Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Screening of differentially expressed genes in three Plasmodium falciparum parasite lines [RNA-seq]

ABSTRACT: Screening of differentially expressed genes in three Plasmodium falciparum parasite lines [RNA-seq]

PROVIDER: PRJNA592366 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR10555668_1.fastq.gz	Fastqsanger.gz
	SRR10555668_2.fastq.gz	Fastqsanger.gz
	SRR10555669_1.fastq.gz	Fastqsanger.gz
	SRR10555669_2.fastq.gz	Fastqsanger.gz
	SRR10555670_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 6

Similar Datasets

Screening of differentially expressed genes in three Plasmodium falciparum parasite lines

Project description:Screening of differentially expressed genes in three Plasmodium falciparum parasite lines

| PRJNA595386 | ENA

Screening of differentially expressed genes in three Plasmodium falciparum parasite lines [expression]

Project description:Screening of differentially expressed genes in three Plasmodium falciparum parasite lines [expression]

| PRJNA593289 | ENA

Time course transcriptome of Plasmodium falciparum parasite of 3D7 strain

Project description:The time course transcriptome were generated in Plasmodium falciparum parasite of 3D7 strain by collecting RNA samples every 2 hours during 48 hours of the full intraerythrocytic developmental cycle.

2020-10-20 | GSE149865 | GEO

Screening of differentially expressed genes in three Plasmodium falciparum parasite lines [RNA-seq]

Project description:We performed RNA-Seq analysis with synchronized 0-6h ring stage parasites of three P.falciparum lines within their third life cycle, to study the change of expression profiling when knocking down PfSWIB. The comparison analysis on screening of differentially expressed genes was done in parasite lines including 3D7(wild type: blank control), PfSWIB (wild type: self-control) and PfSWIB∆ (PfSWIB knockdown). Approximately 10.8% of the transcripts showed up-regulation between the PfSWIB-KD and two WT parasite, whereas 11.9% showed down-regulation (Fold change>1.5, P<0.05). Hierarchical clustering of differentially expressed genes uncovered several transcription factors such as PfApiAP2 family and PfSir2B, as well as certain histone modification enzymes, which proved to be involved in regulating on var gene transcription. We further screened out a number of var genes which exhibited differential expression among different lines, and performed qPCR on 44 diﬀerentially expressed vars in the PfSWIB vs PfSWIB∆ comparison group based on the RNA-seq results, to study the transcription patterns of upsA-, upsB- and upsC-subtype var genes. We found that most upsA- and upsC- type vars were significant down-regulated in PfSWIB∆ line. In contrast, the expression pattern of partial upsB vars presented a distinct change in PfSWIB∆ line. The RNA-seq and qPCR analysis provide a better understanding of the mechanism and function of PfSWIB on regulating the expression switching and clonal variation of var gene family contributing to the pathogenesis in malaria parasites.

2020-02-18 | GSE141155 | GEO

Discovery of telomere repeat-binding factor in the malaria parasite Plasmodium falciparum

Project description:ChIP-seq experiments were performed for the putative telomere repeat-binding factor (PfTRF) in the malaria parasite Plasmodium falciparum strain 3D7. The gene encoding this factor (PF3D7_1209300) was endogenously tagged with either a GFP- or a 3xHA-tag and these transgenic parasite lines were used in ChIP-sequencing experiments. Sequencing of the ChIP and input libraries showed enrichment of PfTRF at all telomere-repeat containing chromosome ends (reference genome Plasmodium falciparum 3D7 from PlasmoDB version 6.1) as well as in all upsB var promoters.In addition,PfTRF was enriched at seven additional, intra-chromosomal sites and called in the PfTRF-HA ChIP-seq only. Plasmodium falciparum 3D7 parasites were generated with -GFP or -3xHA C-terminal tagged TRF (PF3D7_1209300). Nuclei were isolated from formaldehyde cross-linked schizont-stage transgenic parasites and used to prepare chromatin. Chromatin immunoprecipitations were performed using mouse anti-GFP (Roche Diagnostics, #11814460001) or rat anti-HA 3F10 (Roche Diagnostics, #12158167001). Sequencing libraries were prepared according to a Plasmodium-optimized library preparation procedure including KAPA polymerase-mediated PCR amplification.

2016-07-15 | E-GEOD-76537 | biostudies-arrayexpress

High resolution time course transcriptome of Plasmodium falciparum parasite 3D7 strain by RNA-seq

Project description:The time course transcriptome of Plasmodium falciparum 3D7 parasite strain was generated by collecting RNA samples every 2 hours during full Intraerythrocytic Developmental Cycle.

2020-10-20 | GSE150484 | GEO

Discovery of Telomere Repeat-binding Zinc finger protein in the malaria parasite Plasmodium falciparum

Project description:ChIP-seq experiments were performed for the putative Telomere Repeat-binding Zinc finger protein (PfTRZ) in the malaria parasite Plasmodium falciparum strain 3D7. The gene encoding this factor (PF3D7_1209300) was endogenously tagged with either a GFP- or a 3xHA-tag and these transgenic parasite lines were used in ChIP-sequencing experiments. Sequencing of the ChIP and input libraries showed enrichment of PfTRZ at all telomere-repeat containing chromosome ends (reference genome Plasmodium falciparum 3D7 from PlasmoDB version 6.1) as well as in all upsB var promoters.In addition,PfTRZ was enriched at seven additional, intra-chromosomal sites and called in the PfTRZ-HA ChIP-seq only.

2016-07-15 | GSE76537 | GEO

Screening of differentially expressed genes in three Plasmodium falciparum parasite lines

Project description:This SuperSeries is composed of the SubSeries listed below.

2020-02-18 | GSE141959 | GEO

Identification of antimalarial compounds that inhibit Apicomplexan AP2 transcription factor proteins in the human malaria parasite Plasmodium falciparum

Project description:Transcription time course of Plasmodium falciparum parasite asexual blood stage progression in the presence of antimalarial drug CID5750730 (Compound C)

2022-05-13 | GSE202876 | GEO