GEO DataSets

(Submitter supplied) Histone variants are key components of the epigenetic code and evolved to perform specific functions in transcriptional regulation, DNA repair, chromosome segregation and other fundamental processes. H2B.Z is a rare, apicomplexan-specific variant of histone H2B. Here we show that in Plasmodium falciparum H2B.Z localises to euchromatic intergenic regions throughout intraerythrocytic development and together with H2A.Z forms a double-variant nucleosomes subtype. more...

Organism:

Plasmodium falciparum 3D7

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL15857

6 Samples

Download data: GFF

(Submitter supplied) This experiment highlights the extreme sequence bias generated by standard PCR amplication of sequencing libraries and decribes an adapted T7-polymerase based amplification method, which results in non-baised, representative libraries for Illumina sequencing

Organism:

Plasmodium falciparum 3D7

Type:

Other

Platform:

GPL10866

4 Samples

Download data: BED, GFF

(Submitter supplied) This experiment characterizes the localisation of H2A.Z, H3K9ac and H3K4me3 in the epigenome of the human malaria parasite, P. falciparum at 4 different stages of intraerythrocytic development.

Organism:

Plasmodium falciparum 3D7

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL10866

17 Samples

Download data: BED, GFF

(Submitter supplied) This experiment characterizes the transcriptome of the human malaria parasite, P. falciparum at 8 different stages of the intraerythrocytic cycle

Organism:

Plasmodium falciparum 3D7

Type:

Expression profiling by high throughput sequencing

Platform:

GPL10866

8 Samples

Download data: GFF, TXT

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

Organism:

Plasmodium falciparum 3D7

Type:

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

Platform:

GPL10866

29 Samples

Download data: BED, GFF, TXT

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

Organism:

Plasmodium falciparum

Type:

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

Platform:

GPL26835

36 Samples

Download data: BW

(Submitter supplied) Chromatin structure is a basal epigenetic mechanism that determines cellular fate by organizing the dynamic gene expression during the cell development and proliferation. The nuclear members of the evolutionarily conserved actin-related protein (ARPs) superfamily are major components of nucleosome remodelingcomplexes in the nucleus. In the human malaria parasites, Plasmodium falciparum, comparative genome analysis reveals that two canonical actins and three orthologues of ARPs including PfArp1, PfArp4, and PfArp6 are encoded in the genome of this parasite. more...

Organism:

Plasmodium falciparum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26835

18 Samples

Download data: TXT

(Submitter supplied) Chromatin structure is a basal epigenetic mechanism that determines cellular fate by organizing the dynamic gene expression during the cell development and proliferation. The nuclear members of the evolutionarily conserved actin-related protein (ARPs) superfamily are major components of nucleosome remodelingcomplexes in the nucleus. In the human malaria parasites, Plasmodium falciparum, comparative genome analysis reveals that two canonical actins and three orthologues of ARPs including PfArp1, PfArp4, and PfArp6 are encoded in the genome of this parasite. more...

Organism:

Plasmodium falciparum

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL26835

4 Samples

Download data: BW

(Submitter supplied) Chromatin structure is a basal epigenetic mechanism that determines cellular fate by organizing the dynamic gene expression during the cell development and proliferation. The nuclear members of the evolutionarily conserved actin-related protein (ARPs) superfamily are major components of nucleosome remodelingcomplexes in the nucleus. In the human malaria parasites, Plasmodium falciparum, comparative genome analysis reveals that two canonical actins and three orthologues of ARPs including PfArp1, PfArp4, and PfArp6 are encoded in the genome of this parasite. more...

Organism:

Plasmodium falciparum

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL26835

4 Samples

Download data: BW

(Submitter supplied) Chromatin structure is a basal epigenetic mechanism that determines cellular fate by organizing the dynamic gene expression during the cell development and proliferation. The nuclear members of the evolutionarily conserved actin-related protein (ARPs) superfamily are major components of nucleosome remodeling complexes in the nucleus. In the human malaria parasites, Plasmodium falciparum, comparative genome analysis reveals that two canonical actins and three orthologues of ARPs including PfArp1, PfArp4, and PfArp6 are encoded in the genome of this parasite. more...

Organism:

Plasmodium falciparum

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL26835

10 Samples

Download data: BW

(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) Background: Epigenetic modifications of histones and regulation of chromatin structure have been implicated in regulation of virulence gene families in P. falciparum. To better understand chromatin-mediated gene regulation, we used a high-density oligonucleotide microarray to map the position and enrichment of nucleosomes across the entire genome of P. falciparum at three time points of the intra-erythrocytic developmental cycle (IDC) in vitro. more...

Organism:

Plasmodium falciparum

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL9610

6 Samples

Download data: CEL, TXT

(Submitter supplied) Chromatin is composed of DNA wrapped around nucleosomes, complexes consisting of highly basic proteins called histones. Histone variants are non-canonical variants of histones that have specific functions. The Apicomplexan parasite Toxoplasma gondii possesses conserved histone variants CenH3, H3.3, H2A.Z, H2A.X, as well as the parasite-specific H2B variant, H2BV (or H2B.Z). We surveyed the genome-wide distribution of T. more...

Organism:

Toxoplasma gondii RH

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL24058

23 Samples

Download data: BED, BROADPEAK, BW, NARROWPEAK

(Submitter supplied) Chromatin is composed of DNA wrapped around nucleosomes, complexes consisting of highly basic proteins called histones. Histone variants are non-canonical variants of histones that have specific functions. The Apicomplexan parasite Toxoplasma gondii possesses conserved histone variants CenH3, H3.3, H2A.Z, H2A.X, as well as the parasite-specific H2B variant, H2BV (or H2B.Z). We surveyed the genome-wide distribution of T. more...

Organism:

Toxoplasma gondii RH; Toxoplasma gondii ME49

Type:

Genome binding/occupancy profiling by genome tiling array

Platforms:

GPL15564 GPL15563

10 Samples

Download data: GFF, PAIR, TXT

(Submitter supplied) During red-blood-cell-stage infection of Plasmodium falciparum, the parasite undergoes repeated rounds of replication, egress, and invasion. Erythrocyte invasion involves specific interactions between host cell receptors and parasite ligands and coordinated expression of genes specific to this step of the life cycle. We show that a parasite-specific bromodomain protein, PfBDP1, binds to chromatin at transcriptional start sites of invasion-related genes and directly controls their expression. more...

Organism:

Plasmodium falciparum

Type:

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

Platform:

GPL21078

22 Samples

Download data: TXT, XLS

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

Organism:

Plasmodium falciparum; Plasmodium falciparum 3D7

Type:

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

Platforms:

GPL11248 GPL21078

66 Samples

Download data: GPR

(Submitter supplied) Erythrocyte invasion is an essential step in the life cycle of the malaria parasite Plasmodium falciparum that involves specific interactions between host cell receptors and parasite ligands. How the parasite regulates the expression of invasion-related genes is to date largely unknown. Here we show that a novel, parasite-specific bromodomain protein (PfBDP1) binds to chromatin at the transcriptional start site of invasion-related genes and directly controls their expression. more...

Organism:

Plasmodium falciparum 3D7; Plasmodium falciparum

Type:

Expression profiling by array

Platform:

GPL11248

8 Samples

Download data: GPR

(Submitter supplied) To study the bromodomain protein PfBDP1 in the malaria parasite P. falciparum, a transgenic parasite line was generated (PfBDP1DD) in which PfBDP1 was tagged with a haemagglutinin tag and a ligand regulatable FKBP destabilization domain that allowed conditional knockdown of PfBDP1 by removal of the stabilizing ligand Shld1 from cultures. Shld1 was removed 30 hours post invasion (hpi) and the cells allowed to reinvade fresh red blood cells. more...

Organism:

Plasmodium falciparum; Plasmodium falciparum 3D7

Type:

Expression profiling by array

Platform:

GPL11248

36 Samples

Download data: GPR

(Submitter supplied) Histone variant H2A.Z-containing nucleosomes are incorporated at most eukaryotic promoters. This incorporation is mediated by the conserved SWR1 complex, which replaces histone H2A in canonical nucleosomes with H2A.Z in an ATP-dependent manner. Here, we show that promoter-proximal nucleosomes are highly heterogeneous for H2A.Z in Saccharomyces cerevisiae, with substantial representation of nucleosomes containing one, two, or no H2A.Z molecules. more...

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL11034

5 Samples

Download data: TXT

(Submitter supplied) Investigation of genome-wide gene expression changes in Plasmodium falciparum overexpressing PfMYST compared to the wild-type strain 3D7. After introducing a single copy of the full-length PfMYST expression cassette into the parasite genome, parasites showed higher levels of H4-K5, -K8, and -K12 acetylation, a faster progression of intraerythrocytic developmental cycle (IDC), and shorter schizont development time (duration), which led to significantly fewer merozoites developed in mature schizonts than the control. more...

Organism:

Plasmodium falciparum; Plasmodium falciparum 3D7

Type:

Expression profiling by array

Platform:

GPL15768

12 Samples

Download data: PAIR, TXT