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Sample GSM2789840 Query DataSets for GSM2789840
Status Public on Sep 26, 2017
Title 2605688_TimePoint3_Whole Blood
Sample type SRA
 
Source name Whole Blood
Organisms Macaca mulatta; Plasmodium cynomolgi strain B
Characteristics time point: 3
gender: Male
non human primate individual id: ROh14
infected with: Plasmodium cynomolgi strain B
Treatment protocol The experiment included, 1 pre-inoculation day, 35 experiment days, and 10 post-experiment days. Pre- and post-experiment days were used to prepare subjects and administer post-experiment curative treatments respectively. 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.
Growth protocol Animals approved for use were moved into experimental housing 10 days prior to the start of the experiment.
Extracted molecule total RNA
Extraction protocol Whole blood (3 ml) was collected in Tempus tubes (Applied Biosystems) that also preserve mRNA; these samples include erythrocytes, platelets and granulocytes in addition to mononuclear lymphocytes. RNA was extracted using Tempus-Spin RNA isolation kits. The quality of all RNA samples was confirmed using a Bioanalyzer, with an RNA Integrity Number (RIN) greater than 8 recorded for all samples.
Approximately 1 μg of total RNA per sample was converted to double-stranded cDNA using poly-A beads to enrich for mRNA, and Illumina TruSeq Stranded mRNA Sample Prep kits to generate strand-specific libraries. As a quality control, 92 spike-in RNAs of known concentration and GC proportions (ERCC Spike-In Control, Life Technologies) were added to constitute approximately 1% of the total RNA for each library. Adapters were ligated to facilitate multiplexed sequencing on an Illumina HiSeq3000 at the Yerkes Genomics Core, aiming for 50 million paired-end 100 base pair (bp) reads per library.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 3000
 
Data processing Bases were called with Illumina RTA (Real-Time Analysis, v2.7.7) with default parameters. Illumina bcl2fastq v2.17.1.14 was used for demultiplexing. FASTQC (v0.10.1) was used to assess data quality, but the data were not filtered at this stage.
Reads were mapped to a composite reference assembly consisting of host, parasite, and ERCC control references with STAR (v2.5.2b) with default alignment parameters. Note all values for ERCC abundances will be zero as no spike ins were included in sequenced samples. See readme for details.
Abundance estimation of raw read counts per transcript was done internally with STAR using the algorithm of htseq-count.
Genome_build: RNA-Seq reads were mapped to both a host and parasite genome. Host: An early version of a new  assembly (as of 5/2014) of the rhesus macaque (MacaM assembly, v4.0, created by Aleksey Zimin at the University of Maryland, Rob Norgren at the University of Nebraska Medical Center and their colleagues. The MacaM assembly has been deposited in GenBank under BioProject accession PRJNA214746. Parasite: Plasmodium cynomolgi B strain genome assembly was used. The assembly has been deposited in GenBank under the BioProject accession PRJNA187987.
Supplementary_files_format_and_content: Excel files contain raw counts at the gene level, for each individual. Raw counts are further classified by experimental Time Point (1-3), and Specimen Type (Whole Blood).
Supplementary_files_format_and_content: Host and Parasite Raw Read Counts Column headers are defined as follows: 'Gene ID': Identifiers of all Genes in the annotation. 'Gene Symbol': Symbols of all Genes in the annotation. 'Raw File List / Sample Identifier / Abundances': Samples were sequenced across multiple lanes, some samples were sequenced at extra depth, all fastq files are listed for each sample. Raw read counts of all genes, from the raw files listed in the column header. The raw file names and sample identifer both contain information regarding Specimen Type, NHP ID, and Time Point. Notes: There are 15 columns representing 5 animals for Time Points T01, T01B, and T03. There is an read count entry per sample for every gene that appears in the annotation. For genes where there was no detection of expression by reads that mapped to their loci, the raw count is 0."
 
Submission date Sep 21, 2017
Last update date May 15, 2019
Contact name Mary Galinski
Organization name Emory University
Department Vaccine Center at Yerkes
Lab Galinski Lab
Street address 954 Gatewood Road
City Atlanta
State/province GA
ZIP/Postal code 30329
Country USA
 
Platform ID GPL25691
Series (2)
GSE94274 An Integrated Approach to Understanding Host-Pathogen Interactions
GSE104101 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.
Relations
BioSample SAMN07682372
SRA SRX3203812

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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