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SRX1122152: GSM1833978: Day 10, Animal 76; Bos taurus; RNA-Seq
1 ILLUMINA (Illumina Genome Analyzer II) run: 6M spots, 436.6M bases, 258.1Mb downloads

Submitted by: Gene Expression Omnibus (GEO)
Study: Correlative gene expression to protective seroconversion in Rift Valley Fever vaccinates
show Abstracthide Abstract
Rift Valley Fever Virus (RVFV), a negative-stranded RNA virus, is the etiological agent of the vector-borne zoonotic disease, Rift Valley Fever (RVF). In both humans and livestock, protective immunity can be achieved through vaccination. Earlier and more recent vaccine trials in cattle and sheep demonstrated a strong neutralizing antibody and total IgG response induced by the RVFV vaccine, MP-12. From previous work, protective immunity in sheep and cattle vaccinates normally occurs from 7 to 21 days after inoculation with MP-12. While the serology and protective response induced by MP-12 has been studied, little attention has been paid to the underlying molecular and genetic events occurring prior to the serologic immune response. To address this, we isolated RNA from whole blood from vaccinates over a time course of 21 days before and after inoculation during a recent vaccine trial with MP-12. This RNA time course was deeply sequenced by RNASeq and bioinformatically analyzed. Our results revealed time-dependent activation or repression of numerous gene ontologies and pathways related to immune response and regulation. Additional analyses identified a correlative relationship between specific genes related to immune activity and protective immunity prior to serologic detection of antibody response. These data provide an important proof of concept for identifying molecular and genetic components underlying the immune response to vaccination and protection prior to serologic detection. Overall design: Experimental Animals: Healthy, 4 – 6 month old Bos taurus heifer and steer calves were used in the present study. The calves were seronegative to both bovine viral diarrhea and bovine leukemia virus by antigen capture enzyme-linked immunosorbent assay (ELISA) analyses done at the Texas Veterinary Medical Diagnostic Laboratory, College Station, Texas and had no detectable neutralizing antibodies to RVFV by PRNT80 at the time of vaccination. The animal experiments were performed under an Institutional Animal Care and Use Committee approved protocol #2010-192. Vaccines: The authentic recombinant MP-12 (MP12) is an attenuated RVFV vaccine prepared for use in humans by the U. S. Army Medical Research Institute of Infectious Diseases. Vaccines were propagated and prepared at University of Texas Medical Branch in Galveston, TX. Experimental Design: The calves were housed in an ABSL2 Ag biocontainment facility where they were randomized into test groups and acclimated to the facility for 14 days. Animals were inoculated either subcutaneously (s.c.) or intramuscularly (i.m.) with 1x105 PFU of MP-12 (3 animals in each group). Whole blood was collected prior to inoculation on Days 0 through 7, 10, 14, 21 and preserved for serum neutralization studies (PRNT) or total RNA purification for RNASeq analysis. Experimentally determined PRNT values were used to determine the “serologic response status” for animals “unvaccinated”, “vaccinated, not protected”, or “vaccinated, protected” with animals having a serum dilution ration of >1:80 being considered protected. Only RNA samples that met the minimum quality and quantity thresholds were used for the sequencing analysis. Rectal temperatures were recorded each time blood was collected and their health status was documented daily. At the end of the respective studies, the calves were euthanized with pentobarbital sodium (120 mg/kg i.v.). All calves were healthy and clinically normal at the termination of the respective studies. Morrill, John C., Richard C. Laughlin, Nandadeva Lokugamage, Jing Wu, Roberta Pugh, Pooja Kanani, L. Garry Adams, Shinji Makino, C. J. Peters. Immunogenicity of a Recombinant Rift Valley Fever MP-12 Vaccine Candidate in Calves. Vaccine. 2013. doi:10.1016/j.vaccine.2013.08.003. 238. Morrill, John C., Richard C. Laughlin, Nandadeva Lokugamage, Roberta Pugh, Elena Sbrana, William J. Weise, L. Garry Adams, Shinji Makino and C. J. Peters.. Safety and Immunogenicity of Recombinant Rift Valley Fever MP-12 Vaccine Candidates in Sheep. Vaccine 10.1016/j.vaccine.2012.10.118, 2012.
Sample: Day 10, Animal 76
SAMN03940539 • SRS1014761 • All experiments • All runs
Organism: Bos taurus
Library:
Instrument: Illumina Genome Analyzer II
Strategy: RNA-Seq
Source: TRANSCRIPTOMIC
Selection: cDNA
Layout: SINGLE
Construction protocol: Whole blood was collected at DAY 0–7, 10, 14 and 21 and immediately mixed at a 3:5 (blood:buffer) ratio with RNALater (Invitrogen). Samples were stored at –20°C until processing. To purify RNA, frozen samples were thawed at 37°C, centrifuged at 2000xG, and supernatant discarded. Remaining cell pellets were subjected to two rounds of treatment with Red Blood Cell Lysing Buffer per manufacturer’s instructions (Sigma). RNA from resulting cell pellet was initially extracted by Trizol (Invitrogen) followed by treatment with RNeasy Kit with on-column DNase digestion (Qiagen). Purified RNA was quantified by spectrophotometry on a NanoDrop (Thermo, USA) and by electrophoresis with a BioAnalyzer 2100 (Agilent, USA). Only samples with an RNA Integrity Number (RIN) greater than 8.0 were used for RNASeq analysis. All RNASeq sequencing was performed at the Texas A&M Genetics and Bioinformatics Center following manufacturer’s instructions. cDNA was generated from RNA samples of sufficient quantity and quality with Ovation RNA-Seq System (NuGen, USA), sheared by focused ultrasound (Covartis, USA) and made into barcoded (multiplexed) libraries with Encore Rapid Library System (NuGen, USA). Samples were quantified, diluted, pooled re-analyzed with a Bioanalyzer and loaded onto a Genome Analyzer II High-throughput sequencer (Illumina, USA).
Experiment attributes:
GEO Accession: GSM1833978
Links:
Runs: 1 run, 6M spots, 436.6M bases, 258.1Mb
Run# of Spots# of BasesSizePublished
SRR21315905,980,266436.6M258.1Mb2016-09-16

ID:
1636166

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