title: HSV1-5h-rep1-B

status: Public on Nov 24 2009

type: RNA

city: Atlanta

first: Julia

middle: K

last: Hilliard

state: GA

address: 50 Decatur St

department: Biology

country: USA

institute: Georgia State University

description: Gene expression data from HSV-1 5 hour post infection.

hyb_protocol: Fragmented cRNA was hybridized to HG-U133A chip at 45º for 16 hrs. Following hybridization, microarry was washed and stained with strepavidin-conjugated phycoerythrin (SAPE) by using Affymetrix GeneChip Fluidic Station 400. Staining intensity was amplified by using a biotinlylated anti-streptavidin antibody followed by a second SAPE stain.

scan_protocol: Microarray was scanned by Agilent G2500A GeneArray Scanner.

data_processing: Data was analyzed with GeneChip Operating Software 1.4 using Affymetrix default analysis setting and global scaling (scaling factor of 500) as normalization method.

label: Biotin

molecule: total RNA

organism: Homo sapiens

source_name: Human foreskin fibroblast, HSV-1, 5 hour

label_protocol: Biotinylated cRNA was generated by Enzo BioArray High Yield RNA transcript Labeling Kit (Affymetrix) according to manufacturer’s instructions.

growth_protocol: HFF cells were grown in Eagle's mimimum essential medium with 0.1mM non-essential amino acids, 1.0mM sodium pyruvate and Earle's BBS, 90%; fetal bovine serum, 10%.

extract_protocol: Total RNA was extracted by QIAGEN's RNeasy Total RNA Isolation kit according to the manufacturer's instructions.Two-cycle cDNA synthesis were performed using SuperScript Choice system(Invitrogen Life Technologies) according to manufacturer’s instructions.

treatment_protocol: Human foreskin fibroblast (HFF) cells (ATCC, CRL-2097) were infected with HSV-1 at m.o.i. of 10 at 4ºC for 1 hour and 37ºC for 4 hours.

tag: HSV-1 MacIntyre strain


title: Mock-1h-rep2-B

description: Gene expression data from mock infected cells 1 hour post infection.

source_name: Human foreskin fibroblast, mock, 1 hour

treatment_protocol: Human foreskin fibroblast (HFF) cells (ATCC, CRL-2097) were mock infected at 4ºC for 1 hour.

tag: Uninfected control


title: Mock-1h-rep1-B


title: Mock-5h-rep1-B

description: Gene expression data from mock infected cells 5 hour post infection.

source_name: Human foreskin fibroblast, mock, 5 hour

treatment_protocol: Human foreskin fibroblast (HFF) cells (ATCC, CRL-2097) were mock infected at 4ºC for 1 hour and 37ºC for 4 hours.


title: Mock-3h-rep2-B

description: Gene expression data from mock infected cells 3 hour post infection.

source_name: Human foreskin fibroblast, mock, 3 hour

treatment_protocol: Human foreskin fibroblast (HFF) cells (ATCC, CRL-2097) were mock infected at 4ºC for 1 hour and 37ºC for 2 hours.


title: HSV1-1h-rep2-B

description: Gene expression data from HSV-1 1 hour post infection.

source_name: Human foreskin fibroblast, HSV-1, 1 hour

treatment_protocol: Human foreskin fibroblast (HFF) cells (ATCC, CRL-2097) were infected with HSV-1 at m.o.i. of 10 at 4ºC for 1 hour.


title: Mock-5h-rep2-B


title: BV-5h-rep1-B

description: Gene expression data from B virus 5 hour post infection.

source_name: Human foreskin fibroblast, B virus, 5 hour

treatment_protocol: Human foreskin fibroblast (HFF) cells (ATCC, CRL-2097) were infected with B virus at m.o.i. of 10 at 4ºC for 1 hour and 37ºC for 4 hours.

tag: B virus strain:E2490


title: HSV1-3h-rep2-B

description: Gene expression data from HSV-1 3 hour post infection.

treatment_protocol: Human foreskin fibroblast (HFF) cells (ATCC, CRL-2097) were infected with B virus at m.o.i. of 10 at 4ºC for 1 hour and 37ºC for 2 hours.


title: BV-3h-rep2-B

description: Gene expression data from B virus 3 hour post infection.

source_name: Human foreskin fibroblast, B virus, 3 hour


title: Mock-3h-rep1-B


title: BV-1h-rep1-B

description: Gene expression data from B virus 1 hour post infection.

source_name: Human foreskin fibroblast, B virus, 1 hour

treatment_protocol: Human foreskin fibroblast (HFF) cells (ATCC, CRL-2097) were infected with B virus at m.o.i. of 10 at 4ºC for 1 hour.


title: HSV1-5h-rep2-B


title: BV-3h-rep1-B


title: HSV1-3h-rep1-B

source_name: Human foreskin fibroblast, HSV-1, 3 hour


title: Mock-5h-rep1-A


title: HSV1-1h-rep1-B


title: BV-5h-rep2-B


title: Mock-3h-rep2-A


title: Mock-1h-rep1-A


title: Mock-1h-rep2-A


title: BV-1h-rep2-B


title: HSV1-3h-rep1-A

treatment_protocol: Human foreskin fibroblast (HFF) cells (ATCC, CRL-2097) were infected with HSV-1 at m.o.i. of 10 at 4ºC for 1 hour and 37ºC for 2 hours.


title: HSV1-5h-rep2-A


title: HSV1-3h-rep2-A


title: Mock-5h-rep2-A


title: Mock-3h-rep1-A


title: HSV1-5h-rep1-A


title: HSV1-1h-rep2-A


title: HSV1-1h-rep1-A


title: BV-5h-rep2-A


title: BV-5h-rep1-A


title: BV-3h-rep1-A


title: MCF10A-MycChIPchip-ectopicMyc-rep6_chipB

type: genomic

city: Toronto

first: Paul

middle: C

last: Boutros

state: Ontario

address: 101 College Street, Suite 800

country: Canada

institute: Ontario Institute for Cancer Research

hyb_protocol: A 5 µg Cy5-labeled and 5 µg of Cy3-labeled DNAs were combined in a total volume of 158 µl. The 158 µl were mixed with 50 µl of 1 mg/ml of Human Cot-1 DNA, 52 µl of 10x Agilent Blocking Agent, 260 µl of 2x Agilent Hybridization Buffer. Samples were heated at 95°C for 3 min, and then incubated at 37°C for 30 min. 490 µl of the sample were applied to the 1x244 promoter array assembled in a chamber and incubated in a rotisserie hybridization oven at 65°C and 20 r.p.m. for 40 h. After hybridization the microarray slide was washed with Oligo aCGH/ChIP-on-chip Wash Buffer for 5 min at room temperature, followed by a wash for 5 min at 31°C.

scan_protocol: Agilent Feature Extraction software v9.5 was used.

data_processing: Microarray data was scanned using the Agilent Feature Extraction Software (v9.5) and then loaded into the R statistical environment (v2.7.2) using the limma package (v2.14.7). Array data was pre-processed using variance-stabilizing normalization with default parameterization. Pre-processing employed the vsn package (v3.6.0) again in the R statistical environment. The raw and pre-processed data were subjected to a series of quality-control measures: all arrays were included in subsequent analyses. Significance-testing employed t-tests to compare the antibody and control channels, followed by an Empirical Baye’s moderation of standard error and a false-discovery rate adjustment for multiple-testing.

molecule: genomic DNA

source_name: Myc ChIP-chip of exponentially growing MCF10A cells with ectopic MYC expression

label_protocol: WGA amplified DNA (4 µg) was hybridized to Agilent 2x244 promoter arrays at the UHN microarray center (Toronto, Canada).  Arrays were labeled using the Agilent Genomic DNA Labelling Kit and hybridized using the aCGH Hybridization Kit following the ChIP-on-chip v10 protocol as follows: for each 1x244 promoter array, 2 µg of DNA was brought to 26 µl final volume.  5 µl of Random Primers (supplied with Agilent Genomic DNA Labeling Kit PLUS) was added and the mix was incubated at 95°C for 3 min, then on ice for 5 min. The 31 µl were mixed with the Labeling Mix to a final volume of 50 µl (10 µl of 5x Buffer, 5 µl of 10x dNTP, 3 µl of 1 mM Cyanine 3-UTP or 1 mM Cyanine 5-dUTP, 1 µl of Exo-Klenow fragment) and incubated at 37°C for 2 h. The enzyme was then inactivated at 65°C for 10 min. The labeled Genomic DNA was cleaned with Microcon columns (Millipore, Microcon YM-30) and eluted with 80.5 µl of 1x TE.

growth_protocol: MCF10A cells were grown asynchronously in a humidified incubator at 37 degrees C and 5% CO2 in a 1:1 mixture of Dulbecco's modified Eagle's medium and F12 medium (DMEM-F12) supplemented with 5% horse serum, hydrocortisone (0.5 ug/mL), insulin (10 ug/mL), epidermal growth factor (20 ng/mL), and cholera toxin (100 ng/mL).

extract_protocol: Entire ChIP samples were used for the library generation and subsequent amplification. For the library preparation and the amplification (round 1), GenomePlex Complete WGA kit was used (Sigma WGA2) as directed.  Samples were then purified using QIAquick PCR Purification kit (Qiagen 28106) and 10 ng of then proceeded to the reamplification step (round 2). GenomePlex WGA amplification Kit was used (Sigma WGA3) as directed, and samples were then purified using QIAquick PCR Purification kit (Qiagen 28106).

treatment_protocol: Exponentially growing MCF10A cells were cross-linked with 1% formaldehyde for 15 min at 37°C. The cross-linking reaction was quenched by addition of glycine to a final concentration of 0.125 M for 15 min, followed by two washes with phosphate-buffered saline (PBS). Cells were resuspended in cell lysis buffer (5 mM PIPES pH 8, 85 mM KCl, 0.5% [v/v] NP40, 1 mM PMSF, 10 µg/ml aprotinin, 10 µg/ml leupeptin) for 10 min on ice and then pelleted (5000 r.p.m., 5 min, 4°C). The pellet was resuspended in 1 ml of nuclei lysis buffer (50mM Tris–HCl pH 8.1, 10mM EDTA, 1% SDS, 1 mM PMSF, 10 µg/ml aprotinin, 10 µg/ml leupeptin) for 10 min on ice and then sonicated with 11 pulses (setting high, 30 s per pulse, 30 s on ice between pulses) from a BioRuptor Sonicator (Diagenode, BioRuptor 200, UCD-200 TM-EX) to generate fragments between 100 and 500 bp. Lysates were centrifuged for 10 min at 1,000 rpm at 4°C. Supernatants were diluted into an equal volume with IP dilution buffer (0.01% SDS, 1.1% Triton-X100, 1.2 mN EDTA, 16.7 mM Tris–HCl pH 8.1, 0.2% Sarkosyl, 1 mM PMSF, 10 µg/ml aprotinin, 10 µg/ml leupeptin) and precleared for 30 min at 4°C with protein G-PLUS agarose beads (Santa Cruz Biotechnology, Santa Cruz, CA, USA, sc-2002). Prior to use, G-PLUS agarose beads were blocked with salmon sperm DNA at a final concentration of 50 µg/ml and rotated overnight at 4°C. Diluted and cleared extracts corresponding to 10 x 106 MCF10A cells were incubated and rotated at 4°C for 12–16 h with each  1.5 µg normal rabbit IgG (Santa Cruz Biotechnology sc-2027), or home-made purified N262.  50 µl of salmon sperm DNA preblocked Protein G-PLUS agarose beads were added to each sample, incubated on a rotating platform at 4°C for 3 h. Each pellet was washed once with 1.4 ml of sonication buffer and then twice with 1.4 ml of high salt buffer (0.1% [v/v] SDS, 1% [v/v] Triton X-100, 1 mM EDTA, 50 mM HEPES, 500 mM NaCl, 0.1% [w/v] sodium deoxycholate) and then once with 1.4 ml LiCl Buffer (250 mM LiCl, 1% [v/v] NP-40, 1% [w/v] sodium deoxycholate, 1 mM EDTA, 1 mM Tris pH 8) and finally twice with 1.4 ml TE pH 8 (10 mM Tris pH8, 1 mM EDTA). For each wash, the pellets were mixed for 5 min at room temperature then pelleted (3000 r.p.m., 30 s, room temperature). After the last wash, the pellets were eluted in 300 µl of Elution buffer (1% [w/v] SDS, 10 mM Tris pH 8, 5 mM EDTA), incubated at 65°C for 15 min, and then pelleted (3000 r.p.m., 3 min, room temperature). Cross-links were reversed in the presence of 200 mM NaCl at 65°C over-night and samples were treated with RNase A (Sigma R5500). After ethanol precipitation, the samples were resuspended in 100 µl of TE (10 mM Tris, pH 7.5, 1 mM EDTA), 25 µl of 5x proteinase K buffer (1.25% SDS, 50 mM Tris, pH 7.5, 25 mM EDTA), and 1.5 µl of proteinase K (Roche 1413783) and incubated at 42°C for 2 h.  Samples were then column purified sample using Qiagen Qiaquick PCR purification Kit, and eluted in 30 uL of Buffer EB.

tag: CellLine

value: MCF10A, GrowthPhase:Exponential, EctopicGeneExpression:MYC, ChIPAntibody:Myc, ArrayBatch:2

source_name: IgG ChIP-chip of exponentially growing MCF10A cells with ectopic MYC expression

value: MCF10A, GrowthPhase:Exponential, EctopicGeneExpression:MYC, ChIPAntibody:IgG, ArrayBatch:2


title: BV-1h-rep1-A


title: MCF10A-MycChIPchip-ectopicMyc-rep7_chipB


title: MCF10A-MycChIPchip-ectopicMyc-rep4_chipB

value: MCF10A, GrowthPhase:Exponential, EctopicGeneExpression:MYC, ChIPAntibody:Myc, ArrayBatch:1

value: MCF10A, GrowthPhase:Exponential, EctopicGeneExpression:MYC, ChIPAntibody:IgG, ArrayBatch:1


title: MCF10A-MycChIPchip-ectopicMyc-rep5_chipB


title: MCF10A-MycChIPchip-ectopicMyc-rep8_chipB


title: MCF10A-MycChIPchip-ectopicMyc-rep3_chipB


title: BV-1h-rep2-A


title: MCF10A-MycChIPchip-ectopicMyc-rep1_chipB


title: MCF10A-MycChIPchip-ectopicMyc-rep2_chipB


title: BV-3h-rep2-A


title: MCF10A-MycChIPchip-ectopicGFP-rep4_chipB

source_name: Myc ChIP-chip of exponentially growing MCF10A cells with ectopic GFP expression

value: MCF10A, GrowthPhase:Exponential, EctopicGeneExpression:GFP, ChIPAntibody:Myc, ArrayBatch:1

source_name: IgG ChIP-chip of exponentially growing MCF10A cells with ectopic GFP expression

value: MCF10A, GrowthPhase:Exponential, EctopicGeneExpression:GFP, ChIPAntibody:IgG, ArrayBatch:1


title: MCF10A-MycChIPchip-ectopicGFP-rep8_chipB

value: MCF10A, GrowthPhase:Exponential, EctopicGeneExpression:GFP, ChIPAntibody:Myc, ArrayBatch:2

value: MCF10A, GrowthPhase:Exponential, EctopicGeneExpression:GFP, ChIPAntibody:IgG, ArrayBatch:2


title: MCF10A-MycChIPchip-ectopicGFP-rep7_chipB


title: MCF10A-MycChIPchip-ectopicGFP-rep10_chipB


title: MCF10A-MycChIPchip-ectopicMyc-rep9_chipB


title: MCF10A-MycChIPchip-ectopicGFP-rep1_chipB


title: MCF10A-MycChIPchip-ectopicGFP-rep9_chipB


title: MCF10A-MycChIPchip-ectopicMyc-rep10_chipB


title: MCF10A-MycChIPchip-ectopicGFP-rep5_chipB


title: MCF10A-MycChIPchip-ectopicGFP-rep6_chipB


title: MCF10A-MycChIPchip-ectopicGFP-rep3_chipB


title: MCF10A-MycChIPchip-ectopicGFP-rep2_chipB


title: MCF10A-MycChIPchip-ectopicMyc-rep10_chipA


title: Liver_stand_PCN_4

status: Public on Nov 20 2009

city: Ljubljana

first: Peter

last: Juvan

address: Zaloska 4

department: Institute of Biochemistry

country: Slovenia

institute: Faculty of Medicine, University of Ljubljana

description: No additional data.

hyb_protocol: Channel 1 sample was mixed with channel 2 sample hybridization buffer was added (final concentration was 3xSSC, 0.2% SDS) and samples were denatured. Using LifterSlip cover glasses (Erie Scientific Company, Portsmouth, NH, USA) samples were hybridized for 16h at 65ºC in a water bath using humidified hybridization chambers (HybChambers, GeneMachines, San Carlos, CA, USA). Prior hybridizations Steroltalk v2 slides were pre-hybridized for 1 hour at 42ºC in 5xSSC, 0.1%SDS and 1%BSA, then washed at room temperature for 5 min in 2xSSC and 0.1%SDS, 3 min in 0.2xSSC and 2 min in MilliQ water and dried by centrifugation. After hybridization slides were washed at room temperature for 5 min in 2xSSC and 0.5%SDS, 5 min in 0.5xSSC, 5 min in 0.05xSSC, and then dried using vacuum centrifuge.

scan_protocol: Slides were scanned using Tecan LS200 scanner (Tecan Group Ltd., Maennedorf, CH). Images were analyzed using Array-Pro Analyzer 4.5 (Media Cybernetics, Bethesda, MD, USA). The median feature and local background intensities were extracted together with the estimates of their standard deviation

data_processing: Data filtration and normalization was done in Orange (http://magix.fri.uni-lj.si/orange/). Only features with foreground to background ratio higher than 1.5 and coefficient of variation (CV, ratio between standard deviation of the background and the median feature intensity) lower than 0.5 in both channels were used for further analysis, other were filtered out. Log2 ratios were normalized using LOWESS fit to spike in control RNAs according to their average intensity. For normalization, two types of spike in controls were used: custom-made Firefly luciferase and commercial Lucidea Universal ScoreCard.

organism: Mus musculus

source_name: liver, standard diet, PCN

label_protocol: To 20 μg of sample total RNA we added spike in RNA: 250 pg of Firefly Luciferase mRNA (Promega, Madison, WI, USA), and 0.5 μL of test spike mix from Lucidea Universal ScoreCard kit. We reverse-transcribed mRNA to amino-allyl cDNA using 2.5 μg of Oligo dT (Invitrogen, Carlsbad, CA, USA), 400U of SuperScriptTM III Reverse Transcriptase (Invitrogen, Carlsbad, CA, USA) and 1μL of 10mM amino-allyl dUTP (Sigma, St Louis, MI, USA) according to the manufacturer’s protocol. Reaction was stopped after 2 hours by adding 10 μL of 0.5 M EDTA and of 1M NaOH and incubation at 65ºC for 15 min. 10 μL of 1 M HCl was added and cDNA was purified using MinElute PCR Purification Kit (Qiagen GmBH, Hilden, D) according to manufacturer’s protocol with exception of using a phosphate buffer (5mM KPO4 pH 8.5 in 80% ethanol) for washing step and MilliQ water for elution. Purified amino-allyl cDNA was dried and resuspended in 4.5 μL of 0.2 M Na2CO3 (pH 9.0) and 4.5 μL of cyanin dye in DMSO (Amersham Biosciences, GE Healthcare UK limited, Little Chalfont, UK). Labeling reaction was incubated at room temperature for two hours. Next we added 35 μL of 0.1 M Na acetate (pH 5.2) and purified reaction using MinElute PCR Purification Kit (Qiagen GmBH, Hilden, D) according to manufacturer’s protocol. Labeled cDNA was eluted in water and 1 μL was used for analyses using ND-1000 spectrophotometer (Nanodrop Technologies, Wilmington, Delaware, USA).

growth_protocol: Mouse was housed in normal light-cycle room, maintained on standard rodent chow (diet 3430, Provimi Kliba SA, Kaiseraugst, CH), and was allowed water and food ad libitum.

extract_protocol: Left lateral lobes of livers were snap frozen in liquid nitrogen and stored at -80ºC. Total RNA was isolated using TRI-reagent (Sigma, St Louis, MI, USA) according to the manufacturer’s protocol and purified by ethanol precipitation.

treatment_protocol: Mouse was injected one i.p. injection of 40 mg/kg PCN in corn oil in the morning. After 24 hours animal was euthanized using CO2 suffocation.

tag: Strain

tag: Gender

value: female

tag: Age

value: 18-19 weeks

tag: Tissue

value: liver

source_name: liver, reference 3

label_protocol: Labeling protocol is the same as for channel 1 with exception of adding a reference spike mix from Lucidea Universal ScoreCard kit.

growth_protocol: Mix of samples used in experiment: mice on standard diet.

extract_protocol: Mix of all samples used in experiment: all isolated using TRI-reagent (Sigma, St Louis, MI, USA) according to the manufacturer’s protocol and purified by ethanol precipitation.

treatment_protocol: Mix of RNA samples from mice treated with vehicle and PCN.


title: Liver_stand_PCN_2

description: No additional data.


title: Liver_stand_PCN_6

description: No additional data.


title: Liver_stand_PCN_3

description: No additional data.


title: MCF10A-MycChIPchip-ectopicMyc-rep3_chipA


title: MCF10A-MycChIPchip-ectopicMyc-rep2_chipA


title: MCF10A-MycChIPchip-ectopicMyc-rep8_chipA


title: MCF10A-MycChIPchip-ectopicGFP-rep8_chipA


title: MCF10A-MycChIPchip-ectopicGFP-rep10_chipA


title: MCF10A-MycChIPchip-ectopicMyc-rep6_chipA


title: MCF10A-MycChIPchip-ectopicMyc-rep7_chipA


title: Liver_stand_controlPCN_4

description: No additional data.

source_name: liver, standard diet, control

treatment_protocol: Mouse was treated with one i.p. injection of vehicle (corn oil, Sigma, St Louis, MI, USA) in the morning. After 24 hours animal was euthanized using CO2 suffocation.

value: 19 weeks


title: Liver_stand_controlPCN_2

description: No additional data.


title: MCF10A-MycChIPchip-ectopicGFP-rep6_chipA


title: Liver_chol_rosuva_5

description: No additional data.

source_name: liver, cholesterol diet, rosuvastatin

growth_protocol: Mouse was housed in normal light-cycle room, maintained on standard rodent chow (diet 3430, Provimi Kliba SA, Kaiseraugst, CH), and was allowed water and food ad libitum. One week prior treatment diet was switched to a 1% (w/w) cholesterol diet (diet Western 24769, Provimi Kliba SA, Kaiseraugst, CH).

treatment_protocol: Mouse was treated with one peroral application of 20 mg/kg rosuvastatin in tap water in the morning. After 24 hours animal was euthanized using CO2 suffocation.

value: 16 weeks

source_name: liver, reference 2

growth_protocol: Mix of all samples used in experiment: all mice on cholesterol diet.

treatment_protocol: Mix of all samples used in experiment: mice treated with vehicle, rosuvastatin and atorvastatin.


title: Liver_chol_rosuva_6

description: No additional data.


title: Liver_chol_rosuva_3

description: No additional data.


title: Liver_chol_rosuva_1

description: No additional data.


title: Liver_chol_water_6

description: No additional data.

source_name: liver, cholesterol diet, water

treatment_protocol: Mouse was treated with one peroral application of vehicle (tap water) in the morning. After 24 hours animal was euthanized using CO2 suffocation.


title: Liver_chol_rosuva_2

description: No additional data.


title: Liver_chol_atorva_3

description: No additional data.

source_name: liver, cholesterol diet, atorvastatin

treatment_protocol: Mouse was treated with one peroral application of 40 mg/kg atorvastatin in tap water in the morning. After 24 hours animal was euthanized using CO2 suffocation


title: Liver_chol_atorva_2

description: No additional data.


title: Liver_chol_atorva_6

description: No additional data.


title: Liver_chol_atorva_4

description: No additional data.


title: MCF10A-MycChIPchip-ectopicMyc-rep4_chipA


title: Liver_chol_water_1

description: No additional data.


title: MCF10A-MycChIPchip-ectopicMyc-rep5_chipA


title: MCF10A-MycChIPchip-ectopicGFP-rep9_chipA


title: MCF10A-MycChIPchip-ectopicGFP-rep7_chipA


title: MCF10A-MycChIPchip-ectopicMyc-rep9_chipA


title: MCF10A-MycChIPchip-ectopicGFP-rep3_chipA


title: MCF10A-MycChIPchip-ectopicGFP-rep5_chipA


title: MCF10A-MycChIPchip-ectopicGFP-rep1_chipA


title: MCF10A-MycChIPchip-ectopicGFP-rep2_chipA


title: MCF10A-MycChIPchip-ectopicMyc-rep1_chipA


title: Liver_stand_PCN_5

description: No additional data.


title: MCF10A-MycChIPchip-ectopicGFP-rep4_chipA


title: Liver_stand_PCN_1

description: No additional data.


title: Liver_stand_controlPCN_6

description: No additional data.


title: Liver_stand_TCPOBOP_3

description: No additional data.

source_name: liver, standard diet, TCPOBOP

growth_protocol: Mouse was housed in normal light-cycle room, maintained on standard rodent chow (diet 3430, Provimi Kliba SA, Kaiseraugst, CH), and were allowed water and food ad libitum.

treatment_protocol: Mouse was injected one i.p. injection of 3 mg/kg TCPOBOP (Bayer Ag, Wuppertal, Germany) in corn oil in the morning. After 24 hours animal was euthanized using CO2 suffocation.

source_name: liver, reference 1

growth_protocol: Mix of all samples used in experiment: mice on standard and cholesterol diet.

treatment_protocol: Mix of all samples used in experiment: mice treated with vehicle, TCPOBOP and PCN.


title: Liver_chol_TCPOBOP_6

description: No additional data.

source_name: liver, cholesterol diet, TCPOBOP

growth_protocol: Mouse was housed in normal light-cycle room, maintained on standard rodent chow (diet 3430, Provimi Kliba SA, Kaiseraugst, CH), and were allowed water and food ad libitum. One week prior treatment diet was switched to a 1% (w/w) cholesterol diet (diet Western 24769, Provimi Kliba SA, Kaiseraugst, CH).

value: 18 weeks


title: Liver_chol_water_5

description: No additional data.


title: Liver_chol_rosuva_4

description: No additional data.


title: Liver_chol_water_4

description: No additional data.


title: Liver_chol_water_3

description: No additional data.


title: Liver_chol_water_2

description: No additional data.


title: Liver_stand_controlPCN_3

description: No additional data.


title: Liver_chol_TCPOBOP_1

description: No additional data.


title: Liver_chol_PCN_4

description: No additional data.

source_name: liver, cholesterol diet, PCN


title: Liver_stand_controlPCN_1

description: No additional data.


title: Liver_chol_PCN_5

description: No additional data.


title: Liver_stand_TCPOBOP_6

description: No additional data.


title: Liver_chol_atorva_5

description: No additional data.


title: Liver_chol_atorva_1

description: No additional data.


title: Liver_stand_controlPCN_5

description: No additional data.


title: Liver_stand_TCPOBOP_4

description: No additional data.


title: Liver_chol_PCN_2

description: No additional data.


title: Liver_stand_TCPOBOP_5

description: No additional data.


title: Liver_chol_control_4

description: No additional data.

source_name: liver, cholesterol diet, control

treatment_protocol: Mouse was injected one i.p. injection of vehicle (corn oil, Sigma, St Louis, MI, USA) in the morning. After 24 hours animal was euthanized using CO2 suffocation.


title: Liver_chol_control_3

description: No additional data.


title: Liver_stand_control_5

description: No additional data.


title: Liver_chol_TCPOBOP_4

description: No additional data.


title: Liver_stand_control_3

description: No additional data.


title: Liver_chol_control_1

description: No additional data.


title: Liver_chol_TCPOBOP_2

description: No additional data.


title: Liver_chol_TCPOBOP_5

description: No additional data.


title: Liver_stand_TCPOBOP_2

description: No additional data.


title: Liver_stand_control_6

description: No additional data.


title: Liver_chol_TCPOBOP_3

description: No additional data.


title: Liver_stand_TCPOBOP_1

description: No additional data.


title: Liver_chol_PCN_6

description: No additional data.


title: Liver_stand_control_4

description: No additional data.


title: Liver_chol_PCN_3

description: No additional data.


title: Liver_chol_PCN_1

description: No additional data.


title: Liver_chol_control_5

description: No additional data.


title: Liver_chol_control_6

description: No additional data.


title: bre1_array2

status: Public on Nov 19 2009

city: San Francisco

first: William

last: Hwang

state: CA

address: Lim Lab - Box 0525, 35 Medical Center Way

department: Neurosurgery

institute: UCSF

description: bre1 vs wild-type

hyb_protocol: See Venkatasubrahmanyam S et al. PNAS 2007 Oct 16; 104(42):16609-14. PMID: 17925448

data_processing: Log2 of bre1/WT ratio, normalized for total signal in each channel.

molecule: polyA RNA

organism: Saccharomyces cerevisiae

tag: log phase

tag: YPAD

source_name: wild-type


title: Liver_chol_control_2

description: No additional data.


title: CW (28-071) vs. OSU (28-091) on female embryos 28 dpf Array #039

status: Public on Nov 12 2009

city: West Lafayette

first: Peng

last: Xu

state: IN

address: 915 W State St

institute: Purdue University

hyb_protocol: Invitrogen Indirect cDNA Labeling System version 3 (http://web.uvic.ca/grasp/microarray/array.html)

scan_protocol: Following hybridization and slide washing, microarray signals were detected with the Scanarray 4000 Microarray Scanner (Perkin Elmer, Waltham, MA) at excitation wavelengths 540 nm for Cy3 and 633 nm for Cy5, 10 µm resolution and laser power settings 70 – 90%, photo multiplier tube (PMT) gain 80-90%.

data_processing: Microarray image files were processed in ImaGene 6.1 (BioDiscovery, El Segundo, CA) with default parameters. Briefly, the signal values and local background values of each spot were obtained from the ImaGene image segmentation algorithms. Each spot was flagged for quality with flags for “good spot”, “empty spot”, or “poor spot”. Raw data from ImaGene were collated for data analysis in SAS and SAS JMP Genomics (SAS Institute, Cary, NC). Prior to data analysis, local background-subtracted signals for each spot on each slide were natural log-transformed and then standardized by subtracting the median value of all the spots except “poor” spots flagged by ImaGene.

organism: Oncorhynchus mykiss

source_name: Female CW embryo on 28 dpf (sample#: 28-071)

growth_protocol: After fertilization, embryos were incubated in re-circulating stack egg incubators in a constant 11ºC climate-controlled room before sample collection.

extract_protocol: Total RNA was extracted from each frozen rainbow trout embryo using TRI reagent followed by RNeasy kit (Qiagen) purification.

treatment_protocol: A fourth generation backcross (BC4) family was made at Washington State University, using marker assisted selection to select for third-generation backcross (BC3) individuals possessing the allele for fast development (from the Clearwater (CW) clonal line) for crossing with the Oregon State University (OSU) rainbow trout clonal line, which possesses alleles for slower development at the major embryonic development rate QTL (Nichols et al., 2007). Briefly, sperm from an XY BC3 male with the OSU/CW genotype at the major embryonic development rate QTL was utilized to fertilize eggs from an OSU female at Washington State University. Backcross individuals were sampled at 15 days, 19 days and 28 days post-fertilization (dpf), which roughly correspond to the development stages of eyed and yolk vascularizaiton, caudal flexing and beginning of hatching, respectively. After fertilization, embryos were incubated in re-circulating stack egg incubators in a constant 11ºC climate-controlled room. Genetic markers tightly linked to the major embryonic development rate QTL were used to identify the genotype of each embryo.

tag: Female embryo on 28 dpf (sample#

value: 28-071), possessing CW allele (fast-developing allele) on rainbow trout embryonic development rate QTL

source_name: Female OSU embryo on 28 dpf (sample#: 28-091)

value: 28-091), possessing OSU allele (slow-developing allele) on rainbow trout embryonic development rate QTL


title: Liver_stand_control_1

description: No additional data.


title: CW (15-043) vs. OSU (15-078) on female embryos 15 dpf Array #035

data_processing: background values of each spot were obtained from the ImaGene image segmentation algorithms. Each spot was flagged for quality with flags for “good spot”, “empty spot”, or “poor spot”. Raw data from ImaGene were collated for data analysis in SAS and SAS JMP Genomics (SAS Institute, Cary, NC). Prior to data analysis, local background-subtracted signals for each spot on each slide were natural log-transformed and then standardized by subtracting the median value of all the spots except “poor” spots flagged by ImaGene.

source_name: Female CW embryo on 15dpf (sample#: 15-043)

label_protocol: Invitrogen Indirect cDNA Labeling System version 3 (http://web.uvic.ca/grasp/microarray/array.html)

tag: Female embryo on 15 dpf (sample#

value: 15-043), possessing CW allele (fast-developing allele) on rainbow trout embryonic development rate QTL

source_name: Female OSU embryo on 15dpf (sample#: 15-078)

value: 15-078), possessing OSU allele (slow-developing allele) on rainbow trout embryonic development rate QTL


title: Liver_stand_control_2

description: No additional data.


title: CW (28-081) vs. OSU (28-070) on male embryos 28 dpf Array #033

source_name: Male OSU embryo on 28 dpf (sample#: 28-070)

tag: Male embryo on 28 dpf (sample#

value: 28-070), possessing OSU allele (slow-developing allele) on rainbow trout embryonic development rate QTL

source_name: Male CW embryo on 28 dpf (sample#: 28-081)

value: 28-081), possessing CW allele (fast-developing allele) on rainbow trout embryonic development rate QTL


title: CW (28-063) vs. OSU (28-068) on male embryos 28 dpf Array #023

source_name: Male CW embryo on 28 dpf (sample#: 28-063)

value: 28-063), possessing CW allele (fast-developing allele) on rainbow trout embryonic development rate QTL

source_name: Male OSU embryo on 28 dpf (sample#: 28-068)

value: 28-068), possessing OSU allele (slow-developing allele) on rainbow trout embryonic development rate QTL


title: bre1_array4

description: bre1 vs wild-type

scan_protocol: See Venkatasubrahmanyam S et al. PNAS 2007 Oct 16; 104(42):16609-14. PMID: 17925448


title: bre1_array3

description: bre1 vs wild-type

label_protocol:
See Venkatasubrahmanyam S et al.
PNAS 2007 Oct 16; 104(42):16609-14.
PMID: 17925448


title: CW (28-087) vs. OSU (28-030) on male embryos 28 dpf Array #028

source_name: Male OSU embryo on 28 dpf (sample#: 28-030)

value: 28-030), possessing OSU allele (slow-developing allele) on rainbow trout embryonic development rate QTL

source_name: Male CW embryo on 28 dpf (sample#: 28-087)

value: 28-087), possessing CW allele (fast-developing allele) on rainbow trout embryonic development rate QTL


title: bre1_array1

description: bre1 vs wild-type

extract_protocol:
See Venkatasubrahmanyam S et al.
PNAS 2007 Oct 16; 104(42):16609-14.
PMID: 17925448


title: CW (19-072) vs. OSU (19-061) on male embryos 19 dpf Array #022

description: CW (19-072) vs. OSU (19-061)  male embryos 19 dpf

source_name: Male OSU embryo on 19dpf (sample#: 19-061)

tag: Male embryo on 19dpf (sample#

value: 19-061), possessing OSU allele (slow-developing allele) on rainbow trout embryonic development rate QTL

source_name: Male CW embryo on 19dpf (sample#: 19-072)

value: 19-072), possessing CW allele (fast-developing allele) on rainbow trout embryonic development rate QTL


title: CW (15-037) vs. OSU (15-032) on female embryos 15 dpf Array #013

source_name: Female OSU embryo on 15dpf (sample#: 15-032)

growth_protocol: After fertilization, embryos were incubated in re-circulating stack egg incubators in a constant 11 degree climate-controlled room before sample collection.

tag: Female embryo on 15dpf (sample#

value: 15-032), possessing OSU allele (slow-developing allele) on rainbow trout embryonic development rate QTL

source_name: Female CW embryo on 15dpf (sample#: 15-037)

value: 15-037), possessing CW allele (fast-developing allele) on rainbow trout embryonic development rate QTL


title: CW (19-045) vs. OSU (19-046) on male embryos 19 dpf Array #019

description: CW (19-045) vs. OSU (19-046)  male embryos 19 dpf

source_name: Male CW embryo on 19dpf (sample#: 19-045)

value: 19-045), possessing CW allele (fast-developing allele) on rainbow trout embryonic development rate QTL

source_name: Male OSU embryo on 19dpf (sample#: 19-046)

value: 19-046), possessing OSU allele (slow-developing allele) on rainbow trout embryonic development rate QTL


title: CW (19-026) vs. OSU (19-050) on female embryos 19 dpf Array #029

description: CW (19-026) vs. OSU (19-050)  female embryos 19 dpf

source_name: Female OSU embryo on 19dpf (sample#: 19-050)

tag: Female embryo on 19dpf (sample#

value: 19-050), possessing OSU allele (slow-developing allele) on rainbow trout embryonic development rate QTL

source_name: Female CW embryo on 19dpf (sample#: 19-026)

value: 19-026), possessing CW allele (fast-developing allele) on rainbow trout embryonic development rate QTL


title: CW (19-062) vs. OSU (19-029) on female embryos 19 dpf Array #040

description: CW (19-062) vs. OSU (19-029)  female embryos 19 dpf

source_name: Female CW embryo on 19dpf (sample#: 19-062)

value: 19-062), possessing CW allele (fast-developing allele) on rainbow trout embryonic development rate QTL

source_name: Female OSU embryo on 19dpf (sample#: 19-029)

value: 19-029), possessing OSU allele (slow-developing allele) on rainbow trout embryonic development rate QTL


title: CW (28-041) vs. OSU (28-042) on female embryos 28 dpf Array #038

source_name: Female OSU embryo on 28 dpf (sample#: 28-042)

label_protocol: Indirect cDNA Labeling System version 3 (http://web.uvic.ca/grasp/microarray/array.html)

value: 28-042), possessing OSU allele (slow-developing allele) on rainbow trout embryonic development rate QTL

source_name: Female CW embryo on 28 dpf (sample#: 28-041)

value: 28-041), possessing CW allele (fast-developing allele) on rainbow trout embryonic development rate QTL


title: CW (28-051) vs. OSU (28-080) on female embryos 28 dpf Array #036

source_name: Female CW embryo on 28 dpf (sample#: 28-051)

value: 28-051), possessing CW allele (fast-developing allele) on rainbow trout embryonic development rate QTL

source_name: Female OSU embryo on 28 dpf (sample#: 28-080)

value: 28-080), possessing OSU allele (slow-developing allele) on rainbow trout embryonic development rate QTL


title: CW (28-060) vs. OSU (28-038) on male embryos 28 dpf Array #037

source_name: Male CW embryo on 28 dpf (sample#: 28-060)

value: 28-060), possessing CW allele (fast-developing allele) on rainbow trout embryonic development rate QTL

source_name: Male OSU embryo on 28 dpf (sample#: 28-038)

value: 28-038), possessing OSU allele (slow-developing allele) on rainbow trout embryonic development rate QTL


title: CW (28-040) vs. OSU (28-037) on female embryos 28 dpf Array #026

source_name: Female OSU embryo on 28 dpf (sample#: 28-037)

value: 28-037), possessing OSU allele (slow-developing allele) on rainbow trout embryonic development rate QTL

source_name: Female CW embryo on 28 dpf (sample#: 28-040)

value: 28-040), possessing CW allele (fast-developing allele) on rainbow trout embryonic development rate QTL


title: CW (15-038) vs. OSU (15-051) on male embryos 15 dpf Array #018

source_name: Male OSU embryo on 15dpf (sample#: 15-051)

tag: Male embryo on 15 dpf (sample#

value: 15-051), possessing OSU allele (slow-developing allele) on rainbow trout embryonic development rate QTL

source_name: Male CW embryo on 15dpf (sample#: 15-038)

value: 15-038), possessing CW allele (fast-developing allele) on rainbow trout embryonic development rate QTL


title: CW (15-041) vs. OSU (15-066) on male embryos 15 dpf Array #041

source_name: Male CW embryo on 15dpf (sample#: 15-041)

value: 15-041), possessing CW allele (fast-developing allele) on rainbow trout embryonic development rate QTL

source_name: Male OSU embryo on 15dpf (sample#: 15-066)

value: 15-066), possessing OSU allele (slow-developing allele) on rainbow trout embryonic development rate QTL


title: CD9 transduced RASM cells, biological replicate 1.

city: Memphis

first: Celia

last: Longhurst

state: TN

address: 956 Court Avenue Room H300

department: Medicine

institute: UTHSC

description: Gene expression data from cells harvested after adhesion to FN for 6 hours

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

label: biotin

organism: Rattus norvegicus

source_name: Rat aortic vascular smooth muscle cells transiently transduced with adenovirus containing human CD9 cDNA

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: RASM cells were isolated from Sprague-Dawley rats and cultured in DMEM 10% FBS growth media. RASM cells were used at passage 9 in the described experiments.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: RASM cells grown to 80% confluence were infected with either Ad-CD9 or Ad-LACZ control in DMEM media. Seventy-two hours post transduction, RASM cells were harvested and replated on cell culture plates coated with 10ug/ml human plasma FN for 6 hours when adhered cells were washed and total RNA was extracted using TriZol (Sigma)

tag: Rat vascular aortic smooth muscle cells


title: CW (15-026) vs. OSU (15-029) on female embryos 15 dpf Array #014

source_name: Female OSU embryo on 15dpf (sample#: 15-029)

value: 15-029), possessing OSU allele (slow-developing allele) on rainbow trout embryonic development rate QTL

source_name: Female CW embryo on 15dpf (sample#: 15-026)

value: 15-026), possessing CW allele (fast-developing allele) on rainbow trout embryonic development rate QTL


title: CW (15-062) vs. OSU (15-071) on female embryos 15 dpf Array #017

source_name: Female OSU embryo on 15dpf (sample#: 15-071)

value: 15-071), possessing OSU allele (slow-developing allele) on rainbow trout embryonic development rate QTL

source_name: Female CW embryo on 15dpf (sample#: 15-062)

value: 15-062), possessing CW allele (fast-developing allele) on rainbow trout embryonic development rate QTL


title: serotype 11 reference strain

status: Public on Nov 11 2009

city: Wuhan

first: Lu

last: Li

email: sakura.tree@163.com, xuzf@mail.hzau.edu.cn, xuzhuofei@sohu.com, kobe2071@tom.com

state: Hubei

address: Shizishan Street 1

country: China

institute: Huazhong Agricultural University

description: reference strain of serotype 11 and control strain JL03,harvested bacteria cells grown overnight

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent Oligo aCGH Hybridization Kit) were added, and samples were applied to microarrays enclosed in Agilent hybridization chambers. After hybridization, slides were washed sequential

scan_protocol: Scanned on an Agilent G2565BA scanner. Images were quantified using Agilent Feature Extraction Software (version 9.5).

data_processing: Z-normalized by computing the formula:Z(x)=(x-μ)／σ, where x is the log of a measured CGH ratio, μ is the mean and σ is the standard deviation of the population of such log ratios. The module ChARM in the MultiExperiment Viewer was used.

organism: Actinobacillus pleuropneumoniae

source_name: genomic DNA from strain 56153

label_protocol: Add 5 µl of random primers (supplied with Agilent Genomic DNA labeling kit PLUS) to each digested reaction tube at 95°C for 50 min, then incubate on ice for 5 min. Add 21 µl of labeling master mix containing 10X dNTP 5 µl, 5X Buffer 10 µl,Cy3/Cy5–dUTP(1mM) 3 µl,Exo-Klenow fragment 1 µl,Nuclease-free water 2 µl. Incubate at 37°C for 2 h, then at 65°C for 10 min.

extract_protocol: Genomic DNA was extracted by using DNeasy Tissue Kit following manufacture's instructions.

value: serotype 11

source_name: genomic DNA from strain JL03

value: serotype 3


title: serotype 13 reference strain

description: reference strain of serotype 13 and control strain JL03,harvested bacteria cells grown overnight

source_name: genomic DNA from strain N-273

value: serotype 13


title: serotype 12 reference strain

description: reference strain of serotype 12 and control strain JL03,harvested bacteria cells grown overnight

source_name: genomic DNA from strain 1096

value: serotype 12


title: Lac Z transduced RASM cells, biological replicate 2.

source_name: Rat aortic vascular smooth muscle cells transiently transduced with adenovirus containing Lac Z cDNA


title: serotype 7 reference strain

description: reference strain of serotype 7 and control strain JL03,harvested bacteria cells grown overnight

source_name: genomic DNA from strain WF83

value: serotype 7


title: CW (15-030) vs. OSU (15-076) on male embryos 15 dpf Array #031

source_name: Male CW embryo on 15dpf (sample#: 15-030)

value: 15-030), possessing CW allele (fast-developing allele) on rainbow trout embryonic development rate QTL

source_name: Male OSU embryo on 15dpf (sample#: 15-076)

value: 15-076), possessing OSU allele (slow-developing allele) on rainbow trout embryonic development rate QTL


title: CW (19-052) vs. OSU (19-023) on female embryos 19 dpf Array #010

source_name: Female CW embryo on 19dpf (sample#: 19-052)

value: 19-052), possessing CW allele (fast-developing allele) on rainbow trout embryonic development rate QTL

source_name: Female OSU embryo on 19dpf (sample#: 19-023)

value: 19-023), possessing OSU allele (slow-developing allele) on rainbow trout embryonic development rate QTL


title: CW (19-060) vs. OSU (19-077) on male embryos 19 dpf Array #011

source_name: Male CW embryo on 19dpf (sample#: 19-060)

value: 19-060), possessing CW allele (fast-developing allele) on rainbow trout embryonic development rate QTL

source_name: Male OSU embryo on 19dpf (sample#: 19-077)

value: 19-077), possessing OSU allele (slow-developing allele) on rainbow trout embryonic development rate QTL


title: CW (19-085) vs. OSU (19-030) on male embryos 19 dpf Array #027

description: CW (19-085) vs. OSU (19-030)  male embryos 19 dpf

source_name: Male OSU embryo on 19dpf (sample#: 19-030)

value: 19-030), possessing OSU allele (slow-developing allele) on rainbow trout embryonic development rate QTL

source_name: Male CW embryo on 19dpf (sample#: 19-085)

value: 19-085), possessing CW allele (fast-developing allele) on rainbow trout embryonic development rate QTL


title: CW (15-048) vs. OSU (15-028) on male embryos 15 dpf Array #034

source_name: Male CW embryo on 15dpf (sample#: 15-048)

value: 15-048), possessing CW allele (fast-developing allele) on rainbow trout embryonic development rate QTL

source_name: Male OSU embryo on 15dpf (sample#: 15-028)

value: 15-028), possessing OSU allele (slow-developing allele) on rainbow trout embryonic development rate QTL


title: serotype 5a reference strain

description: reference strain of serotype 5a and control strain JL03,harvested bacteria cells grown overnight

source_name: genomic DNA from strain K17

value: serotype 5a


title: serotype 3 reference strain

description: reference strain of serotype 3 and control strain JL03,harvested bacteria cells grown overnight

source_name: genomic DNA from strain S1421


title: serotype 8 reference strain

description: reference strain of serotype 8 and control strain JL03,harvested bacteria cells grown overnight

source_name: genomic DNA from strain 405

value: serotype 8

source_name: genomic DNA from strain JL03


title: serotype 5b reference strain

description: reference strain of serotype 5b and control strain JL03,harvested bacteria cells grown overnight

source_name: genomic DNA from strain L20

value: serotype 5b


title: serotype 10 reference strain

description: reference strain of serotype 10 and control strain JL03,harvested bacteria cells grown overnight

source_name: genomic DNA from strain D13039

value: serotype 10

value: serotype 3


title: serotype 2 reference strain

description: reference strain of serotype 2 and control strain JL03,harvested bacteria cells grown overnight

source_name: genomic DNA from strain 4226

value: serotype 2


title: serotype 6 reference strain

description: reference strain of serotype 6 and control strain JL03,harvested bacteria cells grown overnight

source_name: genomic DNA from strain Femφ

value: serotype 6


title: serotype 9 reference strain

description: reference strain of serotype 9 and control strain JL03,harvested bacteria cells grown overnight

source_name: genomic DNA from strain CVJ13261

value: serotype 9


title: CD9 transduced RASM cells, biological replicate 2.

source_name: Rat aortic vascular smooth muscle cells transiently transduced with adenovirus containing human CD9 cDNA


title: CW (19-021) vs. OSU (19-015) on female embryos 19 dpf Array #015

description: CW (19-021) vs. OSU (19-015)  female embryos 19 dpf

source_name: Female OSU embryo on 19dpf (sample#: 19-015)

value: 19-015), possessing OSU allele (slow-developing allele) on rainbow trout embryonic development rate QTL

source_name: Female CW embryo on 19dpf (sample#: 19-021)

value: 19-021), possessing CW allele (fast-developing allele) on rainbow trout embryonic development rate QTL


title: Lac Z transduced RASM cells, biological replicate 1.

source_name: Rat aortic vascular smooth muscle cells transiently transduced with adenovirus containing Lac Z cDNA


title: serotype 4 reference strain

description: reference strain of serotype 4 and control strain JL03,harvested bacteria cells grown overnight

source_name: genomic DNA from strain M62

value: serotype 4


title: Em-4-3 trpl

status: Public on Nov 05 2009

city: Seattle

first: Nina

middle: Reda

last: Salama

state: WA

address: 1100 Fairview Ave. N

department: Division of Human Biology

institute: Fred Hutchinson Cancer Research Center

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2005-12/65830.gif

hyb_protocol: not provided

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1050, 8310; Software: type: feature extraction; Performer: Nina,,Salama Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2005-11-16; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.0; Parameter Scan Power = 100; Parameter PMT Volts = 570; Parameter Laser on time = 75841; Parameter Laser Power = 3.45; Parameter Scan Time = 15:27:31; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 32.92; Performer: Nina,,Salama Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2005-11-16; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.0; Parameter Pixel Size = 10; Parameter PMT Volts = 540; Parameter Scan Power = 100; Parameter Laser on time = 76270; Parameter Laser Power = 3.74; Parameter Scan Time = 15:27:31; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 32.92; Performer: Nina,,Salama

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

organism: Helicobacter pylori

source_name: 500 ng 26695/J99 genomic DNA mix

label_protocol: 500 ng of genomic DNA of a reference sample (equimolar mix of 26695 and J99) was labeled with Cy3

extract_protocol: Genomic DNA extracted from reference strains 26695 and J99, and then mixed in equimolar concentrations.

tag: Equimolar mix of strains 26695/J99

tag: Reference DNA

label_protocol: 500 ng of genomic DNA of each test strain was labeled with Cy5

extract_protocol: Initial strain isolation from antral biopsies performed at Emory and culture sweeps sent to FHCRC (Seattle) for analysis. Single colony isolates (4) from each patient antral biopsy were isolated and profiled using RAPD. A single clone of each RAPD type detected in each patient (1-2) were analyzed. Genomic DNA was extracted and analyzed on duplicate arrays.

tag: Test Strain

tag: Emory strain Em-4-3


title: Em-18-1 dupl

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2008-10/81753.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 2070, 35460; Software: type: feature extraction; Performer: Nina,,Salama 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 Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.1; Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 33.65; Performer: Nina,,Salama 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 Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.1; Parameter Pixel Size = 10; Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 33.65; Performer: Nina,,Salama

tag: Emory strain Em-18-1


title: Em-27-2 dupl

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2005-12/65787.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1020, 35470; Software: type: feature extraction; Performer: Nina,,Salama Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2005-10-12; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.0; Parameter Scan Power = 100; Parameter PMT Volts = 530; Parameter Laser on time = 75118; Parameter Laser Power = 3.53; Parameter Scan Time = 08:13:17; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 32.03; Performer: Nina,,Salama Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2005-10-12; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.0; Parameter Pixel Size = 10; Parameter PMT Volts = 600; Parameter Scan Power = 100; Parameter Laser on time = 75546; Parameter Laser Power = 3.69; Parameter Scan Time = 08:13:17; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 32.03; Performer: Nina,,Salama

tag: Emory strain Em-27-2


title: Em-28-3

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2005-12/65788.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1880, 8080; Software: type: feature extraction; Performer: Nina,,Salama Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2005-07-11; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.0; Parameter Scan Power = 100; Parameter PMT Volts = 650; Parameter Laser on time = 68603; Parameter Laser Power = 3.44; Parameter Scan Time = 14:32:24; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 31.70; Performer: Nina,,Salama Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2005-07-11; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.0; Parameter Pixel Size = 10; Parameter PMT Volts = 830; Parameter Scan Power = 100; Parameter Laser on time = 68629; Parameter Laser Power = 3.68; Parameter Scan Time = 14:32:24; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 31.70; Performer: Nina,,Salama

tag: Emory strain Em-28-3


title: Em-4-3 dupl

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2005-12/65829.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 960, 8600; Software: type: feature extraction; Performer: Nina,,Salama Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2005-06-16; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.0; Parameter Scan Power = 100; Parameter PMT Volts = 480; Parameter Laser on time = 67642; Parameter Laser Power = 3.51; Parameter Scan Time = 11:50:04; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 31.91; Performer: Nina,,Salama Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2005-06-16; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.0; Parameter Pixel Size = 10; Parameter PMT Volts = 500; Parameter Scan Power = 100; Parameter Laser on time = 67700; Parameter Laser Power = 3.72; Parameter Scan Time = 11:50:04; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 31.91; Performer: Nina,,Salama


title: Em-34-3

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2005-12/65806.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1720, 8720; Software: type: feature extraction; Performer: Nina,,Salama Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2005-07-15; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.0; Parameter Scan Power = 100; Parameter PMT Volts = 520; Parameter Laser on time = 68950; Parameter Laser Power = 3.43; Parameter Scan Time = 13:58:36; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 31.64; Performer: Nina,,Salama Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2005-07-15; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.0; Parameter Pixel Size = 10; Parameter PMT Volts = 550; Parameter Scan Power = 100; Parameter Laser on time = 68976; Parameter Laser Power = 3.70; Parameter Scan Time = 13:58:36; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 31.64; Performer: Nina,,Salama

tag: Emory strain Em-34-3


title: Em-21-3

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2005-12/65778.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1160, 35550; Software: type: feature extraction; Performer: Nina,,Salama Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2005-10-05; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.0; Parameter Scan Power = 100; Parameter PMT Volts = 480; Parameter Laser on time = 74899; Parameter Laser Power = 3.45; Parameter Scan Time = 10:02:24; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 26.24; Performer: Nina,,Salama Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2005-10-05; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.0; Parameter Pixel Size = 10; Parameter PMT Volts = 570; Parameter Scan Power = 100; Parameter Laser on time = 75290; Parameter Laser Power = 3.51; Parameter Scan Time = 10:02:24; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 26.24; Performer: Nina,,Salama

tag: Emory strain Em-21-3


title: Em-22-2 dupl

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2005-12/65781.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1560, 34740; Software: type: feature extraction; Performer: Nina,,Salama Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2005-07-11; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.0; Parameter Scan Power = 100; Parameter PMT Volts = 650; Parameter Laser on time = 68608; Parameter Laser Power = 3.44; Parameter Scan Time = 14:37:16; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 31.82; Performer: Nina,,Salama Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2005-07-11; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.0; Parameter Pixel Size = 10; Parameter PMT Volts = 760; Parameter Scan Power = 100; Parameter Laser on time = 68633; Parameter Laser Power = 3.70; Parameter Scan Time = 14:37:16; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 31.82; Performer: Nina,,Salama

tag: Emory strain Em-22-2


title: Em-10-4

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2005-12/65754.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 200, 8440; Software: type: feature extraction; Performer: Nina,,Salama Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2005-08-26; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.0; Parameter Scan Power = 100; Parameter PMT Volts = 510; Parameter Laser on time = 71645; Parameter Laser Power = 3.45; Parameter Scan Time = 14:40:38; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 31.64; Performer: Nina,,Salama Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2005-08-26; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.0; Parameter Pixel Size = 10; Parameter PMT Volts = 560; Parameter Scan Power = 100; Parameter Laser on time = 71782; Parameter Laser Power = 3.70; Parameter Scan Time = 14:40:38; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 31.64; Performer: Nina,,Salama

tag: Emory strain Em-10-4


title: Em-44-1 dupl

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2005-12/65834.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1790, 35060; Software: type: feature extraction; Performer: Nina,,Salama Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2005-10-28; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.0; Parameter Scan Power = 100; Parameter PMT Volts = 470; Parameter Laser on time = 75735; Parameter Laser Power = 3.46; Parameter Scan Time = 12:33:26; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 33.50; Performer: Nina,,Salama Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2005-10-28; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.0; Parameter Pixel Size = 10; Parameter PMT Volts = 590; Parameter Scan Power = 100; Parameter Laser on time = 76164; Parameter Laser Power = 3.77; Parameter Scan Time = 12:33:26; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 33.50; Performer: Nina,,Salama

tag: Emory strain Em-44-1


title: Em-45-4 dupl

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2005-12/65836.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1640, 8630; Software: type: feature extraction; Performer: Nina,,Salama Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2005-10-28; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.0; Parameter Scan Power = 100; Parameter PMT Volts = 480; Parameter Laser on time = 75744; Parameter Laser Power = 3.46; Parameter Scan Time = 12:43:18; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 33.59; Performer: Nina,,Salama Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2005-10-28; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.0; Parameter Pixel Size = 10; Parameter PMT Volts = 560; Parameter Scan Power = 100; Parameter Laser on time = 76173; Parameter Laser Power = 3.77; Parameter Scan Time = 12:43:18; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 33.59; Performer: Nina,,Salama

tag: Emory strain Em-45-4


title: Em-24-4 dupl

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2005-12/65785.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1240, 9200; Software: type: feature extraction; Performer: Nina,,Salama Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2005-10-12; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.0; Parameter Scan Power = 100; Parameter PMT Volts = 520; Parameter Laser on time = 75113; Parameter Laser Power = 3.46; Parameter Scan Time = 08:09:03; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 31.94; Performer: Nina,,Salama Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2005-10-12; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.0; Parameter Pixel Size = 10; Parameter PMT Volts = 580; Parameter Scan Power = 100; Parameter Laser on time = 75542; Parameter Laser Power = 3.68; Parameter Scan Time = 08:09:03; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 31.94; Performer: Nina,,Salama

tag: Emory strain Em-24-4


title: Em-3-3 dupl

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2005-12/65802.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 780, 8730; Software: type: feature extraction; Performer: Nina,,Salama Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2005-06-16; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.0; Parameter Scan Power = 100; Parameter PMT Volts = 480; Parameter Laser on time = 67640; Parameter Laser Power = 3.54; Parameter Scan Time = 11:47:39; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 31.91; Performer: Nina,,Salama Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2005-06-16; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.0; Parameter Pixel Size = 10; Parameter PMT Volts = 500; Parameter Scan Power = 100; Parameter Laser on time = 67699; Parameter Laser Power = 3.72; Parameter Scan Time = 11:47:39; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 31.91; Performer: Nina,,Salama

tag: Emory strain Em-3-3


title: Em-11-1

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2005-12/65756.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1020, 9130; Software: type: feature extraction; Performer: Nina,,Salama Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2005-09-29; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.0; Parameter Scan Power = 100; Parameter PMT Volts = 510; Parameter Laser on time = 74638; Parameter Laser Power = 3.46; Parameter Scan Time = 15:20:36; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 34.20; Performer: Nina,,Salama Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2005-09-29; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.0; Parameter Pixel Size = 10; Parameter PMT Volts = 600; Parameter Scan Power = 100; Parameter Laser on time = 75028; Parameter Laser Power = 3.78; Parameter Scan Time = 15:20:36; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 34.20; Performer: Nina,,Salama

tag: Emory strain Em-11-1


title: Em-42-3 dupl

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2005-12/65827.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1790, 35060; Software: type: feature extraction; Performer: Nina,,Salama Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2005-10-28; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.0; Parameter Scan Power = 100; Parameter PMT Volts = 470; Parameter Laser on time = 75730; Parameter Laser Power = 3.46; Parameter Scan Time = 12:28:41; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 33.47; Performer: Nina,,Salama Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2005-10-28; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.0; Parameter Pixel Size = 10; Parameter PMT Volts = 590; Parameter Scan Power = 100; Parameter Laser on time = 76158; Parameter Laser Power = 3.76; Parameter Scan Time = 12:28:41; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 33.47; Performer: Nina,,Salama

tag: Emory strain Em-42-3


title: Em-17-1 dupl

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2005-12/65769.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 2200, 8650; Software: type: feature extraction; Performer: Nina,,Salama Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2005-11-30; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.0; Parameter Scan Power = 100; Parameter PMT Volts = 500; Parameter Laser on time = 76314; Parameter Laser Power = 3.49; Parameter Scan Time = 13:22:08; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 33.41; Performer: Nina,,Salama Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2005-11-30; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.0; Parameter Pixel Size = 10; Parameter PMT Volts = 580; Parameter Scan Power = 100; Parameter Laser on time = 76742; Parameter Laser Power = 3.75; Parameter Scan Time = 13:22:08; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 33.41; Performer: Nina,,Salama

tag: Equimolar mix of strains 26695/J99

tag: Emory strain Em-17-1


title: Em-28-3 dupl

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2005-12/65789.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1020, 8960; Software: type: feature extraction; Performer: Nina,,Salama Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2005-10-12; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.0; Parameter Scan Power = 100; Parameter PMT Volts = 540; Parameter Laser on time = 75131; Parameter Laser Power = 3.47; Parameter Scan Time = 08:26:53; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 32.37; Performer: Nina,,Salama Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2005-10-12; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.0; Parameter Pixel Size = 10; Parameter PMT Volts = 640; Parameter Scan Power = 100; Parameter Laser on time = 75560; Parameter Laser Power = 3.70; Parameter Scan Time = 08:26:53; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 32.37; Performer: Nina,,Salama

tag: Reference DNA

tag: Test Strain


title: serotype 1 reference strain

description: reference strain of serotype 1 and control strain JL03,harvested bacteria cells grown overnight

scan_protocol: Scanned on an Agilent G2565BA scanner. Images were quantified using Agilent Feature Extraction Software (version 9.5).

source_name: genomic DNA from strain 4074

tag: Strain

value: serotype 1


title: Em-21-3 dupl

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2005-12/65779.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1540, 8070; Software: type: feature extraction; Performer: Nina,,Salama Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2005-06-24; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.0; Parameter Scan Power = 100; Parameter PMT Volts = 670; Parameter Laser on time = 68164; Parameter Laser Power = 3.59; Parameter Scan Time = 10:27:34; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 31.94; Performer: Nina,,Salama Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2005-06-24; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.0; Parameter Pixel Size = 10; Parameter PMT Volts = 840; Parameter Scan Power = 100; Parameter Laser on time = 68190; Parameter Laser Power = 3.71; Parameter Scan Time = 10:27:34; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 31.94; Performer: Nina,,Salama


title: Em-31-2 dupl

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2005-12/65798.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1020, 9510; Software: type: feature extraction; Performer: Nina,,Salama Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2005-10-12; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.0; Parameter Scan Power = 100; Parameter PMT Volts = 530; Parameter Laser on time = 75139; Parameter Laser Power = 3.47; Parameter Scan Time = 08:34:07; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 32.49; Performer: Nina,,Salama Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2005-10-12; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.0; Parameter Pixel Size = 10; Parameter PMT Volts = 650; Parameter Scan Power = 100; Parameter Laser on time = 75568; Parameter Laser Power = 3.70; Parameter Scan Time = 08:34:07; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 32.49; Performer: Nina,,Salama

tag: Emory strain Em-31-2


title: Em-16-4 dupl

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2005-12/65767.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1380, 34910; Software: type: feature extraction; Performer: Nina,,Salama Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2005-06-24; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.0; Parameter Scan Power = 100; Parameter PMT Volts = 720; Parameter Laser on time = 68152; Parameter Laser Power = 3.49; Parameter Scan Time = 10:15:40; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 31.61; Performer: Nina,,Salama Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2005-06-24; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.0; Parameter Pixel Size = 10; Parameter PMT Volts = 840; Parameter Scan Power = 100; Parameter Laser on time = 68178; Parameter Laser Power = 3.68; Parameter Scan Time = 10:15:40; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 31.61; Performer: Nina,,Salama

tag: Emory strain Em-16-4


title: Em-32-4

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2005-12/65799.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1720, 34750; Software: type: feature extraction; Performer: Nina,,Salama Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2005-07-13; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.0; Parameter Scan Power = 100; Parameter PMT Volts = 620; Parameter Laser on time = 68899; Parameter Laser Power = 3.46; Parameter Scan Time = 13:02:31; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 32.06; Performer: Nina,,Salama Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2005-07-13; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.0; Parameter Pixel Size = 10; Parameter PMT Volts = 750; Parameter Scan Power = 100; Parameter Laser on time = 68925; Parameter Laser Power = 3.71; Parameter Scan Time = 13:02:31; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 32.06; Performer: Nina,,Salama

tag: Emory strain Em-32-4


title: Em-23-4 dupl

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2005-12/65783.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1790, 8430; Software: type: feature extraction; Performer: Nina,,Salama Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2005-07-11; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.0; Parameter Scan Power = 100; Parameter PMT Volts = 650; Parameter Laser on time = 68616; Parameter Laser Power = 3.44; Parameter Scan Time = 14:46:53; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 32.03; Performer: Nina,,Salama Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2005-07-11; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.0; Parameter Pixel Size = 10; Parameter PMT Volts = 710; Parameter Scan Power = 100; Parameter Laser on time = 68642; Parameter Laser Power = 3.70; Parameter Scan Time = 14:46:53; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 32.03; Performer: Nina,,Salama

tag: Emory strain Em-23-4


title: Em-46-3 dupl

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2005-12/65838.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1560, 34900; Software: type: feature extraction; Performer: Nina,,Salama Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2005-10-28; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.0; Parameter Scan Power = 100; Parameter PMT Volts = 450; Parameter Laser on time = 75751; Parameter Laser Power = 3.46; Parameter Scan Time = 12:49:41; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 33.62; Performer: Nina,,Salama Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2005-10-28; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.0; Parameter Pixel Size = 10; Parameter PMT Volts = 610; Parameter Scan Power = 100; Parameter Laser on time = 76180; Parameter Laser Power = 3.78; Parameter Scan Time = 12:49:41; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 33.62; Performer: Nina,,Salama

tag: Emory strain Em-46-3


title: Em-10-1

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2005-12/65752.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 960, 35320; Software: type: feature extraction; Performer: Nina,,Salama Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2005-09-16; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.0; Parameter Scan Power = 100; Parameter PMT Volts = 500; Parameter Laser on time = 73436; Parameter Laser Power = 3.47; Parameter Scan Time = 12:44:08; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 33.38; Performer: Nina,,Salama Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2005-09-16; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.0; Parameter Pixel Size = 10; Parameter PMT Volts = 570; Parameter Scan Power = 100; Parameter Laser on time = 73696; Parameter Laser Power = 3.76; Parameter Scan Time = 12:44:08; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 33.38; Performer: Nina,,Salama

tag: Emory strain Em-10-1


title: Em-35-4 dupl

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2005-12/65811.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 2070, 35270; Software: type: feature extraction; Performer: Nina,,Salama Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2005-11-23; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.0; Parameter Scan Power = 100; Parameter PMT Volts = 560; Parameter Laser on time = 76144; Parameter Laser Power = 3.44; Parameter Scan Time = 11:38:43; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 33.71; Performer: Nina,,Salama Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2005-11-23; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.0; Parameter Pixel Size = 10; Parameter PMT Volts = 570; Parameter Scan Power = 100; Parameter Laser on time = 76573; Parameter Laser Power = 3.76; Parameter Scan Time = 11:38:43; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 33.71; Performer: Nina,,Salama

tag: Emory strain Em-35-4


title: Em-51-2 dupl

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2005-12/65849.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 2230, 35220; Software: type: feature extraction; Performer: Nina,,Salama Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2005-11-23; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.0; Parameter Scan Power = 100; Parameter PMT Volts = 580; Parameter Laser on time = 76166; Parameter Laser Power = 3.44; Parameter Scan Time = 12:00:52; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 33.90; Performer: Nina,,Salama Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2005-11-23; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.0; Parameter Pixel Size = 10; Parameter PMT Volts = 590; Parameter Scan Power = 100; Parameter Laser on time = 76595; Parameter Laser Power = 3.76; Parameter Scan Time = 12:00:52; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 33.90; Performer: Nina,,Salama

tag: Emory strain Em-51-2


title: Em-16-4

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2005-12/65766.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1330, 35470; Software: type: feature extraction; Performer: Nina,,Salama Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2005-09-29; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.0; Parameter Scan Power = 100; Parameter PMT Volts = 500; Parameter Laser on time = 74655; Parameter Laser Power = 3.46; Parameter Scan Time = 15:37:58; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 34.17; Performer: Nina,,Salama Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2005-09-29; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.0; Parameter Pixel Size = 10; Parameter PMT Volts = 550; Parameter Scan Power = 100; Parameter Laser on time = 75046; Parameter Laser Power = 3.82; Parameter Scan Time = 15:37:58; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 34.17; Performer: Nina,,Salama


title: Em-18-3 dupl

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2005-12/65773.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1560, 8000; Software: type: feature extraction; Performer: Nina,,Salama Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2005-06-24; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.0; Parameter Scan Power = 100; Parameter PMT Volts = 680; Parameter Laser on time = 68155; Parameter Laser Power = 3.50; Parameter Scan Time = 10:18:55; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 31.73; Performer: Nina,,Salama Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2005-06-24; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.0; Parameter Pixel Size = 10; Parameter PMT Volts = 840; Parameter Scan Power = 100; Parameter Laser on time = 68181; Parameter Laser Power = 3.69; Parameter Scan Time = 10:18:55; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 31.73; Performer: Nina,,Salama

tag: Emory strain Em-18-3


title: Em-20-1

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2008-10/81725.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1400, 33960; Software: type: feature extraction; Performer: Nina,,Salama 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 Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.0; Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 26.69; Performer: Nina,,Salama 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 Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.0; Parameter Pixel Size = 10; Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 26.69; Performer: Nina,,Salama

tag: Emory strain Em-20-1


title: Em-49-1 trpl

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2005-12/65845.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1570, 34930; Software: type: feature extraction; Performer: Nina,,Salama Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2005-11-30; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.0; Parameter Scan Power = 100; Parameter PMT Volts = 510; Parameter Laser on time = 76319; Parameter Laser Power = 3.50; Parameter Scan Time = 13:27:30; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 33.41; Performer: Nina,,Salama Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2005-11-30; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.0; Parameter Pixel Size = 10; Parameter PMT Volts = 540; Parameter Scan Power = 100; Parameter Laser on time = 76748; Parameter Laser Power = 3.75; Parameter Scan Time = 13:27:30; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 33.41; Performer: Nina,,Salama

tag: Emory strain Em-49-1