title: E1_vehicle control pool vs vehicle control #1

description: 3T3-L1 Adipocytes: Vehicle control pool vs. PPARg Ligand

source_name: E1_vehicle control pool

value: 3T3-L1 Adipocytes

source_name: vehicle control #1


title: Rsp 50ng - 15%

status: Public on Jun 30 2012

type: genomic

city: Madison

first: Safak

last: Yilmaz

state: Wisconsin

address: 2 University Houses

country: USA

institute: UW-Madison

description: Hybridization of labeled and fragmented R. sphaeroides 16S rRNA gene with 15% formamide.  Total RNA in hybridization buffer is 50 ng.

hyb_protocol: 5 ng or 50ng of labeled target was hybridized with the microarray in 10 microliters of custom hybridization buffer (1M Na+, 20 mM Tris [pH=7.2], 0.02% SDS, and variable amounts of formamide) using a Nimblegen mixer matching the arrays used (see www.nimblegen.com).

scan_protocol: Scanning was performed with an Axon 4000B laser scanner and GenePix Pro 6.0 software (Molecular Devices, Sunnyvale, CA).  The wavelength and PMT gain were set at 532 nm and 430, respectively.  Two lines were averaged.  Fluorescence data was saved in TIFF files and processed using Nimblescan software (see www.nimblegen.com).

data_processing: Raw data (.pair files) was analyzed using Matlab (The MathWorks, Natick, MA).  For each probe, the average intensity of three replicates were calculated after the elimination of outliers based on a standard deviation test. The average of control (Nonsense) probes was subtracted from all averages to obtain background-corrected results.

molecule: genomic DNA

organism: Cereibacter sphaeroides 2.4.1

source_name: Rhodobacter sphaeroides 2.4.1 wild-type

label_protocol:
Cloning protocol: For each organism, 16S rRNA gene was amplified with 27f and 1492r primers and cloned using TOPO10 cloning kit (Invitrogen, Carlsbad, CA).   The clones were sequenced to find operons that matched the GenBank sequences in accession codes used during probe design.  One matching clone for each organism was subsequently re-amplified with 27f and 1492r primers and purified using a QIAquick spin column (Qiagen, City, State) for the next step.
Cloned and purified 16S rRNA genes were Cy3-labeled using random prime amplification with Klenow fragment and a decalabel DNA labeling kit (Fermentas, St Leon-Rot, Germany).  A previously published protocol was followed (Loy, A. et al. 2011. PCR mutation detection protocols. Methods in Molecular Biolology. Vol. 688, pp. 187-206).

growth_protocol:
E. coli was grown to mid-log phase (O.D.600nm 0.3-0.4) in Lennox LB broth (Becton Dickinson, Franklin Lakes, NJ) at 37°C.
R. sphaeroides was phototrophically grown to mid-log phase (100-150 kletts) in Sistrom's minimal medium (Sistrom, W. 1960. Journal of General Microbiology. 22:778-785) amended with 33.9 mM succinate .

extract_protocol: Genomic DNA was extracted using Ultra Clean Soil DNA (MoBio Laboratories, Solana Beach, CA).

tag: genotype

value: Wild Type

tag: phenotype

value: normal

tag: accession

tag: hybridization buffer (formamide content)

value: 15% formamide

tag: hybridization buffer (total rna)

value: 50 ng


title: E1_vehicle control pool vs COOH (3870 nM) #1

type: RNA

city: Rahway

first: Yejun

last: Tan

state: NJ

address: 126 E. Lincoln Ave, POBox 2000

department: Molecular Profiling

institute: Merck & Co.

hyb_protocol: Microarrays are incubated at 40°C for 48 hours in a rotating carousel.  Hybridizations to custom Agilent microarrays are completed as previously described (Hughes et al.Nat Biotech (2001), 19(4):342-7).  Microarrays are washed to remove non-specific hybridized sample. Afterwards, microarrays are dried in an ozone-free nitrogen chamber.

scan_protocol: Microarrays are scanned using the Agilent LP2 laser scanner. The scanner output is a Tiff file, which contains the quantitative hybridization data from each individual microarray. The Tiff files are then processed using Rosetta custom feature extraction software.

data_processing: Data were processed using the Rosetta Resolver® system. Rosetta's custom feature extraction software performs error modeling before data are loaded into the Resolver system. The Resolver system performs a squeeze operation that combines replicates of the same sequence in an array while applying error weighting. The error weighting consists of adjusting for additive and multiplicative noise. A P-value is generated and propagated throughout the system. The P-value represents the probability that a gene is expressed. The Resolver system allows users to set thresholds, below which genes of a P-value are considered to be significantly expressed. The Resolver system also combines multiple arrays using a squeezing process. If multiple spots reference one sequence, summarization is performed using an error-weighted average as described in Roland Stoughton and Hongyue Dai, Statistical Combining of Cell Expression Profiles. US Patent #6,351,712, February 26, 2002.

molecule: total RNA

organism: Mus musculus

label_protocol: custom automated version of the aminoallyl MessageAmp II kit from Ambion.

extract_protocol: Qiagen RNeasy spin columns with DNAse treatment

tag: cell type


title: Rsp 50ng - 10%

description: Hybridization of labeled and fragmented R. sphaeroides 16S rRNA gene with 10% formamide.  Total RNA in hybridization buffer is 50 ng.

value: 10% formamide


title: Patient CLL17 Time point TP1

city: Scottsdale

first: Esteban

last: Braggio

state: AZ

address: 13208 East Shea Boulevard, MCRB 3-024

department: Biochemistry

institute: Mayo Clinic

hyb_protocol: Aliquouts of agilent Oligo aCGH hybridization kit were added to the samples as recommended by the manafacture. Samples were heat at 95C for 3 minutes, then 37C for 30 minutes. Samples were dispense in the arrays and hybridized at 65C for 40 hours in a hybrization oven at 20rpm.

scan_protocol: Scanned on DNA Microarray Scanner (Agilent Technologies). Images were quantified using Agilent Feature Extraction Software (version 9.5).

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

organism: Homo sapiens

source_name: Patient CLL17 Time point TP1

label_protocol: 1ug of tumor and reference DNA were independently labeled with Agilent Genomic DNA labeling Kit PLUS as recommended by the manafacture. Cy5 dye was used to label tumor DNA samples and Cy3 to label reference DNA samples. Next, labeled genomic reactions were cleaned-up with Microcon YM-30 columns

extract_protocol: Genomic DNA was obtained from frozen tumors using the Puregene Core A kit (Qiagen) according to manufacturer’s recommendations.

tag: pathology

value: CLL

tag: Stage

value: Diagnosis or near diagnosis

tag: primary therapy

tag: secondary therapy

tag: tertiary therapy

tag: tissue

value: Peripheral blood

source_name: Female reference DNA sample

tag: sample type

value: reference DNA


title: C.elegans_8days_GC2-1

city: Tsukuba

first: Akira

last: Higashibata

state: Ibaraki

department: Department of Space Biology and Microgravity Sciences

country: Japan

institute: Japan Aerospace Exploration Agency

hyb_protocol: Labeled cRNA (1.65 µg/sample) was hybridized to a C. elegans oligo microarray using a gene expression hybridization kit at 65 °C for 17 hours.

scan_protocol: Array were scanned with an Agilent Scanner and processed with Agilent Feature Extraction Software.

data_processing: Microarray data were analyzed using Gene Spring software (Agilent Technologies). Normalized data were produced by "Normalize to 75 percentile sift protocol’’ and "baseline to median of control sample protocol’’. Arrays were filtered on expression (20-100)th percentile in raw data.

organism: Caenorhabditis elegans

source_name: Ground control

label_protocol: Total RNA was amplified using the Low Input Quick Amp Labeling Kit protocol. Cy3 labeled cRNA was produced according to manufacturer's protocol.

growth_protocol: Approximately 50 L1 larvae were grown in 2 mL M9. Worms were cultured in 12 mL S basal medium contained bacterial feeds for 8days.

extract_protocol: Worms were homogenized with four rounds of 20-second beating at 5000 rpm in a Micro Smash TM MS-100 bead beater with 3 minutes of cooling on ice between rounds. Total RNA was extracted using an Isogen RNA purification kit following the manufacturer’s protocol.

tag: strain

value: N2 wild type

tag: developmental stage

value: adult


title: C.elegans_8days_GC1-1


title: Eco 50ng - 45%

description: Hybridization of labeled and fragmented E. coli 16S rRNA gene with 45% formamide.  Total RNA in hybridization buffer is 50 ng.

organism: Escherichia coli K-12

source_name: Escherichia coli K12 wild-type

value: 45% formamide


title: Rsp 50ng - 5%

description: Hybridization of labeled and fragmented R. sphaeroides 16S rRNA gene with 5% formamide.  Total RNA in hybridization buffer is 50 ng.

value: 5% formamide


title: C.elegans_8days_microG3-1

source_name: microG


title: Eco 50ng - 32.5%

description: Hybridization of labeled and fragmented E. coli 16S rRNA gene with 32.5% formamide.  Total RNA in hybridization buffer is 50 ng.

value: 32.5% formamide


title: Rsp 50ng - 0%

description: Hybridization of labeled and fragmented R. sphaeroides 16S rRNA gene with 0% formamide.  Total RNA in hybridization buffer is 50 ng.

value: 0% formamide


title: C.elegans_8days_microG1-1


title: Patient CLL13 Time point TP3 sample C

source_name: Patient CLL13 Time point TP3 sample C

value: Progressive disease

value: Pentostatin, cyclophosphamide and rituximab (PCR)

value: Leukeran/CpG

value: Rituxan/Solu-Medrol


title: C.elegans_8days_microG2-1


title: Patient CLL14 Time point TP2

source_name: Patient CLL14 Time point TP2


title: Patient CLL13 Time point TP3 sample B

source_name: Patient CLL13 Time point TP3 sample B


title: Patient CLL12 Time point TP3

source_name: Patient CLL12 Time point TP3


title: Eco 50ng - 15%

description: Hybridization of labeled and fragmented E. coli 16S rRNA gene with 15% formamide.  Total RNA in hybridization buffer is 50 ng.

value: Wild Type

value: normal

value: 15% formamide


title: Eco 50ng - 25%

description: Hybridization of labeled and fragmented E. coli 16S rRNA gene with 25% formamide.  Total RNA in hybridization buffer is 50 ng.

value: 25% formamide

value: 50 ng


title: Eco 50ng - 20%

description: Hybridization of labeled and fragmented E. coli 16S rRNA gene with 20% formamide.  Total RNA in hybridization buffer is 50 ng.

value: 20% formamide


title: Patient CLL12 Time point TP1

source_name: Patient CLL12 Time point TP1

value: CLL

value: Diagnosis or near diagnosis

value: Peripheral blood

value: reference DNA


title: C.elegans_8days_1G2-1

value: N2 wild type

value: adult


title: Patient CLL13 Time point TP3 sample A

source_name: Patient CLL13 Time point TP3 sample A

value: Nonce


title: C.elegans_8days_1G1-1


title: C.elegans_8days_GC3-2


title: Eco 50ng - 10%

description: Hybridization of labeled and fragmented E. coli 16S rRNA gene with 10% formamide.  Total RNA in hybridization buffer is 50 ng.

value: 10% formamide


title: C.elegans_8days_1G3-1


title: Eco 50ng - 5%

description: Hybridization of labeled and fragmented E. coli 16S rRNA gene with 5% formamide.  Total RNA in hybridization buffer is 50 ng.

value: 5% formamide


title: Patient CLL15 Time point TP1

source_name: Patient CLL15 Time point TP1


title: Patient CLL15 Time point TP2

source_name: Patient CLL15 Time point TP2

value: Progressive disease


title: Patient CLL13 Time point TP2

source_name: Patient CLL13 Time point TP2


title: C.elegans_8days_GC2-2


title: Patient CLL14 Time point TP3

source_name: Patient CLL14 Time point TP3

value: Pentostatin, cyclophosphamide and rituximab (PCR)


title: Patient CLL11 Time point TP2

source_name: Patient CLL11 Time point TP2


title: Eco 5ng - 45%

description: Hybridization of labeled and fragmented E. coli 16S rRNA gene with 45% formamide.  Total RNA in hybridization buffer is 5 ng.

value: Wild Type

value: 45% formamide

value: 5 ng


title: C.elegans_8days_GC1-2


title: C.elegans_8days_microG3-2


title: C.elegans_8days_microG2-2


title: Eco 5ng - 20%

description: Hybridization of labeled and fragmented E. coli 16S rRNA gene with 20% formamide.  Total RNA in hybridization buffer is 5 ng.

value: normal


title: Patient CLL12 Time point TP2

source_name: Patient CLL12 Time point TP2


title: Eco 5ng - 25%

description: Hybridization of labeled and fragmented E. coli 16S rRNA gene with 25% formamide.  Total RNA in hybridization buffer is 5 ng.

value: 25% formamide


title: Eco 5ng - 32.5%

description: Hybridization of labeled and fragmented E. coli 16S rRNA gene with 32.5% formamide.  Total RNA in hybridization buffer is 5 ng.

value: 32.5% formamide


title: Patient CLL10 Time point TP2

source_name: Patient CLL10 Time point TP2

value: CLL


title: C.elegans_8days_1G2-2


title: Patient CLL11 Time point TP3

source_name: Patient CLL11 Time point TP3

source_name: Female reference DNA sample


title: Patient CLL9 Time point TP2

source_name: Patient CLL9


title: Patient CLL8 Time point TP3 sample C

source_name: Patient CLL8

value: Leukeran

value: Avastin


title: Eco 5ng - 15%

description: Hybridization of labeled and fragmented E. coli 16S rRNA gene with 15% formamide.  Total RNA in hybridization buffer is 5 ng.

source_name: Escherichia coli K12 wild-type

value: 15% formamide


title: Eco 50ng - 0%

description: Hybridization of labeled and fragmented E. coli 16S rRNA gene with 0% formamide.  Total RNA in hybridization buffer is 50 ng.

value: 0% formamide

value: 50 ng


title: C.elegans_8days_1G1-2

value: N2 wild type

value: adult


title: Patient CLL10 Time point TP1

source_name: Patient CLL10

value: Diagnosis or near diagnosis

value: Peripheral blood

value: reference DNA


title: C.elegans_8days_microG1-2

source_name: microG


title: Eco 5ng - 5%

description: Hybridization of labeled and fragmented E. coli 16S rRNA gene with 5% formamide.  Total RNA in hybridization buffer is 5 ng.

value: Wild Type

value: 5% formamide


title: C.elegans_8days_1G3-2


title: Patient CLL9 Time point TP1


title: Eco 5ng - 10%

description: Hybridization of labeled and fragmented E. coli 16S rRNA gene with 10% formamide.  Total RNA in hybridization buffer is 5 ng.

value: 10% formamide

value: 5 ng


title: alpha2 KO, rep1

city: San Francisco

first: Lauren

middle: N

last: Booth

state: CA

address: 600 16th Street, N374

department: Micobiology and Immunology

institute: University of California, San Francisco

hyb_protocol: Equal amounts of the Cy3- and Cy5-labeled cDNA was hybridized to the array overnight, as described in the Agilent protocol. Following hybridization, the arrays were washed as specified by Agilent.

scan_protocol: Arrays were scanned at 5 μm, averaging 2 lines, with an Axon GenePix 4000A scanner.

data_processing: Arrays were gridded using GenePix Pro version 5.1. Global Lowess normalization analysis was performed for each array using a Goulphar script (The R Foundation for Statistical Computing). Normalized data was collapsed by averaging the result for all duplicate probes.

organism: Kluyveromyces lactis

source_name: alpha2 KO, alpha cell

label_protocol: 1.3 μg of cDNA was dried and resuspended in 5 μL 0.1 M sodium bicarbonate. An equivalent volume of Cy3 or Cy5 dye (Amersham) was added (dyes were resuspended in 60 μL of DMSO) and the reaction incubated at 65° for 20 minutes in the dark. Labeled cDNAs were purified using a Clean and Concentrator -5 kit (Zymo Research).

extract_protocol: RNA was isolated and reverse transcribed as previously described (Mitrovich, Q. M., Tuch, B. B., Guthrie, C. & Johnson, A. D. Computational and experimental approaches double the number of known introns in the pathogenic yeast Candida albicans. Genome Res 17, 492-502 (2007) (PMID 17351132)) with the exception that the RNA isolation protocol was scaled to 50 mL cultures and that SuperScript II (Invitrogen) was used. Additionally, reverse transcription reactions were performed on either individual samples or on RNA in which an equivalent amount of each RNA sample was pooled.

treatment_protocol: Yeast were grown in liquid phosphate starvation media for 10 hours.

value: alpha

value: alpha2 knockout

tag: growth condition

value: phosphate starvation

source_name: WT, alpha cell

value: wild-type


title: Eco 5ng - 0%

description: Hybridization of labeled and fragmented E. coli 16S rRNA gene with 0% formamide.  Total RNA in hybridization buffer is 5 ng.

value: normal


title: Patient CLL8 Time point TP3 sample A

value: CLL

value: Progressive disease

value: Pentostatin, cyclophosphamide and rituximab (PCR)


title: Patient CLL8 Time point TP1


title: a2 KO, rep2

source_name: WT, a cell

value: a

source_name: a2 KO, a cell

value: a2 knockout


title: Patient CLL8 Time point TP2


title: Spleen DC rep 3

city: Milan

first: Francesca

last: Granucci

address: Piazza della Scienza 2

country: Italy

institute: University of Milano-Bicocca

description: gene expression data from spleen DCs

hyb_protocol: Five micrograms of biotinylated cRNA were hybridized to the Affymetryx GeneChip Mouse Genome 430A 2.0 arrays.

scan_protocol: GeneChips were scanned using the GeneChip scanner 3000

data_processing:
Data handling was mainly done using Bioconductor 2.6. The Robust Multichip Average (RMA), method was employed to calculate probe set intensity. To filter out noisy data before the selection of differentially expressed genes a filter was applied based on a Inter Quantile Range (IQR) greater than 0.25.
The identification of differentially expressed genes was addressed using Linear Models for Microarray Data (LIMMA) and a discovery rate correction of the p-value (Benjamini-Hochberg). The corrected p-value selected in the analysis is p.value less or equal to 0.01.

label: biotin

source_name: sorted CD11c+ conventional DCs from spleen

label_protocol: Biotinylated cDNA was prepared from 2ng of total RNA and fragmented according to the Nugen protocol (WT-Ovation Pico RNA Amplification System)

extract_protocol: Total RNA was extracted by the double extraction protocol: RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction (TRIzol Invitrogen) followed by a Qiagen RNeasy clean-up procedure  Because of the small amount of the cells, 20 ng of Qiagen RNA carrier was used in every extraction. Total RNA concentration was calculated by Quant-IT RiboGreen (Invitrogen). Total RNA integrity was assessed by Agilent Bioanalyzer (Pico kit) and the RNA Integrity Number (RIN) was calculated. Only high-quality RNA preparations, with RIN greater than 8.4, were used for microarray analysis.

value: BALB/c

value: CD11c+ conventional dendritic cells from spleen


title: DNA_Normal_S

city: Birmingham

first: Yan

last: Sanders

state: AL

address: 901 19th Street S

institute: University of Alabama at Birmingham

description: Normal

hyb_protocol: The fragmented DNA was then hybridized to the BeadChip.  A single-base pair extension reaction was then performed, followed by staining with a detectable fluorescent dye label.

scan_protocol: The resulting products were imaged with the iScan Reader from Illumina.

data_processing:
Methylation at each locus was determined by calculating the percent of total signal from each lous that was represented by the mehylation probe using the GenomeStudio software.
matrix signal intensities value definition: Unmethylated and methylated signal intensities

label: Cy5 and Cy3

source_name: lung tissue

label_protocol: Genomic DNA was amplified and fragmented.

extract_protocol: genomic DNA was extracted and purified from lung tissue samples using Qiagen DNeasy Kit according to standard instructions

value: lung

tag: disease status

value: Normal


title: Spleen DC rep 1

description: gene expression data from spleen DCs


title: alpha2 KO, rep2

tag: genotype


title: a2 KO, rep1


title: DNA_IPF_5

description: IPF

value: IPF


title: DNA_IPF_9

description: IPF


title: Patient CLL7 Time point TP1

source_name: Patient CLL7

value: Diagnosis or near diagnosis

value: Peripheral blood

value: reference DNA


title: Lymph node DC rep 3

description: gene expression data from lymph node DCs

source_name: sorted CD11c+ conventional DCs from lymph nodes

value: CD11c+ conventional dendritic cells from lymph node


title: Patient CLL7 Time point TP2


title: Halobacterium salinarum NRC-1, 160min after CuSO4 addition, set 2, replicate 3

city: Seattle

first: Wyming

middle: Lee

last: Pang

state: WA

address: 401 Terry Ave N

institute: Institute for Systems Biology

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-35

scan_protocol: The arrays were scanned using the Perkin Elmer ScanArray 5000 scanner. The images were acquired with ScanArray Express 3.0.1 software at 10um resolution.  All scans were performed at 95% laser power with a varying PMT percentage. For high-low scanning, the low scans were adjusted so that the brightest spots were around 75% of maximum intensity in each channel. Then the high scans were adjusted to a maximum of 20% higher PMT than their corresponding low scans.

data_processing: Spotfinding was performed by MolecularWare AnalyzerDG Pro version 2.50 software. Intensities were normalized between the Alexa 546 and Alexa 647 channels by scaling all intensities in one channel.  Raw array intensity processing was performed using the SLIMArray pipeline which reported log10 ratio values of sample RNA expression relative to reference RNA.  Further analysis was done using the statistical analysis environment R.  Expression levels from pre-treatment and 0 timepoints were averaged.  This average value was then subtracted from the full time course set to produce pre-treatment normalized data.  Pre-treatement normalized data was used to determine replicate experiment statistics (expression averages and standard deviations).

label: Alexa 547, Alexa 647

organism: Halobacterium salinarum NRC-1

source_name: Halobacterium salinarum NRC-1, CuSO4

growth_protocol: Batch H. salinarum cultures were grown aerobically in 1.5L of rich medium to an OD600 of 0.6-0.8 using a New Brunswick BioFlo III bioreactor.  Cultures were then switch to chemostatic mode upon Copper (II) sulfate treatment.

extract_protocol: Total DNA-free RNA prepared using the Absolutely RNA miniprep kit (Stratagene) and analyzed by PCR to rule out DNA contamination, with Agilent Bioanalyzer to verify integrity, and in the spectrophotometer for quantification.

treatment_protocol: Copper (II) sulfate was added at time 0min to a final concentration of 0.85mM.

tag: copper concentration (mm)

tag: treatment

value: Copper (II) sulfate

tag: time (min)

label: Alexa 647, Alexa 547

source_name: Halobacterium salinarum NRC-1, Standard Reference

value: unperturbed H. salinarum batch culture in rich medium at OD600 0.6-0.8


title: DNA_IPF_4

description: IPF


title: DNA_IPF_2

description: IPF


title: Patient CLL6 Time point TP2

source_name: Patient CLL6


title: Patient CLL6 Time point TP3

source_name: Female reference DNA sample


title: Halobacterium salinarum NRC-1, 40min after CuSO4 addition, set 2, replicate 3

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-35


title: Lymph node DC rep 2


title: Lymph node DC rep 1


title: Patient CLL5 Time point TP1

source_name: Patient CLL5


title: Patient CLL8 Time point TP3 sample B

source_name: Patient CLL8

value: Leukeran


title: Cardiac septum_heart_healthy (4158307035_H)

city: Umeå

first: Nina

last: Gennebäck

address: NUS 6M

department: Public health and clinical medicin/medicin

country: Sweden

institute: Umeå University

hyb_protocol: Performed according to Illumina protocol

scan_protocol: Illumina Beadstation 500GX according to Illumina protocol

data_processing:
Cubic spline normalization, subtracted background.
Illumina Genomestudio was used

source_name: Cardiac septum_heart_healthy

label_protocol: Illumina TotalPrep RNA Amplification Kit was used

extract_protocol: Cardiac tissue was put in RNAlater

tag: gender

value: control

tag: disease state


title: Patient CLL5 Time point TP3

tag: pathology

value: CLL

value: Progressive disease


title: Halobacterium salinarum NRC-1, 20min after CuSO4 addition, set 2, replicate 3


title: knockout rep-3

city: Boston

first: Pere

last: Puigserver

address: 450 Brookline Av. CLSB-11144

institute: Dana-Farber Cancer Institute

description: Gene expression data from knockout soleus

hyb_protocol: The fragmented cRNA was added to a hybridization solution containing several biotinylated control oligonucleotides (for quality control), and hybridized to a microarray chip overnight at 45°C. The hybridization solution was then removed. The chips were transferred to a fluidics instrument that performs washes to remove cRNA that has not hybridized to its complementary oligonucleotide probe. The bound cRNA was then fluorescently labeled using phycoerythrin-conjugated streptavidin (SAPE); additional fluors are then added using biotinylated anti-streptavidin antibody and additional SAPE.

scan_protocol: Each cRNA bound at its complementary oligonucleotide was excited using a confocal laser scanner, GCS3000, and the positions and intensities of the fluorescent emissions were captured.

data_processing: The data were analyzed with RMA (Gene Pattern's ExpressionFileCreator version 8). Parameters: method RMA quantile normalization yes background correct yes compute present absent calls no normalization method none value to scale to clm file annotate probes yes The data were analyzed with RMA (Gene Pattern's ExpressionFileCreator version 8). Parameters: method RMA quantile normalization yes background correct yes compute present absent calls no normalization method none value to scale to clm file annotate probes yes.

source_name: Mouse soleus

label_protocol: The double-stranded cDNA was used as the template in an in vitro transcription (IVT) reaction catalyzed by T7 polymerase and containing biotinylated CTP and UTP in addition to the four unmodified ribonucleoside triphosphates. The biotinylated complementary RNA (cRNA) waas purified from the IVT reaction mixture using magnetic particles. The cRNA was quantified spectrophotometrically and purity of the cRNA is also assessed by spectrophometric measurements. The purified cRNA was fragmented in order to facilitate the subsequent hybridization step.    Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

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

value: skeletal muscle

value: mixed background (C57Bl/6 and 129)

value: Yin Yang 1 (YY1) knockout

tag: age

value: 6 months


title: Halobacterium salinarum NRC-1, 5min after CuSO4 addition, set 2, replicate 3


title: DNA_Normal_L

description: Normal

value: lung


title: Patient CLL5 Time point TP2

tag: Stage

tag: primary therapy


title: knockout rep-4


title: Cardiac septum_heart_healthy (4158307036_H)

value: male


title: knockout rep-2


title: Cardiac septum_heart_healthy (4158307042_F)

value: female


title: Halobacterium salinarum NRC-1, 0min after CuSO4 addition, set 2, replicate 3


title: Halobacterium salinarum NRC-1, 10min after CuSO4 addition, set 2, replicate 3


title: knockout rep-1


title: Patient CLL4 Time point TP3

source_name: Patient CLL4

value: Pentostatin, cyclophosphamide and rituximab (PCR)

tag: secondary therapy

tag: tertiary therapy


title: Cardiac septum_heart_healthy (4158307042_E)


title: Cardiac septum_HCM (4158307036_B)

source_name: Cardiac septum_HCM

value: HCM


title: Halobacterium salinarum NRC-1, prior to CuSO4 addition, set 2, replicate 3


title: Halobacterium salinarum NRC-1 Dura3, 80min after CuSO4 addition, set 1, replicate 2

source_name: Halobacterium salinarum NRC-1 Dura3, CuSO4

value: NRC-1 Dura3


title: Halobacterium salinarum NRC-1 Dura3, 160min after CuSO4 addition, set 1, replicate 2


title: Spleen DC rep 2

description: gene expression data from spleen DCs

value: BALB/c

tag: cell type

value: CD11c+ conventional dendritic cells from spleen


title: Halobacterium salinarum NRC-1 Dura3, 40min after CuSO4 addition, set 1, replicate 2

tag: strain

value: Copper (II) sulfate

value: unperturbed H. salinarum batch culture in rich medium at OD600 0.6-0.8


title: Cardiac septum_HCM (4310479091_C)


title: Patient CLL1 Time point TP1

source_name: DNA tumor sample

value: Diagnosis or near diagnosis

tag: tissue

value: Peripheral blood

tag: sample type

value: reference DNA


title: Patient CLL3 Time point TP2

source_name: Patient CLL3

value: CLL

value: Progressive disease


title: Patient CLL3 Time point TP3


title: Halobacterium salinarum NRC-1 Dura3, 10min after CuSO4 addition, set 1, replicate 2


title: Cardiac septum_heart_healthy (4158307036_F)

value: control


title: Cardiac septum_HCM (4310479091_B)


title: Halobacterium salinarum NRC-1 Dura3, 5min after CuSO4 addition, set 1, replicate 2


title: wild type rep-3

description: Gene expression data from wild type soleus

value: skeletal muscle

value: mixed background (C57Bl/6 and 129)

value: wild type

value: 6 months


title: wild type rep-2


title: Cardiac septum_HCM (4158307036_D)

value: female


title: Cardiac septum_HCM (4158307036_A)

value: HCM


title: MDA-MB-231 1 μg/ml DLL4-FC+DMSO 6 hours Treatment Replicate 3

city: Singapore

first: Kian Leong

last: LEE

state: Singapore

address: #07-21, 8 College Road

department: Duke-NUS Medical School

country: Singapore

institute: National University of Singapore (NUS)

description: Chua SW, Vijayakumar P, Nissom PM, Yam CY, Wong VV, Yang H: A novel normalization method for effective removal of systematic variation in microarray data. Nucleic acids research 2006, 34(5):e38.

hyb_protocol: 750ng of each cRNA sample was hybridized to HumanRef-8 v3 Expression BeadChip microarrays (Illumina) as per manufacturer specifications.

scan_protocol: Microarrays were scanned on the BeadArray Reader (Illumina, USA) at scan factor 1 as per manufacturer specifications.

data_processing: Raw intensity values were subjected to background subtraction on the BeadStudio Data Analysis Software (Illumina) and normalized using the cross-correlation method (Chua et al., 2006). Differential gene expression was identified based on a fold change cutoff of >1.5 compared to the average of the Fc controls for each cell line.

source_name: MDA-MB-231, ER-, mutated p53, basal, breast cancer, 1 μg/ml DLL4-FC, 6 hours

label_protocol: 500ng of total RNA from each sample was reverse transcribed into cDNA and in vitro transcribed into biotin-labelled cRNA using the Illumina TotalPrep RNA Amplification kit (Ambion).

growth_protocol: MCF7 and MDA-MB-231 cells were maintained and expanded in DMEM with 10% FBS and 1% of PEST (Invitrogen) in 5% CO2 at 37°C.

extract_protocol: Total RNA was extracted from all treated MCF7 and MDA-MB-231 cells after 6 hours ligand stimulation using the RNeasy Mini kit (Qiagen) according to manufacturer instructions. RNA quality was assessed on the 2100 Bioanalyser (Agilent) using the RNA 6000 Nano Chip kit (Agilent) for intact 18S and 28S ribosomal peaks without significant degradation (RNA Integrity Number >9) for all samples.

treatment_protocol: For each array sample, 5 million cells were plated either on 1 μg/ml JAGGED1-Fc or 1 μg/ml DLL4-Fc or 1 μg/ml Fc as control with or without 5 μM DAPT or DMSO as the carrier control

tag: cell line

tag: estrogen receptor status

value: Negative

tag: p53 status

value: Mutant

tag: cancer type

value: Breast

tag: cancer subtype

value: Basal

value: 1 μg/ml DLL4-FC

tag: duration

value: 6 hours


title: Patient CLL4 Time point TP2

value: Peripheral blood


title: Patient CLL4 Time point TP1

value: Diagnosis or near diagnosis

value: reference DNA


title: Halobacterium salinarum NRC-1 Dura3, 0min after CuSO4 addition, set 1, replicate 2

value: NRC-1 Dura3

tag: copper concentration (mm)

tag: treatment

value: Copper (II) sulfate

tag: time (min)

value: unperturbed H. salinarum batch culture in rich medium at OD600 0.6-0.8


title: Patient CLL2 Time point TP3

tag: pathology

value: CLL

tag: Stage

value: Progressive disease

value: Pentostatin, cyclophosphamide and rituximab (PCR)


title: Patient CLL2 Time point TP2

source_name: Patient CLL2

tag: primary therapy

tag: secondary therapy


title: wild type rep-1

value: skeletal muscle

value: mixed background (C57Bl/6 and 129)

tag: genotype

value: wild type

tag: age

value: 6 months


title: Cardiac septum_HCM (4158307042_B)

tag: gender

value: female

tag: disease state

value: HCM


title: Patient CLL1 Time point TP2

tag: tertiary therapy

tag: tissue

tag: sample type


title: Halobacterium salinarum NRC-1 Dura3, prior to CuSO4 addition, set 1, replicate 2

tag: strain


title: Halobacterium salinarum NRC-1 Dura3, 20min after CuSO4 addition, set 1, replicate 2


title: Halobacterium salinarum NRC-1 Dura3, 160min after CuSO4 addition, set 1, replicate 1


title: MDA-MB-231 1 μg/ml DLL4-FC+DMSO 6 hours Treatment Replicate 2

tag: cell line

tag: estrogen receptor status

value: Negative

tag: p53 status

value: Mutant

tag: cancer type

value: Breast

tag: cancer subtype

value: Basal

value: 1 μg/ml DLL4-FC


title: Cardiac septum_HCM (4158307042_D)

value: male


title: Halobacterium salinarum NRC-1, 80min after CuSO4 addition, set 2, replicate 3

tag: copper concentration (mm)

tag: treatment

value: Copper (II) sulfate

tag: time (min)


title: Halobacterium salinarum NRC-1 Dura3, 80min after CuSO4 addition, set 1, replicate 1

value: NRC-1 Dura3

value: unperturbed H. salinarum batch culture in rich medium at OD600 0.6-0.8


title: Halobacterium salinarum NRC-1 Dura3, 40min after CuSO4 addition, set 1, replicate 1


title: SKBR3-R_1uM_Lapatinib_3

city: Houston

first: Prahlad

last: Ram

state: TEXAS

address: 7435 Fannin St, Unit 950

institute: UT MDACC

description: To export to gene expression data based on unique gene, we used Sample Gene Profile option of Illumina BeadStudio software. The whole 48697 probes on the Human-6 beadChip ver. 2 were used.

hyb_protocol: Labeled, amplified material (750 ng per array) was hybridized to the Illumina HumanHT-12 V3.0 expression beadchip according to the Manufacturer's instructions (Illumina, Inc., San Diego, CA).

scan_protocol: Arrays were scanned with an Illumina Bead array Reader confocal scanner (BeadStation 500GXDW; Illumina, Inc., San Diego, CA) according to the Manufacturer's instructions

data_processing: Array data processing were performed on Illumina BeadStudio software. We normalized gene expression data using Quantile normalization and log2 transformatoin. To export to a data matrix, Sample Gene Profile option of this software was used.

label: Biotin

source_name: human breast cancer cell line

label_protocol: Biotin-labeled cRNA samples for hybridization were prepared according to Illumina's recommended sample labeling procedure: 500 ng of total RNA was used for cDNA synthesis, followed by an amplification/labeling step (in vitro transcription) to synthesize biotin-labeled cRNA using the Illumina. TotalPrep RNA Amplification kit (Ambion Inc., Austin, TX). cRNA concentrations using spectrophotometer (Nanodrop, ND-1000)

extract_protocol: Total RNA was isolated from tissues with mirVana RNA Isolation labeling kit (Ambion Inc) according to the manufacturer protocol. RNA quality and integrity were confirmed by ExperionTM Automated Electrophoresis System (BIO-RAD)

value: SKBR3 resistant

value: 1uM Lapatinib


title: MDA-MB-231 1 μg/ml DLL4-FC+DMSO 6 hours Treatment Replicate 1

tag: duration

value: 6 hours


title: MDA-MB-231 1 μg/ml JAGGED1-FC + 5 μM DAPT 6 hours Treatment Replicate 3

source_name: MDA-MB-231, ER-, mutated p53, basal, breast cancer, 1 μg/ml JAGGED1-FC, 5 μM DAPT, 6 hours

value: 1 μg/ml JAGGED1-FC + 5 μM DAPT


title: Halobacterium salinarum NRC-1 Dura3, 20min after CuSO4 addition, set 1, replicate 1


title: Halobacterium salinarum NRC-1 Dura3, 5min after CuSO4 addition, set 1, replicate 1


title: Halobacterium salinarum NRC-1 Dura3, 10min after CuSO4 addition, set 1, replicate 1


title: MDA-MB-231 1 μg/ml JAGGED1-FC + 5 μM DAPT 6 hours Treatment Replicate 1


title: Halobacterium salinarum NRC-1 Dura3, 0min after CuSO4 addition, set 1, replicate 1


title: Halobacterium salinarum NRC-1 Dura3, prior to CuSO4 addition, set 1, replicate 1


title: Cardiac septum_HCM (4158307036_C)


title: SKBR3-R_1uM_Lapatinib_2


title: SKBR3-R_1uM_Lapatinib_1


title: MDA-MB-231 1 μg/ml JAGGED1-FC + 5 μM DAPT 6 hours Treatment Replicate 2


title: SKBR3-R_0.1uM_Lapatinib_2

value: 0.1uM Lapatinib


title: MDA-MB-231 1 μg/ml JAGGED1-FC+DMSO 6 hours Treatment Replicate 3

source_name: MDA-MB-231, ER-, mutated p53, basal, breast cancer, 1 μg/ml JAGGED1-FC, 6 hours

value: 1 μg/ml JAGGED1-FC


title: SKBR3-R_0.1uM_Lapatinib_1


title: MDA-MB-231 1 μg/ml JAGGED1-FC+DMSO 6 hours Treatment Replicate 1


title: MDA-MB-231 1 μg/ml DLL4-FC + 5 μM DAPT 6 hours Treatment Replicate 2

source_name: MDA-MB-231, ER-, mutated p53, basal, breast cancer, 1 μg/ml DLL4-FC, 5 μM DAPT, 6 hours

value: 1 μg/ml DLL4-FC + 5 μM DAPT


title: SKBR3-R_0.1uM_Lapatinib_3


title: MDA-MB-231 1 μg/ml JAGGED1-FC+DMSO 6 hours Treatment Replicate 2


title: Halobacterium salinarum NRC-1, 160min after CuSO4 addition, set 1, replicate 3

source_name: Halobacterium salinarum NRC-1, CuSO4

source_name: Halobacterium salinarum NRC-1, Standard Reference


title: MDA-MB-231 1 μg/ml FC+DMSO 6 hours Control Replicate 3

source_name: MDA-MB-231, ER-, mutated p53, basal, breast cancer, 1 μg/ml FC, 6 hours

value: 1 μg/ml FC


title: SKBR3-R_Control_3

value: basal conditions


title: SKBR3-R_Control_2


title: MDA-MB-231 1 μg/ml FC+DMSO 6 hours Control Replicate 2

value: Negative

value: Mutant


title: SKBR3-R_Control_1


title: Halobacterium salinarum NRC-1, 80min after CuSO4 addition, set 1, replicate 3


title: MDA-MB-231 1 μg/ml FC+DMSO 6 hours Control Replicate 1

value: Breast

value: Basal


title: SKBR3_1uM_Lapatinib_2

value: SKBR3 parental


title: Halobacterium salinarum NRC-1, 40min after CuSO4 addition, set 1, replicate 3

value: Copper (II) sulfate


title: MCF7 1 μg/ml DLL4-FC + 5 μM DAPT 6 hours Treatment Replicate 3

source_name: MCF7, ER+, wild-type p53, luminal type B, breast cancer, 1 μg/ml DLL4-FC, 5 μM DAPT, 6 hours

value: Positive

value: Wild-type

value: Luminal type B


title: SKBR3_1uM_Lapatinib_3

value: 1uM Lapatinib


title: Halobacterium salinarum NRC-1, 20min after CuSO4 addition, set 1, replicate 3

value: unperturbed H. salinarum batch culture in rich medium at OD600 0.6-0.8


title: SKBR3_1uM_Lapatinib_1


title: Halobacterium salinarum NRC-1, 10min after CuSO4 addition, set 1, replicate 3


title: Halobacterium salinarum NRC-1, 5min after CuSO4 addition, set 1, replicate 3


title: MCF7 1 μg/ml DLL4-FC + 5 μM DAPT 6 hours Treatment Replicate 2

value: 6 hours


title: MCF7 1 μg/ml DLL4-FC + 5 μM DAPT 6 hours Treatment Replicate 1


title: Halobacterium salinarum NRC-1, 0min after CuSO4 addition, set 1, replicate 3


title: MCF7 1 μg/ml DLL4-FC+DMSO 6 hours Treatment Replicate 3

source_name: MCF7, ER+, wild-type p53, luminal type B, breast cancer, 1 μg/ml DLL4-FC, 6 hours

value: 1 μg/ml DLL4-FC


title: MCF7 1 μg/ml JAGGED1-FC + 5 μM DAPT 6 hours Treatment Replicate 3

source_name: MCF7, ER+, wild-type p53, luminal type B, breast cancer, 1 μg/ml JAGGED1-FC, 5 μM DAPT, 6 hours

value: 1 μg/ml JAGGED1-FC + 5 μM DAPT


title: MDA-MB-231 1 μg/ml DLL4-FC + 5 μM DAPT 6 hours Treatment Replicate 3

value: 1 μg/ml DLL4-FC + 5 μM DAPT


title: SKBR3_Control_2


title: MCF7 1 μg/ml JAGGED1-FC + 5 μM DAPT 6 hours Treatment Replicate 2


title: Halobacterium salinarum NRC-1, 320min after CuSO4 addition, replicate 2


title: MCF7 1 μg/ml DLL4-FC+DMSO 6 hours Treatment Replicate 1


title: Halobacterium salinarum NRC-1, 160min after CuSO4 addition, replicate 2


title: SKBR3_0.1uM_Lapatinib_1

value: 0.1uM Lapatinib


title: MDA-MB-231 1 μg/ml DLL4-FC + 5 μM DAPT 6 hours Treatment Replicate 1


title: SKBR3_0.1uM_Lapatinib_2


title: MCF7 1 μg/ml DLL4-FC+DMSO 6 hours Treatment Replicate 2


title: SKBR3_0.1uM_Lapatinib_3


title: SKBR3_Control_1

value: basal conditions


title: Halobacterium salinarum NRC-1, prior to CuSO4 addition, set 1, replicate 3


title: SKBR3_Control_3


title: MCF7 1 μg/ml JAGGED1-FC + 5 μM DAPT 6 hours Treatment Replicate 1


title: Halobacterium salinarum NRC-1, 80min after CuSO4 addition, replicate 2


title: Halobacterium salinarum NRC-1, 40min after CuSO4 addition, replicate 2


title: A549 cells_treated with Silica (0 µg/ml)_24 hours_rep5

city: Morgantown

first: Rajendran

last: Sellamuthu

state: WV

address: 1095 Willowdale Rd

department: HELD

description:
24H_A549_Si(0)_18
The labeling and hybridization of the microarrays were performed at the National Institute for Occupational Safety and Health (NIOSH), Morgantown, WV, and scanning was performed at the Center for Genomics Sciences, Alleghney-Singer Research Institute, Pittsburgh, PA.

hyb_protocol: Employing materials and protocols provided by Illumina, Inc., San Diego, CA, 750 ng of labeled cRNA sample was hybridized to the Sentrix Human HT-12 V3 BeadChip (Illumina, Inc.) for 20 hrs at 58C. Following hybridization, microarrays were washed to remove unbound and non-specifically hybridized target molecules, and stained with Cy3-streptavidin conjugate (Illumina, Inc).

scan_protocol: The arrays were scanned with the Illumina BeadStation 500 platform following the protocol provided by the manufacturer (Illumina, Inc).

data_processing: Array data were extracted using Illumina's BeadStudio software (Framework version 3.0.19.0). Normalization and statistical analysis of the expression data were carried out in R/Bioconductor using the ‘lumi’ and ‘limma’ packages. The ‘lumi’ Bioconductor package covered the data input, quality control, force positive background correction, variance stabilization, normalization and gene annotation (http://bioconductor.org/packages/2.2/bioc/vignettes/lumi/inst/doc/lumi.pdf). Robust spline normalization was used to generate the values in the matrix table. After normalization, Lumi code deletes undetected genes, resulting in a subset of genes detected on the array. A linear model analysis using the 'limma' package in R was conducted to identify differentially expressed genes. p values were calculated and log fold changes were converted to standard fold changes. Resulting raw p-values were corrected for false discovery rate using the Benjamini-Hochberg method.

source_name: A549 cells, Silica (0 µg/ml) treated, 24 hours

label_protocol: Biotin-labeled cRNA was generated from 375 ng RNA samples each by employing the Illumina TotalPrep RNA Amplification Kit (Ambion, Inc, Austin, TX).

extract_protocol: Total RNA was isolated from A549 cells using the RNeasy Mini Kit (Qiagen, Inc, Valencia, CA) with on-column DNA digestion following the manufacturer's instructions.

treatment_protocol: Human lung epithelial cells were grown overnight in F-12K medium. Subsequently, the cells were treated with crystalline silica (0 or 200 µg/ml) in serum-free medium for 24 hours, followed by total RNA isolation.

tag: cell type

value: lung epithelial cells

tag: treatment duration

value: 24 hrs


title: A549 cells_treated with Silica (200 µg/ml)_24 hours_rep1

description:
24H_A549_Si(200)_13
The labeling and hybridization of the microarrays were performed at the National Institute for Occupational Safety and Health (NIOSH), Morgantown, WV, and scanning was performed at the Center for Genomics Sciences, Alleghney-Singer Research Institute, Pittsburgh, PA.

source_name: A549 cells, Silica (200 µg/ml) treated, 24 hours

value: 200 µg/ml crystalline silica


title: A549 cells_treated with Silica (200 µg/ml)_24 hours_rep4

description:
24H_A549_Si(200)_17
The labeling and hybridization of the microarrays were performed at the National Institute for Occupational Safety and Health (NIOSH), Morgantown, WV, and scanning was performed at the Center for Genomics Sciences, Alleghney-Singer Research Institute, Pittsburgh, PA.


title: MCF7 1 μg/ml JAGGED1-FC+DMSO 6 hours Treatment Replicate 3

source_name: MCF7, ER+, wild-type p53, luminal type B, breast cancer, 1 μg/ml JAGGED1-FC, 6 hours

value: Breast

value: 1 μg/ml JAGGED1-FC


title: Halobacterium salinarum NRC-1, 20min after CuSO4 addition, replicate 2

value: Copper (II) sulfate


title: A549 cells_treated with Silica (200 µg/ml)_24 hours_rep5

description:
24H_A549_Si(200)_18
The labeling and hybridization of the microarrays were performed at the National Institute for Occupational Safety and Health (NIOSH), Morgantown, WV, and scanning was performed at the Center for Genomics Sciences, Alleghney-Singer Research Institute, Pittsburgh, PA.


title: Halobacterium salinarum NRC-1, 10min after CuSO4 addition, replicate 2


title: A549 cells_treated with Silica (0 µg/ml)_24 hours_rep4

description:
24H_A549_Si(0)_17
The labeling and hybridization of the microarrays were performed at the National Institute for Occupational Safety and Health (NIOSH), Morgantown, WV, and scanning was performed at the Center for Genomics Sciences, Alleghney-Singer Research Institute, Pittsburgh, PA.


title: Halobacterium salinarum NRC-1, 5min after CuSO4 addition, replicate 2


title: MCF7 1 μg/ml JAGGED1-FC+DMSO 6 hours Treatment Replicate 1

value: Positive


title: MCF7 1 μg/ml JAGGED1-FC+DMSO 6 hours Treatment Replicate 2

value: Wild-type


title: Halobacterium salinarum NRC-1, 0min after CuSO4 addition, replicate 2


title: Halobacterium salinarum NRC-1, prior to CuSO4 addition, replicate 2


title: MCF7 1 μg/ml FC+DMSO 6 hours Control Replicate 2

source_name: MCF7, ER+, wild-type p53, luminal type B, breast cancer, 1 μg/ml FC, 6 hours

value: Luminal type B

value: 1 μg/ml FC


title: MCF7 1 μg/ml FC+DMSO 6 hours Control Replicate 3


title: A549 cells_treated with Silica (0 µg/ml)_24 hours_rep3

description:
24H_A549_Si(0)_16
The labeling and hybridization of the microarrays were performed at the National Institute for Occupational Safety and Health (NIOSH), Morgantown, WV, and scanning was performed at the Center for Genomics Sciences, Alleghney-Singer Research Institute, Pittsburgh, PA.


title: MCF7 1 μg/ml FC+DMSO 6 hours Control Replicate 1


title: BreedProfile HS 04

city: Dummerstorf

first: Klaus

last: Wimmers

address: Wilhelm-Stahl-Allee 2

country: Germany

institute: Leibniz Institute for Farm Animal Biology (FBN)

description: Gene expression data from isolated SCF

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 42°C on Affymetrix GeneChip Bovine Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Scanning using the GeneChip scanner 3000 were performed according to Affymetrix protocols

data_processing: Data were analysed with Affymetrix GCOS 1.1.1 software using global scaling to a target signal of 500 and Affymetrix Expression Console 1.1

organism: Bos taurus

source_name: Subcutaneous fat

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 0.5 ug total RNA (Expression Analysis Technical Manual, 2009, Affymetrix).

extract_protocol: Total RNA was isolated using TRI Reagent (Sigma, Taufkirchen, Germany) according to the manufacturer’s protocol. After DNaseI treatment the RNA was cleaned up using the RNeasy Kit (Qiagen, Hilden, Germany).

treatment_protocol: Energy rich feeding (Gotoh et al. 2009)

tag: breed

value: Holstein

tag: adipose depot

value: Subcutaneous fat


title: BreedProfile HS 05

description: Gene expression data from isolated SCF


title: Halobacterium salinarum NRC-1, 80min after CuSO4 addition, replicate 1

value: unperturbed H. salinarum batch culture in rich medium at OD600 0.6-0.8


title: A549 cells_treated with Silica (200 µg/ml)_24 hours_rep3

description:
24H_A549_Si(200)_15
The labeling and hybridization of the microarrays were performed at the National Institute for Occupational Safety and Health (NIOSH), Morgantown, WV, and scanning was performed at the Center for Genomics Sciences, Alleghney-Singer Research Institute, Pittsburgh, PA.


title: A549 cells_treated with Silica (200 µg/ml)_24 hours_rep2

description:
24H_A549_Si(200)_14
The labeling and hybridization of the microarrays were performed at the National Institute for Occupational Safety and Health (NIOSH), Morgantown, WV, and scanning was performed at the Center for Genomics Sciences, Alleghney-Singer Research Institute, Pittsburgh, PA.


title: Halobacterium salinarum NRC-1, 40min after CuSO4 addition, replicate 1


title: BreedProfile HS 03

description: Gene expression data from isolated IMF

source_name: Intramuscular

value: Intramuscular


title: A549 cells_treated with Silica (0 µg/ml)_24 hours_rep1

description:
24H_A549_Si(0)_14
The labeling and hybridization of the microarrays were performed at the National Institute for Occupational Safety and Health (NIOSH), Morgantown, WV, and scanning was performed at the Center for Genomics Sciences, Alleghney-Singer Research Institute, Pittsburgh, PA.


title: BreedProfile HS 02

description: Gene expression data from isolated IMF


title: A549 cells_treated with Silica (0 µg/ml)_24 hours_rep2

description:
24H_A549_Si(0)_15
The labeling and hybridization of the microarrays were performed at the National Institute for Occupational Safety and Health (NIOSH), Morgantown, WV, and scanning was performed at the Center for Genomics Sciences, Alleghney-Singer Research Institute, Pittsburgh, PA.


title: BreedProfile HS 06

description: Gene expression data from isolated SCF


title: BreedProfile HS 01

description: Gene expression data from isolated IMF


title: BreedProfile JB 06

description: Gene expression data from isolated SCF

value: Japanese Black


title: Lymphoblastic lymphoma remission 10SA_Hind

city: Monza

first: Antonella

last: Lettieri

address: via Pergolesi 33

institute: Tettamanti Research Center

description: Hybridized to 50K_Hind

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.

data_processing:
The SNP arrays raw data were acquired by the Affymetrix GCOS software (version 1.4) and SNP calls were generated by the GTYPE software (version 4.0). The recommended QC and SNP call rate thresholds were used (BRLMM algorithm). Paired copy number analysis was performed using three different algorithms: PartekGS, CRMA and CNAG. The aberration segments provided by Partek Genomics Suite 6.08 software were generated using the genomic segmentation algorithm at a p-value of 0.001 and a signal to noise ratio of 0.3 and a minimum of ten genomic markers. The segmentation data were then filtered for p-value ≤ 0.01. Copy-number values obtained by Robust Multichip Analysis (CRMAv.2) were generated by normalizing each tumor’s probe set intensity to that of its paired normal reference. Raw copy number was estimated by using the CRMA algorithm (Bengtsson et al., 2008). Copy number segmentation of log2 ratios was performed in R using the DNA copy number package v1.16.0 which applies CBS (Circular Binary Segmentation) (Venkatraman and Olshen, 2007). Genomic copy numbers were also calculated using the CNAG v2.0 software package which relies on the Hidden Markov Model (HMM) analysis (Nannya et al., 2005). Copy number values ≤ 1.7 and ≥ 2.3 were considered losses and gains, respectively.[Combined_Hind_Xba_matrix provided as supplementary file on Series records]
primary data description : Genotype Call (SNP call): AA, AB, BB, NC, and NoCall; 'Signal' = Summarized signal

source_name: Lymphoblastic lymphoma remission

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: Normal and tumor genomic DNA of T-ALL patients was extracted from freshly isolated BM-MNC by a commercial procedure (Puregene Blood kit, Gentra Systems, Minneapolis, MN), and genomic DNA from T-LBL patients was obtained from nucleated cells isolated by differential lysis using the QIAamp tissue kit (Qiagen, Hilden, Germany)

tag: disease type

value: T-LBL

value: remission

value: diagnostic bone marrow aspirates or tumor tissue


title: Halobacterium salinarum NRC-1, 20min after CuSO4 addition, replicate 1


title: Lymphoblastic lymphoma remission 11AS_Hind

description: Hybridized to 50K_Hind

tag: tissue


title: A549 cells_treated with Silica (0 µg/ml)_2 hours_rep5

description:
2H_A549_Si(0)_6
The labeling and hybridization of the microarrays were performed at the National Institute for Occupational Safety and Health (NIOSH), Morgantown, WV, and scanning was performed at the Center for Genomics Sciences, Alleghney-Singer Research Institute, Pittsburgh, PA.

source_name: A549 cells, Silica (0 µg/ml) treated, 2 hours

treatment_protocol: Human lung epithelial cells were grown overnight in F-12K medium. Subsequently, the cells were treated with crystalline silica (0 or 200 µg/ml) in serum-free medium for 2 hours, followed by total RNA isolation.

value: lung epithelial cells

value: 2 hrs


title: Lymphoblastic lymphoma remission 13BP_Hind

description: Hybridized to 50K_Xba

tag: sample type


title: BreedProfile JB 05

description: Gene expression data from isolated SCF


title: Lymphoblastic lymphoma remission 9AM_Hind

description: Hybridized to 50K_Hind


title: Halobacterium salinarum NRC-1, 10min after CuSO4 addition, replicate 1

tag: strain


title: A549 cells_treated with Silica (200 µg/ml)_2 hours_rep1

description:
2H_A549_Si(200)_1
The labeling and hybridization of the microarrays were performed at the National Institute for Occupational Safety and Health (NIOSH), Morgantown, WV, and scanning was performed at the Center for Genomics Sciences, Alleghney-Singer Research Institute, Pittsburgh, PA.

source_name: A549 cells, Silica (200 µg/ml) treated, 2 hours

tag: cell line

value: 200 µg/ml crystalline silica


title: Halobacterium salinarum NRC-1, 5min after CuSO4 addition, replicate 1


title: Halobacterium salinarum NRC-1, 0min after CuSO4 addition, replicate 1


title: A549 cells_treated with Silica (0 µg/ml)_2 hours_rep4

description:
2H_A549_Si(0)_5
The labeling and hybridization of the microarrays were performed at the National Institute for Occupational Safety and Health (NIOSH), Morgantown, WV, and scanning was performed at the Center for Genomics Sciences, Alleghney-Singer Research Institute, Pittsburgh, PA.


title: Halobacterium salinarum NRC-1, prior to CuSO4 addition, replicate 1


title: BreedProfile JB 04

description: Gene expression data from isolated SCF


title: BreedProfile JB 03

description: Gene expression data from isolated IMF


title: A549 cells_treated with Silica (0 µg/ml)_2 hours_rep3

description:
2H_A549_Si(0)_3
The labeling and hybridization of the microarrays were performed at the National Institute for Occupational Safety and Health (NIOSH), Morgantown, WV, and scanning was performed at the Center for Genomics Sciences, Alleghney-Singer Research Institute, Pittsburgh, PA.


title: Lymphoblastic lymphoma remission 6TA_Hind

description: Hybridized to 50K_Hind


title: BreedProfile JB 02

description: Gene expression data from isolated IMF


title: A549 cells_treated with Silica (200 µg/ml)_2 hours_rep3

description:
2H_A549_Si(200)_4
The labeling and hybridization of the microarrays were performed at the National Institute for Occupational Safety and Health (NIOSH), Morgantown, WV, and scanning was performed at the Center for Genomics Sciences, Alleghney-Singer Research Institute, Pittsburgh, PA.


title: A549 cells_treated with Silica (200 µg/ml)_2 hours_rep2

description:
2H_A549_Si(200)_2
The labeling and hybridization of the microarrays were performed at the National Institute for Occupational Safety and Health (NIOSH), Morgantown, WV, and scanning was performed at the Center for Genomics Sciences, Alleghney-Singer Research Institute, Pittsburgh, PA.


title: Lymphoblastic lymphoma remission 3MM_Hind

description: Hybridized to 50K_Hind


title: Lymphoblastic lymphoma remission 5NL_Hind

description: Hybridized to 50K_Hind


title: BreedProfile JB 01

description: Gene expression data from isolated IMF


title: Lymphoblastic lymphoma remission 2NP_Hind

description: Hybridized to 50K_Hind


title: Panc3.014 cancer cell line, EYA2-overexpressing rep2

city: Baltimore

first: AUDREY

last: VINCENT

state: MD

address: 1550 Orleans Street, CRBII

department: Pathology

institute: Johns Hopkins University

description: AVin-EGA-B2-1a-hsExon1_(HuEx-1_0-st-v2).CEL

hyb_protocol: Samples were hybridized with the GeneChip Human Exon 1.0 ST Arrays (Affymetrix) and scanned at the JHMI Microarray Core Facility

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix)

data_processing: Relative gene expression values were obtained after using the Tukey biweight method to normalize the raw intensity measurements of all probe sets with Partek Genomics Suite v6.3 beta (Partek Inc., St. Louis MO).

label_protocol: Single stranded cDNA was generated from the amplified cRNA using the WT cDNA Synthesis kit (Affymetrix) and then fragmented and labeled using the WT Terminal Labeling Kit (Affymetrix)

growth_protocol: Cells were maintained in culture at 37degrees C in DMEM containing 10% FBS and 2% penicillin-streptomycin.  3ug/ml Blasticidine was added to stable transfectant culture medium.

extract_protocol: RNA was isolated from cell cultures using the Ambion mirVana RNA extraction kit, according to the manufacturer's instructions

tag: gender

value: Male

tag: carcinoma type

value: Pancreatic ductal adenocarcinoma

tag: tissue derivation

value: Primary pancreatic tumor

tag: tumor stage

value: IIB

tag: transfectant

value: pcDNA6.2/cLumio-DEST-EYA2 vector


title: Lymphoblastic lymphoma remission 1BD_Hind

description: Hybridized to 50K_Hind


title: A549 cells_treated with Silica (0 µg/ml)_2 hours_rep1

description:
2H_A549_Si(0)_1
The labeling and hybridization of the microarrays were performed at the National Institute for Occupational Safety and Health (NIOSH), Morgantown, WV, and scanning was performed at the Center for Genomics Sciences, Alleghney-Singer Research Institute, Pittsburgh, PA.

tag: treatment


title: Panc3.014 cancer cell line, EYA2-overexpressing rep1

description: AVin-EGA-D4-1a-hsExon1_(HuEx-1_0-st-v2).CEL


title: A549 cells_treated with Silica (200 µg/ml)_2 hours_rep4

description:
2H_A549_Si(200)_5
The labeling and hybridization of the microarrays were performed at the National Institute for Occupational Safety and Health (NIOSH), Morgantown, WV, and scanning was performed at the Center for Genomics Sciences, Alleghney-Singer Research Institute, Pittsburgh, PA.


title: A549 cells_treated with Silica (200 µg/ml)_2 hours_rep5

description:
2H_A549_Si(200)_6
The labeling and hybridization of the microarrays were performed at the National Institute for Occupational Safety and Health (NIOSH), Morgantown, WV, and scanning was performed at the Center for Genomics Sciences, Alleghney-Singer Research Institute, Pittsburgh, PA.


title: A549 cells_treated with Silica (0 µg/ml)_2 hours_rep2

description:
2H_A549_Si(0)_2
The labeling and hybridization of the microarrays were performed at the National Institute for Occupational Safety and Health (NIOSH), Morgantown, WV, and scanning was performed at the Center for Genomics Sciences, Alleghney-Singer Research Institute, Pittsburgh, PA.


title: Acute leukemia remission 2422_Hind

description: Hybridized to 50K_Hind

source_name: Acute leukemia remission

value: T-ALL


title: Acute leukemia remission 1928_Hind

description: Hybridized to 50K_Hind


title: Panc3.014 cancer cell line, control rep2

description: AVin-EGA-B1-1a-hsExon1_(HuEx-1_0-st-v2).CEL

source_name: Panc3.014 cancer cell line, control

value: Empty pcDNA6.2/cLumio-DEST vector


title: Acute leukemia remission 1870_Hind

description: Hybridized to 50K_Hind


title: Panc3.014 cancer cell line, control rep1

description: AVin-EGA-A4-1a-hsExon1_(HuEx-1_0-st-v2).CEL


title: Acute leukemia remission 1847_Hind

description: Hybridized to 50K_Hind


title: A549 cells_treated with Silica (0 µg/ml)_6 hours_rep1c

description:
6H_A549_Si(0)_19
The labeling and hybridization of the microarrays were performed at the National Institute for Occupational Safety and Health (NIOSH), Morgantown, WV, and scanning was performed at the Center for Genomics Sciences, Alleghney-Singer Research Institute, Pittsburgh, PA.

source_name: A549 cells, Silica (0 µg/ml) treated, 6 hours

treatment_protocol: Human lung epithelial cells were grown overnight in F-12K medium. Subsequently, the cells were treated with crystalline silica (0 or 50 µg/ml) in serum-free medium for 6 hours, followed by total RNA isolation.

value: 6 hrs


title: Panc3.014 cancer cell line, parental

description: AVin-EGA-B3-1a-hsExon1_(HuEx-1_0-st-v2).CEL

source_name: Panc3.014 cancer cell line, parental

value: Not transfected


title: Acute leukemia remission 1520_Hind

description: Hybridized to 50K_Hind


title: Acute leukemia remission 1238_Hind

description: Hybridized to 50K_Hind


title: A549 cells_treated with Silica (50 µg/ml)_6 hours_rep1

description:
6H_A549_Si(50)_1
The labeling and hybridization of the microarrays were performed at the National Institute for Occupational Safety and Health (NIOSH), Morgantown, WV, and scanning was performed at the Center for Genomics Sciences, Alleghney-Singer Research Institute, Pittsburgh, PA.

source_name: A549 cells, Silica (50 µg/ml) treated, 6 hours

value: 50 µg/ml crystalline silica


title: RNA_IPF_3

description: IPF

hyb_protocol: The cRNA was then hybridized to a human HT-12 BeadChip and stained with strepavidin-Cy3 for visualization.

scan_protocol: Scanned using the Illumina iScan.

data_processing: Quantile normalized, no background subtraction

source_name: IPF

label_protocol: Total RNA was converted to cDNA by reverse transcription, followed by second-strand synthesis to generate double-stranded cDNA.  After purification, the cDNA was converted to biotin-labeled cRNA.

extract_protocol: Rneasy

value: lung

tag: disease status

value: IPF


title: A549 cells_treated with Silica (50 µg/ml)_6 hours_rep3

description:
6H_A549_Si(50)_3
The labeling and hybridization of the microarrays were performed at the National Institute for Occupational Safety and Health (NIOSH), Morgantown, WV, and scanning was performed at the Center for Genomics Sciences, Alleghney-Singer Research Institute, Pittsburgh, PA.


title: DUH23 24 #2 Skeletal Muscle

city: Tübingen

first: Yingguang Frank

last: Chan

address: Max-Planck-Ring 9

institute: Friedrich Miescher Laboratory

description: Gene expression at age 44-45d in skeletal muscle

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.5.1.1 (Agilent) using default parameters (protocol GE1_105_Dec08 and Grid: 014868_D_F_20080627) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

molecule: polyA RNA

source_name: Skeletal muscle, male 44-45d

label_protocol: Muscle and liver cDNA samples were hybridized on a Mouse GE 4x44k Microarray (Agilent Technologies, Inc., Waldbronn, Germany) according to manufacturer’s recommendations. Three technical replicate each was done on pooled cDNA samples from each mouse line.

growth_protocol: Mice from each line were fed ad libitum with standard laboratory conditions

extract_protocol: Mouse tissue samples (muscle and liver) were collected from 44 and 45 days old males from each of the nine out of thirteen lines (5 High lines: BEHi, DUHi, EDHi, MUHi, ROHi and 4 Control lines: BELi, EDLi, MULi and ROLi; n=23 total) at the University of Edinburgh. Frozen tissue samples were stored at -80ºC until use. Tissues were dissociated using TissueLyser II with steel beads (both Qiagen) following manufacturers’ instructions. mRNA was extracted and purified using TRIzol Reagent and the PureLink RNA Mini Kit (Life Technologies GmbH, Darmstadt, Germany). cDNA was synthesized using Maxima First Strand cDNA synthesis kit (Thermo Fisher Scientific, St. Leon-Rot, Germany).

tag: phenotype

value: high body weight

tag: genetic background

value: mixed

tag: weight

value: Skeletal muscle

tag: age

value: male

tag: line

value: DUI


title: A549 cells_treated with Silica (0 µg/ml)_6 hours_rep4c

description:
6H_A549_Si(0)_23
The labeling and hybridization of the microarrays were performed at the National Institute for Occupational Safety and Health (NIOSH), Morgantown, WV, and scanning was performed at the Center for Genomics Sciences, Alleghney-Singer Research Institute, Pittsburgh, PA.

tag: cell type

value: lung epithelial cells

tag: treatment duration


title: RNA_IPF_S

description: IPF

tag: tissue


title: Panc2.5 cancer cell line, parental

description: AVin-EGA-C1-1a-hsExon1_(HuEx-1_0-st-v2).CEL

source_name: Panc2.5 cancer cell line, parental

value: Female

value: Pancreatic ductal adenocarcinoma


title: Panc2.5 cancer cell line, control

description: AVin-EGA-D1-1a-hsExon1_(HuEx-1_0-st-v2).CEL

source_name: Panc2.5 cancer cell line, control

value: Primary pancreatic tumor

value: IIB


title: A549 cells_treated with Silica (50 µg/ml)_6 hours_rep2

description:
6H_A549_Si(50)_2
The labeling and hybridization of the microarrays were performed at the National Institute for Occupational Safety and Health (NIOSH), Morgantown, WV, and scanning was performed at the Center for Genomics Sciences, Alleghney-Singer Research Institute, Pittsburgh, PA.


title: RNA_IPF_C

description: IPF


title: Acute leukemia remission 1433_Hind

description: Hybridized to 50K_Hind

tag: disease type

value: T-ALL

tag: sample type

value: remission

value: diagnostic bone marrow aspirates or tumor tissue


title: A549 cells_treated with Silica (0 µg/ml)_6 hours_rep2c

description:
6H_A549_Si(0)_21
The labeling and hybridization of the microarrays were performed at the National Institute for Occupational Safety and Health (NIOSH), Morgantown, WV, and scanning was performed at the Center for Genomics Sciences, Alleghney-Singer Research Institute, Pittsburgh, PA.

tag: cell line

value: 6 hrs


title: Panc2.5 cancer cell line, EYA2-overexpressing

description: AVin-EGA-D2-1a-hsExon1_(HuEx-1_0-st-v2).CEL

tag: gender

tag: carcinoma type

value: pcDNA6.2/cLumio-DEST-EYA2 vector


title: Acute leukemia remission 1015_Hind

description: Hybridized to 50K_Hind


title: RNA_IPF_2

description: IPF

value: lung


title: DUH23 24 #3 Skeletal Muscle


title: DUH23 24 #1 Skeletal Muscle


title: A549 cells_treated with Silica (0 µg/ml)_6 hours_rep3c

description:
6H_A549_Si(0)_22
The labeling and hybridization of the microarrays were performed at the National Institute for Occupational Safety and Health (NIOSH), Morgantown, WV, and scanning was performed at the Center for Genomics Sciences, Alleghney-Singer Research Institute, Pittsburgh, PA.


title: EDL20 21 #3 Skeletal Muscle

value: low body weight

value: PLI


title: A549 cells_treated with Silica (50 µg/ml)_6 hours_rep4

description:
6H_A549_Si(50)_4
The labeling and hybridization of the microarrays were performed at the National Institute for Occupational Safety and Health (NIOSH), Morgantown, WV, and scanning was performed at the Center for Genomics Sciences, Alleghney-Singer Research Institute, Pittsburgh, PA.

value: 50 µg/ml crystalline silica


title: Halobacterium salinarum NRC-1, 160min after CuSO4 addition, replicate 1

source_name: Halobacterium salinarum NRC-1, CuSO4

tag: strain

tag: copper concentration (mm)

value: Copper (II) sulfate

tag: time (min)

source_name: Halobacterium salinarum NRC-1, Standard Reference

value: unperturbed H. salinarum batch culture in rich medium at OD600 0.6-0.8


title: Wild type_ 8hr

city: Gainesville

first: Zhonglin

last: Mou

state: FL

address: 981 Museum Road

department: Microbiology and Cell Science & Plant Molecular and Cellular  Biology

institute: University of Florida

description: Gene expression 8 hr after Pst DC3000/avrRpt2 infection

hyb_protocol: For each array, 1.65 μg of Cy 3 labeled cRNA was fragmented and hybridized with rotation at 65°C for 17 hr.  Samples were hybridized to Arabidopsis 4 × 44k arrays (Agilent Technologies).  The arrays were washed according to the manufacturer’s protocol.

scan_protocol: The arrays were scanned on a G2505B scanner (Agilent Technologies).

data_processing:
Data were extracted using Feature Extraction 10.1.1.1 software (Agilent Technologies).
Data (individual signal intensity values) obtained from the 8 microarray probes were log transformed (using 2 as the base) and normalized between individual samples by scaling the individual log-transformed signal intensities so that all datasets had comparable lower quartile, median and upper quartile values. Normalized, log2 signals generated using MATLAB.

organism: Arabidopsis thaliana

source_name: Wild type, infected, 8hr

label_protocol: cDNA was synthesized from 200 ng of total RNA and used as a template for in vitro transcription in the presence of T7 RNA Polymerase and cyanine labeled CTP’s using the Quick Amp Labeling kit (Agilent Technologies) according the manufacturer’s protocol.  The amplified, labeled complementary RNA (cRNA) was purified using the RNeasy Mini kit (Qiagen, Valencia, CA).

growth_protocol: Arabidopsis seeds were sown on autoclaved soil (Metro-Mix 200, Grace-Sierra, Malpitas, CA) and vernalized at 4°C for 3 days.  Plants were germinated and grown at 23 to 25°C under a 16-hr-light/8-hr-dark regime.

extract_protocol: About 100 mg leaf tissues were ground into a fine powder in liquid nitrgen and resuspended in 500 μL 80°C water-saturated phenol and 500 μL 80°C extraction buffer (100 mM LiCl, 100 mM Tris pH 8.0, 10 mM EDTA, 1% SDS).  After brief vortexing and centrifugation at 14,000 rpm for 5 min, the aqueous phase was transferred to another cold tube containing 500 μL of 24:1 chloroform:isoamyl alcohol.  After vortexing and centrifugation, the aqueous phase was transferred to a DEPC-treated tube with 1/10 volume of 3 M NaOAc and 2 volume of 100% ethanol.  The tube was inverted to mix and placed at -80°C for 30 min and then spun at 14,000 rpm for 15 min.  After removing the supernatant, the pellet was washed with 80% ethanol, dried briefly, and resuspended in DEPC-treated water.

treatment_protocol: Leaves of 4-week-old plats were inoculated with a 1 mL needless syringe by pressure-infiltration and leaf tissues were collected at the indicated time points.

tag: genotype/variation

value: Wild type

tag: infection

value: avirulent bacterial pathogen Pst DC3000/avrRpt2

tag: time point

value: 8 hr

value: leaf


title: Wild type_ 4hr

description: Gene expression 4 hr after Pst DC3000/avrRpt2 infection

source_name: Wild type, infected, 4hr

value: 4 hr


title: Lymphoblastic lymphoma diagnosis 13BP_Hind

description: Hybridized to 50K_Hind

source_name: Lymphoblastic lymphoma diagnosis

value: T-LBL

value: diagnosis


title: A549 cells_treated with Silica (0 µg/ml)_6 hours_rep5c

description:
6H_A549_Si(0)_24
The labeling and hybridization of the microarrays were performed at the National Institute for Occupational Safety and Health (NIOSH), Morgantown, WV, and scanning was performed at the Center for Genomics Sciences, Alleghney-Singer Research Institute, Pittsburgh, PA.

value: lung epithelial cells

tag: treatment


title: At-med16-1_24hr

description: Gene expression 24 hr after Pst DC3000/avrRpt2 infection

source_name: At-med16-1, infected, 24hr

value: 24 hr


title: Acute leukemia remission 757_Hind

description: Hybridized to 50K_Hind

value: T-ALL

value: remission

value: diagnostic bone marrow aspirates or tumor tissue


title: EDH17 18 #2 Skeletal Muscle

tag: phenotype

value: high body weight

tag: genetic background

value: mixed

tag: weight

value: Skeletal muscle

tag: age

value: male

value: PHI


title: A549 cells_treated with Silica (200 µg/ml)_6 hours_rep3

description:
6H_A549_Si(200)_10
The labeling and hybridization of the microarrays were performed at the National Institute for Occupational Safety and Health (NIOSH), Morgantown, WV, and scanning was performed at the Center for Genomics Sciences, Alleghney-Singer Research Institute, Pittsburgh, PA.

source_name: A549 cells, Silica (200 µg/ml) treated, 6 hours

treatment_protocol: Human lung epithelial cells were grown overnight in F-12K medium. Subsequently, the cells were treated with crystalline silica (0, 100, 200, 400 µg/ml) in serum-free medium for 6 hours, followed by total RNA isolation.

tag: cell type

value: 200 µg/ml crystalline silica

tag: treatment duration

value: 6 hrs


title: At-med16-1_ 8hr

source_name: At-med16-1, infected, 8hr

value: avirulent bacterial pathogen Pst DC3000/avrRpt2

value: 8 hr

tag: tissue


title: EDL20 21 #1 Skeletal Muscle

value: low body weight

tag: line

value: PLI


title: EDL20 21 #2 Skeletal Muscle

tag: gender


title: Wild type_ 24hr

source_name: Wild type, infected, 24hr

value: Wild type

value: leaf


title: A549 cells_treated with Silica (50 µg/ml)_6 hours_rep5

description:
6H_A549_Si(50)_6
The labeling and hybridization of the microarrays were performed at the National Institute for Occupational Safety and Health (NIOSH), Morgantown, WV, and scanning was performed at the Center for Genomics Sciences, Alleghney-Singer Research Institute, Pittsburgh, PA.

tag: cell line

value: lung epithelial cells

value: 50 µg/ml crystalline silica


title: Lymphoblastic lymphoma diagnosis 10SA_Hind

description: Hybridized to 50K_Hind

tag: disease type

value: T-LBL

tag: sample type

value: diagnosis


title: EDH17 18 #1 Skeletal Muscle

value: high body weight


title: Lymphoblastic lymphoma diagnosis 5NL_Hind

description: Hybridized to 50K_Hind

value: diagnostic bone marrow aspirates or tumor tissue


title: Lymphoblastic lymphoma diagnosis 11AS_Hind

description: Hybridized to 50K_Hind


title: Lymphoblastic lymphoma diagnosis 6TA_Hind

description: Hybridized to 50K_Hind


title: Lymphoblastic lymphoma diagnosis 3MM_Hind

description: Hybridized to 50K_Hind


title: EDH17 18 #3 Skeletal Muscle

value: mixed

value: Skeletal muscle


title: ROL15 16 #3 Skeletal Muscle

value: male

value: ROLi


title: At-med16-1_4hr

source_name: At-med16-1, infected, 4hr

value: 4 hr


title: Lymphoblastic lymphoma diagnosis 9AM_Hind

description: Hybridized to 50K_Hind


title: Wild type_0hr

description: Gene expression 0 hr after Pst DC3000/avrRpt2 infection

source_name: Wild type, infected, 0hr

value: avirulent bacterial pathogen Pst DC3000/avrRpt2

value: 0 hr


title: A549 cells_treated with Silica (100 µg/ml)_6 hours_rep5

description:
6H_A549_Si(100)_6
The labeling and hybridization of the microarrays were performed at the National Institute for Occupational Safety and Health (NIOSH), Morgantown, WV, and scanning was performed at the Center for Genomics Sciences, Alleghney-Singer Research Institute, Pittsburgh, PA.

source_name: A549 cells, Silica (100 µg/ml) treated, 6 hours

value: 100 µg/ml crystalline silica

value: 6 hrs


title: ROL15 16 #1 Skeletal Muscle

description: Gene expression at age 44-45d in skeletal muscle

value: low body weight


title: ROH12 13 #2 Skeletal Muscle

value: ROHi


title: ROL15 16 #2 Skeletal Muscle


title: A549 cells_treated with Silica (0 µg/ml)_6 hours_rep4b

description:
6H_A549_Si(0)_11
The labeling and hybridization of the microarrays were performed at the National Institute for Occupational Safety and Health (NIOSH), Morgantown, WV, and scanning was performed at the Center for Genomics Sciences, Alleghney-Singer Research Institute, Pittsburgh, PA.

source_name: A549 cells, Silica (0 µg/ml) treated, 6 hours

value: lung epithelial cells


title: ROH12 13 #3 Skeletal Muscle


title: ROH12 13 #1 Skeletal Muscle


title: A549 cells_treated with Silica (0 µg/ml)_6 hours_rep1b

description:
6H_A549_Si(0)_7
The labeling and hybridization of the microarrays were performed at the National Institute for Occupational Safety and Health (NIOSH), Morgantown, WV, and scanning was performed at the Center for Genomics Sciences, Alleghney-Singer Research Institute, Pittsburgh, PA.


title: MUL9 10 #3 Skeletal Muscle

value: MULi


title: At-med16-1_0hr

source_name: At-med16-1, infected, 0hr

value: leaf


title: Lymphoblastic lymphoma diagnosis 1BD_Hind

description: Hybridized to 50K_Hind

value: T-LBL

value: diagnosis


title: Lymphoblastic lymphoma diagnosis 2NP_Hind

description: Hybridized to 50K_Hind

value: diagnostic bone marrow aspirates or tumor tissue


title: Acute leukemia diagnosis 2422_Hind

description: Hybridized to 50K_Hind

source_name: Acute leukemia diagnosis

value: T-ALL


title: Wild type_12hr_rep1

description: Gene expression 12 hr after Pst DC3000/avrRpt2 infection

data_processing:
Data were extracted using Feature Extraction 10.1.1.1 software (Agilent Technologies).
Data (individual signal intensity values) obtained from the 36 microarray probes were log transformed (using 2 as the base) and normalized between individual samples by scaling the individual log-transformed signal intensities so that all datasets had comparable lower quartile, median and upper quartile values. Normalized, log2 signals generated using MATLAB.

source_name: Wild type, infected, 12hr, replicate 1

value: Wild type

value: 12 hr


title: Wild type_12hr_rep3

source_name: Wild type, infected, 12hr, replicate 3


title: Acute leukemia diagnosis 1928_Hind

description: Hybridized to 50K_Hind


title: A549 cells_treated with Silica (400 µg/ml)_6 hours_rep2

description:
6H_A549_Si(400)_3
The labeling and hybridization of the microarrays were performed at the National Institute for Occupational Safety and Health (NIOSH), Morgantown, WV, and scanning was performed at the Center for Genomics Sciences, Alleghney-Singer Research Institute, Pittsburgh, PA.

source_name: A549 cells, Silica (400 µg/ml) treated, 6 hours

value: 400 µg/ml crystalline silica


title: A549 cells_treated with Silica (400 µg/ml)_6 hours_rep1

description:
6H_A549_Si(400)_2
The labeling and hybridization of the microarrays were performed at the National Institute for Occupational Safety and Health (NIOSH), Morgantown, WV, and scanning was performed at the Center for Genomics Sciences, Alleghney-Singer Research Institute, Pittsburgh, PA.


title: A549 cells_treated with Silica (200 µg/ml)_6 hours_rep1

description:
6H_A549_Si(200)_8
The labeling and hybridization of the microarrays were performed at the National Institute for Occupational Safety and Health (NIOSH), Morgantown, WV, and scanning was performed at the Center for Genomics Sciences, Alleghney-Singer Research Institute, Pittsburgh, PA.

value: 200 µg/ml crystalline silica


title: Wild type_12hr_rep2

source_name: Wild type, infected, 12hr, replicate 2

value: avirulent bacterial pathogen Pst DC3000/avrRpt2


title: Acute leukemia diagnosis 1847_Hind

description: Hybridized to 50K_Hind


title: Wild type_8hr_rep3

source_name: Wild type, infected, 8hr, replicate 3

value: 8 hr


title: A549 cells_treated with Silica (400 µg/ml)_6 hours_rep5

description:
6H_A549_Si(400)_6
The labeling and hybridization of the microarrays were performed at the National Institute for Occupational Safety and Health (NIOSH), Morgantown, WV, and scanning was performed at the Center for Genomics Sciences, Alleghney-Singer Research Institute, Pittsburgh, PA.


title: Wild type_8hr_rep1

source_name: Wild type, infected, 8hr, replicate 1


title: MUL9 10 #2 Skeletal Muscle

source_name: Skeletal muscle, male 44-45d

value: mixed

value: Skeletal muscle

value: male


title: MUL9 10 #1 Skeletal Muscle

value: low body weight


title: Acute leukemia diagnosis 1520_Hind

description: Hybridized to 50K_Hind


title: Wild type_8hr_rep2

source_name: Wild type, infected, 8hr, replicate 2


title: A549 cells_treated with Silica (0 µg/ml)_6 hours_rep3b

description:
6H_A549_Si(0)_9
The labeling and hybridization of the microarrays were performed at the National Institute for Occupational Safety and Health (NIOSH), Morgantown, WV, and scanning was performed at the Center for Genomics Sciences, Alleghney-Singer Research Institute, Pittsburgh, PA.

value: lung epithelial cells

value: 6 hrs


title: MUH7 8 #3 Skeletal Muscle

value: high body weight

value: MUHi


title: A549 cells_treated with Silica (100 µg/ml)_6 hours_rep1

description:
6H_A549_Si(100)_1
The labeling and hybridization of the microarrays were performed at the National Institute for Occupational Safety and Health (NIOSH), Morgantown, WV, and scanning was performed at the Center for Genomics Sciences, Alleghney-Singer Research Institute, Pittsburgh, PA.

value: 100 µg/ml crystalline silica


title: Acute leukemia diagnosis 1870_Hind

description: Hybridized to 50K_Hind

value: diagnosis

value: diagnostic bone marrow aspirates or tumor tissue


title: Acute leukemia diagnosis 1433_Hind

description: Hybridized to 50K_Hind

value: T-ALL


title: Acute leukemia diagnosis 1238_Hind

description: Hybridized to 50K_Hind


title: MUH7 8 #2 Skeletal Muscle


title: Wild type_4hr_rep3

description: Gene expression 4 hr after Pst DC3000/avrRpt2 infection

source_name: Wild type, infected, 4hr, replicate 3

value: Wild type

value: 4 hr

value: leaf


title: A549 cells_treated with Silica (200 µg/ml)_6 hours_rep2

description:
6H_A549_Si(200)_9
The labeling and hybridization of the microarrays were performed at the National Institute for Occupational Safety and Health (NIOSH), Morgantown, WV, and scanning was performed at the Center for Genomics Sciences, Alleghney-Singer Research Institute, Pittsburgh, PA.

source_name: A549 cells, Silica (200 µg/ml) treated, 6 hours

value: 200 µg/ml crystalline silica


title: Acute leukemia diagnosis 757_Hind

description: Hybridized to 50K_Hind


title: Wild type_4hr_rep2

source_name: Wild type, infected, 4hr, replicate 2

value: avirulent bacterial pathogen Pst DC3000/avrRpt2


title: A549 cells_treated with Silica (100 µg/ml)_6 hours_rep2

description:
6H_A549_Si(100)_2
The labeling and hybridization of the microarrays were performed at the National Institute for Occupational Safety and Health (NIOSH), Morgantown, WV, and scanning was performed at the Center for Genomics Sciences, Alleghney-Singer Research Institute, Pittsburgh, PA.


title: Wild type_4hr_rep1

source_name: Wild type, infected, 4hr, replicate 1


title: MUH7 8 #1 Skeletal Muscle

value: mixed


title: BEL4 5 #3 Skeletal Muscle

value: Skeletal muscle

value: BELi


title: A549 cells_treated with Silica (100 µg/ml)_6 hours_rep4

description:
6H_A549_Si(100)_5
The labeling and hybridization of the microarrays were performed at the National Institute for Occupational Safety and Health (NIOSH), Morgantown, WV, and scanning was performed at the Center for Genomics Sciences, Alleghney-Singer Research Institute, Pittsburgh, PA.


title: Acute leukemia diagnosis1015_Hind

description: Hybridized to 50K_Hind


title: Wild type_0hr_rep2

source_name: Wild type, infected, 0hr, replicate 2

value: 0 hr


title: npr1_12hr_rep3

source_name: npr1, infected, 24hr, replicate 3

value: 12 hr


title: A549 cells_treated with Silica (200 µg/ml)_6 hours_rep5

description:
6H_A549_Si(200)_12
The labeling and hybridization of the microarrays were performed at the National Institute for Occupational Safety and Health (NIOSH), Morgantown, WV, and scanning was performed at the Center for Genomics Sciences, Alleghney-Singer Research Institute, Pittsburgh, PA.

value: lung epithelial cells

value: 6 hrs


title: Wild type_0hr_rep1

description: Gene expression 0 hr after Pst DC3000/avrRpt2 infection

source_name: Wild type, infected, 0hr, replicate 1


title: Lymphoblastic lymphoma remission 13BP_Xba

description: Hybridized to 50K_Xba

source_name: Lymphoblastic lymphoma remission

value: T-LBL

value: remission


title: Wild type_0hr_rep3

source_name: Wild type, infected, 0hr, replicate 3


title: BEL4 5 #2 Skeletal Muscle

value: low body weight

value: male


title: A549 cells_treated with Silica (400 µg/ml)_6 hours_rep4

description:
6H_A549_Si(400)_5
The labeling and hybridization of the microarrays were performed at the National Institute for Occupational Safety and Health (NIOSH), Morgantown, WV, and scanning was performed at the Center for Genomics Sciences, Alleghney-Singer Research Institute, Pittsburgh, PA.

value: 400 µg/ml crystalline silica


title: A549 cells_treated with Silica (400 µg/ml)_6 hours_rep3

description:
6H_A549_Si(400)_4
The labeling and hybridization of the microarrays were performed at the National Institute for Occupational Safety and Health (NIOSH), Morgantown, WV, and scanning was performed at the Center for Genomics Sciences, Alleghney-Singer Research Institute, Pittsburgh, PA.


title: Lymphoblastic lymphoma remission 11AS_Xba

description: Hybridized to 50K_Xba

value: diagnostic bone marrow aspirates or tumor tissue


title: Lymphoblastic lymphoma remission 10SA_Xba

description: Hybridized to 50K_Xba


title: BEL4 5 #1 Skeletal Muscle

description: Gene expression at age 44-45d in skeletal muscle


title: npr1_12hr_rep2

source_name: npr1, infected, 24hr, replicate 2


title: BEH2 3 #2 Skeletal Muscle

value: high body weight

value: BEHi


title: npr1_12hr_rep1

source_name: npr1, infected, 24hr, replicate 1

value: leaf


title: BEH2 3 #3 Skeletal Muscle


title: Lymphoblastic lymphoma remission 9AM_Xba

description: Hybridized to 50K_Xba


title: Lymphoblastic lymphoma remission 6TA_Xba

description: Hybridized to 50K_Xba


title: A549 cells_treated with Silica (0 µg/ml)_6 hours_rep2b

description:
6H_A549_Si(0)_8
The labeling and hybridization of the microarrays were performed at the National Institute for Occupational Safety and Health (NIOSH), Morgantown, WV, and scanning was performed at the Center for Genomics Sciences, Alleghney-Singer Research Institute, Pittsburgh, PA.

source_name: A549 cells, Silica (0 µg/ml) treated, 6 hours


title: A549 cells_treated with Silica (200 µg/ml)_6 hours_rep4

description:
6H_A549_Si(200)_11
The labeling and hybridization of the microarrays were performed at the National Institute for Occupational Safety and Health (NIOSH), Morgantown, WV, and scanning was performed at the Center for Genomics Sciences, Alleghney-Singer Research Institute, Pittsburgh, PA.

value: 200 µg/ml crystalline silica


title: EDH17 18 #1 Liver

description: Gene expression at age 44-45d in liver

source_name: Liver, male 44-45d

value: mixed

value: Liver

value: PHI


title: npr1_8hr_rep2

description: Gene expression 8 hr after Pst DC3000/avrRpt2 infection

source_name: npr1, infected, 8hr, replicate 2

value: avirulent bacterial pathogen Pst DC3000/avrRpt2

value: 8 hr


title: npr1_8hr_rep3

source_name: npr1, infected, 8hr, replicate 3


title: ROL15 16 #3 Liver

description: Gene expression at age 44-45d in liver

value: ROLi


title: A549 cells_treated with Silica (800 µg/ml)_6 hours_rep1

description:
6H_A549_Si(800)_13
The labeling and hybridization of the microarrays were performed at the National Institute for Occupational Safety and Health (NIOSH), Morgantown, WV, and scanning was performed at the Center for Genomics Sciences, Alleghney-Singer Research Institute, Pittsburgh, PA.

source_name: A549 cells, Silica (800 µg/ml) treated, 6 hours

treatment_protocol: Human lung epithelial cells were grown overnight in F-12K medium. Subsequently, the cells were treated with crystalline silica (0 or 800 µg/ml) in serum-free medium for 6 hours, followed by total RNA isolation.

value: lung epithelial cells

value: 800 µg/ml crystalline silica

value: 6 hrs


title: ROL15 16 #2 Liver

description: Gene expression at age 44-45d in liver

value: low body weight


title: Lymphoblastic lymphoma remission 5NL_Xba

description: Hybridized to 50K_Xba

value: T-LBL

value: remission


title: A549 cells_treated with Silica (100 µg/ml)_6 hours_rep3

description:
6H_A549_Si(100)_3
The labeling and hybridization of the microarrays were performed at the National Institute for Occupational Safety and Health (NIOSH), Morgantown, WV, and scanning was performed at the Center for Genomics Sciences, Alleghney-Singer Research Institute, Pittsburgh, PA.

source_name: A549 cells, Silica (100 µg/ml) treated, 6 hours

value: 100 µg/ml crystalline silica


title: A549 cells_treated with Silica (800 µg/ml)_6 hours_rep4

description:
6H_A549_Si(800)_16
The labeling and hybridization of the microarrays were performed at the National Institute for Occupational Safety and Health (NIOSH), Morgantown, WV, and scanning was performed at the Center for Genomics Sciences, Alleghney-Singer Research Institute, Pittsburgh, PA.


title: BEH2 3 #1 Skeletal Muscle

source_name: Skeletal muscle, male 44-45d

value: high body weight

value: Skeletal muscle

value: male


title: A549 cells_treated with Silica (0 µg/ml)_6 hours_rep4

description:
6H_A549_Si(0)_35
The labeling and hybridization of the microarrays were performed at the National Institute for Occupational Safety and Health (NIOSH), Morgantown, WV, and scanning was performed at the Center for Genomics Sciences, Alleghney-Singer Research Institute, Pittsburgh, PA.


title: Lymphoblastic lymphoma remission 2NP_Xba

description: Hybridized to 50K_Xba

value: diagnostic bone marrow aspirates or tumor tissue


title: npr1_4hr_rep3

source_name: npr1, infected, 4hr, replicate 3

value: 4 hr

value: leaf


title: A549 cells_treated with Silica (0 µg/ml)_6 hours_rep5b

description:
6H_A549_Si(0)_12
The labeling and hybridization of the microarrays were performed at the National Institute for Occupational Safety and Health (NIOSH), Morgantown, WV, and scanning was performed at the Center for Genomics Sciences, Alleghney-Singer Research Institute, Pittsburgh, PA.


title: npr1_4hr_rep2

description: Gene expression 4 hr after Pst DC3000/avrRpt2 infection

source_name: npr1, infected, 4hr, replicate 2


title: DUH23 24 #2 Liver

description: Gene expression at age 44-45d in liver

value: mixed

value: Liver

value: DUI


title: Lymphoblastic lymphoma remission 3MM_Xba

description: Hybridized to 50K_Xba


title: A549 cells_treated with Silica (0 µg/ml)_6 hours_rep5

description:
6H_A549_Si(0)_36
The labeling and hybridization of the microarrays were performed at the National Institute for Occupational Safety and Health (NIOSH), Morgantown, WV, and scanning was performed at the Center for Genomics Sciences, Alleghney-Singer Research Institute, Pittsburgh, PA.


title: DUH23 24 #3 Liver

description: Gene expression at age 44-45d in liver


title: npr1_4hr_rep1

source_name: npr1, infected, 4hr, replicate 1

value: avirulent bacterial pathogen Pst DC3000/avrRpt2


title: A549 cells_treated with Silica (800 µg/ml)_6 hours_rep5

description:
6H_A549_Si(800)_17
The labeling and hybridization of the microarrays were performed at the National Institute for Occupational Safety and Health (NIOSH), Morgantown, WV, and scanning was performed at the Center for Genomics Sciences, Alleghney-Singer Research Institute, Pittsburgh, PA.

value: lung epithelial cells


title: npr1_8hr_rep1

source_name: npr1, infected, 8hr, replicate 1

value: 8 hr


title: A549 cells_treated with Silica (0 µg/ml)_6 hours_rep3

description:
6H_A549_Si(0)_33
The labeling and hybridization of the microarrays were performed at the National Institute for Occupational Safety and Health (NIOSH), Morgantown, WV, and scanning was performed at the Center for Genomics Sciences, Alleghney-Singer Research Institute, Pittsburgh, PA.

value: 6 hrs


title: Lymphoblastic lymphoma remission 1BD_Xba

description: Hybridized to 50K_Xba


title: Acute leukemia remission 2422_Xba

description: Hybridized to 50K_Xba

source_name: Acute leukemia remission

value: T-ALL


title: EDL20 21 #3 Liver

description: Gene expression at age 44-45d in liver

value: low body weight

value: PLI


title: Acute leukemia remission 1928_Xba

description: Hybridized to 50K_Xba

value: remission


title: DUH23 24 #1 Liver

description: Gene expression at age 44-45d in liver

value: high body weight


title: A549 cells_treated with Silica (800 µg/ml)_6 hours_rep3

description:
6H_A549_Si(800)_15
The labeling and hybridization of the microarrays were performed at the National Institute for Occupational Safety and Health (NIOSH), Morgantown, WV, and scanning was performed at the Center for Genomics Sciences, Alleghney-Singer Research Institute, Pittsburgh, PA.

value: 800 µg/ml crystalline silica


title: EDL20 21 #1 Liver

description: Gene expression at age 44-45d in liver

value: male


title: npr1_0hr_rep2

description: Gene expression 0 hr after Pst DC3000/avrRpt2 infection

source_name: npr1, infected, 0hr, replicate 2

value: 0 hr


title: Acute leukemia remission 1870_Xba

description: Hybridized to 50K_Xba

value: diagnostic bone marrow aspirates or tumor tissue


title: A549 cells_treated with Silica (800 µg/ml)_6 hours_rep2

description:
6H_A549_Si(800)_14
The labeling and hybridization of the microarrays were performed at the National Institute for Occupational Safety and Health (NIOSH), Morgantown, WV, and scanning was performed at the Center for Genomics Sciences, Alleghney-Singer Research Institute, Pittsburgh, PA.


title: Acute leukemia remission 1520_Xba

description: Hybridized to 50K_Xba


title: npr1_0hr_rep3

source_name: npr1, infected, 0hr, replicate 3

value: leaf


title: Atelp2_12hr_rep2

description: Gene expression 12 hr after Pst DC3000/avrRpt2 infection

source_name: Atelp2, infected, 12hr, replicate 2

value: 12 hr


title: Acute leukemia remission 1847_Xba

description: Hybridized to 50K_Xba


title: npr1_0hr_rep1

source_name: npr1, infected, 0hr, replicate 1


title: A549 cells_treated with Silica (0 µg/ml)_6 hours_rep2

description:
6H_A549_Si(0)_32
The labeling and hybridization of the microarrays were performed at the National Institute for Occupational Safety and Health (NIOSH), Morgantown, WV, and scanning was performed at the Center for Genomics Sciences, Alleghney-Singer Research Institute, Pittsburgh, PA.


title: EDH17 18 #3 Liver

description: Gene expression at age 44-45d in liver

value: mixed

value: Liver

value: PHI


title: Atelp2_12hr_rep3

source_name: Atelp2, infected, 12hr, replicate 3

value: avirulent bacterial pathogen Pst DC3000/avrRpt2


title: EDL20 21 #2 Liver

description: Gene expression at age 44-45d in liver


title: A549 cells_treated with Silica (0 µg/ml)_6 hours_rep1

description:
6H_A549_Si(0)_31
The labeling and hybridization of the microarrays were performed at the National Institute for Occupational Safety and Health (NIOSH), Morgantown, WV, and scanning was performed at the Center for Genomics Sciences, Alleghney-Singer Research Institute, Pittsburgh, PA.

source_name: A549 cells, Silica (0 µg/ml) treated, 6 hours

value: lung epithelial cells


title: Acute leukemia remission 1433_Xba

description: Hybridized to 50K_Xba


title: Atelp2_12hr_rep1

source_name: Atelp2, infected, 12hr, replicate 1


title: Acute leukemia remission 1238_Xba

description: Hybridized to 50K_Xba


title: TBCF121838 - late exp. - replicate 2

city: Hannover

first: Jens

last: Klockgether

address: Carl-Neuberg-Str. 1

department: Ped. Pneumology

institute: Hannover Medical School

description: gene expression late exp. growth phase phase

hyb_protocol: Labelled cDNA was hybridized onto GeneChip P. aeruginosa Genome Arrays by incubating at 50°C for 16 h at 60 rpm (Affymetrix GeneChip Hybridization Oven 640)

scan_protocol: Microarrays were scanned using the Affymetrix GeneChip Operation Software Version 1.4 (Affymetrix GeneChip Scanner GCS 30) and data were processed using Agilent Scan Control and Feature Extraction Software

data_processing: Data were analyzed with the Affymetrix Microarray Suite software 5.0 using default parameters. The average microarray hybridization signal intensity was scaled to 150.

organism: Pseudomonas aeruginosa

source_name: TBCF121838 late exp.

label_protocol: Terminal labeling was performed following the Affymetrix standard protocol (GeneChip DNA Labeling Reagent, P/N900542)

growth_protocol: Preliminary cultures of the respective P. aeruginosa strains were inoculated from a -80°C stock culture and incubated at 37°C at 250 rpm in LB medium to an optical density (600 nm) of about 2.0. Aliquot of 0.2 mL were then added to 20 mL fresh LB medium in 100 mL flasks (three per strain)  and incubated at 37°C. When reaching the required optical densities. 10 m Lsamples were taken from the cultures and used for cell harvest and subsequent parallel extraction of total RNA

extract_protocol: Total RNA extraction was performed according the manufacturer's protocol provided by Qiagen for bacteria.

tag: strain

tag: growth phase

value: late exponential

tag: source

value: cystic fibrosis patient airways


title: TBCF121838 - late exp. - replicate 1


title: EDH17 18 #2 Liver

description: Gene expression at age 44-45d in liver

source_name: Liver, male 44-45d


title: Atelp2_8hr_rep3

description: Gene expression 8 hr after Pst DC3000/avrRpt2 infection

source_name: Atelp2, infected, 8hr, replicate 3

tag: genotype/variation

tag: infection

tag: time point

value: 8 hr


title: TBCF10839 - late exp. - replicate 2

source_name: TBCF10839 late exp.


title: ROH12 13 #2 Liver

description: Gene expression at age 44-45d in liver

tag: phenotype

tag: genetic background

value: ROHi


title: ROL15 16 #1 Liver

description: Gene expression at age 44-45d in liver

value: low body weight

tag: weight

tag: age

value: ROLi


title: ROH12 13 #3 Liver

description: Gene expression at age 44-45d in liver

value: high body weight