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 click on “Browse” on the left menu, then expand the “Browse by Public Projects” arrows.  Browse through list of public projects to “A Systems Biology Approach to Emerging Respiratory Viral Diseases”.

2.  Raw data from quantitative proteomics experiments can be accessed at the PNNL.  Once at the site, click on “Browse Available Data” from the Site Links on the left side of the page, and then select “By Publication”. Then scroll down to the “Systems Virology Contract Data” folder. 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.

 In order to access the raw data, you will need to register for an account here.

 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 dataThese 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.Calu3 cells

SARS CoV

 A/VN1203/04

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

 NA 
Mouse AMT tag dataThese 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.C57Bl6 mice

MA15 SARS

 A/VN1203/04

 
 PRIDE http://www.ebi.ac.uk/pride/init.do NA 
 ICL004Time Points = 0, 3, 7, 12, 18, and 24 hrs post infection, N=3 for infected and time match mock samples Calu-3 cells A/VN1203/04 http://omics.pnl.gov/Normalized matrix and Significant peptide list J Proteome Res 9(11):5748-56
ICL006Time Points = 0h, 3h, 7h, 12h, 18h, 24h, 30h, 36h and 48h post infection.  N=3 for infected and time match mock samplesCalu-3 cells A/CA04/09 http://omics.pnl.gov/ Normalized matrix and Significant peptide list  
SCL003Time Points = 0h, 3h, 7h, 12h, 24h, 30h, 36h and 48h post infection, N=3 for infected and time match mock samplesCalu-3 cellsSARS CoVhttp://omics.pnl.gov/  Bioinformatics 27(20):2866-72
  SCL005Time Points = 0h, 3h, 7h, 12h, 24h, 30h, 36h, 48h, 54h, 60h and 72 h 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 lists 
 SM001Four Doses = 100, 1000, 10000, & 100000 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 
 C57Bl6 mice MA15 SARS http://omics.pnl.gov/Normalized matrix and Significant peptide and protein lists  
  IM001Three Doses = 100, 1000, & 10000 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
 C57Bl6 mice A/VN1203/04 http://omics.pnl.gov/Normalized matrix and Significant peptide list  
IM004Dose = 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
C57Bl6 mice VN1203 HA avirulent  http://omics.pnl.gov/ Normalized matrix and Significant peptide list