environment exhibited what appeared to be programmed changes during the late trophozoite and schizont stages of the intraerythrocytic cycle.

Organism:

Plasmodium falciparum; Anopheles gambiae

Type:

Expression profiling by array

Platform:

GPL1321

9 Samples

Download data: CEL, CSV

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

Organism:

Plasmodium falciparum

Type:

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

Platforms:

GPL26835 GPL26836

111 Samples

Download data: BW, HIC

(Submitter supplied) We performed Hi-C assay to address the interaction of central var genes in ruf6-var pairs，subtelomeric upsA-subtype var genes and other HP1-associated genes

Organism:

Plasmodium falciparum

Type:

Other

Platform:

GPL26835

2 Samples

Download data: HIC

(Submitter supplied) We adopted the technique of Chromatin Isolate by RNA Purification combined with high-throughput sequencing (ChIRP-seq) to gain mechanistic insight into the transcriptionally regulatory role of the trans-acting RUF6 ncRNA in detail

Organism:

Plasmodium falciparum

Type:

Other

Platforms:

GPL26835 GPL26836

9 Samples

Download data: BW

(Submitter supplied) We carried out chromatin immunoprecipitation followed by deep sequencing (ChIP-seq) to explore the difference of the genome-wide dynamics of histone modifications and HP1 in PfRrp6-DD-1C line.

Organism:

Plasmodium falciparum

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL26835

23 Samples

Download data: BW