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A Systems Biology Approach to Emerging Respiratory Viral Diseases

ABSTRACT: This submission corresponds to peptides identified from proteomics analysis of tryptic digests of lung homogenates from C57Bl/6 mice infected with avian influenza (A/VN/1203/04). Mice were infected at 10e2, 10e3, or 10e4 pfu (n = 5 each) and sacrificed at 1, 2, 4, and 7 d post-infection. Aliquots of lung proteins were combined to create two pools corresponding to early (1 and 2 d post-infection) and late (4 and 7 d post-infection) infection and each pool was then subjected to tryptic digestion, followed by strong-cation exchange fractionation, resulting in 24 fractions each. Capillary LC-MS/MS analysis was then performed on each fraction. This submission corresponds to proteomics data collected from capillary LC-MS/MS analysis of the early infection pool. The MS/MS datasets were searched with SEQUEST using no enzyme search rules, and the peptide identification results were filtered using the following cutoffs; XCorr >= 1.6, 2.4, or 3.2 for 1+, 2+, or 3+ for fully tryptic peptides, and >= 4.3 or 4.7 for 2+ or 3+ partially tryptic or non-tryptic protein terminal peptides. Additionally, to reduce the total data size to a reasonable level, each spectrum was filtered to only include the top 100 most abundant ions in each 100 m/z-wide window. This submission is the aggregation of 24 individual LC-MS/MS analyses into one pseudo dataset. More information can be found at the following web sites: https://www.systemsvirology.org/project/home/begin.view? http://omics.pnl.gov

INSTRUMENT(S): instrument model, LTQ

ORGANISM(S): Homo Sapiens (human) Mus Musculus (mouse)

TISSUE(S): Permanent Cell Line Cell, Calu-3 Cell

DISEASE(S): Severe Acute Respiratory Syndrome,Swine Influenza,Avian Influenza

SUBMITTER: Gordon Anderson

PROVIDER: PRD000594 | Pride | 2012-01-17

REPOSITORIES: Pride

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			Action	DRS
	PRIDE_Exp_Complete_Ac_19855.pride.mgf.gz	Mgf
	PRIDE_Exp_Complete_Ac_19855.pride.mztab.gz	Mztab
	PRIDE_Exp_Complete_Ac_19855.xml.gz	Xml
	PRIDE_Exp_Complete_Ac_19856.pride.mgf.gz	Mgf
	PRIDE_Exp_Complete_Ac_19856.pride.mztab.gz	Mztab

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Project description:We conducted a genome-wide survey of genes in Ae. aegypti females that are transcriptionally responsive upon challenge with dengue virus (serotype-2). The array was designed with 60-mer oligos specific to 16,092 gene transcripts of gene build AaegL1.1 (www. vectorbase.org). The hybridizations were performed at NimbleGen. We provided total RNA purified from the infected and control samples to NimbleGen. To identify dengue-specific transcription response (DTR) genes of MS and MR females upon infection with DENV2-JAM1409, a total of 15 independent samples (12 test samples and 3 control samples) were used for array hybridizations. These consisted of four DENV2 infected samples (MS-3hr, MR-3hr, MS-18hr and MR-18hr, post-infection, respectively) and a control sample that consisted of RNA isolated at the same time points following uninfected blood meals and pooled across strains and time of sampling. Three independent biological replicates were prepared for each of the above five samples were used for hybridizations. The Ae. aegypti genes responsive to dengue infection were identified in MOYO-S (MS) and MOYO-R (MR) females, upon challenging them with DENV serotype-2, by a genome-wide transcriptome analysis carried out using the NimbleGen oligonucleotide microarray format. We profiled gene expressions of Aedes aegypti mosquitoes, strain MOYO-S (MS, susceptible to dengue virus) and MOYO-R (MR, refractory to dengue virus) at 3 hr and 18 hr after infection with dengue virus (seroptype-2). The test samples were prepared in parallel to the control samples. The control samples were derived from females fed with normal blood that was not mixed with dengue (mock infection). The test samples were prepared from females that were fed with blood mixed with dengue virus (infectious meal). A total of 12 test samples were prepared that represented three biological replicates of dengue infected MS females at 3hr and 18 post-infection times; and MR females at 3hr and 18hr post-infection times. The test samples were compared to a common uninfected control that was prepared by pooling equal amount RNA of the individual control of both strains and both post-infection time points (MS at 3hr, MS at 18 hr, MR at 3hr and MR at 18hr). The control-pool strategy ensured us to identify genes that were responsive in response to dengue infection but not due to genetic differences between the two strains or developmental changes between the two post-infection time points. A total of 3 control pools were used in our array expression studies. Control-1 was prepared from RNA isolated from individual controls set up along with each of the test samples (MS at 3hr, MS at 18 hr, MR at 3hr and MR at 18hr) for the first biological replication. Similarly, control-2 was prepared from individual controls set up along with each of the test samples (MS at 3hr, MS at 18 hr, MR at 3hr and MR at 18hr) for the second biological replication. And control-3 was prepared from individual controls set up along with each of the test samples (MS at 3hr, MS at 18 hr, MR at 3hr and MR at 18hr) for the third biological replication. Thus, the three control pools represented three biological replicates corresponding to the three biological replicates of the test samples.

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A Systems Biology Approach to Emerging Respiratory Viral Diseases

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