Project PXD007775

PRIDE Assigned Tags:
Biomedical Dataset

Summary

Title

Experiment 23: Macaca mulatta infected with Plasmodium cynomolgi B strain to produce and integrate clinical, hematological, parasitological, and omics measures of acute primary infection and relapses.

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.

Sample Processing Protocol

(1) Allow samples to gently thaw on ice. (2). Label two clean collection tubes and one C18 cartridge (Nest Group, MacroSpin Column – SMM SS18V) per sample. (3) Wash each cartridge with 450ul of 100% methanol. Spin tubes at 500g for 3 minutes and discard flowthrough. (4) Repeat steps 3 and 3a using the following solutions: a. 100% ACN, b. 80% ACN in 0.1% FA, c. 0.1% FA – three times. (5) Add 400ul of thawed sample peptides to their cartridge and disrupt C18 as needed to ensure binding. (6) Spin peptides at 500g for 3 minutes and reapply to cartridge once before discarding flowthrough into biohazardous waste. (7) Repeat steps 5-6 until all peptides have been applied to cartridge twice. (8) Wash cartridge with 450ul of 0.1% FA, spin at 500g for 3 minutes, and discard flowthrough. (9) Repeat step 8 three additional times. (10) Move each cartridge to its’ second collection tube. (11) Add 300ul of 80% ACN in 0.1% FA to cartridge to elute peptides. (11a) Spin tubes at 500g for 3 minutes and transfer peptides to final tube. (12) Repeat steps 11 and 11a once before concentrating peptides in speed vacuum. Refer to the SOP_Prot_MS_Step1.docx document for the protocol described in full detail. See the readme E23M99PRMmCyDaRC_Readme_XXXXXXX_pride.txt for further experimental details.

Data Processing Protocol

Prepare sequence databases according to the protocols described in SOP_Prot_DBCreation_Step2.docx and SOP_Prot_ProValT_DatabaseConfig_Step5.docx. Create Proteome Discoverer Workflow and Byonic Parameters File according to the protocol described in SOP_Prot_ProteinIDParams_Step3.docx. Perform identification of proteins using search engines according to the protocol described in SOP_Prot_ProteinID_Step4.docx. Perform proteome validation using ProValT according to the protocol described in SOP_Prot_ProteomeValidation_Step6.docx. Generate final report as described in SOP_Prot_ProteomeReportGeneration_Step7.docx. The software tools used: ProValT (v. PROVALT_3.1.05_08-31-16 or greater), Proteome Discoverer v2.1, Byonic v2.9, NuSep FASTA Manager 1.2.1. For the full data processing workflow, refer to UGA_Proteomics_Workflow_04-25-17.pptx and the beforementioned SOP files. See the readme E23M99PRMmCyDaRC_Readme_XXXXXXX_pride.txt for further experimental details.

Contact

Jessica Kissinger, Institute of Bioinformatics, University of Georgia
Mary R. Galinski, Emory University ( lab head )

Submission Date

11/03/2019

Publication Date

13/03/2019

Corresponding dataset(s) in other omics resources

http://plasmodb.org/plasmo/mahpic.jsp

Publication

Publication pending