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
ECL001
Time Points = 0, 3, 7, 12, 18, and 24 hrs post infection
N = 3 for infected and time matched mock samples
MOI of 5.0
Calu-3 cells  HCoV-EMC (MERS CoV) GEO Accession GSE45042DE gene listMBio. 2013 Apr30; 4(3) 
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 of 1.0
Calu-3 cells A/VN1203/04

GEO Accession GSE33142

NA

BMC Systems Biol. 2011;5:190

ICL004
Time Points = 0, 3, 7, 12, 18, and 24 hrs post infection
N = 3 for infected and time match mock samples
MOI of 1.0
Calu-3 cellsA/VN1203/04GEO Accession GSE28166DE gene list

 J Virol. 85(21):10955-67

BMC Systems Biol. 2011;5:190

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 of 3.0
Calu-3 cells A/CA/04/09 H1N1GEO Accession GSE37571DE gene list PLoS One. 2013 Jul 25;8(7) 
ICL010
A/Netherlands/602/09 and mock-infected
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 of 3.0
Calu-3 cells

 A/Netherlands/602/09 A/California/04/2009  H1N1

GEO Accession GSE40844

  PLoS One. 2013 Jul 25;8(7)
ICL011
Time Points = 0, 3, 7, 12, 18, and 24 hours post infection
N = 3 for infected and time match mock samples
 Calu-3 cellsPB2-627E and PB1-F2 del mutants of A/VN/1203/04 H5N1 GEO Accession GSE43203 DE gene list 
ICL012
Time Points = 0, 3, 7, 12, 18, and 24 hours post infection
N = 3 for infected and time match mock samples
 Calu-3 cellsNS1trunc of A/VN/1203/04 H5N1 GEO Accession GSE43204DE gene list 
SCL005
Time Points = 0, 3, 7, 12, 24, 30, 36, 48, 54, 60, and 72 hours post infection
N = 3 for infected and time match mock samples
MOI of 5.0
 Calu-3 cells SARS CoV and delta ORF6 SARSGEO Accession  GSE33267DE gene list

 PLoS One. 2013 Jul 25;8(7)

J Virol. 2013 Apr;87(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
GEO Accession GSE37827DE gene list 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 ExoNIGEO Accession GSE48142 DE gene list 
SM001
20 week-old C57BL/6 mice
mouse adapted strain of SARS-CoV, MA15
Four Doses = 10^2, 10^3, 10^4, and 10^5 (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 MA15 SARSGEO Accession GSE33266DE gene list 
SM003
20 week-old C57BL/6 mice
Infected with: MA15 at 10^4 or 10^5 PFU (4 animal/time point) icSARS at 10^5 PFU (5 animals/time point), Bat SRBD at 10^4 PFU (5 animals/time point), mock infected (4-5 animals/time point)
Time points = 1, 2, 4, and 7 days post infection
Weight loss and animal survival were also monitored
C57BL/6 mice  Wild Type SARS MA15, icSARS CoV and SARS Bat SRBD mutant virusesGEO Accession GSE50000  DE gene list 
SM004
20 week-old C57BL/6 mice (TIMP1 and Serpine1 (PAI1) knock-out mice)
SARS MA15 virus
Infections were done at 10^4 PFU or time-matched mock infected.
Time points = 4 and 7 days post infection
2 - 4 animals/dose/time point
Weight loss and animal survival were also monitored
C57BL/6 mice - TIMP1 or Serpine1 knock-out miceSARS-CoV (MA15) GEO Accession GSE51386  DE gene list 
SM007
20 week-old C57BL/6 or CXCR3 KO mice
SARS-CoV (MA15)
Dosage = 10^5 PFU or mock infected
Time points = 2 (N=3), 4 (N=3), and 7 (N=4) days post infection. 
Equivalent numbers of time matched mock animals
C57BL/6 mice or CXCR3 knockout mice  SARS-CoV (MA15)GEO Accession GSE50878

DE gene list

this list is for ST001 which contains IM010, SM007, SM015, SM019, and SM020

 
SM009
20 week old C57BL6 or PLAT knockout mice
SARS-CoV (MA15)
Dosage = 10^5 PFU or mock infected 
Time points = 4 and 7 days post infection.
2 - 4 mice/dose/time point
C57BL/6 or PLAT knockout miceSARS-CoV (MA15)GEO Accession GSE51387 DE gene list 
SM012
20 week-old C57BL/6
MA15 at doses of 10^4 or 10^5 PFU, deltaORF6 at 10^5 PFU, ExoN at 10^4 PFU or mock infected
Arrays not run on ExoN due to RNA quality
Time points = 1, 2, 4, and 7 days post infection
3 mice/dose/time point
3 mice/time point for time matched mocks
C57BL/6 micewild type SARS MA15 or SARS deltaORF6 and ExoN mutant viruses  GEO Accession GSE49262DE gene list 
SM014
20 week-old C57BL/6
Dosage = 10^5 PFU or mock infected
Time points = 1, 2, 4, and 7 days post infection
4 mice/dose/time point
3 mice/time point for time matched mocks
C57BL/6 micewild type SARS MA15 or SARS nsp16 mutant virus  GEO Accession GSE49263 DE gene list 
SM015
10-week-old C57BL/6 mice or Tnfrsf1a/1b knockout mice
Arrays were only done on samples from Tnfrsf1a/1b KO mice
Dosage = 10^5 PFU or mock infected
Time Points = 4 and 7 days post infection
C57BL/6 mice, Tnfrsf1a/1b knockout miceSARS-CoV (MA15) GEO Accession GSE40840 

DE gene list

this list is for ST001 which contains IM010, SM007, SM015, SM019, and SM020

 
SM019
10 wk old C57BL/6 mice
IRF3, Tnfrsf1b  or Indo KO mice
Infected with MA15 at a dosage = 10^5 PFU
Time Points = 5 and 7 days post infection (infected and mock-infected)
C57BL/6 mice SARS MA15  GEO Accession GSE40824

DE gene list

this list is for ST001 which contains IM010, SM007, SM015, SM019, and SM020

 
SM020
10 wk old C57BL/6 mice or KEPI (ppp1r14c) KO mice 
Infected with SARS MA15
Dosage = 10^5 PFU
Time Points = 5 and 7 days post infection (infected and mock-infected)
C57BL/6 mice or KEPI (ppp1r14c) KO mice SARS MA15  GEO Accession GSE40827

DE gene list

this list is for ST001 which contains IM010, SM007, SM015, SM019, and SM020

 
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 H1N1 GEO Accession GSE37569DE gene list

BMC Systems Biology 2013, 7:69 

IM001
20 week-old C57BL/6 mice
A/VN1203/04
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 miceA/VN1203/04GEO Accession GSE33263DE gene list

BMC Systems Biol. 2011;5:190

 BMC Systems Biol. 2013;7:69

IM002
Three H1N1 virus strains: NJ/8/76, Mex4482/2009, and Brisbane/59/2007plus mock
Dosage =  10^6 PFU 
Time Points = 1, 3, and 5 days post infection
3 mouse lungs/time point for infections
2 mouse lungs/time point for time matched mocks
BALB/c mice Three H1N1 Strains: NJ/8/76,
Mex4482/2009, and
Brisbane/59/2007 (seasonal) 
GEO Accession GSE36328DE gene list 
IM004
20 week-old C57BL/6 mice
VN1203 HA avirulent mutant virus
Three Doses = 10^3, 10^4, and 10^5 PFU (ARRAYS WERE ONLY DONE ON 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
 

VN1203 HA avirulent mutant

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

GEO Accession GSE37572DE gene 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) GEO Accession GSE43301DE gene listBMC Systems Biol. 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 PFU
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 mice VN1203 PB1-F2 Deletion 

GEO Accession

IM006A - GSE43302

IM006B - GSE44441 

IM006A -  DE gene list

IM006B - DE gene list

BMC Systems Biol. 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

 GEO Accession  GSE44445DE gene listBMC Systems Biol. 2013, 7:69
IM009
6-8 week-old BALB/c mice
Two viruses (MA-A/CA/04/09 , A/CA/04/09) plus a time matched mock:
Dosage = 10^6 PFU
Time Points = 1, 3, and 5 days post infection
3 mice/treatment/day
BALB/c mice  MA-A/CA/04/09 and A/CA/04/09 (H1N1) GEO Accession GSE36328DE gene listJ Virol. 2012 Jul;86(13):7192-206
IM010
6 week-old IDO1 KO (bottleneck), TNFRSF1B (hub) KO or WT C57BL/6 mice
Infect with A/VN1203/04
MLD50 group:  0.1, 1, 10 and 100 PFU (three mice per group). Mouse body weights and survival were assessed over a 14 day period
Lung tissue harvest group:  Mock or 1000 PFU, 3 mice per group per day, collect tissues for virus titer and RNA harvest on days 2 and 6.  Body weights were also collected each day.
IDO1 KO, TNFRSF1B KO or WT C57BL/6 mice A/Vietnam/1203/04 H5N1GEO Accession GSE40792

DE gene list

this list is for ST001 which contains IM010, SM007, SM015, SM019, and SM020

 
SHAE002
SARS Time Points = 0, 12, 24, 36, 48, 60, 72, 84, and 96 hours post infection
H1N1 Time points = 0, 6, 12, 18, 24, 36, and 48 hours post infection
Infection was done at an MOI of 2.
N = 3 or 4 when possible, HAE cultures were infected/condition/time point
Replicates: 3 or 4 different HAE, plated at the same time using the same cell stock
Time matched mocks done in triplicate from same cell stock as rest of samples.
Culture medium (the same as what the virus stock is in) will be used for the mock infections.
Primary Human Cells - HAE culturesSARS-CoV, SARS-dORF6, SARS-BatSRBD, H1N1 CA04 2009 

 GEO Accession GSE47960

SHAE002, 003 and 004 grouped in a GEO Superseries = GSE47963

DE gene listPLoS One. 2013 Jul 25;8(7) 
SHAE003
SARS Time Points = 0, 12, 24, 36, 48, 60, 72, 84, and 96 hours post infection
SARS-dORF6 and SARS-BatSRBD Time Points = 0, 24, 48, 60, 72, 84 and 96 hours post infection 
H1N1 Time points = 0, 6, 12, 18, 24, 36, and 48 hours post infection
Infection was done at an MOI of 2.
Four HAE cultures were infected per condition per time point
Replicates: 4 different HAE, plated at the same time using the same cell stock
Time matched mocks done in triplicate from same cell stock as rest of samples
Culture medium (the same as what the virus stock is in) will be used for the mock infections
Primary Human Cells - HAE culturesSARS-CoV, SARS-dORF6 or SARS-BatSRBD, H1N1 CA04 2009

 GEO Accession GSE47961

SHAE002, 003 and 004 grouped in a GEO Superseries = GSE47963

DE gene listPLoS One. 2013 Jul 25;8(7) 
SHAE004
SARS Time Points = 0, 12, 24, 36, 48, 60, 72, 84, and 96 hours post infection
H1N1 Time points = 0, 6, 12, 18, 24, 36, and 48 hours post infection
SARS = MOI of 2; H1N1 =  MOI of 1
Three HAE cultures were infected per condition per time point
Replicates: 3 different HAE, plated at the same time using the same cell stock
Time matched mocks done in triplicate from same cell stock as rest of samples
Culture medium (the same as what the virus stock is in) will be used for the mock infections
Primary Human Cells - HAE culturesSARS-CoV, SARS-dORF6 or SARS-BatSRBD, H1N1 CA04 2009 

 GEO Accession GSE47962

SHAE002, 003 and 004 grouped in a GEO Superseries = GSE47963

DE gene list

PLoS One. 2013 Jul 25;8(7)