Available Data Sets 

 Please notify us when our data is utilized in publications (honey@uw.edu) and acknowledge the Systems Virology Center, NIAID Contract No. HHSN272200800060C when using these data.

Use the listing below and the associated links to access the following information for Systems Virology proteomics data sets. 

  1. Raw data files can be accessed through PRoteomics IDEntifications Database (PRIDE, see Note 1), the Pacific Northwest National Laboratory ´╗┐´╗┐Biological MS Data and Software Distribution website (PNNL, See Note 2) or by contacting the Systems Virology Center representative, Tom Metz (thomas.metz@pnnl.gov).  An FTP transfer can be arranged for large data sets.

  2. We have Agilent array data from many of these same samples; they can be found here.

Notes:

1. To find Systems Virology data on the PRIDE website type in "A Systems Biology Approach to Emerging Respiratory Viral Disease" in the Search box.

2.  Raw data from quantitative proteomics experiments can be accessed at the PNNL.  Once at the site, click on “Project Data” from the Additional Resources section on the left side of the page. Click on “Systems Virology Contract Data”. Data from each experiment is contained within its own folder (e.g. “ICL004: A/VN1203/04- and mock-infected Calu-3 cell time course”), and raw data will be within Experiment sub-folders.

Raw data files can be accessed by contacting Systems Virology Center representative, Tom Metz (thomas.metz@pnnl.gov).

A tutorial of the AMT Tag Proteomic Approach developed by PNNL can be found here.  Tools for use with this method (Decon2ls and VIPER) are available here. Decon2ls is used to deisotope high resolution MS data for subsequent matching to the AMT tag database. VIPER matches the Decon2ls output to the AMT tag database.



Proteomic Data Set Listing 

 

DATA SET NAMEDESCRIPTIONMODEL SYSTEMVIRUS(S)RAW DATA FILES

  PROCESSED

DATA 

PUBLICATIONS
Calu 3 cell AMT tag data
These data correspond to those peptide identifications used to create peptide accurate mass and time (AMT) tag databases for human lung endothelial cells (Calu-3). The AMT tag databases are then used for identifying peptides in high throughput quantitative analyses.
Calu-3 cells

SARS CoV

 A/VN1203/04

PRIDE http://www.ebi.ac.uk/pride/init.do

 NA 
Mouse AMT tag data
These data correspond to those peptide identifications used to create peptide accurate mass and time (AMT) tag databases for mouse lung homogenates.  The AMT tag databases are then used for identifying peptides in high throughput quantitative analyses.
C57BL/6 mice

MA15 SARS

 A/VN1203/04

 PRIDE http://www.ebi.ac.uk/pride/init.do NA 
ICL004
Time Points = 0, 3, 7, 12, 18, and 24 hrs post infection
N = 3 for infected and time match mock samples
MOI = 1
Calu-3 cells A/VN1203/04http://omics.pnl.gov/Normalized matrix and Significant peptide listJ Proteome Res 9(11):5748-56
ICL006
Time Points = 0, 3, 7, 12, 18, 24, 30, 36, and 48 hrs post infection 
N = 3 for infected and time match mock samples
MOI = 3.0
Calu-3 cellsA/CA04/09http://omics.pnl.gov/ Normalized matrix and Significant peptide list  PLoS One. 2013 Jul 25;8(7)
ICL010
Time Points mock-infected = 0, 3, 7, 12, 18, 24, 30, 36, and 48 hours post infection
Time Points A/California/04/2009 = 0, 12, 24, and 48 hours post infection
MOI = 3.0
Calu-3 cells A/Netherlands/602/09 A/California/04/2009  H1N1 http://omics.pnl.gov/Normalized matrix and Significant protein and peptide lists PLoS One. 2013 Jul 25;8(7)
ICL011
Time Points = 0, 3, 7, 12, 18, and 24 hrs post infection
N = 3 for infected and time match mock samples
Calu-3 cells PB2-627E and PB1-F2 del mutants of A/VN/1203/04 H5N1http://omics.pnl.gov/Normalized matrix and Significant peptide and protein list 
ICL012
Time Points = 0, 3, 7, 12, 18, and 24 hrs post infection
N = 3 for infected and time match mock samples
Calu-3 cells NS1trunc of A/VN/1203/04 H5N1http://omics.pnl.gov/Normalized matrix and Significant peptide and protein lists 
ECL002
Time Points = 0, 7, 12, 18, and 24 hrs post infection
N = 4 for infected and time matched mock samples
MOI = 5.0
Calu-3 cellsHCoV-EMChttp://omics.pnl.gov/ Normalized matrix and Significant peptide and protein lists 
SCL003
Time Points = 0, 3, 7, 12, 24, 30, 36, and 48 hrs post infection
N = 3 for infected and time match mock samples
Calu-3 cellsSARS CoVhttp://omics.pnl.gov/  Bioinformatics 27(20):2866-72
SCL005
Time Points = 0, 3, 7, 12, 24, 30, 36, 48, 54, 60, and 72 hrs post infection
N = 3 for infected and time match mock samples
Calu-3 2B4 cells  SARS CoV deltaORF6 SARS http://omics.pnl.gov/Normalized matrix and Significant peptide and protein listsPLoS One. 2013 Jul 25;8(7)
SCL006
Time Points = 0, 7, 12, 24, 30, 36, 48, 54, 60, and 72 hours post infection 
N = 3 for infected and time match mock samples 
MOI of 1.0
Calu-3 cells SARS CoV and
Bat SRBD
 http://omics.pnl.gov/Normalized matrix and Significant peptide and protein lists PLoS One. 2013 Jul 25;8(7)
SCL008
Time Points (Protein samples) = 0, 24, 48, and 72 hours post infection
N = 4 for infected and time match mock samples
MOI of 1 for icSARS ExoNI and MOI of 5 for wild type virus and icSARS-deltaNSP16
 Calu-3 2B4 cellsicSARS CoV, icSARS deltaNSP16 or icSARS ExoNI  http://omics.pnl.gov/ Normalized matrix and Significant peptide and protein lists 
SM001
Four Doses = 10^2, 10^3, 10^4, and 10^5 PFU
Time points of 1, 2, 4, and 7 days post infection
5 mice/dose/time point
3 mice/time point for time matched mocks 
C57BL/6 miceMA15 SARShttp://omics.pnl.gov/Normalized matrix and Significant peptide and protein listsMBio. 2013 Aug 6;4(4) 
CA04M001
20 week-old C57BL/6 mice
A/CA/04/2009 H1N1
Three Doses = 10^3, 10^4, 10^5, and 10^6 PFU 
Time points = 1, 2, 4, and 7 days post infection
3 - 4 mice/time point for infections
3 mice/time point for time matched mocks
C57BL/6 miceA/CA/04/2009 H1N1http://omics.pnl.gov/Normalized matrix and Significant peptide and protein lists BMC Systems Biology 2013, 7:69
IM001
Three Doses = 10^2, 10^3,  and 10^4 PFU 
Time points of 1, 2, 4, and 7 days post infection
5 mice/dose/time point
3 mice/time point for time matched mocks
C57BL/6 mice A/VN1203/04 http://omics.pnl.gov/Normalized matrix and Significant peptide list  BMC Systems Biology 2013, 7:69
IM004
Dosage = 10^4 PFU
Time points = 1, 2, 4, and 7 days post infection
5 mice/dose/time point
3 mice/time point for time matched mocks
C57BL/6 mice VN1203 HA avirulent  http://omics.pnl.gov/ Normalized matrix and Significant peptide list  
IM005
20 week old C57BL/6 mice
VN1203 PB2 627E
Dosage = 10^4 PFU
Time points = 1, 2, 4, and 7 days post infection
5 mice/time point for infections
3 mice/time point for time matched mocks
C57BL/6 mice PB2-627E: A/Vietnam/1203-CIP048_RG2/2004 (H5N1)http://omics.pnl.gov/Normalized matrix and Significant protein and peptide lists BMC Systems Biology 2013, 7:69
IM006A and B
20 week old C57BL/6 mice
VN1203 PB1-F2 Del
Three doses = 10^2, 10^3, and 10^4
Microarrays and proteomics only done on 10^3 (IM006A) and 10^4 (IM006B) PFU
Time points = 1, 2, 4, and 7 days post infection
5 mice/time point for infections
3 mice/time point for time matched mocks
 C57BL/6 miceVN1203 PB1-F2 Deletion http://omics.pnl.gov/Normalized matrix and significant protein and peptide lists BMC Systems Biology 2013, 7:69
IM007
20 week-old C57BL/6 mice
VN1203 NS1-trunc
Three doses = 10^2, 10^3, and 10^4 PFU
Time points = 1, 2, 4, and 7 days post infection
5 mice/time point for infections
3 mice/time point for time matched mocks
C57BL/6 mice 

NS1trunc124 mutation in the wild type

A/Vietnam/1203/2004 (H5N1) virus

 http://omics.pnl.gov/

Normalized matrix and Significant protein and peptide lists

 BMC Systems Biology 2013, 7:69