title: wildtype under low Mg2+ Ca2+ VS high Mg2+ Ca2+ replicate3

status: Public on Jul 16 2008

city: Davis

first: Malinee

last: Sriariyanun

state: CA

address: 451 East Health Sciences Drive

department: Plant Pathology

institute: University of California, Davis

description: Biologiacl replicate3 of 3

hyb_protocol: Probes were resuspended in 28 ul of preheated 1X hybridization buffer (5X SSC, 0.1% SDS, 1% BSA) at 42°C. To block non-specific hybridization, add 2 ul salmon sperm DNA (10 ug/ul) into the solution. Labeled probes were denatured by heating mixture at 95 °C for 3 mins and snap cool on ice for 30 seconds. Probed were applied into injector to hybridize with printed slides. Samples were hybridized for 16 hours (42°C in humidified water bath), sequentially washed with 42°C preheated low stringency wash buffer (2x SSC and 0.1% SDS) 5 minutes, then washed with high stringency wash buffer (0.1x SSC and 0.1% SDS) 5 minutes. Slides were transferred to 0.1x SSC buffer and agitated for 5 mins (2times) and dried under N2 (5 min, 30C). Slides were kept under N2 until scanning.

scan_protocol: Hybridized microarray slides were imaged using a GenePix 4000B dual laser microarray scanner (Axon Instruments, USA) at 5 µm resolution. Slides were imaged using 100% laser power for both lasers (532 and 635 nm).

data_processing:
All images were processed using GenePix software (Axon Instruments, USA) for element identification and quantitation. The metadata associated with the hybridizations, along with the “raw” intensities obtained from the GenePix quantitation.
LMGene package (Rocke DM 2004) that is code for R analysis was used to normalize our data as we described in Seo et al 2008.

organism: Xanthomonas oryzae pv. oryzae PXO99A

source_name: Total RNA from Xoo PXO99A cultured in modified M9 media containing low Mg2+ Ca2+ concentration (10 uM) labeled with Cyanine-5.

label_protocol: 100 ng of total RNA were amplified by using MessageAmpTM II – Bacteria kit (Ambion Inc., CA, USA) according to manufacturer’s protocol. The purified amplified RNA was used as template for generating labelled cDNA probe by using SuperScript TM Indirect cDNA Labelling System (Invitrogen, CA, USA). 500 ng of aRNA was mixed with 5 µg Anchor Oligo(dT)20 Primer and 3 µg Random hexamers, incubated in 70 oC thermal cycler for 10 mins, and then place on ice for 5 mins. First-Strand cDNA synthesis master mix (containing 6 µl 5X First-Strand buffer, 5 mM DTT, 1.5 µl dNTP mix including amino-modified nucleotides, 40 units RNaseOUTTM, 800 units SuperScriptTM III RT) was added in 30 µl reaction, and incubated in 46 oC thermal cycler for 3 hrs. Synthesized cDNA was hydrolysed in 70 oC for 10 mins with 15 µl of 1 N NaOH, and then neutralized with 15 µl of 1 N HCl. cDNA was next purified by adding 20 µl 3 M sodium acetate, pH 5.2 to adjust pH and followed the S.N.A.P.TM Column purification protocol and proceed directly to ethanol precipitation. Purified first-strand cDNA was resuspended in 5 µl of 2X Coupling buffer to incorporate with either Cy3TM or Cy5TM dye solution and 5 µl of DMSO (Amersham Biosciences, NJ, USA), incubated in the dark for 1 hr, and finally labelled cDNA was purified, again, with S.N.A.P.TM Column. 50 pMol of each labelled cDNA samples were mixed with their counter-dye-partner samples until ready to precede to array hybridization.

growth_protocol: Cells were grown at 28 0C with shaking at 200 rpm, in nutrient-rich PSB media containing 10 g of peptone, 10 g of sucrose, 1 g of L-glutamic acid (monosodium salt). Bacterial cells were cultured in PSB media until OD600 is 0.2, washed twice, and immediately transfer into modified M9 media containing either low and high Mg2+ and Ca2+ (10 uM, 10 mM) for 16 hrs. Cells were washed twice and harvested. Three separated cultures were used for each microarray studies

extract_protocol: A bacterial 1010-cells culture was harvested in a centrifuge tube and cell pellets were frozen in -80 0C immediately until RNA isolation. RNA was isolated using Trizol reagent (Invitrogen Corp.) and protocol is described in manufacturer manual. The RNA samples were treated with DNaseI (10 units, Promega Corp., Madison, WI, U.S.A.) for 30 mins at 37 0C, followed by column purification using RNeasy mini kit (Qiagen, Germantown, MD, U.S.A.). The quality of RNA was determined by gel electrophoresis on a 1% agarose gel and verified visually on a Nanodrop, or by Agilent 2100 Bioanalyzer (Agilent Technologies). The quantity of total RNA and mRNA were determined by measuring the absorbance at 260nm and 280nm. In addition, the level of protein contamination in the RNA was measured by using A260/A280 ratio.

tag: cultured in PSB until OD =0.2 and incubated in modified M9 media 16 hrs

source_name: Total RNA from Xoo PXO99A cultured in modified M9 media containing high Mg2+ Ca2+ concentration (10 mM) labeled with Cyanine-3.


title: wildtype under low Mg2+ Ca2+ VS high Mg2+ Ca2+ replicate3, counter dye swap

type: RNA

country: USA

description: Biologiacl replicate3 of 3

molecule: total RNA

source_name: Total RNA from Xoo PXO99A cultured in modified M9 media containing high Mg2+ Ca2+ concentration (10 mM) labeled with Cyanine-5.

source_name: Total RNA from Xoo PXO99A cultured in modified M9 media containing low Mg2+ Ca2+ concentration (10 uM) labeled with Cyanine-3.


title: wildtype under low Mg2+ Ca2+ VS high Mg2+ Ca2+ replicate2, counter dye swap

description: Biologiacl replicate2 of 3


title: wildtype under low Mg2+ Ca2+ VS high Mg2+ Ca2+ replicate2

description: Biologiacl replicate2 of 3


title: wildtype under low Mg2+ Ca2+ VS high Mg2+ Ca2+ replicate1, counter dye swap

description: Biologiacl replicate1 of 3


title: wildtype under low Mg2+ Ca2+ VS high Mg2+ Ca2+ replicate1

description: Biologiacl replicate1 of 3


title: phoP knockout under low Mg2+ Ca2+ VS high Mg2+ Ca2+ replicate3

description: Biologiacl replicate3 of 3

source_name: Total RNA from Xoo phoP knockout mutant cultured in modified M9 media containing low Mg2+ Ca2+ concentration (10 uM) labeled with Cyanine-5.

source_name: Total RNA from Xoo phoP knockout mutant cultured in modified M9 media containing high Mg2+ Ca2+ concentration (10 mM) labeled with Cyanine-3.


title: NHDF 24hr Mock A

status: Public on Jul 17 2008

city: Cambridge

first: Kate

last: Rubins

state: MA

address: Nine Cambridge Center

institute: Whitehead Institute for Biomedical Research

description:
Simple annotation: Normal tissue, Fibroblasts
Image: http://smd.stanford.edu/MicroArray/gifs/2005-04/60853.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 = 39.01; Parameter Scan Time = 14:45:04; Parameter PMT Volts = 550; Parameter Scan Date = 2005-03-07; Parameter Pixel Size = 10; Parameter Laser on time = 208243; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.41; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; 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 = 39.01; Parameter Scan Time = 14:45:04; Parameter PMT Volts = 650; Parameter Scan Date = 2005-03-07; Parameter Pixel Size = 10; Parameter Laser on time = 573047; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.95; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; 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)

organism: Homo sapiens

source_name: Stratagene Universal Human Reference RNA, 1 round of amp(Ambion MessageAmp), 6/27/02

label_protocol: not provided

extract_protocol: not provided

source_name: NHDF 24hr Mock A

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: NHDF 24hr Mock A

tag: Compound Based Treatment

tag: Infection

tag: Cell Line

value: Primary Human Fibroblast

tag: Measurement

value: time(relative) 24 h


title: phoP knockout under low Mg2+ Ca2+ VS high Mg2+ Ca2+ replicate3, counter dye swap

description: Biologiacl replicate3 of 3

source_name: Total RNA from Xoo phoP knockout mutant cultured in modified M9 media containing high Mg2+ Ca2+ concentration (10 mM) labeled with Cyanine-5.

source_name: Total RNA from Xoo phoP knockout mutant cultured in modified M9 media containing low Mg2+ Ca2+ concentration (10 uM) labeled with Cyanine-3.


title: phoP knockout under low Mg2+ Ca2+ VS high Mg2+ Ca2+ replicate2, counter dye swap

description: Biologiacl replicate2 of 3


title: NHDF TNFa A

description:
Simple annotation: Normal tissue, Fibroblasts
Image: http://smd.stanford.edu/MicroArray/gifs/2005-04/60855.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 = 39.23; Parameter Scan Time = 15:19:11; Parameter PMT Volts = 525; Parameter Scan Date = 2005-03-07; Parameter Pixel Size = 10; Parameter Laser on time = 208278; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.42; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; 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 = 39.23; Parameter Scan Time = 15:19:11; Parameter PMT Volts = 600; Parameter Scan Date = 2005-03-07; Parameter Pixel Size = 10; Parameter Laser on time = 573082; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.97; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Kate,,Rubins

tag: Stratagene Universal Human Reference RNA, 1 round of amp(Ambion MessageAmp), 6/27/02

source_name: NHDF TNFa A

tag: NHDF TNFa A

value: Tumor necrosis factor alpha 0.6 pM


title: NHDF 24hr IFNa A

description:
Simple annotation: Normal tissue, Fibroblasts
Image: http://smd.stanford.edu/MicroArray/gifs/2005-04/60854.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 = 39.16; Parameter Scan Time = 15:02:49; Parameter PMT Volts = 530; Parameter Scan Date = 2005-03-07; Parameter Pixel Size = 10; Parameter Laser on time = 208261; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.42; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; 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 = 39.16; Parameter Scan Time = 15:02:49; Parameter PMT Volts = 600; Parameter Scan Date = 2005-03-07; Parameter Pixel Size = 10; Parameter Laser on time = 573065; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.96; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Kate,,Rubins

source_name: NHDF 24hr IFNa A

tag: NHDF 24hr IFNa A

value: Interferon alpha 0.6 pM


title: NHDF 0hr B

description:
Simple annotation: Normal tissue, Fibroblasts
Image: http://smd.stanford.edu/MicroArray/gifs/2005-04/60852.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 = 38.61; Parameter Scan Time = 13:29:51; Parameter PMT Volts = 555; Parameter Scan Date = 2005-03-07; Parameter Pixel Size = 10; Parameter Laser on time = 208169; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.41; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; 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 = 38.61; Parameter Scan Time = 13:29:51; Parameter PMT Volts = 640; Parameter Scan Date = 2005-03-07; Parameter Pixel Size = 10; Parameter Laser on time = 572972; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.90; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Kate,,Rubins

source_name: NHDF 0hr B

tag: NHDF 0hr B

value: time(relative) 0 h


title: phoP knockout under low Mg2+ Ca2+ VS high Mg2+ Ca2+ replicate1

description: Biologiacl replicate1 of 3


title: phoP knockout under low Mg2+ Ca2+ VS high Mg2+ Ca2+ replicate1, counter dye swap

description: Biologiacl replicate1 of 3


title: phoP knockout VS wildtype under M9 media with low Mg2+ Ca2 replicate3

description: Biologiacl replicate3 of 3


title: phoP knockout VS wildtype under M9 media with low Mg2+ Ca2 replicate3, counter dye swap

description: Biologiacl replicate3 of 3


title: phoP knockout under low Mg2+ Ca2+ VS high Mg2+ Ca2+ replicate2

description: Biologiacl replicate2 of 3


title: phoP knockout VS wildtype under M9 media with low Mg2+ Ca2 replicate2, counter dye swap

description: Biologiacl replicate2 of 3


title: Xac infiltrated leaves at 48h_biol replicate 2

city: Campinas

first: Celso

middle: Eduardo

last: Benedetti

state: São Paulo

address: R. Giuseppe Maximo Scolfaro, 10000

department: Center for Molecular and Structural Biology

country: Brazil

institute: Brazilian Synchrotron Light Laboratory

description: To identify defense response genes, sweet orange leaves were infiltrated with water (mock control) and bacterial pathogens Xanthomonas axonopodis pv. citri and Xanthomonas axonopodis pv. aurantifolii.

hyb_protocol: After fragmentation, 15 µg of cRNA were hybridized for 16hs at 45ºC on a GeneChip hybridization oven 640. Subsequently, genechips were washed and stained in the Affymetrix fluidics station 450.

scan_protocol: Scanned using the Affymetrix genechip scanner 7G.

data_processing: All data were acquired and processed using the GeneChip Operating Software (GCOS - Affymetrix). The CEL files of each hybridization chip were obtained with the GCOS and subsequently imported to the ArrayAssist software (Stratagene) for further normalization and statistical analyses. The matrix tables containing the statistical data for each experiment were performed through the significance analysis (“Multiple treatments vs Control”) of the ArrayAssist. These microarray-hybridization comparisons identified the genes with 3.0 or 2.0 fold change up- or down- regulation with a p-value ≤ 0.05.

label: biotin

organism: Citrus sinensis

source_name: Xac infiltrated leaves at 48h

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 0.4 µg of mRNA (Expression Analysis Technical Manual, Affymetrix 2005-2006).

growth_protocol: Six-month-old plants of sweet orange (C. sinensis) “Pêra” cultivar were obtained from certified nurseries and kept in growth room at 25-28oC under 14h/day fluorescent light.

extract_protocol: Total RNA was extracted from sweet orange leaves at different time intervals after water and bacterial infiltration treatments using Trizol (Invitrogen), followed by mRNA purification with FastTrack 2.0 (Invitrogen).

treatment_protocol: Plant leaves were infiltrated with suspensions of Xac (strain 306, da Silva et al., 2002) or Xaa pathotype C (strain ICMP 8435). Bacterial cells grown in LB medium without NaCl (LBON) for 48h at 28oC and 200 rpm were recovered by centrifugation and ressuspended in sterile water (OD600nm= 0.6). Leaf sectors were infiltrated with approximately 0.3 mL of the bacterial suspensions or water as control.

tag: adult leaves


title: phoP knockout VS wildtype under M9 media with low Mg2+ Ca2 replicate1, counter dye swap

description: Biologiacl replicate1 of 3


title: Xac infiltrated leaves at 6h_biol replicate 1

source_name: Xac infiltrated leaves at 6h


title: NHDF p[IC] A

description:
Simple annotation: Normal tissue, Fibroblasts
Image: http://smd.stanford.edu/MicroArray/gifs/2005-04/60856.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 = 39.34; Parameter Scan Time = 15:44:59; Parameter PMT Volts = 510; Parameter Scan Date = 2005-03-07; Parameter Pixel Size = 10; Parameter Laser on time = 208304; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.42; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; 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 = 39.34; Parameter Scan Time = 15:44:59; Parameter PMT Volts = 620; Parameter Scan Date = 2005-03-07; Parameter Pixel Size = 10; Parameter Laser on time = 573107; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.96; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Kate,,Rubins

source_name: NHDF p[IC] A

tag: NHDF p[IC] A

value: polyinosinic-polycytidylic acid potassium salt 100ug/mL


title: Xac infiltrated leaves at 48h_biol replicate 1


title: phoP knockout VS wildtype under M9 media with low Mg2+ Ca2 replicate1

description: Biologiacl replicate1 of 3


title: Killed MPX 2   HeLa

description:
Simple annotation: Normal tissue, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs/2005-09/63900.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 = 27.88; Parameter Scan Time = 23:53:42; Parameter PMT Volts = 399; Parameter Scan Date = 2005-09-02; Parameter Pixel Size = 10; Parameter Laser on time = 4888; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4200A 01 Autoloader; Parameter Laser Power = 2.44; 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 = 27.88; Parameter Scan Time = 23:53:42; Parameter PMT Volts = 547; Parameter Scan Date = 2005-09-02; Parameter Pixel Size = 10; Parameter Laser on time = 4888; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4200A 01 Autoloader; Parameter Laser Power = 1.89; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 80; Parameter Scanning software = AxImageIO; Performer: Kate,,Rubins

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

source_name: Killed MPX 2 HeLa cells infected with Killed MPX in vitro 5.5.05

value: Inactivated Monkeypox Zaire virus

value: HeLa

value: time(relative) 2 h


title: Xaa infiltrated leaves at 48h_biol replicate 2

source_name: Xaa infiltrated leaves at 48h


title: NHDF 0hr A

description:
Simple annotation: Normal tissue, Fibroblasts
Image: http://smd.stanford.edu/MicroArray/gifs/2005-04/60851.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 = 38.29; Parameter Scan Time = 13:10:12; Parameter PMT Volts = 545; Parameter Scan Date = 2005-03-07; Parameter Pixel Size = 10; Parameter Laser on time = 208148; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.40; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; 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 = 38.29; Parameter Scan Time = 13:10:12; Parameter PMT Volts = 650; Parameter Scan Date = 2005-03-07; Parameter Pixel Size = 10; Parameter Laser on time = 572952; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.89; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Kate,,Rubins

source_name: NHDF 0hr A

tag: NHDF 0hr A


title: Xaa infiltrated leaves at 6h_biol replicate 1

source_name: Xaa infiltrated leaves at 6h


title: Xaa infiltrated leaves at 6h_biol replicate 2


title: larynx_normal_8

city: Manhasset

first: James

middle: Allen

last: DeVoti

state: NY

address: 350 Community Drive, Rm 140

department: Immunology and Inflammation

institute: Feinstein Institute for Medical Research

description: Papillomas and adjacent tissues were analyzed and matched sets were compared with the goal to find genes that might be important in the pathophysiology of recurrent respiratory papillomatosis.

hyb_protocol: Gene Chip 450 fluidics station Protocol as per manufacturer (Affymetrix, Santa Clara, CA).

scan_protocol: Gene Chip 3000 scanner

data_processing: Affymetrix MAS 5.0 software

label: Biotin

source_name: Laryngeal Biopsy

label_protocol: BioArray High Yield RNA Transcript Labeling Kit (Enzo Life Sciences Inc., Farmingdale, NY).

extract_protocol: RNeasy spin columns (Qiagen,Valencia, CA)

tag: patient 8 normal


title: larynx_papilloma_12

tag: patient 12 papilloma


title: water infiltrated leaves at 6h_biol replicate 1

source_name: water infiltrated leaves at 6h


title: larynx_papilloma_7

tag: patient 7 papilloma


title: larynx_normal_12

tag: patient 12 normal


title: water infiltrated leaves at 48h_biol replicate 2

source_name: water infiltrated leaves at 48h


title: larynx_papilloma_11

tag: patient 11 papilloma


title: Xaa infiltrated leaves at 48h_biol replicate 1


title: Xac infiltrated leaves at 6h_biol replicate 2


title: larynx_papilloma_10

tag: patient 10 papilloma


title: larynx_normal_11

tag: patient 11 normal


title: larynx_normal_7

tag: patient 7 normal


title: larynx_normal_9

tag: patient 9 normal


title: larynx_papilloma_9

tag: patient 9 papilloma


title: water infiltrated leaves at 48h_biol replicate 1


title: water infiltrated leaves at 6h_biol replicate 2


title: larynx_normal_10

tag: patient 10 normal


title: MCF-7 vs MCF-7Epi at dose 11

city: Sudbury

first: Baoqing

last: Guo

state: ON

address: 41 Ramsey Lake Road

department: Tumor Biology

country: Canada

institute: Advanced Medical Research Institute of Canada

description: This 'sample' represents 6 hybridizations (combining 3 dye-flip pairs)

hyb_protocol: To prepare the hybridization solution for arrays, 5 ul of yeast tRNA (10 mg/ml) and 5 ul of sonicated salmon sperm DNA (10 mg/ml) were added for every 100 ul of DIG Easy Hyb  solution (Roche Diagnostics). Four hundred microliter of this solution were prepared for every six arrays processed. After incubation of the hybridization solution at 650C for 2 min and subsequent cooling to room temperature, 50 ul of this solution was added to each of the labeled cDNA samples. The samples were then incubated for 2 min at 650C, and brought to room temperature. Lifter slips (25x60 mm; Erie Scientific) were placed on Hu1.7k8 microarray slides (University Health Network), after which the hybridization solution containing the labeled cDNAs was carefully applied by capillary action. Each slide was placed on a platform in a hybridization chamber containing DIG Easy Hyb solution at the bottom. The chamber was then  wrapped in plastic wrap and incubated at 370C for 8–18 h. After hybridization, the arrays were immersed in 1x SSC to remove the coverslip, after which each array was washed three times in 1xSSC, 0.1% SDS for 10 min at 500C, with occasional mixing. A separate washing chamber was used for each wash. The arrays were then rinsed six times in 1x SSC and dried by centrifugation at 500 rpm for 5 min.

scan_protocol: Hybridized and washed arrays were scanned on an Axon 4000B dual laser scanner (532 nm/633 nm wavelengths). The voltage across the photo-multiplier tubes was adjusted until the intensity ratio of the red and green acquisition histograms was between 0.9 and 1.1 (when all fluorescent signals above 200 units were included in the analysis). The fluorescence intensities for each feature (spot) on the array were determined using  the GenePix Pro program (version 6.0) from Axon Instruments, using the gal file supplied by the University Health Network Microarray Centre to generate GenePix result GPR files

data_processing: After feature extraction of GPR files, the data were normalized, background subtracted through a process of Read flip-dye data file pairs, total intensity normalization followed by flip-dye consistency checking using TIGR MIDAS. Background subtraction and conversion of microarray files from .gpr to .mev was carried out using TIGR’s Express Converter™ software for both integrated and median intensities and converted files were loaded into TIGR’s Microarray Data Analysis System™ (MIDAS) with forward and reverse arrays undergoing combination, total intensity normalization, and flip-dye consistency checking protocols. The normalized data were analyzed and clustered using a in-house algorithm for significant  change in gene expression, (Villeneuve DJ, Parissenti AM: The use of DNA microarrays to investigate the pharmacogenomics of drug response in living systems. Curr Top Med Chem 4: 2004), Computational cross-validation was conducted using software from the Institute for Genomics Research (TIGR) at Stanford University (http://www.tigr.org/software/microarray.shtml). Arrays comparing gene expression between MCF-7DOX-2 or MCF-7EPI cells and MCF-7CC cells and cross dose analysis were performd using TIGR’s Multi-experiment Viewer (MeV) software using integrated intensity values. In order to eliminate analysis of weak-fluorescing (gray) spots, two-colour, low intensity cutoff filters were set at 1.0 for both the Cy3 and Cy5 dyes. Filter generated gene sets were then designated as primary data sources with “data not found” or “in multiple clusters” intensity points being removed to enrich for named gene values. Selection for up- (red) and down- (green) regulated genes was accomplished using a one-class SAM (Significance Analysis of Microarrays) analysis with all default settings [S0 values, K-nearest neighbours imputer] .

label: Cy3, Cy5

source_name: Parent MCF-7 cells

label_protocol: To each RNA preparation (10 ug), 8 ul of 5 x First Strand Reaction Buffer (Invitrogen Laboratories, 2.5 ul of T20-VN mRNA primer (100 pmol/ll), 3 ul of a mixture of 20 mM dATP, dCTP,and dGTP, 1 ul of 2 mM dCTP, 4 ul of 0.1M DTT, and 2 ul of either Cy3- or Cy5-labelled dCTP (1 mM concentration) was added in a final volume of 40 ul. After thorough mixing, each sample was incubated at 650C for 5 min and subsequently at 420C for 5 min using two preset water baths covered with aluminum foil to prevent quenching of the light-sensitive Cy3 and Cy5 dyes. Two microliter of Superscript II reverse transcriptase (Invitrogen Laboratories), were then added to each sample and the tubes incubated at 420C for 2–3 h. After brief centrifugation and incubation on ice, 5 ul of 50 mM EDTA (pH 8) and 2 ul of 10 N NaOH were added, after which the samples were incubated at 650C for 20 min. After the incubation period, 4 ul of 5M ammonium acetate was added and the Cy3 and Cy5 samples combined. One hundred microliter of isopropanol were added and the labelled nucleic acids precipitated on ice for 30 min. The precipitated nucleic acids were harvested by centrifugation at 13,000 g for 5 min. The isopropanol was poured off and the pellet was washed twice with 300 ul of ice cold 70% ethanol. The samples were again harvested by centrifugation, and the ethanol removed by pipetting. Five microliter of water were then added to solubilize the labelled cDNAs.

extract_protocol: Five independent preparations of total RNA were isolated from cells at each selection dose using Qiagen RNeasy™ mini kit  following manufacturer protocol   The 3 highest quality RNA preparations from drug-selected or co-cultured control cells at each selection dose were used in cDNA microarray experiments (six arrays per selection dose)

tag: human breast adenocacinoma cancer cells

label: Cy5, Cy3

source_name: Epirubicin selected to dose 11


title: MCF-7 vs MCF-7Epi at dose 12

source_name: Epirubicin selected to dose 12


title: MCF-7 vs MCF-7Epi at dose 10

source_name: Epirubicin selected to dose 10


title: MCF-7 vs MCF-7Epi at dose 9

source_name: Epirubicin selected to dose 9


title: MCF-7 vs MCF-7Epi at dose 8

source_name: Epirubicin selected to dose 8


title: larynx_normal_6

tag: patient 6 normal


title: larynx_papilloma_5

tag: patient 5 papilloma


title: MCF-7 vs MCF-7Epi at dose 7

source_name: Epirubicin selected to dose 7


title: larynx_papilloma_6

tag: patient 6 papilloma


title: MCF-7 vs MCF-7Dox-2 at dose 12

source_name: Doxorubicin selected to dose 12


title: MCF-7 vs MCF-7Dox-2 at dose 9

source_name: Doxorubicin selected to dose 9


title: larynx_normal_5

tag: patient 5 normal


title: MCF-7 vs MCF-7Dox-2 at dose 10

source_name: Doxorubicin selected to dose 10


title: MCF-7 vs MCF-7Dox-2 at dose 11

source_name: Doxorubicin selected to dose 11


title: MCF-7 vs MCF-7Dox-2 at dose 8

source_name: Doxorubicin selected to dose 8


title: MCF-7 vs MCF-7Dox-2 at dose 7

source_name: Doxorubicin selected to dose 7


title: larynx_papilloma_3

tag: papilloma patient 3


title: larynx_papilloma_2

tag: Papilloma, Patient 2


title: larynx_normal_4

tag: patient 4 normal


title: larynx_normal_2

tag: Normal patient 2


title: larynx_normal_3

source_name: Larynx Biopsy

tag: Normal, Patient 3


title: larynx_normal_1

source_name: Laryngeal Biopsy

tag: Normal, Patient 1


title: larynx_papilloma_1

tag: Papilloma, Patient 1


title: Red soft berry B14 from plant 1 cluster proximal position, biological rep 1

status: Public on Jul 15 2008

city: Vancouver

first: Steven

middle: T.

last: Lund

state: BC

address: 241 - 2205 East Mall

department: Wine Research Centre

institute: The University of British Columbia

description: One goal of this study was to determine the association between the global transcriptome state and phenotypic variables frequently used in berry staging such as color and firmness, so we defined the four time-points (development series) by color/firmness combinations: green hard (GH), green soft (GS), pink soft (PS) and red soft (RS)

hyb_protocol: Following fragmentation, 14 µg of cRNA from one berry was hybridized for 16 hr at 45ºC on each GeneChip Vitis (Grape) Genome Arrays . GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned with an Affymetrix GeneArray 3000 7G scanner.

data_processing: The raw data were background adjusted, normalized and log2-transformed using the Bioconductor GCRMA package.

organism: Vitis vinifera

source_name: grape berry near maturation

label_protocol: Biotin -labeled cRNA was prepared according to the manufacturer’s protocol (Affymetrix, Santa Clara, CA).

growth_protocol: Dormant shoot cuttings of V. vinifera cv. Cabernet Sauvignon clone 15 were collected from a commercial vineyard near Osoyoos, BC, in January, 2006, and then transported on wet ice and stored at 4ºC.For fruit cluster propagation, a technique similar to that reported by Mullins and Rajasekaran (1981) was employed, as follows.  The basipetal ends of several cuttings were scored with a razor blade and then placed in heated soil within a 4ºC walk-in cooler to promote root formation but inhibit bud break.  After adventitious roots became visible, cuttings were moved to the greenhouse and potted in a mixture of 75% peat and 25% perlite (pH 7.0).  On average, after nine days at 20-25ºC under a 16 h photoperiod, bud break occurred and a single cluster formed on the resulting shoot.  Two shoots bearing healthy clusters were selected for experimentation.

extract_protocol: Total RNA was isolated as described in Reid et al. 2006 (PMID: 17105665).  One RNA extraction was done for each of 32 berries.

treatment_protocol: Seleted grape berries were snap frozen upon harvest, prior to RNA extraction.

tag: Cultivar

value: Cabernet sauvignon


title: Red soft berry C30 from plant 2 cluster proximal position, biological rep 2


title: Red soft berry C31 from plant 2 cluster distal position, biological rep 2


title: Red soft berry C29 from plant 2 cluster proximal position, biological rep 1


title: Pink soft berry C27 from plant 2 cluster distal position, biological rep 2

source_name: grape berry post ripening initiation


title: Red soft berry A7 from plant 2 cluster distal position, biological rep 1


title: larynx_papilloma_4

tag: patient 4 papilloma


title: Red soft berry C15 from plant 1 cluster distal position, biological rep 1


title: Pink soft berry C11 from plant 1 cluster distal position, biological rep 1


title: Pink soft berry B13 from plant 2 cluster distal position, biological rep 1


title: phoP knockout VS wildtype under M9 media with low Mg2+ Ca2 replicate2

description: Biologiacl replicate2 of 3

source_name: Total RNA from Xoo phoP knockout mutant cultured in modified M9 media containing low Mg2+ Ca2+ concentration (10 uM) labeled with Cyanine-5.

tag: cultured in PSB until OD =0.2 and incubated in modified M9 media 16 hrs

source_name: Total RNA from Xoo PXO99A cultured in modified M9 media containing low Mg2+ Ca2+ concentration (10 uM) labeled with Cyanine-3.


title: E3

city: Leiden

first: John

last: van Tuyn

address: Albinusdreef 2

department: Cardiology

country: Netherlands

institute: Leiden university Medical Center

description: Normal (not transduced)

hyb_protocol: standard Illumina protocol

scan_protocol: standard Illumina protocol

data_processing: Raw data normalized using global variance stabilization normalization (VSN)

source_name: CMPCs

label_protocol: standard Illumina protocol

extract_protocol: NucleoSpin RNA II purification kit (Macherey Nagel)

tag: cardiomyocyte progenitor cells (CMPCs), ScaI+ cells isolated from human fetal heart


title: Red soft berry C16 from plant 1 cluster distal position, biological rep 2


title: Pink soft berry C12 from plant 1 cluster distal position, biological rep 2


title: Red soft berry C13 from plant 1 cluster proximal position, biological rep 2


title: Pink soft berry B23 from plant 1 cluster proximal position, biological rep 2


title: Pink soft berry C25 from plant 2 cluster proximal position, biological rep 1


title: Pink soft berry C26 from plant 2 cluster proximal position, biological rep 2


title: E2

description: Normal (not transduced)


title: Pink soft berry B8 from plant 1 cluster proximal position, biological rep 1


title: D3

description: overexpressing LacZ (tranduction control)


title: Green soft berry C22 from plant 2 cluster proximal position, biological rep 2

source_name: grape berry during ripening initiation


title: Green soft berry C23 from plant 2 cluster distal position, biological rep 1


title: Green soft berry A22 from plant 2 cluster proximal position, biological rep 1


title: D2


title: E1

description: Normal (not transduced)


title: Green soft berry C24 from plant 2 cluster distal position, biological rep 2


title: C3

description: overexpressing human SM-MYOCD (smooth muscle specific myocardin isoform) also expressed upstream tiny ORF


title: Green soft berry A21 from plant 1 cluster proximal position, biological rep 2


title: D1


title: Green soft berry A23 from plant 1 cluster distal position, biological rep 1


title: Green soft berry C7 from plant 1 cluster distal position, biological rep 2


title: Green soft berry B10 from plant 1 cluster proximal position, biological rep 1


title: C2


title: larynx_papilloma_8

tag: patient 8 papilloma


title: Green hard berry B12 from plant 2 cluster distal position, biological rep 1

source_name: grape berry before ripening initiation


title: A4

description: overexpressing human CM-MYOCD


title: B1

description: overexpressing human SM-MYOCD (smooth muscle specific myocardin isoform)


title: B3


title: Green hard berry C17 from plant 2 cluster proximal position, biological rep 2


title: Green hard berry C3 from plant 1 cluster distal position, biological rep 1


title: A2

description: A2 overexpressing huamn CM-MYOCD


title: HK24/2 control

city: New York

first: Mayte

last: Suarez-Farinas

address: 1425 Madison Ave, L2-70C, Box 1077,

institute: Mount SinaiSchool of Medicine

hyb_protocol: Quiagen single amplification protocol

scan_protocol: Hewlett-Packard GeneArray Scanner G25Time: 0Time: 0A.

data_processing: GCRMA (using gcrma package from R/Bioconductor)

source_name: HK24/2 untreated

label_protocol: Quiagen single amplification protocol

extract_protocol: Cells lysed in RLT with Beta-2-mercaptoethanol

tag: Cytokine

value: control

tag: KC-Source


title: Green hard berry C19 from plant 2 cluster distal position, biological rep 2


title: C1


title: Green hard berry C4 from plant 1 cluster distal position, biological rep 2


title: A3

description: overexpressing huamn CM-MYOCD


title: Green hard berry B21 from plant 1 cluster proximal position, biological rep 1


title: Green hard berry C1 from plant 1 cluster proximal position, biological rep 2


title: Green hard berry B9 from plant 2 cluster proximal position, biological rep 1


title: B2


title: A1

description: A1 overexpressing human CM-MYOCD


title: HK24/2 IL17

source_name: HK24/2 treated with IL17


title: HK24/2 IL22

source_name: HK24/2 treated with IL22


title: HK12/2 control

source_name: HK12/2 untreated


title: HK12/2 IFNg

source_name: HK12/2 treated with IFNg

value: IFNg

value: HK12/2, IFNg


title: HK23/2 IL22

source_name: HK23/2 treated with IL22


title: Myoepithelioma_case_5

status: Public on Jul 14 2008

type: genomic

city: Lund

first: Karolin

middle: H

last: Nord

address: BMC C13

department: Dept of Clinical Genetics

country: Sweden

institute: Lund University

description: Genomic imbalances in myoepithelioma

hyb_protocol: Arrays were hybridized and washed as described in Heidenblad et al. (Oncogene 2006;25:7106-16)

scan_protocol: Arrays were scanned in Agilent Microarray scanner

data_processing: Primary data were collected using the GenePix Pro 4.0 software, and the quantified data matrix was deposited into the web-based database BioArray Software Environment (BASE), where filtering and normalization were performed.

molecule: genomic DNA

source_name: Case 5

label_protocol: BioPrime array CGH labeling module (Invitrogen, Carlsbad, CA, USA)

extract_protocol: DNeasy Tissue Kit (Qiagen, Valencia, CA, USA)

tag: Genomic DNA from fresh frozen tumor biopsy

source_name: Promega reference male DNA (Promega, Madison, WI, USA)

tag: Pooled lymphoblastoid genomic DNA from ten male individuals


title: Myoepithelioma_case_6

description: Genomic imbalances in myoepithelioma

source_name: Case 6


title: HK24/2 IFNg

source_name: HK24/2 treated with IFNg


title: HK12/2 IL22

source_name: HK12/2 treated with IL22


title: Myoepithelioma_case_3

description: Genomic imbalances in myoepithelioma

source_name: Case 3


title: HK12/2 IL17

source_name: HK12/2 treated with IL17


title: HK23/2 control

source_name: HK23/2 untreated


title: HK23/2 IL17

source_name: HK23/2 treated with IL17


title: MUTZ3 shMRP4 DC_immature_Gain70

status: Public on Jul 12 2008

city: Namur

first: jean-pierre

last: gillet

address: 61 Rue de Bruxelles

department: URPhyM

country: Belgium

institute: University of Namur

description: For more details, please see Rieneke van de Ven, Blood in press

hyb_protocol: Hybridization, quantification and data analysis were performed as described by de Longueville et al. Toxicol Sci 2003; 75:378-392 and Biochem Pharmacol 2002; 64:137-149. and provided in the DualChip microarray protocol of direct labelling.

scan_protocol: Briefly, after hybridization, the detection was performed using a Cy3-conjugated anti-biotin IgG antibody (Jackson Immuno Research Laboratories, USA). The arrays were scanned with the ScanArray 4000 XL laser confocal scanner (Applied Biosystems, USA) at a resolution of 10 µm. To maximize the dynamic range of microarrays, the same arrays were scanned using different photomultiplier settings (PMT). The use of different intensities (termed gains) allows the quantification of genes that are expressed at both high and low copy numbers.

data_processing: After image acquisition, the scanned 16-bit image was used to quantify the signal intensities with ImaGene 5.5 software (BioDiscovery, USA) and the file was imported into the DualChip software provided by Eppendorf (Hamburg, Germany).  The signal intensities were normalized by housekeeping genes and internal standards.

source_name: MUTZ3-shMRP4,immature DC,day 7

label_protocol: A concentration of 10 µg was chosen for preparation of labeled cDNA, for more details please see de Longueville F et al. Biochem Pharmacol 2002;64:137– 49.

growth_protocol: MUTZ3 and MUTZ3-shMRP4 cell lines were seeded in MEM alpha (Lonza, Belgium) supplemented with 20% FCS (Hyclone, Sweden) and 10% conditioned medium from the 5637 renal carcinoma cell line.

extract_protocol: RNA was isolated from cell pellets using RNAbee (5 million cells/ml) following manufacturer's protocol

treatment_protocol: immature DC were cultured from MUTZ3 or MUTZ3_shMRP4 cells in MEM alpha supplemented with 20% FCS, 100ng/ml GM-CSF, 10ng/ml IL4 and 2.5ng/ml TNFalpha for 7 days

tag: MUTZ3 cell line, stable retroviral transductant, pRetroSuper.GFP.shMRP4, GFP positive, immature DC, cultured from p47


title: MUTZ3 shMRP4 DC_immature_Gain50


title: Myoepithelioma_case_1

description: Genomic imbalances in myoepithelioma

source_name: Case 1


title: HK23/2 IFNg

source_name: HK23/2 treated with IFNg


title: Myoepithelioma_case_2

description: Genomic imbalances in myoepithelioma

source_name: Case 2


title: MUTZ3 shMRP4 DC_immature_Gain100


title: MUTZ3 DC_immature_Gain70

source_name: MUTZ3,immature DC,day 7

tag: MUTZ3 cell line, immature DC, cultured from passage 17


title: MUTZ3 DC_immature_Gain50


title: E2F3 +/- Involution Day 4 rep2

status: Public on Jul 11 2008

city: East Lansing

first: Eran

last: Andrechek

state: MI

address: 2120 BPS Building

department: Physiology

institute: Michigan State University

description: Three mice were taken for each genotype at each timepoint (Involution day 0, 1, 2, 3 and 4) and RNA was prepared from the mammary glands.

hyb_protocol: protocol attached below (from Duke Institute fro Genome Sciences and Policy Microarray Facility) http://www.genome.duke.edu/cores/microarray/services/spotted-arrays/protocols/

scan_protocol: Axon Genepix Scanner (Genepix 4000B)

data_processing: Data was analysed with GeneSpring 7 data software package (Silicon Genetics). Each data set was normalised using Lowess intensity-dependent normalisation and then subject to ANOVA. ANOVA was used to eliminate genes that had no signal call in one (or more) of the repeats after Lowess normalization at each of the time points.

organism: Mus musculus

source_name: Mammary Gland

label_protocol: Abion_AmpII protocol (attached below) (from Duke Institute fro Genome Sciences and Policy Microarray Facility) http://www.genome.duke.edu/cores/microarray/services/spotted-arrays/protocols/

extract_protocol: Briefly, mammary gland RNA was prepped through CsCl ultracentrafugation.

tag: E2F3 +/- Involution Day 4 rep2

source_name: Total RNA from mouse reference library

extract_protocol: Total RNA extracted from mouse reference library

tag: reference


title: E2F3 +/- Involution Day 4 rep3

tag: E2F3 +/- Involution Day 4 rep3


title: E2F3 +/- Involution Day 4 rep1

tag: E2F3 +/- Involution Day 4 rep1


title: E2F3 +/- Involution Day 3 rep3

tag: E2F3 +/- Involution Day 3 rep3


title: MUTZ3 DC_immature_Gain100


title: mouse embryonic stem cell replicate 4

first: Vanessa

last: Hall

address: Solvegatan 17

description:
mESC4
murine embryonic stem cells
Amplified cRNA was hybridized to a nylon GEArray containing 263 stem cell related genes (SuperArray Biosciences)

hyb_protocol: Purified cRNA was hybrdized to nylon arrays for 18h at 60 degrees celsius.

scan_protocol: Chemiluminescence detection was performed using CDP star and captured on a Kodak 3000 CCD camera

data_processing:
Data was analyzed using GEAsuite software available from Superarray Biosciences
Normalized signal intensity using GEAsuite software tool. Normalized spot brightness. VALUEs represent Normalized against housekeeping gene, Gapdh and subtracted background.

source_name: blastocyst

label_protocol: 1.5ug of total RNA was reverse transcribed to produce cRNA and labelled with ubiquitin-biotin.

growth_protocol: cells were cultured in-vitro prior to analysis according to standard pre-defined protocols. Cells were harvested for RNA extraction by using Trypsin/EDTA, rinsed in PBS, and resuspended in cell lysis buffer

extract_protocol: Total RNA was extracted using Trizol/chloroform extraction. Purified RNA was also treated with Dnase to avoid any possibly DNA contamination

treatment_protocol: Cells subjected to reprogramming were exposed to streptolysin-O to permeabilize cell membranes for 30 mins and then exposed to Xenopus egg extract for 45 mins at 37 degrees.

tag: 5 days


title: reprogrammed bone marrow stem cells replicate 1

description:
XenBMSC2
murine stromal cells exposed to Xenopus extract
Amplified cRNA was hybridized to a nylon GEArray containing 263 stem cell related genes (SuperArray Biosciences)

source_name: bone marrow

tag: 6 weeks


title: reprogrammed bone marrow stem cells replicate 2

description:
XenBMSC3
murine stromal cells exposed to Xenopus extract
Amplified cRNA was hybridized to a nylon GEArray containing 263 stem cell related genes (SuperArray Biosciences)


title: E2F3 +/- Involution Day 2 rep3

tag: E2F3 +/- Involution Day 2 rep3


title: E2F3 +/- Involution Day 2 rep2

tag: E2F3 +/- Involution Day 2 rep2


title: E2F3 +/- Involution Day 3 rep2

tag: E2F3 +/- Involution Day 3 rep2


title: mouse embryonic stem cell replicate 5

description:
mESC5
murine embryonic stem cells
Amplified cRNA was hybridized to a nylon GEArray containing 263 stem cell related genes (SuperArray Biosciences)


title: E2F3 +/- Involution Day 1 rep3

tag: E2F3 +/- Involution Day 1 rep3


title: E2F3 +/- Involution Day 1 rep2

tag: E2F3 +/- Involution Day 1 rep2


title: E2F3 +/- Involution Day 2 rep1

tag: E2F3 +/- Involution Day 2 rep1


title: E2F3 +/- Lactation rep3

tag: E2F3 +/- Lactation rep3


title: E2F3 +/- Involution Day 1 rep1

tag: E2F3 +/- Involution Day 1 rep1


title: E2F3 +/- Involution Day 3 rep1

tag: E2F3 +/- Involution Day 3 rep1


title: E2F3 +/- Lactation rep2

tag: E2F3 +/- Lactation rep2


title: mouse embryonic stem cell replicate 3

description:
mESC3
murine embryonic stem cells
Amplified cRNA was hybridized to a nylon GEArray containing 263 stem cell related genes (SuperArray Biosciences)


title: mouse embryonic stem cell replicate 1

description:
mESC1
murine embryonic stem cells
Amplified cRNA was hybridized to a nylon GEArray containing 263 stem cell related genes (SuperArray Biosciences)


title: mouse embryonic stem cell replicate 2

description:
mESC2
murine embryonic stem cells
Amplified cRNA was hybridized to a nylon GEArray containing 263 stem cell related genes (SuperArray Biosciences)


title: WT Involution Day 4 rep1

tag: WT Involution Day 4 rep1


title: bone marrow stem cell replicate 4

description:
BMSC5
murine bone marrow stromal cells cultured in-vitro
Amplified cRNA was hybridized to a nylon GEArray containing 263 stem cell related genes (SuperArray Biosciences)


title: WT Involution Day 4 rep2

tag: WT Involution Day 4 rep2

tag: reference


title: Glycodelin-induced changes in MCF-7 breast cancer cells

city: Helsinki

first: Hannu

last: Koistinen

address: PO Box 63

department: Clinical Chemistry

country: Finland

institute: University of Helsinki

description: Recent reports suggest that glycodelin induces epithelial differentiation. Little is known about the mechanisms involved in this process. To elucidate this we transfected glycodelin-negative MCF-7 breast cancer cells with glycodelin cDNA. Cells transfected with a vector in which glycodelin cDNA was in antisense orientation were used as non-glycodelin-producing controls. Oligo microarray was performed to study gene expression changes between glycodelin-transfected and control cells.

hyb_protocol: According to the manufacturer's instructions (Agilent Technologies).

scan_protocol: Agilent DNA Microarray Scanner according to the manufacturer's instructions (Agilent Technologies).

data_processing: Data normalization and ratio calculation was performed by Feature Extraction software (v 6.1.1) using default settings.

source_name: MCF-7 control cells

label_protocol: The labeling was carried out from 20 µg of total RNA using direct labeling method according to the manufacturer's instructions (Agilent Technologies).

extract_protocol: RNA from 8 cell clones were purified using Phase lock gel (Eppendorf), DNase treated and analyzed using Agilent Technologies 2100 Bioanalyzer.

tag: Human breast cancer MCF-7 cells, transfected with glycodelin cDNA in antisense orientation (i.e. control cells).

source_name: Glycodelin-transfected MCF-7 cells

tag: Human breast cancer MCF-7 cells, transfected with glycodelin cDNA (i.e. glycodelin-producing cells).


title: WT Involution Day 3 rep3

tag: WT Involution Day 3 rep3


title: WT Involution Day 4 rep3

tag: WT Involution Day 4 rep3


title: E2F3 +/- Lactation rep1

tag: E2F3 +/- Lactation rep1


title: WT Involution Day 3 rep2

tag: WT Involution Day 3 rep2


title: bone marrow stem cell replicate 1

description:
BMSC2
murine bone marrow stromal cells cultured in-vitro
Amplified cRNA was hybridized to a nylon GEArray containing 263 stem cell related genes (SuperArray Biosciences)

tag: 6 weeks


title: bone marrow stem cell replicate 3

description:
BMSC4
murine bone marrow stromal cells cultured in-vitro
Amplified cRNA was hybridized to a nylon GEArray containing 263 stem cell related genes (SuperArray Biosciences)


title: bone marrow stem cell replicate 2

description:
BMSC3
murine bone marrow stromal cells cultured in-vitro
Amplified cRNA was hybridized to a nylon GEArray containing 263 stem cell related genes (SuperArray Biosciences)


title: WT Involution Day 2 rep3

tag: WT Involution Day 2 rep3


title: WT Involution Day 3 rep1

tag: WT Involution Day 3 rep1


title: WT Involution Day 2 rep1

tag: WT Involution Day 2 rep1


title: WT Involution Day 2 rep2

tag: WT Involution Day 2 rep2


title: WT Involution Day 1 rep1

tag: WT Involution Day 1 rep1


title: cI_24h_12h_rep2

status: Public on Jul 10 2008

city: Cologne

first: Bernhard

last: Gerstmayer

address: Stockheimer Weg 1

country: Germany

institute: Miltenyi Biotec GmbH

description: 100 µg of total RNA from transplanted and untreated (control) rat kidneys were labeled by reverse transcription with Cy5 and Cy3 fluorescence, respectively.

scan_protocol: Image capture and signal quantification were done with the ScanArray3000 (GSI Lumonics, Watertown, MA) and ImaGene software version 4.1 (BioDiscovery, Los Angeles, CA)

data_processing: normalized log2 ratio of means defined as Ch2/Ch1

organism: Rattus norvegicus

source_name: normal untreated kidneys

tag: control, strain F344

source_name: kidney_rep2, transplanted

tag: strain LEW, transplanted kidney subjected to 24 hours of cold ischemia, organ harvesting after 12 hours


title: WT Involution Day 1 rep3

tag: WT Involution Day 1 rep3


title: WT Lactation rep2

tag: WT Lactation rep2


title: WT Lactation rep3

tag: WT Lactation rep3

tag: reference


title: WT Involution Day 1 rep2

tag: WT Involution Day 1 rep2


title: cI_24h_12h_rep1

source_name: kidney_rep1, transplanted


title: WT Lactation rep1

tag: WT Lactation rep1


title: cI_20min_6months_rep2

tag: strain LEW, transplanted kidney subjected to 20 min of cold ischemia, organ harvesting after 6 months


title: cI_20min_6months_rep3

source_name: kidney_rep3, transplanted


title: cI_20min_12h_rep3

tag: strain LEW, transplanted kidney subjected to 20 min of cold ischemia, organ harvesting after 12 hours


title: cI_24h_6m_rep1

tag: strain LEW, transplanted kidney subjected to 24 hours of cold ischemia, organ harvesting after 6 months


title: cI_20min_6months_rep1


title: cI_24h_6m_rep2


title: cI_20min_12h_rep1

tag: strain LEW, transplanted kidney subjected to 20 of min cold ischemia, organ harvesting after 12 hours


title: mESCs_p400ChIP_array2

city: Berkeley

first: Jason

middle: T

last: Huff

address: 211 Koshland Hall

department: Plant & Microbial Biology

institute: University of California, Berkeley

description: The p400 IP and input samples were split and hybridized separately to the two arrays of the MM8 NimbleGen promoter set.

hyb_protocol: Labeling, hybridization of amplified input and immunoprecipitated samples to Mouse MM8 promoter arrays and scanning were performed at NimbleGen Systems Inc.

data_processing: Raw Cy5 and Cy3 intensity values were extracted from the NimbleGen “pair” files for each of the two microarrays in the MM8 promoter set. Normalization of log2(ratio) probe values was performed using functions in the R (http://www.r-project.org) package "limma" in Bioconductor (Gentleman et al., 2004; Smyth, 2004). A variety of normalization methods were tested in comparison to the NimbleGen method. The final normalized values reflect fitting of an intensity-dependent loess curve only to the control probes and then normalizing the chromosomal probes to the fit without background subtraction (using the “loess” method in the normalizeWithinArrays() function). This method yielded normalized log2(IP/input) values with a large dynamic range and empirical distributions most similar between the two arrays of the promoter set.

source_name: p400 ChIP

extract_protocol: 1 mg of extract was processed for chromatin IP as described in the methods (Fazzio et al., 2008). 4 ng of the resulting immunoprecipitated (IP) DNA was amplified using a BioPrime Array CGH kit (Invitrogen), omitting fluorescent nucleotides and using 120 uM of each dNTP.

treatment_protocol: One 10 cm dish was cross-linked and processed for ChIP.

tag: Mouse embryonic stem cell line E14

source_name: input material

extract_protocol: 4 ng of input DNA was amplified using a BioPrime Array CGH kit (Invitrogen), omitting fluorescent nucleotides and using 120 uM of each dNTP.


title: cI_20min_12h_rep2


title: DBA smoked mouse_1

city: Genoa

first: Paolo

last: Fardin

address: Largo G. Gaslini 5

department: Molecular Biology

country: Italy

institute: Istiuto Giannina Gaslini

description: The mice were housed in groups of two to four in macrolon cages. Room temperature ranged between 22°C and 24°C, the relative humidity ranged between 40% and 50%; food and water were supplied ad libitum.

hyb_protocol: Hybridization was carried out for 16 hr at 45oC. Chips were then washed with 6x SSPE and stained with streptavidin-phycoerythrin according to Affymetrix’s guidelines.

scan_protocol: Chips were scanned using a confocal microscope scanner with the 560-nm long-pass filter (HP GeneArray Scanner 2500) according to Affymetrix’s guidelines.

data_processing: Expression values were quantified using the statistical algorithms implemented in Affymetrix Micrarray Suite 5.0. Array signals were scaled to an average intensity of 100 and the resulting data were analyzed by GeneSpring Expression Analysis Software (version Gx 7.3).

source_name: smoked lung

label_protocol: 15 µg of RNA were reverse-transcribed into cDNA using SuperScript II kit (Invitrogen Life Technologies, Irvine CA) with an oligo(dT)24 primer containing a T7 polymerase promoter site at 3’ purchased from the MWG Biotech (Ebersberg, Germany). cDNA was purified by phenol-chloroform extraction followed by ethanol precipitation and resuspended in DEPC water. Labeled cRNA was synthesized using the in vitro transcription reaction in the presence of biotin-11-CTP and biotin-16-UTP, and the BioAssay High Yield RNA Transcript Labeling Kit (Enzo Diagnostics, Farmingdale, NY). Biotin-labeled cRNA was cleaned up using the Qiagen RNeasy Mini Kit (Qiagen, Hilden, Germany) and ethanol precipitation.

extract_protocol: Total RNA was extracted from mice lungs using Trizol (Invitrogen Life technologies, Irvine, CA) according to the manufacturer’s instructions.

tag: DBA/2 three month-old male mice exposed to the smoke from three cigarettes/day, 5 days/week for 4 weeks


title: C57 control mouse_1

source_name: normal lung

tag: C57Bl/6J three month-old male mice


title: C57 smoked mouse_1

tag: C57Bl/6J three month-old male mice exposed to the smoke from three cigarettes/day, 5 days/week for 4 weeks


title: DBA control mouse_1

tag: DBA/2 three month-old male mice


title: ICR smoked mouse_1

tag: ICR three month-old male mice exposed to the smoke from three cigarettes/day, 5 days/week for 4 weeks


title: Upper respiratory tract infection (Viro3P12-247)

status: Public on Jul 09 2008

city: San Francisco

first: Joe

last: DeRisi

department: Biochemistry and Biophysics

institute: University of California, San Francisco

description: RdABC amplified RNA from Nasal Lavage

hyb_protocol: standard overnight hybridization

scan_protocol: Axon 4000 scanner

data_processing: Median feature intensity minus median background intensity. The data analysis software used is E-Predict, which normalizes the data using a variety of measures: sum, quadratic, unit-vector, or no normalization (please see Urisman A, Fischer KF, Chiu CY, Kistler AL, Beck  S, Wang D, DeRisi JL.E-Predict: a computational strategy for species identification based on observed DNA microarray hybridization patterns.Genome Biol. 2005;6(9):R78. Epub 2005 Aug 30).  E-Predict is public access.  For the purposes of this paper, sum-normalized intensities were used in the analysis.

organism: Viruses

source_name: RdABC amplified RNA from Nasal Lavage

label_protocol: Rd C Cy3 incorporation

extract_protocol: RNeasy followed by DNAse treatment

tag: Upper respiratory tract infection


title: No respiratory symptoms (Viro3P12-243)

description: RdABC amplified RNA from Nasal Lavage

tag: No respiratory symptoms


title: Bronchiolitis (Viro3P12-244)

description: RdABC amplified RNA from Nasal Lavage

tag: Bronchiolitis


title: Pneumonia (Viro3P12-246)

description: RdABC amplified RNA from Nasal Lavage

tag: Pneumonia


title: ICR control mouse_1

tag: ICR three month-old male mice


title: Pneumonia (Viro3P12-242)

description: RdABC amplified RNA from Nasal Lavage


title: Pneumonia (Viro3P12-245)

description: RdABC amplified RNA from Nasal Lavage


title: mESCs_p400ChIP_array1

scan_protocol: Labeling, hybridization of amplified input and immunoprecipitated samples to Mouse MM8 promoter arrays and scanning were performed at NimbleGen Systems Inc.


title: No respiratory symptoms (Viro3P12-147)

description: RdABC amplified RNA from Nasal Lavage


title: No respiratory symptoms (Viro3P12-241)

description: RdABC amplified RNA from Nasal Lavage


title: Bronchiolitis (Viro3P12-146)

description: RdABC amplified RNA from Nasal Lavage


title: No respiratory symptoms (Viro3P12-139)

description: RdABC amplified RNA from Nasal Lavage


title: Upper respiratory tract infection (Viro3P12-144)

description: RdABC amplified RNA from Nasal Lavage


title: Upper respiratory tract infection (Viro3P12-138)

description: RdABC amplified RNA from Nasal Lavage


title: No respiratory symptoms (Viro3P12-145)

description: RdABC amplified RNA from Nasal Lavage


title: Pneumonia (Viro3P12-149)

description: RdABC amplified RNA from Nasal Lavage


title: No respiratory symptoms (Viro3P12-135)

description: RdABC amplified RNA from Nasal Lavage


title: Pneumonia (Viro3P12-136)

description: RdABC amplified RNA from Nasal Lavage


title: Upper respiratory tract infection (Viro3P12-148)

description: RdABC amplified RNA from Nasal Lavage


title: Asthma (Viro3P12-137)

description: RdABC amplified RNA from Nasal Lavage

tag: Asthma


title: No respiratory symptoms (Viro3P12-132)

description: RdABC amplified RNA from Nasal Lavage


title: Pneumonia (Viro3P12-130)

description: RdABC amplified RNA from Nasal Lavage


title: Pneumonia (Viro3P12-133)

description: probe 70 oligo

source_name: probe 70 oligo


title: Upper respiratory tract infection (Viro3P12-129)

description: RdABC amplified RNA from Nasal Lavage


title: Upper respiratory tract infection (Viro3P12-134)

description: RdABC amplified RNA from Nasal Lavage


title: No respiratory symptoms (Viro3P12-124)

description: RdABC amplified RNA from Nasal Lavage


title: Upper respiratory tract infection (Viro3P12-126)

description: RdABC amplified RNA from Nasal Lavage


title: Pneumonia (Viro3P12-122)

description: RdABC amplified RNA from Nasal Lavage


title: Pneumonia (Viro3P12-060)

description: RdABC amplified RNA from Nasal Lavage


title: Asthma (Viro3P12-123)

description: RdABC amplified RNA from Nasal Lavage


title: Pneumonia (Viro3P11-260)

description: RdABC amplified RNA from Nasal Lavage


title: No respiratory symptoms (Viro3P12-055)

description: RdABC amplified RNA from Nasal Lavage


title: Upper respiratory tract infection (Viro3P12-125)

description: RdABC amplified RNA from Nasal Lavage


title: Pneumonia (Viro3P12-057)

description: RdABC amplified RNA from Nasal Lavage


title: Upper respiratory tract infection (Viro3P12-127)

description: RdABC amplified RNA from Nasal Lavage


title: Bronchiolitis (Viro3P12-131)

description: RdABC amplified RNA from Nasal Lavage


title: Pneumonia (Viro3P11-259)

description: RdABC amplified RNA from Nasal Lavage


title: Pneumonia (Viro3P12-128)

description: RdABC amplified RNA from Nasal Lavage


title: Croup (Viro3P12-058)

description: RdABC amplified RNA from Nasal Lavage

tag: Croup


title: Pneumonia (Viro3P11-261)

description: RdABC amplified RNA from Nasal Lavage


title: Upper respiratory tract infection (Viro3P11-256)

description: RdABC amplified RNA from Nasal Lavage


title: Upper respiratory tract infection (Viro3P12-059)

description: RdABC amplified RNA from Nasal Lavage


title: No respiratory symptoms (Viro3P12-056)

description: RdABC amplified RNA from Nasal Lavage


title: Bronchiolitis (Viro3P11-258)

description: RdABC amplified RNA from Nasal Lavage


title: Upper respiratory tract infection (Viro3P11-257)

description: RdABC amplified RNA from Nasal Lavage


title: No respiratory symptoms (Viro3P11-250)

description: RdABC amplified RNA from Nasal Lavage


title: No respiratory symptoms (Viro3P11-254)

description: RdABC amplified RNA from Nasal Lavage


title: Upper respiratory tract infection (Viro3P11-249)

description: RdABC amplified RNA from Nasal Lavage


title: Pneumonia (Viro3P11-243)

description: RdABC amplified RNA from Nasal Lavage


title: Bronchiolitis (Viro3P11-252)

description: RdABC amplified RNA from Nasal Lavage


title: Pneumonia (Viro3P11-244)

description: RdABC amplified RNA from Nasal Lavage


title: No respiratory symptoms (Viro3P11-255)

description: RdABC amplified RNA from Nasal Lavage


title: No respiratory symptoms (Viro3P11-240)

description: RdABC amplified RNA from Nasal Lavage


title: Bronchiolitis (Viro3P11-248)

description: RdABC amplified RNA from Nasal Lavage


title: No respiratory symptoms (Viro3P11-237)

description: RdABC amplified RNA from Nasal Lavage


title: Pneumonia (Viro3P11-246)

description: RdABC amplified RNA from Nasal Lavage


title: Upper respiratory tract infection (Viro3P11-247)

description: RdABC amplified RNA from Nasal Lavage


title: Upper respiratory tract infection (Viro3P11-251)

description: RdABC amplified RNA from Nasal Lavage


title: Croup (Viro3P11-253)

description: RdABC amplified RNA from Nasal Lavage


title: No respiratory symptoms (Viro3P11-241)

description: RdABC amplified RNA from Nasal Lavage


title: No respiratory symptoms (Viro3P11-242)

description: RdABC amplified RNA from Nasal Lavage


title: Asthma (Viro3P11-245)

description: RdABC amplified RNA from Nasal Lavage


title: Upper respiratory tract infection (Viro3P11-239)

description: RdABC amplified RNA from Nasal Lavage


title: Pneumonia (Viro3P11-232)

description: RdABC amplified RNA from Nasal Lavage


title: Bronchiolitis (Viro3P11-233)

description: RdABC amplified RNA from Nasal Lavage


title: Pneumonia (Viro3P11-230)

description: RdABC amplified RNA from Nasal Lavage


title: Pneumonia (Viro3P11-238)

description: RdABC amplified RNA from Nasal Lavage


title: Bronchiolitis (Viro3P11-236)

description: RdABC amplified RNA from Nasal Lavage


title: Pneumonia (Viro3P11-234)

description: RdABC amplified RNA from Nasal Lavage


title: Upper respiratory tract infection (Viro3P11-231)

description: RdABC amplified RNA from Nasal Lavage


title: Bronchiolitis (Viro3P11-229)

description: RdABC amplified RNA from Nasal Lavage


title: Bronchiolitis (Viro3P11-225)

description: RdABC amplified RNA from Nasal Lavage


title: Bronchiolitis (Viro3P11-222)

description: RdABC amplified RNA from Nasal Lavage


title: No respiratory symptoms (Viro3P11-228)

description: RdABC amplified RNA from Nasal Lavage


title: No respiratory symptoms (Viro3P11-226)

description: RdABC amplified RNA from Nasal Lavage


title: Bronchiolitis (Viro3P11-201)

description: RdABC amplified RNA from Nasal Lavage


title: No respiratory symptoms (Viro3P11-227)

description: RdABC amplified RNA from Nasal Lavage


title: No respiratory symptoms (Viro3P11-202)

description: RdABC amplified RNA from Nasal Lavage


title: No respiratory symptoms (Viro3P11-223)

description: RdABC amplified RNA from Nasal Lavage


title: No respiratory symptoms (Viro3P11-203)

description: RdABC amplified RNA from Nasal Lavage


title: Upper respiratory tract infection (Viro3P11-204)

description: RdABC amplified RNA from Nasal Lavage


title: Asthma (Viro3P11-221)

description: RdABC amplified RNA from Nasal Lavage


title: Pneumonia (Viro3P11-200)

description: RdABC amplified RNA from Nasal Lavage


title: Bronchiolitis (Viro3P11-207)

description: RdABC amplified RNA from Nasal Lavage


title: Pneumonia (Viro3P11-208)

description: RdABC amplified RNA from Nasal Lavage


title: Bronchiolitis (Viro3P11-206)

description: RdABC amplified RNA from Nasal Lavage


title: Bronchiolitis (Viro3P11-205)

description: RdABC amplified RNA from Nasal Lavage


title: No respiratory symptoms (Viro3P11-224)

description: RdABC amplified RNA from Nasal Lavage


title: Bronchiolitis (Viro3P11-199)

description: RdABC amplified RNA from Nasal Lavage


title: Pneumonia (Viro3P11-198)

description: RdABC amplified RNA from Nasal Lavage


title: Pneumonia (Viro3P11-197)

description: RdABC amplified RNA from Nasal Lavage


title: No respiratory symptoms (Viro3P11-210)

description: RdABC amplified RNA from Nasal Lavage


title: Asthma (Viro3P11-194)

description: RdABC amplified RNA from Nasal Lavage


title: No respiratory symptoms (Viro3P11-191)

description: RdABC amplified RNA from Nasal Lavage


title: Pneumonia (Viro3P11-195)

description: RdABC amplified RNA from Nasal Lavage


title: No respiratory symptoms (Viro3P11-184)

description: RdABC amplified RNA from Nasal Lavage


title: No respiratory symptoms (Viro3P11-193)

description: RdABC amplified RNA from Nasal Lavage


title: No respiratory symptoms (Viro3P11-188)

description: RdABC amplified RNA from Nasal Lavage


title: Bronchiolitis (Viro3P11-190)

description: RdABC amplified RNA from Nasal Lavage


title: Pneumonia (Viro3P11-189)

description: RdABC amplified RNA from Nasal Lavage


title: Pneumonia (Viro3P11-178)

description: RdABC amplified RNA from Nasal Lavage


title: Bronchiolitis (Viro3P11-196)

description: RdABC amplified RNA from Nasal Lavage


title: No respiratory symptoms (Viro3P11-192)

description: RdABC amplified RNA from Nasal Lavage


title: Pneumonia (Viro3P11-177)

description: RdABC amplified RNA from Nasal Lavage


title: Bronchiolitis (Viro3P11-187)

description: RdABC amplified RNA from Nasal Lavage


title: Pneumonia (Viro3P11-183)

description: RdABC amplified RNA from Nasal Lavage


title: No respiratory symptoms (Viro3P11-180)

description: RdABC amplified RNA from Nasal Lavage


title: No respiratory symptoms (Viro3P11-185)

description: RdABC amplified RNA from Nasal Lavage


title: Upper respiratory tract infection (Viro3P11-176)

description: RdABC amplified RNA from Nasal Lavage


title: No respiratory symptoms (Viro3P11-182)

description: RdABC amplified RNA from Nasal Lavage


title: No respiratory symptoms (Viro3P11-179)

description: RdABC amplified RNA from Nasal Lavage


title: Pneumonia (Viro3P11-181)

description: RdABC amplified RNA from Nasal Lavage


title: Upper respiratory tract infection (Viro3P11-186)

description: RdABC amplified RNA from Nasal Lavage


title: Bronchiolitis (Viro3P11-174)

description: RdABC amplified RNA from Nasal Lavage


title: Pneumonia (Viro3P11-175)

description: RdABC amplified RNA from Nasal Lavage


title: Bronchiolitis (Viro3P11-173)

description: RdABC amplified RNA from Nasal Lavage


title: No respiratory symptoms (Viro3P11-162)

description: RdABC amplified RNA from Nasal Lavage


title: No respiratory symptoms (Viro3P11-166)

description: RdABC amplified RNA from Nasal Lavage


title: No respiratory symptoms (Viro3P11-169)

description: RdABC amplified RNA from Nasal Lavage


title: Upper respiratory tract infection (Viro3P11-168)

description: RdABC amplified RNA from Nasal Lavage


title: No respiratory symptoms (Viro3P11-165)

description: RdABC amplified RNA from Nasal Lavage


title: No respiratory symptoms (Viro3P11-163)

description: RdABC amplified RNA from Nasal Lavage


title: No respiratory symptoms (Viro3P11-171)

description: RdABC amplified RNA from Nasal Lavage


title: Upper respiratory tract infection (Viro3P11-161)

description: RdABC amplified RNA from Nasal Lavage


title: Bronchiolitis (Viro3P11-164)

description: RdABC amplified RNA from Nasal Lavage


title: No respiratory symptoms (Viro3P11-160)

description: RdABC amplified RNA from Nasal Lavage


title: Croup (Viro3P11-150)

description: RdABC amplified RNA from Nasal Lavage


title: No respiratory symptoms (Viro3P11-159)

description: RdABC amplified RNA from Nasal Lavage


title: Pneumonia (Viro3P11-157)

description: RdABC amplified RNA from Nasal Lavage


title: No respiratory symptoms (Viro3P11-149)

description: RdABC amplified RNA from Nasal Lavage


title: Upper respiratory tract infection (Viro3P11-136)

description: RdABC amplified RNA from Nasal Lavage


title: Asthma (Viro3P11-137)

description: RdABC amplified RNA from Nasal Lavage


title: Croup (Viro3P11-148)

description: RdABC amplified RNA from Nasal Lavage


title: No respiratory symptoms (Viro3P11-146)

description: RdABC amplified RNA from Nasal Lavage


title: Pneumonia (Viro3P11-147)

description: probe 70 oligo


title: No respiratory symptoms (Viro3P11-132)

description: RdABC amplified RNA from Nasal Lavage


title: Upper respiratory tract infection (Viro3P11-135)

description: RdABC amplified RNA from Nasal Lavage


title: Upper respiratory tract infection (Viro3P11-130)

description: RdABC amplified RNA from Nasal Lavage


title: Upper respiratory tract infection (Viro3P11-134)

description: RdABC amplified RNA from Nasal Lavage


title: No respiratory symptoms (Viro3P11-120)

description: RdABC amplified RNA from Nasal Lavage


title: Pneumonia (Viro3P11-122)

description: RdABC amplified RNA from Nasal Lavage


title: No respiratory symptoms (Viro3P11-119)

description: RdABC amplified RNA from Nasal Lavage


title: Bronchiolitis (Viro3P11-133)

description: RdABC amplified RNA from Nasal Lavage


title: Bronchiolitis (Viro3P11-123)

description: RdABC amplified RNA from Nasal Lavage


title: Pneumonia (Viro3P11-114)

description: RdABC amplified RNA from Nasal Lavage


title: Pneumonia (Viro3P11-128)

description: RdABC amplified RNA from Nasal Lavage


title: Asthma (Viro3P11-121)

description: RdABC amplified RNA from Nasal Lavage


title: Upper respiratory tract infection (Viro3P11-126)

description: RdABC amplified RNA from Nasal Lavage


title: No respiratory symptoms (Viro3P11-127)

description: RdABC amplified RNA from Nasal Lavage


title: Asthma (Viro3P11-125)

description: RdABC amplified RNA from Nasal Lavage


title: Pneumonia (Viro3P11-113)

description: RdABC amplified RNA from Nasal Lavage


title: Pneumonia (Viro3P11-129)

description: RdABC amplified RNA from Nasal Lavage


title: No respiratory symptoms (Viro3P11-124)

description: RdABC amplified RNA from Nasal Lavage


title: Upper respiratory tract infection (Viro3P11-112)

description: RdABC amplified RNA from Nasal Lavage


title: No respiratory symptoms (Viro3P11-106)

description: RdABC amplified RNA from Nasal Lavage


title: Pneumonia (Viro3P11-110)

description: RdABC amplified RNA from Nasal Lavage


title: Bronchiolitis (Viro3P11-107)

description: RdABC amplified RNA from Nasal Lavage


title: Upper respiratory tract infection (Viro3P11-109)

description: RdABC amplified RNA from Nasal Lavage


title: Bronchiolitis (Viro3P11-108)

description: RdABC amplified RNA from Nasal Lavage


title: Upper respiratory tract infection (Viro3P11-111)

description: RdABC amplified RNA from Nasal Lavage


title: Asthma (Viro3P11-098)

description: RdABC amplified RNA from Nasal Lavage


title: Pneumonia (Viro3P11-100)

description: RdABC amplified RNA from Nasal Lavage


title: Bronchiolitis (Viro3P11-094)

description: RdABC amplified RNA from Nasal Lavage


title: Upper respiratory tract infection (Viro3P11-090)

description: RdABC amplified RNA from Nasal Lavage


title: Bronchiolitis (Viro3P11-097)

description: RdABC amplified RNA from Nasal Lavage


title: Asthma (Viro3P11-093)

description: RdABC amplified RNA from Nasal Lavage


title: Pneumonia (Viro3P11-099)

description: RdABC amplified RNA from Nasal Lavage


title: No respiratory symptoms (Viro3P11-101)

description: RdABC amplified RNA from Nasal Lavage


title: Bronchiolitis (Viro3P11-091)

description: RdABC amplified RNA from Nasal Lavage


title: Bronchiolitis (Viro3P11-089)

description: RdABC amplified RNA from Nasal Lavage


title: Upper respiratory tract infection (Viro3P11-088)

description: RdABC amplified RNA from Nasal Lavage


title: Pneumonia (Viro3P11-095)

description: RdABC amplified RNA from Nasal Lavage


title: Asthma (Viro3P11-092)

description: RdABC amplified RNA from Nasal Lavage


title: No respiratory symptoms (Viro3P11-087)

description: RdABC amplified RNA from Nasal Lavage


title: No respiratory symptoms (Viro3P11-086)

description: RdABC amplified RNA from Nasal Lavage


title: Pneumonia (Viro3P11-105)

description: RdABC amplified RNA from Nasal Lavage


title: Pneumonia (Viro3P11-081)

description: RdABC amplified RNA from Nasal Lavage


title: Upper respiratory tract infection (Viro3P11-079)

description: RdABC amplified RNA from Nasal Lavage


title: No respiratory symptoms (Viro3P11-084)

description: RdABC amplified RNA from Nasal Lavage


title: No respiratory symptoms (Viro3P11-085)

description: RdABC amplified RNA from Nasal Lavage


title: Upper respiratory tract infection (Viro3P11-083)

description: RdABC amplified RNA from Nasal Lavage


title: Bronchiolitis (Viro3P11-082)

description: RdABC amplified RNA from Nasal Lavage


title: Upper respiratory tract infection (Viro3P11-080)

description: RdABC amplified RNA from Nasal Lavage


title: No respiratory symptoms (Viro3P11-069)

description: RdABC amplified RNA from Nasal Lavage


title: Bronchiolitis (Viro3P11-096)

description: RdABC amplified RNA from Nasal Lavage


title: Pneumonia (Viro3P11-076)

description: RdABC amplified RNA from Nasal Lavage


title: Bronchiolitis (Viro3P11-061)

description: RdABC amplified RNA from Nasal Lavage


title: Upper respiratory tract infection (Viro3P11-065)

description: RdABC amplified RNA from Nasal Lavage


title: Upper respiratory tract infection (Viro3P11-066)

description: RdABC amplified RNA from Nasal Lavage


title: Asthma (Viro3P11-070)

description: RdABC amplified RNA from Nasal Lavage


title: Pneumonia (Viro3P11-068)

description: RdABC amplified RNA from Nasal Lavage


title: No respiratory symptoms (Viro3P11-078)

description: RdABC amplified RNA from Nasal Lavage


title: No respiratory symptoms (Viro3P11-054)

description: RdABC amplified RNA from Nasal Lavage


title: Asthma (Viro3P11-056)

description: RdABC amplified RNA from Nasal Lavage


title: Asthma (Viro3P11-051)

description: RdABC amplified RNA from Nasal Lavage


title: Bronchiolitis (Viro3P11-059)

description: RdABC amplified RNA from Nasal Lavage


title: No respiratory symptoms (Viro3P11-064)

description: RdABC amplified RNA from Nasal Lavage


title: No respiratory symptoms (Viro3P11-050)

description: RdABC amplified RNA from Nasal Lavage


title: Pneumonia (Viro3P11-049)

description: RdABC amplified RNA from Nasal Lavage


title: No respiratory symptoms (Viro3P11-063)

description: RdABC amplified RNA from Nasal Lavage


title: No respiratory symptoms (Viro3P11-067)

description: RdABC amplified RNA from Nasal Lavage


title: Bronchiolitis (Viro3P11-048)

description: RdABC amplified RNA from Nasal Lavage


title: No respiratory symptoms (Viro3P11-055)

description: RdABC amplified RNA from Nasal Lavage


title: No respiratory symptoms (Viro3P11-058)

description: RdABC amplified RNA from Nasal Lavage


title: Pneumonia (Viro3P11-052)

description: RdABC amplified RNA from Nasal Lavage


title: Bronchiolitis (Viro3P11-047)

description: probe 70 oligo


title: Asthma (Viro3P11-057)

description: RdABC amplified RNA from Nasal Lavage


title: No respiratory symptoms (Viro3P11-053)

description: RdABC amplified RNA from Nasal Lavage


title: No respiratory symptoms (Viro3P11-060)

description: RdABC amplified RNA from Nasal Lavage


title: Upper respiratory tract infection (Viro3P11-045)

description: probe 70 oligo


title: No respiratory symptoms (Viro3P11-046)

description: RdABC amplified RNA from Nasal Lavage


title: Pneumonia (Viro3P11-062)

description: RdABC amplified RNA from Nasal Lavage


title: Pneumonia (Viro3P11-043)

description: RdABC amplified RNA from Nasal Lavage


title: Bronchiolitis (Viro3P11-044)

description: RdABC amplified RNA from Nasal Lavage