title: TNT_35ppm_Rep2 vs TNT_7ppm_Rep3

source_name: mRNA from worm (Rep#2) treated with 35 ppm of TNT labeled with Cyanine-3 (green)

source_name: mRNA from worm (Rep#3) treated with 7 ppm of TNT labeled with Alex Fluor 647 (red)


title: TNT_35ppm_Rep2 vs TNT_7ppm_Rep2

status: Public on Oct 15 2007

type: RNA

city: Vicksburg

first: Ping

last: Gong

state: MS

address: 3909 Halls Ferry Road

department: Environmental Laboratory

country: USA

institute: US Army ERDC

description: A RNAlater-ICE fixed worm was chopped into 8-10 pieces in equal length. Total RNA was isolated using Qiagen RNeasy Mini Kit from each of the 8-10 pieces and was pooled as one biological replicate representing each individual earthworm. The pooled total RNA was purified to obtain mRNA using NucleoTrap Nucleic Acid Purification Kit (BD Biosciences).

hyb_protocol: Labeled cDNA probes for both channels (Genisphere) were added to the array, covered with a glass cover slip, which was then placed in a 50-ml tube. A few drops of water was also added into the tube to keep the air moisture. The capped tube was incubated at 55oC in a hybridization oven without rotation overnight (ca. 16 hr). Arrays were post-hyb washed according to manufacture's instruction (Genisphere).

scan_protocol: Arrays were scanned at 5-um resolution using VersArray ChipReader (Bio-Rad).

data_processing: A spot was flagged out if (1) its raw signal intensity was below its background level, (2) it overlapped with other spots, or (3) it was stained or over-saturated. The filtered spot intensity data were normalized by (1) subtraction of background intensity, (2) cross-channel LOWESS (local regression), and (3) centering to each channel's median spot intensity.

molecule: polyA RNA

organism: Eisenia fetida

label_protocol: 30 ng mRNA was reverse-transcribed into cDNA and labeled using Genisphere 3DNA 900 Expression Array Detection Cy3 kit.

extract_protocol: RNeasy kit (Qiagen)

tag: Adult earthowrms exposed in soil for 28 days.

tag: Worms were snap frozen in liquid nitrogen.

tag: Worm tissue was fixed in RNAlater-ICE (Ambion).

source_name: mRNA from worm (Rep#2) treated with 7 ppm of TNT labeled with Alex Fluor 647 (red)

label_protocol: 30 ng mRNA was reverse transcribed into cDNA and labeled using Genisphere 3DNA 900 Expression Array Detection Alex Fluor 647 kit.

tag: Worm tissue was fixed in RNAlater-ICe (Ambion).


title: TNT_35ppm_Rep3 vs TNT_7ppm_Rep4

source_name: mRNA from worm (Rep#3) treated with 35 ppm of TNT labeled with Cyanine-3 (green)

source_name: mRNA from worm (Rep#4) treated with 7 ppm of TNT labeled with Alex Fluor 647 (red)


title: TNT_139ppm_Rep5 vs TNT_0ppm_Rep1

source_name: mRNA from worm (Rep#5) treated with 139 ppm of TNT labeled with Cyanine-3 (green)

source_name: mRNA from worm (Rep#1) treated with 0 ppm of TNT labeled with Alex Fluor 647 (red)


title: TNT_35ppm_Rep5 vs TNT_7ppm_Rep1

source_name: mRNA from worm (Rep#5) treated with 35 ppm of TNT labeled with Cyanine-3 (green)

source_name: mRNA from worm (Rep#1) treated with 7 ppm of TNT labeled with Alex Fluor 647 (red)


title: LonBKB1-46461

city: manhattan

first: Xiaoyan

last: Tang

email: xtang@ksu.edu, llan@ksu.edu

state: KS

address: 4702 Throckmorton

department: Plant Pathology

institute: Kansas State University

description: Gene expression data from DC3000 when grown in KB (King et al., 1954) to ~0.7x109 cfu/mL.

hyb_protocol: According to the standard protocol provided by NimbleGen Systems Inc., Madison, WS.

data_processing: For each probe on the array, the median signal intensity was calculated using the NimbleGen extraction software. The data were normalized by using quantile normalization (Bolstad et al., 2003)available through the Bioconductor project

label: biotin

molecule: total RNA

organism: Pseudomonas syringae pv. tomato str. DC3000

source_name: Pseudomonas syringae pv. tomato DC3000 lonB mutant r2

extract_protocol: Total RNA was extracted using a modified hot phenol procedure (Aiba et al. 1981), then purified by using RNeasy Midi kit following the manufacture instruction (Qiagen, Valencia, CA).

tag: DC3000 lonB mutant was grown in KB (King et al., 1954) to ~0.7x109 cfu/mL,The bacteria were centrifuged, washed twice with MM (Huynh et al., 1989), and resuspended in MM to 3x108 cfu/mL. The bacteria were cultured in MM for 6 h before being harvested for RNA extraction.


title: TNT_7ppm_Rep3 vs TNT_139ppm_Rep4

source_name: mRNA from worm (Rep#3) treated with 7 ppm of TNT labeled with Cyanine-3 (green)

source_name: mRNA from worm (Rep#4) treated with 139 ppm of TNT labeled with Alex Fluor 647 (red)


title: TNT_7ppm_Rep1 vs TNT_139ppm_Rep1

source_name: mRNA from worm (Rep#1) treated with 7 ppm of TNT labeled with Cyanine-3 (green)

source_name: mRNA from worm (Rep#1) treated with 139 ppm of TNT labeled with Alex Fluor 647 (red)


title: TNT_35ppm_Rep1 vs TNT_7ppm_Rep1

source_name: mRNA from worm (Rep#1) treated with 35 ppm of TNT labeled with Cyanine-3 (green)


title: TNT_0ppm_Rep5 vs TNT_35ppm_Rep1

source_name: mRNA from worm (Rep#5) treated with 0 ppm of TNT labeled with Cyanine-3 (green)

source_name: mRNA from worm (Rep#1) treated with 35 ppm of TNT labeled with Alex Fluor 647 (red)


title: LONB-KB-38962

scan_protocol: According to the standard protocol provided by NimbleGen Systems Inc., Madison, WS.

source_name: Pseudomonas syringae pv. tomato DC3000 lonB mutant


title: LonB-KB-65934

source_name: Pseudomonas syringae pv. tomato DC3000 lonB mutant r3

label_protocol: According to the standard protocol provided by NimbleGen Systems Inc., Madison, WS.


title: CtsR Regulon, ictsR-mcsA vs delta ctsR, log phase

status: Public on Oct 14 2007

city: Ithaca

first: Sarita

last: Raengpradub

state: NY

address: 412 Stocking Hall

department: Food Science

institute: Cornell University

description: Expression profiles were measured from two independent RNA extractions, resulting in four replicate spots per gene (array contains duplicate spots).

hyb_protocol: Microarray slide blocking was performed prior to hybridization. Slides were incubated for 10 min in a solution containing methyl pyrrilidone, succinic anhydride and sodium borate, and then washed in fresh methyl pyrrilidone for 10 min. Successive 1-min washes in nanopure water (once), 0.1% SDS (3 times), nanopure water (5 times), and 95% EtOH (once). The slides were dried by centrifugation and immersed for 1 h in blocking solution (0.1% BSA, 5X SSC, 0.1% SDS) at 42°C. After blocking, the slides were washed for 1 min each in nanopure water (5 times) and 95% EtOH (2 times) and then dried by centrifugation. For the strains to be compared, labeled cDNAs were combined and dried, then resuspended in 50μl of hybridization buffer (5X SSC, 0.1% SDS, 0.1mM dithiothreitol (DTT), 0.5X formamide, 0.06 μg/μl salmon sperm DNA in DEPC-treated water), denatured at 95°C for 5 min then applied to the slides using mSeries LifterSlips™ (Erie Scientific). Following overnight hybridization at 42°C, the slides were washed in 2X SSC+0.1% SDS (5 min at 42˚C), with subsequent 5-min washes at room temperature in 2X SSC+0.1% SDS, 2X SSC, and 0.2X SSC, followed by final rinse in nanopure water. Slides were dried by centrifugation.

scan_protocol: Images were scanned using a GenePix 4000B scanner (Molecular Devices Corp.). Raw TIFF images were automatically gridded and analyzed using GenePix Pro 6.0 software.

data_processing: Analyses of microarray data were performed in R with Bioconductor using LIMMA software (Smyth, 2005). Background correction was performed using the “normexp” method. For normalization within arrays, the data were weighted for the genomic DNA controls and normalized using print-tip loess method (Smyth & Speed, 2003). The data were then scale normalized between arrays. The correlation between duplicate spots was calculated (Smyth et al., 2005) and a linear model was fitted to the normalized log ratios and empirical Bayes statistics were applied for differential expression analysis.

label: Alexa Fluor 635

organism: Listeria monocytogenes

label_protocol: cDNA was synthesized from 10 μg purified total RNA (using random primers) and labeled with Alexa Fluor dyes using the SuperScript Plus Indirect cDNA Labeling System.

growth_protocol: For all experiments, Listeria monocytogenes FSL H6-195 (ictsR-mcsA strain) were grown in BHI broth at 37°C with shaking (250 rpm), followed by inoculation into 5 ml of BHI broth+0.5mM IPTG (1:100 dilution) and growth at 37°C with shaking to an OD600=0.4, then diluted again (1:100) into BHI broth+0.5 mM IPTG and incubated at 37 °C with shaking until an OD600=0.4, then harvested for RNA isolation.

extract_protocol: RNA was isolated from frozen bacterial pellets with the Qiagen RNeasy Midi kit according to the manufacturer’s protocol for enzymatic and mechanical disruption, except that cells treated with lysozyme followed by sonication on ice for three 30 s bursts at 18–21 W (30 s pauses between bursts). RQ1 DNase treatment of total RNA in the presence of RNasin Plus RNA inhibitor (Promega) was performed according to the manufacturer’s protocol, followed by subsequent phenol:chloroform and chloroform extractions. RNA was ethanol-precipitated overnight, centrifuged and washed with 70% ethanol before resuspenson of the final RNA pellet in DEPC-treated water. Total nucleic acid concentration and purity were estimated using absorbance readings (260/280 nm, 260/230 nm) on a NanoDrop ND-1000 spectrophotometer. RNA integrity was checked by agarose gel electrophoresis.

tag: Listeria monocytogenes FSL H6-195 (ictsR-mcsA strain expressing the ctsR-mscA operon in trans under control of an IPTG-inducible promoter) grown at 37°C to log phase (OD600=0.4) in BHI+0.5mM IPTG.

label: Alexa Fluor 532

growth_protocol: For all experiments, Listeria monocytogenes FSL H6-190 (ctsR null mutant)  were grown in BHI broth at 37°C with shaking (250 rpm), followed by inoculation into 5 ml of BHI broth (1:100 dilution) and growth at 37°C with shaking to an OD600=0.4, then diluted again (1:100) into BHI broth and incubated at 37 °C with shaking until an OD600=0.4, then harvested for RNA isolation.

tag: Listeria monocytogenes FSL H6-190 (ctsR null mutant) grown at 37°C to log phase (OD600=0.4).


title: CtsR regulon, 10403S vs delta ctsR, log phase

description: Expression profiles were measured from three independent RNA extractions, resulting in six replicate spots per gene (array contains duplicate spots).

source_name: Listeria monocytogenes 10403S

growth_protocol: For all experiments, Listeria monocytogenes 10403S were grown in BHI broth at 37°C with shaking (250 rpm), followed by inoculation into 5 ml of BHI broth (1:100 dilution) and growth at 37°C with shaking to an OD600=0.4, then diluted again (1:100) into BHI broth and incubated at 37 °C with shaking until an OD600=0.4, then harvested for RNA isolation.

tag: Listeria monocytogenes 10403S grown at 37°C to log phase (OD600=0.4).

source_name: Listeria monocytogenes FSL H6-190 (ctsR null mutant)


title: C57BL/6 VP, biological rep4

status: Public on Oct 12 2007

city: boston

first: qing

last: xu

state: MA

address: 44 binney st

department: Medical Oncology

institute: dana farber cancer institute

description: Gene expression data from ventral prostate of wild type 8 wks old C57BL/6 mice

hyb_protocol: standard procedure carried out at Broad Institute

data_processing: CEL files were normalized with median array intensity using MAS5

organism: Mus musculus

source_name: ventral prostate of wild type C57BL/6 mice

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: standard mouse diet

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

tag: Genotype

value: wild type

tag: Age

value: 8 weeks


title: FVB VP, biological rep3

description: Gene expression data from ventral prostate of wild type 8 wks old FVB mice

scan_protocol: standard procedure carried out at Broad Institute

source_name: ventral prostate of wild type FVB mice


title: C57BL/6 VP, biological rep2


title: 129X1 VP, biological rep4

description: Gene expression data from ventral prostate of wild type 8 wks old 129X1 mice

source_name: ventral prostate of wild type 129X1 mice


title: C57BL/6 VP, biological rep3


title: BALB/c VP, biological rep3

description: Gene expression data from ventral prostate of wild type 8 wks old BALB/c mice

source_name: ventral prostate of wild type BALB/c mice


title: C57BL/6 VP, biological rep1


title: FVB VP, biological rep4


title: BALB/c VP, biological rep1


title: FVB VP, biological rep1


title: BALB/c VP, biological rep4


title: BALB/c VP, biological rep2


title: 129X1 VP, biological rep3


title: 129X1 VP, biological rep2


title: SWR VP, biological rep3

description: Gene expression data from ventral prostate of wild type 8 wks old SWR mice

source_name: ventral prostate of wild type SWR mice


title: FVB VP, biological rep2


title: 129X1 VP, biological rep1


title: SWR VP, biological rep4


title: SWR VP, biological rep2


title: AKR VP, biological rep4

description: Gene expression data from ventral prostate of wild type 8 wks old AKR mice

source_name: ventral prostate of wild type AKR mice


title: Neisseria meningitidis isolate B004-3

status: Public on Oct 11 2007

type: genomic

city: Beijing

first: Junping

last: Peng

address: No 6, Rongjing Eastern Street, BDA

country: China

institute: Chinese center for disease control and prevention

description: CGH

hyb_protocol: Samples were hybridized overnight at 65°C

scan_protocol: The processed slides were scanned with a GenePix 4000B scanner (Axon). Fluorescent spots and the local background intensities were quantified with GenePix Pro 5.0 software (Axon)

data_processing: MIDAS (TIGR) & GACK (Genomotyping Analysis by Charlie Kim, Genome Biology 2002)

molecule: genomic DNA

organism: Neisseria meningitidis

source_name: menB 004

label_protocol: Genomic DNA was  fluorescently labeled by random priming with the Klenow fragment

extract_protocol: Genomic DNA was extracted by using Wizard Genomic DNA Purification Kit (Promega)

tag: Neisseria meningitidis Serogroup B isolate

tag: Neisseria meningitidis Serogroup C isolate (ST4821)


title: AKR VP, biological rep1


title: SWR VP, biological rep1


title: AKR VP, biological rep3


title: AKR VP, biological rep2


title: Neisseria meningitidis isolate B004-2

description: CGH


title: Neisseria meningitidis isolate B004-1

description: CGH


title: Neisseria meningitidis isolate A472-3

description: CGH

source_name: menA 472

tag: Neisseria meningitidis Serogroup A isolate


title: Neisseria meningitidis isolate A472-1

description: CGH


title: Neisseria meningitidis isolate A472-2

description: CGH


title: Neisseria meningitidis isolate A462-3

description: CGH

source_name: menA 462


title: Neisseria meningitidis isolate A362-3

description: CGH

hyb_protocol: Samples were hybridized overnight at 65°C.

scan_protocol: The processed slides were scanned with a GenePix 4000B scanner (Axon). Fluorescent spots and the local background intensities were quantified with GenePix Pro 5.0 software (Axon).

source_name: menA 362

label_protocol: Genomic DNA was  fluorescently labeled by random priming with the Klenow fragment.


title: Neisseria meningitidis isolate A412-3

description: CGH

source_name: menA 412


title: Neisseria meningitidis isolate A462-2

description: CGH


title: Neisseria meningitidis isolate A342-2

description: CGH

source_name: menA 342

tag: Neisseria meningitidis Serogroup a isolate


title: Neisseria meningitidis isolate A342-3

description: CGH


title: Neisseria meningitidis isolate A462-1

description: CGH


title: Neisseria meningitidis isolate A362-2

description: CGH


title: Neisseria meningitidis isolate A362-1

description: CGH


title: Neisseria meningitidis isolate A315-3

description: CGH

hyb_protocol: samples were hybridized overnight at 65°C

data_processing:
MIDAS (TIGR)
GACK (Genomotyping Analysis by Charlie Kim, Genome Biology 2002)

source_name: menA 315


title: Neisseria meningitidis isolate A317-3

description: CGH

data_processing:
MIDAS (TIGR) software
GACK (Genomotyping Analysis by Charlie Kim, Genome Biology 2002)

source_name: menA 317


title: Neisseria meningitidis isolate A307-3

description: CGH

source_name: menA 307


title: Neisseria meningitidis isolate A412-2

description: CGH


title: Neisseria meningitidis isolate A315-1

description: CGH


title: Neisseria meningitidis isolate A317-1

description: CGH


title: Neisseria meningitidis isolate A315-2

description: CGH


title: Neisseria meningitidis isolate A317-2

description: CGH


title: Neisseria meningitidis isolate A307-2

description: CGH


title: Neisseria meningitidis isolate A307-1

description: CGH


title: Neisseria meningitidis isolate A281-2

description: CGH

hyb_protocol: samples were hybridized overnight at 65°C.

source_name: menA 281

extract_protocol:
Genomic DNA was extracted by using Wizard® Genomic DNA Purification
Kit (Promega)


title: Neisseria meningitidis isolate A281-3

description: CGH


title: Neisseria meningitidis isolate A342-1

description: CGH


title: Neisseria meningitidis isolate A281-1

description: CGH


title: rClone-2 B Affy

city: Leuven

first: Fernando

last: Ulloa Montoya

address: Herestraat 49 bus 804

department: Medicine

country: Belgium

institute: Katholieke Universiteit Leuven

description: rat clone 2, biological replicate B, Affymetrix

hyb_protocol: Samples were hybridized to Affymetrix  Rat Expression Set 230A chips (Affymetrix Inc), washed, and scanned at the University of Minnesota Affymetrix Microarray Core Facility as described in the Affymetrix GeneChip Expression Analysis Technical Manual. Protocol EukGE-WS2v4_450

scan_protocol: Array was scanned at the University of Minnesota Affymetrix Microarray Core Facility as described in the Affymetrix GeneChip Expression Analysis Technical Manual. Pixel Size 2.5, Filter 570, Scanner ID 50209060, Number of Scans 1, Scanner Type M10

data_processing: CEL files were loaded into GeneData Expressionist Refiner (GeneData, San Francisco, CA) to assess overall quality and obtain condensed single intensity values per probeset using the Microarray Analysis Suite Statistical algorithm (MAS 5.0). The mean of mean intensity values for all chips (192) was used to normalize the mean intensity of each chip. Normalization Target: 292, Tau: 0.015, Alpha1: 0.04, Alpha2: 0.06

label: Biotin

organism: Rattus norvegicus

source_name: rat clone 2, biological replicate B

label_protocol: 200 ng of total cellular RNA was subjected to double amplification. First round of IVT-based, linear amplification was performed using the RiboAmp OA RNA Amplification Kit (Arcturus, Mountain View, CA) followed by labeling with the Enzo Bioarray HighYield RNA Transcript Labeling Kit (Enzo Diagnostics, Farmingdale, NY) according to manufacturer's instructions

growth_protocol: Fisher rat BM cells were plated on 600w glucose DMEM, 40% MCDB-201, 1X insulin-transferrin-selenium (ITS; Sigma), 1X LA-BSA, 0.05x10-6M dexamethasone (Sigma), 10-4M ascorbic acid 3-phosphate, 100 units of penicillin, 1,000 units of streptomycin, 55 ?M 2-mercaptoethanol, 2 0.000000BS (HyClone; Lot ANL19977), 10ng/mL hPDGF-BB, 10ng/mL mEGF, and 1000 units/mL mLIF in a humidified, 502 and 6% CO2, 37oC incubator. After 4 weeks, CD45+ cells were depleted using a MACS separation CS column, and cells replated at 10 cells/well. Expansion was done by trypsinizing (0.05% trypsin) the cells and replating them every two days at a density of 200 cells/cm2. Cells at population doubling >100 were used for 3 RNA collections for gene arrays

extract_protocol: Total RNA  was extracted using the RNAeasy microkit (Qiagen, Valencia, CA), DNAse treatment was performed on column

tag: Strain

value: Fisher, Sex:Male, Age:Adult, Tissue:Bone marrow (cultured cells), Cell type:Clone isolated using Multipotent Adult Progenitor Cells culture conditions


title: rClone-2 C Affy

description: rat clone 2, biological replicate C, Affymetrix

source_name: rat clone 2, biological replicate C


title: Neisseria meningitidis isolate A263-3

description: CGH

source_name: menA 263


title: Neisseria meningitidis isolate A412-1

description: CGH


title: Neisseria meningitidis isolate A210-3

description: CGH

source_name: menA 210


title: Neisseria meningitidis isolate A263-2

description: CGH


title: Neisseria meningitidis isolate A263-1

description: CGH


title: Neisseria meningitidis isolate A210-1

description: CGH


title: Neisseria meningitidis isolate A200-3

description: CGH

source_name: menA 200


title: Mutant Histone H2A K4,7G replicate 1

city: Pullman

first: John

middle: J.

last: Wyrick

state: WA

address: Biotechnology Life Sciences 241

department: School of Molecular Biosciences

institute: Washington State University

description: Mutant yeast strain Histone H2A K4,7G

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: Affymetrix Microarray Suite version 5.0.

organism: Saccharomyces cerevisiae

source_name: Yeast RNA

label_protocol: Approximately 20 µg of total RNA was processed to produce biotinylated cRNA targets.

extract_protocol: Cells were grown in YPD media until mid-log phase. Cells were harvested at OD600 of 0.5-0.7. Cells were lysed and RNA was extracted by hot acid phenol chloroform and phenol chloroform isoamyl alcohol extraction.

tag: PY018 (mutant Histone H2A K4,7G)


title: Neisseria meningitidis isolate A210-2

description: CGH


title: Mutant Histone H2A^4-20 replicate 3

description: Mutant yeast strain Histone H2A^4-20

tag: PY015 (mutant Histone H2A^4-20)


title: Mutant Histone H2A K4,7G replicate 3

description: Mutant yeast strain Histone H2A K4,7G


title: Neisseria meningitidis isolate A200-1

description: CGH


title: Neisseria meningitidis isolate A200-2

description: CGH


title: Mutant Histone H2A^4-20 replicate 2

description: Mutant yeast strain Histone H2A^4-20


title: Neisseria meningitidis isolate A180-1

description: CGH

source_name: menA 180


title: rMAPC-1 B Affy

description: rat MAPC, clone 1, biological replicate B, Affymetrix

value: Fisher, Sex:Male, Age:Adult, Tissue:Bone marrow (cultured cells), Cell type:Multipotent Adult Progenitor Cells


title: Neisseria meningitidis isolate A180-3

description: CGH

source_name: menC 180


title: rMAPC-1 C Affy

description: rat MAPC, clone 1, biological replicate C, Affymetrix


title: Neisseria meningitidis isolate A180-2

description: CGH


title: rMAPC-1 A Affy

description: rat MAPC, clone 1, biological replicate A, Affymetrix


title: rClone-2 A Affy

description: rat clone 2, biological replicate A, Affymetrix

source_name: rat clone 2, biological replicate A


title: Neisseria meningitidis isolate 630601-3

description: CGH

tag: Neisseria meningitidis Serogroup C isolate


title: Mutant Histone H2A^4-20 replicate 1

description: Mutant yeast strain Histone H2A^4-20


title: Neisseria meningitidis isolate 510603-3

description: CGH


title: Wild-type for H2A^4-20 and H2A K4,7G replicate 3

description: Wild-type yeast strain

tag: PY014 (wild-type Histone H3)


title: Wild-type for H2A^4-20 and H2A K4,7G replicate 2

description: Wild-type yeast strain


title: Mutant Histone H2A K4,7G replicate 2

description: Mutant yeast strain Histone H2A K4,7G


title: Neisseria meningitidis isolate 630601-1

description: CGH


title: Neisseria meningitidis isolate 510603-2

description: CGH


title: Wild-type for H2A^4-20 and H2A K4,7G replicate 1

description: Wild-type yeast strain


title: Neisseria meningitidis isolate 630601-2

description: CGH


title: Neisseria meningitidis isolate 510603-1

description: CGH


title: tra1 P3408A vs. TRA1 SB (array2)

status: Public on Oct 10 2007

city: London

first: Christopher

last: Brandl

state: Ontario

address: 1151 Richmond St.

department: Biochemistry

country: Canada

institute: University of Western Ontario

description: Experiment was performed to analyze the effects of the tra1_P3408A allele on gene expression.  This array is one of two dye-swapped replicates.

hyb_protocol: Hybridization was performed at MOgene LC (St. Louis, MO).  Labeled material was fragmented according to the protocol described in the Agilent processing manual and hybridized overnight with the array in a rotating oven at 60 degrees Celsius in an ozone-free environment.  Wash conditions used were as outlined in the Agilent processing manual.

scan_protocol: Scanning was performed at MOgene LC (St. Louis, MO) using an Agilent scanner.

data_processing: Data processing was performed at MOgene LC (St. Louis, MO).  Feature extraction, normalization and background subtraction of reported values were performed using Agilent software.

source_name: Cy3: CY1507(TRA1::Tn10LUK with 1643(myc-tra1_P3408A-YCplac111))

label_protocol: Labeling was performed at MOgene LC (St. Louis, MO).  Total RNA from yeast was amplified using Agilent's low input linear amplification kit according to the process outlined by the manufacturer (Agilent Technologies).  1-5ug of amplified target cRNA was labeled using the Micromax kit (PerkinElmer, Inc.).  The labeled material was passed through a zymo RNA Clean-up Kit-5 column (Zymo Research Corp., CA) to remove un-incorporated label and eluted in 15-20ul of RNase-free water (Ambion, Inc.).  All of the labeling and post-labeling procedures were conducted in an ozone-free environment to ensure the integrity of the label.

extract_protocol: RNA extraction was performed as described in Mutiu AI, and Brandl CJ (2005) RNA isolation from yeast using silica matrices. J Biomol Tech 16:316-317.

tag: Yeast cells were grown in YP media containing 2% glucose to an A600=2.0.

source_name: Cy5: CY1524(TRA1::Tn10LUK with 1614(myc-TRA1_SB-YCplac111))


title: tra1 SRR3413 vs. TRA1 SB (array2)

source_name: Cy3: CY1531(TRA1::Tn10LUK with 1644(myc-tra1_SRR3413-YCplac111))

source_name: Cy3: CY1524(TRA1::Tn10LUK with 1614(myc-TRA1_SB-YCplac111))


title: TRA1 SB vs. tra1 SRR3413 (array1)

source_name: Cy5: CY1531(TRA1::Tn10LUK with 1644(myc-tra1_SRR3413-YCplac111))


title: tra1 S3463A vs. TRA1 SB (array2)

source_name: Cy5: CY1514(TRA1::Tn10LUK with 1688(myc-tra1_S3463A-YCplac111))


title: TRA1 SB vs. tra1 S3463A (array1)


title: Liver_healthy_cow_early postpartum_7045Cy5

status: Public on Oct 09 2007

city: Urbana

first: Juan

last: Loor

state: IL

address: 1207 West Gregory Drive

department: Animal Sciences

institute: University of Illinois

description: Cow fed ad libitum early postpartum.  Liver RNA was cohybridized with RNA from a pool of bovine tissues.

data_processing: loess normalization, log2 transformation

organism: Bos taurus

source_name: liver, cow, labelled with Cy5

tag: Liver RNA

source_name: reference standard RNA, labelled with Cy3

tag: RNA pool of bovine tissues


title: Liver_ketotic_cow_early postpartum_6870Cy5

description: Cow was feed restricted to 50% of feed intake from 4 days postpartum until onset of ketosis, as determined by thorough clinical examination.  Liver RNA was cohybridized with RNA from a pool of bovine tissues.


title: Liver_ketotic_cow_early postpartum_6607Cy3

source_name: reference RNA labelled with Cy5

source_name: Liver RNA labelled with Cy3


title: TRA1 SB vs. tra1 P3408A (array1)

source_name: Cy5: CY1507(TRA1::Tn10LUK with 1643(myc-tra1_P3408A-YCplac111))


title: Liver_healthy_cow_early postpartum_7187Cy3


title: Liver_healthy_cow_early postpartum_7187Cy5


title: Liver_healthy_cow_early postpartum_7105Cy3


title: Liver_healthy_cow_early postpartum_7050Cy5


title: Liver_ketotic_cow_early postpartum_6886Cy5


title: Liver_healthy_cow_early postpartum_6986Cy5


title: Liver_healthy_cow_early postpartum_7050Cy3


title: Liver_ketotic_cow_early postpartum_6837Cy3

tag: Liver RNA labelled with Cy3


title: Liver_ketotic_cow_early postpartum_6870Cy3


title: Liver_healthy_cow_early postpartum_7045Cy3


title: Liver_ketotic_cow_early postpartum_6837Cy5

tag: Liver RNA labelled with Cy5

tag: RNA pool of bovine tissues labelled with Cy3


title: Liver_healthy_cow_early postpartum_6877Cy3


title: Liver_ketotic_cow_early postpartum_6839Cy3


title: Liver_ketotic_cow_early postpartum_6839Cy5


title: Liver_healthy_cow_early postpartum_7161Cy5

data_processing: unnormalized, log2 transformation

tag: Liver RNA from healthy cow early postpartum

tag: Pool RNA from cattle tissues


title: Liver_ketotic_cow_early postpartum_6724Cy5


title: Liver_ketotic_cow_early postpartum_6886Cy3


title: Liver_ketotic_cow_early postpartum_5866Cy5

tag: Cow from ketotic liver early postpartum

tag: RNA isolated from bovine tissues


title: Liver_ketotic_cow_early postpartum_6607Cy5

tag: RNA from pool of bovine tissues labelled with Cy3


title: Velcade_10nM_24h_TaY

city: Tokyo

first: Junko

middle: H

last: Ohyashiki

address: 6-7-1, Nishishinjuku, Shinjuku-ku

department: Intractable Immune System Diseases Research Center

country: Japan

institute: Tokyo Medical University

description: The proteasome inhibitor, bortezomib (Millennium Pharmaceuticals, Inc., also known as VELCADE or PS-3419), represents a new class of anti-cancer drugs which has been shown to inhibit the growth and/or progression of human cancers.

hyb_protocol: Hybridization Protocol Hybridization was carried out automatically using GeneTAC Hybstation (Genomic Solutions, US) according to the supplier’s instruction. The conditions of hybridization were 55oC for 2 hours, 50oC for 2 hours, and 46oC for 2 hours, then 42oC for 12 hours.

scan_protocol: The　hybridized signals were scanned by GenePix 4000B Microarray Scanner (Axon Instruments, Union City, CA, USA).

data_processing: The scanned dara was normalized, verified and analysed by GeneSifter.

organism: Homo sapiens

label_protocol: 20 microgram of RNA were labeled using a LabelStar Array kit (Qiagen) , according to the supplier’s instruction.

extract_protocol: RNeasy Mini Kit (Qiagen, Germantown, MD, USA)

treatment_protocol: TaY cells were cultured with 10 nM of Velcade for 24hrs.

tag: Velcade treated ATL cells

tag: Mock


title: Liver_healthy_cow_early postpartum_6986Cy3


title: Liver_healthy_cow_early postpartum_7161Cy3

source_name: liver, cow, labelled with Cy3

source_name: reference standard RNA, labelled with Cy5


title: Liver_healthy_cow_early postpartum_7105Cy5


title: Velcade_5nM_72h_TaY

treatment_protocol: TaY cells were cultured with 5 nM of Velcade for 72hrs.


title: Liver_healthy_cow_early postpartum_6877Cy5

description: Cow fed ad libitum early post-partum.  Liver RNA was cohybridized with RNA from a pool of bovine tissues.


title: Liver_ketotic_cow_early postpartum_6724Cy3


title: Velcade_5nM_8h_TaY

treatment_protocol: TaY cells were cultured with 5 nM of Velcade for 8hrs.

source_name: TaY\Mock


title: Velcade_0.5nM_24h_TaY

extract_protocol: TaY cells were cultured with 0.5 nM of Velcade for 24hrs.


title: Velcade_5nM_24h_TaY

treatment_protocol: TaY cells were cultured with 5nM of Velcade for 24hrs.


title: Velcade_0.05nM_24h_TaY

hyb_protocol: Hybridization was carried out automatically using GeneTAC Hybstation (Genomic Solutions, US) according to the supplier’s instruction. The conditions of hybridization were 55oC for 2 hours, 50oC for 2 hours, and 46oC for 2 hours, then 42oC for 12 hours.

data_processing: The scanned data was normalized, verified, and analyzed using the GeneSifter.

treatment_protocol: TaY cells were cultured with 0.05 nM of Velcade for 24hrs.

tag: Velvade treated ATL cells

treatment_protocol: TaY cells were cultured without velcade.


title: 1M-89_16a

status: Public on Oct 08 2007

city: San Francisco

first: Donna

middle: G

last: Albertson

state: CA

department: Comprihensive Cancer Center

institute: University of California San Francisco

description: Used Spot files "HA3.1_clonepos_May04.20060811.txt" & "HA3.1_spotclone.20060807.txt" to analyse the raw images for this sample.

hyb_protocol: Labeled test and reference DNAs together with 100 µg human Cot-1 DNA were hybridized for ~48 hrs at 37º C.

scan_protocol: We acquired 16-bit DAPI, Cy3 and Cy5 images using a custom built CCD camera system (Hamilton et al. 2006. A large field CCD system for quantitative imaging of microarrays. Nuc. Acids Res. 34, e58).

data_processing: We carried out image and data analysis using UCSF SPOT (Jain AN et al. 2002. Fully automatic quantification of microarray image data. Genome Res. 12:325-332). Ratios for each spot were calculated as the total background-corrected fluorescence intensity ratios for the test and reference channels. In addition, array CGH data were corrected for BAC clone specific GC content and in some hybridizations a geometrical dependence of the ratios on the array. Justification of these procedures is presented in Tokuyasu et al. (in preparation). We used the SPROC software to automatically filter the data based on quality criteria, average the log2 ratios of the replicate spots, and assign genome position. Only clones for which two or more spots passed quality criteria and for which the standard deviation of the replicates was less than 0.2 were included in the subsequent analysis. Data were normalized to set the median log2 ratio to zero. Data were derived from two different versions of arrays: HumArray2.0 and HumArray3.1. For compatibility, data are presented in the HumArray 3.1 format.

label_protocol: Genomic DNA (600 ng) was labeled by random priming to incorporate Cy3 dCTP in a 50 µl reaction.

extract_protocol: Cell line DNA was isolated by incubation overnight at 55º C in 3 ml of 1x TE buffer (pH=7.5) supplemented with 0.5 % SDS and 0.1 µg/µl proteinase K, followed by ethanol precipitation after 24 hours.

treatment_protocol: methotrexate resistant colony derived from clone 1M-89

tag: HCT116+chr3, clone 1M-89

source_name: Reference genomic DNA

label_protocol: Genomic DNA (600 ng) was labeled by random priming to incorporate Cy5 dCTP in a 50 µl reaction.

extract_protocol: Reference genomic DNA was isolated from whole blood of healthy male doner. DNA was prepared using standard methods ie. cell lysis and proteinase K digestion followed by ETOH precipitation. Detailed protocol can be found at http://cancer.ucsf.edu/array/protocols/index.php.

tag: gender

value: male,

tag: tissue type

value: blood


title: 1M-89_6


title: 1M-89_c6a


title: 1M-57_2

description: Used Spot files "HA2.0_clonepos_May04.20060811.txt" & "HA2.0_spotclone.20060807.txt" to analyse the raw images for this sample.

treatment_protocol: methotrexate resistant colony derived from clone 1M-57

tag: HCT116+chr3, clone 1M-57


title: 1M-57_5


title: 1M-42_2

treatment_protocol: methotrexate resistant colony derived from clone 1M-42

tag: HCT116+chr3, clone 1M-42


title: 1M-89_4a


title: 1M-89

treatment_protocol: control, without methotrexate treatment


title: 1M-89_2


title: 1M-89_7


title: 1M-84_c1

treatment_protocol: methotrexate resistant colony derived from clone 1M-84

tag: HCT116+chr3, clone 1M-84


title: 1M-84


title: 1M-84_c11a


title: 1M-89_3


title: 1M-89_1a


title: 1M-89_12


title: 1M-84_8a


title: Liver_ketotic_cow_early postpartum_5866Cy3

tag: RNA pool of bovine tissues

tag: Liver RNA


title: 1M-83_10

treatment_protocol: methotrexate resistant colony derived from clone 1M-83

tag: HCT116+chr3, clone 1M-83


title: 1M-83


title: 1M-83_3


title: 1M-83_2


title: 1M-83_1a


title: 1M-83_2a


title: 1M-84_6


title: 1M-75

tag: HCT116+chr3, clone 1M-75


title: 1M-83_c6


title: 1M-75_c10

treatment_protocol: methotrexate resistant colony derived from clone 1M-75


title: 1M-75_c3


title: 1M-73_2

treatment_protocol: methotrexate resistant colony derived from clone 1M-73

tag: HCT116+chr3, clone 1M-73


title: 1M-73


title: 1M-72

tag: HCT116+chr3, clone 1M-72


title: 1M-72_c3

treatment_protocol: methotrexate resistant colony derived from clone 1M-72


title: 1M-72_c5


title: 1M-75_c7a


title: 1M-67_c11

treatment_protocol: methotrexate resistant colony derived from clone 1M-67

tag: HCT116+chr3, clone 1M-67


title: 1M-67_c10


title: 1M-67


title: 1M-57_14


title: 1M-57_12


title: 1M-57_9


title: 1M-57_16


title: 1M-67_c7


title: 1M-57_3a


title: 1M-57


title: 1M-57_c12


title: 1M-57_c10


title: 1M-57_6


title: 1M-57_1


title: 1M-57_c6


title: 1M-45_16

treatment_protocol: methotrexate resistant colony derived from clone 1M-45

tag: HCT116+chr3, clone 1M-45


title: 1M-45


title: 1M-45_c2


title: 1M-45_10


title: 1M-45_6a


title: 1M-45_4a


title: 1M-43

tag: HCT116+chr3, clone 1M-43


title: 1M-45_1a


title: 1M-45_2


title: 1M-45_3a


title: 1M-43_11

treatment_protocol: methotrexate resistant colony derived from clone 1M-43


title: 1M-89_12_expression

description: Image analysis was performed using UCSF Spot (Jain AN et al. 2002. Fully automatic quantification of microarray image data. Genome Res. 12:325-332).

hyb_protocol: Labeled test and reference cDNAs together with 100 µg human Cot-1 DNA were hybridized overnight at 37º C using Genomic Solutions GeneTAC Hybridization Station. Hybridizations were carried out on arrays of printed long oligonucleotides (70mers) containing 21,000 elements (Operon V2.0, printed in the J. David Gladstone Institutes, Genomics Core Laboratory).

scan_protocol: Slides were scanned with an Axon scanner.

data_processing: Ratios for each spot were calculated as the total background-corrected fluorescence intensity ratios for the test and reference channels. Expression data were filtered to exclude all spots with foreground intensity below 500 units in the Cy3 or Cy5 channel and were subsequently median normalized.

label_protocol: Total RNA (20 µg) was reverse transcribed in the presence of aminoallyl-dUTP followed by coupling with Cy3 dye.

extract_protocol: Trizol

label_protocol: Total RNA (20 µg) was reverse transcribed in the presence of aminoallyl-dUTP followed by coupling with Cy5 dye.

treatment_protocol: without methotrexate treatment


title: 1M-43_9a


title: 1M-43_14


title: 1M-43_8a


title: 1M-43_3


title: 1M-43_4a


title: 1M-42


title: 1M-43_1


title: 1M-57_2_expression

source_name: HCT116+chr3, clone 1M-57


title: 1M-57_3a_expression


title: 1M-43_2


title: 1M-89_6_expression


title: 1M-42_c10_expression


title: 1M-42_c10


title: 1M-42_4_expression


title: 1M-42_c7


title: 1M-42_2_expression


title: 1M-42_9_expression

source_name: HCT116+chr3, clone 1M-42


title: 1M-42_c6


title: 1M-34_c5a_expression

treatment_protocol: methotrexate resistant colony derived from clone 1M-34

tag: HCT116+chr3, clone 1M-34


title: 1M-42_17


title: 1M-42_1a_expression


title: 1M-43_12


title: 1M-42_13


title: 1M-42_15a


title: 1M-42_c4a


title: 1M-42_9


title: 1M-34_2a_expression


title: 1M-42_8a


title: 1M-34_4a_expression


title: 1M-34_c11


title: 1M-42_1a


title: 1M-42_3


title: 1M-42_2a

source_name: Genomic DNA (600 ng) was labeled by random priming to incorporate Cy3 dCTP in a 50 µl reaction.


title: 1M-42_4


title: 1M-42_1


title: 1M-39

tag: HCT116+chr3, clone 1M-39


title: 1M-34_c3


title: 1M-34_c8


title: 1M-34


title: 1M-34_c10a


title: 1M-34_3a


title: 1M-34_c5a


title: 1M-34_2a


title: 1M-34_5


title: 1M-34_c2


title: Tomato hp-2dg vs WT (fruit transcriptional comparizon) - XI

city: Rishon Le-Zion

first: Igor

middle: Michael

last: Kolotilin

address: Dereh Ha-Macabim

department: Plant sciences

country: Israel

institute: Volcani inst.

description:
RNA Source:
Representative plants of line n-935 and their normal counterparts were planted in a randomized-block design (3 blocks, 5 plants in each block) in an environmentally controlled greenhouse at the Volcani Center, Bet Dagan, Israel, during the winter seasons of 2004 and 2005 (minimal temperature kept at 15˚C with no supplemental light). At each of 3 developmental stages (mature green, breaker and pink-red) a single fruit was harvested from a randomly chosen plant of each genotype within each block. In each harvest different plants in each block were taken to represent each genotype. Following harvest, equal pericarp samples were cut from the equator region of each fruit. These samples were pooled according to genotype prior to RNA extraction, allowing equal representation of each block in the final sample. A total of 3 harvests taken from each genotype were eventually analyzed– each harvest representing a biological repeat.
RNA Samples:
Total RNA was isolated from ~1g of pericarp tissue of mature-green, breaker and early-red fruits harvested from hp-2dg mutant plants and their normal counterparts using Qiagen RNeasy Midi Kit (Qiagen Inc., Valencia, CA, USA). RNA isolation was according to the manufacturer's recommendations with the following modifications: (1) tissue was pulverized in RLT buffer containing β-mercaptoethanol, and (2) RNA samples were treated, on-column for 1 hour, with DNase I using Qiagen RNase-free DNase Set.
Each RNA sample was subjected to mRNA amplification procedure using MessageAmp aRNA kit (Ambion Inc., Austin, TX, USA). Three μg of total RNA were used in each amplification reaction.
Microarray Experiment Design:
Transcriptional profiling of tomato pericarp tissue of hp-2dg/hp-2dg plants was obtained using direct comparisons with their normal counterparts in each developmental stage separately. Two-color hybridizations were carried out to the TOM1 microarray slide (CGEP website at Cornell).

hyb_protocol: Each RNA sample was subjected to mRNA amplification procedure using MessageAmp aRNA kit (Ambion Inc., Austin, TX, USA). Three μg of total RNA were used in each amplification reaction. Three microgram of amplified mRNA products were subjected to reverse transcription and then labeled with Cy3 and Cy5 (Amersham Biosciences, Uppsala, Sweden) by the indirect amino-allyl method (Invitrogen, Carlsbad, CA, USA). Hybridization of labeled targets to the tomato microarray slide TOM1 was carried out at 42°C for 14 to 16 h using a covered hybridization oven (Amersham Pharmacia, Buckinghamshire, England). Microarray slides were washed seven times for 10 min each: at room temperature in 2XSSC/0.1% SDS- twice, room temperature in 0.2XSSC/0.1% SDS- twice, room temperature with 0.2XSSC- twice, and once in 0.2XSSC at 42°C. Excess fluids were drained from the arrays by centrifugation (5 min at 450g).

scan_protocol: For each developmental stage (mature green, breaker and early-red), 4 hybridizations were carried out, representing 3 independent biological repeats and one technical repeat of swapped dyes. Separate images for each fluorescence dye were acquired using ScanArray 4000 genetic analyzer [GSI Lumonics (Packard / Perkin Elmer), Ramsey MN, USA[. The analyzer scan was carried out at 10 μm resolution per pixel, adjusting the photomultiplier and laser power to achieve an optimal distribution of signals with minimal saturation. Quantification was carried out using QuantArray version 3 software, applying histogram method (Billerica, Packard BioScience, MA, USA). Data analysis was performed using Genespring® 7.2 software (Silicon Genetics, Redwood City, CA, USA), applying per-spot and per-chip normalizations: For each hybridization Lowess curve was fit to the log-intensity versus log-ratio plot. 40% of the data was used to calculate the Lowess fit at each point. This curve was used to adjust the value of the normal genotype for each measurement (control channel). If the control channel was lower than 10 then 10 was used instead. Low-quality data were identified and discarded when their signal to noise ratio was <2.

data_processing: GeneSpring (GeneSpring 7.2; Silicon Genetics, Redwood City, CA) was used for Lowess normalization, where 40% of the data served for smoothing. Channel1 (control channel) values lower than 10 were set to 10. Channel2 was divided by Channel1, and this ratio was Log2 transformed.

organism: Solanum lycopersicum

source_name: WT tomato fruit pericarp, red stage

tag: Line

value: Manapal (Wild Type)

tag: Tissue

value: Fruit pericarp

tag: Developmental stage

value: Red

source_name: hp-2dg tomato mutant fruit pericarp, red stage

value: Manapal (hp-2dg mutant)


title: Tomato hp-2dg vs WT (fruit transcriptional comparizon) - XII (dye swap)

label_protocol: Each RNA sample was subjected to mRNA amplification procedure using MessageAmp aRNA kit (Ambion Inc., Austin, TX, USA). Three μg of total RNA were used in each amplification reaction.

extract_protocol: Total RNA was isolated from ~1g of pericarp tissue of mature-green, breaker and early-red fruits harvested from hp-2dg mutant plants and their normal counterparts using Qiagen RNeasy Midi Kit (Qiagen Inc., Valencia, CA, USA). RNA isolation was according to the manufacturer's recommendations with the following modifications: (1) tissue was pulverized in RLT buffer containing β-mercaptoethanol, and (2) RNA samples were treated, on-column for 1 hour, with DNase I using Qiagen RNase-free DNase Set.


title: Tomato hp-2dg vs WT (fruit transcriptional comparizon) - IX


title: 1M-89_6_32K

description: Used Spot files " HA32K_A.clonepos.20050919.txt" & " HA32K_A.spotclone.20060222.txt" to analyse the raw images for the left subarray and " HA32K_B.clonepos.20050919.txt" & " HA32K_B.spotclone.20060222.txt" for the right subarray.

scan_protocol: We acquired 16-bit DAPI, Cy3 and Cy5 images for both subarrays (A an B) printed on one slide using a custom built CCD camera system (Hamilton et al. 2006. A large field CCD system for quantitative imaging of microarrays. Nuc. Acids Res. 34, e58).

data_processing: We carried out image and data analysis using UCSF SPOT (Jain AN et al. 2002. Fully automatic quantification of microarray image data. Genome Res. 12:325-332). Ratios for each spot were calculated as the total background-corrected fluorescence intensity ratios for the test and reference channels. In addition, array CGH data were corrected for BAC clone specific GC content and in some hybridizations a geometrical dependence of the ratios on the array. Justification of these procedures is presented in Tokuyasu et al. (in preparation). Data were normalized to set the median log2 ratio to zero.

label_protocol: Genomic DNA (800 ng) was labeled by random priming to incorporate Cy3 dCTP in a 50 µl reaction.

tag: HCT116+chr3, clone 1M-89

label_protocol: Genomic DNA (800 ng) was labeled by random priming to incorporate Cy5 dCTP in a 50 µl reaction.

tag: gender

value: male

tag: tissue type


title: Tomato hp-2dg vs WT (fruit transcriptional comparizon) - X


title: 1M-42_9_32K

tag: HCT116+chr3, clone 1M-42


title: 1M-42_c10_32K


title: Tomato hp-2dg vs WT (fruit transcriptional comparizon) - VI

source_name: WT tomato fruit pericarp, breaker stage

value: Breaker

source_name: hp-2dg tomato mutant fruit pericarp, breaker stage


title: Tomato hp-2dg vs WT (fruit transcriptional comparizon) - II

source_name: WT tomato fruit pericarp, mature green stage

value: Mature green

source_name: hp-2dg tomato mutant fruit pericarp, mature green stage


title: Tomato hp-2dg vs WT (fruit transcriptional comparizon) - VII


title: Tomato hp-2dg vs WT (fruit transcriptional comparizon) - I


title: 1M-42_15_32K


title: Tomato hp-2dg vs WT (fruit transcriptional comparizon) - III


title: Tomato hp-2dg vs WT (fruit transcriptional comparizon) - VIII (dye swap)


title: Tomato hp-2dg vs WT (fruit transcriptional comparizon) - V


title: 1M-34_4a


title: 1M-42_13_32K


title: Tomato hp-2dg vs WT (fruit transcriptional comparizon) - IV(dye swap)


title: 1M-42_2a_32K


title: SD, control, rat 14

status: Public on Oct 05 2007

city: Maastricht

first: Arie

last: van Erk

address: PO Box 616

department: BiGCaT Bioinformatics

country: Netherlands

institute: University Maastricht

hyb_protocol: see exp file

scan_protocol: see exp file

source_name: heart muscle

label_protocol: affymetrix 2-cycle cDNA synthesis kit

growth_protocol: animals were kept on a standard diet

extract_protocol: Picopure RNA isolation kit

tag: strain

value: TGR(mRen-2)27 (Ren-2) on Sprague Dawley background; gender:male; age:10 weeks; tissue:biopsy from cardiac left ventricle


title: SD, control, rat 12


title: SD, control, rat 11


title: Ren2, failure, rat 9


title: Ren2, compensated, rat 4


title: Ren2, failure, rat 10


title: Ren2, compensated, rat 2


title: SD, control, rat 13


title: Ren2, compensated, rat 6


title: Ren2, failure, rat 8


title: Ren2, failure, rat 7


title: Ren2, compensated, rat 3


title: Ren2, compensated, rat 5


title: Ren2, compensated, rat 1


title: HP1_SG_C_71667

status: Public on Oct 03 2007

city: Umea

first: Jan

last: Larsson

address: Umea University

department: Molecular Biology

country: Sweden

institute: Umea University

description: Biological replicate 3 of 3

hyb_protocol: NimbleGen standard protocol (http://www.nimblegen.com/products/lit/lit.html).

data_processing: Ratio of Total DNA and ChIP DNA

organism: Drosophila melanogaster

growth_protocol: For ChIP experiments we used Schneider´s Drosophila line 2 cells (ATCC CRL-1963) grown at 25°C in Erlenmeyer-flasks to a density of 0.5-1.5x107 cells/ml in Drosophila SFM medium (Invitrogen) supplemented with 100U/ml of Penicillin G, 100 μg/ml of Streptomycin sulfate and 2 mM of L-glutamine.

extract_protocol: The cells were cross-linked, washed and sonicated as described by (Schwartz, Y.B., Kahn, T.G., Nix, D.A., Li, X.Y., Bourgon, R., Biggin, M. and Pirrotta, V.  2006. Genome-wide analysis of Polycomb targets in Drosophila melanogaster. Nat. Genet. 38: 700-705). For salivary glands we used 250 pairs of salivary glands for each biological replicate. The glands were dissected in PBS and transferred to a 1-2 minute fixation in 2% formaldehyde in (PBS, 0.1% Triton X-100). The glands were then washed in PBS and glycine was added to a final concentration of 0.125 M. The glands were then washed one time in PBS, 1 mM PMSF, protease inhibitor cocktail (Roche) followed by 2 washes in TBS, 1mM PMSF, protease inhibitor cocktail. The samples were homogenized in 500 µl lysis buffer (1% SDS, 10 mM EDTA, 50 mM TRIS-HCl pH 8.1). Approximately 120 µl glass beads were added prior to sonication. The samples were cleared by centrifugation 10 min at 16000 g. For chromatin immunoprecipitation 150 μl of cell lysate was diluted ten-fold in ChIP Dilution buffer (0.01% SDS, 1.1% Triton X-100, 1.2 mM EDTA, 16.7 mM Tris-HCl pH 8.0, 167 mM NaCl), and protein inhibitors were added. The diluted lysate was precleared by incubation with 30 µl (60 µl for salivary glands) of Dynabeads conjugated to Protein A (Dynal), pre-blocked by equilibration in 150 µl ChIP buffer containing 12 µg (24 µg for salivary glands) sonicated herring sperm DNA. The cleared lysates were then incubated with 3 µl anti-POF (rabbit, 4 µl for salivary glands), 3 µl anti-HP1 (291C, Covance, 4 µl for salivary glands) or 4 µl H3K9ac (07-352, Upstate) antibodies overnight at 4C. The antibody complexes were precipitated by incubation with DNA-blocked Protein A Dynabeads for 1 hour at 4C. The beads were washed once with low salt buffer (0.1% SDS, 1% Triton X-100, 2 mM Tris-HCl pH 8.0, 150 mM NaCl), once with high salt buffer (0.1% SDS, 1% Triton X-100, 2 mM Tris-HCl pH 8.0, 500 mM NaCl), once with LiCl-containing buffer (250 mM LiCl, 10 mM Tris-HCl pH 8.0, 1 mM EDTA, 1% NP-40, 1% sodium deoxycholate) and twice with TE Buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA). The protein/DNA complexes were eluted from the antibodies by incubating 2 × 15 minutes at room temperature in 250 µl Elution buffer (1% SDS, 0.1 M NaHCO3) with rotation. NaCl was added to a final concentration of 200 mM and protein/DNA crosslinks were reversed by heating at 65C for 4 hours. 10 µl of 0.5 M EDTA, 20 µl of 1M Tris-HCl pH 6.5 and 1 µl of 20 mg/ml proteinase K were added before an additional incubation at 45C for 1 hour. The DNA was recovered by phenol/chloroform extraction followed by ethanol precipitation. The immunoprecipitated DNA was then dissolved in 20 µl water. The immunoprecipitated DNA and corresponding amounts of input DNA were amplified using ligation mediated PCR. Linkers used and ligation was performed as described by (Strutt, H., Cavalli, G. and Paro, R.  1997. Co-localization of Polycomb protein and GAGA factor on regulatory elements responsible for the maintenance of homeotic gene expression. EMBO J. 16: 3621-3632.). The amplification was done in principal according to (Ren, B. and Dynlacht, B.D.  2004. Use of chromatin immunoprecipitation assays in genome-wide location analysis of mammalian transcription factors. Methods Enzymol. 376: 304-315.) except that we ligated and amplified all immunoprecipitated DNA from each sample and used the Advantage cDNA PCR kit (BD Biosciences) for amplification. The DNA was purified using illustra DNA and Gel band purification kit (GE Healthcare) prior to labeling. To verify that no amplification bias will affect the enrichment profiles we analyzed the ChIP DNA/input DNA ratio prior and after the ligation mediated PCR using real time PCR as described previously (Johansson, A.M., Stenberg, P., Bernhardsson, C. and Larsson, J.  2007. Painting of fourth and chromosome-wide regulation of the 4th chromosome in Drosophila melanogaster. EMBO J. 26: 2307-2316).

tag: Salivary gland, Wild type, mixed sex


title: H3K9ac_S2_C_75533

description: Biological replicate 3 of 3

scan_protocol: NimbleGen standard protocol (http://www.nimblegen.com/products/lit/lit.html).

tag: Schneider 2 embryonic cell-line, Wild type, male


title: POF_SG_C_71666

description: Biological replicate 3 of 3

label_protocol: NimbleGen standard protocol (http://www.nimblegen.com/products/lit/lit.html).


title: HP1_SG_A_71669

description: Biological replicate 1 of 3


title: H3K9ac_S2_A_76741

description: Biological replicate 1 of 3


title: HP1_SG_B_78852

description: Biological replicate 2 of 3


title: POF_SG_A_71668

description: Biological replicate 1 of 3


title: PL27_1 DNA

city: Stanford

first: Jonathan

last: Pollack

address: 269 Campus Drive, CCSR3245A

department: Pathology

institute: Stanford University

description:
Simple annotation: Prostate, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2004-07/53424.gif

hyb_protocol: not provided

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1120, 5480; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Jacques,,Lapointe Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 39.71; Parameter Scan Time = 11:29:46; Parameter PMT Volts = 650; Parameter Scan Date = 2004-06-30; Parameter Pixel Size = 10; Parameter Laser on time = 172596; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.40; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Jacques,,Lapointe Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 39.71; Parameter Scan Time = 11:29:46; Parameter PMT Volts = 750; Parameter Scan Date = 2004-06-30; Parameter Pixel Size = 10; Parameter Laser on time = 537400; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 2.03; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Jacques,,Lapointe

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: Normal male genomic DNA

label_protocol: not provided

extract_protocol: not provided

tag: Normal male genomic DNA

tag: LabeledExtract

source_name: PL27_1 DNA

tag: Prostate genomic DNA; PL27_1 DNA

tag: Prostate genomic DNA; LabeledExtract


title: PL122_1 DNA

description:
Simple annotation: Prostate, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2004-07/53571.gif

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1120, 5480; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Jacques,,Lapointe Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.99; Parameter Scan Time = 10:30:49; Parameter PMT Volts = 650; Parameter Scan Date = 2004-07-06; Parameter Pixel Size = 10; Parameter Laser on time = 173117; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.41; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Jacques,,Lapointe Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.99; Parameter Scan Time = 10:30:49; Parameter PMT Volts = 660; Parameter Scan Date = 2004-07-06; Parameter Pixel Size = 10; Parameter Laser on time = 537921; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.94; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Jacques,,Lapointe

source_name: PL122_1 DNA

tag: Prostate genomic DNA; PL122_1 DNA


title: PL129_1  DNA

description:
Simple annotation: Prostate, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2004-07/53572.gif

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1120, 5560; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Jacques,,Lapointe Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 39.47; Parameter Scan Time = 11:28:14; Parameter PMT Volts = 650; Parameter Scan Date = 2004-07-06; Parameter Pixel Size = 10; Parameter Laser on time = 173176; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.41; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Jacques,,Lapointe Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 39.47; Parameter Scan Time = 11:28:14; Parameter PMT Volts = 680; Parameter Scan Date = 2004-07-06; Parameter Pixel Size = 10; Parameter Laser on time = 537979; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.97; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Jacques,,Lapointe

source_name: PL129_1  DNA

tag: Prostate genomic DNA; PL129_1  DNA


title: PL194_3 DNA

description:
Simple annotation: Prostate, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2004-07/53573.gif

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1120, 5720; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Jacques,,Lapointe Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 39.31; Parameter Scan Time = 11:08:56; Parameter PMT Volts = 650; Parameter Scan Date = 2004-07-06; Parameter Pixel Size = 10; Parameter Laser on time = 173155; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.41; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Jacques,,Lapointe Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 39.31; Parameter Scan Time = 11:08:56; Parameter PMT Volts = 710; Parameter Scan Date = 2004-07-06; Parameter Pixel Size = 10; Parameter Laser on time = 537959; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.93; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Jacques,,Lapointe

source_name: PL194_3 DNA

tag: Prostate genomic DNA; PL194_3 DNA


title: H3K9ac_S2_B_76743

description: Biological replicate 2 of 3


title: POF_SG_B_71672

description: Biological replicate 2 of 3


title: HP1_S2_C_68286

description: Biological replicate 3 of 3


title: PL118_3.2 DNA

description:
Simple annotation: Prostate, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2004-07/53570.gif

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1360, 5480; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Jacques,,Lapointe Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.67; Parameter Scan Time = 10:07:36; Parameter PMT Volts = 650; Parameter Scan Date = 2004-07-06; Parameter Pixel Size = 10; Parameter Laser on time = 173094; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.42; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Jacques,,Lapointe Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.67; Parameter Scan Time = 10:07:36; Parameter PMT Volts = 670; Parameter Scan Date = 2004-07-06; Parameter Pixel Size = 10; Parameter Laser on time = 537898; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.89; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Jacques,,Lapointe

tag: Prostate genomic DNA; PL118_3.2 DNA


title: PL115_2 DNA

description:
Simple annotation: Prostate, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2004-02/49669.gif

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1080, 5200; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Jacques,,Lapointe Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.79; Parameter Scan Time = 10:53:30; Parameter PMT Volts = 650; Parameter Scan Date = 2004-02-03; Parameter Pixel Size = 10; Parameter Laser on time = 148345; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.41; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Jacques,,Lapointe Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.79; Parameter Scan Time = 10:53:30; Parameter PMT Volts = 670; Parameter Scan Date = 2004-02-03; Parameter Pixel Size = 10; Parameter Laser on time = 513249; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 2.11; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Jacques,,Lapointe

source_name: PL115_2 DNA

tag: Prostate genomic DNA; PL115_2 DNA


title: PT176_2 DNA

description:
Simple annotation: Prostate, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2003-12/47166.gif

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1120, 5530; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Jacques,,Lapointe Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.67; Parameter Scan Time = 11:14:38; Parameter PMT Volts = 650; Parameter Scan Date = 2003-11-09; Parameter Pixel Size = 10; Parameter Laser on time = 135314; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.49; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Jacques,,Lapointe Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.67; Parameter Scan Time = 11:14:38; Parameter PMT Volts = 680; Parameter Scan Date = 2003-11-09; Parameter Pixel Size = 10; Parameter Laser on time = 500379; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 2.00; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Jacques,,Lapointe

source_name: PL176_2 DNA

tag: Prostate genomic DNA; PL176_2 DNA


title: PT28_6 DNA

description:
Simple annotation: Prostate, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2004-06/52836.gif

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1280, 5720; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Jacques,,Lapointe Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 39.21; Parameter Scan Time = 10:41:37; Parameter PMT Volts = 650; Parameter Scan Date = 2004-06-03; Parameter Pixel Size = 10; Parameter Laser on time = 167923; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.40; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Jacques,,Lapointe Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 39.21; Parameter Scan Time = 10:41:37; Parameter PMT Volts = 690; Parameter Scan Date = 2004-06-03; Parameter Pixel Size = 10; Parameter Laser on time = 532826; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 2.01; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Jacques,,Lapointe

source_name: PT28_6 DNA

tag: Prostate genomic DNA; PT28_6 DNA


title: HP1_S2_A_67732

description: Biological replicate 1 of 3


title: HP1_S2_B_74589

description: Biological replicate 2 of 3


title: PT235_5 DNA

description:
Simple annotation: Prostate, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2004-06/52835.gif

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1280, 5720; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Jacques,,Lapointe Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 39.11; Parameter Scan Time = 10:27:27; Parameter PMT Volts = 650; Parameter Scan Date = 2004-06-03; Parameter Pixel Size = 10; Parameter Laser on time = 167909; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.46; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Jacques,,Lapointe Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 39.11; Parameter Scan Time = 10:27:27; Parameter PMT Volts = 670; Parameter Scan Date = 2004-06-03; Parameter Pixel Size = 10; Parameter Laser on time = 532813; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 2.00; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Jacques,,Lapointe

source_name: PT235_5 DNA

tag: Prostate genomic DNA; PT235_5 DNA


title: PT180_2 DNA

description:
Simple annotation: Prostate, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2003-12/47168.gif

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1120, 5530; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Jacques,,Lapointe Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 39.34; Parameter Scan Time = 12:14:36; Parameter PMT Volts = 650; Parameter Scan Date = 2003-11-09; Parameter Pixel Size = 10; Parameter Laser on time = 135373; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.38; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Jacques,,Lapointe Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 39.34; Parameter Scan Time = 12:14:36; Parameter PMT Volts = 690; Parameter Scan Date = 2003-11-09; Parameter Pixel Size = 10; Parameter Laser on time = 500438; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 2.05; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Jacques,,Lapointe

source_name: PT180_2 DNA

tag: Prostate genomic DNA; PT180_2 DNA


title: PT174_2 DNA

description:
Simple annotation: Prostate, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2003-12/47165.gif

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1120, 5530; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Jacques,,Lapointe Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.46; Parameter Scan Time = 11:00:45; Parameter PMT Volts = 650; Parameter Scan Date = 2003-11-09; Parameter Pixel Size = 10; Parameter Laser on time = 135299; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.48; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Jacques,,Lapointe Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.46; Parameter Scan Time = 11:00:45; Parameter PMT Volts = 670; Parameter Scan Date = 2003-11-09; Parameter Pixel Size = 10; Parameter Laser on time = 500364; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.99; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Jacques,,Lapointe

source_name: PT174_2 DNA

tag: Prostate genomic DNA; PT174_2 DNA


title: PT173_2 DNA

description:
Simple annotation: Prostate, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2003-11/47161.gif

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 880, 5080; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Jacques,,Lapointe Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 39.37; Parameter Scan Time = 12:59:49; Parameter PMT Volts = 650; Parameter Scan Date = 2003-11-05; Parameter Pixel Size = 10; Parameter Laser on time = 134350; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.39; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Jacques,,Lapointe Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 39.37; Parameter Scan Time = 12:59:49; Parameter PMT Volts = 640; Parameter Scan Date = 2003-11-05; Parameter Pixel Size = 10; Parameter Laser on time = 499415; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 2.26; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Jacques,,Lapointe

source_name: PT173_2 DNA

tag: Prostate genomic DNA; PT173_2 DNA


title: PT21_6 DNA

description:
Simple annotation: Prostate, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2004-07/53421.gif

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1120, 5480; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Jacques,,Lapointe Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 39.55; Parameter Scan Time = 11:10:55; Parameter PMT Volts = 650; Parameter Scan Date = 2004-06-30; Parameter Pixel Size = 10; Parameter Laser on time = 172577; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.40; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Jacques,,Lapointe Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 39.55; Parameter Scan Time = 11:10:55; Parameter PMT Volts = 750; Parameter Scan Date = 2004-06-30; Parameter Pixel Size = 10; Parameter Laser on time = 537381; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 2.02; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Jacques,,Lapointe

source_name: PT21_6 DNA

tag: Prostate genomic DNA; PT21_6 DNA


title: PT126_1 DNA

description:
Simple annotation: Prostate, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2004-06/52834.gif

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1280, 5720; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Jacques,,Lapointe Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 39.49; Parameter Scan Time = 11:12:30; Parameter PMT Volts = 650; Parameter Scan Date = 2004-06-03; Parameter Pixel Size = 10; Parameter Laser on time = 167954; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.39; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Jacques,,Lapointe Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 39.49; Parameter Scan Time = 11:12:30; Parameter PMT Volts = 750; Parameter Scan Date = 2004-06-03; Parameter Pixel Size = 10; Parameter Laser on time = 532857; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 2.08; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Jacques,,Lapointe

source_name: PT126_1 DNA

tag: Prostate genomic DNA; PT126_1 DNA


title: PL114_4 DNA

description:
Simple annotation: Prostate, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2004-02/49668.gif

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1080, 5200; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Jacques,,Lapointe Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.62; Parameter Scan Time = 10:39:04; Parameter PMT Volts = 650; Parameter Scan Date = 2004-02-03; Parameter Pixel Size = 10; Parameter Laser on time = 148331; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.41; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Jacques,,Lapointe Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.62; Parameter Scan Time = 10:39:04; Parameter PMT Volts = 670; Parameter Scan Date = 2004-02-03; Parameter Pixel Size = 10; Parameter Laser on time = 513234; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 2.11; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Jacques,,Lapointe

tag: Normal male genomic DNA

source_name: PL114_4 DNA

tag: Prostate genomic DNA; PL114_4 DNA


title: POF_S2_C_77418

description: Biological replicate 3 of 3

tag: Schneider 2 embryonic cell-line, Wild type, male


title: PT195_3 DNA

description:
Simple annotation: Prostate, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2004-06/52833.gif

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1280, 5960; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Jacques,,Lapointe Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.92; Parameter Scan Time = 12:18:38; Parameter PMT Volts = 650; Parameter Scan Date = 2004-05-28; Parameter Pixel Size = 10; Parameter Laser on time = 167505; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.41; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Jacques,,Lapointe Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.92; Parameter Scan Time = 12:18:38; Parameter PMT Volts = 650; Parameter Scan Date = 2004-05-28; Parameter Pixel Size = 10; Parameter Laser on time = 532408; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.96; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Jacques,,Lapointe

tag: LabeledExtract

source_name: PT195_3 DNA

tag: Prostate genomic DNA; PT195_3 DNA

tag: Prostate genomic DNA; LabeledExtract


title: PT171_2 DNA

description:
Simple annotation: Prostate, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2003-11/47160.gif

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 880, 5080; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Jacques,,Lapointe Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 39.28; Parameter Scan Time = 12:46:30; Parameter PMT Volts = 650; Parameter Scan Date = 2003-11-05; Parameter Pixel Size = 10; Parameter Laser on time = 134337; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.39; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Jacques,,Lapointe Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 39.28; Parameter Scan Time = 12:46:30; Parameter PMT Volts = 640; Parameter Scan Date = 2003-11-05; Parameter Pixel Size = 10; Parameter Laser on time = 499402; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 2.24; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Jacques,,Lapointe

source_name: PT171_2 DNA

tag: Prostate genomic DNA; PT171_2 DNA


title: POF_S2_A_67731

description: Biological replicate 1 of 3

scan_protocol: NimbleGen standard protocol (http://www.nimblegen.com/products/lit/lit.html).


title: PT318_2 DNA

description:
Simple annotation: Prostate, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2004-02/49665.gif

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1080, 5200; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Jacques,,Lapointe Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.15; Parameter Scan Time = 09:59:07; Parameter PMT Volts = 650; Parameter Scan Date = 2004-02-03; Parameter Pixel Size = 10; Parameter Laser on time = 148292; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.40; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Jacques,,Lapointe Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.15; Parameter Scan Time = 09:59:07; Parameter PMT Volts = 670; Parameter Scan Date = 2004-02-03; Parameter Pixel Size = 10; Parameter Laser on time = 513195; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 2.04; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Jacques,,Lapointe

source_name: Normal male genomic DNA

source_name: PT318_2 DNA

tag: Prostate genomic DNA; PT318_2 DNA


title: PT96_1 DNA

description:
Simple annotation: Prostate, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2004-02/49666.gif

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1080, 5200; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Jacques,,Lapointe Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.35; Parameter Scan Time = 10:12:44; Parameter PMT Volts = 650; Parameter Scan Date = 2004-02-03; Parameter Pixel Size = 10; Parameter Laser on time = 148305; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.41; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Jacques,,Lapointe Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.35; Parameter Scan Time = 10:12:44; Parameter PMT Volts = 670; Parameter Scan Date = 2004-02-03; Parameter Pixel Size = 10; Parameter Laser on time = 513208; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 2.04; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Jacques,,Lapointe

source_name: PT96_1 DNA

tag: Prostate genomic DNA; PT96_1 DNA


title: PT102_2 DNA

description:
Simple annotation: Prostate, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2004-02/49667.gif

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1080, 5200; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Jacques,,Lapointe Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.50; Parameter Scan Time = 10:26:16; Parameter PMT Volts = 650; Parameter Scan Date = 2004-02-03; Parameter Pixel Size = 10; Parameter Laser on time = 148319; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.41; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Jacques,,Lapointe Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.50; Parameter Scan Time = 10:26:16; Parameter PMT Volts = 670; Parameter Scan Date = 2004-02-03; Parameter Pixel Size = 10; Parameter Laser on time = 513222; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 2.07; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Jacques,,Lapointe

source_name: PT102_2 DNA

tag: Prostate genomic DNA; PT102_2 DNA


title: POF_S2_B_68300

description: Biological replicate 2 of 3


title: PT190_5 DNA

description:
Simple annotation: Prostate, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2004-06/52831.gif

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1280, 5480; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Jacques,,Lapointe Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.77; Parameter Scan Time = 10:20:49; Parameter PMT Volts = 650; Parameter Scan Date = 2004-05-28; Parameter Pixel Size = 10; Parameter Laser on time = 167388; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.42; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Jacques,,Lapointe Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.77; Parameter Scan Time = 10:20:49; Parameter PMT Volts = 630; Parameter Scan Date = 2004-05-28; Parameter Pixel Size = 10; Parameter Laser on time = 532291; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.98; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Jacques,,Lapointe

source_name: PT190_5 DNA

tag: Prostate genomic DNA; PT190_5 DNA


title: PT191_1 DNA

description:
Simple annotation: Prostate, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2004-06/52832.gif

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1280, 5480; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Jacques,,Lapointe Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.82; Parameter Scan Time = 10:33:40; Parameter PMT Volts = 650; Parameter Scan Date = 2004-05-28; Parameter Pixel Size = 10; Parameter Laser on time = 167400; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.42; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Jacques,,Lapointe Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.82; Parameter Scan Time = 10:33:40; Parameter PMT Volts = 650; Parameter Scan Date = 2004-05-28; Parameter Pixel Size = 10; Parameter Laser on time = 532303; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.98; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Jacques,,Lapointe

source_name: PT191_1 DNA

tag: Prostate genomic DNA; PT191_1 DNA


title: PT138_1 DNA

description:
Simple annotation: Prostate, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2003-11/47159.gif

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 880, 5080; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Jacques,,Lapointe Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 39.25; Parameter Scan Time = 12:33:14; Parameter PMT Volts = 650; Parameter Scan Date = 2003-11-05; Parameter Pixel Size = 10; Parameter Laser on time = 134323; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.39; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Jacques,,Lapointe Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 39.25; Parameter Scan Time = 12:33:14; Parameter PMT Volts = 650; Parameter Scan Date = 2003-11-05; Parameter Pixel Size = 10; Parameter Laser on time = 499388; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 2.22; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Jacques,,Lapointe

source_name: PT138_1 DNA

tag: Prostate genomic DNA; PT138_1 DNA


title: PT130_1 DNA

description:
Simple annotation: Prostate, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2003-11/47156.gif

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 880, 5080; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Jacques,,Lapointe Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.74; Parameter Scan Time = 11:40:36; Parameter PMT Volts = 650; Parameter Scan Date = 2003-11-05; Parameter Pixel Size = 10; Parameter Laser on time = 134271; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.39; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Jacques,,Lapointe Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.74; Parameter Scan Time = 11:40:36; Parameter PMT Volts = 640; Parameter Scan Date = 2003-11-05; Parameter Pixel Size = 10; Parameter Laser on time = 499336; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 2.13; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Jacques,,Lapointe

source_name: PT130_1 DNA

tag: Prostate genomic DNA; PT130_1 DNA


title: PL133_1 DNA

description:
Simple annotation: Prostate, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2003-11/47158.gif

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 880, 5080; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Jacques,,Lapointe Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 39.07; Parameter Scan Time = 12:08:24; Parameter PMT Volts = 650; Parameter Scan Date = 2003-11-05; Parameter Pixel Size = 10; Parameter Laser on time = 134299; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.39; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Jacques,,Lapointe Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 39.07; Parameter Scan Time = 12:08:24; Parameter PMT Volts = 640; Parameter Scan Date = 2003-11-05; Parameter Pixel Size = 10; Parameter Laser on time = 499364; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 2.22; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Jacques,,Lapointe

source_name: PL133_1 DNA

tag: Prostate genomic DNA; PL133_1 DNA