Macaca mulatta
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA412382 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR6107700_1.fastq.gz | Fastqsanger.gz | |||
| SRR6107700_2.fastq.gz | Fastqsanger.gz | |||
| SRR6107710_1.fastq.gz | Fastqsanger.gz | |||
| SRR6107710_2.fastq.gz | Fastqsanger.gz | |||
| SRR6107720_1.fastq.gz | Fastqsanger.gz |
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Project description:Malaria-naive male rhesus macaques (Macaca mulatta), approximately four years of age, were inoculated intravenously with salivary gland sporozoites produced and isolated at the Centers for Disease Control and Prevention from multiple Anopheles species (An. dirus, An. gambiae, and An. stephensi) and then profiled for clinical, hematological, parasitological, immunological, functional genomic, lipidomic, proteomic, and metabolomic measurements. The experiment was designed for about 100 days, with pre- and post-100 day periods to prepare subjects and administer curative treatments respectively. During the 100-day period subjects experienced periods of patent and sub-patent infection. The anti-malarial drug artemether was subcuratively administered to subjects after the initial peak of infection, if subjects were not able to self-resolve. Blood-stage curative artemether was administered to all subjects following peak infection, and following a period of relapse infection. All peaks were clinically determined for each subject. The anti-malarial drugs primaquine and chloroquine were administered to all subjects at the end of the study for curative treatment of the liver and blood-stage infections, respectively. Capillary blood samples were collected daily for the measurement of CBCs, reticulocytes, and parasitemias. Capillary blood samples were collected every other day to obtain plasma for metabolomic analysis. Venous blood and bone marrow samples were collected at seven time points for functional genomic, proteomic, lipidomic, and immunological analyses. Within the MaHPIC, this project is known as ‘Experiment 23’. This is an iteration of Experiment 04 with the same parasite-host combination and sampling and treatment adjustments made, and this is the first in a series of experiments that includes subsequent homologous (Experiment 24, P. cynomolgi B strain) and heterologous (Experiment 25, P. cynomolgi strain ceylonensis) challenges of individuals from the Experiment 23 cohort. One subject was not included in subsequent experiments due to persistent behavioral issues that prevented sample collection. This dataset was produced by Lance Wells at University of Georgia. To access other publicly available results from 'E23' and other MaHPIC Experiments, including clinical results (specifics on drugs administered, diet, and veterinary interventions), and other omics, visit http://plasmodb.org/plasmo/mahpic.jsp . This page will be updated as datasets are released to the public. The experimental design and protocols for this study were approved by the Emory University Institutional Animal Care and Use Committee (IACUC). Refer to the E23 README file for further details of this dataset and its production.
2019-03-13 | PXD007775 | Pride
Project description:Malaria Host Pathogen Interaction Center Experiment 04R: Host and parasite gene transcript abundances, from whole blood, of Macaca mulatta infected Plasmodium cynomolgi treated with artemether over 7 time points in a 100 day study (GSE103507)
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Project description:Malaria Host Pathogen Interaction Center Experiment 04: Host and parasite gene transcript abundances, from whole blood, of Macaca mulatta infected Plasmodium cynomolgi treated with artemether over 7 time points in a 100 day study (GSE99486)
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Project description:MaHPIC Experimental Description: Malaria-naive male rhesus macaques (<i>Macaca mulatta</i>), approximately four years of age, were inoculated intravenously with salivary gland sporozoites produced and isolated at the Centers for Disease Control and Prevention from multiple Anopheles species (<i>An. dirus</i>, <i>An. gambiae</i>, and <i>An. stephensi</i>) and then profiled for clinical, hematological, parasitological, immunological, functional genomic, lipidomic, proteomic, and metabolomic measurements. The experiment was designed for about 100 days, with pre- and post-100 day periods to prepare subjects and administer curative treatments respectively. During the 100-day period subjects experienced periods of patent and sub- patent infection. The anti-malarial drug artemether was subcuratively administered to subjects after the initial peak of infection, if subjects were not able to self-resolve. Blood-stage curative artemether was administered to all subjects following peak infection, and following a period of relapse infection. All peaks were clinically determined for each subject. The anti-malarial drugs primaquine and chloroquine were administered to all subjects at the end of the study for curative treatment of the liver and blood-stage infections, respectively. Capillary blood samples were collected daily for the measurement of CBCs, reticulocytes, and parasitemias. Capillary blood samples were collected every other day to obtain plasma for metabolomic analysis. Venous blood and bone marrow samples were collected at seven time points for functional genomic, proteomic, lipidomic, and immunological analyses. Within the MaHPIC, this project is known as 'Experiment 23'. This is an iteration of Experiment 04 with the same parasite-host combination and sampling and treatment adjustments made, and this is the first in a series of experiments that includes subsequent homologous (Experiment 24, <i>P. cynomolgi</i> B strain) and heterologous (Experiment 25, <i>P. cynomolgi</i> strain ceylonensis) challenges of individuals from the Experiment 23 cohort. One subject was not included in subsequent experiments due to persistent behavioral issues that prevented sample collection. This dataset was produced by Dean Jones at Emory University. To access other publicly available results from E23 and other MaHPIC Experiments, including clinical results (specifics on drugs administered, diet, and veterinary interventions), and other omics, visit <a href='http://plasmodb.org/plasmo/mahpic.jsp' target='_blank'>http://plasmodb.org/plasmo/mahpic.jsp</a>. This page will be updated as datasets are released to the public. The experimental design and protocols for this study were approved by the Emory University Institutional Animal Care and Use Committee (IACUC).<br><br>Linked Studies: <a href='/metabolights/search?freeTextQuery=MaHPIC' target='_blank'><span class='label label-success'>Malaria Host-Pathogen Interaction Center (MaHPIC)</span></a>
2017-12-11 | MTBLS542 | MetaboLights
Project description:Malaria Host Pathogen Interaction Center Experiment 04: Host and parasite gene transcript abundances, from bone marrow aspirate, of Macaca mulatta infected Plasmodium cynomolgi treated with artemether over 7 time points in a 100 day study (GSE94273)
| PRJNA385819 | ENA
Project description:Malaria Host Pathogen Interaction Center Experiment 24: Host and parasite gene transcript abundances, from whole blood, of Macaca mulatta infected Plasmodium cynomolgi B strain treated with artemether over 3 time points in a 46 day study (GSE104101)
| PRJNA408250 | ENA
Project description:Malaria Host Pathogen Interaction Center Experiment 23R: Host and parasite gene transcript abundances, from whole blood, of Macaca mulatta infected Plasmodium cynomolgi B strain treated with artemether over 7 time points in a 100 day study (GSE104223)
| PRJNA412080 | ENA
Project description:MicroRNAs are small non-coding RNAs that are critical in post-transcriptional regulation. According to the latest miRBase (v22), there are 617 annotated pre-miRNAs in Macaca mulatta, which is much less than 1917 in human, although both of these two species are primates. To improve the annotation of miRNAs in Macaca mulatta, we generated 12 small RNA profiles from 8 tissues and perform comprehensive analysis of these profiles. We identified 613 conserved pre-miRNAs that have not been reported in Macaca mulatta and 25 novel miRNAs. Furthermore, we identified 996 editing sites with significant editing levels from 250 pre-miRNAs after analyzing the 12 self-generated and 58 additional published sRNA-seq profiles from different types of organs or tissues. Our results show that the distribution of different miRNA editing types in Macaca mulatta is different from that in human brains. Particularly, there are much more small indel events in miRNAs of Macaca mulatta than in human brains. These results significantly increase our understanding of miRNAs and their editing events in Macaca mulatta.
2019-08-27 | GSE124417 | GEO
Project description:[Original Title] Malaria Host Pathogen Interaction Center Experiment 03: Host and parasite gene transcript abundance measures from bone marrow for Macaca mulatta infected with Plasmodium coatneyi Hackeri strain from 7 time points over a 101 day study of acute, recrudescent, and chronic infections. This project is part of the Malaria Host-Pathogen Interaction Center (MaHPIC) - a transdisciplinary malaria systems biology research program initially supported by an NIH/NIAID contract (# HHSN272201200031C, 2012-2017; see http://www.systemsbiology.emory.edu). The MaHPIC continues with ongoing support from the Defense Advanced Research Project Agency (DARPA) and others. The MaHPIC generates many data types (e.g., clinical, hematological, parasitological, metabolomics, functional genomics, lipidomics, proteomics, immune response, telemetry) and mathematical models, to iteratively test and develop hypotheses related to the complex host-parasite dynamics in the course of malaria in non-human primates (NHPs), and metabolomics data via collaborations with investigators conducting clinical studies in malaria endemic countries, with the overarching goal of better understanding human disease, pathogenesis, and immunity. Curation and maintenance of all data and metadata are the responsibility of the MaHPIC: Mary Galinski mary.galinski@emory.edu (MaHPIC Program Director), Jessica Kissinger jkissinger@uga.edu (MaHPIC Co-Program Director), and Alberto Moreno alberto.moreno@emory.edu (MaHPIC Co-Program Director).
2017-08-24 | GSE103042 | GEO
Project description:Transposable elements (TE) account for more than 50% of human genome. It has been reported that some types of TEs are dynamically regulated in the reprogramming of human cell lines. However, it is largely unknown whether some TEs in Macaca mulatta are also regulated during the reprogramming of cell lines of monkey. Here, we systematically examined the transcriptional activities of TEs during the conversion of Macaca mulatta fibroblast cells to neuroepithelial stem cells (NESCs). Hundreds of TEs were dynamically regulated during the reprogramming of Macaca mulatta fibroblast cells. Furthermore, 60 Long Terminal Repeats (LTRs), as well as some integrase elements, of MacERV3 were transiently activated during the early stages of the conversion process. These LTRs were potentially bound by critical transcription factors for reprogramming, such as KLF4 and ETV5. These results suggest that the transcription of TEs are delicately regulated during the reprogramming of Macaca mulatta fibroblast cells. Although the family of ERVs activated during the reprogramming of fibroblast cells in Macaca mulatta are different from those in the reprogramming of human fibroblast cells, our results suggest that the activation of some ERVs is a conserved mechanism in primates for converting fibroblast cells to stem cells.
2020-12-31 | GSE137692 | GEO