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 to access the following information for Systems Virology Agilent microarray data sets.

  1. Raw data files and the normalized data matrix can be accessed through Gene Expression Omnibus (GEO).  The GEO accession number is provided.
  2. Lists of differentially expressed (DE) genes are available below.  These data and associated metadata can be accessed through Influenza Research Database (IRD) or Virus Pathogen Resource (ViPR).
  3. Metadata for some data sets can be accessed by clicking on the name of the data set in the listing.
  4. Proteomic data sets from many of the same samples can be found on our Proteomic Data page.

ViPR and IRD have additional tools for analysis and visualization of these data.



Microarray Data Set Listing 

 

DATA SET NAMEDESCRIPTIONMODEL SYSTEMVIRUS(S)RAW DATA FILESPROCESSED DATA SETSPUBLICATIONS
ICL002

 Pilot Time course = 0, 1.5, 3, 7, 12 and 24 hrs post infection, N=2 for infected and N =1 for time match mock samples.  MOI=1

Calu-3 cells A/VN1203/04

GEO Accession

GSE33142

NAPMC3229612
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 cellsA/VN1203/04GEO Accession GSE28166 DE gene list

 J Virol. 85(21):10955-67

BMC Syst Biol. 5:190

ICL006Time Points = 0, 3, 7, 12, 18, 24, 30, 36 and 48 hrs post infection. N=3 for infected and time match mock samples. MOI of 3.0
Calu-3 cells A/CA/04/09 H1N1GEO Accession GSE37571DE gene list  
ICL010

 A/Netherlands/602/09 and mock-infected -  0, 3, 7, 12, 18, 24, 30, 36 and 48 hours p. i.  A/California/04/2009 -  0, 12, 24, and 48 hours p. i.  MOI of 3.0

Calu-3 cells

 A/Netherlands/602/09 A/California/04/2009

 

GEO Accession GSE37571  

  
 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 cells SARS CoV and delta ORF6 SARSGEO Accession  GSE33267 DE gene list 
SCL006Time Points = 0, 7, 12, 24, 30, 36, 48, 54, 60 and 72 hrs post infection, N=3 for infected and time match mock samples.  MOI of 1.0Calu-3 cells SARS CoV and
Bat SRBD
GEO Accession GSE37827  DE gene list  
  SM00120 week-old C57black6 mice
mouse adapted strain of SARS-CoV, MA15.
Four Doses = 100, 1000, 10000, & 100000 (PFU) 
Time points of 1, 2, 4 and 7 days.
5 mice/time point for infections
3 mice/time point for time matched mocks
  C57Bl6 mice MA15 SARSGEO Accession GSE33266 DE gene list 
  IM00120 week-old C57black6 mice
A/VN1203/04
Three Doses = 100, 1000, & 10000 (PFU)  
Time points of 1, 2, 4 and 7 days.
5 mice/time point for infections
3 mice/time point for time matched mocks
 C57Bl6 miceA/VN1203/04GEO Accession GSE33263
 DE gene list BMC Syst Biol. 5:190
IM004
20 week-old C57black6 mice
VN1203 HA avirulent mutant virus
Three Doses = 10E3, 10E4, 10E5 PFU (ARRAYS WERE ONLY DONE ON 10E4 PFU)
Time points of 1, 2, 4 and 7 days.
5 mice/time point for infections
3 mice/timepoint for time matched mocks
C57Bl6 mice 

VN1203 HA avirulent mutant

[A/Vietnam/1203-CIP048_RG1/2004(H5N1)]

GEO Accession GSE37572 DE gene list  
CA04M001
20 week-old C57black6 mice
A/CA/04/2009 H1N1
Three Doses = 10E3, 10E4, 10E5 and 10E6 PFU
Time points of 1, 2, 4 and 7 days.
3-4mice/time point for infections
3 mice/timepoint for time matched mocks
C57Bl6 mice A/CA/04/2009 H1N1 

GEO Accession GSE37569 

DE gene list