title: JHB-blood-N-F-006

description:
Simple annotation: Development, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs/2004-02/49247.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1360, 7040; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Paul-Martin,,Holterhus

source_name: Stratagene Reference

tag: Stratagene Reference

tag: Disease State

value: female control

value: time(absolute) 24;8 years


title: PCA_wildtype_rpoN_BR2A

status: Public on Jul 13 2009

type: RNA

city: Amherst

first: Derek

last: Lovley

state: MA

address: University of Massachusetts at Amherst, Dept. of Microbiology, Morrill IV north room 202

department: Microbiology

country: USA

institute: University of Massachusetts Amherst

description: Total RNA (10 ug) was directly labeled with cy5 (pCDrpoN) or cy3 (pCD341)

hyb_protocol: Combimatrix 100 ul volume cap.

scan_protocol: Slide was scanned using GenePix software and a GenePix 4000b scanner.

data_processing:
The raw total intensities were treated as follows to generate the M Log2 ratios for this work.  Background signal was calculated from a set of negative control spots incorporated into the array.  As the negative control sequences are not design specific (ie. are found in all of the ESOAs independent of the organism being sampled) some will inevitably demonstrate strong cross hybridization with the sample of interest.  To avoid this issue the negative control spots were ranked according to their total intensity.  The average of the lowest 30% was calculated.  Background signal was calculated as this mean + 2 standard deviations.  The background signal was then subtracted from the total intensity for each spot.  Probes whose signal was not greater than zero after background subtraction were omitted from further analysis.  For the remaining data, the logged ratios [M=log2 (Ex/Ct)] are then calculated and Lowess global normalization is performed. During the data preprocessing, M vs. A plots before and after normalization, and side-by-side box plots for all arrays are used to assess array quality.(3)  LIMMA mixed model analysis (R-package LIMMA(2))is applied to the normalized logged ratios to identify differentially expressed genes.  Specifically, biological replicates are treated as a randomized block to allow for modeling correlations within them. LIMMA calculates a moderated t statistic for each probe, which is the ratio of the estimated mean logged intensity ratio and the Empirical Bayes estimate of its standard error. The P-value of each oligo is then corrected for multiple comparisons according to Benjamini and Hockberg's procedure(1) to control the false discovery rate. Oligos are ranked according to the adjusted P-values and were called differentially expressed if the adjusted P-values are < 0.001.  Note that multiple oligonucleotide probes from the same gene are analyzed separately and a gene is called differentially expressed if at least half of its probes are called differentially expressed.
1.	Benjamini, Y., and Y. Hochberg. 1995. Controlling the False Discovery Rate - a Practical and Powerful Approach to Multiple Testing. Journal of the Royal Statistical Society Series B-Methodological 57:289-300.
2.	Smyth, G. K. 2004. Linear models and empirical bayes methods for assessing differential expression in microarray experiments. Stat Appl Genet Mol Biol 3:Article3.
3.	Smyth, G. K., and T. Speed. 2003. Normalization of cDNA microarray data. Methods 31:265-73.

molecule: total RNA

organism: Geobacter sulfurreducens

source_name: rpoN overexpressor

label_protocol: Micromax ASAP direct RNA labeling kit

extract_protocol: Qiagen RNEasy Midi protocol

tag: DL1/pCDrpoN was grown in medium containing acetate as the electron donor and fumarate as the electron acceptor.  1mM IPTG was added to induce

tag: rpoN overexpression from plasmid pCDrpoN.

source_name: wildtype (pCD341)

label_protocol: Micromax direct RNA labeling kit

tag: DL1/pCD341 was grown in medium containing acetate as the electron donor and fumarate as the electron acceptor.  1mM IPTG was added to induce

tag: control plasmid pCD341.


title: NRA2, 11_17_06

city: East Lansing

first: Theodora

last: Szasz

state: MI

address: B 445 Life Sciences

department: Pharmacology and Toxicology

institute: Michigan State University

description: Biological replicate 4 of 6

hyb_protocol: Hybridization was performed according to the "CodeLink Gene Expression System: Single-Assay Bioarray Hybridization and Detection" protocol provided by Amersham/GE Healthcare. Ten µg cRNA were fragmented and hybridized to array. Streptavidin-Cy5 conjugate was used for detection.

scan_protocol: Arrays were scanned using the GenePix Array Scanner (Axon Instruments/Molecular Devices) using standard procedures detailed in the "CodeLink Gene Expression System: Single-Assay Bioarray Hybridization and Detection" protocol provided by Amersham/GE Healthcare.

data_processing: Images were acquired using GenePix Pro 6.0 software (Axon Instruments/Molecular Devices), which runs automatic spot-finding algorithms, subtracts background, filters absent and flags low (near background), saturated, noisy or otherwise poor quality spots. Raw intensities of the ~34,000 spots on each array (N=6 for aorta, N=6 for vena cava) were median-normalized as a batch. Normalized intensity values of each spot were averaged and p values were calculated in Microsoft Excel.

label: biotin

organism: Rattus norvegicus

source_name: Sprague-Dawley rat aorta

label_protocol: Labeling was performed according to the "CodeLink Gene Expression System: Manual Labelled cRNA Target Preparation" protocol provided by Amersham/GE Healthcare. Briefly, first-strand cDNA was synthesized starting with one µg DNase-treated total RNA and diluted bacterial mRNA controls. After second-strand synthesis and cDNA purification, cRNA was in vitro transcribed with incorporation of biotin-labeled UTP, purified and assessed for concentration, purity and quality.

extract_protocol: Total RNA was isolated from ~10 mg sections of rat aorta tissue using the MELT TM Total RNA Isolation System (Ambion/Applied Biosystems) according to the manufacturer’s protocol. RNA was then quantified on a NanoDrop spectrophotometer (NanoDrop Technologies/Thermo Fisher Scientific).

tag: Normal (untreated) male Sprague-Dawley rat aorta


title: NRA1, 11_17_06

description: Biological replicate 3 of 6


title: JHB-blood-P-017

city: Kiel

first: Paul-Martin

last: Holterhus

address: Campus Kiel, Schwanenweg 20

department: Pädiatrische Endokrinologie und Diabetologie

country: Germany

institute: Universitätsklinikum Schleswig-Holstein

description:
Simple annotation: Development, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs/2004-04/51379.gif

hyb_protocol: not provided

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1480, 5720; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Paul-Martin,,Holterhus

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

organism: Homo sapiens

source_name: Stratagene Reference (0810006)

label_protocol: We subsequently used 3 ug aRNA, 7.5 ug random-hexamer-primers (Roche), and Cy5-dUTP (0,1 mM) (Amersham, Freiburg, Germany) for Cy5-labeling (pseudo-color red) and 50 ug of human universal reference-RNA (Stratagene; Amsterdam; The Netherlands), 4.5 ug T20VN-primer (TIB MolBiol, Berlin, Germany), and Cy3-dUTP (0,1 mM) (Amersham) for Cy3-labeling (pseudo-color green) to prepare the microarray-probes.

extract_protocol: not provided

tag: Stratagene Reference (0810006)

extract_protocol:
Blood samples were taken at 1:00 pm +/- 1 h (Potassium-EDTA-monovettes, Sarstedt, Numbrecht, Germany) to control for circadian influences on gene expression. Blood was taken from normal male controls, normal female controls as well as different patients with disorders of sex development leading to a dissection of sex chromosomes and external genital phenotype.
All samples were analyzed by a blood cell counter (Beckmann-Coulter, Krefeld, Germany) and white blood cell counts did not differ between the normal males and the normal females (by t-test).
PBMCs were isolated from whole blood using PBS (pH 7.2) and Ficoll (Biochrom, Berlin, Germany) gradient centrifugation. In essence, serum was extracted from whole blood by centrifugation (720 g; 10 min), diluted with 3 ml of PBS and pipetted on top of 5 ml Ficoll. After centrifugation (950 g; 20 min), the cellular interphase was transferred and washed twice with PBS (460 g; 10 min). Total RNA was extracted by TRIZOL (Invitrogen, Karlsruhe, Germany) according to the manufacturer's manual. After extraction and clean-up (RNeasy-Mini-columns, Qiagen, Hilden, Germany), RNA was quantified by spectrophotometry and additionally analyzed for quality by 1% denaturating gel electrophoresis.
Three micrograms of total RNA and 1 ug of T7-oligo(dT)15 were used for linear RNA-amplification. Reverse transcription was done by SuperScript II (400 U) (Invitrogen, Karlsruhe, Germany) at 42degrees C for 90 min. The second-strand synthesis buffer containing RNaseH (2U), DNA-Polymerase-I (40 U), and dNTPs (1 mM) (Roche, Mannheim, Germany) was mixed with the first reaction mixture and subsequently incubated for 2 h at 15degrees C. The reaction was deactivated with 0.05 M NaOH (Merck, Darmstadt, Germany) and 0.1 M EDTA (Merck) and the reaction product was cleaned by phenol-chlorofom-isoamylalcohol (25:24:1) (Merck) and Phase-Lock-Gel-Tubes (Eppendorf, Hamburg, Germany). Subsequently, the in-vitro-transcription-mixture containing T7-RNA-Polymerase (60 U) and NTPs (1 mM) (Roche) was added to the cleaned reaction product and incubated for 5 h at 37degrees C. The resulting aRNA was purified with RNeasy-Mini-columns and quantified by spectrophotometry.

value: 17?-hydroxysteroid-dehydrogenase type III deficiency

tag: Genotype

tag: Measurement

value: time(absolute) 13;3 years

tag: Phenotype


title: JHB-blood-N-M-015

description:
Simple annotation: Development, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs/2004-05/51951.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1760, 7000; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Paul-Martin,,Holterhus

value: male control

value: time(absolute) 42;0 years

value: normal male


title: JHB-blood-P-019

description:
Simple annotation: Development, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs/2004-06/52935.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1280, 5680; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Paul-Martin,,Holterhus

value: gonadal dysgenesis

value: time(absolute) 16;11 years

value: normal female


title: EDL (O157:H7)

status: Public on Jul 11 2009

type: genomic

city: Lethbridge

first: Chad

middle: R

last: Laing

state: Alberta

address: Twp Rd 9-1

department: Laboratory for Foodborne Zoonoses

country: Canada

institute: Public Health Agency of Canada

description: EDL (O157:H7)

hyb_protocol: A 70 μl hybridization solution consisting of 30% formamide, 5x SSC, 0.1% SDS, 0.1mg/ml sonicated Salmon sperm DNA, and equal amounts of test and reference labeled DNAs, each containing at least 30 pmol of incorporated dye, was denatured at 95 oC for 5 min and briefly centrifuged to collect all the contents. DNAs were then hybridized overnight (16 hours) at 42oC

scan_protocol: Arrays were then scanned with a GenePix 4000B scanner (Axon Instruments, Redwood City, CA) or ProScanArray (Perkin Elmer, Shelton, CT) and processed using GenePix Pro 5.0.

data_processing: Data obtained from E. coli O157:H7 microarrays were normalized using the Ratio-based and Lowess methods in Acuity 3.1 (Axon instruments) before analysis. The normalized data for all strains were converted into log2 (Fluor 647/Fluor 546) in Acuity 3.1 and subsequently analyzed in Microsoft Excel. Control, blank, and test spots with a mean intensity below that of the mean of all negative controls were removed from the analysis. The arithmetic mean of the remaining spots across the duplicates was taken to construct the dataset. GACK (Genomotyping Analysis by Charles Kim), was used to generate a cut off value determining the presence or absence of genes, and a dendrogram using the Euclidean distance metric with average linkage was created with tMEV v4.1.

label: Alexa Fluor 647

molecule: genomic DNA

organism: Escherichia coli O157:H7

source_name: Overnight bacterial culture in BHI broth.

label_protocol: 5 μg of test genomic DNA were digested with EcoRV and PstI restriction enzymes, 3 μg of which were labeled with ULYSIS Alexa Fluor 647 dye (Invitrogen, Burlington, ON). Genomic DNA form strains MG1655, Sakai and EDL933, were digested in an analogous fashion, 1 μg of each were combined and labeled with Alexa Fluor 546 dye (Invitrogen, Burlington, ON). This labeled genomic DNA mixture was then used as a reference for all hybridizations. Unincorporated dye was removed using Qiaquick PCR purification kits (Qiagen, Mississauga, ON), according to the manufacturer’s instructions, and DNA was eluted in 30 μl of 0.1x TE buffer. Labeled DNA was vacuum-dried and resuspended in 20 μl of dH2O.

growth_protocol: See the paper Variation in the Genomic islands of porcine enteropathogenic Escherichia coli strains of serogroup O45 revealed by comparative genomic hybridization and PCR by Bruant and Zhang et al. 2009

extract_protocol: The cultures were centrifuged at 8000 rpm for 10 minutes and the pellet was dissolved in 15 mL of 10 mM NaCl, 20 mM Tris-HCl (pH 8.0), 1 mM EDTA, 100 μg/mL proteinase K and 0.5% SDS. This suspension was incubated at 50oC for 2 h and DNA extracted with an equal volume of phenol:chloroform:isoamyl alcohol (25:24:1). Following centrifugation for 10 min at 8000 rpm, the upper phase was removed and precipitated by adding 0.1 volume of 3 M NaOAc (pH 5.2) and 2 volumes of 99% ethanol. The DNA precipitate was then spooled out of the solution using a sterile glass rod, washed with 70% ethanol, and dissolved in 5 mL of TE (10 mM Tris-HCl, 1 mM EDTA, pH 8.0) buffer.

tag: strain

value: EHEC strain

label: Alexa Fluor 546

organism:
Escherichia coli O157:H7 str. EDL933
Escherichia coli O157:H7 str. Sakai
Escherichia coli str. K-12 substr. MG1655

tag: referece

value: The three genomes contributing to the ORFs on the microarray.


title: JHB-blood-N-M-008

description:
Simple annotation: Development, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs/2004-04/51026.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1360, 7640; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Paul-Martin,,Holterhus

value: time(absolute) 25;8 years


title: Sakai (O157:H7)

description: Sakai (O157:H7)

treatment_protocol: See the paper Variation in the Genomic islands of porcine enteropathogenic Escherichia coli strains of serogroup O45 revealed by comparative genomic hybridization and PCR by Bruant and Zhang et al. 2009


title: NRA1, 6_23_06

description: Biological replicate 1 of 6


title: PCA_wildtype_rpoN_BR1A


title: JHB-blood-P-004

description:
Simple annotation: Development, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs/2004-02/49683.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1280, 7160; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Paul-Martin,,Holterhus

value: 5α-reductase type II deficiency

value: time(absolute) 20;4 years


title: PCA_wildtype_rpoN_BR1B


title: 87-4725

organism: Escherichia coli

value: Porcine EPEC strain O45


title: JHB-blood-N-F-009

description:
Simple annotation: Development, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs/2004-03/50332.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1680, 7560; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Paul-Martin,,Holterhus

value: time(absolute) 31;5 years


title: 88-4299


title: 81-4420


title: 89-56-196


title: NRA1_1, 7_8_06

description: Biological replicate 2 of 6


title: 83-2315


title: 86-1390


title: E22

value: Rabbit EPEC strain O103


title: 88-1861


title: 91-19-172


title: HCT116 PS vs DNMT1/DNMT3b DKO

city: Lausanne

first: Eric

last: Paquet

state: Vaud

address: Station 15  CH - 1015

department: Life sciences

country: Switzerland

institute: EPFL

description: Standard Cell Culture, 70% confluent.

hyb_protocol: The protocols supplied by Agilent Technologies were used.

data_processing:
Microarray data were processed using the package limma in BioConductor. The raw data were first background subtracted using the subtract function and the log2 of the remaining intensity was taken. For each array, the DKO/PS ratio was normalized to unity within the 5’ region of the 45S.

The VALUEs represent an average of the log2 DKO/PS ratios from the non-dye-swap and dye-swapped samples.

molecule: nuclear RNA

source_name: HCT116 (PS)

label_protocol: The unamplified nuclear RNAs were directly chemically linked to either Cy3 or Cy5 using the ULS Fluorescent Labeling Kit for Agilent Arrays manufactured by Kreatech Biotechnology following the manufacturer's procedure.

growth_protocol: The HCT116 colorectal carcinoma cell line (parental strain, PS) and the double knockout DNMT1-/-, DNMT3b-/- cell line (clone DKO1) were obtained from B. Vogelstein and were grown as previously described (Rhee et al., 2002).

extract_protocol: Cells were lysed in 10mM Tris-HCl pH7.4, 10mM NaCl, 10mM MgCl2, 0.1% NP40 (IGEPAL CA-630, Sigma I-3021), vortexed at maximum speed for 10 sec, left on ice 10 min, then nuclei recovered by centrifugation 2000rpm (500g), 5 min, 4oC.  RNA was isolated by using Trizol reagent (Invitrogen).

treatment_protocol: None.

tag: cell line

tag: cell type

value: colorectal carcinoma

tag: knockout

source_name: HCT116 DNMT1-/-,DNMT3b-/- (DKO)

value: HCT116, clone DKO1

value: DNMT1, DNMT3b


title: Curcumin-treatment

city: Bangalore

first: Sugandan

last: Sivamani

address: 259, Apurva

department: Microarray Data Analysis

country: India

institute: Genotypic

description: Microarrays were scanned on an Agilent scanner (G2505C) at 100% PMT.Data extraction was carried out with Agilent Feature Extraction software (version 9.1), and normalization was done using linear per array algorithm according to the manufacturer’s protocol

hyb_protocol: The fragmented cRNA were mixed with 25ul of 2x GE Hybridization Buffer (Agilent). About 45ul of the resulting mixture was applied to the Microarray and hybridized at 65degC for 17 hours in an Agilent Microarray Hybridization Chamber (SureHyb: G2534A) with Hybridization Oven. After hybridization, slides were washed with Agilent Gene expression Wash Buffer I for 1 minute at room temperature followed by a 1 min wash with Agilent Gene expression Wash Buffer II for 37C. Slides were finally rinsed with Acetonitrile for cleaning up and drying.

scan_protocol: Laser detection of Cyanine 3 and Cyanine 5 fluorescence is performed using a confocal scanning instrument containing two tuned lasers, which excite Cyanine dyes at the appropriate wavelengths.

data_processing: Feature extracted data was analyzed using GeneSpring GX v 7.3.1 software from Agilent. Normalization of the data was done in GeneSpring GX using the recommended one color Per Chip and Per Gene Data Transformation: Set measurements less than 0.01 to 0.01, Per Chip: Normalize to 50th percentile, Per Gene: Normalize to Specific Samples. Further quality control of normalized data was done using correlation based condition tree to eliminate bad experiments. Differentially regulated Genes were filtered with cutoff of > 1.5 for Up regulation and < 0.55 for Down Regulation were obtained. Differentially regulated genes were clustered using gene tree to identify significant gene expression patterns.

source_name: curcumin-treated human retinoblastoma Y79

label_protocol: T7 promoter based-linear amplification to generate labeled complementary RNA

extract_protocol: The whole of tissue was used for RNA isolation by using Qiagen Rneasy Minikit (Cat No: 74106) as per the manufacturer’s instructions . The RNA was eluted in 30 µl of RNase free water (Ambion, AM9939). RNA concentration and purity was determined at an optical density ratio of 260/280 using the Nanodrop® ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE) and the integrity of total RNA was verified on an Agilent 2100 Bioanalyzer using the RNA 6000 Nano LabChip (Agilent Technologies). RNA was stored at −80 °C until use

treatment_protocol: 20µM curcumin

value: retinoblastoma


title: 247-infected B, d10

city: Glasgow

first: Liam

last: Morrison

address: 120 University Avenue

department: Wellcome Centre for Molecular Parasitology

country: United Kingdom

institute: University of Glasgow

description: Gene expression data from mouse spleen infected with T. brucei STIB247.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip® Mouse Genome 430A 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix Genechip Scanner 3000 7G.

data_processing: Analysis was done using the module Affy of the BioConductor microarray analysis software, with normalisation by the Robust Multichip Average (RMA) method (Irizarry et al., 2003). Analysis of expression differences was carried out using RankProducts (RP)(Breitling et al., 2004).

organism: Mus musculus

source_name: 247-infected spleen, day 10

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

growth_protocol: Infected mice were inoculated via the intraperitoneal route with 1 x 10^4 trypanosomes, and euthanised at day 10 post infection. Spleens were dissected and snap frozen in liquid nitrogen. Spleens from uninfected mice from the same batch were taken in the same way at the same time.

extract_protocol: RNA was extracted using the Qiagen total RNA kit according to the manufacturer's instructions.

treatment_protocol: Spleens were placed in liquid nitrogen immediately post-dissection and stored at -80 degrees until RNA extraction.

value: BALB/c

tag: tissue

value: spleen

tag: infection

value: Trypanosoma brucei STIB247


title: 247-infected A, d10


title: Uveal melanoma, non-invasive

description: Microarrays were scanned on an Agilent scanner (G2505C) at 100% PMT with 10% for lower intensity (XDR Scanning).Data extraction was carried out with Agilent Feature Extraction software (version 9.1), and normalization was done using linear per array algorithm according to the manufacturer’s protocol

hyb_protocol: See Agilent Technologies website for miRNA microarray hybridization and wash protocol: http://www.chem.agilent.com/scripts/LiteraturePDF.asp?iWHID=50500

data_processing: Feature extracted data was analyzed using GeneSpring GX v 10.0.2 software from Agilent. Normalization of the data was done in GeneSpring GX using the recommended Percentile shift normalization (50th percentile) . Further quality control of normalized data was done using correlation based condition tree to eliminate bad experiments. High expressed miRNA's were clustered using gene tree to identify significant gene expression patterns.

source_name: Uveal melanoma, non-invasive

label_protocol:
Ligation of one cyanine3 –pCp molecule to the 3’ end of RNA molecule with
greater than 90% efficiency that generates fluorescent miRNA.

extract_protocol: Mirvana extraction protocol

tag: tissue type

value: Intra ocular tumor sample

value: Uveal melanoma, non-invasive choroidal melanoma

tag: tissue source

value: formalin fixed paraffin embedded sections


title: Scopoletin-treatment

description: Microarrays were scanned on an Agilent scanner (G2505C) at 100% laser power.Data extraction was carried out with Agilent Feature Extraction software (version 9.1), and normalization was done using linear per array algorithm according to the manufacturer’s protocol

source_name: scopoletin-treated human retinoblastoma Y79

treatment_protocol: Human retinoblastoma Y79 cell line collected at 48 hours after scopoletin treatment.


title: uninfected C, d10

description: Gene expression data from uninfected mouse spleen.

source_name: uninfected spleen, day 10

value: uninfected


title: 927-infected C, d10

description: Gene expression data from mouse spleen infected with T. brucei TREU927.

source_name: 927-infected spleen, day 10

value: Trypanosoma brucei TREU927


title: uninfected B, d10


title: Uveal melanoma, invasive

source_name: Uveal melanoma, invasive

value: Uveal melanoma, invasive (confirmed liver metastasis)


title: 247-infected C, d10


title: 927-infected A, d10


title: Untreated control 2

description: Microarrays were scanned on an Agilent scanner (G2565AA) at 100% laser power, 30% PMT.Data extraction was carried out with Agilent Feature Extraction software (version 9.1), and normalization was done using linear per array algorithm according to the manufacturer’s protocol

source_name: untreated human retinoblastoma Y79

treatment_protocol: Untreated human retinoblastoma Y79 cell line cultured in RPMI 1640 supplemented with 10% heat-inactivated fetal calf serum, 0.1 % ciprofloxacin, 2mM L-Glutamine, 1mM sodium pyruvate, 4.5% dextrose and grown in suspension at 37C in 5% CO2 humidified incubator.


title: 86-4220

value: The three genomes contributing to the ORFs on the microarray.


title: 927-infected B, d10


title: uninfected A, d10


title: Cerulenin-treatment

description: Microarrays were scanned on an Agilent scanner (G2505C) at 100%  PMT.Data extraction was carried out with Agilent Feature Extraction software (version 9.1), and normalization was done using linear per array algorithm according to the manufacturer’s protocol

data_processing: Feature extracted data was analyzed using GeneSpring GX v 10.0.2 software from Agilent. Normalization of the data was done in GeneSpring GX using the recommended Percentile shift normalization (75th percentile) and Normalize to baseline of control samples. Further quality control of normalized data was done using correlation based condition tree to eliminate bad experiments. Differentially regulated Genes were filtered with cutoff of Fold > 1 for Up regulation and Fold < -1 for Down Regulation were obtained. Differentially regulated genes were clustered using gene tree to identify significant gene expression patterns.

source_name: cerulenin-treated human retinoblastoma Y79

treatment_protocol: Human retinoblastoma Y79 cell line collected after 7µg/ml cerulenin treatment.


title: Untreated control 1

description: Microarrays were scanned on an Agilent scanner (G2565AA) at 100% laser power, 30% PMT.Data extraction was carried out with Agilent Feature Extraction software (version 9.1), and normalization was done using linear per array algorithm according to the manufacturer’s protocol.

extract_protocol: The whole of tissue was used for RNA isolation by using Qiagen Rneasy Minikit (Cat No: 74106) as per the manufacturer’s instructions . The RNA was eluted in 30 µl of RNase free water (Ambion, AM9939). RNA concentration and purity was determined at an optical density ratio of 260/280 using the Nanodrop® ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE) and the integrity of total RNA was verified on an Agilent 2100 Bioanalyzer using the RNA 6000 Nano LabChip (Agilent Technologies). RNA was stored at −80 °C until use.


title: iPPSC, ID4 passage 7

status: Public on Jul 10 2009

city: Columbia

first: Toshihiko

last: Ezashi

state: MO

address: 240a CS Bond Life Sciences Center

department: Animal Sciences

institute: University of Missouri-Columbia

description: Gene expression data from iPPSC cultured in hESC medium on MEF feeder for 5 days

hyb_protocol: Biotin labeled cRNA samples were fragmented and then hybridized to the Affymetrix GeneChip® Porcine Genome Array.

scan_protocol: The data from microarrays was obtained by scanning microarrays using GeneChip® Scanner 3000.

data_processing: The expression data were extracted using the Micro-Array Suite 5.0 software (Affymetrix).

organism: Sus scrofa

source_name: EGFP-PFF were reprogrammed with four reprogramming genes, OCT4, SOX2, KLF4 and c-MYC, and clonally expanded.

label_protocol: 10 µg each of high quality total RNA was used in double stranded cDNA synthesis and labeling reactions using the GeneChip® Expression 3’-Amplification IVT Labelling Kit (Affymetrix)

growth_protocol: iPPSC at passage 7 cultured in hESC medium on MEF feeder for 5 days

extract_protocol: RNA from 3 iPPSC clones in addition to two porcine fetal fibroblasts (EGFP-PFF) was extracted using STAT-60 reagent.

treatment_protocol: Progenitor EGFP-PFF were cultured in DMEM/10%FBS medium.

value: induced porcine pluripotent stem cells (iPPSC) with lentiviral transduction of four reprogramming genes, OCT4, SOX2, KLF4 and c-MYC


title: EpCAM siRNA

source_name: siRNA-treated human retinoblastoma Y79

treatment_protocol: Human retinoblastoma y79 cell line collected at 48 hours after epcam-sirna treatment to silence epcam gene expression (gene: TACSTD1)


title: Progenitor porcine fetal fibroblast, biological rep2

description: Gene expression data from EGFP-PFF cultured in DMEM/10%FBS medium

source_name: EGFP-PFF derived at day 34 of pregnancy

value: Progenitor porcine fetal fibroblast


title: iPPSC, IC1 passage 7


title: Progenitor porcine fetal fibroblast, biological rep1


title: iPPSC, ID6 passage 7


title: shfy110|MDA134

city: Stanford

first: Jonathan

last: Pollack

state: CA

address: 269 Campus Drive, CCSR3245A

department: Pathology

institute: Stanford University

description:
Simple annotation: Breast, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2004-10/56232.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1800, 5240; Software: type: feature extraction; Performer: Melanie,,Bocanegra Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2004-10-06; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter PMT Volts = 550; Parameter Laser on time = 50407; Parameter Laser Power = 3.52; Parameter Scan Time = 15:07:07; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [94858]; Parameter Focus Position = 0; Parameter Scan Temperature = 30.36; Performer: Melanie,,Bocanegra Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2004-10-06; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.1; Parameter Pixel Size = 10; Parameter PMT Volts = 570; Parameter Scan Power = 100; Parameter Laser on time = 50452; Parameter Laser Power = 3.48; Parameter Scan Time = 15:07:07; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [94858]; Parameter Focus Position = 0; Parameter Scan Temperature = 30.36; Performer: Melanie,,Bocanegra

source_name: Normal human female genomic DNA

label_protocol: not provided

tag: Normal human female genomic DNA

source_name: Breast Tumor Cell Line MDA134 genomic DNA


title: shfk169|SUM190 vs. NF|

description:
Simple annotation: Breast, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2004-09/55863.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 2160, 5480; Software: type: feature extraction; Performer: Jessica,,Kao Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2004-09-23; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter PMT Volts = 650; Parameter Laser on time = 48923; Parameter Laser Power = 3.52; Parameter Scan Time = 13:46:19; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [94858]; Parameter Focus Position = 0; Parameter Scan Temperature = 32.09; Performer: Jessica,,Kao Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2004-09-23; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.1; Parameter Pixel Size = 10; Parameter PMT Volts = 680; Parameter Scan Power = 100; Parameter Laser on time = 48968; Parameter Laser Power = 3.49; Parameter Scan Time = 13:46:19; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [94858]; Parameter Focus Position = 0; Parameter Scan Temperature = 32.09; Performer: Jessica,,Kao

source_name: Breast Tumor Cell Line SUM190 genomic DNA


title: shfk237_sr|MDAMB157 vs. NF|

description:
Simple annotation: Breast, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2004-07/54202.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 2320, 6000; Software: type: feature extraction; Performer: Jessica,,Kao Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2004-05-06; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter PMT Volts = 610; Parameter Laser on time = 33580; Parameter Laser Power = 3.47; Parameter Scan Time = 12:39:53; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [94858]; Parameter Focus Position = 0; Parameter Scan Temperature = 29.62; Performer: Jessica,,Kao Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2004-05-06; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.1; Parameter Pixel Size = 10; Parameter PMT Volts = 650; Parameter Scan Power = 100; Parameter Laser on time = 33623; Parameter Laser Power = 3.53; Parameter Scan Time = 12:39:53; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [94858]; Parameter Focus Position = 0; Parameter Scan Temperature = 29.62; Performer: Jessica,,Kao

source_name: Breast Tumor Cell Line MDAMB157 genomic DNA


title: shfy112|MDA468

description:
Simple annotation: Breast, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2004-10/55939.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1800, 5400; Software: type: feature extraction; Performer: Melanie,,Bocanegra Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2004-09-29; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter PMT Volts = 500; Parameter Laser on time = 50008; Parameter Laser Power = 3.52; Parameter Scan Time = 14:21:52; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [94858]; Parameter Focus Position = 0; Parameter Scan Temperature = 31.39; Performer: Melanie,,Bocanegra Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2004-09-29; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.1; Parameter Pixel Size = 10; Parameter PMT Volts = 530; Parameter Scan Power = 100; Parameter Laser on time = 50053; Parameter Laser Power = 3.50; Parameter Scan Time = 14:21:52; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [94858]; Parameter Focus Position = 0; Parameter Scan Temperature = 31.39; Performer: Melanie,,Bocanegra

source_name: Breast Tumor Cell Line MDA468 genomic DNA


title: SHFY72|HCC70

description:
Simple annotation: Breast, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2005-12/66006.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 2080, 5640; Software: type: feature extraction; Performer: Melanie,,Bocanegra Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2005-12-02; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter PMT Volts = 540; Parameter Laser on time = 68950; Parameter Laser Power = 3.64; Parameter Scan Time = 13:47:05; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [94858]; Parameter Focus Position = 0; Parameter Scan Temperature = 29.78; Performer: Melanie,,Bocanegra Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2005-12-02; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.1; Parameter Pixel Size = 10; Parameter PMT Volts = 500; Parameter Scan Power = 100; Parameter Laser on time = 68995; Parameter Laser Power = 3.41; Parameter Scan Time = 13:47:05; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [94858]; Parameter Focus Position = 0; Parameter Scan Temperature = 29.78; Performer: Melanie,,Bocanegra

source_name: Breast Tumor Cell Line HCC70 genomic DNA


title: SHFY62|HCC712

description:
Simple annotation: Breast, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2005-12/66009.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1920, 5080; Software: type: feature extraction; Performer: Melanie,,Bocanegra Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2005-12-02; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter PMT Volts = 550; Parameter Laser on time = 68978; Parameter Laser Power = 3.66; Parameter Scan Time = 14:15:01; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [94858]; Parameter Focus Position = 0; Parameter Scan Temperature = 30.48; Performer: Melanie,,Bocanegra Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2005-12-02; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.1; Parameter Pixel Size = 10; Parameter PMT Volts = 520; Parameter Scan Power = 100; Parameter Laser on time = 69023; Parameter Laser Power = 3.44; Parameter Scan Time = 14:15:01; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [94858]; Parameter Focus Position = 0; Parameter Scan Temperature = 30.48; Performer: Melanie,,Bocanegra

source_name: Breast Tumor Cell Line HCC712 genomic DNA


title: shfk253_sr|MDA453 vs. NF|

description:
Simple annotation: Breast, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2004-07/54201.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 2200, 5360; Software: type: feature extraction; Performer: Jessica,,Kao Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2004-05-06; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter PMT Volts = 650; Parameter Laser on time = 33569; Parameter Laser Power = 3.47; Parameter Scan Time = 12:29:30; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [94858]; Parameter Focus Position = 0; Parameter Scan Temperature = 29.29; Performer: Jessica,,Kao Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2004-05-06; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.1; Parameter Pixel Size = 10; Parameter PMT Volts = 650; Parameter Scan Power = 100; Parameter Laser on time = 33612; Parameter Laser Power = 3.52; Parameter Scan Time = 12:29:30; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [94858]; Parameter Focus Position = 0; Parameter Scan Temperature = 29.29; Performer: Jessica,,Kao

source_name: Breast Tumor Cell Line MDA453 genomic DNA


title: shfk146|BT-20 vs. NF|

description:
Simple annotation: Breast, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2004-07/54209.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 2360, 5640; Software: type: feature extraction; Performer: Jessica,,Kao Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2004-07-22; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter PMT Volts = 590; Parameter Laser on time = 41350; Parameter Laser Power = 3.52; Parameter Scan Time = 11:52:08; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [94858]; Parameter Focus Position = 0; Parameter Scan Temperature = 28.65; Performer: Jessica,,Kao Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2004-07-22; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.1; Parameter Pixel Size = 10; Parameter PMT Volts = 540; Parameter Scan Power = 100; Parameter Laser on time = 41394; Parameter Laser Power = 3.48; Parameter Scan Time = 11:52:08; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [94858]; Parameter Focus Position = 0; Parameter Scan Temperature = 28.65; Performer: Jessica,,Kao

source_name: Breast Tumor Cell Line BT-20 genomic DNA


title: shfk234|NM vs. NF|

description:
Simple annotation: Breast, Control experiment
Image: http://smd.stanford.edu/MicroArray/gifs/2004-04/51439.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 2160, 5400; Software: type: feature extraction; Performer: Jessica,,Kao Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2004-04-27; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter PMT Volts = 540; Parameter Laser on time = 32713; Parameter Laser Power = 3.46; Parameter Scan Time = 12:08:48; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [94858]; Parameter Focus Position = 0; Parameter Scan Temperature = 27.43; Performer: Jessica,,Kao Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2004-04-27; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.1; Parameter Pixel Size = 10; Parameter PMT Volts = 650; Parameter Scan Power = 100; Parameter Laser on time = 32757; Parameter Laser Power = 3.51; Parameter Scan Time = 12:08:48; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [94858]; Parameter Focus Position = 0; Parameter Scan Temperature = 27.43; Performer: Jessica,,Kao

source_name: Normal human male genomic DNA

tag: Normal human male genomic DNA


title: Liver Study2 336h Vehicle_Control dose 0 - rep 2

status: Public on Jul 29 2009

city: Basel

first: Adrian

middle: B

last: Roth

address: Grenzacherstr 124

department: NCS

institute: Roche

description: Gene expression data from rat liver, vehicle control

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Rat U34a Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.

data_processing: MAS 5 data summarization was carrried out using the simpleaffy package in Bioconductor (call.exprs function). Values were calculated on a linear scale, afterwards a quantile normalization was applied across all arrays.

source_name: Male Wistar Rat Liver

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA (Expression Analysis Technical Manual, Affymetrix).

growth_protocol: All animals received ethical care as specified by Swiss law and in accordance with the 'Guide for the care and use of laboratory animals' published by the NIH. The test facility is fully accredited by the Association for Assessment and Accreditation of Laboratory Animal Care International (AAALAC). The study was based on guidelines proposed by the ICH (International Conference on Harmonisation of Technical Requirements for Registration of Pharmaceuticals for Human Use) and the CPMP (Committee for Proprietary Medicinal Products of the EMEA [European Agency for the Evaluation of Medicinal Products]) and the OECD.

extract_protocol: RNeasy extraction of total RNA was performed according to the manufacturer's instructions (Qiagen).

treatment_protocol: Eight-week-old male Wistar rats were dosed orally (gavage) once daily with the indicated dose of either test compound or vehicle (citric acid buffer) and sacrificed by carbon dioxide asphyxiation 24 hrs after the last dosing. The livers of all animals were excised immediately  and a tissue slice which consisted of ca. ¼ from the bottom of the left lateral lobe was placed in RNALater (Ambion, TX, USA) at 4°C for 24 hrs to allow penetration of the tissue and then stored at -20°C until further processing for gene expression analysis.

tag: gender

value: Male

value: Liver

value: Wistar

tag: treatment

tag: dose amount (mg_per_kg_per_day)

tag: sampling time (hours)


title: KC0231 (T14S3-A1)

city: Cold Spring Harbor

first: Nicholas

last: Navin

state: NY

address: 1 Bungtown Road

institute: Cold Spring Harbor Laboratory

description: This experiment was done in colour reversal.

hyb_protocol: Hybridizations consisted of 35 uL of hybridization solution (37% formamide, 4x SSC, 0.1%SDS, and labeled DNA). Samples were denatured in an MJ Research Tetrad (Bio-Rad, Hercules, CA) at 95 degrees C for 5 min, and then pre-annealed at 37 degrees C for no more than 30 min. The solution was then applied to the microarray and hybridized under a coverslip in an oven at 42 degrees C for 14 to 16 h. Thereafter, slides were washed 1 min in 0.2% SDS/0.2x SSC, 30 sec in 0.2x SSC, and 30 sec in 0.05x SSC. Slides were dried by centrifugation and scanned immediately.

scan_protocol: Scanned on an Axon GenePix 4000B scanner using a pixel size of 5 um. Microarrays were scanned and gridded using GenePix Pro 4.0 software (MDS Analytical Technologies, Toronto, Canada) and data were imported into S-Plus 2000 analysis software (Insightful, Seattle, WA).

data_processing:
The data were normalized using a lowess curve-fitting algorithm, followed by a local normalization (previously described in Hicks et al.). After placement in genome order, the mean of log ratios was computed for color reversal experiments for each sample. Segmentation was performed on the above-described data. Segments are defined as non-overlapping, genomic regions where copy number has changed. Our segmentation method is based on the minimization of the square-sum of differences between log-ratios and means (squared deviation) over segments larger than 6 probes in size. Initially, the segmenter searches for breakpoints that might be boundaries of segments. The first known breakpoint on a given chromosome is its first probe. For a given breakpoint, a 100-probe window to its right is selected. The sum of squared deviations of the flanking probes is calculated for each probe within this window. A probe whose squared deviation value produces a local minimum with respect to its neighbors, and is below a threshold of 95% of the square deviation within a window, is accepted as a new, known breakpoint. Whenever a probe is found below the threshold in the newly defined region, the segmenter recursively breaks said region into two pieces until it cannot find any further breakpoints therein. If no breakpoints are found, the 100- probe window is shifted by half its size and this procedure continues until a chromosome end is reached. Initial segments are constructed using found breakpoints. Each segment and its neighbors are validated for significance by the Kolmogorov-Smirnov (K-S) algorithm. If the p-value of compared segments is less than 10-5, then said segment is accepted as real. If not, the segments are merged. The segmenter also reports statistics such as mean, standard deviation, and median for each segment.

The VALUEs combine the data from both color-reversal (non-dye swap and dye swap) samples.

label_protocol: Briefly, complexity-reduced representations consisting of small (200-1200 bp) fragments were amplified by adapter-mediated PCR of genomic DNA. DNA samples (2 ug) were labeled either with Cy5-dCTP or Cy3-dCTP using Amersham-Pharmacia MegaPrime labeling kit (Amersham Biosciences, Piscataway, NJ), and competitively hybridized to each other on the same slide. Each sample genome was analyzed in duplicate, swapping the Cy5 and Cy3 dyes with the control (i.e. "colour reversal").

extract_protocol: Qiagen Genomic DNA Isolation Kit (cat# 51306).

value: Ductal Breast Carcinoma

value: EBV Immortalized Fibroblast Reference


title: SHFY67|HCC3153

description:
Simple annotation: Breast, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2005-12/66007.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1800, 5400; Software: type: feature extraction; Performer: Melanie,,Bocanegra Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2005-12-02; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter PMT Volts = 540; Parameter Laser on time = 68959; Parameter Laser Power = 3.64; Parameter Scan Time = 13:55:18; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [94858]; Parameter Focus Position = 0; Parameter Scan Temperature = 29.96; Performer: Melanie,,Bocanegra Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2005-12-02; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.1; Parameter Pixel Size = 10; Parameter PMT Volts = 540; Parameter Scan Power = 100; Parameter Laser on time = 69004; Parameter Laser Power = 3.45; Parameter Scan Time = 13:55:18; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [94858]; Parameter Focus Position = 0; Parameter Scan Temperature = 29.96; Performer: Melanie,,Bocanegra

source_name: Breast Tumor Cell Line HCC3153 genomic DNA


title: Virgin mouse myometrium, biological rep3

city: Cincinnati

first: Nathan

last: Salomonis

state: OH

address: 3333 Burnet Avenue

department: Biomedical Informatics

institute: Cincinnati Children's Hospital

description: Exon-junction, exon, constitutive region hybridizing probesets from undifferentiated wild-type E14 embryonic stem cells

hyb_protocol: According to manufacturer's (Affymetrix) recommendations

data_processing: Probeset intensity values for Affymetrix AltMouseA Array(perfect match only custom array) CEL files were obtained using the RMA package from Bioconductor, using the appropriate CDF file

source_name: Virgin mouse myometrium

label_protocol: RNA was converted to cDNA primed with random hexamers using the SuperScript II enzyme (Invitrogen), fragmented with DNAse1 (0.6U/ul) (Amersham Pharmacia Biotech) at 37 C to yield 50-200nt fragements (Agilent Bioanalyzer),  purifie

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

treatment_protocol: mouse myometrium was harvested from adult fvbn mice as described by salomonis et al. genome biol. 2005;6(2): R12.

value: mouse myometrium


title: Virgin mouse myometrium, biological rep4

scan_protocol: According to manufacturer's (Affymetrix) recommendations


title: Virgin mouse myometrium, biological rep2


title: Virgin mouse myometrium, biological rep5


title: Virgin mouse myometrium, biological rep1


title: KC0247 (T14S5-A2)


title: 6 hours postpartum, mouse myometrium, biological rep4

description: Exon-junction, exon, constitutive region hybridizing probesets from undifferentiated wild-type E18 embryonic stem cells

source_name: 6 hours postpartum, mouse myometrium

tag: age

value: 6 hours


title: KC0243 (T14S6-A1)


title: KC0141 (T13S2-A1)


title: KC0229 (T14S2-A1)


title: 6 hours postpartum, mouse myometrium, biological rep2


title: 6 hours postpartum, mouse myometrium, biological rep3


title: KC0143 (T13S3-A2)


title: KC0133 (T13S6-A1)


title: KC0237 (T14S5-A1)


title: KC0233 (T14S4-A1)


title: 18 days gestation, mouse myometrium, biological rep5

source_name: 18 days gestation, mouse myometrium

value: 18 days


title: 6 hours postpartum, mouse myometrium, biological rep1


title: KC0177 (T13N)

value: Normal Matched Breast Tissue


title: KC0137 (T13S5-A1)


title: 18 days gestation, mouse myometrium, biological rep4


title: KC0121 (T13S1-A1)


title: KC0165 (T12S1-A)


title: 14 days gestation, mouse myometrium, biological rep3

source_name: 14 days gestation, mouse myometrium

value: 14 days


title: 14 days gestation, mouse myometrium, biological rep2


title: Wild-type mouse cardiac ventricle, biological rep5

source_name: Wild-type mouse cardiac ventricle

treatment_protocol: Non-transgenic control mouse heart. Cardiac ventrical was harvested from FVBN mice raised on a non-supplemented chow diet.

value: Non-transgenic control mouse heart


title: KC0147 (T13S4-A1)


title: KC0241 (T14S4-A2)


title: KC0253 (T14S6-A2)


title: Wild-type mouse cardiac ventricle, biological rep4


title: Wild-type mouse cardiac ventricle, biological rep3


title: Wild-type mouse cardiac atria, biological rep5

source_name: Wild-type mouse cardiac atria

treatment_protocol: Non-transgenic control mouse heart. Cardiac atria was harvested from FVBN mice raised on a non-supplemented chow diet.


title: Wild-type mouse cardiac ventricle, biological rep1


title: Wild-type mouse cardiac ventricle, biological rep2


title: 18 days gestation, mouse myometrium, biological rep1


title: 14 days gestation, mouse myometrium, biological rep4


title: 14 days gestation, mouse myometrium, biological rep1


title: KC0169 (T12N)


title: 8-week expressing Ro1 mouse cardiac ventricle, biological rep5

treatment_protocol: transgenic mouse heart, expressing the g alpha i coupled receptor, ro1 (rassl or receptor activated solely by a synthetic ligand type opioid 1) protein under the conditional control of the myosin-alpha-heavy chain promoter using the tetracycline transactivator (tta) system. cardiac ventrical was harvested from fvbn mice withdrawn from a doxycycline chow diet for 8-weeks, developing a severe dilated cardiomyopathy. mice were raised (fetal through adulthood) on doxycycline (redfern ch et al. proc natl acad sci u s a. 2000 apr 25;97(9): 4826-31).

value: 8 weeks


title: 18 days gestation, mouse myometrium, biological rep3


title: Wild-type mouse cardiac atria, biological rep3


title: Wild-type mouse cardiac atria, biological rep2


title: 8-week expressing Ro1 mouse cardiac ventricle, biological rep2

value: transgenic mouse heart, expressing the g alpha i coupled receptor, ro1 (rassl or receptor activated solely by a synthetic ligand type opioid 1) protein


title: Wild-type mouse cardiac atria, biological rep1


title: 8-week expressing Ro1 mouse cardiac ventricle, biological rep4


title: 14 days gestation, mouse myometrium, biological rep5


title: Wild-type mouse cardiac atria, biological rep4


title: 8-week expressing Ro1 mouse cardiac ventricle, biological rep3


title: 18 days gestation, mouse myometrium, biological rep2


title: Recovered Ro1 mouse cardiac ventricle, biological rep2

source_name: Recovered Ro1 mouse cardiac ventricle

treatment_protocol: transgenic mouse heart, expressing the g alpha i coupled receptor, ro1 (rassl or receptor activated solely by a synthetic ligand type opioid 1) protein under the conditional control of the myosin-alpha-heavy chain promoter using the tetracycline transactivator (tta) system. cardiac ventrical was harvested from fvbn\ mice withdrawn from a doxycycline chow diet for 8-weeks (developing a severe dilated cardiomyopathy) and then recovered for 4-weeks by re-administration of doxycyline. mice were raised (fetal through adulthood) on doxycycline (redfern ch et al. proc natl acad sci u s a. 2000 apr 25;97(9): 4826-31).


title: 8-week expressing Ro1 mouse cardiac ventricle, biological rep1


title: Recovered Gnaq mouse cardiac ventricle, biological rep2

source_name: Recovered Gnaq mouse cardiac ventricle

treatment_protocol: Transgenic mouse heart, expressing the G alpha q protein under the conditional control of the myosin-alpha-heavy chain promoter using the tetracycline transactivator (tTA) system. Cardiac ventrical was harvested from FVBN mice withdrawn from a doxycycline chow diet for 8-weeks (developing a mild hypertrophic cardiomyopathy) and then recovered for 4-weeks by re-administration of doxycyline. Mice were raised (fetal through adulthood) on doxycycline.


title: Recovered Gnaq mouse cardiac ventricle, biological rep3

value: Transgenic mouse heart, expressing the G alpha q protein


title: Recovered Gnaq mouse cardiac ventricle, biological rep1


title: 8-week expressing Gnaq mouse cardiac ventricle, biological rep4

treatment_protocol: Transgenic mouse heart, expressing the G alpha q protein under the conditional control of the myosin-alpha-heavy chain promoter using the tetracycline transactivator (tTA) system. Cardiac ventrical was harvested from FVBN mice withdrawn from a doxycycline chow diet for 8-weeks, developing a mild hypertrophic cardiomyopathy. Mice were raised (fetal through adulthood) on doxycycline.


title: 8-week expressing MH-tTA control mouse cardiac ventricle, biological rep2

treatment_protocol: single transgenic control mouse heart, expressing the tetracycline transactivator (tta) protein under the control of the myosin-alpha-heavy chain promoter. cardiac ventrical was harvested from fvbn mice withdrawn from a doxycycline chow diet for 8-weeks. mice were raised (fetal through adulthood) on doxycycline (redfern ch et al. proc natl acad sci u s a. 2000 apr 25;97(9): 4826-31).

value: single transgenic control mouse heart


title: 8-week expressing MH-tTA control mouse cardiac ventricle, biological rep1


title: 8-week expressing Gnaq mouse cardiac ventricle, biological rep3


title: Mouse undifferentiated ESCs, biological rep4

source_name: Mouse embryonic stem cell

treatment_protocol: Mouse E14 ESCs were grown in a monolayer on gelatin-coated culture plates, maintained in medium supplemented with 10% FBS, sodium pyruvate, non-essential amino-acids, beta-mercaptoethanol, LIF, and passaged with trypsin.

value: undifferentiated wild-type E14 embryonic stem cells


title: 8-week expressing MH-tTA control mouse cardiac ventricle, biological rep3


title: 8-week expressing MH-tTA control mouse cardiac ventricle, biological rep5


title: Sample NA18635

status: Public on Jul 27 2009

city: San Diego

last: Illumina Inc.

address: 9885 Towne Centre Drive

institute: Illumina Inc.

hyb_protocol: standard Illumina protocol

scan_protocol: standard Illumina protocol

data_processing: standard Illumina protocol

label: C-Bio and A-DNP

label_protocol: standard Illumina protocol

extract_protocol: standard Illumina protocol

tag: sample


title: Mouse undifferentiated ESCs, biological rep1


title: 8-week expressing Gnaq mouse cardiac ventricle, biological rep1


title: 8-week expressing MH-tTA control mouse cardiac ventricle, biological rep4


title: Mouse day 14 embryoid bodies, biological rep4

source_name: Mouse E14 undifferentiated ESCs

treatment_protocol: Mouse E14 ESCs were differentiated to embryoid bodies using the hanging drop method in medium supplemented with 20% FBS, sodium pyruvate, non-essential amino-acids and beta-mercaptoethanol for 14 days.


title: Mouse day 14 embryoid bodies, biological rep5


title: Mouse day 14 embryoid bodies, biological rep3


title: Mouse undifferentiated ESCs, biological rep3


title: 8-week expressing Gnaq mouse cardiac ventricle, biological rep2


title: Recovered Ro1 mouse cardiac ventricle, biological rep1


title: Mouse day 14 embryoid bodies, biological rep1


title: Patient o77 with diffuse large B cell lymphoma

city: Nagoya

first: Masao

last: Seto

state: Aichi

address: Kanokoden 1-1

department: Dept. of molecular medicine

country: Japan

institute: Aichi Cancer Certer Res. Ins.

hyb_protocol: Cy5-sample cRNA and Cy3-common reference cRNA were hybridized to a custom Agilent oligonucleotide microarray, containing a total of 21,619 spots corresponding to 18,175 unique genes, followed by confocal laser scanning (Agilent Technologies).

scan_protocol: Scanned on an Agilent G2565BA scanner. Images were quantified using Agilent Feature Extraction Software (version 9.1.3.1).

data_processing: LOWESS normalized, background subtracted VALUE data obtained from log10 of processed Red signal/processed Green signal. Agilent software was used.

source_name: diffuse large B cell lymphoma

label_protocol: cRNA was generated and labeled with Cy3 or Cy5 (CyDye, Amersham Pharmacia Biotech, Piscataway, NJ) using the Low RNA Fluorescent Linear Amplification kit (Agilent Technologies, Palo Alto, CA).

extract_protocol: Total RNA was extracted using the RNeasy kit (Qiagen, Valencia, CA), followed by treatment with DNase I. Double-stranded cDNA was synthesized from 250 ng of total RNA using MMLV-RT and poly dT primer incorporating the T7 promoter.

tag: annotation

tag: sex

value: M

tag: ipi

value: LI

value: negative

value: positive

tag: a20 status

value: without A20 loss

source_name: Normal lymph node mixture

tag: sample type

value: reference


title: Mouse day 14 embryoid bodies, biological rep2

tag: cell type


title: Patient o76 with diffuse large B cell lymphoma

source_name: diffuse large b cell lymphoma

value: F

value: L


title: Patient o75 with diffuse large B cell lymphoma

value: HI


title: Patient o71 with diffuse large B cell lymphoma

tag: ipi:


title: Patient o67 with diffuse large B cell lymphoma

source_name: diffuse largae B cell lymphoma

value: reactive lymph node


title: Patient o68 with diffuse large B cell lymphoma


title: Patient o70 with diffuse large B cell lymphoma


title: Patient o52 with diffuse large B cell lymphoma


title: KC0153 (T12S3-A)

tag: tissue

value: Ductal Breast Carcinoma

tag: cell line

value: EBV Immortalized Fibroblast Reference


title: KC0159 (T12S2-A)


title: Patient o51 with diffuse large B cell lymphoma


title: KC0117 (T12S4-H)


title: KC0115 (T12S5-H)


title: KC0113 (T12S4-A)


title: KC0102 (T12S5-A)


title: KC0109 (T11S6-A)


title: Patient o45 with diffuse large B cell lymphoma


title: KC0051 (T11S4-A)


title: KC0071 (T11S5-A)


title: Patient o32 with diffuse large B cell lymphoma


title: Patient o41 with diffuse large B cell lymphoma


title: KC0100 (T12S6-H)


title: KC0047 (T11S3-A)


title: MR2624 (T20S3-A)

description: This sample was hybridized to a single array (two color-reversals not performed).

data_processing: The data were normalized using a lowess curve-fitting algorithm, followed by a local normalization (previously described in Hicks et al.). After placement in genome order, the mean of log ratios was computed. Segmentation was performed on the above-described data. Segments are defined as non-overlapping, genomic regions where copy number has changed. Our segmentation method is based on the minimization of the square-sum of differences between log-ratios and means (squared deviation) over segments larger than 6 probes in size. Initially, the segmenter searches for breakpoints that might be boundaries of segments. The first known breakpoint on a given chromosome is its first probe. For a given breakpoint, a 100-probe window to its right is selected. The sum of squared deviations of the flanking probes is calculated for each probe within this window. A probe whose squared deviation value produces a local minimum with respect to its neighbors, and is below a threshold of 95% of the square deviation within a window, is accepted as a new, known breakpoint. Whenever a probe is found below the threshold in the newly defined region, the segmenter recursively breaks said region into two pieces until it cannot find any further breakpoints therein. If no breakpoints are found, the 100- probe window is shifted by half its size and this procedure continues until a chromosome end is reached. Initial segments are constructed using found breakpoints. Each segment and its neighbors are validated for significance by the Kolmogorov-Smirnov (K-S) algorithm. If the p-value of compared segments is less than 10-5, then said segment is accepted as real. If not, the segments are merged. The segmenter also reports statistics such as mean, standard deviation, and median for each segment.

label_protocol: Briefly, complexity-reduced representations consisting of small (200-1200 bp) fragments were amplified by adapter-mediated PCR of genomic DNA. DNA samples (2 ug) were labeled either with Cy5-dCTP or Cy3-dCTP using Amersham-Pharmacia MegaPrime labeling kit (Amersham Biosciences, Piscataway, NJ), and competitively hybridized to each other on the same slide.


title: Patient o28 with diffuse large B cell lymphoma


title: MR2643 (T19S1-A2)


title: KC0044 (T11S2-A)


title: KC0217 (T7S1-A)


title: MR2623 (T20S2-A)


title: MR2622 (T20S1-A)


title: Patient o27 with diffuse large B cell lymphoma


title: MR2646 (T19S3-A2)


title: KC0181 (T8S1-A)


title: KC0037 (T11S1-A)


title: MR2648 (T19S6-A1)


title: Sample NA06991


title: MR2604 (T18S2-A)


title: MR2606 (T18S3-A)


title: MR2644 (T19S4-A1)


title: MR2608 (T18S4-A)


title: Patient o65 with diffuse large B cell lymphoma

source_name: diffuse larga B cell lymphoma

value: heterozygous A20 loss


title: Patient o82 with diffuse large B cell lymphoma

value: heterozygous loss A20 loss


title: MR2642 (T19N)

value: Normal Matched Breast Tissue


title: MR2647 (T19S5-A1)


title: MR2602 (T18S1-A)


title: MR2557 (T17S4-A3)


title: KC0213 (T7S4-A)


title: patient o50 with diffuse large B cell lymphoma


title: MR2556 (T17S3-A1)


title: s854 6dpf GFP- Rep3

city: Pittsburgh

first: Carsten

last: Stuckenholz

state: PA

address: 3501 Fifth Avenue, Room 5065.5B

department: Department of Medicine, Division of Hematology and Oncology

institute: University of Pittsburgh

description: Gastrointestinal organogenesis at different time points in Zebrafish

hyb_protocol: Hybridization cocktail contained 2.2 µg fragmented, biotin-labeled and amplified cDNA, as per manufacturer's protocol (NuGEN). Hybridization protocol used was EukGE-WS2v4 on an Affymetrix GeneChip Fluidics Station 400.

scan_protocol: GeneChips were scanned with an Affymetrix scanner according to the manufacturer's protocol.

data_processing: Expression values were extracted using RMA (http://rmaexpress.bmbolstad.com/). Each array was normalized by log2-transformation, subtraction of median, and division by standard deviation.

organism: Danio rerio

source_name: Dissociated transgenic zebrafish embryos [Tg(XlEef1a1:GFP)s854], flow sorted, 6 dpf

label_protocol: RNA was SPIA amplified into cDNA and labeled with biotin using Ovation (NuGEN) as per manufacturer's instructions.

growth_protocol: Homozygous Tg(XlEef1a1:GFP)s854 zebrafish embryos were grown in standard embryo media supplemented with 0.003% 1-phenyl-2-thiourea (PTU) at 1 dpf to suppress pigmentation and autofluorescence.

extract_protocol: RNA was extracted using Absolutely RNA micropreps (Stratagene). RNA quality was assessed on an Agilent BioAnalyzer.

treatment_protocol: Embryos were washed in 3X in PBST, dissociated in HBBS supplemented with 0.25% Trypsin, 0.1% EDTA, 40 µg/ml Proteinase K, and 10 µg/ml Collagenase using a tissue grinder. Cells were resuspended in TMI Buffer (100 mM NaCl, 5 mM KCL, 5 mM HEPES, pH 7.0, and 1% PEG-20000), passed through a 40 µm cell strainer and FAC sorted based on GFP expression.

tag: Strain

tag: Age

value: 6 dpf

tag: FACS

value: GFP negative


title: KC0225 (T7S3-A)


title: Patient o81 with diffuse large B cell lymphoma

value: M


title: MR2553 (T17S3-A2)


title: s854 6dpf GFP- Rep2


title: s854 6dpf GFP+ Rep3

value: GFP positive


title: KC0221 (T7S2-A)


title: Patient o78 with diffuse large B cell lymphoma

value: LI

value: negative

source_name: Normal lymph npde mixture


title: Patient o57 with diffuse large B cell lymphoma

value: positive


title: KC0209 (T8S5-A)


title: s854 6dpf GFP+ Rep2


title: KC0205 (T8S4-A)


title: MR2554 (T17S2-A1)


title: Patient o73 with diffuse large B cell lymphoma

value: without A20 loss

value: reference


title: s854 4dpf GFP- Rep3

source_name: Dissociated transgenic zebrafish embryos [Tg(XlEef1a1:GFP)s854], flow sorted, 4 dpf

value: 4 dpf


title: KC0201 (T8S3-A)


title: MR2551 (T17S2-A2)


title: MR2552 (T17S1-A1)


title: s854 6dpf GFP+ Rep1


title: s854 4dpf GFP- Rep2


title: MR2299 (T15S4-A)


title: Patient o58 with diffuse large B cell lymphoma

value: L


title: MR2558 (T17S4-A1)


title: s854 6dpf GFP- Rep1


title: KC0185 (T8S2-A)


title: s854 4dpf GFP+ Rep1


title: MR2287 (T15S1-A)


title: MR2403 (T16S2-A)


title: s854 4dpf GFP- Rep1


title: MR2291 (T15S2-A)


title: Patient o49 with diffuse large B cell lymphoma

value: F


title: Patient o54 with diffuse large B cell lymphoma

value: HI


title: MR2406 (T16S4-A)

value: Ductal Breast Carcinoma

value: EBV Immortalized Fibroblast Reference


title: NN626 (T10S6-A1)


title: Patient o39 with diffuse large B cell lymphoma


title: s854 3dpf GFP- Rep2

source_name: Dissociated transgenic zebrafish embryos [Tg(XlEef1a1:GFP)s854], flow sorted, 3 dpf

value: 3 dpf


title: MR2405 (T16S3-A)


title: s854 3dpf GFP+ Rep3


title: MR2402 (T16S1-A)


title: s854 3dpf GFP+ Rep2


title: s854 3dpf GFP- Rep1


title: Patient o37 with diffuse large B cell lymphoma

value: H

value: n/d


title: s854 4dpf GFP+ Rep3


title: NN624 (T10S6-A2)


title: MR2625 (T20S4-A)


title: NN622 (T10S6-D)


title: s854 2dpf GFP- Rep3

source_name: Dissociated transgenic zebrafish embryos [Tg(XlEef1a1:GFP)s854], flow sorted, 2 dpf

value: 2 dpf

value: GFP negative


title: Patient o66 with diffuse large B cell lymphoma

value: M


title: MR2645 (T19S2-A2)


title: NN620 (T10S5-A1)


title: NN618 (T10S5-A2)


title: s854 3dpf GFP+ Rep1

value: GFP positive


title: s854 4dpf GFP+ Rep2


title: Patient o36 with diffuse large B cell lymphoma

value: negative


title: s854 2dpf GFP+ Rep2


title: Patient o34 with diffuse large B cell lymphoma

value: positive


title: s854 2dpf GFP+ Rep3


title: s854 2dpf GFP- Rep1


title: s854 2dpf GFP- Rep2


title: Patient o35 with diffuse large B cell lymphoma

source_name: diffuse large Bcell lymphoma

value: LI

value: without A20 loss


title: Patient o26 with diffuse large B cell lymphoma

value: reference


title: s854 2dpf GFP+ Rep1


title: NN612 (T10S4-A1)


title: Patient o25 with diffuse large B cell lymphoma

value: reactive lymph node


title: patient o80 with diffuse large B cell lymphoma

value: heterozygous loss


title: Patient o79 with diffuse large B cell lymphoma

value: F

value: HI

tag: anntotation


title: Patient o74 with diffuse large B cell lymphoma

source_name: normal lymph node mixture


title: s854 3dpf GFP- Rep3


title: NN614 (T10S4-D)

value: Ductal Breast Carcinoma

value: EBV Immortalized Fibroblast Reference


title: NN616 (T10S5-D)


title: Patient o69 with diffuse large B cell lymphoma


title: patient o62 with diffuse large B cell lymphoma

value: H


title: Patient o72 with diffuse large B cell lymphoma

source_name: diffuse large B cell lynomhoma


title: HCC712|HOP106

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-11/71171.gif

scan_protocol: GenePix

source_name: Common Reference RNA

tag: reference

value: Common Reference RNA


title: HCC1954|HOP113

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-11/71162.gif


title: hop081|UACC893

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-11/71102.gif


title: NN608 (T10S3-H)


title: hop070|MDA361

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-11/71097.gif


title: NN610 (T10S3-D)


title: HCC1007|HOP130

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-11/71153.gif


title: NN604 (T10S2-H)


title: NN860 (T9S6-A)


title: Patient o59 with diffuse large B cell lymphoma


title: HCC1395|HOP154

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-11/71156.gif


title: Patient o61 with diffuse large B cell lymphoma


title: Patient o60 with diffuse large B cell lymphoma


title: HOP126|184A1

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-12/71503.gif

source_name: common reference RNA


title: NN862 (T9N)

value: Normal Matched Breast Tissue


title: NN602 (T10S1-D)


title: Patient o53 with diffuse large B cell lymphoma


title: NN606 (T10S2-D)


title: hop063|Cal51

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-11/71094.gif


title: NN852 (T9S4-A)


title: Patient o48 with diffuse large B cell lymphoma


title: Patient o44 with diffuse large B cell lymphoma


title: NN856 (T9S5-A)


title: Patient o43 with diffuse large B cell lymphoma


title: NN600 (T10S1-H)


title: HCC1599|HOP110

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-11/71160.gif


title: Patient o40 with diffuse large B cell lymphoma


title: NN836 (T6N)


title: hop086|SUM190

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-11/71107.gif


title: hop093|SUM102

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-11/71113.gif


title: NN844 (T9S2-A)

description: This experiment was done in colour reversal.


title: HCC1187|HOP128

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-11/71155.gif


title: HOP146|HTERT

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-12/71504.gif

source_name: common Reference RNA

source_name: HTERT

value: HTERT


title: hop068|HCC1419

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-11/71096.gif


title: NN840 (T9S1-A)


title: MR2295 (T15S3-A)


title: 1143|Shez194s

description:
Simple annotation: Breast, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2006-12/71512.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1880, 4960; Software: type: feature extraction; Performer: Melanie,,Bocanegra Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2004-03-18; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter PMT Volts = 550; Parameter Laser on time = 28498; Parameter Laser Power = 3.46; Parameter Scan Time = 14:41:41; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [94858]; Parameter Focus Position = 0; Parameter Scan Temperature = 30.05; Performer: Melanie,,Bocanegra Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2004-03-18; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.1; Parameter Pixel Size = 10; Parameter PMT Volts = 650; Parameter Scan Power = 100; Parameter Laser on time = 28542; Parameter Laser Power = 3.51; Parameter Scan Time = 14:41:41; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [94858]; Parameter Focus Position = 0; Parameter Scan Temperature = 30.05; Performer: Melanie,,Bocanegra

source_name: Normal human female genomic DNA

tag: Normal human female genomic DNA

source_name: Breast Tumor Cell Line HCC1143 genomic DNA


title: HCC2157|HOP147

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-11/71164.gif


title: NN834 (T6S4-A)


title: NN848 (T9S3-A)


title: NN822 (T6S1-A)


title: HCC38|HOP129

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-11/71169.gif


title: NN830 (T6S3-A)


title: MDA134|HOP115

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-11/71172.gif


title: NN818 (T5S4-A2)


title: NN826 (T6S2-A)


title: HCC1428|HOP149

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-11/71157.gif


title: NN816 (T5S4-A1)


title: HCC1500|HOP109

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-11/71158.gif


title: NN810 (T5S3-A1)


title: 38|Shez192s

description:
Simple annotation: Breast, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2006-12/71510.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1960, 5240; Software: type: feature extraction; Performer: Melanie,,Bocanegra Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2004-03-17; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter PMT Volts = 560; Parameter Laser on time = 28060; Parameter Laser Power = 3.42; Parameter Scan Time = 11:29:56; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [94858]; Parameter Focus Position = 0; Parameter Scan Temperature = 29.74; Performer: Melanie,,Bocanegra Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2004-03-17; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.1; Parameter Pixel Size = 10; Parameter PMT Volts = 650; Parameter Scan Power = 100; Parameter Laser on time = 28104; Parameter Laser Power = 3.50; Parameter Scan Time = 11:29:56; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [94858]; Parameter Focus Position = 0; Parameter Scan Temperature = 29.74; Performer: Melanie,,Bocanegra

source_name: Breast Tumor Cell Line HCC38 genomic DNA


title: hop060|SKBR3

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-11/71093.gif


title: NN812 (T5S3-A2)


title: SUM52|HOP114

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-11/71173.gif


title: 1569|Shez182s

description:
Simple annotation: Breast, cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2006-11/71220.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 2000, 5160; Software: type: feature extraction; Performer: Melanie,,Bocanegra Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2004-02-11; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter PMT Volts = 540; Parameter Laser on time = 22724; Parameter Laser Power = 3.39; Parameter Scan Time = 12:53:07; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [94858]; Parameter Focus Position = 0; Parameter Scan Temperature = 28.92; Performer: Melanie,,Bocanegra Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2004-02-11; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.1; Parameter Pixel Size = 10; Parameter PMT Volts = 650; Parameter Scan Power = 100; Parameter Laser on time = 22767; Parameter Laser Power = 3.53; Parameter Scan Time = 12:53:07; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [94858]; Parameter Focus Position = 0; Parameter Scan Temperature = 28.92; Performer: Melanie,,Bocanegra

source_name: Normal female genomic DNA

tag: Normal female genomic DNA

source_name: Breast Tumor Cell Line HCC1569

tag: Breast Tumor Cell Line HCC1569


title: HCC2688|HOP150

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-11/71167.gif


title: NN806 (T5S2-A1)


title: 202|Shez207s

description:
Simple annotation: Breast, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2006-12/71513.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1640, 4080; Software: type: feature extraction; Performer: Melanie,,Bocanegra Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2004-05-11; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter PMT Volts = 575; Parameter Laser on time = 34318; Parameter Laser Power = 3.45; Parameter Scan Time = 18:00:09; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [94858]; Parameter Focus Position = 0; Parameter Scan Temperature = 30.84; Performer: Melanie,,Bocanegra Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2004-05-11; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.1; Parameter Pixel Size = 10; Parameter PMT Volts = 650; Parameter Scan Power = 100; Parameter Laser on time = 34362; Parameter Laser Power = 3.51; Parameter Scan Time = 18:00:09; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [94858]; Parameter Focus Position = 0; Parameter Scan Temperature = 30.84; Performer: Melanie,,Bocanegra

source_name: Breast Tumor Cell Line 202 genomic DNA

tag: Breast Tumor Cell Line 202 genomic DNA


title: 1007|Shez206s

description:
Simple annotation: Breast, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2006-12/71514.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1640, 5200; Software: type: feature extraction; Performer: Melanie,,Bocanegra Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2004-05-11; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter PMT Volts = 540; Parameter Laser on time = 34329; Parameter Laser Power = 3.45; Parameter Scan Time = 18:10:04; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [94858]; Parameter Focus Position = 0; Parameter Scan Temperature = 31.00; Performer: Melanie,,Bocanegra Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2004-05-11; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.1; Parameter Pixel Size = 10; Parameter PMT Volts = 650; Parameter Scan Power = 100; Parameter Laser on time = 34373; Parameter Laser Power = 3.50; Parameter Scan Time = 18:10:04; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [94858]; Parameter Focus Position = 0; Parameter Scan Temperature = 31.00; Performer: Melanie,,Bocanegra

source_name: Breast Tumor Cell Line HCC1007 genomic DNA


title: HCC3153|HOP107

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-11/71168.gif


title: 1954|Shez193s

description:
Simple annotation: Breast, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2006-12/71511.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1960, 5240; Software: type: feature extraction; Performer: Melanie,,Bocanegra Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2004-03-17; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter PMT Volts = 570; Parameter Laser on time = 28070; Parameter Laser Power = 3.44; Parameter Scan Time = 11:38:17; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [94858]; Parameter Focus Position = 0; Parameter Scan Temperature = 29.87; Performer: Melanie,,Bocanegra Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2004-03-17; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.1; Parameter Pixel Size = 10; Parameter PMT Volts = 650; Parameter Scan Power = 100; Parameter Laser on time = 28114; Parameter Laser Power = 3.50; Parameter Scan Time = 11:38:17; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [94858]; Parameter Focus Position = 0; Parameter Scan Temperature = 29.87; Performer: Melanie,,Bocanegra

source_name: Breast Tumor Cell Line HCC1954 genomic DNA


title: NN526 (T2S1)

description: This experiment was done in colour reversal.


title: shdv122_sr|MCF7 ATCC vs. NF|

description:
Simple annotation: Breast, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2004-07/54186.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1400, 6600; Software: type: feature extraction; Performer: Jessica,,Kao Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2003-06-06; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter PMT Volts = 550; Parameter Laser on time = 93085; Parameter Laser Power = 3.87; Parameter Scan Time = 02:56:50; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 30.81; Performer: Jessica,,Kao Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2003-06-06; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.2.2; Parameter Pixel Size = 10; Parameter PMT Volts = 650; Parameter Scan Power = 100; Parameter Laser on time = 312078; Parameter Laser Power = 3.05; Parameter Scan Time = 02:56:50; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 30.81; Performer: Jessica,,Kao

source_name: Breast Tumor Cell Line MCF7 ATCC genomic DNA


title: hop079|MCF10A

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-11/71100.gif


title: hop084|BT483

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-11/71105.gif


title: NN516 (T4S4)


title: HCC1187|Shez195_Correct_spotreader

description:
Simple annotation: Breast, cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2008-09/81496.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1880, 4800; Software: type: feature extraction; Performer: Melanie,,Bocanegra Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.1; Parameter Scanner Model = GenePix 4000B [94858]; Parameter Focus Position = 0; Parameter Scan Temperature = 30.14; Performer: Melanie,,Bocanegra Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.1; Parameter Pixel Size = 10; Parameter Scanner Model = GenePix 4000B [94858]; Parameter Focus Position = 0; Parameter Scan Temperature = 30.14; Performer: Melanie,,Bocanegra


title: Sample NA18563

tag: sample


title: NN802 (T5S1-A1)


title: RSNA vs. RSND

city: Chicago

first: Wei

last: Xu

state: IL

address: 303 E Chicago Ave, Tarry 4-714

department: Surgery

institute: Northwestern University, Feinberg School of Medicine

description: Biological replicate of RSNA and biological replicate of RSND

hyb_protocol: Each mixed aliquot was transferred to a Microcon YM-30 Centrifugal Filter Unit (Millipore, Billerica, MA) to be concentrated. Before the samples were loaded on the GeneTAC HybStation (Genomic Solutions), 110 μl SlideHyb buffer 3 (Ambion, Austin, TX) was added to each concentrated mixture and subsequently incubated in 70 ºC for 5 minutes. An 18-hour step-down protocol was applied to all hybridizations; briefly, 3 hours at 60 ºC, 3 hours at 55 ºC, 12 hours at 50 ºC. The washing procedure followed the hybridizations, and was performed with three different washing buffers containing SSC buffer (Ambion) and sodium dodecyl sulfate (SDS) under different conditions: 30 seconds in each cycle at 50 ºC for three cycles with medium stringency wash buffer (2 × SSC and 0.1% SDS), 30 seconds in each cycle at 42 ºC for three cycles with high stringency wash buffer (0.2 × SSC and 0.1% SDS), and 30 seconds in each cycle at 42 ºC for three cycles with post wash buffer (0.2 × SSC). All slides were rinsed once in 0.2 × SSC and once in double distilled water after they were downloaded from the HybStation, and immediately dried by centrifugation at 1,000 g for two minutes.

scan_protocol: Hybridized cDNA microarrays were scanned by GenePix 4000B two-laser Scanner (Molecular Devices, Downingtown, PA), and GenePix Pro 6.0 (Molecular Devices) software was then used for image processing and spot intensity file creation.

data_processing: Data were processed with Limma ((Wettenhall and Smyth, 2004) package under R environment. The essential parameters used in the analyses- Background correction: MINIMUM; Within array normalization: LOESS; Between array normalization: Aquantile;

label: Alexa 555

organism: Dreissena polymorpha

source_name: Zebra mussel foot tissue

label_protocol: Started with 10 µg total RNA, the cDNA synthesis and dye labeling were performed by SuperScript Plus Indirect cDNA Labeling Kit (Invitrogen) containing Alexa Fluor 555 & 647 dyes. The Oligo(dT) primer was used in cDNA synthesis. The protocol is based on the manufacturer's instructions.

growth_protocol: The zebra mussels were collected from Zebra mussels used for total RNA extraction were obtained from the Huron River in Ann Arbor, MI, USA (Latitude: 42º16’12’’N; Longitude -83º43’34”W). The mussels were then allowed to acclimate for eight weeks in glass aquaria kept at room temperature and supplied with well water. The mussels were fed a pure culture of the algus Ankistrodesmus falcatus once a week.

extract_protocol: 5-PRIME PerfectPure RNA Tissue Kit (5 PRIME Inc, Gaithersburg, MD) following manufacturer's instructions.

treatment_protocol: Four factors including three environmental factors (temperature, dissolved oxygen level,  and water agitation) and one adhesion status were considered in this study. In each factor, two different levels were created (Table 1), therefore, sixteen treatment groups were obtained (Figure 1). The loop design for hybridization was also shown in Figure 1.

tag: factors

value: RSNA (Room temperature, static water, non-hypoxia, adhesion)

value: foot

label: Alexa 647

value: RSND (Room temperature, static water, non-hypoxia, non-adhesion)


title: hop064|MDA468

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-11/71095.gif


title: shdv146_sr|MDA 361 vs. NF|

description:
Simple annotation: Breast, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2004-07/54188.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1760, 6480; Software: type: feature extraction; Performer: Jessica,,Kao Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2003-07-25; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter PMT Volts = 620; Parameter Laser on time = 106121; Parameter Laser Power = 4.61; Parameter Scan Time = 00:40:05; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 30.29; Performer: Jessica,,Kao Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2003-07-25; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.2.2; Parameter Pixel Size = 10; Parameter PMT Volts = 680; Parameter Scan Power = 100; Parameter Laser on time = 325114; Parameter Laser Power = 2.94; Parameter Scan Time = 00:40:05; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 30.29; Performer: Jessica,,Kao

source_name: Breast Tumor Cell Line MDA361 genomic DNA