Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Gene knockdown in malaria parasites via non-canonical RNAi

ABSTRACT: To introduce a non-canonical RNA interference pathway into Plasmodium berghei (P. berghei), we generated a P. berghei line constitutively expressing the human protein Argonaute 2 (Ago2) and episomally expressed Ago2-dependent short hairpin RNAs (AgoshRNAs) against GFP. Using RNA sequencing (RNA-Seq), we analyzed transcriptomes of wild type parasites (PbGFPcon), Ago2-expressing parasites (PbAgo2) and PbAgo2 parasites expressing a scrambled AgoshRNA (scr) or anti-GFP-AgoshRNA (aGFP). We compared PbAgo2 to wildtype PbGFPcon parasites and find that Ago2 expression interferes with the expression of development-of-zygote-inhibited (DOZI)-dependent transcripts. When comparing PbAgo2 plus scr with PbAgo2 expressing aGFP, we find a clear knockdown of GFP; Other than that, we do not observe a significant off-targeting in these samples besides differential expression of genes belonging to multi-gene families.

ORGANISM(S): Plasmodium berghei

PROVIDER: GSE95534 | GEO | 2019/02/22

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Transcription activated by AP2-Z in early zygote plays an essential role in Plasmodium ookinete development [ChIP-seq]

Project description:To investigate the genome-wide binding sites of early zygote AP2-family transcription factor, AP2-Z in Plasmodium berghei, the chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) analyses were performed. Parasites expressing GFP-fused AP2-Z (AP2-Z::GFP) were harvested at 6 hours post starting ookinete culture (hpoc) and subjected to ChIP-seq experiments using anti-GFP antibody. Binding sites of AP2-Z were determined from the sequence data.

2022-08-05 | GSE198070 | GEO

Global gene expression of the rodent malaria parasites Plasmodium yoelii, Plasmodium berghei and Plasmodium chabaudi blood-stage parasites

Project description:The purpose of this research is to identify and evaluate the global gene expression of the rodent malaria parasites Plasmodium yoelii, Plasmodium berghei and Plasmodium chabaudi blood-stage parasites and specifically compare the blood stage gene expression profiles of samples derived from previous studies on Plasmodium falciparum, Plasmodium vivax and Plasmodium knowlesi

2016-04-08 | GSE80015 | GEO

Comparison of gene expression between wild type and AP2-L KO parasites

Project description:In the rodent malaria parasite Plasmodium berghei, we found that an AP2 family transcription factor designated AP2-L plays a critical role in the development of the liver stage. Using DNA microarray analysis we showed that the expression of several genes, including those of parasitophorous vacuole membrane proteins, was significantly decreased in the early liver stage of AP2-L-depleted parasites. Gene expression of P. berghei liver stages was compared between wild type and AP2-L KO parasites. Liver stage parasites were cultured for 24h using HepG2 cells. Ten and seven biologically independent experiments were performed for wild type and AP2-L KO parasites, respectively.

2012-04-30 | E-GEOD-34877 | biostudies-arrayexpress

RNA Microarray of 36H liver stages of Pb WT and Pb SSPELD Knock out parasites

Project description:Global gene expression profiling of P. berghei liver stages at 36h from WT and Pb SSPELD KO parasites to investigate the changes in RNA expression levels in Pb SSPELD parasites.

2016-09-01 | GSE72399 | GEO

Comparison of gene expression between wild type and AP2-G KO parasites.

Project description:In the rodent malaria parasite Plasmodium berghei, we found that an AP2 family transcription factor designated AP2-L plays a critical role in the development of the liver stage. Using DNA microarray analysis we showed that the expression of several genes, including those of parasitophorous vacuole membrane proteins, was significantly decreased in the early liver stage of AP2-L-depleted parasites. Gene expression of P. berghei sporozoites was compared between wild type and AP2-G KO parasites. Five biologically independent experiments were performed for each genotype.

2012-04-30 | E-GEOD-34806 | biostudies-arrayexpress

Chromatin remodeling events associated with gARID are essential for gametocyte development in Plasmodium [ChIP-seq]

Project description:To investigate the genome-wide binding sites of gARID in gametocytes of Plasmodium berghei, the chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) analyses were performed. Parasites expressing GFP-fused gARID were harvested after treating the infected mice with sulfadiazine and subjected to ChIP-seq experiments using anti-GFP antibody. Binding sites of gARID were determined from the sequence data.

2023-06-30 | GSE235409 | GEO

PbAP2-FG2 and AP2R-2 function together as a transcriptional repressor complex essential for Plasmodium female development [ChIP-seq]

Project description:To investigate the genome-wide binding sites of the transcriptional regulators, PbAP2-FG2 and AP2R-2 in female gametocytes of Plasmodium berghei, the chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) analyses were performed. Parasites expressing GFP-fused PbAP2-FG2 (PbAP2-FG2::GFP) or GFP-fused AP2R-2 (AP2R-2::GFP) were harvested after treating the infected mice with sulfadiazine and subjected to ChIP-seq experiments using anti-GFP antibody. Binding sites of PbAP2-FG2 and AP2R-2 were determined from the sequence data.

2023-02-02 | GSE213775 | GEO

RNA-seq of liver stage-derived parasites from wild-type and TCRδ-/- mice

Project description:P. berghei ANKA parasites were collected from the blood at 74h after infection of wild-type and TCRδ-/- mice with 2x10^4 sporozoites (samples were pooled from 3 mice/ group) and mRNA was sequenced by RNA-seq.

2019-04-11 | E-MTAB-6493 | biostudies-arrayexpress

Transcriptome changes during inducible gametocytogenesis in Plasmodium berghei parasites

Project description:During the malaria infection, Plasmodium parasites invade the host’s red blood cells where they can differentiate into two different life forms. The majority will replicate asexually and infect new erythrocytes. A small percentage, however, will transform into gametocytes – a specialized sexual stage able to survive and develop when taken up by Anopheles mosquito. As the gametocytes ensure the parasite’s transmission to a new host, their generation is an attractive target for new antimalarial interventions. The molecular mechanisms controlling gametocytogenesis, however, remain largely unknown due to the technical challenges: the early gametocytes are morphologically indistinguishable from asexual parasites and present in very low numbers during the infection. Recently, AP2-G - a transcription factor from an apicomplexa-specific apiAP2 family – was described as indispensable for gametocyte commitment in both human malaria parasite Plasmodium falciparum and rodent malaria model Plasmodium berghei. Therefore, we have decided to test whether the overexpression of this factor alone could increase gametocyte production and enable the investigation of uncharacterised, earliest stages of gametocyte development. To this end, we have engineered PBGAMi - a Plasmodium berghei line, in which all parasites were ap2-g deficient by default but able to overexpress it when induced with rapamycin. While the control parasites (PBGAMi R-), as expected, differentiated into asexual forms (schizonts) only, almost all rapamycin-treated parasites (PBGAMi R+) transformed into gametocytes. We used the generated line to perform RNA-seq analysis of the R- and R+ populations at different time points of their development and identify the changes arising between them, mapping the sequence of events leading to the formation of gametocytes.

2018-06-30 | GSE110201 | GEO

Plasmodium falciparum blood stage parasites: control vs PfTRF-depleted parasites

Project description:Transcriptional profiling of transgenic Plasmodium falciparum blood stage parasites expressing the telomere repeat-binding factor PfTRF as a C-terminal GFP-DD fusion (3D7/TRFGFP-ON). The DD (FKBP destabilisation domain) allows for the conditional depletion of fusion proteins in absence of the stabilising ligand Shield-1 (Banaszynski LA, Chen LC, Maynard-Smith LA, Ooi AG, Wandless TJ. A rapid, reversible, and tunable method to regulate protein function in living cells using synthetic small molecules.Cell. 2006 Sep 8;126(5):995-1004). The goal of this experiment was to identify genes differentially expressed in response to PfTRF depletion.

2016-07-14 | GSE84342 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data