title: LW01set3_eds5_Psm_24h

description: eds5 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae ES4326, harvested 24h after infiltration in set3 experiment.

source_name: Arabidopsis thaliana eds5, leaves, 1x10E8 cfu/ml Pseudomonas syringae ES4326-infiltrated, 24h


title: Fully Methylated DNA rep2

status: Public on Jul 21 2008

type: genomic

city: New Haven

first: Annette

last: Molinaro

state: CT

address: 60 College St

country: USA

institute: Yale University

description: Comparison of MeDIP enrichment and input genomic DNA allows the determination of DNA-methylation, according to Weber et al 2005.

hyb_protocol: Standard Nimblegen protocol

scan_protocol: Standard Nimblegen Protocol

data_processing:
Within (Loess based) and between (Quantile based) normalization methods available in the Limma Bioconductor/R library (Ihaka et al. 1996, Gentleman et al. 2004, Smyth et al. 2003, Smyth 2005) as standard methods for two-channel microarrays are applied to determine M and A values.
Smoothed MeDIP enrichment as well as Absolute and Relative Methylation Score are determined using the MEDME R library (Pelizzola et al, 2008).

molecule: genomic DNA

organism: Homo sapiens

source_name: Fully Methylated DNA, MeDIP

label_protocol:
UA whole-genome amplification was applied for producing an unmethylated copy of genomic DNA of normal human melanocytes (REPLI-g Mini Kit, QIAGEN). The amplified unmethylated DNA was treated with CpG methyltransferase (M. SssI, NEB) to add methyl-groups to all cytosine residues within CpG dinucleotides, in order to obtain fully methylated genomic DNA. This has been verified by bisulfite DNA sequencing for eight genomic loci. We confirmed 0% mCpG in unmethylated genomic DNA and 90-100% mCpG in fully methylated DNA
MeDIP was adapted from the previous study (Weber et al. 2005). Genomic DNA was sheared by sonication into 300 to 1200 bp fragments, and methylated DNA was immunoprecipitated by incubating 10 ug of sonicated genomic DNA for 12 hr at 4C with 20 ug of mouse monoclonal antibody against 5-methylcytidine (Eurogentec). Fifty uL of Dynabeads with M-280 sheep antibodies to mouse IgG (Dynal Biotech) were added to the mix and incubated at 4oC for 2hr. Elution was performed two times in 200 uL TE containing 1.0% and 0.67% SDS, respectively, and methylated DNA was then recovered by standard proteinase K/phenol-chlorophorm procedure. DNA was also recovered from the unbound fractions. The remaining DNA from eluted fractions and sonicated input DNA were differentially labeled using fluorescent dyes (Cy3/Cy5) and competitively hybridized to the genomic DNA arrays.

extract_protocol: Normal human melanocytes were cultured from newborn foreskins (NBMEL) in basal medium (OptiMEM supplemented with 5% fetal calf serum and penicillin/streptomycin) enriched with the following ingredients required for proliferation: TPA (20 nM, 12-O-tetradecanoyl phorbol-13-acetate), IBMX (0.1 mM, 3-isobutyl-1-methyl xanthin), cholera toxin (2.5 nM), vanadate (1 µm) and dbcAMP (0.1 mM, N6, 2’-O-dibutyryladenosine 3:5-cyclic monophosphate), termed TICVA (Cheng et al. 2006). The samples were collected according to Health Insurance Portability and Accountability Act (HIPAA) regulations with Human Investigative Committee protocol. Genomic DNA was extracted using DNeasy Blood & Tissue Kit (QIAGEN) according to the manufacturer’s instructions.

tag: Fully Methylated DNA

source_name: Fully Methylated DNA


title: LW01set2_eds5_Psm_24h

status: Public on Jul 18 2008

type: RNA

city: St Paul

first: lin

last: wang

state: MN

address: 350 Cargill building, 1500 Gortner Ave

department: Plant Biology

institute: University of Minnesota

description: eds5 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae ES4326, harvested 24h after infiltration in set2 experiment.

hyb_protocol: Labeled RNA was suspended in hybridization buffer (50% Formamide, 5xSSC, 0.1% SDS, 10 ug Sheared Salmon Sperm DNA (Eppendorf), 50pg calbation oligo)

scan_protocol: Slide was scaned using Genepix4000B with low and high voltages of photomultiplier at 532nm and constant voltage at 635nm.

data_processing:
Note that each Sample corresponds to two GPR files (we use low PMT and high PMT, then combine them).

The median of ratios for each spot was processed by the following linear model: Sij = mu + Ai + Bj + Eij where Sij denotes the log2-transformed, median of ratios for the spot, mu denotes a constant, Ai and Bj denote the effects of i-th gene and j-th subarray. The residual Eij is assumed to be independent and normally distributed. Stable genes-based quantile normalization was applied for slide-to-slide comparisons. LW01_set1_Col-0_Psm_24h, LW01_set1_eds5_Psm_24h, LW01_set1_mpk3_Psm_24h, LW01_set1_mpk6_Psm_24h, LW01_set1_npr_Psm_24h, LW01_set1_pad4_Psm_24h, LW01_set1_sid2_Psm_24h, LW01_set1_tga_Psm_24h, LW01_set2_Col-0_Psm_24h, LW01_set2_eds5_Psm_24h, LW01_set2_mpk3_Psm_24h, LW01_set2_mpk6_Psm_24h, LW01_set2_npr_Psm_24h, LW01_set2_pad4_Psm_24h, LW01_set2_sid2_Psm_24h, LW01_set2_tga_Psm_24h, LW01_set3_Col-0_Psm_24h, LW01_set3_eds5_Psm_24h, LW01_set3_mpk3_Psm_24h, LW01_set3_mpk6_Psm_24h, LW01_set3_npr_Psm_24h, LW01_set3_pad4_Psm_24h, LW01_set3_sid2_Psm_24h, LW01_set3_tga_Psm_24h, LW02_set1_Col-0_Psm_24h, LW02_set1_SALK023199_Psm_24h, LW02_set1_SALK066990_Psm_24h, LW02_set1_coi1_Psm_24h, LW02_set1_dde2_Psm_24h, LW02_set1_ein2_Psm_24h, LW02_set1_jai1_Psm_24h, LW02_set1_jar1_Psm_24h, LW02_set2_Col-0_Psm_24h, LW02_set2_SALK023199_Psm_24h, LW02_set2_SALK066990_Psm_24h, LW02_set2_coi1_Psm_24h, LW02_set2_dde2_Psm_24h, LW02_set2_ein2_Psm_24h, LW02_set2_jai1_Psm_24h, LW02_set2_jar1_Psm_24h, LW02_set3_Col-0_Psm_24h, LW02_set3_SALK023199_Psm_24h, LW02_set3_SALK066990_Psm_24h, LW02_set3_coi1_Psm_24h, LW02_set3_dde2_Psm_24h, LW02_set3_ein2_Psm_24h, LW02_set3_jai1_Psm_24h, LW02_set3_jar1_Psm_24h, LW03_set1_Col-0_Psm_24h, LW03_set1_Col-0_mock_24h, LW03_set1_SALK018487_Psm_24h, LW03_set1_SALK052422_Psm_24h, LW03_set1_SALK084141_Psm_24h, LW03_set1_SALK143063_Psm_24h, LW03_set1_eds1_Psm_24h, LW03_set1_fmo1_Psm_24h, LW03_set2_Col-0_Psm_24h, LW03_set2_Col-0_mock_24h, LW03_set2_SALK018487_Psm_24h, LW03_set2_SALK052422_Psm_24h, LW03_set2_SALK084141_Psm_24h, LW03_set2_SALK143063_Psm_24h, LW03_set2_eds1_Psm_24h, LW03_set2_fmo1_Psm_24h, LW03_set3_Col-0_Psm_24h, LW03_set3_Col-0_mock_24h, LW03_set3_SALK018487_Psm_24h, LW03_set3_SALK052422_Psm_24h, LW03_set3_SALK084141_Psm_24h, LW03_set3_SALK143063_Psm_24h, LW03_set3_eds1_Psm_24h, LW03_set3_fmo1_Psm_24h, LW05_set1_Col-0_Psm-cor-_24h, LW05_set1_Col-0_Psm_24h, LW05_set1_Col-0_mock_24h, LW05_set1_coi1_Psm-cor-_24h, LW05_set1_coi1_Psm_24h, LW05_set1_coi1_mock_24h, LW05_set1_ndr1_Psm_24h, LW05_set1_pbs3_Psm_24h, LW05_set2_Col-0_Psm-cor-_24h, LW05_set2_Col-0_Psm_24h, LW05_set2_Col-0_mock_24h, LW05_set2_coi1_Psm-cor-_24h, LW05_set2_coi1_Psm_24h, LW05_set2_coi1_mock_24h, LW05_set2_ndr1_Psm_24h, LW05_set2_pbs3_Psm_24h, LW05_set3_Col-0_Psm-cor-_24h, LW05_set3_Col-0_Psm_24h, LW05_set3_Col-0_mock_24h, LW05_set3_coi1_Psm-cor-_24h, LW05_set3_coi1_Psm_24h, LW05_set3_coi1_mock_24h, LW05_set3_ndr1_Psm_24h, and LW05_set3_pbs3_Psm_24h were normalized together. Perl scripts for the linear model and the normalization are available for non-commercial research conducted upon request (Fumiaki Katagiri, katagiri@umn.edu). Spots with bad quality (missing, lints, and high background) were flagged as indicated in Flag in the attached .gpr file for this sample.

molecule: total RNA

organism: Arabidopsis thaliana

label_protocol: Following procedure was performed with Amino Allyl MessageAmp aRNA Amplification Kit II (Ambion).First, cDNA was synthesized from 1ug of total RNA.  Next, RNA was in vitro transcribed.  The RNA was then labeled with Alexa555 in coupling reaction.

growth_protocol: Plants were grown in pots with BM-2 soil (Berger Peat Moss Ltd, Quebec, Canada) at a density of 9 plants per pot and kept at 22 degrees Celsius and 75% humidity with a 12 hour day length.

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

treatment_protocol: Individual leaves were infiltrated in the morning using a needle-less syringe with 1x10E8 cfu/ml Pseudomonas syringae ES4326 and harvested 24h later.

tag: Genotype

tag: Tissue

value: leaves

tag: Age

value: 4 week-old

tag: Treatment

tag: Time point


title: LW01set1_sid2_Psm_24h

description: sid2 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae ES4326, harvested 24h after infiltration in set1 experiment.

source_name: Arabidopsis thaliana sid2, leaves, 1x10E8 cfu/ml Pseudomonas syringae ES4326-infiltrated, 24h


title: Highly metastatic 468GFP-LN biorep2

city: London

first: Ann

last: Chambers

state: Ontario

address: 790 Commissioner's Road E

department: Victoria research labs

country: Canada

institute: London Regional Cancer program

description:
Ligation mediated PCR amplified genomic DNA, after restriction with HhaI
Promoter array data from Parental Cell line 468GFP-LN, Second biological replicate

hyb_protocol: Following fragmentation, 7.5 micrograms of Ligation mediated PCR amplified genomic DNA was hybridized as per standard affymetrix protocols for Human Promoter 1.0R arrays. 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 GCOS using Affymetrix default analysis settings and global scaling as normalization method.

label: Biotin/SAPE

label_protocol: Ligation mediated PCR amplified genomic DNA, after restriction with HhaI, was labeled as per Affymetrix standard protocol for Human Promoter 1.0R arrays

growth_protocol: Cells were grown out to three passages in alpha-MEM containing 10% FBS in 5% CO2 to 70 % confluency

extract_protocol: Genomic DNA was extracted using Sigma GeneElute kit using the Manufacturer's protocol

treatment_protocol: No treatment


title: LW01set2_sid2_Psm_24h

description: sid2 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae ES4326, harvested 24h after infiltration in set2 experiment.


title: LW01set2_Col-0_Psm_24h

description: Col-0 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae ES4326, harvested 24h after infiltration in set2 experiment.

source_name: Arabidopsis thaliana Col-0, leaves, 1x10E8 cfu/ml Pseudomonas syringae ES4326-infiltrated, 24h


title: siBmi-1, biological rep3

city: Ann Arbor

first: Elizabeth

middle: R

last: Lawlor

state: MI

address: 1600 Huron Parkway, NCRC Bldg 520

institute: University of Michigan

description: no additional information

hyb_protocol: hybridization to HuEx1.0 microarrays was carried out following the manufacturer’s instructions.

data_processing:
Cell intensity (CEL) file data were quantile-normalized and summarized using the Iterative Probe Logarithmic Intensity Error Estimation (iterPLIER) within Affymetrix Expression Console software.
Sample VALUE column reports iterPLIER transcript level log2 signal intensity.

label: biotin

source_name: ESFT cell line transfected with 50 nM BMI-1-targeted (siBMI1-A: 5’-CCGUCUUAAUUUUCCAUUG-3’ or siBMI1-B: 5’-GCGGUAACCACCAAUCUUC-3’), or negative control (siNS) siRNA oligonucleotides (Ambion, Austin, TX).

label_protocol: Samples were prepared in the CHLA genome core using the GeneChip Whole Transcript (WT) Sense Target Labeling Assay Manual (Affymetrix, Santa Clara)

extract_protocol: RNA was extracted, DNase I treated and purified (RNeasy Minikit, Qiagen, Valencia, CA) from A4573 cells 48 hrs post-siRNA-transfection.

tag: ESFT cell lines were transfected with 50 nM BMI-1-targeted (siBMI1-A

value: 5’-CCGUCUUAAUUUUCCAUUG-3’ or siBMI1-B:5’-GCGGUAACCACCAAUCUUC-3’), or negative control (siNS) siRNA oligonucleotides (Ambion, Austin, TX). For stable knockdown, siBMI1-A and siBMI1-B DNA oligonucleotide sequences were cloned into the pSuper-retro-puro short-hairpin vector backbone (shBMI1-A and shBMI1-B) (Oligoengine, Seattle, WA). Non-silencing sequence (5’-ACGCATGCATGCTTGCTTT-3’) was similarly cloned to act as a negative control {Baek, 2005 #192}. For gain-of-function studies, full-length human BMI-1 cDNA was PCR amplified from TC-71 cells, sequence verified and cloned into pBabe-Puro and pBabe-Hygro retroviral vectors.  Retrovirus production was achieved through tri-transfection of 293FT packaging cells (Invitrogen, Carlsbad,CA) with the appropriate retroviral construct along with the packaging plasmids pHit 60 (MLV gag-pol) and pHit 456 (VSV envelope) (provided by Dr. C. Lutzko, CHLA). Viral supernatants were collected after 48 hrs, target ESFT cell lines infected at MOI’s of 2-4 viral particles/cell, and transduced cells selected in media containing 2 ug/ml puromycin.


title: LW01set2_npr_Psm_24h

description: npr infiltrated with 1x10E8 cfu/ml Pseudomonas syringae ES4326, harvested 24h after infiltration in set2 experiment.

source_name: Arabidopsis thaliana npr, leaves, 1x10E8 cfu/ml Pseudomonas syringae ES4326-infiltrated, 24h

value: npr


title: LW01set1_pad4_Psm_24h

description: pad4 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae ES4326, harvested 24h after infiltration in set1 experiment.

source_name: Arabidopsis thaliana pad4, leaves, 1x10E8 cfu/ml Pseudomonas syringae ES4326-infiltrated, 24h


title: LW01set1_npr_Psm_24h

description: npr infiltrated with 1x10E8 cfu/ml Pseudomonas syringae ES4326, harvested 24h after infiltration in set1 experiment.


title: siBmi-1, biological rep1

description: no additional information

scan_protocol: hybridization to HuEx1.0 microarrays was carried out following the manufacturer’s instructions.


title: siControl, biological rep2

description: no additional information

source_name: ESFT cell line  transfected with  negative control (siNS) siRNA oligonucleotides (Ambion, Austin, TX)


title: LW01set2_pad4_Psm_24h

description: pad4 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae ES4326, harvested 24h after infiltration in set2 experiment.


title: LW01set1_mpk6_Psm_24h

description: mpk6 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae ES4326, harvested 24h after infiltration in set1 experiment.

source_name: Arabidopsis thaliana mpk6, leaves, 1x10E8 cfu/ml Pseudomonas syringae ES4326-infiltrated, 24h


title: LW01set1_mpk3_Psm_24h

description: mpk3 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae ES4326, harvested 24h after infiltration in set1 experiment.

source_name: Arabidopsis thaliana mpk3, leaves, 1x10E8 cfu/ml Pseudomonas syringae ES4326-infiltrated, 24h


title: siBmi-1, biological rep2

description: no additional information


title: siControl, biological rep1

description: no additional information


title: siControl, biological rep3

description: no additional information


title: LW01set1_Col-0_Psm_24h

description: Col-0 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae ES4326, harvested 24h after infiltration in set1 experiment.


title: Thyroid tissue cultured with Poly(I-C) medium for 6 hours

city: Shinjuku-ku

first: Kanji

last: Sato

state: Tokyo

address: Kawada-cho 8-1

department: Institute of Clinical Endocrinology

country: Japan

institute: Tokyo Women's Medical University

description: Thyroid follicles were cultured with or without Poly(I:C) for 6h

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential

scan_protocol: Images were quantified using AgilentMicroarray Scanner

data_processing: LOWESS normalized, background subtracted VALUE data obtained from log2 of processed Red signal/processed Green signal. Agilent software was used.

source_name: human thyroid follicles - untreated

label_protocol: 0.5 µg of total RNA were primed with 2 µl of 100 µM T16P7 DNA primer at 65°C for 10 min, then reversed transcribed at 40°C for 2 h in the presence of Low RNA input linear amplification (Agilent), and 10mM dNDP.

growth_protocol: Thyroid follicles  prepared from patients with Graves' disease  were cultured in medium containing NaI (10-8M) and 0.5% serum in 10cm-dishes coated with agarose gel.

extract_protocol: Total RNA was extracted from thyroid follicles using the RNeasy Minikit (Quiagen, Tokyo, Japan)

treatment_protocol: Total RNA was prepared from thyroid follicles treated with or without poly(I:C).

tag: Poly(I:C) (-)

source_name: human thyroid follicles - treated

tag: Poly(I:C) (25microg/ml)


title: LW01set1_eds5_Psm_24h

description: eds5 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae ES4326, harvested 24h after infiltration in set1 experiment.


title: LW01set2_mpk6_Psm_24h

description: mpk6 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae ES4326, harvested 24h after infiltration in set2 experiment.


title: Newborn normal melanocytes NBMEL_rep2 (genomic)

source_name: Newborn normal melanocytes, MeDIP

label_protocol: MeDIP was adapted from the previous study (Weber et al. 2005). Genomic DNA was sheared by sonication into 300 to 1200 bp fragments, and methylated DNA was immunoprecipitated by incubating 10 ug of sonicated genomic DNA for 12 hr at 4C with 20 ug of mouse monoclonal antibody against 5-methylcytidine (Eurogentec). Fifty uL of Dynabeads with M-280 sheep antibodies to mouse IgG (Dynal Biotech) were added to the mix and incubated at 4oC for 2hr. Elution was performed two times in 200 uL TE containing 1.0% and 0.67% SDS, respectively, and methylated DNA was then recovered by standard proteinase K/phenol-chlorophorm procedure. DNA was also recovered from the unbound fractions. The remaining DNA from eluted fractions and sonicated input DNA were differentially labeled using fluorescent dyes (Cy3/Cy5) and competitively hybridized to the genomic DNA arrays.

tag: Newborn normal melanocytes

source_name: Newborn normal melanocytes


title: SHGU49|CRvs.Panc219|

city: Stanford

first: Kevin

last: Kwei

state: CA

address: 269 Campus Dr.

institute: Stanford

description:
Simple annotation: tumor, Pancreas
Image: http://smd.stanford.edu/MicroArray/gifs/2006-01/66379.gif
Tissue type: Pancreatic

hyb_protocol: not provided

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 2120, 5760; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Murali,,Bashyam Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 29.41; Parameter Scan Time = 09:47:16; Parameter PMT Volts = 470; Parameter Scan Date = 2005-12-08; Parameter Pixel Size = 10; Parameter Laser on time = 69889; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [94858]; Parameter Laser Power = 3.66; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Murali,,Bashyam Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 29.41; Parameter Scan Time = 09:47:16; Parameter PMT Volts = 500; Parameter Scan Date = 2005-12-08; Parameter Pixel Size = 10; Parameter Laser on time = 69934; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [94858]; Parameter Laser Power = 3.46; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Murali,,Bashyam

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

source_name: common reference

label_protocol: not provided

extract_protocol: not provided

tag: common reference

source_name: Panc 219

tag: Panc 219


title: SHFy119|CRvs.Panc217|

description:
Simple annotation: tumor, Pancreas
Image: http://smd.stanford.edu/MicroArray/gifs/2005-10/64453.gif
Tissue type: Pancreatic

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1880, 5480; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Murali,,Bashyam Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 30.87; Parameter Scan Time = 10:30:43; Parameter PMT Volts = 500; Parameter Scan Date = 2004-09-10; Parameter Pixel Size = 10; Parameter Laser on time = 46857; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [94858]; Parameter Laser Power = 3.52; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Murali,,Bashyam Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 30.87; Parameter Scan Time = 10:30:43; Parameter PMT Volts = 500; Parameter Scan Date = 2004-09-10; Parameter Pixel Size = 10; Parameter Laser on time = 46902; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [94858]; Parameter Laser Power = 3.49; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Murali,,Bashyam

source_name: Common Reference

tag: Common Reference


title: SHFU190|CRvs.Panc154|

description:
Simple annotation: tumor, Pancreas
Image: http://smd.stanford.edu/MicroArray/gifs/2006-01/66367.gif
Tissue type: Pancreatic

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1880, 5560; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Murali,,Bashyam Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 30.32; Parameter Scan Time = 09:28:07; Parameter PMT Volts = 500; Parameter Scan Date = 2005-11-23; Parameter Pixel Size = 10; Parameter Laser on time = 67836; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [94858]; Parameter Laser Power = 3.63; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Murali,,Bashyam Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 30.32; Parameter Scan Time = 09:28:07; Parameter PMT Volts = 480; Parameter Scan Date = 2005-11-23; Parameter Pixel Size = 10; Parameter Laser on time = 67881; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [94858]; Parameter Laser Power = 3.44; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Murali,,Bashyam

source_name: Panc 154

tag: Panc 154


title: SHGU214|CR vs.Panc185

description:
Simple annotation: tumor, Pancreas
Image: http://smd.stanford.edu/MicroArray/gifs/2006-09/70415.gif
Tissue type: Pancreatic

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1880, 5240; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Murali,,Bashyam Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.97; Parameter Scan Time = 15:01:38; Parameter PMT Volts = 500; Parameter Scan Date = 2006-08-31; Parameter Pixel Size = 10; Parameter Laser on time = 86165; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [94858]; Parameter Laser Power = 3.72; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Murali,,Bashyam Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.97; Parameter Scan Time = 15:01:38; Parameter PMT Volts = 640; Parameter Scan Date = 2006-08-31; Parameter Pixel Size = 10; Parameter Laser on time = 86210; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [94858]; Parameter Laser Power = 3.40; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Murali,,Bashyam

source_name: Common reference

tag: Common reference


title: SHFy127|CRvs.Panc169|

description:
Simple annotation: tumor, Pancreas
Image: http://smd.stanford.edu/MicroArray/gifs/2005-10/64461.gif
Tissue type: Pancreatic

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 2080, 5480; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Murali,,Bashyam Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.15; Parameter Scan Time = 15:01:14; Parameter PMT Volts = 480; Parameter Scan Date = 2004-09-17; Parameter Pixel Size = 10; Parameter Laser on time = 47768; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [94858]; Parameter Laser Power = 3.52; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Murali,,Bashyam Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.15; Parameter Scan Time = 15:01:14; Parameter PMT Volts = 500; Parameter Scan Date = 2004-09-17; Parameter Pixel Size = 10; Parameter Laser on time = 47813; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [94858]; Parameter Laser Power = 3.49; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Murali,,Bashyam


title: SHFy130|CRvs.Panc218|

description:
Simple annotation: tumor, Pancreas
Image: http://smd.stanford.edu/MicroArray/gifs/2005-10/64468.gif
Tissue type: Pancreatic

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 2080, 5800; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Murali,,Bashyam Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 32.03; Parameter Scan Time = 15:57:52; Parameter PMT Volts = 490; Parameter Scan Date = 2004-09-17; Parameter Pixel Size = 10; Parameter Laser on time = 47824; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [94858]; Parameter Laser Power = 3.51; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Murali,,Bashyam Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 32.03; Parameter Scan Time = 15:57:52; Parameter PMT Volts = 500; Parameter Scan Date = 2004-09-17; Parameter Pixel Size = 10; Parameter Laser on time = 47869; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [94858]; Parameter Laser Power = 3.50; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Murali,,Bashyam


title: SHGU42|CRvs.Panc221|

description:
Simple annotation: tumor, Pancreas
Image: http://smd.stanford.edu/MicroArray/gifs/2006-01/66378.gif
Tissue type: Pancreatic

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 2120, 5560; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Murali,,Bashyam Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 29.68; Parameter Scan Time = 10:03:09; Parameter PMT Volts = 470; Parameter Scan Date = 2005-12-08; Parameter Pixel Size = 10; Parameter Laser on time = 69905; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [94858]; Parameter Laser Power = 3.66; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Murali,,Bashyam Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 29.68; Parameter Scan Time = 10:03:09; Parameter PMT Volts = 500; Parameter Scan Date = 2005-12-08; Parameter Pixel Size = 10; Parameter Laser on time = 69950; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [94858]; Parameter Laser Power = 3.46; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Murali,,Bashyam

source_name: Panc 221

tag: Panc 221


title: SHFy148|CRvs.Bil291|

description:
Simple annotation: tumor, Pancreas
Image: http://smd.stanford.edu/MicroArray/gifs/2005-10/64469.gif
Tissue type: Biliary duct

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 2000, 5560; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Murali,,Bashyam Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.15; Parameter Scan Time = 09:56:33; Parameter PMT Volts = 500; Parameter Scan Date = 2004-09-23; Parameter Pixel Size = 10; Parameter Laser on time = 48716; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [94858]; Parameter Laser Power = 3.51; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Murali,,Bashyam Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.15; Parameter Scan Time = 09:56:33; Parameter PMT Volts = 500; Parameter Scan Date = 2004-09-23; Parameter Pixel Size = 10; Parameter Laser on time = 48761; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [94858]; Parameter Laser Power = 3.51; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Murali,,Bashyam


title: SHFy118|CRvs.Panc201|

description:
Simple annotation: tumor, Pancreas
Image: http://smd.stanford.edu/MicroArray/gifs/2005-10/64452.gif
Tissue type: Pancreatic

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1880, 5480; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Murali,,Bashyam Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 30.63; Parameter Scan Time = 10:16:16; Parameter PMT Volts = 500; Parameter Scan Date = 2004-09-10; Parameter Pixel Size = 10; Parameter Laser on time = 46844; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [94858]; Parameter Laser Power = 3.52; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Murali,,Bashyam Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 30.63; Parameter Scan Time = 10:16:16; Parameter PMT Volts = 470; Parameter Scan Date = 2004-09-10; Parameter Pixel Size = 10; Parameter Laser on time = 46888; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [94858]; Parameter Laser Power = 3.51; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Murali,,Bashyam


title: SHFy124|CRvs.Panc294|

description:
Simple annotation: tumor, Pancreas
Image: http://smd.stanford.edu/MicroArray/gifs/2005-10/64459.gif
Tissue type: Pancreatic

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 2000, 5320; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Murali,,Bashyam Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.76; Parameter Scan Time = 11:51:48; Parameter PMT Volts = 500; Parameter Scan Date = 2004-09-10; Parameter Pixel Size = 10; Parameter Laser on time = 46939; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [94858]; Parameter Laser Power = 3.52; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Murali,,Bashyam Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.76; Parameter Scan Time = 11:51:48; Parameter PMT Volts = 440; Parameter Scan Date = 2004-09-10; Parameter Pixel Size = 10; Parameter Laser on time = 46983; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [94858]; Parameter Laser Power = 3.49; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Murali,,Bashyam


title: SHGU43|CRvs.Panc222|

description:
Simple annotation: tumor, Pancreas
Image: http://smd.stanford.edu/MicroArray/gifs/2006-01/66377.gif
Tissue type: Pancreatic

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 2120, 5560; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Murali,,Bashyam Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 29.93; Parameter Scan Time = 10:25:37; Parameter PMT Volts = 440; Parameter Scan Date = 2005-12-08; Parameter Pixel Size = 10; Parameter Laser on time = 69929; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [94858]; Parameter Laser Power = 3.65; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Murali,,Bashyam Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 29.93; Parameter Scan Time = 10:25:37; Parameter PMT Volts = 500; Parameter Scan Date = 2005-12-08; Parameter Pixel Size = 10; Parameter Laser on time = 69973; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [94858]; Parameter Laser Power = 3.46; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Murali,,Bashyam

source_name: Panc 222

tag: Panc 222


title: SHFy125|CRvs.Panc361|

description:
Simple annotation: tumor, Pancreas
Image: http://smd.stanford.edu/MicroArray/gifs/2005-10/64460.gif
Tissue type: Pancreatic

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 2080, 5640; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Murali,,Bashyam Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.85; Parameter Scan Time = 12:05:16; Parameter PMT Volts = 500; Parameter Scan Date = 2004-09-10; Parameter Pixel Size = 10; Parameter Laser on time = 46952; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [94858]; Parameter Laser Power = 3.52; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Murali,,Bashyam Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.85; Parameter Scan Time = 12:05:16; Parameter PMT Volts = 430; Parameter Scan Date = 2004-09-10; Parameter Pixel Size = 10; Parameter Laser on time = 46997; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [94858]; Parameter Laser Power = 3.49; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Murali,,Bashyam


title: SHGU46|CRvs.Panc196|

description:
Simple annotation: tumor, Pancreas
Image: http://smd.stanford.edu/MicroArray/gifs/2006-01/66374.gif
Tissue type: Pancreatic

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 2120, 5760; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Murali,,Bashyam Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 29.17; Parameter Scan Time = 09:32:09; Parameter PMT Volts = 410; Parameter Scan Date = 2005-12-08; Parameter Pixel Size = 10; Parameter Laser on time = 69875; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [94858]; Parameter Laser Power = 3.67; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Murali,,Bashyam Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 29.17; Parameter Scan Time = 09:32:09; Parameter PMT Volts = 500; Parameter Scan Date = 2005-12-08; Parameter Pixel Size = 10; Parameter Laser on time = 69920; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [94858]; Parameter Laser Power = 3.43; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Murali,,Bashyam

source_name: Panc 196

tag: Panc 196


title: SHFy117|CRvs.Panc198|

description:
Simple annotation: tumor, Pancreas
Image: http://smd.stanford.edu/MicroArray/gifs/2005-10/64451.gif
Tissue type: Pancreatic

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1880, 5560; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Murali,,Bashyam Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 30.29; Parameter Scan Time = 09:59:17; Parameter PMT Volts = 500; Parameter Scan Date = 2004-09-10; Parameter Pixel Size = 10; Parameter Laser on time = 46826; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [94858]; Parameter Laser Power = 3.53; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Murali,,Bashyam Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 30.29; Parameter Scan Time = 09:59:17; Parameter PMT Volts = 520; Parameter Scan Date = 2004-09-10; Parameter Pixel Size = 10; Parameter Laser on time = 46870; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [94858]; Parameter Laser Power = 3.53; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Murali,,Bashyam


title: SHFy116|CRvs.Panc159|

description:
Simple annotation: tumor, Pancreas
Image: http://smd.stanford.edu/MicroArray/gifs/2005-10/64450.gif
Tissue type: Pancreatic

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1880, 5400; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Murali,,Bashyam Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 30.02; Parameter Scan Time = 09:46:10; Parameter PMT Volts = 500; Parameter Scan Date = 2004-09-10; Parameter Pixel Size = 10; Parameter Laser on time = 46814; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [94858]; Parameter Laser Power = 3.53; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Murali,,Bashyam Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 30.02; Parameter Scan Time = 09:46:10; Parameter PMT Volts = 480; Parameter Scan Date = 2004-09-10; Parameter Pixel Size = 10; Parameter Laser on time = 46858; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [94858]; Parameter Laser Power = 3.50; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Murali,,Bashyam


title: SHFY135|CRvs.Bil227|

description:
Simple annotation: tumor, Pancreas
Image: http://smd.stanford.edu/MicroArray/gifs/2006-03/67603.gif
Tissue type: Biliary duct

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 2160, 5480; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Murali,,Bashyam Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 29.04; Parameter Scan Time = 09:51:52; Parameter PMT Volts = 500; Parameter Scan Date = 2004-08-04; Parameter Pixel Size = 10; Parameter Laser on time = 42415; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [94858]; Parameter Laser Power = 3.51; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Murali,,Bashyam Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 29.04; Parameter Scan Time = 09:51:52; Parameter PMT Volts = 430; Parameter Scan Date = 2004-08-04; Parameter Pixel Size = 10; Parameter Laser on time = 42460; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [94858]; Parameter Laser Power = 3.48; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Murali,,Bashyam


title: SHGU189|CRvs.Panc167|

description:
Simple annotation: tumor, Pancreas
Image: http://smd.stanford.edu/MicroArray/gifs/2006-01/66368.gif
Tissue type: Pancreatic

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1880, 5560; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Murali,,Bashyam Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 30.51; Parameter Scan Time = 09:38:07; Parameter PMT Volts = 500; Parameter Scan Date = 2005-11-23; Parameter Pixel Size = 10; Parameter Laser on time = 67846; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [94858]; Parameter Laser Power = 3.66; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Murali,,Bashyam Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 30.51; Parameter Scan Time = 09:38:07; Parameter PMT Volts = 440; Parameter Scan Date = 2005-11-23; Parameter Pixel Size = 10; Parameter Laser on time = 67891; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [94858]; Parameter Laser Power = 3.46; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Murali,,Bashyam

source_name: Panc 167

tag: Panc 167


title: SHGU212|CRvs.Panc178|

description:
Simple annotation: tumor, Pancreas
Image: http://smd.stanford.edu/MicroArray/gifs/2006-09/70413.gif
Tissue type: Pancreatic

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 2080, 5320; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Murali,,Bashyam Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.73; Parameter Scan Time = 14:44:51; Parameter PMT Volts = 540; Parameter Scan Date = 2006-08-31; Parameter Pixel Size = 10; Parameter Laser on time = 86193; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [94858]; Parameter Laser Power = 3.42; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Murali,,Bashyam Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.73; Parameter Scan Time = 14:44:51; Parameter PMT Volts = 500; Parameter Scan Date = 2006-08-31; Parameter Pixel Size = 10; Parameter Laser on time = 86148; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [94858]; Parameter Laser Power = 3.73; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Murali,,Bashyam


title: SHGU50|CRvs.Bil247|

description:
Simple annotation: tumor, Pancreas
Image: http://smd.stanford.edu/MicroArray/gifs/2006-01/66375.gif
Tissue type: Biliary duct

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 2000, 5320; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Murali,,Bashyam Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 29.99; Parameter Scan Time = 10:33:38; Parameter PMT Volts = 470; Parameter Scan Date = 2005-12-08; Parameter Pixel Size = 10; Parameter Laser on time = 69936; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [94858]; Parameter Laser Power = 3.65; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Murali,,Bashyam Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 29.99; Parameter Scan Time = 10:33:38; Parameter PMT Volts = 500; Parameter Scan Date = 2005-12-08; Parameter Pixel Size = 10; Parameter Laser on time = 69981; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [94858]; Parameter Laser Power = 3.46; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Murali,,Bashyam

source_name: Bil 247

tag: Bil 247


title: SHFU188|CRvs.Panc184|

description:
Simple annotation: tumor, Pancreas
Image: http://smd.stanford.edu/MicroArray/gifs/2006-01/66369.gif
Tissue type: Pancreatic

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1880, 5560; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Murali,,Bashyam Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 30.81; Parameter Scan Time = 09:51:47; Parameter PMT Volts = 500; Parameter Scan Date = 2005-11-23; Parameter Pixel Size = 10; Parameter Laser on time = 67859; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [94858]; Parameter Laser Power = 3.65; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Murali,,Bashyam Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 30.81; Parameter Scan Time = 09:51:47; Parameter PMT Volts = 440; Parameter Scan Date = 2005-11-23; Parameter Pixel Size = 10; Parameter Laser on time = 67904; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [94858]; Parameter Laser Power = 3.46; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Murali,,Bashyam

source_name: Panc 184

tag: Panc 184


title: SHGU44|CRvs.Bil287|

description:
Simple annotation: tumor, Pancreas
Image: http://smd.stanford.edu/MicroArray/gifs/2006-01/66376.gif
Tissue type: Biliary duct

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 2000, 5560; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Murali,,Bashyam Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 30.05; Parameter Scan Time = 10:42:13; Parameter PMT Volts = 500; Parameter Scan Date = 2005-12-08; Parameter Pixel Size = 10; Parameter Laser on time = 69944; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [94858]; Parameter Laser Power = 3.65; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Murali,,Bashyam Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 30.05; Parameter Scan Time = 10:42:13; Parameter PMT Volts = 500; Parameter Scan Date = 2005-12-08; Parameter Pixel Size = 10; Parameter Laser on time = 69989; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [94858]; Parameter Laser Power = 3.45; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Murali,,Bashyam

source_name: Bil 287

tag: Bil 287


title: SHFy123|CRvs.Bil265|

description:
Simple annotation: tumor, Pancreas
Image: http://smd.stanford.edu/MicroArray/gifs/2005-10/64458.gif
Tissue type: Biliary duct

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1880, 5560; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Murali,,Bashyam Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.61; Parameter Scan Time = 11:34:05; Parameter PMT Volts = 500; Parameter Scan Date = 2004-09-10; Parameter Pixel Size = 10; Parameter Laser on time = 46921; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [94858]; Parameter Laser Power = 3.52; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Murali,,Bashyam Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.61; Parameter Scan Time = 11:34:05; Parameter PMT Volts = 450; Parameter Scan Date = 2004-09-10; Parameter Pixel Size = 10; Parameter Laser on time = 46965; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [94858]; Parameter Laser Power = 3.50; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Murali,,Bashyam


title: SHFy136|CRvs.Panc410|

description:
Simple annotation: tumor, Pancreas
Image: http://smd.stanford.edu/MicroArray/gifs/2005-10/64472.gif
Tissue type: Pancreatic

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 2080, 5400; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Murali,,Bashyam Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 32.86; Parameter Scan Time = 17:24:13; Parameter PMT Volts = 480; Parameter Scan Date = 2004-09-17; Parameter Pixel Size = 10; Parameter Laser on time = 47910; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [94858]; Parameter Laser Power = 3.53; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Murali,,Bashyam Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 32.86; Parameter Scan Time = 17:24:13; Parameter PMT Volts = 500; Parameter Scan Date = 2004-09-17; Parameter Pixel Size = 10; Parameter Laser on time = 47955; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [94858]; Parameter Laser Power = 3.52; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Murali,,Bashyam


title: SHGU215|CRvs.Panc374|

description:
Simple annotation: tumor, Pancreas
Image: http://smd.stanford.edu/MicroArray/gifs/2006-01/66380.gif
Tissue type: Pancreatic

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 2080, 5440; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Murali,,Bashyam Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 28.52; Parameter Scan Time = 11:12:42; Parameter PMT Volts = 500; Parameter Scan Date = 2005-12-11; Parameter Pixel Size = 10; Parameter Laser on time = 70185; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [94858]; Parameter Laser Power = 3.67; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Murali,,Bashyam Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 28.52; Parameter Scan Time = 11:12:42; Parameter PMT Volts = 460; Parameter Scan Date = 2005-12-11; Parameter Pixel Size = 10; Parameter Laser on time = 70230; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [94858]; Parameter Laser Power = 3.40; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Murali,,Bashyam

source_name: Panc 374

tag: Panc 374


title: SHGU51|CRvs.Bil301|

description:
Simple annotation: tumor, Pancreas
Image: http://smd.stanford.edu/MicroArray/gifs/2006-01/66382.gif
Tissue type: Biliary duct

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 2200, 5720; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Murali,,Bashyam Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 30.20; Parameter Scan Time = 10:59:58; Parameter PMT Volts = 470; Parameter Scan Date = 2005-12-08; Parameter Pixel Size = 10; Parameter Laser on time = 69963; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [94858]; Parameter Laser Power = 3.65; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Murali,,Bashyam Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 30.20; Parameter Scan Time = 10:59:58; Parameter PMT Volts = 500; Parameter Scan Date = 2005-12-08; Parameter Pixel Size = 10; Parameter Laser on time = 70008; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [94858]; Parameter Laser Power = 3.46; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Murali,,Bashyam

source_name: Bil 301

tag: Bil 301


title: SHGU47|CRvs.Panc194|

description:
Simple annotation: tumor, Pancreas
Image: http://smd.stanford.edu/MicroArray/gifs/2006-01/66373.gif
Tissue type: Pancreatic

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 2120, 6080; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Murali,,Bashyam Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 29.04; Parameter Scan Time = 09:23:18; Parameter PMT Volts = 400; Parameter Scan Date = 2005-12-08; Parameter Pixel Size = 10; Parameter Laser on time = 69866; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [94858]; Parameter Laser Power = 3.67; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Murali,,Bashyam Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 29.04; Parameter Scan Time = 09:23:18; Parameter PMT Volts = 500; Parameter Scan Date = 2005-12-08; Parameter Pixel Size = 10; Parameter Laser on time = 69911; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [94858]; Parameter Laser Power = 3.41; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Murali,,Bashyam

source_name: Panc 194

tag: Panc 194


title: SHFy134|CRvs.Panc354|

description:
Simple annotation: tumor, Pancreas
Image: http://smd.stanford.edu/MicroArray/gifs/2005-10/64471.gif
Tissue type: Pancreatic

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 2080, 5800; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Murali,,Bashyam Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 32.67; Parameter Scan Time = 17:05:04; Parameter PMT Volts = 500; Parameter Scan Date = 2004-09-17; Parameter Pixel Size = 10; Parameter Laser on time = 47891; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [94858]; Parameter Laser Power = 3.53; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Murali,,Bashyam Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 32.67; Parameter Scan Time = 17:05:04; Parameter PMT Volts = 480; Parameter Scan Date = 2004-09-17; Parameter Pixel Size = 10; Parameter Laser on time = 47936; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [94858]; Parameter Laser Power = 3.52; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Murali,,Bashyam


title: SHFy121|CRvs.Panc235|

description:
Simple annotation: tumor, Pancreas
Image: http://smd.stanford.edu/MicroArray/gifs/2005-10/64455.gif
Tissue type: Pancreatic

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1880, 5480; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Murali,,Bashyam Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.30; Parameter Scan Time = 11:03:57; Parameter PMT Volts = 500; Parameter Scan Date = 2004-09-10; Parameter Pixel Size = 10; Parameter Laser on time = 46891; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [94858]; Parameter Laser Power = 3.52; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Murali,,Bashyam Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.30; Parameter Scan Time = 11:03:57; Parameter PMT Volts = 470; Parameter Scan Date = 2004-09-10; Parameter Pixel Size = 10; Parameter Laser on time = 46935; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [94858]; Parameter Laser Power = 3.51; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Murali,,Bashyam


title: SHGU186|CRvs.Panc266|

description:
Simple annotation: tumor, Pancreas
Image: http://smd.stanford.edu/MicroArray/gifs/2006-01/66371.gif
Tissue type: Pancreatic

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 2200, 6080; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Murali,,Bashyam Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.39; Parameter Scan Time = 10:10:07; Parameter PMT Volts = 500; Parameter Scan Date = 2005-11-23; Parameter Pixel Size = 10; Parameter Laser on time = 67878; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [94858]; Parameter Laser Power = 3.65; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Murali,,Bashyam Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.39; Parameter Scan Time = 10:10:07; Parameter PMT Volts = 430; Parameter Scan Date = 2005-11-23; Parameter Pixel Size = 10; Parameter Laser on time = 67923; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [94858]; Parameter Laser Power = 3.45; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Murali,,Bashyam

source_name: Panc 266

tag: Panc 266


title: SHGU52|CRvs.Panc365|

description:
Simple annotation: tumor, Pancreas
Image: http://smd.stanford.edu/MicroArray/gifs/2006-01/66381.gif
Tissue type: Pancreatic

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 2080, 5720; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Murali,,Bashyam Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 28.68; Parameter Scan Time = 11:20:43; Parameter PMT Volts = 500; Parameter Scan Date = 2005-12-11; Parameter Pixel Size = 10; Parameter Laser on time = 70194; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [94858]; Parameter Laser Power = 3.67; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Murali,,Bashyam Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 28.68; Parameter Scan Time = 11:20:43; Parameter PMT Volts = 440; Parameter Scan Date = 2005-12-11; Parameter Pixel Size = 10; Parameter Laser on time = 70239; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [94858]; Parameter Laser Power = 3.42; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Murali,,Bashyam

source_name: Panc 365

tag: Panc 365


title: SHFy120|CRvs.Panc226|

description:
Simple annotation: tumor, Pancreas
Image: http://smd.stanford.edu/MicroArray/gifs/2005-10/64454.gif
Tissue type: Pancreatic

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1880, 5480; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Murali,,Bashyam Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.15; Parameter Scan Time = 10:50:45; Parameter PMT Volts = 500; Parameter Scan Date = 2004-09-10; Parameter Pixel Size = 10; Parameter Laser on time = 46877; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [94858]; Parameter Laser Power = 3.52; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Murali,,Bashyam Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.15; Parameter Scan Time = 10:50:45; Parameter PMT Volts = 430; Parameter Scan Date = 2004-09-10; Parameter Pixel Size = 10; Parameter Laser on time = 46922; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [94858]; Parameter Laser Power = 3.49; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Murali,,Bashyam


title: SHGU187|CRvs.Panc224|

description:
Simple annotation: tumor, Pancreas
Image: http://smd.stanford.edu/MicroArray/gifs/2006-01/66370.gif
Tissue type: Pancreatic

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 2200, 6080; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Murali,,Bashyam Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.09; Parameter Scan Time = 10:00:04; Parameter PMT Volts = 500; Parameter Scan Date = 2005-11-23; Parameter Pixel Size = 10; Parameter Laser on time = 67868; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [94858]; Parameter Laser Power = 3.66; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Murali,,Bashyam Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.09; Parameter Scan Time = 10:00:04; Parameter PMT Volts = 450; Parameter Scan Date = 2005-11-23; Parameter Pixel Size = 10; Parameter Laser on time = 67913; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [94858]; Parameter Laser Power = 3.41; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Murali,,Bashyam

source_name: common reference

tag: common reference

source_name: Panc 224

tag: Panc 224


title: SHFy133|CRvs.Panc325|

description:
Simple annotation: tumor, Pancreas
Image: http://smd.stanford.edu/MicroArray/gifs/2005-10/64470.gif
Tissue type: Pancreatic

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 2080, 5800; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Murali,,Bashyam Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 32.52; Parameter Scan Time = 16:50:56; Parameter PMT Volts = 500; Parameter Scan Date = 2004-09-17; Parameter Pixel Size = 10; Parameter Laser on time = 47878; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [94858]; Parameter Laser Power = 3.51; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Murali,,Bashyam Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 32.52; Parameter Scan Time = 16:50:56; Parameter PMT Volts = 490; Parameter Scan Date = 2004-09-17; Parameter Pixel Size = 10; Parameter Laser on time = 47922; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [94858]; Parameter Laser Power = 3.53; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Murali,,Bashyam

source_name: Common Reference

tag: Common Reference


title: SHFy122|CRvs.Panc254|

description:
Simple annotation: tumor, Pancreas
Image: http://smd.stanford.edu/MicroArray/gifs/2005-10/64456.gif
Tissue type: Pancreatic

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1880, 5480; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Murali,,Bashyam Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.48; Parameter Scan Time = 11:21:12; Parameter PMT Volts = 500; Parameter Scan Date = 2004-09-10; Parameter Pixel Size = 10; Parameter Laser on time = 46908; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [94858]; Parameter Laser Power = 3.52; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Murali,,Bashyam Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.48; Parameter Scan Time = 11:21:12; Parameter PMT Volts = 450; Parameter Scan Date = 2004-09-10; Parameter Pixel Size = 10; Parameter Laser on time = 46953; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [94858]; Parameter Laser Power = 3.51; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Murali,,Bashyam


title: Mock 2   Mph

status: Public on Jul 17 2008

city: Cambridge

first: Kate

last: Rubins

state: MA

address: Nine Cambridge Center

institute: Whitehead Institute for Biomedical Research

description:
Simple annotation: Normal tissue, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/65410.gif

scan_protocol: Rubins 2003 - Data filtering and analysis; Array images were scanned using an Axon Scanner 4000A (Axon Instruments, Union City, CA), and image analysis was performed using GenePix Pro version 3.0.6.89 (Axon Instruments, Union City, CA).  Grids were manually aligned and features were found using the software feature extraction.  Features were visually inspected for blemishes and removed from downstream analysis.    Data were uploaded to the Stanford Microarray Database (http://genome-www5.stanford.edu/)  and normalized using regression correlation.  Data were expressed as the log2 ratio of fluorescence intensities of the sample and the reference, for each element on the array.    Data were filtered to exclude elements that did not have a regression correlation of Cy5 to Cy3 signal over the pixels spanning the array element of ??0.6 and intensity/background ratio of ??2.5 in at least 80% of the arrays.    For each gene, the expression levels over the timecourse for each monkey were ??time-zerotransformed?? by subtracting the average of the pre-infection baseline expression level from that animal so that the values of each timepoint represent changes relative to the uninfected samples.    The genes whose expression varied from the uninfected baseline by at least 3 fold in at least 3 samples were selected for further analysis.    The data were hierarchically clustered using the Cluster program (http://rana.lbl.gov/EisenSoftware.htm) and displayed using TreeView (http://rana.lbl.gov/EisenSoftware.htm).; Protocol Type = Feature Extraction; Software: type: feature extraction; Performer: Kate,,Rubins Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 27.19; Parameter Scan Time = 17:45:08; Parameter PMT Volts = 436; Parameter Scan Date = 2005-10-31; Parameter Pixel Size = 10; Parameter Laser on time = 12503; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4200A 01 Autoloader; Parameter Laser Power = 1.25; Parameter Scan Power = 80; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Kate,,Rubins Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 27.19; Parameter Scan Time = 17:45:08; Parameter PMT Volts = 455; Parameter Scan Date = 2005-10-31; Parameter Pixel Size = 10; Parameter Laser on time = 12503; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4200A 01 Autoloader; Parameter Laser Power = 1.72; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 80; Parameter Scanning software = AxImageIO; Performer: Kate,,Rubins

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

source_name: Mock 2 Mph cells Mock Infected in vitro 5.5.05

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

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

tag: Compound Based Treatment

tag: Infection

tag: Cell Line

value: Primary Human Monocyte

tag: Measurement

value: time(relative) 2 h


title: MPX plus Poly [IC] at 4 Hrs PI 12   Mph

description:
Simple annotation: Normal tissue, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/65338.gif

scan_protocol: Rubins 2003 - Data filtering and analysis; Array images were scanned using an Axon Scanner 4000A (Axon Instruments, Union City, CA), and image analysis was performed using GenePix Pro version 3.0.6.89 (Axon Instruments, Union City, CA).  Grids were manually aligned and features were found using the software feature extraction.  Features were visually inspected for blemishes and removed from downstream analysis.    Data were uploaded to the Stanford Microarray Database (http://genome-www5.stanford.edu/)  and normalized using regression correlation.  Data were expressed as the log2 ratio of fluorescence intensities of the sample and the reference, for each element on the array.    Data were filtered to exclude elements that did not have a regression correlation of Cy5 to Cy3 signal over the pixels spanning the array element of ??0.6 and intensity/background ratio of ??2.5 in at least 80% of the arrays.    For each gene, the expression levels over the timecourse for each monkey were ??time-zerotransformed?? by subtracting the average of the pre-infection baseline expression level from that animal so that the values of each timepoint represent changes relative to the uninfected samples.    The genes whose expression varied from the uninfected baseline by at least 3 fold in at least 3 samples were selected for further analysis.    The data were hierarchically clustered using the Cluster program (http://rana.lbl.gov/EisenSoftware.htm) and displayed using TreeView (http://rana.lbl.gov/EisenSoftware.htm).; Protocol Type = Feature Extraction; Software: type: feature extraction; Performer: Kate,,Rubins Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 28.13; Parameter Scan Time = 15:14:02; Parameter PMT Volts = 449; Parameter Scan Date = 2005-10-31; Parameter Pixel Size = 10; Parameter Laser on time = 12352; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4200A 01 Autoloader; Parameter Laser Power = 1.56; Parameter Scan Power = 80; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Kate,,Rubins Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 28.13; Parameter Scan Time = 15:14:02; Parameter PMT Volts = 434; Parameter Scan Date = 2005-10-31; Parameter Pixel Size = 10; Parameter Laser on time = 12352; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4200A 01 Autoloader; Parameter Laser Power = 1.71; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 80; Parameter Scanning software = AxImageIO; Performer: Kate,,Rubins

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

source_name: Killed MPX 24 HeLa cells infected with Mock in vitro 5.5.05

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

value: Monkeypox Zaire virus

value: time(relative) 12 h


title: Mock 1   Mph

description:
Simple annotation: Normal tissue, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/65409.gif

scan_protocol: Rubins 2003 - Data filtering and analysis; Array images were scanned using an Axon Scanner 4000A (Axon Instruments, Union City, CA), and image analysis was performed using GenePix Pro version 3.0.6.89 (Axon Instruments, Union City, CA).  Grids were manually aligned and features were found using the software feature extraction.  Features were visually inspected for blemishes and removed from downstream analysis.    Data were uploaded to the Stanford Microarray Database (http://genome-www5.stanford.edu/)  and normalized using regression correlation.  Data were expressed as the log2 ratio of fluorescence intensities of the sample and the reference, for each element on the array.    Data were filtered to exclude elements that did not have a regression correlation of Cy5 to Cy3 signal over the pixels spanning the array element of ??0.6 and intensity/background ratio of ??2.5 in at least 80% of the arrays.    For each gene, the expression levels over the timecourse for each monkey were ??time-zerotransformed?? by subtracting the average of the pre-infection baseline expression level from that animal so that the values of each timepoint represent changes relative to the uninfected samples.    The genes whose expression varied from the uninfected baseline by at least 3 fold in at least 3 samples were selected for further analysis.    The data were hierarchically clustered using the Cluster program (http://rana.lbl.gov/EisenSoftware.htm) and displayed using TreeView (http://rana.lbl.gov/EisenSoftware.htm).; Protocol Type = Feature Extraction; Software: type: feature extraction; Performer: Kate,,Rubins Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 27.38; Parameter Scan Time = 17:26:36; Parameter PMT Volts = 431; Parameter Scan Date = 2005-10-31; Parameter Pixel Size = 10; Parameter Laser on time = 12485; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4200A 01 Autoloader; Parameter Laser Power = 1.54; Parameter Scan Power = 80; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Kate,,Rubins Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 27.38; Parameter Scan Time = 17:26:36; Parameter PMT Volts = 455; Parameter Scan Date = 2005-10-31; Parameter Pixel Size = 10; Parameter Laser on time = 12485; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4200A 01 Autoloader; Parameter Laser Power = 1.72; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 80; Parameter Scanning software = AxImageIO; Performer: Kate,,Rubins

source_name: Mock 1 Mph cells Mock Infected in vitro 5.5.05

value: time(relative) 1 h


title: Mock 0b   Mph

description:
Simple annotation: Normal tissue, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/65413.gif

scan_protocol: Rubins 2003 - Data filtering and analysis; Array images were scanned using an Axon Scanner 4000A (Axon Instruments, Union City, CA), and image analysis was performed using GenePix Pro version 3.0.6.89 (Axon Instruments, Union City, CA).  Grids were manually aligned and features were found using the software feature extraction.  Features were visually inspected for blemishes and removed from downstream analysis.    Data were uploaded to the Stanford Microarray Database (http://genome-www5.stanford.edu/)  and normalized using regression correlation.  Data were expressed as the log2 ratio of fluorescence intensities of the sample and the reference, for each element on the array.    Data were filtered to exclude elements that did not have a regression correlation of Cy5 to Cy3 signal over the pixels spanning the array element of ??0.6 and intensity/background ratio of ??2.5 in at least 80% of the arrays.    For each gene, the expression levels over the timecourse for each monkey were ??time-zerotransformed?? by subtracting the average of the pre-infection baseline expression level from that animal so that the values of each timepoint represent changes relative to the uninfected samples.    The genes whose expression varied from the uninfected baseline by at least 3 fold in at least 3 samples were selected for further analysis.    The data were hierarchically clustered using the Cluster program (http://rana.lbl.gov/EisenSoftware.htm) and displayed using TreeView (http://rana.lbl.gov/EisenSoftware.htm).; Protocol Type = Feature Extraction; Software: type: feature extraction; Performer: Kate,,Rubins Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 27.13; Parameter Scan Time = 18:46:20; Parameter PMT Volts = 449; Parameter Scan Date = 2005-10-31; Parameter Pixel Size = 10; Parameter Laser on time = 12564; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4200A 01 Autoloader; Parameter Laser Power = 1.23; Parameter Scan Power = 80; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Kate,,Rubins Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 27.13; Parameter Scan Time = 18:46:20; Parameter PMT Volts = 472; Parameter Scan Date = 2005-10-31; Parameter Pixel Size = 10; Parameter Laser on time = 12564; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4200A 01 Autoloader; Parameter Laser Power = 1.73; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 80; Parameter Scanning software = AxImageIO; Performer: Kate,,Rubins

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

value: time(relative) 0 h