P.falciparum 3D7 transcriptome-50
Ontology highlight
ABSTRACT:
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR006177_1.fastq.gz | Fastqsanger.gz | |||
| ERR006177_2.fastq.gz | Fastqsanger.gz | |||
| ERR006178_1.fastq.gz | Fastqsanger.gz | |||
| ERR006178_2.fastq.gz | Fastqsanger.gz | |||
| ERR006179_1.fastq.gz | Fastqsanger.gz |
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Project description:Investigation of whole genome gene expression level changes in Plasmodium falciparum 3D7 delta-PfPuf2 mutant, compared to the wild-type strain 3D7. The mutation engineered into this strain render tanslational control. The mutants analyzed in this study are further described in Miao J, Li J, Fan Q, Li X, Li X, Cui L.2010. The Puf-family RNA-binding protein PfPuf2 regulates sexual development and sex differentiation in the malaria parasite Plasmodium falciparum. J Cell Sci. 123(7):1039-49 (PMID 20197405). A 12 chip study using total RNA recovered from six separate wild-type cultures of Plasmodium falciparum 3D7 at gametocyte stage III (three cultures) and stage V (three cultures) and six separate cultures of dalta PfPuf2 mutant at gametocyte stage III (three cultures) and stage V (three cultures). Each chip measures the expression level of 5,367 genes from Plasmodium falciparum 3D7 with 45-60 mer probes with two replicates on final array of 71618 probes.
2012-07-05 | E-GEOD-39124 | biostudies-arrayexpress
Project description:Plasmodium falciparum blood stage parasites: control vs PfTRF-depleted parasites
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Project description:New insights into the blood-stage transcriptome of Plasmodium falciparum using RNA-Seq was published in 2010 (Otto et al. Molecular Microbiology 2010, April;67 (1), pp. 12-24). Here in collaboration with Manuel Llinas (Princetown University) we are utilising advances in RNA-Seq to gain further understanding of Plasmodium falciparum blood-stage transcription. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/
2013-03-05 | E-ERAD-86 | biostudies-arrayexpress
Project description:This experiment studies the effect of knocking out the transcriptional regulator SIR2 in 3D7 parasites. RNA was harvested from ring-stage parasites at 8 hours post-infection. Keywords = SIR2 Keywords = epigenetic regulation Keywords = antigenic variation Keywords = var Keywords = Plasmodium falciparum Keywords: other
2005-03-08 | GSE2369 | GEO
Project description:The parasite Plasmodium falciparum is responsible for severe malaria, which is still one of the major causes of death in developing countries. To provide a new RNA-seq reference dataset for its blood-stage transcriptome according to current guidelines and best practices, we performed a time course experiment with three independent biological replicates of synchronized P. falciparum 3D7 cells, that were cultivated at a haematocrit of 5% in human O+ erythrocytes. RNA-seq samples were taken at 8 developmental stages including young ring stage (8 hpi), late ring stage/early trophozoite (16 hpi), mid-age trophozoite (24 hpi), late trophozoite (32 hpi), early schizont (40 hpi), schizont (44 hpi), late schizont (48 hpi) and purified merozoites (0 hpi). Red blood cell pellets were lysed with Trizol and total RNA was purified using column-based purification (PureLink RNA Kit) including DNase treatment on the column and controlling for absence of genomic DNA contamination using qPCR. Whole blood total RNA samples were depleted of human globin mRNA using magnetic bead isolation technology (GLOBINclear kit). After RNA sample quality control and optimized cDNA libraries preparation for AT-biased genomes for Illumina sequencing, RNA-seq was performed at BGI Genomics (Shenzhen, China) on HiSeq 4000 to generate 100 bp paired-end sequencing reads.
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Project description:The asexual forms of the malaria parasite Plasmodium falciparum are uniquely adapted for chronic persistence in human red blood cells, continuously evading the immune system using an epigenetically regulated process. However, parasite survival on a population level also requires transmission of sexual parasite forms to subsequent human hosts. Here, we reveal that the essential nuclear gene, P. falciparum histone deacetylase 2 (PfHda2), silences specific subsets of genes involved in antigenic variation or conversion to sexual stages. Two parallel timecourses resulting in a total of 22 samples (11 wildtype, 11 PfHda2 knockdown) were hybridized against a Cy3-labeled reference pool of 3D7 mixed stage parasites on a two-color array.
2014-02-11 | E-GEOD-54806 | biostudies-arrayexpress
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
Project description:Calcium is a universal second messenger molecule which plays a significant role in several biological processes. Presence of calcium sensors (calmodulins) and calcium-dependent protein kinases in Plasmodium species suggests an important role of calcium-dependent signaling pathways in the regulation of cellular processes in the malaria parasites. Evidence for the transcriptional response of Plasmodium falciparum asexual blood stages to the well-known calcium ionophore A23187 has been presented here. P. falciparum 3D7 strain was cultured as described by Bozdech Z, Llinas M, Pulliam BL, Wong ED, Zhu J, DeRisi JL: The transcriptome of the intraerythrocytic developmental cycle of Plasmodium falciparum. PLoS Biol 2003, 1(1):E5. Calcium ionophore treatment was done as follows. Parasites at schizont stage were treated with 5 μM of calcium ionophore, A23187 for 30 minutes, 1 hour, 2 hours, 4 hours and 6 hours. Total RNA from each of the time points was isolated and aminoallyl-cDNA was synthesized using reverse transcriptase system (Fermentas). cDNA made from the treated parasites were labeled with Cy5 (GE-Amersham). A reference pool was made by mixing equal amount of cDNA from the parasites collected at 6 hours interval throughout the 48 hours life cycle and was labeled with Cy3 (GE-Amersham). The samples were then hybridized on a spotted cDNA chip platform comprising 10166 MOEs representing 5363 coding sequences as described in Hu G, Cabrera A, Kono M, Mok S, Chaal BK, Haase S, Engelberg K, Cheemadan S, Spielmann T, Preiser PR, Gilberger TW, Bozdech Z: Transcriptional profiling of growth perturbations of the human malaria parasite Plasmodium falciparum. Nat Biotechnol, 2009. 28(1): p. 91-8. The data was normalized and filtered with the condition, signal intensity>background intensity + 2 SD of background intensity) using NOMAD.
2012-07-14 | E-GEOD-33797 | biostudies-arrayexpress
Project description:Calcium is a universal second messenger molecule which plays a significant role in several biological processes. Presence of calcium sensors (calmodulins) and calcium-dependent protein kinases in Plasmodium species suggests an important role of calcium-dependent signaling pathways in the regulation of cellular processes in the malaria parasites. Evidence for the transcriptional response of Plasmodium falciparum asexual blood stages to the well-known calcium ionophore ionomycin has been presented here. P. falciparum 3D7 strain was cultured as described by Bozdech Z, Llinas M, Pulliam BL, Wong ED, Zhu J, DeRisi JL: The transcriptome of the intraerythrocytic developmental cycle of Plasmodium falciparum. PLoS Biol 2003, 1(1):E5. Calcium ionophore treatment was done as follows. Parasites at schizont stage were treated with 5 μM of calcium ionophore, ionomycin for 30 minutes, 1 hour, 2 hours, 4 hours and 6 hours. Total RNA from each of the time points was isolated and aminoallyl-cDNA was synthesized using reverse transcriptase system (Fermentas). cDNA made from the treated parasites were labeled with Cy5 (GE-Amersham). A reference pool was made by mixing equal amount of cDNA from the parasites collected at 6 hours interval throughout the 48 hours life cycle and was labeled with Cy3 (GE-Amersham). The samples were then hybridized on a spotted cDNA chip platform comprising 10166 MOEs representing 5363 coding sequences as described in Hu G, Cabrera A, Kono M, Mok S, Chaal BK, Haase S, Engelberg K, Cheemadan S, Spielmann T, Preiser PR, Gilberger TW, Bozdech Z: Transcriptional profiling of growth perturbations of the human malaria parasite Plasmodium falciparum. Nat Biotechnol, 2009. 28(1): p. 91-8. The data was normalized and filtered with the condition, signal intensity>background intensity + 2 SD of background intensity) using NOMAD.
2012-07-14 | E-GEOD-33796 | biostudies-arrayexpress
Project description:The asexual forms of the malaria parasite Plasmodium falciparum are uniquely adapted for chronic persistence in human red blood cells, continuously evading the immune system using an epigenetically regulated process. However, parasite survival on a population level also requires transmission of sexual parasite forms to subsequent human hosts. Here, we reveal that the essential nuclear gene, P. falciparum histone deacetylase 2 (PfHda2), silences specific subsets of genes involved in antigenic variation or conversion to sexual stages.
2014-02-11 | GSE54806 | GEO