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| Status |
Public on Sep 01, 2017 |
| Title |
2231891_TimePoint4_WholeBlood |
| Sample type |
SRA |
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| Source name |
Whole blood
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| Organisms |
Macaca mulatta; Plasmodium coatneyi |
| Characteristics |
tissue: Whole blood
time point: 4
gender: Male
mahpic non human primate individual id: RZe13
parasite strain: P. coatneyi strain Hackeri
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| Treatment protocol |
The NHPs were given sub-curative treatment with Artemether during the experiment. After the 101-day experimental period, NHPs were treated with blood-stage curative doses of Artemether.
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| Growth protocol |
Animals approved for use were moved into experimental housing 10 days prior to the start of the experiment.
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| 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 3-plex sequencing on an Illumina HiSeq2000 at the Yerkes Genomics Core, aiming for 80 million paired-end 100 base pair (bp) reads per library.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 1000 |
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| Description |
Note that raw counts are provided for the parasite processed files. Normalized abundance measurements are provided for the host processed files.
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| 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.
Abundance estimation of raw read counts per transcript was done internally with STAR using the algorithm of htseq-count.
Normalized expression (normalized read counts) was performed with DESeq2 (v1.10.1)
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 accession PRJNA214746. Parasite: Plasmodium coatneyi strain Hackeri genome assembly was used. The assembly has been deposited in GenBank under the accession PRJNA329102.
Supplementary_files_format_and_content: Excel files contain normalized transcript abundances at the gene level, for each individual. Abundances are further classified by experimental Time Point (1-7), and Specimen Type (Whole Blood). Gene expression normalization is performed using the gene level expression files withby using the DESeq2 standard library size normalization method (estimateSizeFactors) with default parameters. See standard operating procedures provided in supplementary files for details. Note that raw counts are also provided as supplementary files.
Supplementary_files_format_and_content: Host DESeq2Normalized 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 1 / Raw File 2 / Sample Identifier / Abundances': DESeq2 normalized 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 35 columns representing 5 animals for Time Points T01-T07 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.
Supplementary_files_format_and_content: Host 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 1 / Raw File 2 / Sample Identifier / Abundances': 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 35 columns representing 5 animals for Time Points T01-T07 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.
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| Submission date |
Aug 29, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Mary Galinski |
| Organization name |
Emory University
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| Department |
Vaccine Center at Yerkes
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| Lab |
Galinski Lab
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| Street address |
954 Gatewood Road
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| City |
Atlanta |
| State/province |
GA |
| ZIP/Postal code |
30329 |
| Country |
USA |
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| Platform ID |
GPL25689 |
| Series (2) |
| GSE94274 |
An Integrated Approach to Understanding Host-Pathogen Interactions |
| GSE103259 |
Malaria Host Pathogen Interaction Center Experiment 03: Host and parasite gene transcript abundance measures from whole blood for Macaca mulatta infected with Plasmodium coatneyi Hackeri strain from 7 time points over a 101 day study |
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| Relations |
| BioSample |
SAMN07573147 |
| SRA |
SRX3146247 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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