P. vivax: proof-of-principle global transcription analysis from two wild isolates
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PROVIDER: PRJNA107065 | ENA |
REPOSITORIES: ENA
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Project description:The complete genome sequence of the P. vivax Sal-1 strain allowed the design of a first version array representing 1 oligo/2 kb of coding sequences (http://zblab.sbs.ntu.edu.sg/vivax/index.html). Here, proof-of-principle experiments using total RNA of parasites obtained from the Sal-1 strain, from P. falciparum and from parasites obtained directly from two human patients are presented. Keywords: expression profiles
2008-04-12 | GSE11075 | GEO
Project description:The complete genome sequence of the P. vivax Sal-1 strain allowed the design of a first version array representing 1 oligo/2 kb of coding sequences (http://zblab.sbs.ntu.edu.sg/vivax/index.html). Here, proof-of-principle experiments using total RNA of parasites obtained from the Sal-1 strain, from P. falciparum and from parasites obtained directly from two human patients are presented. To determine the extent of cross-hybridization of P. falciparum with P. vivax, and to determine overlaps in expression profiles of the P. vivax Sal1 monkey-adapted strain vs wild isolates, single dual hybridization analyses were performed.
2008-04-12 | E-GEOD-11075 | biostudies-arrayexpress
Project description:Pre-clinical proof of principle for orally delivered Th17 antagonist miniproteins
| PRJNA1096346 | ENA
Project description:Proof of principle and optimization experiment on cardioid with10X-based-iPS2-seq was performed on two batches of hPSC-derived cardioids at day 7.5 and pooled together after sample multiplexing. hPSC were primed and treated with Tetracycline 5 days prior cardiac differentiation. CG000388 Rev B (when multiplexing) User Guide was followed with sample multiplexing, provided information of the multiplexing for the cellranger aggr is provided. Sequencing has been performed on a Nextseq 1000 on a P2 Illumina kit 100 cycles. Sequencing run: Read1, 28 cycles; Index1, 10 cycles; Index2, 10 cycles, Read2, 90 cycles.
2025-10-27 | E-MTAB-14066 | biostudies-arrayexpress
Project description:Proof of principle for iPS2-10X-seq: timecourse experiment during 2D cardiac differentiation
| PRJEB75579 | ENA
Project description:Proof of principle for iPS2-10X-seq: cardioids experiment during 3D cardiac differentiation
| PRJEB75583 | ENA
Project description:Plasmodium vivax is the most geographically widespread human malaria parasite causing approximately 130-435 million infections annually. It is an economic burden in many parts of the world and poses a public health challenge along with the other Plasmodium sp. The biology of this parasite is very little understood. Emerging evidences of severe complications due to infections by this parasite provides an impetus to focus research on the same. Investigating this parasite directly from the infected patients is the most feasible way to study its biology and any pathogenic mechanisms which may exist. Gene expression studies of this parasite directly obtained from the patients has provided evidence of gene regulation resulting in varying amount of transcript levels in the different blood stages. However, the mechanisms regulating gene expression in malaria parasites are not well understood. Discovery of natural antisense transcripts (NATs) in P. falciparum has suggested that these might play an important role in regulating gene expression. We report here the genome-wide occurrence of NATs in P. vivax parasites from patients with differing clinical symptoms. A total of 1348 NATs against annotated gene loci have been detected using a custom designed strand specific microarray. Majority of NATs identified from this study shows positive correlation with the expression pattern of the sense transcript. Our data also shows condition specific expression patterns of varying S and AS transcript levels. Genes with AS transcripts enrich to various biological processes. This is the first report detailing the presence of NATs from clinical isolates of P. vivax. The data suggests differential regulation of gene expression in diverse clinical conditions and would lead to future detailed investigations of genome regulation.
2014-01-16 | GSE45165 | GEO
Project description:Plasmodium vivax is the most geographically widespread human malaria parasite causing approximately 130-435 million infections annually. It is an economic burden in many parts of the world and poses a public health challenge along with the other Plasmodium sp. The biology of this parasite is very little understood. Emerging evidences of severe complications due to infections by this parasite provides an impetus to focus research on the same. Investigating this parasite directly from the infected patients is the most feasible way to study its biology and any pathogenic mechanisms which may exist. Gene expression studies of this parasite directly obtained from the patients has provided evidence of gene regulation resulting in varying amount of transcript levels in the different blood stages. However, the mechanisms regulating gene expression in malaria parasites are not well understood. Discovery of natural antisense transcripts (NATs) in P. falciparum has suggested that these might play an important role in regulating gene expression. We report here the genome-wide occurrence of NATs in P. vivax parasites from patients with differing clinical symptoms. A total of 1348 NATs against annotated gene loci have been detected using a custom designed strand specific microarray. Majority of NATs identified from this study shows positive correlation with the expression pattern of the sense transcript. Our data also shows condition specific expression patterns of varying S and AS transcript levels. Genes with AS transcripts enrich to various biological processes. This is the first report detailing the presence of NATs from clinical isolates of P. vivax. The data suggests differential regulation of gene expression in diverse clinical conditions and would lead to future detailed investigations of genome regulation. Plasmodium vivax isolates were collected from patients (n = 8) with differing clinical conditions.The patients exhibited symptoms categorized as un-complicated (n =1) or complicated malaria (n = 7). Criteria for determination of complicated disease were based on World Health Organization year 2010 guidelines. Microarray array based transcriptional profiling was carried out to detect prevalence of natural antisense transcripts.
2014-01-16 | E-GEOD-45165 | biostudies-arrayexpress
Project description:Proof of principle and optimization experiment on 10X-based-iPS2-seq was performed in two experiments: The first explorative experiment (H001AS5) was performed on two batches of hPSC and hPSC-derived cardiomyocytes at day 23 and pooled together. hPSC were not treated with Tetracycline or primed for this experiment. Tetracycline has been administered throughout the differentiation. All batches were filtered and counted by a hemocytometer with trypan blue to assess vitality (all over 95% vital); then, they were pooled in the same tube before loading the 10X chip. hPSC and hPSC-derived cells were loaded on different days on separate 10X chips G as 16000 cells aiming as target cell recovery of 10000. The second exploratory experiment (H001AS7) is a time course from Day 0 to Day 12. Day 0 hPSC were primed and treated with Tetracycline 5 days prior library preparation. Then Day 2, Day 6 and Day 12 were treated with Tetracycline throughout and 5 day prior cardiac differentation. Sequencing has been performed for H001AS5 on a Illumina NextSeq 500 using two High Output Kits v2.5 (150 Cycles), for H001AS8 on a NextSeq 2000 on P3 Illumina kit 100 cycles. Sequencing run: Read1, 28 cycles; Index1, 10 cycles; Index2, 10 cycles, Read2, 90 cycles.
2025-10-27 | E-MTAB-14065 | biostudies-arrayexpress
Project description:This project contains RNA-sequencing reads of Plasmodium vivax derived directly from clinical patients. Here, we aim to characterize the gene expression patterns in patients with various parasite compositions. Patients (n=10) were recruited from two malaria endemic areas in Thailand. Ten RNA samples were treated with DNase, followed by Epicentre Globin-Zero Gold kit to deplete rRNA and globin transcript. The RNA-seq libraries were sequenced on an Illumina HiSeq4000 platform to generate approximately 60 million paired-end reads of 150 bp for each sample.
2019-06-30 | E-MTAB-6753 | biostudies-arrayexpress