Plasmodium falciparum CNV-SNP chip optimization
Ontology highlight
ABSTRACT:
ORGANISM(S): Plasmodium falciparum
PROVIDER: GSE28287 | GEO | 2011/04/01
SECONDARY ACCESSION(S): PRJNA139367
REPOSITORIES: GEO
Similar Datasets
Project description:Optimize SNP genotyping probes and demonstrate a new P. falciparum microarray platform that includes CGH and resequencing probes on the same chip 3D7 common reference; lab samples: HB3, Dd2, SC05, 7C126; field patient samples: M1176, M1069, M1094, M1321, M1064, M1111
2011-04-01 | E-GEOD-28287 | biostudies-arrayexpress
Project description:A custom resequencing array for analysis of field isolates of plasmdium falciparum was created. Test of DNA with genotypes known at all loci genotyped by the microarray as well as test of accuracy correlation with amounts of DNA added to each array
2014-03-28 | GSE56305 | GEO
Project description:A custom resequencing array for analysis of field isolates of plasmdium falciparum was created. Test of DNA with genotypes known at all loci genotyped by the microarray as well as test of accuracy correlation with amounts of DNA added to each array Comparison of test DNA from lab and clinical isolates between genotyped generated by next-generation sequencing and this new custom DNA microarray.
2014-03-28 | E-GEOD-56305 | biostudies-arrayexpress
Project description:Plasmodium falciparum drug resistance genotyping in Uganda 2018-2019
| PRJNA655702 | ENA
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:Background: The cytoadherence of Plasmodium falciparum is thought to be mediated by variant surface antigens (VSA), encoded by var, rif, stevor and pfmc-2tm genes. The last three families have rarely been studied in the context of cytoadherence. As most VSA genes are unique, the variability among sequences has impeded the functional study of VSA across different P. falciparum strains. However, many P. falciparum genomes have recently been sequenced, allowing the development of specific microarray probes to each VSA gene. Methods: All VSA sequences from the HB3, Dd2 and IT/FCR3 genomes were extracted using HMMer. Oligonucleotide probes were designed with OligoRankPick and added to the 3D7-based microarray chip. As a proof of concept, IT/R29 parasites were selected for and against rosette formation and the transcriptomes of isogenic rosetting and non-rosetting parasites were compared by microarray. Results: From each parasite strain 50-56 var genes, 125-132 rif genes, 26-33 stevor genes and 3-8 pfmc-2tm genes were identified. The ability of the VSA-supplemented microarray chip to detect cytoadherence-related genes was assessed using P. falciparum clone IT/R29, in which rosetting is known to be mediated by PfEMP1 encoded by ITvar9. Whole transcriptome analysis showed that the most highly upregulated gene in rosetting parasites was ITvar9 (19 to 429-fold upregulated over six time points). Only one rif gene (IT4rifA_042) was upregulated by more than 4-fold (5-fold at 12 hours post-invasion), and no stevor or pfmc-2tm genes were upregulated by more than 2-fold. 49 non-VSA genes were upregulated in rosetting parasites by more than 3-fold in at least two time-points, although none as markedly as ITvar9. Conclusions: We demonstrate that the VSA of newly sequenced P. falciparum strains can be added to the 3D7-based microarray chip, allowing the analysis of the entire transcriptome of multiple strains. For the rosetting clone IT/R29, the striking transcriptional upregulation of ITvar9 was confirmed, and the data did not support the involvement of other VSA families in rosette formation.
2011-07-01 | GSE28990 | GEO
Project description:PSAC drug selection resequencing in Plasmodium falciparum
| PRJNA237619 | ENA
Project description:Plasmodium falciparum custom resequencing array testing and validation
| PRJNA242877 | ENA
Project description:Transcriptomic Analysis of Cultured Sporozoites of P. falciparum
2013-12-03 | GSE52867 | GEO
Project description:Transcriptomic Analysis of Cultured Sporozoites of P. falciparum RNA-seq reads from each of three developmental stages (2 replicates per sample) were mapped to the reference Plasmodium falciparum genome, and gene expression levels were calculated for each sample.
2013-12-03 | E-GEOD-52867 | biostudies-arrayexpress