GEO DataSets

(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) 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:

Expression profiling by array

Platform:

GPL26985

18 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) 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) 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 falciparum; Plasmodium knowlesi; Plasmodium vivax; Plasmodium berghei

Type:

Genome binding/occupancy profiling by high throughput sequencing

6 related Platforms

26 Samples

Download data: BEDGRAPH

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

Organism:

Plasmodium falciparum

Type:

Expression profiling by array; Genome variation profiling by array

Platforms:

GPL11248 GPL11250

135 Samples

Download data: GPR

(Submitter supplied) Study of chromatin changes of P. falciparum in response to changes in the levels of histone H4 acetylations especially H4K8ac using chromatin immunoprecipitation coupled to microarray chip (ChIP-on-chip)

Organism:

Plasmodium falciparum

Type:

Genome variation profiling by array

Platform:

GPL11250

39 Samples

Download data: GPR, TXT

(Submitter supplied) Transcriptional analaysis of P. falciparum in response to changes in the levels of histone H4 acetylations especially H4K8ac

Organism:

Plasmodium falciparum

Type:

Expression profiling by array

Platform:

GPL11248

96 Samples

Download data: GPR, TXT

(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

(Submitter supplied) We carried out RNA Immunoprecipitation followed by deep sequencing (RIP-seq) to explore the difference of direct target substrates of PfRrp6 and RNA exosome core

Organism:

Plasmodium falciparum

Type:

Other

Platform:

GPL26835

20 Samples

Download data: XLSX