title: Testicle tissue, Porcine, L_004442

source_name: Testicle tissue, Porcine, High androstenone, biomat-id 2081

value: Landrace, Gender:Male, Tissue:Testicle, High androstenone, biomat-id 2081

source_name: Testicle tissue, Porcine, Low androstenone, biomat-id 6303

value: Landrace, Gender:Male, Tissue:Testicle, Low androstenone, biomat-id 6303


title: Testicle tissue, Porcine, L_004367

status: Public on Nov 26 2007

type: RNA

city: Tjele

first: Jakob

last: Hedegaard

address: PO-box 50

department: Department of Genetics and Biotechnology

country: Denmark

institute: Aarhus University, Faculty of Agricultural Sciences

description: High and low androstenone testicle tissue samples were prepared from Landrace boars slaughtered at approximately 100kg

hyb_protocol: Two labeled RNA extract batches, corresponding to two independent RNA extractions, were hybridized to cDNA microarrays on a Discovery XT hybridization station from Ventana. The slides were hybridized in a Discovery XT hybridization station (Ventana Discovery Systems, Tucson, AZ, USA). Transfer Chip Prep-2 from 4 ºC to room temperature 1 hour before use. Prepare ChipSpread by mixing equal volumes of ChipSpread A (20 mg/mL BSA, 4x SSC, 0.5 mg/mL sodium azide) and B (formamide; 2 mg/mL SDS) and incubate at room temperature for 1 hour before use. A total of 2.5 mL is needed per slide. Print labels, trim them and place them on the slides. Mix the Chip Map reagents (Chip Prep-1, -2 and - 3) by inversion, remove the cap and place the reagents in the Discovery. Place the slides in the machine and initiate the run. Cover slide with 2.5 mL ChipSpread when the message appears (after few minutes). The machine now runs for app. 1.5 hours to pre-hybridize the slides. Heat a waterbath to 90°C or use a PCR machine. Mix the Chiphybe80, add 200 µL to the sample (<20 µL) and mix carefully. Heat the sample mixture at 90°C for 3 minutes and mix carefully by pipetting. Press ""button"" on the machine which then prepares the slides for hybridization. When the message appears apply the samples onto the slides and press ""button"" and the machine hybridizes at 48 ºC for 6 hours. Wipe oil from backside of slides using a clean-room napkin and place slides in the slide-holder from the High Throughput Wash Station (Telechem, cat.no. HTW) placed in a mTub filled with RiboWash. If processing more than 20 slides, place equal number of slides in two slide-holders and continue in parallel. Transfer the slide-holder to a HTW filled with RiboWash and wash for 2 min with magnetic stirring at 700 rpm. Refill the HTW with RiboWash and repeat the wash. Dip the slide-holder in 2x SSC filled in a mTub (200 mL 20x SSC, Elga H2O + 1800 mL water). Transfer the slide-holder to a HTW filled with 2x SSC and wash for 2 min with magnetic stirring at 700 rpm. Refill the HTW with 2x SSC and repeat the wash. Dip the slide-holder 10 times in 0.1x SSC filled in a mTub (5 mL 20x SSC, Elga H2O + 995 mL water) and leave the holder submerged in 0.1x SSC. Transfer the slides to a mBox slide holder placed in a mTub filled with Elga H2O. Dry arrays by centrifugation (at 300 x g for 4 min placed in a mBox)

scan_protocol: Scanner: ScanArray Express HT system (Perkin Elmer), 5 µm resolution, 100 % laser power and PMT adjusted individually for each channel. Image analysis software: ScanArray Express (version 3.0, Perkin Elmer) using the histogram method with default settings.

data_processing: The edwards method of the limma Bioconductor package was used for background correction, and the printtip loess method was used for normalizing the expression log-ratios. The empirical Bayes statistics of limma was used to assess differential expression.

molecule: total RNA

organism: Sus scrofa

source_name: Testicle tissue, Porcine, High androstenone, biomat-id 18572

label_protocol: 20 µg total RNA was labelled by using the Superscript Indirect cDNA Labeling System (Invitrogen) in combination with ARES cDNA labeling kits (Molecular Probes/Invitrogen) following the enclosed protocols. Spike-in RNA from the Lucidea Universal ScoreCard (Amersham Biosciences) was added to the cDNA reactions. ""Green"" spike-in RNA was added to the samples labeled with Alexa-594 and ""red"" spike-in RNA was added to the samples labeled with Alexa-488.

extract_protocol: Total-RNA extractions with DNase treatment using RNeasy Midi Kit from Qiagen

tag: Breed

value: Landrace, Gender:Male, Tissue:Testicle, High androstenone, biomat-id 18572

source_name: Testicle tissue, Porcine, Low androstenone, biomat-id 11499

value: Landrace, Gender:Male, Tissue:Testicle, Low androstenone, biomat-id 11499


title: Testicle tissue, Porcine, D_004121

description: High and low androstenone testicle tissue samples were prepared from Duroc boars slaughtered at approximately 100kg

source_name: Testicle tissue, Porcine, High androstenone, biomat-id 2635

value: Duroc, Gender:Male, Tissue:Testicle, High androstenone, biomat-id 2635

source_name: Testicle tissue, Porcine, Low androstenone, biomat-id 3057

value: Duroc, Gender:Male, Tissue:Testicle, Low androstenone, biomat-id 3057


title: Testicle tissue, Porcine, D_004169

source_name: Testicle tissue, Porcine, High androstenone, biomat-id 19418

value: Duroc, Gender:Male, Tissue:Testicle, High androstenone, biomat-id 19418

source_name: Testicle tissue, Porcine, Low androstenone, biomat-id 22960

value: Duroc, Gender:Male, Tissue:Testicle, Low androstenone, biomat-id 22960


title: Testicle tissue, Porcine, D_004244

source_name: Testicle tissue, Porcine, Low androstenone, biomat-id 3063

value: Duroc, Gender:Male, Tissue:Testicle, Low androstenone, biomat-id 3063

source_name: Testicle tissue, Porcine, High androstenone, biomat-id 1213

value: Duroc, Gender:Male, Tissue:Testicle, High androstenone, biomat-id 1213


title: Testicle tissue, Porcine, L_004619

source_name: Testicle tissue, Porcine, Low androstenone, biomat-id 8330

value: Landrace, Gender:Male, Tissue:Testicle, Low androstenone, biomat-id 8330

source_name: Testicle tissue, Porcine, High androstenone, biomat-id 5439

value: Landrace, Gender:Male, Tissue:Testicle, High androstenone, biomat-id 5439


title: Testicle tissue, Porcine, L_004473

source_name: Testicle tissue, Porcine, High androstenone, biomat-id 20877

value: Landrace, Gender:Male, Tissue:Testicle, High androstenone, biomat-id 20877

source_name: Testicle tissue, Porcine, Low androstenone, biomat-id 509

value: Landrace, Gender:Male, Tissue:Testicle, Low androstenone, biomat-id 509


title: Testicle tissue, Porcine, D_004350

source_name: Testicle tissue, Porcine, Low androstenone, biomat-id 7911

value: Duroc, Gender:Male, Tissue:Testicle, Low androstenone, biomat-id 7911

source_name: Testicle tissue, Porcine, High androstenone, biomat-id 3776

value: Duroc, Gender:Male, Tissue:Testicle, High androstenone, biomat-id 3776


title: Testicle tissue, Porcine, L_004398

source_name: Testicle tissue, Porcine, High androstenone, biomat-id 18955

value: Landrace, Gender:Male, Tissue:Testicle, High androstenone, biomat-id 18955

source_name: Testicle tissue, Porcine, Low androstenone, biomat-id 14983

value: Landrace, Gender:Male, Tissue:Testicle, Low androstenone, biomat-id 14983


title: Testicle tissue, Porcine, L_004527

source_name: Testicle tissue, Porcine, Low androstenone, biomat-id 8350

value: Landrace, Gender:Male, Tissue:Testicle, Low androstenone, biomat-id 8350

source_name: Testicle tissue, Porcine, High androstenone, biomat-id 9168

value: Landrace, Gender:Male, Tissue:Testicle, High androstenone, biomat-id 9168


title: Testicle tissue, Porcine, L_004404

source_name: Testicle tissue, Porcine, High androstenone, biomat-id 15513

value: Landrace, Gender:Male, Tissue:Testicle, High androstenone, biomat-id 15513

source_name: Testicle tissue, Porcine, Low androstenone, biomat-id 7121

value: Landrace, Gender:Male, Tissue:Testicle, Low androstenone, biomat-id 7121


title: Testicle tissue, Porcine, D_004152

source_name: Testicle tissue, Porcine, High androstenone, biomat-id 13140

value: Duroc, Gender:Male, Tissue:Testicle, High androstenone, biomat-id 13140

source_name: Testicle tissue, Porcine, Low androstenone, biomat-id 3061

value: Duroc, Gender:Male, Tissue:Testicle, Low androstenone, biomat-id 3061


title: Testicle tissue, Porcine, D_004275

source_name: Testicle tissue, Porcine, Low androstenone, biomat-id 2089

value: Duroc, Gender:Male, Tissue:Testicle, Low androstenone, biomat-id 2089

source_name: Testicle tissue, Porcine, High androstenone, biomat-id 6570

value: Duroc, Gender:Male, Tissue:Testicle, High androstenone, biomat-id 6570


title: Testicle tissue, Porcine, L_004602

source_name: Testicle tissue, Porcine, Low androstenone, biomat-id 7687

value: Landrace, Gender:Male, Tissue:Testicle, Low androstenone, biomat-id 7687

source_name: Testicle tissue, Porcine, High androstenone, biomat-id 11864

value: Landrace, Gender:Male, Tissue:Testicle, High androstenone, biomat-id 11864


title: Testicle tissue, Porcine, D_004077

source_name: Testicle tissue, Porcine, High androstenone, biomat-id 20354

value: Duroc, Gender:Male, Tissue:Testicle, High androstenone, biomat-id 20354

source_name: Testicle tissue, Porcine, Low androstenone, biomat-id 7700

value: Duroc, Gender:Male, Tissue:Testicle, Low androstenone, biomat-id 7700


title: Small intestine, RNA batch 2, Digestive tissue, Porcine, 5 Hampshire boars, Healthy, 5 months old

status: Public on Nov 21 2007

city: Aarhus

first: Henrik

last: Hornshøj

address: Brendstrupgårdsvej 100

department: Department of Molecular Medicine

institute: Aarhus University

description: The porcine tissue samples were prepared from five healthy Hampshire boars at age four to six months. All five boars were represented in each tissue sample in order to minimize any effect of genetic variation on the expression profiles.

hyb_protocol: Two labeled RNA extract batches, corresponding to two independent RNA extractions, were hybridized to cDNA microarrays in two rounds on a Discovery XT hybridization station from Ventana.

scan_protocol: Scanned and converted into TIFF images using Scanner and ScanArray Express from Perkin Elmer

data_processing: Spot identification and spot intensity quantification was done using GenePix Pro version 6.0. The print tip loess method of the limma Bioconductor package was used for normalizing the expression log-ratios.

source_name: Small intestine, Digestive tissue, Porcine, Healthy

label_protocol: 20 micrograms total RNA labeled with Alexa 594 usimicrograms total RNA SuperScript Indirect cDNA labelimicrograms total RNA System from Invitrmicrograms total RNAen

extract_protocol: Total-RNA extractions using RNeasy Maxi Kit from Qiagen

value: Hampshire, Gender:male, Age:5 months

source_name: Reference, Reference tissue, Porcine, Healthy

value: Hampshire, Gender:male, Age:5 months, Reference:pooled labeled RNA extracts from all tissue samples


title: Semitendinosus, RNA batch 2, Muscle tissue, Porcine, 5 Hampshire boars, Healthy, 5 months old

source_name: Semitendinosus, Muscle tissue, Porcine, Healthy


title: Biceps femoris, RNA batch 2, Muscle tissue, Porcine, 5 Hampshire boars, Healthy, 5 months old

source_name: Biceps femoris, Muscle tissue, Porcine, Healthy


title: Skin, RNA batch 1, Skin tissue, Porcine, 5 Hampshire boars, Healthy, 5 months old

source_name: Skin, Skin tissue, Porcine, Healthy


title: Stomach, RNA batch 1, Digestive tissue, Porcine, 5 Hampshire boars, Healthy, 5 months old

source_name: Stomach, Digestive tissue, Porcine, Healthy


title: Lung, RNA batch 2, Lung tissue, Porcine, 5 Hampshire boars, Healthy, 5 months old

source_name: Lung, Lung tissue, Porcine, Healthy


title: Kidney, RNA batch 2, Kidney tissue, Porcine, 5 Hampshire boars, Healthy, 5 months old

source_name: Kidney, Kidney tissue, Porcine, Healthy


title: Cerebellum, RNA batch 1, Brain tissue, Porcine, 5 Hampshire boars, Healthy, 5 months old

source_name: Cerebellum, Brain tissue, Porcine, Healthy


title: Supraspinatus, RNA batch 2, Muscle tissue, Porcine, 5 Hampshire boars, Healthy, 5 months old

source_name: Supraspinatus, Muscle tissue, Porcine, Healthy


title: Vastus intermedius, RNA batch 1, Muscle tissue, Porcine, 5 Hampshire boars, Healthy, 5 months old

source_name: Vastus intermedius, Muscle tissue, Porcine, Healthy


title: Vastus intermedius, RNA batch 2, Muscle tissue, Porcine, 5 Hampshire boars, Healthy, 5 months old


title: Fat, RNA batch 2, Fat tissue, Porcine, 5 Hampshire boars, Healthy, 5 months old

source_name: Fat, Fat tissue, Porcine, Healthy


title: Semimembranosus, RNA batch 1, Muscle tissue, Porcine, 5 Hampshire boars, Healthy, 5 months old

source_name: Semimembranosus, Muscle tissue, Porcine, Healthy


title: Spleen, RNA batch 1, Spleen tissue, Porcine, 5 Hampshire boars, Healthy, 5 months old

source_name: Spleen, Spleen tissue, Porcine, Healthy


title: Testicle tissue, Porcine, D_004213

source_name: Testicle tissue, Porcine, Low androstenone, biomat-id 24860

value: Duroc, Gender:Male, Tissue:Testicle, Low androstenone, biomat-id 24860

source_name: Testicle tissue, Porcine, High androstenone, biomat-id 11503

value: Duroc, Gender:Male, Tissue:Testicle, High androstenone, biomat-id 11503


title: Liver, RNA batch 2, Liver tissue, Porcine, 5 Hampshire boars, Healthy, 5 months old

source_name: Liver, Liver tissue, Porcine, Healthy


title: Large intestine, RNA batch 1, Digestive tissue, Porcine, 5 Hampshire boars, Healthy, 5 months old

source_name: Large intestine, Digestive tissue, Porcine, Healthy


title: Infraspinatus, RNA batch 1, Muscle tissue, Porcine, 5 Hampshire boars, Healthy, 5 months old

source_name: Infraspinatus, Muscle tissue, Porcine, Healthy

source_name: Reference, Reference tissue, Porcine, Healthy


title: Infraspinatus, RNA batch 2, Muscle tissue, Porcine, 5 Hampshire boars, Healthy, 5 months old


title: Pancreas, RNA batch 1, Endocrine tissue, Porcine, 5 Hampshire boars, Healthy, 5 months old

source_name: Pancreas, Endocrine tissue, Porcine, Healthy


title: Frontal cortext, RNA batch 1, Brain tissue, Porcine, 5 Hampshire boars, Healthy, 5 months old

source_name: Frontal cortext, Brain tissue, Porcine, Healthy


title: Pancreas, RNA batch 2, Endocrine tissue, Porcine, 5 Hampshire boars, Healthy, 5 months old


title: Heart, RNA batch 1, Muscle tissue, Porcine, 5 Hampshire boars, Healthy, 5 months old

source_name: Heart, Muscle tissue, Porcine, Healthy


title: Semitendinosus, RNA batch 1, Muscle tissue, Porcine, 5 Hampshire boars, Healthy, 5 months old

source_name: Semitendinosus, Muscle tissue, Porcine, Healthy


title: Heart, RNA batch 2, Muscle tissue, Porcine, 5 Hampshire boars, Healthy, 5 months old


title: Thyroid gland, RNA batch 2, Endocrine tissue, Porcine, 5 Hampshire boars, Healthy, 5 months old

source_name: Thyroid gland, Endocrine tissue, Porcine, Healthy


title: Stomach, RNA batch 2, Digestive tissue, Porcine, 5 Hampshire boars, Healthy, 5 months old

source_name: Stomach, Digestive tissue, Porcine, Healthy


title: Large intestine, RNA batch 2, Digestive tissue, Porcine, 5 Hampshire boars, Healthy, 5 months old


title: Pituitary gland, RNA batch 2, Endocrine tissue, Porcine, 5 Hampshire boars, Healthy, 5 months old

source_name: Pituitary gland, Endocrine tissue, Porcine, Healthy


title: Lung, RNA batch 1, Lung tissue, Porcine, 5 Hampshire boars, Healthy, 5 months old

source_name: Lung, Lung tissue, Porcine, Healthy


title: Longissimus dorsi, RNA batch 2, Muscle tissue, Porcine, 5 Hampshire boars, Healthy, 5 months old

source_name: Longissimus dorsi, Muscle tissue, Porcine, Healthy


title: Biceps femoris, RNA batch 1, Muscle tissue, Porcine, 5 Hampshire boars, Healthy, 5 months old

source_name: Biceps femoris, Muscle tissue, Porcine, Healthy


title: Fat, RNA batch 1, Fat tissue, Porcine, 5 Hampshire boars, Healthy, 5 months old

source_name: Fat, Fat tissue, Porcine, Healthy


title: Kidney, RNA batch 1, Kidney tissue, Porcine, 5 Hampshire boars, Healthy, 5 months old

source_name: Kidney, Kidney tissue, Porcine, Healthy


title: Testicle tissue, Porcine, D_004190

source_name: Testicle tissue, Porcine, High androstenone, biomat-id 5464

value: Duroc, Gender:Male, Tissue:Testicle, High androstenone, biomat-id 5464

source_name: Testicle tissue, Porcine, Low androstenone, biomat-id 11025

value: Duroc, Gender:Male, Tissue:Testicle, Low androstenone, biomat-id 11025


title: codY S.pneu TIGR4 164685

status: Public on Nov 20 2007

city: Groningen

first: Anne

middle: de

last: Jong

address: Nijenborgh 7

department: Molecular Genetics

country: Netherlands

institute: university of Groningen

description: codY-mutant of Streptococcus pneumoniae versus Wild type

hyb_protocol: Hybridization (16 h at 45 °C) of labeled cDNA was performed in Ambion Slidehyb #1 hybridization buffer (Ambion Europe) on superamine glass slides (Array-It; SMMBC), containing technical replicates.

scan_protocol: Slides were scanned using the Genepix 4200AL DNA micro array slide scanner. Quantification of the signal of the spots on slides was done with ArrayPro 4.5.

data_processing: Slide data were processed and normalized using MicroPreP, and CyberT implementation of the Student's t test (PMID: 15130795).

organism: Streptococcus pneumoniae TIGR4

source_name: wt OD 0.1

label_protocol: Synthesis of cDNA and indirect Cy-3/Cy-5-dCTPs labeling of 15–20 µg of total RNA was performed with the CyScribe Post labeling kit (Amersham Biosciences) according to the supplier's instructions

extract_protocol: 500 ml of THY-broth was inoculated with 10-20 colonies from agar plates, and these cultures were statically grown at 37°C. Samples for RNA isolation were taken when the cultures reached an optical density (OD600) of either 0.1 or 0.2 (early and mid-log growth, respectively). RNA was isolated and purified using the High Pure RNA isolation kit (Roche diagnostics) as described (PMID: 17085554). Contaminating genomic DNA was removed by treatment with RNase-free DNase I (Roche diagnostics). RNA was isolated from three replicate cultures. Synthesis, subsequent labeling of cDNA, and microarray hybridization was performed as described (PMID: 17085554 and 15907200). In all cases, dye-swapping was performed with one of the three biological replicates.

tag: prep 6

organism: Streptococcus pneumoniae

source_name: dcodY OD 0.1

tag: prep 5


title: codY S.pneu TIGR4 164683

label_protocol: Synthesis of cDNA and indirect Cy-3/Cy-5-dCTPs labeling of 15–20 µg of total RNA was performed with the CyScribe Post labeling kit (Amersham Biosciences) according to the supplier's instructions.

tag: prep 3


title: codY S.pneu TIGR4 164684

source_name: dcody OD 0.2

source_name: wt OD 0.2


title: codY S.pneu TIGR4 164682

tag: prep 1

tag: prep 4


title: Cerebellum, RNA batch 2, Brain tissue, Porcine, 5 Hampshire boars, Healthy, 5 months old

source_name: Cerebellum, Brain tissue, Porcine, Healthy

source_name: Reference, Reference tissue, Porcine, Healthy


title: Pituitary gland, RNA batch 1, Endocrine tissue, Porcine, 5 Hampshire boars, Healthy, 5 months old


title: Triceps brachii, RNA batch 2, Muscle tissue, Porcine, 5 Hampshire boars, Healthy, 5 months old

source_name: Triceps brachii, Muscle tissue, Porcine, Healthy


title: Small intestine, RNA batch 1, Digestive tissue, Porcine, 5 Hampshire boars, Healthy, 5 months old

source_name: Small intestine, Digestive tissue, Porcine, Healthy


title: Supraspinatus, RNA batch 1, Muscle tissue, Porcine, 5 Hampshire boars, Healthy, 5 months old

source_name: Supraspinatus, Muscle tissue, Porcine, Healthy


title: Triceps brachii, RNA batch 1, Muscle tissue, Porcine, 5 Hampshire boars, Healthy, 5 months old


title: Spleen, RNA batch 2, Spleen tissue, Porcine, 5 Hampshire boars, Healthy, 5 months old

source_name: Spleen, Spleen tissue, Porcine, Healthy


title: Skin, RNA batch 2, Skin tissue, Porcine, 5 Hampshire boars, Healthy, 5 months old

source_name: Skin, Skin tissue, Porcine, Healthy


title: Longissimus dorsi, RNA batch 1, Muscle tissue, Porcine, 5 Hampshire boars, Healthy, 5 months old

source_name: Longissimus dorsi, Muscle tissue, Porcine, Healthy


title: codY S.pneu TIGR4 164687

source_name: dcodY OD 0.2


title: Thyroid gland, RNA batch 1, Endocrine tissue, Porcine, 5 Hampshire boars, Healthy, 5 months old

source_name: Thyroid gland, Endocrine tissue, Porcine, Healthy


title: Liver, RNA batch 1, Liver tissue, Porcine, 5 Hampshire boars, Healthy, 5 months old

source_name: Liver, Liver tissue, Porcine, Healthy


title: Frontal cortext, RNA batch 2, Brain tissue, Porcine, 5 Hampshire boars, Healthy, 5 months old

source_name: Frontal cortext, Brain tissue, Porcine, Healthy


title: Semimembranosus, RNA batch 2, Muscle tissue, Porcine, 5 Hampshire boars, Healthy, 5 months old

source_name: Semimembranosus, Muscle tissue, Porcine, Healthy


title: muscle_HRT_follow-up_1092_2

status: Public on Nov 19 2007

city: Jyväskylä

first: Eija

last: Pöllänen

address: PO Box 35/Viveca

department: Department of Health Sciences

country: Finland

institute: University of Jyväskylä

description: This sample presents follow-up sample of ID_1092_2 individual, who belonged to hormone replacement therapy group (HRT) of "HRT and excercise"-intervention

hyb_protocol: Employing protocols by Illumina Inc.; hybridization: 17 h at 55 degC

scan_protocol: Using an Illumina BeadReader containin two lasers: 532 nm and 635 nm and performing with 0.8 microns resolution.

data_processing: The raw data was acquired by the BeadStudio Direct Hybridization V.1.5.0.34 (Illumina inc) and quantile normalized with Inforsense KDE 3.1 (InforSense Inc.) software.

organism: Homo sapiens

source_name: vastus lateralis muscle, HRT user, follow-up

label_protocol: Illumina RNA amplification kit (Ambion Inc., #I1755) was used according to manufacturer’s instructions. Input amount: 500 ng of total RNA.

extract_protocol: Frozen muscle biopsy samples were homogenized in Trizol-reagent (Invitrogen Inc.) with aid of FastPrep FP120 -apparatus (MP Biomedicals). Manufacturer’s protocol was followed through the isolation procedure.

tag: Gender

value: female

tag: menopausal status

value: early postmenopausal


title: muscle_non-HRT_baseline_1302_2

description: This sample presents baseline sample of ID_1302_2 individual, who belonged to no hormone replacement therapy group (non-HRT) of "HRT and excercise"-intervention

source_name: vastus lateralis muscle, non-HRT user, baseline


title: muscle_HRT_follow-up_551_2

description: This sample presents follow-up sample of ID_551_2 individual, who belonged to hormone replacement therapy group (HRT) of "HRT and excercise"-intervention


title: muscle_HRT_baseline_551_2

description: This sample presents baseline sample of ID_551 individual, who belonged to hormone replacement therapy group (HRT) of "HRT and excercise"-intervention

source_name: vastus lateralis muscle, HRT user, baseline


title: muscle_HRT_baseline_1092_2

description: This sample presents baseline sample of ID_1092_2 individual, who belonged to hormone replacement therapy group (HRT) of "HRT and excercise"-intervention


title: codY S.pneu TIGR4 164681

scan_protocol: Slides were scanned using the Genepix 4200AL DNA micro array slide scanner. Quantification of the signal of the spots on slides was done with ArrayPro 4.5

tag: OD 0.1 prep 1

tag: OD 0.1 prep 4


title: human_intracranial_artery_5

city: Detroit

first: Gerard

last: Tromp

state: MI

address: 3309 Scott Hall, 540 East Canfield Ave

department: Center for Molecular Medicine and Genetics

country: USA

institute: Wayne State University School of Medicine

description: Intracranial arteries obtained from autopsy for mRNA expression analysis

hyb_protocol: 1.5 micrograms of labeled cRNA was used for hybridization, and microarrays were washed and stained using standard Illumina BeadChip 6 X 2 protocol, Doc. # 11176837 Rev. E

scan_protocol: Scanned on Illumina BeadStation 500GX using standard Illumina protocol

data_processing: Cubic spline normalization using Illumina BeadStudio Version 1.5.0.34

label: biotin, streptavidin-Cy3

source_name: Total RNA from human intracranial artery, non-aneurysm

label_protocol: 154 ng of total RNA was amplified and labeled using the Illumina TotalPrep RNA Amplification Kit (Cat #IL1791), manual version 0606

extract_protocol: Guanidinium isothiocyanate, cesium chloride centrifugation (Sambrook Molecular Cloning:  a laboratory manual)

tag: Tissue

value: Intracranial artery (non-aneurysm)

tag: Source Disease Status

value: non-aneurysm

tag: Individual/Pool

value: Individual

tag: Age

value: 23 years

value: Male

tag: Vessel

value: secondary and tertiary branches middle cerebral artery

tag: Ethnicity

value: African American


title: human_intracranial_artery_2

label_protocol: 151 ng of total RNA was amplified and labeled using the Illumina TotalPrep RNA Amplification Kit (Cat #IL1791), manual version 0606

value: 47 years

value: internal carotid artery and primary branch middle cerebral artery


title: human_intracranial_artery_1

label_protocol: 150 ng of total RNA was amplified and labeled using the Illumina TotalPrep RNA Amplification Kit (Cat #IL1791), manual version 0606

value: 52 years


title: human_intracranial_artery_3

label_protocol: 152 ng of total RNA was amplified and labeled using the Illumina TotalPrep RNA Amplification Kit (Cat #IL1791), manual version 0606

value: 34 years


title: codY S.pneu TIGR4 164686

source_name: dcody OD 0.1

source_name: wt OD 0.1


title: Stage1, Immediately post-cardioplegic arrest, Replicate3

city: Toronto

first: Sara

last: Arab

state: ONT

address: 610 University Avenue

department: Cardiology

country: Canada

institute: Toronto General Hospital

description: All the chips were controlled for presence of any defect before scanning.

hyb_protocol: Hybridization was performed according to standard Affymetrix instructions at the Genomic Core Facility at the Hospital for Sick Children. Affymetrix standard protocol

scan_protocol: Affymetrix standard protocol using MAS5.0.

data_processing: GeneSpring version 7.0 from Agilent.

label: Biotin

source_name: Heart

label_protocol:
Labeling was performed according to standard Affymetrix instructions at the Genomic Core Facility at the Hospital for Sick Children.
Affymetrix standard protocol

extract_protocol: Total RNA (TRNA) was isolated utilizing Trizol Reagent (GIBCO/BRL) following the manufacturer's protocol.  The quality of TRNA was assessed using the Agilent 2100 Bioanalyzer (version A.02.01S1232, Agilent Technologies).  Only RNA with the OD ratio of 1.99-2.0 at 260/280 was used for microarray analysis.

tag: Sample was taken immediately after cardiac arrest following administration of standard hyperkalemic, cold blood cardioplegia (30ml/kg), which was repeated (20ml/kg) every 20 minutes

tag: All myocardial samples were taken from the RVOT through the tricuspid valve


title: Stage1, Immediately post-cardioplegic arrest, Replicate4


title: BQS252 thiolutin t20min replicate 1

status: Public on Nov 17 2007

city: Burjassot

first: Jose

middle: E.

last: Perez-Ortin

state: Valencia

address: Dr. Moliner 50

department: Bioquimica y Biologia Molecular

country: Spain

institute: Universitat de Valencia

description:
Filters were stripped by pouring 3X150 ml boiling stripping buffer (5 mM sodium phosphate, pH 7.5, 0.1% SDS) over the
membrane. The first time, the stripping buffer was immediately changed while after the second and third washes the filters
were left to cool at room temperature. To ensure that radioactivity had been eliminated, the filters were either checked
with a Geiger counter or re-scanned with a Phosphorimager.

hyb_protocol: Hybridization Solution was: 5XSSC, 5XDenhart’s, 0.5% SDS and 100 µg herring sperm DNA/ml. The hybridization protocol used was as follows. Filters were inserted in 12.5X2.5-cm flat-bottom plastic tubes and pre-hybridized in a rotator oven with 5 ml pre-hybridization solution (the same as used for hybridization but without the radioactive sample) at 65ºC. The pre-hybridization solution was then replaced with 5 ml of the same solution containing 3X10exp6 dpm/mL of radioactive sample and hybridized for 44h. Washing conditions were: 1h at 65ºC for 20 min in 2XSSC, 0.1% SDS, and twice at 65ºC for 30 min in 0.2XSSC, 0.1% SDS.

scan_protocol: Images were acquired using a FujiFilm FLA3000 Phosphorimager.

data_processing: Raw image quantization background subtracted

organism: Saccharomyces cerevisiae

source_name: yeast strain FY1679 derived  growing in exponential phase treated with 3 µ/mL thiolutin t20min

label_protocol: About 30-40 µg of total RNA were reverse transcribed into cDNA by adding 200 us of RT polymerase SuperScript II and random hexamers (Invitrogen), 1 µL RNaseOUT (Invitrogen), 6 µL 5X First Strand Buffer (Invitrogen), 1.5 µL dNTP mix (16 mM dATP, dTTP, dGTP, and 100 µM dCTP) and 5 µL [α-33P]dCTP (3000 Ci/mmol, 10 µCi/microL) in a final reaction volume of 30 µL. The labeling reaction was incubated for 1 h at 43ºC. 1 µL of EDTA 0.5 M was added to stop the reaction. The labeled cDNAs were purified by a S300-HR MicroSpin column (Amersham BioSciences).

growth_protocol: Total RNA from BQS252 yeast strain growing in exponential phase in YPD (yeast extract 1%; peptone 2%,glucose 2%)

extract_protocol:
Total RNA from yeast cells was prepared as described by
Sherman et al. [1986], but using a multiple-sample automated
device (Fast-Prep, BIO101) to break the cells.
Sherman F, Fink GR, Hicks JB (1986) Methods in yeast genetics.
Spring Harbor Cold Laboratory Press, Cold Spring Harbor, New York

treatment_protocol: 20 minutes after the addition of thiolutin 3 µ/mL

tag: Total RNA from BQS252 yeast strain (Mat a, ura3-52 derived from FY1679) growing in exponential phase in YPD


title: BQS252 thiolutin t10min replicate 1

source_name: yeast strain FY1679 derived  growing in exponential phase treated with 3 µ/mL thiolutin t10min

treatment_protocol: 10 minutes after the addition of thiolutin 3 µ/mL


title: Stage 3, after 5 min. Reperfusion, Replicate3

description: All the chips were controlled for presence of any defect before scanning

scan_protocol: MAS5.0 Affymetrix standard protocol

data_processing: GeneSpring version 7.0 from Agilent

tag: Sample was taken at 5 minutes after reperfusion prior to right atrial closure.

tag: All myocardial samples were taken from the RVOT through the tricuspid valve.


title: Stage 3, after 5 min. Reperfusion, Replicate2


title: Stage 3, after 5 min. Reperfusion, Replicate1


title: BQS252_thiolutin_3ug t30min replicate 1

source_name: yeast strain FY1679 derived growing in exponential phase treated with 3 µ/mL thiolutin t30min

treatment_protocol: 30 minutes after the addition of thiolutin 3 µ/mL


title: Stage2, End-ischemia, Replicate3

scan_protocol: Affymetrix standard protocol

tag: End-ischemia sample was taken at 50 minutes of cardiac arrest.


title: BQS252 thiolutin t45min replicate 1

description:
Filters were stripped by pouring 3X150 ml boiling stripping buffer (5 mM sodium phosphate, pH 7.5, 0.1% SDS) over the membrane. The first time, the stripping buffer was immediately changed while after the second and third washes the filters were left to cool at room temperature. To ensure that radioactivity had been eliminated, the filters were either checked
with a Geiger counter or re-scanned with a Phosphorimager.

source_name: yeast strain FY1679 derived  growing in exponential phase treated with 3 µ/mL thiolutin t45min

treatment_protocol: 45 minutes after the addition of thiolutin 3 µ/mL


title: Stage1, Immediately post-cardioplegic arrest, Replicate1


title: Stage1, Immediately post-cardioplegic arrest, Replicate2


title: BQS252_thiolutin_t0min_replicate 1

source_name: yeast strain FY1679 derived  growing in exponential phase treated with 3 µ/mL thiolutin t0min


title: Stage 3, after 5 min. Reperfusion, Replicate4


title: Stage2, End-ischemia, Replicate4


title: human_intracranial_artery_4

label_protocol: 153 ng of total RNA was amplified and labeled using the Illumina TotalPrep RNA Amplification Kit (Cat #IL1791), manual version 0606


title: Stage2, End-ischemia, Replicate1


title: 60293_23ZN

status: Public on Nov 15 2007

city: Research Triangle Park

first: Urmila

middle: P

last: Kodavanti

state: NC

address: 109 TW Alexander Drive

department: NHEERL, ETD

institute: USEPA

description: Saline suspension which contained zinc sulfate (14.5ug/ml), replicate #3.

hyb_protocol: see Affymetrix technical manual

scan_protocol: see Affymetrix technical manual

data_processing: MAS 5.0

label: biotin

organism: Rattus norvegicus

source_name: Rattus norvegicus heart, intratracheal zinc sulfate

label_protocol: see Affymetrix technical manual

extract_protocol: Total heart RNA was isolated from tissues snap-frozen in liquid nitrogen by homogenization in TriReagent (Sigma, St Louis, MO) and dissolved in 50ul diethylpyrocarbonate treated water.

treatment_protocol: Rats in each group were randomized by body weight into 6 groups (n=8) for each time point. Each particle sample was suspended in sterile saline at desired concentration and was mixed continuously for 20 min prior to their use. To prepare soluble fraction, PM saline suspension was centrifuged at 12, 000 x g in cold for 10 min and the supernatant fluid was filtered through a Teflon syringe filter unit (0.25 um pore size). This filtered fraction was termed as leachable fraction (PM-L). Similarly zinc sulfate was dissolved in sterile saline to give 33.4 ug zinc per ml. All fractions, including saline were intratracheally instilled once per week at 1 ml/kg volume under halothane anesthesia

tag: Healthy, male, 12-14 week old, Wistar Kyoto rats


title: 60289_19HP11LC

description: Saline suspension which contained soluble zinc leachate components, replicate #3.

source_name: Rattus norvegicus heart, intratracheal zinc leachate

tag: Healthy, male, 12-14 week old, Wistar Kyoto rats.


title: 60292_22ZN

description: Saline suspension which contained zinc sulfate (14.5ug/ml), replicate #2.


title: 60291_21ZN

description: Saline suspension which contained zinc sulfate (14.5ug/ml), replicate #1.


title: 60294_24ZN

description: Saline suspension which contained zinc sulfate (14.5ug/ml), replicate #4.


title: 60290_20HP11LC

description: Saline suspension which contained soluble zinc leachate components, replicate #4.


title: 60284_14HP11LD

description: Saline suspension which contained insoluble components plus water soluble zinc (7.25ug/mg zinc) and also a small amount of water-soluble nickel (1.5 ug/mg), replicate #2.

source_name: Rattus norvegicus heart, intratracheal 7.25 ug/mg zinc


title: 60286_16HP11LD

description: Saline suspension which contained insoluble components plus water soluble zinc (7.25ug/mg zinc) and also a small amount of water-soluble nickel (1.5 ug/mg), replicate #4.

source_name: Rattus norvegicus heart, intratracheal 7.25 ug/mg zinc.


title: 60283_13HP11LD

description: Saline suspension which contained insoluble components plus water soluble zinc (7.25ug/mg zinc) and also a small amount of water-soluble nickel (1.5 ug/mg), replicate #1.


title: 60288_18HP11LC

description: Saline suspension which contained soluble zinc leachate components, replicate #2.


title: 60285_15HP11LD

description: Saline suspension which contained insoluble components plus water soluble zinc (7.25ug/mg zinc) and also a small amount of water-soluble nickel (1.5 ug/mg), replicate #3.


title: 60279_9HP11HD

description: Saline suspension which contained insoluble components plus water soluble zinc (14.5ug/mg zinc) and also a small amount of water-soluble nickel (3.0 ug/mg), replicate #1

source_name: Rattus norvegicus heart, intratracheal 14.5 ug/mg zinc


title: 60282_12HP11HD

description: Saline suspension which contained insoluble components plus water soluble zinc (14.5ug/mg zinc) and also a small amount of water-soluble nickel (3.0 ug/mg), replicate #4.


title: 60287_17HP11LC

description: Saline suspension which contained soluble zinc leachate components, replicate #1.


title: 60281_11HP11HD

description: Saline suspension which contained insoluble components plus water soluble zinc (14.5ug/mg zinc) and also a small amount of water-soluble nickel (3.0 ug/mg), replicate #3.


title: 60280_10HP11HD

description: Saline suspension which contained insoluble components plus water soluble zinc (14.5ug/mg zinc) and also a small amount of water-soluble nickel (3.0 ug/mg), replicate #2.


title: C-lim aerobic chemostat with phenylalanine as N-source 1

city: Delft

first: Jean-Marc

last: Daran

address: Julianalaan 67

department: Department of Biotechnology

institute: Delft University of Technology

hyb_protocol: [Fluidics] Protocol	EukGE-WS2v4

scan_protocol: [Scanner] Pixel Size	3 Filter	570 Number of Scans	2 Scanner Type	HP

data_processing: MAS 5.1

label: SAPE

molecule: polyA RNA

source_name: chemostat culture with phenylalanine as N-source

label_protocol: Sampling of cells from chemostats, probe preparation and hybridization to Affymetrix GeneChip® Microarrays was performed as described by Piper et al (Piper et al., 2002).

growth_protocol:
The prototrophic S. cerevisiae strain CEN.PK113-7D (MATa) (1,2) was grown at 30°C in 1.0-liter working volume chemostats (3). Cultures were fed with a synthetic medium (4) that supported glucose-limited growth. The glucose concentration in the reservoir medium was 7.5 g·l-1. The nitrogen source was used, at the following concentration: L-phenylalanine, 5.0 g·l-1. When an amino acid served as nitrogen source, the synthetic medium was supplemented with 6.6 g·l-l K2SO4. The dilution rate was set at 0.10 h-1. The pH was measured online and kept constant at 5.0 by the automatic addition of 2 M KOH with the use of an Applikon ADI 1030 biocontroller. Stirrer speed was 800 rpm and the airflow was 0.5 l.min-1. Dissolved oxygen tension was measured online with an Ingold model 34 100 3002 probe, and was above 50% air saturation. A condenser connected to a cryostat set at 2 °C cooled the off-gas, and oxygen and carbon dioxide were measured off-line. Steady-state samples for arrays were taken after 10 to 14 volume changes to minimize the impact of evolutionary adaptation that occurs after long term cultivation (5,6). Dry weight, metabolite-, and gas profiles were constant over at least 3 volume changes prior to sampling for RNA extraction.
(1) van Dijken et al. 2000. An interlaboratory comparison of physiological and genetic properties of four Saccharomyces cerevisiae strains. Enzyme Microb Technol 26(9,10): 706-714.
(2) Daran-Lapujade P et al. 2003. Comparative genotyping of the Saccharomyces cerevisiae laboratory strains S288C and CEN.PK113-7D using oligonucleotide microarrays. FEMS Yeast Res 4: 285-296.
(3) van den Berg et al. 1996. The two acetyl-coenzyme A synthetases of Saccharomyces cerevisiae differ with respect to kinetic properties and transcriptional regulation. J Biol Chem 271: 28953-28959.
(4) Verduyn et al. 1992. Effect of benzoic acid on metabolic fluxes in yeasts: a continuous-culture study on the regulation of respiration and alcoholic fermentation. Yeast 8: 501-17.
(5) Ferea et al. 1999. Systematic changes in gene expression patterns following adaptive evolution in yeast. Proc Natl Acad Sci U S A 96: 9721-9726.
(6) Jansen et al. 2004. Prolonged maltose-limited cultivation of Saccharomyces cerevisiae selects for cells with improved maltose affinity and hypersensitivity. Appl Environ Microbiol 70: 1956-1963.

tag: The prototrophic S. cerevisiae strain CEN.PK113-7D (MATa) (1)


title: 60274_4SALINE

description: Intratracheal saline, replicate #4

source_name: Rattus norvegicus heart, intratracheal saline


title: 60275_5MSH

description: Intratracheal Mount St. Helen's (MSH) ash which does not contain any water-soluble zinc or other metals such that we can delineate any cardiac effect secondary to pulmonary deposition of these particles as these fine mode particles themselves are not likely to translocate to the heart, replicate #1

source_name: Rattus norvegicus heart, intratracheal Mt. St. Helen ash


title: 60469_1SALINE-2

description: Intratracheal saline, replicate #1

tag: Healthy, male 12-14 week old, Wistar Kyoto rats


title: 60277_7MSH

description: Intratracheal Mount St. Helen's (MSH) ash which does not contain any water-soluble zinc or other metals such that we can delineate any cardiac effect secondary to pulmonary deposition of these particles as these fine mode particles themselves are not likely to translocate to the heart, replicate #3


title: 60273_3SALINE

description: Intratracheal saline replicate #3


title: 60278_8MSH

description: Intratracheal Mount St. Helen's (MSH) ash which does not contain any water-soluble zinc or other metals such that we can delineate any cardiac effect secondary to pulmonary deposition of these particles as these fine mode particles themselves are not likely to translocate to the heart, replicate #4


title: 60272_2SALINE

description: Intratracheal saline replicate #2


title: Stage2, End-ischemia, Replicate2

description: All the chips were controlled for presence of any defect before scanning.


title: HDF/Hs578T co-culture 2

status: Public on Nov 14 2007

city: Basel

first: Martin

last: Buess

state: CH

address: Petersgraben 4

department: Medizinische Onkologie

country: Switzerland

institute: University Hospital Basel

description:
Simple annotation: Cell-line, co-culture
Image: http://smd.stanford.edu/MicroArray/gifs/2005-04/60692.gif

hyb_protocol: not provided

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1280, 6120; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Martin,,Buess 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 = 39.24; Parameter Scan Time = 14:49:24; Parameter PMT Volts = 560; Parameter Scan Date = 2005-04-04; Parameter Pixel Size = 10; Parameter Laser on time = 214377; 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: Martin,,Buess 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 = 39.24; Parameter Scan Time = 14:49:24; Parameter PMT Volts = 620; Parameter Scan Date = 2005-04-04; Parameter Pixel Size = 10; Parameter Laser on time = 579181; 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: Martin,,Buess

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: stratagene human reference

label_protocol:
MessageAmpII; Total RNA was amplified using the Message AmpTM II aRNA Kit (Ambion, Austin, TX), according to the manufacturer's instructions.; Protocol Type = Amplification; Performer: Martin,,Buess
amplified RNA dircect inocorporaton; The protocol was modified for amplified RNA: 1. 6ug of amplified RNA and 10ug of random hexamer primer were mixed in a total volume of 15.4 ul. Then the described protocol was followed.; Protocol Type = Labeling; Performer: Martin,,Buess

extract_protocol: not provided

tag: StratageneRef; RNA for the reference was pooled from 11 cell lines - obtained from Stratagene.; Protocol Type = Biological Sample; Performer

value: Martin,,Buess

label_protocol:
MessageAmp II; RNA was amplified using the Message AmpTM II aRNA Kit (Ambion, Austin, TX) according to the manufacturer's instructions.; Protocol Type = Amplification; Performer: Martin,,Buess
amplified RNA direct incorporation method; The protocol was modified for amplified RNA:  6ug of amplified RNA was mixed with 10ug of random hexamer primer pd(N)6( Procuct number 27-2166-01, Amersham Biosciences) in a total volume of 15.4 ul. Then the protocol was followed as described; Protocol Type = Labeling; Performer: Martin,,Buess

growth_protocol: Co-culture conditions; Human mammary epithelial cells (HMEC) (Cambrex Bio Science Walkersville, Inc) were expanded in mammary epithelial basal medium supplemented with bovine pituitary extract, human EGF, insulin and antibiotics (Clonetics, Cambrex Bio Science Walkersville, Inc). MCF-7, T47D, MDA-MB231, MDA-MB436, SKBR-3,  Hs578T, BT549, CCL-171, HTB-125 (ATTC) and HDF (Cambrex Bio Science Walkersville, Inc) were propagated in DMEM supplemented with 10% FBS (HyClone, Logan UT), glutamine, 100U/ml penicillin and 100 μg/ml streptomycin (GIBCO, Grand Island, N.Y.). For co-culture experiments the cells were cultivated for 48 hours at 50,000 cells/cm2 in endothelial basal media (CAMBREX Bio Science Rockland, Inc Rockland, Maine) with 0.2% FBS, which was a good universal media for all cells involved. Separated co-cultures were kept in Transwell? chambers 0.4μm pore size (Costar, Corning Inc. Corning, NY). Cells negatively tested for mycoplasma infection using MycoAlert Tm (CAMBREX Bio Science Rocland, Inc Rockland, Maine) and VenorGem? (SIGMA, Saint Louis, Missouri) mycoplasma detection kits according to the manufacturer?s instructions.; Protocol Type = Biological Sample; Performer: Martin,,Buess

extract_protocol: RNeasy; Total RNA was isolated using the RNeasy mini kit (QIAGEN), according to the manufacturer's instructions.; Protocol Type = Extract preparation; Performer: Martin,,Buess

tag: LabeledExtract


title: 60276_6MSH

description: Intratracheal Mount St. Helen's (MSH) ash which does not contain any water-soluble zinc or other metals such that we can delineate any cardiac effect secondary to pulmonary deposition of these particles as these fine mode particles themselves are not likely to translocate to the heart, replicate #2


title: CCL-171 /T47D  co-culture 2

description:
Simple annotation: Cell-line, co-culture
Image: http://smd.stanford.edu/MicroArray/gifs/2005-02/59138.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1250, 5220; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Martin,,Buess Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 32.25; Parameter Scan Time = 18:06:49; Parameter PMT Volts = 600; Parameter Scan Date = 2005-02-04; Parameter Pixel Size = 10; Parameter Laser on time = 215831; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 3.02; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Martin,,Buess Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 32.25; Parameter Scan Time = 18:06:49; Parameter PMT Volts = 610; Parameter Scan Date = 2005-02-04; Parameter Pixel Size = 10; Parameter Laser on time = 434837; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.48; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Martin,,Buess


title: CCL-171 /MDA-MB436 co-culture 2

description:
Simple annotation: Cell-line, co-culture
Image: http://smd.stanford.edu/MicroArray/gifs/2005-02/59136.gif

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1360, 5220; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Martin,,Buess Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 32.13; Parameter Scan Time = 17:22:27; Parameter PMT Volts = 620; Parameter Scan Date = 2005-02-04; Parameter Pixel Size = 10; Parameter Laser on time = 215788; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.88; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Martin,,Buess Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 32.13; Parameter Scan Time = 17:22:27; Parameter PMT Volts = 620; Parameter Scan Date = 2005-02-04; Parameter Pixel Size = 10; Parameter Laser on time = 434794; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.48; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Martin,,Buess

label_protocol: not provided

tag: stratagene human reference


title: CCL-171 /T47D co-culture 1

description:
Simple annotation: Cell-line, co-culture
Image: http://smd.stanford.edu/MicroArray/gifs/2005-02/59137.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1280, 5230; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Martin,,Buess Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 32.19; Parameter Scan Time = 17:45:00; Parameter PMT Volts = 600; Parameter Scan Date = 2005-02-04; Parameter Pixel Size = 10; Parameter Laser on time = 215809; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 3.02; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Martin,,Buess Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 32.19; Parameter Scan Time = 17:45:00; Parameter PMT Volts = 600; Parameter Scan Date = 2005-02-04; Parameter Pixel Size = 10; Parameter Laser on time = 434815; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.48; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Martin,,Buess


title: HDF/ MDA-MB436 co-culture 1

description:
Simple annotation: Cell-line, co-culture
Image: http://smd.stanford.edu/MicroArray/gifs/2005-04/60688.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1320, 6000; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Martin,,Buess 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 = 39.10; Parameter Scan Time = 14:17:11; Parameter PMT Volts = 580; Parameter Scan Date = 2005-04-04; Parameter Pixel Size = 10; Parameter Laser on time = 214345; 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: Martin,,Buess 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 = 39.10; Parameter Scan Time = 14:17:11; Parameter PMT Volts = 620; Parameter Scan Date = 2005-04-04; Parameter Pixel Size = 10; Parameter Laser on time = 579149; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 2.09; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Martin,,Buess


title: HDF/T47D co-culture 1

description:
Simple annotation: Cell-line, co-culture
Image: http://smd.stanford.edu/MicroArray/gifs/2005-04/60690.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1360, 5680; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Martin,,Buess 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 = 38.87; Parameter Scan Time = 13:32:57; Parameter PMT Volts = 580; Parameter Scan Date = 2005-04-04; Parameter Pixel Size = 10; Parameter Laser on time = 214300; 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: Martin,,Buess 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 = 38.87; Parameter Scan Time = 13:32:57; Parameter PMT Volts = 600; Parameter Scan Date = 2005-04-04; Parameter Pixel Size = 10; Parameter Laser on time = 579104; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 2.12; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Martin,,Buess


title: CCL-171 monoculture 8

description:
Simple annotation: Cell-line, Controls
Image: http://smd.stanford.edu/MicroArray/gifs/2005-02/59135.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1380, 6020; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Martin,,Buess Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.67; Parameter Scan Time = 15:57:06; Parameter PMT Volts = 620; Parameter Scan Date = 2005-02-04; Parameter Pixel Size = 10; Parameter Laser on time = 215703; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 3.14; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Martin,,Buess Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.67; Parameter Scan Time = 15:57:06; Parameter PMT Volts = 610; Parameter Scan Date = 2005-02-04; Parameter Pixel Size = 10; Parameter Laser on time = 434709; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.49; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Martin,,Buess


title: CCL-171 /HS578T co-culture 1

description:
Simple annotation: Cell-line, co-culture
Image: http://smd.stanford.edu/MicroArray/gifs/2005-02/59139.gif

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1350, 5770; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Martin,,Buess Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.36; Parameter Scan Time = 15:23:42; Parameter PMT Volts = 600; Parameter Scan Date = 2005-02-04; Parameter Pixel Size = 10; Parameter Laser on time = 215669; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 3.40; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Martin,,Buess Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.36; Parameter Scan Time = 15:23:42; Parameter PMT Volts = 620; Parameter Scan Date = 2005-02-04; Parameter Pixel Size = 10; Parameter Laser on time = 434675; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.49; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Martin,,Buess


title: HDF/T47D co-culture 2

description:
Simple annotation: Cell-line, co-culture
Image: http://smd.stanford.edu/MicroArray/gifs/2005-04/60826.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1240, 6880; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Martin,,Buess 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 = 15:01:06; Parameter PMT Volts = 560; Parameter Scan Date = 2005-04-04; Parameter Pixel Size = 10; Parameter Laser on time = 214388; 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: Martin,,Buess 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 = 15:01:06; Parameter PMT Volts = 620; Parameter Scan Date = 2005-04-04; Parameter Pixel Size = 10; Parameter Laser on time = 579192; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 2.14; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Martin,,Buess


title: HDF/MDA-MB436 co-culture 2

description:
Simple annotation: Cell-line, co-culture
Image: http://smd.stanford.edu/MicroArray/gifs/2005-04/60689.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1320, 6200; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Martin,,Buess 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 = 39.18; Parameter Scan Time = 14:27:51; Parameter PMT Volts = 580; Parameter Scan Date = 2005-04-04; Parameter Pixel Size = 10; Parameter Laser on time = 214355; 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: Martin,,Buess 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 = 39.18; Parameter Scan Time = 14:27:51; Parameter PMT Volts = 620; Parameter Scan Date = 2005-04-04; Parameter Pixel Size = 10; Parameter Laser on time = 579159; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 2.10; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Martin,,Buess

source_name: HDF/ MDA-MB436

tag: HDF/ MDA-MB436


title: HDF/Hs578T co-culture 1

description:
Simple annotation: Cell-line, co-culture
Image: http://smd.stanford.edu/MicroArray/gifs/2005-04/60691.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1280, 6120; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Martin,,Buess 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 = 39.22; Parameter Scan Time = 14:39:09; Parameter PMT Volts = 560; Parameter Scan Date = 2005-04-04; Parameter Pixel Size = 10; Parameter Laser on time = 214366; 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: Martin,,Buess 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 = 39.22; Parameter Scan Time = 14:39:09; Parameter PMT Volts = 620; Parameter Scan Date = 2005-04-04; Parameter Pixel Size = 10; Parameter Laser on time = 579170; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 2.12; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Martin,,Buess


title: HDF/BT549 co-culture 2

description:
Simple annotation: Cell-line, co-culture
Image: http://smd.stanford.edu/MicroArray/gifs/2005-04/60687.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1120, 6520; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Martin,,Buess 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 = 13:20:18; Parameter PMT Volts = 580; Parameter Scan Date = 2005-04-04; Parameter Pixel Size = 10; Parameter Laser on time = 214288; 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: Martin,,Buess 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 = 13:20:18; Parameter PMT Volts = 600; Parameter Scan Date = 2005-04-04; Parameter Pixel Size = 10; Parameter Laser on time = 579092; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 2.10; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Martin,,Buess


title: HTB-125/Hs578T co-culture 2

description:
Simple annotation: Cell-line, co-culture
Image: http://smd.stanford.edu/MicroArray/gifs/2005-03/59636.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1100, 5750; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Martin,,Buess Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.76; Parameter Scan Time = 13:15:18; Parameter PMT Volts = 600; Parameter Scan Date = 2005-02-24; Parameter Pixel Size = 10; Parameter Laser on time = 220233; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.96; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Martin,,Buess Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.76; Parameter Scan Time = 13:15:18; Parameter PMT Volts = 610; Parameter Scan Date = 2005-02-24; Parameter Pixel Size = 10; Parameter Laser on time = 439239; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.49; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Martin,,Buess


title: HTB-125/T47D co-culture 1

description:
Simple annotation: Cell-line, co-culture
Image: http://smd.stanford.edu/MicroArray/gifs/2005-03/59637.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1260, 5420; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Martin,,Buess Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 30.94; Parameter Scan Time = 10:06:00; Parameter PMT Volts = 600; Parameter Scan Date = 2005-02-24; Parameter Pixel Size = 10; Parameter Laser on time = 220044; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 3.14; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Martin,,Buess Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 30.94; Parameter Scan Time = 10:06:00; Parameter PMT Volts = 620; Parameter Scan Date = 2005-02-24; Parameter Pixel Size = 10; Parameter Laser on time = 439051; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.49; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Martin,,Buess


title: CCL-171/BT549 co-culture 1

description:
Simple annotation: Cell-line, co-culture
Image: http://smd.stanford.edu/MicroArray/gifs/2005-04/60825.gif

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1430, 6000; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Martin,,Buess Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 32.06; Parameter Scan Time = 17:09:55; Parameter PMT Volts = 610; Parameter Scan Date = 2005-02-04; Parameter Pixel Size = 10; Parameter Laser on time = 215775; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.69; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Martin,,Buess Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 32.06; Parameter Scan Time = 17:09:55; Parameter PMT Volts = 630; Parameter Scan Date = 2005-02-04; Parameter Pixel Size = 10; Parameter Laser on time = 434781; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.48; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Martin,,Buess


title: HTB-125/SKBR3 co-culture 2

description:
Simple annotation: Cell-line, co-culture
Image: http://smd.stanford.edu/MicroArray/gifs/2005-03/59630.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1100, 5750; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Martin,,Buess Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.70; Parameter Scan Time = 12:03:50; Parameter PMT Volts = 600; Parameter Scan Date = 2005-02-24; Parameter Pixel Size = 10; Parameter Laser on time = 220162; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.88; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Martin,,Buess Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.70; Parameter Scan Time = 12:03:50; Parameter PMT Volts = 610; Parameter Scan Date = 2005-02-24; Parameter Pixel Size = 10; Parameter Laser on time = 439168; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.47; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Martin,,Buess

source_name: HTB/ SKBR3

tag: HTB/ SKBR3


title: HDF7/BT549 co-culture 1

description:
Simple annotation: Cell-line, co-culture
Image: http://smd.stanford.edu/MicroArray/gifs/2005-04/60686.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1320, 6440; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Martin,,Buess 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 = 39.08; Parameter Scan Time = 14:06:08; Parameter PMT Volts = 580; Parameter Scan Date = 2005-04-04; Parameter Pixel Size = 10; Parameter Laser on time = 214334; 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: Martin,,Buess 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 = 39.08; Parameter Scan Time = 14:06:08; Parameter PMT Volts = 600; Parameter Scan Date = 2005-04-04; Parameter Pixel Size = 10; Parameter Laser on time = 579137; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 2.09; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Martin,,Buess


title: HTB-125/BT549 co-culture 2

description:
Simple annotation: Cell-line, co-culture
Image: http://smd.stanford.edu/MicroArray/gifs/2005-03/59634.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1320, 6030; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Martin,,Buess Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 30.60; Parameter Scan Time = 09:41:35; Parameter PMT Volts = 600; Parameter Scan Date = 2005-02-24; Parameter Pixel Size = 10; Parameter Laser on time = 220020; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.62; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Martin,,Buess Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 30.60; Parameter Scan Time = 09:41:35; Parameter PMT Volts = 610; Parameter Scan Date = 2005-02-24; Parameter Pixel Size = 10; Parameter Laser on time = 439026; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.49; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Martin,,Buess


title: HTB-125/MDA-MB436 co-culture 2

description:
Simple annotation: Cell-line, co-culture
Image: http://smd.stanford.edu/MicroArray/gifs/2005-03/59631.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1320, 5560; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Martin,,Buess Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 30.45; Parameter Scan Time = 09:28:21; Parameter PMT Volts = 600; Parameter Scan Date = 2005-02-24; Parameter Pixel Size = 10; Parameter Laser on time = 220006; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.23; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Martin,,Buess Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 30.45; Parameter Scan Time = 09:28:21; Parameter PMT Volts = 620; Parameter Scan Date = 2005-02-24; Parameter Pixel Size = 10; Parameter Laser on time = 439013; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.50; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Martin,,Buess


title: HTB-125/SKBR3 co-culture 3

description:
Simple annotation: Cell-line, co-culture
Image: http://smd.stanford.edu/MicroArray/gifs/2005-03/59632.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1100, 5750; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Martin,,Buess Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.79; Parameter Scan Time = 12:52:18; Parameter PMT Volts = 600; Parameter Scan Date = 2005-02-24; Parameter Pixel Size = 10; Parameter Laser on time = 220210; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 3.01; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Martin,,Buess Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.79; Parameter Scan Time = 12:52:18; Parameter PMT Volts = 620; Parameter Scan Date = 2005-02-24; Parameter Pixel Size = 10; Parameter Laser on time = 439216; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.48; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Martin,,Buess

source_name: HTB-125/ SKBR3

tag: HTB-125/ SKBR3


title: CCL-171 / MDA-MB 436 co-culture 1

description:
Simple annotation: Cell-line, co-culture
Image: http://smd.stanford.edu/MicroArray/gifs/2005-02/59133.gif

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1320, 4880; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Martin,,Buess Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.00; Parameter Scan Time = 14:42:59; Parameter PMT Volts = 620; Parameter Scan Date = 2005-02-04; Parameter Pixel Size = 10; Parameter Laser on time = 215628; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.92; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Martin,,Buess Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.00; Parameter Scan Time = 14:42:59; Parameter PMT Volts = 600; Parameter Scan Date = 2005-02-04; Parameter Pixel Size = 10; Parameter Laser on time = 434634; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.52; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Martin,,Buess


title: HTB-125/ Hs578T co-culture 1

description:
Simple annotation: Cell-line, co-culture
Image: http://smd.stanford.edu/MicroArray/gifs/2005-03/59635.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1410, 5310; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Martin,,Buess Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.45; Parameter Scan Time = 11:13:00; Parameter PMT Volts = 600; Parameter Scan Date = 2005-02-24; Parameter Pixel Size = 10; Parameter Laser on time = 220110; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.53; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Martin,,Buess Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.45; Parameter Scan Time = 11:13:00; Parameter PMT Volts = 620; Parameter Scan Date = 2005-02-24; Parameter Pixel Size = 10; Parameter Laser on time = 439116; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.49; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Martin,,Buess


title: HTB-125/BT549 co-culture 1

description:
Simple annotation: Cell-line, co-culture
Image: http://smd.stanford.edu/MicroArray/gifs/2005-03/59633.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1260, 5420; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Martin,,Buess Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.03; Parameter Scan Time = 10:17:06; Parameter PMT Volts = 600; Parameter Scan Date = 2005-02-24; Parameter Pixel Size = 10; Parameter Laser on time = 220055; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 3.27; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Martin,,Buess Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.03; Parameter Scan Time = 10:17:06; Parameter PMT Volts = 620; Parameter Scan Date = 2005-02-24; Parameter Pixel Size = 10; Parameter Laser on time = 439062; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.49; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Martin,,Buess


title: HTB-125/T47D co-culture 2

description:
Simple annotation: Cell-line, co-culture
Image: http://smd.stanford.edu/MicroArray/gifs/2005-03/59638.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1450, 6060; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Martin,,Buess Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.12; Parameter Scan Time = 10:28:26; Parameter PMT Volts = 600; Parameter Scan Date = 2005-02-24; Parameter Pixel Size = 10; Parameter Laser on time = 220065; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.88; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Martin,,Buess Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.12; Parameter Scan Time = 10:28:26; Parameter PMT Volts = 630; Parameter Scan Date = 2005-02-24; Parameter Pixel Size = 10; Parameter Laser on time = 439072; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.48; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Martin,,Buess


title: HTB-125/MCF-7 co-culture 3

description:
Simple annotation: Cell-line, co-culture
Image: http://smd.stanford.edu/MicroArray/gifs/2005-03/59625.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1100, 5750; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Martin,,Buess Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.73; Parameter Scan Time = 12:14:13; Parameter PMT Volts = 600; Parameter Scan Date = 2005-02-24; Parameter Pixel Size = 10; Parameter Laser on time = 220172; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.53; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Martin,,Buess Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.73; Parameter Scan Time = 12:14:13; Parameter PMT Volts = 610; Parameter Scan Date = 2005-02-24; Parameter Pixel Size = 10; Parameter Laser on time = 439178; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.48; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Martin,,Buess


title: HTB-125/MDA-MB231 co-culture 1

description:
Simple annotation: Cell-line, co-culture
Image: http://smd.stanford.edu/MicroArray/gifs/2005-03/59626.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1260, 5020; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Martin,,Buess Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 30.75; Parameter Scan Time = 09:53:02; Parameter PMT Volts = 600; Parameter Scan Date = 2005-02-24; Parameter Pixel Size = 10; Parameter Laser on time = 220031; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.65; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Martin,,Buess Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 30.75; Parameter Scan Time = 09:53:02; Parameter PMT Volts = 610; Parameter Scan Date = 2005-02-24; Parameter Pixel Size = 10; Parameter Laser on time = 439037; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.49; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Martin,,Buess


title: CCL-171 monoculture 7

description:
Simple annotation: Cell-line, Controls
Image: http://smd.stanford.edu/MicroArray/gifs/2005-02/59132.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1380, 5520; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Martin,,Buess Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.94; Parameter Scan Time = 16:31:26; Parameter PMT Volts = 610; Parameter Scan Date = 2005-02-04; Parameter Pixel Size = 10; Parameter Laser on time = 215737; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.70; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Martin,,Buess Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.94; Parameter Scan Time = 16:31:26; Parameter PMT Volts = 620; Parameter Scan Date = 2005-02-04; Parameter Pixel Size = 10; Parameter Laser on time = 434744; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.49; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Martin,,Buess


title: HTB-125/MDA-MB231co-culture 2

description:
Simple annotation: Cell-line, co-culture
Image: http://smd.stanford.edu/MicroArray/gifs/2005-03/59627.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1410, 5310; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Martin,,Buess Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.36; Parameter Scan Time = 11:02:21; Parameter PMT Volts = 600; Parameter Scan Date = 2005-02-24; Parameter Pixel Size = 10; Parameter Laser on time = 220100; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.59; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Martin,,Buess Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.36; Parameter Scan Time = 11:02:21; Parameter PMT Volts = 620; Parameter Scan Date = 2005-02-24; Parameter Pixel Size = 10; Parameter Laser on time = 439106; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.48; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Martin,,Buess


title: HTB-125/MDA-MB436 co-culture 1

description:
Simple annotation: Cell-line, co-culture
Image: http://smd.stanford.edu/MicroArray/gifs/2005-03/59628.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1240, 4880; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Martin,,Buess Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.61; Parameter Scan Time = 11:37:42; Parameter PMT Volts = 600; Parameter Scan Date = 2005-02-24; Parameter Pixel Size = 10; Parameter Laser on time = 220135; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.83; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Martin,,Buess Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.61; Parameter Scan Time = 11:37:42; Parameter PMT Volts = 630; Parameter Scan Date = 2005-02-24; Parameter Pixel Size = 10; Parameter Laser on time = 439141; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.49; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Martin,,Buess


title: HTB-125/HMEC co-culture 1

description:
Simple annotation: Cell-line, co-culture
Image: http://smd.stanford.edu/MicroArray/gifs/2005-03/59622.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1370, 5680; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Martin,,Buess Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.55; Parameter Scan Time = 11:26:28; Parameter PMT Volts = 610; Parameter Scan Date = 2005-02-24; Parameter Pixel Size = 10; Parameter Laser on time = 220124; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.78; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Martin,,Buess Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.30; Parameter Scan Time = 10:51:33; Parameter PMT Volts = 620; Parameter Scan Date = 2005-02-24; Parameter Pixel Size = 10; Parameter Laser on time = 439095; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.48; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Martin,,Buess


title: HTB-125 monoculture 2

description:
Simple annotation: Cell-line, Controls
Image: http://smd.stanford.edu/MicroArray/gifs/2005-03/59621.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1410, 5910; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Martin,,Buess Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.30; Parameter Scan Time = 10:51:33; Parameter PMT Volts = 600; Parameter Scan Date = 2005-02-24; Parameter Pixel Size = 10; Parameter Laser on time = 220089; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.84; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Martin,,Buess Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.30; Parameter Scan Time = 10:51:33; Parameter PMT Volts = 620; Parameter Scan Date = 2005-02-24; Parameter Pixel Size = 10; Parameter Laser on time = 439095; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.48; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Martin,,Buess

source_name: HTB

tag: HTB


title: HDF/MCF-7 co-culture 3

description:
Simple annotation: Cell-line, co-culture
Image: http://smd.stanford.edu/MicroArray/gifs/2004-11/57143.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1240, 5600; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Martin,,Buess Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 32.74; Parameter Scan Time = 10:56:55; Parameter PMT Volts = 580; Parameter Scan Date = 2004-11-02; Parameter Pixel Size = 10; Parameter Laser on time = 203455; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 3.62; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.2; Parameter Scanning software = AxImageIO; Performer: Martin,,Buess Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 32.74; Parameter Scan Time = 10:56:55; Parameter PMT Volts = 580; Parameter Scan Date = 2004-11-02; Parameter Pixel Size = 10; Parameter Laser on time = 422390; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.61; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Martin,,Buess