title: MPX 6   Mph

description:
Simple annotation: Normal tissue, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/65426.gif

scan_protocol: Rubins 2003 - Data filtering and analysis; Array images were scanned using an Axon Scanner 4000A (Axon Instruments, Union City, CA), and image analysis was performed using GenePix Pro version 3.0.6.89 (Axon Instruments, Union City, CA).  Grids were manually aligned and features were found using the software feature extraction.  Features were visually inspected for blemishes and removed from downstream analysis.    Data were uploaded to the Stanford Microarray Database (http://genome-www5.stanford.edu/)  and normalized using regression correlation.  Data were expressed as the log2 ratio of fluorescence intensities of the sample and the reference, for each element on the array.    Data were filtered to exclude elements that did not have a regression correlation of Cy5 to Cy3 signal over the pixels spanning the array element of ??0.6 and intensity/background ratio of ??2.5 in at least 80% of the arrays.    For each gene, the expression levels over the timecourse for each monkey were ??time-zerotransformed?? by subtracting the average of the pre-infection baseline expression level from that animal so that the values of each timepoint represent changes relative to the uninfected samples.    The genes whose expression varied from the uninfected baseline by at least 3 fold in at least 3 samples were selected for further analysis.    The data were hierarchically clustered using the Cluster program (http://rana.lbl.gov/EisenSoftware.htm) and displayed using TreeView (http://rana.lbl.gov/EisenSoftware.htm).; Protocol Type = Feature Extraction; Software: type: feature extraction; Performer: Kate,,Rubins Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 27.38; Parameter Scan Time = 16:12:27; Parameter PMT Volts = 426; Parameter Scan Date = 2005-10-31; Parameter Pixel Size = 10; Parameter Laser on time = 12411; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4200A 01 Autoloader; Parameter Laser Power = 1.52; Parameter Scan Power = 80; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Kate,,Rubins Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 27.38; Parameter Scan Time = 16:12:27; Parameter PMT Volts = 438; Parameter Scan Date = 2005-10-31; Parameter Pixel Size = 10; Parameter Laser on time = 12411; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4200A 01 Autoloader; Parameter Laser Power = 1.71; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 80; Parameter Scanning software = AxImageIO; Performer: Kate,,Rubins

source_name: MPX 6 Mph cells inf w MPX in vitro 5.5.05


title: MPX 1   Mph

status: Public on Jul 17 2008

type: RNA

city: Cambridge

first: Kate

last: Rubins

state: MA

address: Nine Cambridge Center

country: USA

institute: Whitehead Institute for Biomedical Research

description:
Simple annotation: Normal tissue, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/65424.gif

hyb_protocol: not provided

scan_protocol: Rubins 2003 - Data filtering and analysis; Array images were scanned using an Axon Scanner 4000A (Axon Instruments, Union City, CA), and image analysis was performed using GenePix Pro version 3.0.6.89 (Axon Instruments, Union City, CA).  Grids were manually aligned and features were found using the software feature extraction.  Features were visually inspected for blemishes and removed from downstream analysis.    Data were uploaded to the Stanford Microarray Database (http://genome-www5.stanford.edu/)  and normalized using regression correlation.  Data were expressed as the log2 ratio of fluorescence intensities of the sample and the reference, for each element on the array.    Data were filtered to exclude elements that did not have a regression correlation of Cy5 to Cy3 signal over the pixels spanning the array element of ??0.6 and intensity/background ratio of ??2.5 in at least 80% of the arrays.    For each gene, the expression levels over the timecourse for each monkey were ??time-zerotransformed?? by subtracting the average of the pre-infection baseline expression level from that animal so that the values of each timepoint represent changes relative to the uninfected samples.    The genes whose expression varied from the uninfected baseline by at least 3 fold in at least 3 samples were selected for further analysis.    The data were hierarchically clustered using the Cluster program (http://rana.lbl.gov/EisenSoftware.htm) and displayed using TreeView (http://rana.lbl.gov/EisenSoftware.htm).; Protocol Type = Feature Extraction; Software: type: feature extraction; Performer: Kate,,Rubins Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 27.38; Parameter Scan Time = 15:35:20; Parameter PMT Volts = 417; Parameter Scan Date = 2005-10-31; Parameter Pixel Size = 10; Parameter Laser on time = 12374; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4200A 01 Autoloader; Parameter Laser Power = 1.52; Parameter Scan Power = 80; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Kate,,Rubins Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 27.38; Parameter Scan Time = 15:35:20; Parameter PMT Volts = 432; Parameter Scan Date = 2005-10-31; Parameter Pixel Size = 10; Parameter Laser on time = 12374; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4200A 01 Autoloader; Parameter Laser Power = 1.72; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 80; Parameter Scanning software = AxImageIO; Performer: Kate,,Rubins

data_processing: VALUE is Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)

molecule: total RNA

organism: Homo sapiens

source_name: Stratagene UHR, 1 round of amp(Ambion MessageAmp) 8/9/05, spiked in MPX/VAC

label_protocol: not provided

extract_protocol: not provided

source_name: MPX 1 Mph cells inf w MPX in vitro 5.5.05

label_protocol:
Rubins 2003 - Ambion Message Amp I; FIRST STRAND CDNA SYNTHESIS: In PCR reaction tube, mix: Amount Reagent 0.1 - 5ug  Total RNA 1uL T7 Oligo (dT) primer 11uL Nuclease free water  70oC for 10 min in a thermocycler with lid on, but not clamped down.   Centrifuge briefly.   Prepare in a Master Mix and keep at room temperature: Amount Reagent 2uL 10X First Strand Buffer 1uL Ribonuclease Inhibitor 4uL dNTP Mix Gently pipette or flick to mix, and then centrifuge briefly.  Incubate master mix at 42oC for 2 minutes prior to adding to reaction tubes.   Add to the master mix: Amount Reagent 1uL Reverse Transcriptase  Quickly transfer 8ul of above Master Mix to each RNA sample, mix by pipetting.   42oC for 2 hours in thermocycler with lid on, but not clamped down.   Centrifuge briefly, place on ice, and immediately proceed to next step  SECOND STRAND SYNTHESIS: Amount Reagent 63uL Nuclease free water 10uL 10X Second Strand Buffer 4uL dNTP Mix 2uL DNA Polymerase 1uL RNase H Add 80uL to each tube. Gently pipette or flick to mix, and then centrifuge briefly.  16oC for 2 hours in thermocycler with lid completely off.    DS cDNA CLEANUP: Preheat the 5mL bottle of water at 50oC for at least 10 minutes. Place filter cartridge in a 2mL tube and add 100ul of cDNA Binding Buffer. Incubate at room temperature for 5 min.  Transfer 100uL reaction from strip-8 PCR tubes into 1.5ml Eppendorf tubes. Add 250uL of cDNA binding buffer to each cDNA sample, mix by pipetting. Add the mix to the filter cartridge. Centrifuge for 1 min at 10,000 x g. Discard flow-through.  Add 650ul of cDNA wash buffer. Centrifuge for 1 min. at 10,000 x g. Discard flow-through. Centrifuge again for 1 min at 10,000 x g to remove trace amounts of ethanol.  Transfer filter cartridge to fresh 2mL tube Add 50uL of preheated water to the center of the column.   Incubate at room temperature for 2 minutes. Centrifuge for 1 minute at 10,000 x g. Repeat elution with a second 50ul of preheated water. Centrifuge for 1 minute at 10,000 x g.   Transfer to strip-8 PCR tubes and mark a line for 8uL Concentrate the purified cDNA to < 8uL by drying in a vacuum centrifuge on high heat.   Resuspend cDNA up to 8uL with H20, mix well, and keep on ice or store at ?20oC.  IN VITRO TRANSCRIPTION  Prepare the following master mix: Amount Reagent 8uL T7 NTP mix (75 mM each) 2uL T7 10X Reaction Buffer 2uL T7 Enzyme Mix Add 12uL to each tube. Gently pipette or flick to mix, and then centrifuge briefly.  37oC for 6 hours in hybridization oven.  Add to each reaction: Amount Reagent 2uL DNaseI  Gently pipette or flick to mix, and then centrifuge briefly.  37oC for 30min in hybridization oven   aRNA PURIFICATION  Preheat 5mL bottle of nuclease free water at 50oC for at least 10 minutes.  Immediately before staring aRNA purification., equilibrate 1 filter cartridge per aRNA sample Place filter cartridge in a 2mL tube and add 100ul of aRNA Binding Buffer. Incubate at room temperature for 5 min.  Add 78uL aRNA Elution Solution to each IVT mix to bring final volume up to 100uL.   Add 350uL of aRNA Binding Buffer to each aRNA sample. Add 250uL of ACS grade 95% ethanol to each sample. Mix by pipetting or gentle vortexing.  Apply entire sample to the equilibrated filter cartridge.  Centrifuge for 1 minute at 10,000 x g.   Discard flow-through but re-use tube.  Add 650uL aRNA Wash Buffer to each filter.   Centrifuge for 1 minute at 10,000 x g.   Discard flow-through but re-use tube. Centrifuge again for 1 min at 10,000 x g Transfer cartridge to a fresh 2mL tube.  Elute aRNA by adding 50uL preheated (50oC) water to center of column.  Incubate at room temperature for 2 min.  Centrifuge for 1 minute at 10,000 x g.  Repeat elution with a second 50uL of preheated water. Centrifuge for 1 minute at 10,000 x g.   Store aRNA at ?80oC.; Protocol Type = Amplification; Performer: Kate,,Rubins
Rubins 2003 - Labeling Amplified RNA - Direct Incorporation of Cy Dyes; Preparation of Fluorescent DNA Probe from Amplified mRNA  1. To anneal primer, mix 3-4ug of amplified mRNA with 10ug of random hexamer primer in a total volume of 15.4ul:    mRNA 3-4ug  pdN6 (5 ug/uL) 2uL ddH2O (DEPC) to 15.4 uL Total volume: 15.4 uL  2. Heat to 65oC for 10 min and cool on ice.   3. Add 14.6uL reaction mixture (Master Mix or separate) to each RNA/hexamer mix Reaction mixture  5X first-strand buffer 6.0uL  0.1M DTT 3.0uL Unlabeled dNTPs (low dTTP) 0.6uL Cy3 or Cy5 (1 mM, Amersham) 3.0uL Superscript II (200 U/uL, Gibco BRL) 2.0uL Total volume: 14.6uL   4. Incubate at 42oC for 1 hr.   5. Add 1 uL SSII (RT booster) to each sample. Incubate for an additional 1 hr.   6. Degrade RNA by addition 15uL of 0.1N NaOH and incubate at 65-70oC for 10 min.   7. Neutralize by addition of 15uL of 0.1N HCl.  8. Add 380uL of TE (10mM Tris, 1mM EDTA) to a Microcon YM-30 column.  Next add the 60uL of Cy5 probe and the 60??l of Cy3 probe to the same Microcon.  9. WASH 1: Spin 7-8 min. at 14,000g (=RCF).  Remove flow through and save to a separate tube.  10. WASH 2: Add 450ul 1X TE and spin 7-8 min. at 14,000g. Remove flow through and save to the separate tube.  11.  WASH 3: Add to centricon: 1X TE 450uL 1ug/uL Cot1 human DNA (Gibco-BRL) 20 uL 10ug/uL  polyA RNA (Sigma, #P9403) 2 uL 10ug/uL  tRNA (Gibco-BRL, #15401-011) 2 uL Spin 7-10 min. at 14,000g. Look for nice concentration of the "colored probe" in the centricon. Try to concentrate to a volume of less than 25uL. This volume is attained when the center of the membrane is dry and the probe forms a ring of liquid at the edges of the membrane.  Make sure not to dry the membrane completely!  12. Invert the centricon into a clean tube and spin briefly at 14,000 RPM to recover the probe.; Protocol Type = Labeling; Performer: Kate,,Rubins

extract_protocol: Rubins 2003 - Trizol Extraction of Total RNA from PBMCs; 1. Make sure the area is clean and free of any RNases.  Keep the samples cold or on ice as much as possible to prevent RNA degradation.   Use only RNase free tubes and RNase free, aerosol-barrier pipette tips throughout the whole experiment.  2. Add 1mL of Trizol to the frozen PBMC pellet.   3. If the Trizol was added to the PBMCs before freezing, thaw the Trizol/PBMCs on the benchtop for 5-10 minutes.  4. Vortex and transfer to 1.5ml microfuge tubes if not already in them.  5. Add 0.2 mls chloroform per 1 ml Trizol.  Vortex or shake vigorously and incubate at room temp. for 2-3 minutes.  6. Centrifuge at 12,000g for 15 minutes at 4C.  7. Transfer the aqueous phase to a fresh tube.  (The volume will be about 60% of the volume of Trizol.)  Note:  If isolating DNA, save the organic phase.  Add 1uL of 1ug/uL Linear Acrylamide if RNA yield is expected to be low.  8. Add 0.5 mLs of isopropanol per 1 ml Trizol used.  Incubate at room temp. for 10 minutes.   9. Centrifuge at top speed (14,000rpm) for 10 minutes at 4C.    10. The RNA pellet will be visible at the bottom of the tube.  Use the vacuum to very carefully aspirate the supernatant. Alternatively, carefully suck off the supernatant with a pipette. Discard supernatant. Check that the pellet is visible at the bottom of the tube.  11. WASH 1: Wash the pellet with 1 ml 70% EtOH.  Centrifuge at top speed 14,000g for 5-7 minutes.  12. Use the vacuum to very carefully aspirate the supernatant. Alternatively, carefully suck off the supernatant with a pipette. Discard supernatant. Check that the pellet is visible at the bottom of the tube.  13. WASH 2:  Wash the pellet with 1 ml 70% EtOH.  Centrifuge at top speed 14,000g for 5-7 minutes.  14. Use the vacuum to very carefully aspirate the supernatant. Alternatively, carefully suck off the supernatant with a pipette. Discard supernatant. Check that the pellet is visible at the bottom of the tube.  15. Air dry pellet shortly, until no EtOH is visible (2-5 minutes).  Do not overdry!  16. Resuspend the pellet in 20uls of DEPC H2O.  Store at ?80C.  17. Check RNA quality and quantity by denaturing gel and OD spec (260nm and 260/280 ratio).; Protocol Type = Extract preparation; Performer: Kate,,Rubins

tag: Compound Based Treatment

tag: Infection

value: Monkeypox Zaire virus

tag: Cell Line

value: Primary Human Monocyte

tag: Measurement

value: time(relative) 1 h


title: Mock 0c   Mph

description:
Simple annotation: Normal tissue, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/65423.gif

scan_protocol: Rubins 2003 - Data filtering and analysis; Array images were scanned using an Axon Scanner 4000A (Axon Instruments, Union City, CA), and image analysis was performed using GenePix Pro version 3.0.6.89 (Axon Instruments, Union City, CA).  Grids were manually aligned and features were found using the software feature extraction.  Features were visually inspected for blemishes and removed from downstream analysis.    Data were uploaded to the Stanford Microarray Database (http://genome-www5.stanford.edu/)  and normalized using regression correlation.  Data were expressed as the log2 ratio of fluorescence intensities of the sample and the reference, for each element on the array.    Data were filtered to exclude elements that did not have a regression correlation of Cy5 to Cy3 signal over the pixels spanning the array element of ??0.6 and intensity/background ratio of ??2.5 in at least 80% of the arrays.    For each gene, the expression levels over the timecourse for each monkey were ??time-zerotransformed?? by subtracting the average of the pre-infection baseline expression level from that animal so that the values of each timepoint represent changes relative to the uninfected samples.    The genes whose expression varied from the uninfected baseline by at least 3 fold in at least 3 samples were selected for further analysis.    The data were hierarchically clustered using the Cluster program (http://rana.lbl.gov/EisenSoftware.htm) and displayed using TreeView (http://rana.lbl.gov/EisenSoftware.htm).; Protocol Type = Feature Extraction; Software: type: feature extraction; Performer: Kate,,Rubins Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 26.88; Parameter Scan Time = 21:59:35; Parameter PMT Volts = 434; Parameter Scan Date = 2005-10-31; Parameter Pixel Size = 10; Parameter Laser on time = 12758; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4200A 01 Autoloader; Parameter Laser Power = 2.30; Parameter Scan Power = 80; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Kate,,Rubins Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 26.88; Parameter Scan Time = 21:59:35; Parameter PMT Volts = 457; Parameter Scan Date = 2005-10-31; Parameter Pixel Size = 10; Parameter Laser on time = 12758; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4200A 01 Autoloader; Parameter Laser Power = 1.71; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 80; Parameter Scanning software = AxImageIO; Performer: Kate,,Rubins

tag: Stratagene UHR, 1 round of amp(Ambion MessageAmp) 8/9/05, spiked in MPX/VAC

source_name: Mock 0c Mph cells Mock Infected in vitro 5.5.05

value: time(relative) 0 h


title: VAC 24   Mph

description:
Simple annotation: Normal tissue, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/65422.gif

scan_protocol: Rubins 2003 - Data filtering and analysis; Array images were scanned using an Axon Scanner 4000A (Axon Instruments, Union City, CA), and image analysis was performed using GenePix Pro version 3.0.6.89 (Axon Instruments, Union City, CA).  Grids were manually aligned and features were found using the software feature extraction.  Features were visually inspected for blemishes and removed from downstream analysis.    Data were uploaded to the Stanford Microarray Database (http://genome-www5.stanford.edu/)  and normalized using regression correlation.  Data were expressed as the log2 ratio of fluorescence intensities of the sample and the reference, for each element on the array.    Data were filtered to exclude elements that did not have a regression correlation of Cy5 to Cy3 signal over the pixels spanning the array element of ??0.6 and intensity/background ratio of ??2.5 in at least 80% of the arrays.    For each gene, the expression levels over the timecourse for each monkey were ??time-zerotransformed?? by subtracting the average of the pre-infection baseline expression level from that animal so that the values of each timepoint represent changes relative to the uninfected samples.    The genes whose expression varied from the uninfected baseline by at least 3 fold in at least 3 samples were selected for further analysis.    The data were hierarchically clustered using the Cluster program (http://rana.lbl.gov/EisenSoftware.htm) and displayed using TreeView (http://rana.lbl.gov/EisenSoftware.htm).; Protocol Type = Feature Extraction; Software: type: feature extraction; Performer: Kate,,Rubins Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 26.88; Parameter Scan Time = 21:41:06; Parameter PMT Volts = 432; Parameter Scan Date = 2005-10-31; Parameter Pixel Size = 10; Parameter Laser on time = 12739; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4200A 01 Autoloader; Parameter Laser Power = 1.54; Parameter Scan Power = 80; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Kate,,Rubins Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 26.88; Parameter Scan Time = 21:41:06; Parameter PMT Volts = 447; Parameter Scan Date = 2005-10-31; Parameter Pixel Size = 10; Parameter Laser on time = 12739; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4200A 01 Autoloader; Parameter Laser Power = 1.71; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 80; Parameter Scanning software = AxImageIO; Performer: Kate,,Rubins

source_name: VAC 24 Mph cells inf w VAC in vitro 5.5.05

value: Vaccinia Western Reserve virus

value: time(relative) 12 h


title: VAC 12   Mph

description:
Simple annotation: Normal tissue, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/65421.gif

scan_protocol: Rubins 2003 - Data filtering and analysis; Array images were scanned using an Axon Scanner 4000A (Axon Instruments, Union City, CA), and image analysis was performed using GenePix Pro version 3.0.6.89 (Axon Instruments, Union City, CA).  Grids were manually aligned and features were found using the software feature extraction.  Features were visually inspected for blemishes and removed from downstream analysis.    Data were uploaded to the Stanford Microarray Database (http://genome-www5.stanford.edu/)  and normalized using regression correlation.  Data were expressed as the log2 ratio of fluorescence intensities of the sample and the reference, for each element on the array.    Data were filtered to exclude elements that did not have a regression correlation of Cy5 to Cy3 signal over the pixels spanning the array element of ??0.6 and intensity/background ratio of ??2.5 in at least 80% of the arrays.    For each gene, the expression levels over the timecourse for each monkey were ??time-zerotransformed?? by subtracting the average of the pre-infection baseline expression level from that animal so that the values of each timepoint represent changes relative to the uninfected samples.    The genes whose expression varied from the uninfected baseline by at least 3 fold in at least 3 samples were selected for further analysis.    The data were hierarchically clustered using the Cluster program (http://rana.lbl.gov/EisenSoftware.htm) and displayed using TreeView (http://rana.lbl.gov/EisenSoftware.htm).; Protocol Type = Feature Extraction; Software: type: feature extraction; Performer: Kate,,Rubins Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 26.94; Parameter Scan Time = 21:22:32; Parameter PMT Volts = 436; Parameter Scan Date = 2005-10-31; Parameter Pixel Size = 10; Parameter Laser on time = 12721; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4200A 01 Autoloader; Parameter Laser Power = 1.24; Parameter Scan Power = 80; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Kate,,Rubins Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 26.94; Parameter Scan Time = 21:22:32; Parameter PMT Volts = 448; Parameter Scan Date = 2005-10-31; Parameter Pixel Size = 10; Parameter Laser on time = 12721; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4200A 01 Autoloader; Parameter Laser Power = 1.71; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 80; Parameter Scanning software = AxImageIO; Performer: Kate,,Rubins

source_name: VAC 12 Mph cells inf w VAC in vitro 5.5.05


title: MPX 2   Mph

description:
Simple annotation: Normal tissue, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/65425.gif

scan_protocol: Rubins 2003 - Data filtering and analysis; Array images were scanned using an Axon Scanner 4000A (Axon Instruments, Union City, CA), and image analysis was performed using GenePix Pro version 3.0.6.89 (Axon Instruments, Union City, CA).  Grids were manually aligned and features were found using the software feature extraction.  Features were visually inspected for blemishes and removed from downstream analysis.    Data were uploaded to the Stanford Microarray Database (http://genome-www5.stanford.edu/)  and normalized using regression correlation.  Data were expressed as the log2 ratio of fluorescence intensities of the sample and the reference, for each element on the array.    Data were filtered to exclude elements that did not have a regression correlation of Cy5 to Cy3 signal over the pixels spanning the array element of ??0.6 and intensity/background ratio of ??2.5 in at least 80% of the arrays.    For each gene, the expression levels over the timecourse for each monkey were ??time-zerotransformed?? by subtracting the average of the pre-infection baseline expression level from that animal so that the values of each timepoint represent changes relative to the uninfected samples.    The genes whose expression varied from the uninfected baseline by at least 3 fold in at least 3 samples were selected for further analysis.    The data were hierarchically clustered using the Cluster program (http://rana.lbl.gov/EisenSoftware.htm) and displayed using TreeView (http://rana.lbl.gov/EisenSoftware.htm).; Protocol Type = Feature Extraction; Software: type: feature extraction; Performer: Kate,,Rubins Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 27.38; Parameter Scan Time = 15:53:58; Parameter PMT Volts = 418; Parameter Scan Date = 2005-10-31; Parameter Pixel Size = 10; Parameter Laser on time = 12392; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4200A 01 Autoloader; Parameter Laser Power = 1.53; Parameter Scan Power = 80; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Kate,,Rubins Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 27.38; Parameter Scan Time = 15:53:58; Parameter PMT Volts = 434; Parameter Scan Date = 2005-10-31; Parameter Pixel Size = 10; Parameter Laser on time = 12392; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4200A 01 Autoloader; Parameter Laser Power = 1.71; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 80; Parameter Scanning software = AxImageIO; Performer: Kate,,Rubins

source_name: MPX 2 Mph cells inf w MPX in vitro 5.5.05

value: time(relative) 2 h


title: VAC 2   Mph

description:
Simple annotation: Normal tissue, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/65420.gif

scan_protocol: Rubins 2003 - Data filtering and analysis; Array images were scanned using an Axon Scanner 4000A (Axon Instruments, Union City, CA), and image analysis was performed using GenePix Pro version 3.0.6.89 (Axon Instruments, Union City, CA).  Grids were manually aligned and features were found using the software feature extraction.  Features were visually inspected for blemishes and removed from downstream analysis.    Data were uploaded to the Stanford Microarray Database (http://genome-www5.stanford.edu/)  and normalized using regression correlation.  Data were expressed as the log2 ratio of fluorescence intensities of the sample and the reference, for each element on the array.    Data were filtered to exclude elements that did not have a regression correlation of Cy5 to Cy3 signal over the pixels spanning the array element of ??0.6 and intensity/background ratio of ??2.5 in at least 80% of the arrays.    For each gene, the expression levels over the timecourse for each monkey were ??time-zerotransformed?? by subtracting the average of the pre-infection baseline expression level from that animal so that the values of each timepoint represent changes relative to the uninfected samples.    The genes whose expression varied from the uninfected baseline by at least 3 fold in at least 3 samples were selected for further analysis.    The data were hierarchically clustered using the Cluster program (http://rana.lbl.gov/EisenSoftware.htm) and displayed using TreeView (http://rana.lbl.gov/EisenSoftware.htm).; Protocol Type = Feature Extraction; Software: type: feature extraction; Performer: Kate,,Rubins Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 26.94; Parameter Scan Time = 21:04:04; Parameter PMT Volts = 442; Parameter Scan Date = 2005-10-31; Parameter Pixel Size = 10; Parameter Laser on time = 12702; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4200A 01 Autoloader; Parameter Laser Power = 1.21; Parameter Scan Power = 80; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Kate,,Rubins Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 26.94; Parameter Scan Time = 21:04:04; Parameter PMT Volts = 449; Parameter Scan Date = 2005-10-31; Parameter Pixel Size = 10; Parameter Laser on time = 12702; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4200A 01 Autoloader; Parameter Laser Power = 1.73; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 80; Parameter Scanning software = AxImageIO; Performer: Kate,,Rubins

source_name: VAC 2 Mph cells inf w VAC in vitro 5.5.05


title: g-MPX 12 hr Mf 7.29

description:
Simple annotation: Normal tissue, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs/2004-08/55146.gif

scan_protocol: Rubins 2003 - Data filtering and analysis; Array images were scanned using an Axon Scanner 4000A (Axon Instruments, Union City, CA), and image analysis was performed using GenePix Pro version 3.0.6.89 (Axon Instruments, Union City, CA).  Grids were manually aligned and features were found using the software feature extraction.  Features were visually inspected for blemishes and removed from downstream analysis.    Data were uploaded to the Stanford Microarray Database (http://genome-www5.stanford.edu/)  and normalized using regression correlation.  Data were expressed as the log2 ratio of fluorescence intensities of the sample and the reference, for each element on the array.    Data were filtered to exclude elements that did not have a regression correlation of Cy5 to Cy3 signal over the pixels spanning the array element of ??0.6 and intensity/background ratio of ??2.5 in at least 80% of the arrays.    For each gene, the expression levels over the timecourse for each monkey were ??time-zerotransformed?? by subtracting the average of the pre-infection baseline expression level from that animal so that the values of each timepoint represent changes relative to the uninfected samples.    The genes whose expression varied from the uninfected baseline by at least 3 fold in at least 3 samples were selected for further analysis.    The data were hierarchically clustered using the Cluster program (http://rana.lbl.gov/EisenSoftware.htm) and displayed using TreeView (http://rana.lbl.gov/EisenSoftware.htm).; Protocol Type = Feature Extraction; Software: type: feature extraction; Performer: Kate,,Rubins Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 32.67; Parameter Scan Time = 03:11:14; Parameter PMT Volts = 610; Parameter Scan Date = 2004-08-28; Parameter Pixel Size = 10; Parameter Laser on time = 188014; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 3.34; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.2; Parameter Scanning software = AxImageIO; Performer: Kate,,Rubins Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 32.67; Parameter Scan Time = 03:11:14; Parameter PMT Volts = 680; Parameter Scan Date = 2004-08-28; Parameter Pixel Size = 10; Parameter Laser on time = 406982; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.67; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Kate,,Rubins

source_name: Stratagene UHR RNA, 1 round of amp(Ambion MessageAmp), 6/27/02, spiked in MPX/VAC 8/26/04

source_name: g-MPX 12 hr Primary Human Macrophages infected with Killed Monkeypox-Zaire in vitro 7.29.04

value: Inactivated Monkeypox Zaire virus


title: MPX 24   Mph

description:
Simple annotation: Normal tissue, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/65428.gif

scan_protocol: Rubins 2003 - Data filtering and analysis; Array images were scanned using an Axon Scanner 4000A (Axon Instruments, Union City, CA), and image analysis was performed using GenePix Pro version 3.0.6.89 (Axon Instruments, Union City, CA).  Grids were manually aligned and features were found using the software feature extraction.  Features were visually inspected for blemishes and removed from downstream analysis.    Data were uploaded to the Stanford Microarray Database (http://genome-www5.stanford.edu/)  and normalized using regression correlation.  Data were expressed as the log2 ratio of fluorescence intensities of the sample and the reference, for each element on the array.    Data were filtered to exclude elements that did not have a regression correlation of Cy5 to Cy3 signal over the pixels spanning the array element of ??0.6 and intensity/background ratio of ??2.5 in at least 80% of the arrays.    For each gene, the expression levels over the timecourse for each monkey were ??time-zerotransformed?? by subtracting the average of the pre-infection baseline expression level from that animal so that the values of each timepoint represent changes relative to the uninfected samples.    The genes whose expression varied from the uninfected baseline by at least 3 fold in at least 3 samples were selected for further analysis.    The data were hierarchically clustered using the Cluster program (http://rana.lbl.gov/EisenSoftware.htm) and displayed using TreeView (http://rana.lbl.gov/EisenSoftware.htm).; Protocol Type = Feature Extraction; Software: type: feature extraction; Performer: Kate,,Rubins Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 27.25; Parameter Scan Time = 16:49:36; Parameter PMT Volts = 412; Parameter Scan Date = 2005-10-31; Parameter Pixel Size = 10; Parameter Laser on time = 12448; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4200A 01 Autoloader; Parameter Laser Power = 1.53; Parameter Scan Power = 80; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Kate,,Rubins Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 27.25; Parameter Scan Time = 16:49:36; Parameter PMT Volts = 449; Parameter Scan Date = 2005-10-31; Parameter Pixel Size = 10; Parameter Laser on time = 12448; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4200A 01 Autoloader; Parameter Laser Power = 1.71; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 80; Parameter Scanning software = AxImageIO; Performer: Kate,,Rubins

source_name: MPX 24 Mph cells inf w MPX in vitro 5.5.05

value: time(relative) 24 h


title: VAC 1   Mph

description:
Simple annotation: Normal tissue, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/65419.gif

scan_protocol: Rubins 2003 - Data filtering and analysis; Array images were scanned using an Axon Scanner 4000A (Axon Instruments, Union City, CA), and image analysis was performed using GenePix Pro version 3.0.6.89 (Axon Instruments, Union City, CA).  Grids were manually aligned and features were found using the software feature extraction.  Features were visually inspected for blemishes and removed from downstream analysis.    Data were uploaded to the Stanford Microarray Database (http://genome-www5.stanford.edu/)  and normalized using regression correlation.  Data were expressed as the log2 ratio of fluorescence intensities of the sample and the reference, for each element on the array.    Data were filtered to exclude elements that did not have a regression correlation of Cy5 to Cy3 signal over the pixels spanning the array element of ??0.6 and intensity/background ratio of ??2.5 in at least 80% of the arrays.    For each gene, the expression levels over the timecourse for each monkey were ??time-zerotransformed?? by subtracting the average of the pre-infection baseline expression level from that animal so that the values of each timepoint represent changes relative to the uninfected samples.    The genes whose expression varied from the uninfected baseline by at least 3 fold in at least 3 samples were selected for further analysis.    The data were hierarchically clustered using the Cluster program (http://rana.lbl.gov/EisenSoftware.htm) and displayed using TreeView (http://rana.lbl.gov/EisenSoftware.htm).; Protocol Type = Feature Extraction; Software: type: feature extraction; Performer: Kate,,Rubins Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 27.00; Parameter Scan Time = 20:42:40; Parameter PMT Volts = 444; Parameter Scan Date = 2005-10-31; Parameter Pixel Size = 10; Parameter Laser on time = 12681; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4200A 01 Autoloader; Parameter Laser Power = 1.33; Parameter Scan Power = 80; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Kate,,Rubins Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 27.00; Parameter Scan Time = 20:42:40; Parameter PMT Volts = 481; Parameter Scan Date = 2005-10-31; Parameter Pixel Size = 10; Parameter Laser on time = 12681; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4200A 01 Autoloader; Parameter Laser Power = 1.73; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 80; Parameter Scanning software = AxImageIO; Performer: Kate,,Rubins

source_name: VAC 1 Mph cells inf w VAC in vitro 5.5.05


title: EBOV 1 hr FibroS100

description:
Simple annotation: Normal tissue, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs/2004-08/55219.gif

scan_protocol: Rubins 2003 - Data filtering and analysis; Array images were scanned using an Axon Scanner 4000A (Axon Instruments, Union City, CA), and image analysis was performed using GenePix Pro version 3.0.6.89 (Axon Instruments, Union City, CA).  Grids were manually aligned and features were found using the software feature extraction.  Features were visually inspected for blemishes and removed from downstream analysis.    Data were uploaded to the Stanford Microarray Database (http://genome-www5.stanford.edu/)  and normalized using regression correlation.  Data were expressed as the log2 ratio of fluorescence intensities of the sample and the reference, for each element on the array.    Data were filtered to exclude elements that did not have a regression correlation of Cy5 to Cy3 signal over the pixels spanning the array element of ??0.6 and intensity/background ratio of ??2.5 in at least 80% of the arrays.    For each gene, the expression levels over the timecourse for each monkey were ??time-zerotransformed?? by subtracting the average of the pre-infection baseline expression level from that animal so that the values of each timepoint represent changes relative to the uninfected samples.    The genes whose expression varied from the uninfected baseline by at least 3 fold in at least 3 samples were selected for further analysis.    The data were hierarchically clustered using the Cluster program (http://rana.lbl.gov/EisenSoftware.htm) and displayed using TreeView (http://rana.lbl.gov/EisenSoftware.htm).; Protocol Type = Feature Extraction; Software: type: feature extraction; Performer: Kate,,Rubins Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 32.49; Parameter Scan Time = 10:49:57; Parameter PMT Volts = 650; Parameter Scan Date = 2004-08-29; Parameter Pixel Size = 10; Parameter Laser on time = 189493; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.55; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.2; Parameter Scanning software = AxImageIO; Performer: Kate,,Rubins Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 32.49; Parameter Scan Time = 10:49:57; Parameter PMT Volts = 670; Parameter Scan Date = 2004-08-29; Parameter Pixel Size = 10; Parameter Laser on time = 408462; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.67; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Kate,,Rubins

tag: Stratagene UHR RNA, 1 round of amp(Ambion MessageAmp), 6/27/02, spiked in MPX/VAC 8/26/04

source_name: EBOV 1 hr Primary Human Skin Fibroblasts S100 infected with Ebola-Zaire in vitro 7.29.04

value: Ebola Zaire virus

value: Primary Human Fibroblast


title: Killed MPX 24   Mph

description:
Simple annotation: Normal tissue, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/65418.gif

scan_protocol: Rubins 2003 - Data filtering and analysis; Array images were scanned using an Axon Scanner 4000A (Axon Instruments, Union City, CA), and image analysis was performed using GenePix Pro version 3.0.6.89 (Axon Instruments, Union City, CA).  Grids were manually aligned and features were found using the software feature extraction.  Features were visually inspected for blemishes and removed from downstream analysis.    Data were uploaded to the Stanford Microarray Database (http://genome-www5.stanford.edu/)  and normalized using regression correlation.  Data were expressed as the log2 ratio of fluorescence intensities of the sample and the reference, for each element on the array.    Data were filtered to exclude elements that did not have a regression correlation of Cy5 to Cy3 signal over the pixels spanning the array element of ??0.6 and intensity/background ratio of ??2.5 in at least 80% of the arrays.    For each gene, the expression levels over the timecourse for each monkey were ??time-zerotransformed?? by subtracting the average of the pre-infection baseline expression level from that animal so that the values of each timepoint represent changes relative to the uninfected samples.    The genes whose expression varied from the uninfected baseline by at least 3 fold in at least 3 samples were selected for further analysis.    The data were hierarchically clustered using the Cluster program (http://rana.lbl.gov/EisenSoftware.htm) and displayed using TreeView (http://rana.lbl.gov/EisenSoftware.htm).; Protocol Type = Feature Extraction; Software: type: feature extraction; Performer: Kate,,Rubins Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 27.00; Parameter Scan Time = 20:21:32; Parameter PMT Volts = 437; Parameter Scan Date = 2005-10-31; Parameter Pixel Size = 10; Parameter Laser on time = 12660; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4200A 01 Autoloader; Parameter Laser Power = 1.46; Parameter Scan Power = 80; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Kate,,Rubins Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 27.00; Parameter Scan Time = 20:21:32; Parameter PMT Volts = 623; Parameter Scan Date = 2005-10-31; Parameter Pixel Size = 10; Parameter Laser on time = 12660; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4200A 01 Autoloader; Parameter Laser Power = 1.73; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 80; Parameter Scanning software = AxImageIO; Performer: Kate,,Rubins

source_name: Killed MPX 24 Mph cells inf w Killed MPX in vitro 5.5.05


title: MPX 12   Mph

description:
Simple annotation: Normal tissue, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/65427.gif

scan_protocol: Rubins 2003 - Data filtering and analysis; Array images were scanned using an Axon Scanner 4000A (Axon Instruments, Union City, CA), and image analysis was performed using GenePix Pro version 3.0.6.89 (Axon Instruments, Union City, CA).  Grids were manually aligned and features were found using the software feature extraction.  Features were visually inspected for blemishes and removed from downstream analysis.    Data were uploaded to the Stanford Microarray Database (http://genome-www5.stanford.edu/)  and normalized using regression correlation.  Data were expressed as the log2 ratio of fluorescence intensities of the sample and the reference, for each element on the array.    Data were filtered to exclude elements that did not have a regression correlation of Cy5 to Cy3 signal over the pixels spanning the array element of ??0.6 and intensity/background ratio of ??2.5 in at least 80% of the arrays.    For each gene, the expression levels over the timecourse for each monkey were ??time-zerotransformed?? by subtracting the average of the pre-infection baseline expression level from that animal so that the values of each timepoint represent changes relative to the uninfected samples.    The genes whose expression varied from the uninfected baseline by at least 3 fold in at least 3 samples were selected for further analysis.    The data were hierarchically clustered using the Cluster program (http://rana.lbl.gov/EisenSoftware.htm) and displayed using TreeView (http://rana.lbl.gov/EisenSoftware.htm).; Protocol Type = Feature Extraction; Software: type: feature extraction; Performer: Kate,,Rubins Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 27.31; Parameter Scan Time = 16:30:57; Parameter PMT Volts = 430; Parameter Scan Date = 2005-10-31; Parameter Pixel Size = 10; Parameter Laser on time = 12429; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4200A 01 Autoloader; Parameter Laser Power = 1.52; Parameter Scan Power = 80; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Kate,,Rubins Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 27.31; Parameter Scan Time = 16:30:57; Parameter PMT Volts = 450; Parameter Scan Date = 2005-10-31; Parameter Pixel Size = 10; Parameter Laser on time = 12429; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4200A 01 Autoloader; Parameter Laser Power = 1.72; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 80; Parameter Scanning software = AxImageIO; Performer: Kate,,Rubins

source_name: MPX 12 Mph cells inf w MPX in vitro 5.5.05


title: EBOV 0 hr FibroS100

description:
Simple annotation: Normal tissue, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs/2004-08/55217.gif

scan_protocol: Rubins 2003 - Data filtering and analysis; Array images were scanned using an Axon Scanner 4000A (Axon Instruments, Union City, CA), and image analysis was performed using GenePix Pro version 3.0.6.89 (Axon Instruments, Union City, CA).  Grids were manually aligned and features were found using the software feature extraction.  Features were visually inspected for blemishes and removed from downstream analysis.    Data were uploaded to the Stanford Microarray Database (http://genome-www5.stanford.edu/)  and normalized using regression correlation.  Data were expressed as the log2 ratio of fluorescence intensities of the sample and the reference, for each element on the array.    Data were filtered to exclude elements that did not have a regression correlation of Cy5 to Cy3 signal over the pixels spanning the array element of ??0.6 and intensity/background ratio of ??2.5 in at least 80% of the arrays.    For each gene, the expression levels over the timecourse for each monkey were ??time-zerotransformed?? by subtracting the average of the pre-infection baseline expression level from that animal so that the values of each timepoint represent changes relative to the uninfected samples.    The genes whose expression varied from the uninfected baseline by at least 3 fold in at least 3 samples were selected for further analysis.    The data were hierarchically clustered using the Cluster program (http://rana.lbl.gov/EisenSoftware.htm) and displayed using TreeView (http://rana.lbl.gov/EisenSoftware.htm).; Protocol Type = Feature Extraction; Software: type: feature extraction; Performer: Kate,,Rubins Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 32.34; Parameter Scan Time = 10:26:40; Parameter PMT Volts = 680; Parameter Scan Date = 2004-08-29; Parameter Pixel Size = 10; Parameter Laser on time = 189470; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.92; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.2; Parameter Scanning software = AxImageIO; Performer: Kate,,Rubins Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 32.34; Parameter Scan Time = 10:26:40; Parameter PMT Volts = 750; Parameter Scan Date = 2004-08-29; Parameter Pixel Size = 10; Parameter Laser on time = 408438; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.68; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Kate,,Rubins

source_name: EBOV 0 hr Primary Human Skin Fibroblasts S100 infected with Ebola-Zaire in vitro 7.29.04


title: g-MPX 24 hr Mf 7.29

description:
Simple annotation: Normal tissue, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs/2004-08/55147.gif

scan_protocol: Rubins 2003 - Data filtering and analysis; Array images were scanned using an Axon Scanner 4000A (Axon Instruments, Union City, CA), and image analysis was performed using GenePix Pro version 3.0.6.89 (Axon Instruments, Union City, CA).  Grids were manually aligned and features were found using the software feature extraction.  Features were visually inspected for blemishes and removed from downstream analysis.    Data were uploaded to the Stanford Microarray Database (http://genome-www5.stanford.edu/)  and normalized using regression correlation.  Data were expressed as the log2 ratio of fluorescence intensities of the sample and the reference, for each element on the array.    Data were filtered to exclude elements that did not have a regression correlation of Cy5 to Cy3 signal over the pixels spanning the array element of ??0.6 and intensity/background ratio of ??2.5 in at least 80% of the arrays.    For each gene, the expression levels over the timecourse for each monkey were ??time-zerotransformed?? by subtracting the average of the pre-infection baseline expression level from that animal so that the values of each timepoint represent changes relative to the uninfected samples.    The genes whose expression varied from the uninfected baseline by at least 3 fold in at least 3 samples were selected for further analysis.    The data were hierarchically clustered using the Cluster program (http://rana.lbl.gov/EisenSoftware.htm) and displayed using TreeView (http://rana.lbl.gov/EisenSoftware.htm).; Protocol Type = Feature Extraction; Software: type: feature extraction; Performer: Kate,,Rubins Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 32.58; Parameter Scan Time = 01:33:05; Parameter PMT Volts = 620; Parameter Scan Date = 2004-08-28; Parameter Pixel Size = 10; Parameter Laser on time = 187916; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.96; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.2; Parameter Scanning software = AxImageIO; Performer: Kate,,Rubins Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 32.58; Parameter Scan Time = 01:33:05; Parameter PMT Volts = 680; Parameter Scan Date = 2004-08-28; Parameter Pixel Size = 10; Parameter Laser on time = 406884; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.65; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Kate,,Rubins

source_name: g-MPX 24 hr Primary Human Macrophages infected with Killed Monkeypox-Zaire in vitro 7.29.04


title: MPX 24 hr FibroS100

description:
Simple annotation: Normal tissue, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs/2004-08/55216.gif

scan_protocol: Rubins 2003 - Data filtering and analysis; Array images were scanned using an Axon Scanner 4000A (Axon Instruments, Union City, CA), and image analysis was performed using GenePix Pro version 3.0.6.89 (Axon Instruments, Union City, CA).  Grids were manually aligned and features were found using the software feature extraction.  Features were visually inspected for blemishes and removed from downstream analysis.    Data were uploaded to the Stanford Microarray Database (http://genome-www5.stanford.edu/)  and normalized using regression correlation.  Data were expressed as the log2 ratio of fluorescence intensities of the sample and the reference, for each element on the array.    Data were filtered to exclude elements that did not have a regression correlation of Cy5 to Cy3 signal over the pixels spanning the array element of ??0.6 and intensity/background ratio of ??2.5 in at least 80% of the arrays.    For each gene, the expression levels over the timecourse for each monkey were ??time-zerotransformed?? by subtracting the average of the pre-infection baseline expression level from that animal so that the values of each timepoint represent changes relative to the uninfected samples.    The genes whose expression varied from the uninfected baseline by at least 3 fold in at least 3 samples were selected for further analysis.    The data were hierarchically clustered using the Cluster program (http://rana.lbl.gov/EisenSoftware.htm) and displayed using TreeView (http://rana.lbl.gov/EisenSoftware.htm).; Protocol Type = Feature Extraction; Software: type: feature extraction; Performer: Kate,,Rubins Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 32.25; Parameter Scan Time = 10:15:29; Parameter PMT Volts = 670; Parameter Scan Date = 2004-08-29; Parameter Pixel Size = 10; Parameter Laser on time = 189459; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.77; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.2; Parameter Scanning software = AxImageIO; Performer: Kate,,Rubins Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 32.25; Parameter Scan Time = 10:15:29; Parameter PMT Volts = 790; Parameter Scan Date = 2004-08-29; Parameter Pixel Size = 10; Parameter Laser on time = 408427; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.67; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Kate,,Rubins

source_name: MPX 24 hr Primary Human Skin Fibroblasts S100 infected with Ebola-Zaire in vitro 7.29.04


title: g-MPX 8 hr Mf 7.29

description:
Simple annotation: Normal tissue, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs/2004-08/55145.gif

scan_protocol: Rubins 2003 - Data filtering and analysis; Array images were scanned using an Axon Scanner 4000A (Axon Instruments, Union City, CA), and image analysis was performed using GenePix Pro version 3.0.6.89 (Axon Instruments, Union City, CA).  Grids were manually aligned and features were found using the software feature extraction.  Features were visually inspected for blemishes and removed from downstream analysis.    Data were uploaded to the Stanford Microarray Database (http://genome-www5.stanford.edu/)  and normalized using regression correlation.  Data were expressed as the log2 ratio of fluorescence intensities of the sample and the reference, for each element on the array.    Data were filtered to exclude elements that did not have a regression correlation of Cy5 to Cy3 signal over the pixels spanning the array element of ??0.6 and intensity/background ratio of ??2.5 in at least 80% of the arrays.    For each gene, the expression levels over the timecourse for each monkey were ??time-zerotransformed?? by subtracting the average of the pre-infection baseline expression level from that animal so that the values of each timepoint represent changes relative to the uninfected samples.    The genes whose expression varied from the uninfected baseline by at least 3 fold in at least 3 samples were selected for further analysis.    The data were hierarchically clustered using the Cluster program (http://rana.lbl.gov/EisenSoftware.htm) and displayed using TreeView (http://rana.lbl.gov/EisenSoftware.htm).; Protocol Type = Feature Extraction; Software: type: feature extraction; Performer: Kate,,Rubins Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 32.55; Parameter Scan Time = 01:01:36; Parameter PMT Volts = 620; Parameter Scan Date = 2004-08-28; Parameter Pixel Size = 10; Parameter Laser on time = 187884; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.87; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.2; Parameter Scanning software = AxImageIO; Performer: Kate,,Rubins Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 32.55; Parameter Scan Time = 01:01:36; Parameter PMT Volts = 680; Parameter Scan Date = 2004-08-28; Parameter Pixel Size = 10; Parameter Laser on time = 406853; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.66; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Kate,,Rubins

source_name: g-MPX 8 hr Primary Human Macrophages infected with Killed Monkeypox-Zaire in vitro 7.29.04

value: time(relative) 8 h


title: EBOV 0 Pool FibroS100

description:
Simple annotation: Normal tissue, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs/2004-08/55218.gif

scan_protocol: Rubins 2003 - Data filtering and analysis; Array images were scanned using an Axon Scanner 4000A (Axon Instruments, Union City, CA), and image analysis was performed using GenePix Pro version 3.0.6.89 (Axon Instruments, Union City, CA).  Grids were manually aligned and features were found using the software feature extraction.  Features were visually inspected for blemishes and removed from downstream analysis.    Data were uploaded to the Stanford Microarray Database (http://genome-www5.stanford.edu/)  and normalized using regression correlation.  Data were expressed as the log2 ratio of fluorescence intensities of the sample and the reference, for each element on the array.    Data were filtered to exclude elements that did not have a regression correlation of Cy5 to Cy3 signal over the pixels spanning the array element of ??0.6 and intensity/background ratio of ??2.5 in at least 80% of the arrays.    For each gene, the expression levels over the timecourse for each monkey were ??time-zerotransformed?? by subtracting the average of the pre-infection baseline expression level from that animal so that the values of each timepoint represent changes relative to the uninfected samples.    The genes whose expression varied from the uninfected baseline by at least 3 fold in at least 3 samples were selected for further analysis.    The data were hierarchically clustered using the Cluster program (http://rana.lbl.gov/EisenSoftware.htm) and displayed using TreeView (http://rana.lbl.gov/EisenSoftware.htm).; Protocol Type = Feature Extraction; Software: type: feature extraction; Performer: Kate,,Rubins Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 32.43; Parameter Scan Time = 10:37:54; Parameter PMT Volts = 690; Parameter Scan Date = 2004-08-29; Parameter Pixel Size = 10; Parameter Laser on time = 189481; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 3.09; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.2; Parameter Scanning software = AxImageIO; Performer: Kate,,Rubins Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 32.43; Parameter Scan Time = 10:37:54; Parameter PMT Volts = 740; Parameter Scan Date = 2004-08-29; Parameter Pixel Size = 10; Parameter Laser on time = 408449; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.67; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Kate,,Rubins

source_name: EBOV 0 Pool Primary Human Skin Fibroblasts S100 infected with Ebola-Zaire in vitro 7.29.04


title: Mock 12 hr Mf 7.29

description:
Simple annotation: Normal tissue, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs/2004-08/55141.gif

scan_protocol: Rubins 2003 - Data filtering and analysis; Array images were scanned using an Axon Scanner 4000A (Axon Instruments, Union City, CA), and image analysis was performed using GenePix Pro version 3.0.6.89 (Axon Instruments, Union City, CA).  Grids were manually aligned and features were found using the software feature extraction.  Features were visually inspected for blemishes and removed from downstream analysis.    Data were uploaded to the Stanford Microarray Database (http://genome-www5.stanford.edu/)  and normalized using regression correlation.  Data were expressed as the log2 ratio of fluorescence intensities of the sample and the reference, for each element on the array.    Data were filtered to exclude elements that did not have a regression correlation of Cy5 to Cy3 signal over the pixels spanning the array element of ??0.6 and intensity/background ratio of ??2.5 in at least 80% of the arrays.    For each gene, the expression levels over the timecourse for each monkey were ??time-zerotransformed?? by subtracting the average of the pre-infection baseline expression level from that animal so that the values of each timepoint represent changes relative to the uninfected samples.    The genes whose expression varied from the uninfected baseline by at least 3 fold in at least 3 samples were selected for further analysis.    The data were hierarchically clustered using the Cluster program (http://rana.lbl.gov/EisenSoftware.htm) and displayed using TreeView (http://rana.lbl.gov/EisenSoftware.htm).; Protocol Type = Feature Extraction; Software: type: feature extraction; Performer: Kate,,Rubins Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 32.31; Parameter Scan Time = 23:52:13; Parameter PMT Volts = 620; Parameter Scan Date = 2004-08-27; Parameter Pixel Size = 10; Parameter Laser on time = 187815; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.70; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.2; Parameter Scanning software = AxImageIO; Performer: Kate,,Rubins Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 32.31; Parameter Scan Time = 23:52:13; Parameter PMT Volts = 650; Parameter Scan Date = 2004-08-27; Parameter Pixel Size = 10; Parameter Laser on time = 406783; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.65; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Kate,,Rubins

source_name: Mock 12 hr Primary Human Macrophages Mock Infected in vitro 7.29.04


title: VAC 0 Pool Mf 7.29

description:
Simple annotation: Normal tissue, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs/2004-08/55149.gif

scan_protocol: Rubins 2003 - Data filtering and analysis; Array images were scanned using an Axon Scanner 4000A (Axon Instruments, Union City, CA), and image analysis was performed using GenePix Pro version 3.0.6.89 (Axon Instruments, Union City, CA).  Grids were manually aligned and features were found using the software feature extraction.  Features were visually inspected for blemishes and removed from downstream analysis.    Data were uploaded to the Stanford Microarray Database (http://genome-www5.stanford.edu/)  and normalized using regression correlation.  Data were expressed as the log2 ratio of fluorescence intensities of the sample and the reference, for each element on the array.    Data were filtered to exclude elements that did not have a regression correlation of Cy5 to Cy3 signal over the pixels spanning the array element of ??0.6 and intensity/background ratio of ??2.5 in at least 80% of the arrays.    For each gene, the expression levels over the timecourse for each monkey were ??time-zerotransformed?? by subtracting the average of the pre-infection baseline expression level from that animal so that the values of each timepoint represent changes relative to the uninfected samples.    The genes whose expression varied from the uninfected baseline by at least 3 fold in at least 3 samples were selected for further analysis.    The data were hierarchically clustered using the Cluster program (http://rana.lbl.gov/EisenSoftware.htm) and displayed using TreeView (http://rana.lbl.gov/EisenSoftware.htm).; Protocol Type = Feature Extraction; Software: type: feature extraction; Performer: Kate,,Rubins Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 32.67; Parameter Scan Time = 02:02:41; Parameter PMT Volts = 620; Parameter Scan Date = 2004-08-28; Parameter Pixel Size = 10; Parameter Laser on time = 187946; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 3.18; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.2; Parameter Scanning software = AxImageIO; Performer: Kate,,Rubins Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 32.67; Parameter Scan Time = 02:02:41; Parameter PMT Volts = 680; Parameter Scan Date = 2004-08-28; Parameter Pixel Size = 10; Parameter Laser on time = 406914; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.67; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Kate,,Rubins

source_name: VAC 0 Pool Primary Human Macrophages infected with Vaccinia WR in vitro 7.29.04


title: g-MPX 4 hr Mf 7.29

description:
Simple annotation: Normal tissue, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs/2004-08/55144.gif

scan_protocol: Rubins 2003 - Data filtering and analysis; Array images were scanned using an Axon Scanner 4000A (Axon Instruments, Union City, CA), and image analysis was performed using GenePix Pro version 3.0.6.89 (Axon Instruments, Union City, CA).  Grids were manually aligned and features were found using the software feature extraction.  Features were visually inspected for blemishes and removed from downstream analysis.    Data were uploaded to the Stanford Microarray Database (http://genome-www5.stanford.edu/)  and normalized using regression correlation.  Data were expressed as the log2 ratio of fluorescence intensities of the sample and the reference, for each element on the array.    Data were filtered to exclude elements that did not have a regression correlation of Cy5 to Cy3 signal over the pixels spanning the array element of ??0.6 and intensity/background ratio of ??2.5 in at least 80% of the arrays.    For each gene, the expression levels over the timecourse for each monkey were ??time-zerotransformed?? by subtracting the average of the pre-infection baseline expression level from that animal so that the values of each timepoint represent changes relative to the uninfected samples.    The genes whose expression varied from the uninfected baseline by at least 3 fold in at least 3 samples were selected for further analysis.    The data were hierarchically clustered using the Cluster program (http://rana.lbl.gov/EisenSoftware.htm) and displayed using TreeView (http://rana.lbl.gov/EisenSoftware.htm).; Protocol Type = Feature Extraction; Software: type: feature extraction; Performer: Kate,,Rubins Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 32.58; Parameter Scan Time = 00:40:58; Parameter PMT Volts = 620; Parameter Scan Date = 2004-08-28; Parameter Pixel Size = 10; Parameter Laser on time = 187864; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.85; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.2; Parameter Scanning software = AxImageIO; Performer: Kate,,Rubins Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 32.58; Parameter Scan Time = 00:40:58; Parameter PMT Volts = 680; Parameter Scan Date = 2004-08-28; Parameter Pixel Size = 10; Parameter Laser on time = 406832; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.66; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Kate,,Rubins

source_name: g-MPX 4 hr Primary Human Macrophages infected with Killed Monkeypox-Zaire in vitro 7.29.04

value: time(relative) 4 h


title: g-MPX 2 hr Mf 7.29

description:
Simple annotation: Normal tissue, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs/2004-08/55143.gif

scan_protocol: Rubins 2003 - Data filtering and analysis; Array images were scanned using an Axon Scanner 4000A (Axon Instruments, Union City, CA), and image analysis was performed using GenePix Pro version 3.0.6.89 (Axon Instruments, Union City, CA).  Grids were manually aligned and features were found using the software feature extraction.  Features were visually inspected for blemishes and removed from downstream analysis.    Data were uploaded to the Stanford Microarray Database (http://genome-www5.stanford.edu/)  and normalized using regression correlation.  Data were expressed as the log2 ratio of fluorescence intensities of the sample and the reference, for each element on the array.    Data were filtered to exclude elements that did not have a regression correlation of Cy5 to Cy3 signal over the pixels spanning the array element of ??0.6 and intensity/background ratio of ??2.5 in at least 80% of the arrays.    For each gene, the expression levels over the timecourse for each monkey were ??time-zerotransformed?? by subtracting the average of the pre-infection baseline expression level from that animal so that the values of each timepoint represent changes relative to the uninfected samples.    The genes whose expression varied from the uninfected baseline by at least 3 fold in at least 3 samples were selected for further analysis.    The data were hierarchically clustered using the Cluster program (http://rana.lbl.gov/EisenSoftware.htm) and displayed using TreeView (http://rana.lbl.gov/EisenSoftware.htm).; Protocol Type = Feature Extraction; Software: type: feature extraction; Performer: Kate,,Rubins Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 32.49; Parameter Scan Time = 00:19:18; Parameter PMT Volts = 620; Parameter Scan Date = 2004-08-28; Parameter Pixel Size = 10; Parameter Laser on time = 187842; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.72; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.2; Parameter Scanning software = AxImageIO; Performer: Kate,,Rubins Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 32.49; Parameter Scan Time = 00:19:18; Parameter PMT Volts = 670; Parameter Scan Date = 2004-08-28; Parameter Pixel Size = 10; Parameter Laser on time = 406810; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.65; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Kate,,Rubins

source_name: g-MPX 2 hr Primary Human Macrophages infected with Killed Monkeypox-Zaire in vitro 7.29.04


title: MPX 1 hr FibroS100

description:
Simple annotation: Normal tissue, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs/2004-08/55211.gif

scan_protocol: Rubins 2003 - Data filtering and analysis; Array images were scanned using an Axon Scanner 4000A (Axon Instruments, Union City, CA), and image analysis was performed using GenePix Pro version 3.0.6.89 (Axon Instruments, Union City, CA).  Grids were manually aligned and features were found using the software feature extraction.  Features were visually inspected for blemishes and removed from downstream analysis.    Data were uploaded to the Stanford Microarray Database (http://genome-www5.stanford.edu/)  and normalized using regression correlation.  Data were expressed as the log2 ratio of fluorescence intensities of the sample and the reference, for each element on the array.    Data were filtered to exclude elements that did not have a regression correlation of Cy5 to Cy3 signal over the pixels spanning the array element of ??0.6 and intensity/background ratio of ??2.5 in at least 80% of the arrays.    For each gene, the expression levels over the timecourse for each monkey were ??time-zerotransformed?? by subtracting the average of the pre-infection baseline expression level from that animal so that the values of each timepoint represent changes relative to the uninfected samples.    The genes whose expression varied from the uninfected baseline by at least 3 fold in at least 3 samples were selected for further analysis.    The data were hierarchically clustered using the Cluster program (http://rana.lbl.gov/EisenSoftware.htm) and displayed using TreeView (http://rana.lbl.gov/EisenSoftware.htm).; Protocol Type = Feature Extraction; Software: type: feature extraction; Performer: Kate,,Rubins Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.70; Parameter Scan Time = 09:14:42; Parameter PMT Volts = 670; Parameter Scan Date = 2004-08-29; Parameter Pixel Size = 10; Parameter Laser on time = 189398; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.88; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.2; Parameter Scanning software = AxImageIO; Performer: Kate,,Rubins Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.70; Parameter Scan Time = 09:14:42; Parameter PMT Volts = 730; Parameter Scan Date = 2004-08-29; Parameter Pixel Size = 10; Parameter Laser on time = 408367; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.69; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Kate,,Rubins

source_name: MPX 1 hr Primary Human Skin Fibroblasts S100 infected with Monkeypox-Zaire in vitro 7.29.04


title: MPX 0 Pool FibroS100

description:
Simple annotation: Normal tissue, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs/2004-08/55210.gif

scan_protocol: Rubins 2003 - Data filtering and analysis; Array images were scanned using an Axon Scanner 4000A (Axon Instruments, Union City, CA), and image analysis was performed using GenePix Pro version 3.0.6.89 (Axon Instruments, Union City, CA).  Grids were manually aligned and features were found using the software feature extraction.  Features were visually inspected for blemishes and removed from downstream analysis.    Data were uploaded to the Stanford Microarray Database (http://genome-www5.stanford.edu/)  and normalized using regression correlation.  Data were expressed as the log2 ratio of fluorescence intensities of the sample and the reference, for each element on the array.    Data were filtered to exclude elements that did not have a regression correlation of Cy5 to Cy3 signal over the pixels spanning the array element of ??0.6 and intensity/background ratio of ??2.5 in at least 80% of the arrays.    For each gene, the expression levels over the timecourse for each monkey were ??time-zerotransformed?? by subtracting the average of the pre-infection baseline expression level from that animal so that the values of each timepoint represent changes relative to the uninfected samples.    The genes whose expression varied from the uninfected baseline by at least 3 fold in at least 3 samples were selected for further analysis.    The data were hierarchically clustered using the Cluster program (http://rana.lbl.gov/EisenSoftware.htm) and displayed using TreeView (http://rana.lbl.gov/EisenSoftware.htm).; Protocol Type = Feature Extraction; Software: type: feature extraction; Performer: Kate,,Rubins Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.58; Parameter Scan Time = 09:00:42; Parameter PMT Volts = 660; Parameter Scan Date = 2004-08-29; Parameter Pixel Size = 10; Parameter Laser on time = 189384; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.97; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.2; Parameter Scanning software = AxImageIO; Performer: Kate,,Rubins Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.58; Parameter Scan Time = 09:00:42; Parameter PMT Volts = 700; Parameter Scan Date = 2004-08-29; Parameter Pixel Size = 10; Parameter Laser on time = 408352; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.68; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Kate,,Rubins

source_name: Stratagene UHR RNA, 1 round of amp(Ambion MessageAmp), 6/27/02, spiked in MPX/VAC 8/26/04

source_name: MPX 0 Pool Primary Human Skin Fibroblasts S100 infected with Monkeypox-Zaire in vitro 7.29.04


title: MPX 8 hr FibroS100

description:
Simple annotation: Normal tissue, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs/2004-08/55214.gif

scan_protocol: Rubins 2003 - Data filtering and analysis; Array images were scanned using an Axon Scanner 4000A (Axon Instruments, Union City, CA), and image analysis was performed using GenePix Pro version 3.0.6.89 (Axon Instruments, Union City, CA).  Grids were manually aligned and features were found using the software feature extraction.  Features were visually inspected for blemishes and removed from downstream analysis.    Data were uploaded to the Stanford Microarray Database (http://genome-www5.stanford.edu/)  and normalized using regression correlation.  Data were expressed as the log2 ratio of fluorescence intensities of the sample and the reference, for each element on the array.    Data were filtered to exclude elements that did not have a regression correlation of Cy5 to Cy3 signal over the pixels spanning the array element of ??0.6 and intensity/background ratio of ??2.5 in at least 80% of the arrays.    For each gene, the expression levels over the timecourse for each monkey were ??time-zerotransformed?? by subtracting the average of the pre-infection baseline expression level from that animal so that the values of each timepoint represent changes relative to the uninfected samples.    The genes whose expression varied from the uninfected baseline by at least 3 fold in at least 3 samples were selected for further analysis.    The data were hierarchically clustered using the Cluster program (http://rana.lbl.gov/EisenSoftware.htm) and displayed using TreeView (http://rana.lbl.gov/EisenSoftware.htm).; Protocol Type = Feature Extraction; Software: type: feature extraction; Performer: Kate,,Rubins Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 32.09; Parameter Scan Time = 09:52:22; Parameter PMT Volts = 670; Parameter Scan Date = 2004-08-29; Parameter Pixel Size = 10; Parameter Laser on time = 189435; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.66; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.2; Parameter Scanning software = AxImageIO; Performer: Kate,,Rubins Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 32.09; Parameter Scan Time = 09:52:22; Parameter PMT Volts = 680; Parameter Scan Date = 2004-08-29; Parameter Pixel Size = 10; Parameter Laser on time = 408404; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.66; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Kate,,Rubins

source_name: MPX 8 hr Primary Human Skin Fibroblasts S100 infected with Monkeypox-Zaire in vitro 7.29.04


title: MPX 2 hr FibroS100

description:
Simple annotation: Normal tissue, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs/2004-08/55212.gif

scan_protocol: Rubins 2003 - Data filtering and analysis; Array images were scanned using an Axon Scanner 4000A (Axon Instruments, Union City, CA), and image analysis was performed using GenePix Pro version 3.0.6.89 (Axon Instruments, Union City, CA).  Grids were manually aligned and features were found using the software feature extraction.  Features were visually inspected for blemishes and removed from downstream analysis.    Data were uploaded to the Stanford Microarray Database (http://genome-www5.stanford.edu/)  and normalized using regression correlation.  Data were expressed as the log2 ratio of fluorescence intensities of the sample and the reference, for each element on the array.    Data were filtered to exclude elements that did not have a regression correlation of Cy5 to Cy3 signal over the pixels spanning the array element of ??0.6 and intensity/background ratio of ??2.5 in at least 80% of the arrays.    For each gene, the expression levels over the timecourse for each monkey were ??time-zerotransformed?? by subtracting the average of the pre-infection baseline expression level from that animal so that the values of each timepoint represent changes relative to the uninfected samples.    The genes whose expression varied from the uninfected baseline by at least 3 fold in at least 3 samples were selected for further analysis.    The data were hierarchically clustered using the Cluster program (http://rana.lbl.gov/EisenSoftware.htm) and displayed using TreeView (http://rana.lbl.gov/EisenSoftware.htm).; Protocol Type = Feature Extraction; Software: type: feature extraction; Performer: Kate,,Rubins Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.88; Parameter Scan Time = 09:28:53; Parameter PMT Volts = 670; Parameter Scan Date = 2004-08-29; Parameter Pixel Size = 10; Parameter Laser on time = 189412; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.96; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.2; Parameter Scanning software = AxImageIO; Performer: Kate,,Rubins Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.88; Parameter Scan Time = 09:28:53; Parameter PMT Volts = 690; Parameter Scan Date = 2004-08-29; Parameter Pixel Size = 10; Parameter Laser on time = 408380; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.69; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Kate,,Rubins

source_name: MPX 2 hr Primary Human Skin Fibroblasts S100 infected with Monkeypox-Zaire in vitro 7.29.04


title: VAC 0 hr Mf 7.29

description:
Simple annotation: Normal tissue, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs/2004-08/55148.gif

scan_protocol: Rubins 2003 - Data filtering and analysis; Array images were scanned using an Axon Scanner 4000A (Axon Instruments, Union City, CA), and image analysis was performed using GenePix Pro version 3.0.6.89 (Axon Instruments, Union City, CA).  Grids were manually aligned and features were found using the software feature extraction.  Features were visually inspected for blemishes and removed from downstream analysis.    Data were uploaded to the Stanford Microarray Database (http://genome-www5.stanford.edu/)  and normalized using regression correlation.  Data were expressed as the log2 ratio of fluorescence intensities of the sample and the reference, for each element on the array.    Data were filtered to exclude elements that did not have a regression correlation of Cy5 to Cy3 signal over the pixels spanning the array element of ??0.6 and intensity/background ratio of ??2.5 in at least 80% of the arrays.    For each gene, the expression levels over the timecourse for each monkey were ??time-zerotransformed?? by subtracting the average of the pre-infection baseline expression level from that animal so that the values of each timepoint represent changes relative to the uninfected samples.    The genes whose expression varied from the uninfected baseline by at least 3 fold in at least 3 samples were selected for further analysis.    The data were hierarchically clustered using the Cluster program (http://rana.lbl.gov/EisenSoftware.htm) and displayed using TreeView (http://rana.lbl.gov/EisenSoftware.htm).; Protocol Type = Feature Extraction; Software: type: feature extraction; Performer: Kate,,Rubins Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 32.58; Parameter Scan Time = 01:45:31; Parameter PMT Volts = 620; Parameter Scan Date = 2004-08-28; Parameter Pixel Size = 10; Parameter Laser on time = 187928; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.93; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.2; Parameter Scanning software = AxImageIO; Performer: Kate,,Rubins Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 32.58; Parameter Scan Time = 01:45:31; Parameter PMT Volts = 680; Parameter Scan Date = 2004-08-28; Parameter Pixel Size = 10; Parameter Laser on time = 406896; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.66; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Kate,,Rubins

source_name: VAC 0 hr Primary Human Macrophages infected with Vaccinia WR in vitro 7.29.04


title: Mock 2 hr Mf 7.29

description:
Simple annotation: Normal tissue, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs/2004-08/55139.gif

scan_protocol: Rubins 2003 - Data filtering and analysis; Array images were scanned using an Axon Scanner 4000A (Axon Instruments, Union City, CA), and image analysis was performed using GenePix Pro version 3.0.6.89 (Axon Instruments, Union City, CA).  Grids were manually aligned and features were found using the software feature extraction.  Features were visually inspected for blemishes and removed from downstream analysis.    Data were uploaded to the Stanford Microarray Database (http://genome-www5.stanford.edu/)  and normalized using regression correlation.  Data were expressed as the log2 ratio of fluorescence intensities of the sample and the reference, for each element on the array.    Data were filtered to exclude elements that did not have a regression correlation of Cy5 to Cy3 signal over the pixels spanning the array element of ??0.6 and intensity/background ratio of ??2.5 in at least 80% of the arrays.    For each gene, the expression levels over the timecourse for each monkey were ??time-zerotransformed?? by subtracting the average of the pre-infection baseline expression level from that animal so that the values of each timepoint represent changes relative to the uninfected samples.    The genes whose expression varied from the uninfected baseline by at least 3 fold in at least 3 samples were selected for further analysis.    The data were hierarchically clustered using the Cluster program (http://rana.lbl.gov/EisenSoftware.htm) and displayed using TreeView (http://rana.lbl.gov/EisenSoftware.htm).; Protocol Type = Feature Extraction; Software: type: feature extraction; Performer: Kate,,Rubins Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 32.16; Parameter Scan Time = 23:23:08; Parameter PMT Volts = 600; Parameter Scan Date = 2004-08-27; Parameter Pixel Size = 10; Parameter Laser on time = 187786; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.92; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.2; Parameter Scanning software = AxImageIO; Performer: Kate,,Rubins Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 32.16; Parameter Scan Time = 23:23:08; Parameter PMT Volts = 670; Parameter Scan Date = 2004-08-27; Parameter Pixel Size = 10; Parameter Laser on time = 406754; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.65; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Kate,,Rubins

source_name: Mock 2 hr Primary Human Macrophages Mock Infected in vitro 7.29.04


title: Mock 4 hr Mf 7.29

description:
Simple annotation: Normal tissue, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs/2004-08/55140.gif

scan_protocol: Rubins 2003 - Data filtering and analysis; Array images were scanned using an Axon Scanner 4000A (Axon Instruments, Union City, CA), and image analysis was performed using GenePix Pro version 3.0.6.89 (Axon Instruments, Union City, CA).  Grids were manually aligned and features were found using the software feature extraction.  Features were visually inspected for blemishes and removed from downstream analysis.    Data were uploaded to the Stanford Microarray Database (http://genome-www5.stanford.edu/)  and normalized using regression correlation.  Data were expressed as the log2 ratio of fluorescence intensities of the sample and the reference, for each element on the array.    Data were filtered to exclude elements that did not have a regression correlation of Cy5 to Cy3 signal over the pixels spanning the array element of ??0.6 and intensity/background ratio of ??2.5 in at least 80% of the arrays.    For each gene, the expression levels over the timecourse for each monkey were ??time-zerotransformed?? by subtracting the average of the pre-infection baseline expression level from that animal so that the values of each timepoint represent changes relative to the uninfected samples.    The genes whose expression varied from the uninfected baseline by at least 3 fold in at least 3 samples were selected for further analysis.    The data were hierarchically clustered using the Cluster program (http://rana.lbl.gov/EisenSoftware.htm) and displayed using TreeView (http://rana.lbl.gov/EisenSoftware.htm).; Protocol Type = Feature Extraction; Software: type: feature extraction; Performer: Kate,,Rubins Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 32.22; Parameter Scan Time = 23:34:06; Parameter PMT Volts = 600; Parameter Scan Date = 2004-08-27; Parameter Pixel Size = 10; Parameter Laser on time = 187797; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.95; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.2; Parameter Scanning software = AxImageIO; Performer: Kate,,Rubins Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 32.22; Parameter Scan Time = 23:34:06; Parameter PMT Volts = 670; Parameter Scan Date = 2004-08-27; Parameter Pixel Size = 10; Parameter Laser on time = 406765; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.66; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Kate,,Rubins

source_name: Mock 4 hr Primary Human Macrophages Mock Infected in vitro 7.29.04