title: TTO rep2 dye-swap

city: Las Cruces

first: John

middle: Eric

last: Gustafson

state: NM

department: Biology and Molecular Biology Program

institute: New Mexico State University

hyb_protocol: Arrays were blocked in 1% SDS, 5 X SSC and 1 mg/ml BSA at 42C for 1 h. Arrays were then washed 2X for 5 min in 0.1X SSC and 2X for 30 sec in sterile double-distilled water. Arrays were hybirdized to Cy-labeled cDNAs denatured at 05C in 10 mM EDTA for 5 min and mixed with 40 ul hybridization buffer (Ambion) before loading under a caverslip on the array and sealing in hybridization cassettes. Hybridization was carried out at 47C for 18 h. Afterwards, array slides were washed in 2X SSC, 0.5% SDS at 37C for 5 min, followed by stringency washes 2X in 0.1X SSC at 37C for 2.5 min each, and 2X in 0.1X SSC at room temperature for 2.5 min each.

scan_protocol: Arrays were scanned using an Axon 4000b, and images analyzed using Spotfinder.

data_processing: Array intensity data was log2-transformed, and normalized using the Lowess algorithm. Statistical analysis was performed using a significance analysis of microarrays (SAM, MultiExperiment Viewer, ver. 4.0) unpaired contrast. A d-statistic was calculated for each gene based on repeated permutations, and a false discovery rate FDR of 0.01 was used to assign a critical cutoff for significance.

organism: Staphylococcus aureus

source_name: Treatment

label_protocol: Amino-allyl labeled cDNA was dried and then suspended in 0.1 M sodium carbonate (pH 9.3) and coupled with Cy5. Uncoupled dye was removed by column purification (Qiagen).

growth_protocol: MHB cultures OD580nm = 0.4 at 37ºC, 200 rpm

extract_protocol: Samples were added to RNA Protect (Qiagen, Valencia, CA) and processed according to the manufacturer's instructions. Cells were harvested by centrifugation (8,000 X g, 20 min, 4C) and then resuspended in 1 ml Trizol (Invitrogen, Carlsbad, CA) and processed in an FP120 FastPrep cell disruptor (MP Biomedicals, Irvine, CA). Chloroform was subsequently added to the lysates, followed by centrifugation (16,000 X g, 15 min, 4C) and RNA was precipitated 1:1 (vol/vol) in 100% ethyl alcohol. The RNA was then purified using the RNeasy™ kit (Qiagen) according to the manufacturer's instructions. Contaminating DNA was removed from purified RNA using DNAfree (Ambion, Austin, TX). cDNA was produced using SuperScript II Reverse Transcriptase (Invitrogen) from 2 µg of total RNA combined with random hexamers, 0.25 mM deoxynucleoside triphosphate, and 0.25 mM aminoallyl-dUTP.

treatment_protocol: TTO treated (0.25% vv) for 15 min.

tag: strain

value: TTO

source_name: Control

label_protocol: Amino-allyl labeled cDNA was dried and then suspended in 0.1 M sodium carbonate (pH 9.3) and coupled with Cy3. Uncoupled dye was removed by column purification (Qiagen).

treatment_protocol: No TTO treatment


title: TTO rep2

status: Public on Apr 26 2012

type: RNA

country: USA

molecule: total RNA

tag: treatment


title: zebrafish at ZT8, DD condition

city: Shanghai

first: Haifang

last: Wang

address: 320 yueyang road

department: CAS-MPG Partner institute for Computational Biology

country: China

institute: Shanghai institute for biology science

hyb_protocol: Cy3-labeled cRNA (800ng each) were hybridized to the zebrafish microarray (G5219F, Agilent) for 17 h at 65°C.

scan_protocol: The hybridized microarrays were then washed according to the manufacturer’s protocol. Microarray results were extracted using Agilent G2565BA Scanner and Feature Extraction software (v10.5.1, Agilent), and subsequently analyzed by Gene-Spring GX software (v11.0.1, Agilent).

data_processing: Data were extracted using Feature Extraction software (v10.5.1, Agilent) and Gene-Spring GX software (v11.0.1, Agilent).

organism: Danio rerio

source_name: whole body

label_protocol: Purified total RNA of each sample was amplified and labeled with a fluorescent dye Cyanine 3 (Cy3) using a low-RNA input linear amplification kit following the manufacturer's protocol (5184-3523, Agilent).

extract_protocol: Total RNA of larval sample was extracted using Trizol (Invitrogen) according to the manufacturer’s instruction. The quantity and quality of the RNA samples were assessed with a NanoDrop ND-1000 spectrometer (NanoDrop Technologies) and an Agilent 2100 bioanalyzer (Agilent).

tag: tissue

value: larva

tag: gender

value: male

tag: time

value: DD condition


title: AB32_pCDH_vectorControl_Vehicle2

city: Westmead

first: J

middle: Dinny

last: Graham

state: NSW

address: 176 Hawkesbury Rd

department: Westmead Institute for Medical Research

country: Australia

institute: University of Sydney

description: Replicate 2

hyb_protocol: 750ng biotin-labeled sample was hybridized to each HT-12 array using Illumina reagents and standard procedure

scan_protocol: The standard Illumina scanning protocol was used

data_processing: The data were background subtracted and normalized using the cubic spline normalization method using Illumina Genome Studio software

label: biotin

organism: Homo sapiens

source_name: MCF-10A clone AB32 cells grown in monolayer culture, transduced 48h with pCDH empty vector virus then treated 24h with ethanol vehicle (0.1%)

label_protocol: 500ng total RNA per sample was amplified and biotin labeled using Invitrogen Illumina total Prep reagents, following the standard protocol

growth_protocol: Cells were grown in standard recommended media in monolayer cultures at 37C and 5% CO2 for 24h prior to viral transduction and treatment

extract_protocol: Total RNA was isolated using Invitrogen RNaqueous reagents and following the standard protocol

treatment_protocol: Cells were transduced with empty vector (pCDH) or FOXA1 expression viral particles 48h, then treated with 10nM ORG2058 or ethanol vehicle (0.1% final in growth medium) for the indicated times, followed by harvesting by trypsinization and centrifugation.

value: breast

tag: cell line

tag: transduced virus


title: AB32-Vehicle_control_Replicate1

description: Replicate 1

source_name: MCF-10A clone AB32 grown in monolayer culture, treated 24h with ethanol vehicle

growth_protocol: Cells were grown in standard recommended media in monolayer cultures at 37C and 5% CO2 to 70% confluent prior to treatment

treatment_protocol: Cells were treated with 10nM ORG2058 or ethanol vehicle (0.1% final in growth medium) for the times indicated, followed by harvesting by trypsinization and centrifugation.


title: zebrafish at ZT12, DD condition


title: TTO rep1 dye-swap


title: T-47D-6h_10nMORG2058_Replicate2

description: Replicate 2

source_name: T-47D breast cancer cells grown in monolayer culture, treated 6h with 10nM ORG2058


title: zebrafish at ZT36, LD condition

value: LD condition


title: T-47D-6h_10nMORG2058_Replicate3

description: Replicate 3


title: zebrafish at ZT4, DD condition


title: zebrafish at ZT40, LD condition


title: T-47D-24h_10nMORG2058_Replicate2

description: Replicate 2

source_name: T-47D breast cancer cells grown in monolayer culture, treated 24h with 10nM ORG2058


title: zebrafish at ZT32, LD condition


title: T-47D-6h_10nMORG2058_Replicate1

description: Replicate 1


title: NHM_dark_d492_treat_rep1

city: Sharnbrook

first: Fei Ling

last: Lim

state: Bedfordshire

address: Colworth Science Park

country: United Kingdom

institute: Unilever

description: SLC24A5 knockdown treatment

hyb_protocol: The Agilent Hybridisation Kit (catalogue number 5188-5242) was used in conjunction with Agilent human whole genome Oligo Arrays (catalogue number G4112F).  2μg of the labelled sample RNA were used for hybridisation according to the Agilent One-Color Microarray-Based Gene Expression Analysis Protocol. The hybridisation was performed for 17 h at 65 ºC with 10 rpm rotation. Slides were then washed for 1 min at 22 ºC in Wash Solution 1 (catalogue number 5188-5325), followed by 1 min in Wash Solution 2 that was pre-warmed to 37 ºC (catalogue number 5188-5326) as described in the manufacturer’s manual. Slides were then washed in acetonitrile (Fisher cat# A/0630/PB15) for 1 min followed by 30s in Agilent Stabilisation and Drying Solution (catalogue number 5185-5979).

scan_protocol: The slides were scanned with the Agilent G2565BA Microarray Scanner System.

data_processing: For data extraction and quality control, the Agilent G2567AA Feature Extraction Software (v.9.1) was used.

source_name: Cultured melanocytes

label_protocol: 300ng RNA and 3µl (1:5000 dilution) Agilent One-Color RNA Spike-In RNA were labelled with reagents supplied in the Agilent Low RNA Input Linear Amplification Kit PLUS, One-Color according to Manufacturer’s instructions as follows:  Primers were annealed to template by mixing 1.2 µl T7 Promoter Primer, 200ng RNA and 2µl spike in control (in a volume of 11.5µl), denatured at 65ºC for 10min followed by incubation at 4ºC for 5min. First Strand Buffer (to 1X), DTT (to 10mM), dNTP (to 0.5mM), MMLV (1µl) and RNaseOut (0.5 µl) were then added to make up the cDNA synthesis reaction (20µl), which was incubated for 2h at 40 ºC. After 15 min denaturation at 65ºC, the reaction was made up to 80µl with the addition of Cyanine 3-CTP (to 0.3mM), Transcription Buffer (to 1X), DTT (to 10mM), NTP (8µl), PEG (to 4%), RNaseOUT (0.5µl), Inorganic Phosphatase (0.6µl), and T7 RNA Polymerase (0.8µl) and incubated for 2h at 40 ºC to synthesise the fluorescent labelled cRNA.  The labelled cRNA was purified with the RNeasy Mini Kit (Qiagen Ltd, Crawley, UK) according to Manufacturer’s protocol.

growth_protocol: Melanocytes from lightly and darkly pigmented donors were plated in 6-well plates at 100000 cells per well (2ml volume) and cultured for 24h in Medium 254 + HMGS1 supplement (Invitrogen Ltd) at 9% CO2, 37ºC.

extract_protocol: Total RNA was isolated using Qiagen RNeasy kit, as per the manufacturers instructions. The integrity of the RNA was confirmed with analysis by the Agilent 2100 bioanalyser using the RNA 6000 nano LabChip kit.

treatment_protocol: Cells were incubated with transfection reagents for 6h; 2μl/ml Lipofectamine 2000 in Opti-MEM medium (Invitrogen Ltd, Paisley, UK), plus siRNA duplex at a final concentration of 50nM. Cells were returned to the normal culture medium for 5d. siRNA treatments comprised; Stealth™ RNA-mediated interference duplexes (Invitrogen Ltd, Paisley, UK) targeting nucleotides 185-210 (termed 185) and 492-517 (termed 492) of SLC24A5. A negative control siRNA duplex treatment comprised comprised Allstars (termed All*) non-targeting siRNA (Qiagen Ltd, Crawley, UK).Additional negative control treatments comprised lipofectamine alone and and unchallenged melanocytes, cultured alongside the cellular treatments. All treatments and controls were conducted in triplicate in both cell lines.

tag: treatment type

value: siRNA 492 to SLC24A5

tag: pigmentation level

value: Darkly pigmented


title: TTO rep1


title: Mono-cultured K. vulgare Cells, Replicate 2

city: Wuxi

first: Zhu

last: Yibo

state: Jiangsu

address: Lihu Road 1800#

institute: Jiangnan University

description:
Mono-cultured-rep2
Common reference design.

hyb_protocol: A total of 1μg of Cy3-labeled and Cy5-labeled cRNA was prepared for fragmentation adding 11 μl 10 × Blocking Agent and 2.2 μl of 25× Fragmentation Buffer, heated at 60 °C for 30 min, and finally diluted by addition of 55μl 2× GE Hybridization buffer. A volume of 100 μl of hybridization solution was then dispensed in the gasket slide and assembled to the gene expression microarray slide. The slides were incubated for 17 h at 65°C in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned using the Agilent DNA microarray scanner (part number G2505B) following Agilent Technology’s guidelines.

data_processing: Agilent Feature Extraction Software (version 10.5.1.1) was used to analyze acquired array images. Lowess normalization and subsequent data processing was performed using the Agilent GeneSpring GX v11.5.1 software. Following Lowess normalization of the raw data, genes for which at least 8 out of 16 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis. Differentially expressed genes with statistical significance were identified through Volcano Plot filtering. The threshold we used to screen up- or downregulated genes was defined by Fold Change ≥2 and P-value <0.05.

organism: Ketogulonicigenium vulgare WSH-001

source_name: Mono-cultured K. vulgare cells

label_protocol: Sample labeling and hybridization reactions were performed according to the Agilent Two-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology). Briefly, for each sample, 1 μg of total RNA was linearly amplified and labeled with Cy5-dCTP and sample of common reference with Cy3-dCTP. Labelled cRNAs were purified with the Qiagen RNeasy Mini Kit, and sample concentration and specific activity (pmol Cy5/Cy3 per μg cRNA) were measured in a NanoDrop® ND-8000 spectrophotometer.

growth_protocol: The mono-culture of K. vulgare was grown at 30 °C in the well-defined chemical medium at pH 7.0, 200rpm for 18 h.

extract_protocol: The mono- and co-cultures were sampled after 18-h fermentation (mid-log phase) and added to RNAProtect® Bacterial Reagent (Qiagen, Valencia, CA) according to the manufacturer’s instructions. Bacterial cells were treated with lysozyme stock solution (40 mg ml-1 in 30 mM pH 8.0 Tris/EDTA buffer) and protease K at 25oC for 10 min (vortex 10 s for every 2 min). Total RNA was isolated and purified using the RNeasy Mini kit (Qiagen) according to the manufacturer’s protocol. Total RNA binding on the RNeasy spin column membrane were treated with RNase-Free DNase Set (Qiagen) to remove remaining DNA. The concentration and purity of the total RNA were assessed by Nanodrop® ND-8000 (Thermo Fisher), and the integrity of the RNA was assessed using standard denaturing agarose gel electrophoresis.

treatment_protocol: The mixture of K. vulgare and B. megaterium was grown at 30 °C in the well-defined chemical medium at pH 7.0, 200 rpm for 18 h until cells were at their mid-log phase.

tag: growth condition

value: mono-culture

tag: growth phase

value: mid-logarithmic

organism:
Priestia megaterium
Ketogulonicigenium vulgare WSH-001

source_name: Pooled 3 co-cultured and 3 mono-cultured cells

value: co-culture with Bacillus megaterium and mono-culture

tag: sample type

value: reference


title: Co-cultured K. vulgare Cells, Replicate 3

description:
Co-cultured-rep3
Common reference design.

source_name: Co-cultured K. vulgare cells

value: co-culture with Bacillus megaterium


title: Co-cultured K. vulgare Cells, Replicate 2

description:
Co-cultured-rep2
Common reference design.


title: zebrafish at ZT20, DD condition


title: Mono-cultured K. vulgare Cells, Replicate 1

description:
Mono-cultured-rep1
Common reference design.


title: zebrafish at ZT28, LD condition


title: T-47D-Vehicle_control_Replicate2

description: Replicate 2

source_name: T-47D breast cancer cells grown in monolayer culture, treated 24h with ethanol vehicle


title: T-47D-2h_10nMORG2058_Replicate2

description: Replicate 2

source_name: T-47D breast cancer cells grown in monolayer culture, treated 2h with 10nM ORG2058


title: Strain 195_With Ammonium_rep1

city: Berkeley

first: Patrick

last: Lee

state: CA

address: 209 O'Brien Hall

department: Civil and Environmental Engineering

institute: University of California, Berkeley

hyb_protocol: According to the protocols outlined in section 3, chapter 3 of the Affymetrix GeneChip Expression Analysis Technical Manual (Affymetrix, Santa Clara, CA).

data_processing: Data analysis was performed using the MAS5.0 algorithm and each microarray was normalized with global scaling to a value of 2500.

label: Biotin

organism: Dehalococcoides mccartyi 195

source_name: Dehalococcoides ethenogenes 195 grown with ammonium

growth_protocol: Cells were grown in defined minimal medium (He et al. 2007. Appl. Environ. Microbiol. 73: 2847-2853) at 34oC. Trichloroethene was provided as the electron acceptor, acetate as the carbon source, and hydrogen as the electron donor.

extract_protocol: Cells were collected by vacuum-filtration onto 0.22 mm, 47 mm Durapore membrane filters. Total RNA was extracted from frozen filters using the RNeasy Mini Kit (Qiagen, Valencia, CA) according to the manufacturer's instructions and processed as described in Lee et al. 2009. Appl. Environ. Microbiol. 75: 7551-7555.

treatment_protocol: Cultures were grown with or without ammonium as described in Lee et al. 2009. Appl. Environ. Microbiol. 75: 7551-7555 and harvested when cells reached late exponential growth phase.

tag: bacteria

value: Pure culture

value: with ammonium


title: Strain 195_With Ammonium_rep3

scan_protocol: According to the protocols outlined in section 3, chapter 3 of the Affymetrix GeneChip Expression Analysis Technical Manual (Affymetrix, Santa Clara, CA).


title: Strain 195_With Ammonium_rep2

label_protocol: According to the protocols outlined in section 3, chapter 3 of the Affymetrix GeneChip Expression Analysis Technical Manual (Affymetrix, Santa Clara, CA).


title: Mono-cultured K. vulgare Cells, Replicate 3

description:
Mono-cultured-rep3
Common reference design.


title: T-47D-Vehicle_control_Replicate3

description: Replicate 3


title: zebrafish at ZT16, LD condition


title: zebrafish at ZT24, LD condition


title: AB32_FOXA1_overexpression_Vehicle1

description: Replicate 1

source_name: MCF-10A clone AB32 cells grown in monolayer culture, transduced 48h with pCDH-CMV-FOXA1-EF1-copGFP virus then treated 24h with ethanol vehicle (0.1%)


title: 24h E.coli-infected, anti-LIF-treated lungs, biological rep2

city: Boston

first: Lee

last: Quinton

state: MA

address: 72 E Concord St

institute: Boston University School of Medicine

hyb_protocol: 5 ug of labeled sense strand DNA were hybridized for 17h at 45 degrees C on a Genechip Mouse Gene Array 1.0 ST Array.  GeneChips were washed and stainied in the Affymetrix Fluiidix Station 450.

scan_protocol: Arrays were scanned using the Affymetrix GeneChip Scanner 3000 7GPlus.

data_processing: CEL files were summarized using the Affymetrix Expression Console (version 1.1). The RMA (Robust Multi-Array Analysis) algorithm was used to generate gene-level data.

organism: Mus musculus

source_name: 24h_E.coli-infection + anti-LIF-treated lungs

label_protocol: Fragmented, biotinlyated sense strand DNA were prepared from 200 ng total RNA using the WT Target labeling kit according to the manufacturer's protocol (Affymetrix)

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions (Life Technologies).  RNA was further purified using the the Qiagen RNEasy kit with the optional DNAse treatment.

value: Lung

tag: infection

value: intratracheal instillation of E. coli (10^6 CFU)

tag: antibody included in the instillate

value: anti-LIF


title: 24h E.coli-infected, anti-LIF-treated lungs, biological rep3


title: T-47D-Vehicle_control_Replicate1

description: Replicate 1


title: Co-cultured K. vulgare Cells, Replicate 1

description:
Co-cultured-rep1
Common reference design.


title: Strain 195_Without Ammonium_rep3

source_name: Dehalococcoides ethenogenes 195 grown without ammonium

value: without ammonium


title: zebrafish at ZT12, LD condition

value: larva

value: male


title: 24h E.coli-infected, control IgG-treated lungs, biological rep1

source_name: 24h_E.coli-infection + control IgG-treated lungs

value: Control IgG


title: T-47D-2h_10nMORG2058_Replicate3

description: Replicate 3

value: breast


title: 24h E.coli-infected, anti-LIF-treated lungs, biological rep1


title: zebrafish at ZT0, LD condition

value: LD condition


title: T-47D-2h_10nMORG2058_Replicate1

description: Replicate 1


title: Strain 195_Without Ammonium_rep1


title: Strain 195_Without Ammonium_rep2


title: Uninfected control IgG-treated lungs, biological rep2

source_name: 24h_vehicle + control IgG-treated lungs

value: intratracheal instillation of  vehicle (PBS control)


title: 24h E.coli-infected, control IgG-treated lungs, biological rep2


title: zebrafish at ZT4, LD condition

source_name: whole body


title: Uninfected control IgG-treated lungs, biological rep3


title: zebrafish at ZT8, LD condition


title: Uninfected control IgG-treated lungs, biological rep1


title: ndvB knockout biofilm; biological replicate 2

city: Ottawa

first: Trevor

last: Beaudoin

state: Ontario

address: 451 Smyth Road

country: Canada

institute: University of Ottawa

description: Gene expression data from biofilms

hyb_protocol: Following fragmentation, cDNA was hybridized on GeneChip PA01 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station. Performed at Stemcore Labratories  of the OHRI

scan_protocol: GeneChips were scanned using a GeneArray Scanner at Stemcore Labratories (OHRI)

data_processing:
The data were analyzed using R statistical framework with bioconductor packages. Robust microarray analyisis (RMA) and microarrary analysis software 5.0 (MAS5.0) was used in the analysis
Data was processed as Mas5.0 and RMA signal intensities and genes that were shown to be significantly different using both methods were chosen for further study

organism: Pseudomonas aeruginosa PA14

source_name: Biofilm PA14

label_protocol: Biotinylated cDNA was prepared according to the standard Affymetrix protocol f(Expression Analysis Technical Manual, Affymetrix) at Stemcore Labratories of the Ottawa Health Research Institute (OHRI).

growth_protocol: 48 hour biofilm growth of given culture using Kadouri drip fed method. Cells were grown on 6-well polystyrene plates at 37 degrees celsius in M63 media supplemented with arginine and magnesium.

extract_protocol: RNA was extracted using PureLink Micro-to-Midi total RNA purification system (Invitrogen)

treatment_protocol: Biofilm cells were washed with fresh media and then extracted into 1mL of fresh media and spun down at 12000xg. Each biological replicate consisted of two wells of biofilm grown cells

tag: genotype

value: ndvB KO


title: Wild-type biofilm; biological replicate 3

description: Gene expression data from biofilms

value: wild type


title: ndvB knockout biofilm; biological replicate 1

description: Gene expression data from biofilms


title: 24h E.coli-infected, control IgG-treated lungs, biological rep3


title: ndvB knockout biofilm; biological replicate 3

description: Gene expression data from biofilms


title: zebrafish at ZT20, LD condition


title: Liver_Stormwater_Rep4

status: Public on Apr 25 2012

city: Gainesville

first: Ignacio

middle: Alejandro

last: Rodriguez-Jorquera

state: Florida

address: Mowry Drive 471

department: Soil and Water Science

institute: University of Florida

description:
Storm_04
Gene expression after 48 hours of exposure to whole surface waters effluents in male liver of FHM

hyb_protocol: Also performed according to the Agilent protocol no. G4140-90040

scan_protocol: Microarrays were kept in the dark until scanning on an Agilent G2505B microarray scanner.

data_processing: Data extraction was performed using Agilent Feature Extraction software (v9.5) and was used as a composite of two scans (one at 10 and the other at 100 PMT (Agilent G2505 B Microarray Scanner) to extend the dynamic range. Raw expression data (gProcessedSignal) were imported into JMP Genomics v5 (SAS, Cary, NC). During import, data were log2-transformed and all control and non-uniform spots were removed prior to the final analysis. Raw intensity data for each microarray were normalized by LOESS before performing ANOVA. Differentially regulated transcripts were identified using a one-way analysis of variance.

organism: Pimephales promelas

label_protocol: Agilent protocol titled One-color microarrays- based  gene expression analysis (document no. G4140-90040 v6.5) was used to label 1000 ng total RNA.

extract_protocol: Total RNA was extracted using the RNA STAT-60 reagent (Tel-Test, Friendswood, TX, USA), reconstituted in RNAsecure (Ambion), and DNase-treated with Turbo DNA-free (Ambion), following manufacturers’ protocols.  RNA quantity for microarray analysis was measured using the NanoDrop ND-1000 (Nanodrop Technologies, Wilmington, DE) and RNA quality was evaluated using the Agilent 2100 BioAnalyzer with the RNA 6000 Nanochip. RNA integrity values (RIN) were between 8.0 and 9.9 for all samples used in the analysis.

tag: exposed to surface water from

value: a lake (stormwater)

value: Liver


title: Liver_Control_Rep2

description:
Ctl_02
Gene expression after 48 hours of exposure to whole surface waters effluents in male liver of FHM

tag: exposed to

value: carbon filtered, dechlorinated tap water (control)


title: Liver_Stormwater_Rep2

description:
Storm_02
Gene expression after 48 hours of exposure to whole surface waters effluents in male liver of FHM


title: Wild-type biofilm; biological replicate 1

description: Gene expression data from biofilms


title: Liver_Wastewater_Rep2

description:
Waste_02
Gene expression after 48 hours of exposure to whole surface waters effluents in male liver of FHM

value: a wastewater treatment plant (wastewater)


title: Liver_Wastewater_Rep4

description:
Waste_04
Gene expression after 48 hours of exposure to whole surface waters effluents in male liver of FHM


title: Liver_Streamwater_Rep3

description:
Stream_03
Gene expression after 48 hours of exposure to whole surface waters effluents in male liver of FHM

value: downstream of a wastewater treatment plant (streamwater)


title: Liver_Stormwater_Rep3

description:
Storm_03
Gene expression after 48 hours of exposure to whole surface waters effluents in male liver of FHM


title: Liver_Control_Rep3

description:
Ctl_03
Gene expression after 48 hours of exposure to whole surface waters effluents in male liver of FHM


title: Liver_Wastewater_Rep3

description:
Waste_03
Gene expression after 48 hours of exposure to whole surface waters effluents in male liver of FHM


title: Liver_Streamwater_Rep4

description:
Stream_04
Gene expression after 48 hours of exposure to whole surface waters effluents in male liver of FHM


title: Liver_Wastewater_Rep1

description:
Waste_01
Gene expression after 48 hours of exposure to whole surface waters effluents in male liver of FHM


title: mitfa morpholino knockdown at 50 hpf,rep1

scan_protocol: The hybridized microarrays were then washed according to the manufacturer’s protocol. Microarray results were extracted using Agilent G2565BA Scanner.

tag: treatment

value: mitfa knockdown

tag: age

value: 50 hpf


title: Liver_Streamwater_Rep2

description:
Stream_02
Gene expression after 48 hours of exposure to whole surface waters effluents in male liver of FHM

tag: gender

tag: tissue


title: Liver_Control_Rep1

description:
Ctl_01
Gene expression after 48 hours of exposure to whole surface waters effluents in male liver of FHM


title: Liver_Streamwater_Rep1

description:
Stream_01
Gene expression after 48 hours of exposure to whole surface waters effluents in male liver of FHM


title: mitfa Morpholino control at 48 hpf

value: mitfa morpholino control

value: 48 hpf


title: Wild-type biofilm; biological replicate 2

description: Gene expression data from biofilms


title: Liver_Stormwater_Rep1

description:
Storm_01
Gene expression after 48 hours of exposure to whole surface waters effluents in male liver of FHM


title: mitfa morpholino knockdown at 48 hpf

value: larva


title: Col-0 rep2

city: Cologne

first: Bruno

last: Huettel

address: Carl-von-Linne-Weg 10

department: MPI Plant Breeding

country: Germany

institute: Max Planck Genome Centre Cologne

description: Gene expression data from 7 days old wild type seedlings

hyb_protocol: After fragmentation, 7.5 ug of ds-cDNA was hybridized for 16 hr at 45C on GeneChip Arabidopsis Tiling 1.0R Array. GeneChips were washed and stained with Fluidics Script FS450_0001 in the Affymetrix Fluidics Station 450.

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

data_processing: Data was processed in R as described in Naouar et al. Quantitative RNA expression analysis with Affymetrix Tiling 1.0R arrays identifies new E2F target genes. Plant J (2009) vol. 57 (1) pp. 184-94. Probe-level data were pre-processed using the RMA algorithm (Irizarry et al., 2003), which involves three steps: (i) background correction – where an error component of the intensities is estimated and eliminated; (ii) quantile normalization – where every slide is normalized to have the same cumulative frequency distribution; and (iii) summarization, using the median polish algorithm – where the median values per probe set, adjusted for slide differences, are calculated. RMA ignores the MM probes. On the basis of an empirical Bayes moderated t-statistic for the contrasts (Smyth, 2004), as implemented in the Bioconductor package limma, P values were calculated and then transformed into false-discovery rates, or Q values according to the method described by Storey and Tibshirani (2003), as implemented in the R package qvalue. We compared the results obtained with RMA and those obtained with a mixed-effect anova model (Wolfinger et al., 2001) as a summarization step, after background adjustment (convolution) and quantile normalization had been performed as described for RMA.

organism: Arabidopsis thaliana

source_name: Arabidopsis Col-0 seedlings 7 days after germination

label_protocol: 1 μg of total RNA was reverse transcribed into cDNA using an oligo(dT)-T7 primer, and was then converted into cRNA and linearly amplified by T7 in vitro transcription reaction using the standard Ambion protocol (MessageAmp aRNA Kit, Ambion). cRNA was then reverse transcribed with random primers to dUTP-containing ds cDNA (WT ds cDNA Synthesis Kit, catalog no. 900813; Affymetrix). Fragmentation and labeling was performed with the GeneChip WT double-stranded DNA Terminal Labeling Kit (catalog no. 900812, Affymetrix)

growth_protocol: Seedlings were grown in solid medium containing ½ concentration of macro elements and 0.5% sucrose in Petri-dishes at 22°C, 120 mol/m2s light intensity and 8h light/16h dark period. Seedling were collected at 4h after the start of the light period in liquid nitrogen for RNA preparation

extract_protocol:
Whole seedling were collected for RNA preparation.
Total RNA was isolated with RNeasy Mini kit supplied with RNase-Free DNase set (Qiagen) according to the manufacturer's instructions.

value: young seedlings

tag: genotype/variation

value: wild type control

tag: cultivar

value: germinated seedlings 7 days after sawing collected at 4h after the start of the light period using a photoperiod of 8h light and 16h dark with 120 mol/m2s light intensity at 22°C


title: mitfa Morpholino control at 50 hpf

value: male


title: mitfa morpholino knockdown at 50 hpf,rep 2


title: Col-0 rep3


title: wild type zebrafish at 48 hpf


title: wild type zebrafish at 50 hpf

scan_protocol: The hybridized microarrays were then washed according to the manufacturer’s protocol. Microarray results were extracted using Agilent G2565BA Scanner


title: aca8 aca10 rep3

description: Gene expression data from 7 days old aca8 aca10 mutant seedlings

source_name: Arabidopsis aca8 aca10 mutant seedlings 7 days after germination


title: T-47D-24h_10nMORG2058_Replicate1

description: Replicate 1

source_name: T-47D breast cancer cells grown in monolayer culture, treated 24h with 10nM ORG2058

value: breast

tag: cell line


title: aca8 aca10 rep1


title: Col-0 rep1


title: aca8 aca10 rep2


title: patient 50 TGR2 Response

city: Milano

first: Francesca

last: Falcetta

address: Via La Masa, 19

department: Oncology

country: Italy

institute: Istituto di ricerche farmacologiche Mario Negri

hyb_protocol: 100 ngs of total RNA enriched in miRNA fraction was Cy5-hybridized with a miRNA hybridization kit according to the manufacturer’s instructions (Agilent Technologies)

scan_protocol: Laser confocal scanner (G2565BA, Agilent Technologies)

data_processing: Data were extracted from scanned images using Agilent Feature Extraction software version 11. After elimination of outlier spot signals, raw intensity values for each of spots for every probes were averaged and the nonspecific intesity value was substracted.  Probes that produced a signal undistinguishable from the nonspecific value in all arrays were taken off. Log 2 values of probes were normalized by Invariant method.

source_name: Rectal tumor samples

label_protocol: 100 ngs of total RNA enriched in miRNA fraction was Cy5-labeled with a miRNA labelling kit according to the manufacturer’s instructions (Agilent Technologies)

extract_protocol: Frozen primary tumor tissues (100 mg) were homogenized at 8000 RPM in a Ultraturrax T 10 at 4°C with 1 ml of Trizol until to obtain a totally liquid phase and total RNA was extracted and purified using Ambion mirVana RNA isolation kit (Applied Biosystems, Italy) according to the manufacturer’s instructions. RNA was measured by NanoDrop, ND-1000 Specthophotometer (NanoDrop Technologies, USA) and quality assessed by Agilent Bioanalyzer Assay (Agilent Technologies, Germany).

treatment_protocol: Thirty-eight patients with histological diagnosis of rectal adenocarcinoma invading through the intestinal wall or with pelvic lymph node involvement as measured by endorectal ultrasonography (uT3/uT4 or any uT/N+) was treated with neoadjuvant chemo-radiotherapy. Capecitabine was given orally at 825 mg/m2 b.i.d. (two administrations each 12 h apart), from day 1 to 14 every 21 days. Oxaliplatin was administered i.v. at 50 mg/m2, diluted in 500 ml of glucose solution as a 120-min infusion, at days 1 and 8 of each 21-day cycle. Pelvic conformal RT was delivered at the daily dose of 1.8 Gy, 5 days a week, up to 45 Gy in 5 weeks. After surgery, further 4 months of adjuvant chemotherapy with CAP or weekly 5-FU–leucovorin were proposed to all the patients. The oral (CAP) or the i.v. (5-FU–leucovorin) regimen was a patient choice.

tag: tumor stage

tag: group

value: B

tag: outcome

value: other response

value: rectal cancer tumor

value: capecitabine + oxaliplatin in combination with  45 Gy of pelvic conformal radiotherapy


title: IM004_HAavirulent_10^4pfu_2d_2

city: Seattle

first: Michael

last: Katze

state: WA

address: Rosen Building 960 Republican St.

department: Microbiology

institute: University of Washington

description:
Sample name: 251486831459_1_3
Mice infect with Influenza A/VN/1203/04 HA avirulent at 10^4 PFU

hyb_protocol: The Agilent One-Color Microarray-Based Gene Expression Analysis Protocol was followed for hybridization and array washing. Two hundred fifty ng of each RNA sample was hybridized to one Agilent 4X44K human HG (Design ID 014850) array.

scan_protocol: Dry slides were scanned on an Agilent DNA microarray scanner (Model G2505B) using the XDR setting.

data_processing: Raw images were analyzed using the Agilent Feature Extraction software (version 9.5.3.1) and the GE1-v5_95_Feb07 extraction protocol. All arrays were required to pass Agilent QC flags. Extracted raw data were background corrected using the norm-exp method and quantile normalized using Agi4x44PreProcess and RMA Bioconductor packages.

label_protocol: The Agilent One-Color Microarray-Based Gene Expression Analysis Protocol was followed for the Cy3-cDNA probe preparation.

growth_protocol: Twenty-week-old C57BL/6 mice were infected by intranasal instillation of 10^4PFU of  A/Vietnam/1203-CIP048_RG1/2004 HA avirulent in 50 µl of PBS or mock-infected with PBS alone.  At days 1, 2, 4 and 7 days post-infection, lungs were harvested.

extract_protocol: All TRIzol lysates were processed simultaneously: they were phase-separated, and RNA was isolated from the aqueous phase (diluted 2 fold with RLT buffer) using Qiagen RNeasy Mini columns and the manufacturer’s recommended protocol (Qiagen Inc., Valencia, CA). RNA quality was assessed on an Agilent 2100 Bioanalyzer using the nanochip format, and only intact RNA was used for microarray analyses.

treatment_protocol: Specific lobs of the lung from each animal were harvested and briefly rinse tissue in cold (4ºC) PBS. Following the RNAlater (Ambion) protocol, tissue was cut into small chunks (<0.5cm in any single dimension) and place immediately into a 10-20 volumes (w/v) (e.g. 100mg/ml) RNAlater. After a 4ºC incubation for overnight, samples were stored at -80ºC further processing. Lung tissue was removed from RNAlater, washed in a small volume of Trizol, homogenized in 10-20 volumes (w/v) TRIzol and stored at -80°C until RNA isolation.

tag: strain

value: Female

tag: sample collection time post infection

value: 2 day

value: 20 week old

value: Influenza A/VN/1203/04 HA avirulent

tag: virus dose

value: lung


title: IM004_HAavirulent_10^4pfu_1d_1

description:
Sample name: 251486831605_1_4
Mice infect with Influenza A/VN/1203/04 HA avirulent at 10^4 PFU

value: 1 day

tag: infection


title: IM004_HAavirulent_10^4pfu_1d_5

description:
Sample name: 251486831474_1_2
Mice infect with Influenza A/VN/1203/04 HA avirulent at 10^4 PFU


title: IM004_HAavirulent_10^4pfu_4d_1

description:
Sample name: 251486831460_1_4
Mice infect with Influenza A/VN/1203/04 HA avirulent at 10^4 PFU

value: 4 day


title: IM004_HAavirulent_10^4pfu_1d_2

description:
Sample name: 251486831603_1_1
Mice infect with Influenza A/VN/1203/04 HA avirulent at 10^4 PFU


title: IM004_HAavirulent_10^4pfu_2d_5

description:
Sample name: 251486831606_1_2
Mice infect with Influenza A/VN/1203/04 HA avirulent at 10^4 PFU


title: IM004_HAavirulent_10^4pfu_1d_4

description:
Sample name: 251486831475_1_2
Mice infect with Influenza A/VN/1203/04 HA avirulent at 10^4 PFU


title: IM004_HAavirulent_10^4pfu_2d_3

description:
Sample name: 251486831605_1_2
Mice infect with Influenza A/VN/1203/04 HA avirulent at 10^4 PFU


title: patient 48 TGR3 Response


title: patient 49 TGR4 Response


title: IM004_HAavirulent_10^4pfu_4d_3

description:
Sample name: 251486831606_1_1
Mice infect with Influenza A/VN/1203/04 HA avirulent at 10^4 PFU


title: IM004_HAavirulent_10^4pfu_4d_2

description:
Sample name: 251486831605_1_1
Mice infect with Influenza A/VN/1203/04 HA avirulent at 10^4 PFU


title: IM004_HAavirulent_10^4pfu_2d_1

description:
Sample name: 251486831603_1_4
Mice infect with Influenza A/VN/1203/04 HA avirulent at 10^4 PFU


title: patient 44 TGR2 Response


title: patient 45 TGR2 Not Complete Response


title: patient 47 TGR3 Response

value: female


title: patient 46 TGR1

value: A

value: pathologic complete response


title: IM004_HAavirulent_10^4pfu_7d_1

description:
Sample name: 251486831605_1_3
Mice infect with Influenza A/VN/1203/04 HA avirulent at 10^4 PFU

value: 7 day


title: IM004_HAavirulent_10^4pfu_4d_5

description:
Sample name: 251486831602_1_2
Mice infect with Influenza A/VN/1203/04 HA avirulent at 10^4 PFU


title: IM004_HAavirulent_10^4pfu_7d_2

description:
Sample name: 251486831460_1_3
Mice infect with Influenza A/VN/1203/04 HA avirulent at 10^4 PFU


title: IM004_HAavirulent_10^4pfu_4d_4

description:
Sample name: 251486831603_1_2
Mice infect with Influenza A/VN/1203/04 HA avirulent at 10^4 PFU


title: Hypothalamus-Control+Saline (Cy5) x Control+high (Cy3)

city: Tsukuba

first: RANDEEP

last: RAKWAL

state: Ibaraki

address: 1-1-1 Tennodai

department: Institute of Health and Sport Sciences

country: Japan

institute: University of Tsukuba

hyb_protocol: hybridization_Kit: in situ hybridization plus

scan_protocol: Scanner: Agilent DNA microarray Scaner

data_processing: Software: Feature Extraction ver 9.5.3.1

organism: Rattus norvegicus

source_name: Treatment Cy3

label_protocol: Manual: Low RNA Input Linear Amplification kit standard protocol

growth_protocol: This part of the experiment was conducted in accordance with the Guidelines for the Care and Use of Laboratory Animals at the National Institute of Advanced Industrial Science and Technology (AIST), Japan. Nine male 10-weeks-old Wistar rats (300-350 g BW) were housed in acrylic cages (3/cage) at 24ºC and given access to tap water and laboratory chow ad libitum.

extract_protocol: kit: QIAGEN, Rneasy Mini

value: Wistar

value: 9 weeks

value: male

value: Hypothalamus

source_name: Control Cy5

treatment_protocol: Saline

value: saline


title: Hypothalamus-Control+Saline (Cy5) x Control+low (Cy3)


title: IM004_HAavirulent_10^4pfu_1d_3

description:
Sample name: 251486831459_1_2
Mice infect with Influenza A/VN/1203/04 HA avirulent at 10^4 PFU


title: IM004_HAavirulent_10^4pfu_7d_3

description:
Sample name: 251486831606_1_3
Mice infect with Influenza A/VN/1203/04 HA avirulent at 10^4 PFU


title: IM004_HAavirulent_10^4pfu_2d_4

description:
Sample name: 251486831460_1_2
Mice infect with Influenza A/VN/1203/04 HA avirulent at 10^4 PFU


title: patient 43 TGR1

value: rectal cancer tumor

value: capecitabine + oxaliplatin in combination with  45 Gy of pelvic conformal radiotherapy


title: IM004_HAavirulent_10^4pfu_7d_5

description:
Sample name: 251486831458_1_4
Mice infect with Influenza A/VN/1203/04 HA avirulent at 10^4 PFU

value: Female


title: IM004_HAavirulent_10^4pfu_7d_4

description:
Sample name: 251486831602_1_3
Mice infect with Influenza A/VN/1203/04 HA avirulent at 10^4 PFU

value: 20 week old


title: patient 40 TGR1


title: patient 41 TGR1


title: Cerebral cortex-Control+Saline (Cy5) x Control+high (Cy3)

value: Cerebral cortex


title: Ventral striatum-Control+Saline (Cy5) x Control+low (Cy3)

value: Ventral striatum


title: Cerebral cortex-Control+Saline (Cy5) x Control+low (Cy3)


title: IM004_mock_2d_1

description:
Sample name: 251486831602_1_4
Time-matched mock

value: 2 day

value: mock

value: control

value: lung


title: patient 32 TGR2 Response

value: B

value: other response


title: Hippocampus-Control+Saline (Cy5) x Control+low (Cy3)

value: Wistar

value: Hippocampus


title: patient 42 TGR3 Not Complete Response

value: male


title: Amygdala-Control+Saline (Cy5) x Control+low (Cy3)

value: 9 weeks

value: Amygdala


title: IM004_mock_1d_2

description:
Sample name: 251486831458_1_2
Time-matched mock

value: 1 day


title: IM004_mock_2d_2

description:
Sample name: 251486831474_1_3
Time-matched mock


title: Hippocampus-Control+Saline (Cy5) x Control+high (Cy3)

value: saline


title: Hypothalamus-Control+Saline (Cy3) x Control+low (Cy5)

source_name: Control Cy3

value: Hypothalamus

source_name: Treatment Cy5


title: Midbrain-Control+Saline (Cy5) x Control+low (Cy3)

value: midbrain


title: Ventral striatum-Control+Saline (Cy5) x Control+high (Cy3)


title: Hypothalamus-Control+Saline (Cy3) x Control+high (Cy5)


title: Amygdala-Control+Saline (Cy3) x Control+low (Cy5)


title: patient 31 TGR2 Response

value: rectal cancer tumor

value: capecitabine + oxaliplatin in combination with  45 Gy of pelvic conformal radiotherapy


title: Amygdala-Control+Saline (Cy5) x Control+high (Cy3)


title: Amygdala-Control+Saline (Cy3) x Control+high (Cy5)


title: Hippocampus-Control+Saline (Cy3) x Control+low (Cy5)


title: IM004_mock_1d_3

description:
Sample name: 251486831460_1_1
Time-matched mock

value: Female

value: 20 week old


title: patient 30 TGR2 Response

value: female


title: Ventral striatum-Control+Saline (Cy3) x Control+high (Cy5)

value: Ventral striatum


title: Midbrain-Control+Saline (Cy3) x Control+low (Cy5)


title: Hippocampus-Control+Saline (Cy3) x Control+high (Cy5)


title: Cerebral cortex-Control+Saline (Cy3) x Control+low (Cy5)

value: Cerebral cortex


title: Ventral striatum-Control+Saline (Cy3) x Control+low (Cy5)


title: Cerebral cortex-Control+Saline (Cy3) x Control+high (Cy5)


title: Midbrain-Control+Saline (Cy5) x Control+high (Cy3)


title: Midbrain-Control+Saline (Cy3) x Control+high (Cy5)


title: IM004_mock_2d_3

description:
Sample name: 251486831458_1_1
Time-matched mock

value: 2 day

value: mock

value: control

value: lung


title: IM004_mock_4d_1

description:
Sample name: 251486831458_1_3
Time-matched mock

value: 4 day


title: patient 29 TGR2 Response

value: male

value: B

value: other response


title: patient 28 TGR3 Not Complete Response


title: IM004_mock_4d_3

description:
Sample name: 251486831475_1_4
Time-matched mock


title: ime4-/- yeast grown in YPD rep2

city: Tel-Hashomer

first: Sharon

last: Moshitch-Moshkovitz

address: Laboratory wing

department: Cancer Research Center

country: Israel

institute: Sheba Medical Center

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

scan_protocol: affymetrix scanner

data_processing: Feature intensity values from scanned arrays were normalized and reduced to expression summaries using the RMA algorithm. Control probes, probesets with an interquartile range below 0.1 were removed;

organism: Saccharomyces cerevisiae

source_name: ime4-/- cells vegetative growth

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 600 ng total RNA (Affymetrix wt_sensetarget_label_manual)

growth_protocol: Yeast are grown vegetatively in YPD (Yeast extract, Peptone, Dextrose) medium

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

treatment_protocol: For sporulation yeast cells were transferred to SM (sporulation medium, 1% Kacetate)

tag: growth medium

value: YPD


title: ime4-/- yeast grown in SPO rep1

source_name: ime4-/- cells 4 hrs after transfer to meiosis-inducing media

value: SPO


title: WT yeast grown in SPO rep3

source_name: WT cells 4 hrs after transfer to meiosis-inducing media

value: wild type


title: ime4-/- yeast grown in YPD rep1


title: ime4-/- yeast grown in SPO rep2


title: WT yeast grown in SPO rep1


title: WT yeast grown in SPO rep2


title: WT yeast grown in YPD rep2

source_name: WT cells vegetative growth


title: IM004_mock_4d_2

description:
Sample name: 251486831474_1_1
Time-matched mock


title: patient 24 TGR2 Not Complete Response

value: rectal cancer tumor

value: capecitabine + oxaliplatin in combination with  45 Gy of pelvic conformal radiotherapy


title: patient 27 TGR4 Not Complete Response


title: IM004_mock_7d_2

description:
Sample name: 251486831475_1_1
Time-matched mock

value: Female

value: 7 day

value: 20 week old


title: WT yeast grown in YPD rep1


title: Human_Osteosarcoma_Non-Metastatic_HOS_Parental Line

city: Houston

first: Alexander

last: Yu

state: TX

department: Pediatrics

institute: Baylor College of Medicine

description: Gene expression data from non-metastatic parental cell line HOS

hyb_protocol: The labelled RNA was hybridized with the Human U133 plus 2 array using the GeneChip hybridization, wash and stain kit (Affymetrix).

scan_protocol: The hybridization signals were obtained from the GeneChip 7G Scanner (Affymetrix).

data_processing: The data was normalized using the Robust Multichip Average (RMA).  RMA consists of three steps: a background adjustment, quantile normalization and summarization (Irizarry, R.A., et al., Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics, 2003. 4(2): p. 249-64.).  The quality of the arrays data was assessed through affyQCReport (Parman, C., C. Halling, and R. Gentleman, affyQCReport: QC Report Generation for affyBatch objects. R package version 1.32.0.).  The microarray data was then analyzed using the S-score algorithm, which is a comparative method for gene expression data analysis that uses probe level data.  The microarray data was then analyzed using the S-score algorithm, which is a comparative method for gene expression data analysis that uses probe level data to calculate p-value of differential expression for each gene (Kennedy, R.E., K.J. Archer, and M.F. Miles, Empirical validation of the S-Score algorithm in the analysis of gene expression data. BMC Bioinformatics, 2006. 7: p. 154.).  Differential gene expression was defined as genes with a p-value (generated by Sscore, described in data processing section above) less than 0.05 and a 2-fold or greater difference in normalized fluorescence intensity between the 143B (numerator) and HOS (denominator), and LM7 (numerator) and SaOS-2 (denominator) cells.

source_name: Organ: Bone, Disease: Osteosarcoma, Non-metastatic tumor

label_protocol: The purified RNA were labelled by the Genechip 3” IVT express kit (Affymetrix, Santa Clara, CA) following the manufacturer’s protocol.

growth_protocol: The cell lines were maintained in GIBCO Minimum Essential Media supplemented with 10% fetal bovine serum at 37oC in 5% CO2, and they were tested to be mycoplasma-free.

extract_protocol: The TRIzol reagent (Invitrogen, San Diego, CA) was used to extract RNA from the cell lines, and the RNA was further purified by the RNeasy kit (QIAGEN, Valencia, CA).

value: HOS

tag: cell type

value: osteosarcoma

tag: origin

value: Derived from an osteosarcoma of a 13 year-old girl.

tag: metastatic potential

value: Low


title: Human_Osteosarcoma_ Metastatic_143B_Subline of HOS

description: Gene expression data from metastatic subline derived from HOS

source_name: Organ: Bone, Disease: Osteosarcoma, metastatic tumor

value: Developed from HOS by a Ki-RAS oncogene transformation.

value: High


title: patient 26 TGR1

value: male

value: A

value: pathologic complete response

tag: treatment


title: Human_Osteosarcoma_ Metastatic_LM7_Subline of SaOS-2

description: Gene expression data from metastatic subline derived from SaOS-2

value: Developed by injecting human SAOS-2 osteosarcoma cells into nude mice and isolating rare pulmonary metastases in culture which were then re-injected.


title: IM004_mock_7d_3

description:
Sample name: 251486831459_1_1
Time-matched mock

tag: gender

tag: age

value: mock

value: control

value: lung


title: IM004_mock_7d_1

description:
Sample name: 251486831603_1_3
Time-matched mock

tag: tissue


title: patient 25 TGR1

value: rectal cancer tumor

value: capecitabine + oxaliplatin in combination with  45 Gy of pelvic conformal radiotherapy


title: patient 23 TGR1

value: female


title: patient 17 TGR3 Response

value: B

value: other response


title: patient 14 TGR4 Response


title: patient 16 TGR3 Response


title: CA04M001_mock_7d_3

description:
Sample name: 251486831452_1_3
Time-matched mock

growth_protocol: Twenty-week-old C57BL/6 mice were infected by intranasal instillation of 10^3, 10^4, 10^5 and 10^6 PFU of A/CA04/2009 in 50 µl of PBS or mock-infected with PBS alone.  At days 1, 2, 4 and 7 days post-infection, lungs were harvested.

value: Female

value: 7 day

value: 20 week old


title: patient 13 TGR3 Not Complete Response


title: wild type IL-2 17 h rep 4

city: Bethesda

first: Peng

last: Li

state: MD

address: 9000 Rockville Pike

department: NHLBI

institute: NIH

description:
17h, wt
after 17h IL-2 induction

hyb_protocol: Fragmented RNA was assessed for relative length on Agilent 2100 bioanalyzer and hybridized to Affymetrix Mouse 430 2.0 chips for 16 hours.

scan_protocol: Affymetrix GeneChip scanner

data_processing: Intensities were pre-processed with MAS5.0, and further processed with variance stablization transformation (S10)

source_name: T cell

label_protocol: Biotin labeled with Affymetrix's IVT labeling kits (Affymetrix, Santa Clara, CA).

growth_protocol: Pre-activated splenic T cells (5x1e+6) were rested overnight

extract_protocol: Total RNA was extracted from cultured EPC with an RNAqueous micro RNA isolation kit (Ambion, Austin, TX).  Cells were lysed in buffer containing guanidinium thiocyanate.

treatment_protocol: Not treated or treated with 100 U/ml of IL-2 for 2, 6, or 17 hr

tag: genotype

value: wild type

value: T cell

tag: time


title: CA04M001_mock_7d_1

description:
Sample name: 251486831456_1_3
Time-matched mock


title: patient 18 TGR2 Response

tag: tumor stage


title: Human_Osteosarcoma_Non-Metastatic_SaOS-2_Parental Line

description: Gene expression data from non-metastatic parental cell line SaOS-2

tag: cell line

value: osteosarcoma

value: Derived from an osteosarcoma of an 11 year old female Caucasian.

value: Low


title: wild type IL-2 17 h rep 5

description:
17h, wt
after 17h IL-2 induction


title: wild type IL-2 17 h rep 3

description:
17h, wt
after 17h IL-2 induction


title: CA04M001_mock_7d_2

description:
Sample name: 251486831450_1_4
Time-matched mock


title: CA04M001_mock_4d_3

description:
Sample name: 251486831433_1_2
Time-matched mock

value: 4 day


title: patient 12 TGR2 Not Complete Response

value: male

tag: group

tag: outcome


title: patient 11 TGR3 Response


title: CA04M001_mock_4d_2

description:
Sample name: 251486831436_1_1
Time-matched mock

tag: strain

tag: sample collection time post infection

value: mock

value: control


title: STAT5 double knocked in IL-2 17 h rep 5

description:
17h, double knocked in
STAT5 double knocked in

value: STAT5 double knocked in


title: STAT5 double knocked in IL-2 17 h rep 4


title: wild type IL-2 17 h rep 2

description:
17h, wt
after 17h IL-2 induction


title: CA04M001_mock_4d_1

description:
Sample name: 251486831430_1_2
Time-matched mock

tag: infection

tag: virus dose

value: lung


title: patient 10 TGR3 Response

value: female

value: rectal cancer tumor

value: capecitabine + oxaliplatin in combination with  45 Gy of pelvic conformal radiotherapy


title: CA04M001_mock_1d_2

description:
Sample name: 251486831452_1_4
Time-matched mock

value: Female

value: 1 day


title: CA04M001_mock_2d_1

description:
Sample name: 251486831438_1_2
Time-matched mock

value: 2 day

value: 20 week old


title: patient 9 TGR1

value: A

value: pathologic complete response


title: patient 8 TGR1


title: CA04M001_mock_2d_2

description:
Sample name: 251486831451_1_3
Time-matched mock


title: CA04M001_mock_1d_1

description:
Sample name: 251486831432_1_3
Time-matched mock


title: IM004_mock_1d_1

description:
Sample name: 251486831606_1_4
Time-matched mock


title: wild type IL-2 17 h rep 1

description:
17h, wt
after 17h IL-2 induction

value: wild type

tag: cell type

value: T cell


title: CA04M001_10^6_7d_5

description:
Sample name: 251486831433_1_4
A/CA/04/2009 infected with 10^6 PFU

value: 7 day


title: STAT5 double knocked in IL-2 17 h rep 1


title: patient 7 TGR3 Not Complete Response

value: male

value: B

value: other response


title: patient 6 TGR2 Response


title: patient 5 TGR2 Response


title: wild type IL-2 6 h rep 3

description:
6h, wt
after 6h IL-2 induction

value: 6 h


title: CA04M001_10^6_7d_4

description:
Sample name: 251486831436_1_3
A/CA/04/2009 infected with 10^6 PFU

value: lung


title: wild type IL-2 6 h rep 4

description:
6h, wt
after 6h IL-2 induction


title: White Blood Cell HFCSD 27 weeks male 4

first: Junko

last: Takahashi

address: 1-1-1 Umezono

institute: National Institute of Advanced Industrial Science and Technology　(AIST)

description: gene expression analysis performed on a white blood cell (LeukoLock) preparation from a male 27 weeks high-fat, high-cholesterol, and high-sucrose diet miniature pig.

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60ºC 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-020109 Porcine Gene Expression Microarray (44K) for 17 hours at 65ºC in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed for 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37ºC GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Hybridized microarray slides washed according to the manufacturer’s instructions were scanned with an Agilent DNA Microarray Scanner (#G2565BA, Agilent Technologies, Santa Clara, CA) at 5 micron resolution.

data_processing: The scanned images were analyzed numerically using the Agilent Feature Extraction Software version 9.5.3.1 (Agilent) using default parameters (protocol GE1_105_Dec08 and Grid: 020109_D_F_20090417) to obtain background subtracted and spatially detrended processed signal intensities. Features flagged with not positive and significant or flagged with not above significant were considered as unexpressed genes. The quantile normalization method was used in our microarray analysis.

organism: Sus scrofa

source_name: Blood

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Whole blood RNA was extracted using the PAXgene RNA Isolation kit from whole blood preserved in Paxgene tubes (Qiagen). RNA of white blood cell was extracted from whole blood using the LeukoLock Total RNA Isolation kit (Ambion, Austin, TX). Isolation was performed according to the manufacturer’s protocol. RNA was quantified using a NanoDrop-1000 spectrophotometer and its quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Paxgene tube conservation at -80ºC

value: white blood cell

value: high-cholesterol high-sucrose diet HFCSD

value: 27 weeks

tag: breed

value: miniature pig


title: STAT5 double knocked in IL-2 17 h rep 2

value: STAT5 double knocked in


title: patient 4 TGR2 Response

value: female

value: rectal cancer tumor

value: capecitabine + oxaliplatin in combination with  45 Gy of pelvic conformal radiotherapy


title: wild type IL-2 6 h rep 2

description:
6h, wt
after 6h IL-2 induction


title: STAT5 double knocked in IL-2 17 h rep 3


title: White Blood Cell HFCSD 27 weeks male 1


title: CA04M001_10^6_7d_1

description:
Sample name: 251486831427_1_1
A/CA/04/2009 infected with 10^6 PFU

value: Female

value: 20 week old


title: wild type IL-2 6 h rep 1

description:
6h, wt
after 6h IL-2 induction

value: wild type

value: T cell


title: CA04M001_10^6_7d_2

description:
Sample name: 251486831437_1_1
A/CA/04/2009 infected with 10^6 PFU

value: 7 day


title: White Blood Cell HFCSD 27 weeks male 2

value: male


title: CA04M001_10^6_7d_3

description:
Sample name: 251486831429_1_1
A/CA/04/2009 infected with 10^6 PFU


title: wild type IL-2 6 h rep 5

description:
6h, wt
after 6h IL-2 induction


title: White Blood Cell HFCSD 27 weeks male 3


title: STAT5 double knocked in IL-2 6 h rep 5

description:
6h, double knocked in
STAT5 double knocked in


title: patient 2 TGR2 Response

value: B

value: other response


title: patient 3 TGR2 Response


title: patient 1 TGR2 Not Complete Response


title: STAT5 double knocked in IL-2 6 h rep 3

value: 6 h


title: White Blood Cell HFCD 27 weeks male 3

description: gene expression analysis performed on a white blood cell (LeukoLock) preparation from a male 27 weeks high-fat and high-cholesterol diet miniature pig.

value: white blood cell

value: high-cholesterol diet HFCD


title: White Blood Cell HFCD 27 weeks male 4

value: 27 weeks


title: White Blood Cell HFCD 27 weeks male 2

value: miniature pig


title: STAT5 double knocked in IL-2 6 h rep 2

value: STAT5 double knocked in


title: STAT5 double knocked in IL-2 6 h rep 4


title: CA04M001_10^6_4d_1

description:
Sample name: 251486831437_1_2
A/CA/04/2009 infected with 10^6 PFU

value: 4 day

value: lung


title: CA04M001_10^6_4d_2

description:
Sample name: 251486831451_1_1
A/CA/04/2009 infected with 10^6 PFU


title: White Blood Cell control 27 weeks male 4

description: gene expression analysis performed on a white blood cell (LeukoLock) preparation from a male 27 weeks control diet miniature pig.

value: control


title: CA04M001_10^6_2d_4

description:
Sample name: 251486831450_1_2
A/CA/04/2009 infected with 10^6 PFU

value: Female

value: 2 day


title: CA04M001_10^6_4d_3

description:
Sample name: 251486831426_1_2
A/CA/04/2009 infected with 10^6 PFU

value: 20 week old


title: wild type IL-2 2 h rep 5

description:
2h, wt
after 2h IL-2 induction

value: wild type

value: T cell

value: 2 h


title: White Blood Cell HFCD 27 weeks male 1

value: male


title: CA04M001_10^6_2d_3

description:
Sample name: 251486831434_1_1
A/CA/04/2009 infected with 10^6 PFU


title: White Blood Cell control 27 weeks male 1


title: STAT5 double knocked in IL-2 6 h rep 1


title: wild type IL-2 2 h rep 3

description:
2h, wt
after 2h IL-2 induction


title: CA04M001_10^6_2d_1

description:
Sample name: 251486831435_1_3
A/CA/04/2009 infected with 10^6 PFU


title: CA04M001_10^6_1d_4

description:
Sample name: 251486831438_1_1
A/CA/04/2009 infected with 10^6 PFU

value: 1 day


title: White Blood Cell control 27 weeks male 2


title: wild type IL-2 2 h rep 4

description:
2h, wt
after 2h IL-2 induction


title: White Blood Cell control 27 weeks male 3


title: STAT5 double knocked in IL-2 2 h rep 5

description:
2h, double knocked in
STAT5 double knocked in


title: CA04M001_10^5_7d_5

description:
Sample name: 251486831451_1_2
A/CA/04/2009 infected with 10^5 PFU

value: 7 day


title: STAT5 double knocked in IL-2 2 h rep 4


title: CA04M001_10^5_7d_4

description:
Sample name: 251486831438_1_3
A/CA/04/2009 infected with 10^5 PFU


title: Whole Blood HFCD 27 weeks male 3

description: gene expression analysis performed on a whole blood (PAXgene) preparation from a male 27 weeks high-fat and high-cholesterol diet miniature pig.

value: whole blood


title: Whole Blood HFCSD 27 weeks male 3

description: gene expression analysis performed on a whole blood (PAXgene) preparation from a male 27 weeks high-fat, high-cholesterol, and high-sucrose diet miniature pig.

value: high-cholesterol high-sucrose diet HFCSD


title: CA04M001_10^6_1d_3

description:
Sample name: 251486831457_1_3
A/CA/04/2009 infected with 10^6 PFU


title: Whole Blood HFCSD 27 weeks male 1

value: 27 weeks


title: Whole Blood HFCSD 27 weeks male 2

value: miniature pig


title: CA04M001_10^6_1d_1

description:
Sample name: 251486831435_1_4
A/CA/04/2009 infected with 10^6 PFU


title: STAT5 double knocked in IL-2 2 h rep 2

value: STAT5 double knocked in


title: CA04M001_10^5_7d_3

description:
Sample name: 251486831453_1_3
A/CA/04/2009 infected with 10^5 PFU


title: wild type IL-2 2 h rep 1

description:
2h, wt
after 2h IL-2 induction


title: wild type IL-2 2 h rep 2

description:
2h, wt
after 2h IL-2 induction


title: CA04M001_10^6_2d_2

description:
Sample name: 251486831454_1_4
A/CA/04/2009 infected with 10^6 PFU


title: Whole Blood HFCD 27 weeks male 2

value: high-cholesterol diet HFCD


title: STAT5 double knocked in IL-2 2 h rep 3


title: CA04M001_10^5_7d_2

description:
Sample name: 251486831457_1_4
A/CA/04/2009 infected with 10^5 PFU

value: lung


title: Whole Blood HFCD 27 weeks male 1


title: STAT5 double knocked in IL-2 2 h rep 1


title: wild type control 0 h rep 4

description:
0hr, wt
control without IL-2 induction

value: control

value: 0 h


title: Whole Blood control 27 weeks male 4

description: gene expression analysis performed on a whole blood (PAXgene) preparation from a male 27 weeks control diet miniature pig.


title: Whole Blood control 27 weeks male 3


title: CA04M001_10^5_4d_3

description:
Sample name: 251486831456_1_4
A/CA/04/2009 infected with 10^5 PFU

value: Female

value: 4 day


title: wild type control 0 h rep 2

description:
0hr, wt
control without IL-2 induction

value: wild type


title: Whole Blood HFCSD 19 weeks male 3

description: gene expression analysis performed on a whole blood (PAXgene) preparation from a male 19 weeks high-fat, high-cholesterol, and high-sucrose diet miniature pig.

value: 19 weeks


title: CA04M001_10^5_4d_4

description:
Sample name: 251486831453_1_4
A/CA/04/2009 infected with 10^5 PFU

value: 20 week old


title: STAT5 double knocked in control 0 h rep 2

description:
0hr, double knocked in
STAT5 double knocked in

value: T cell


title: wild type control 0 h rep 1

description:
0hr, wt
control without IL-2 induction


title: Whole Blood HFCD 19 weeks male 4

description: gene expression analysis performed on a whole blood (PAXgene) preparation from a male 19 weeks high-fat and high-cholesterol diet miniature pig.

value: male


title: Whole Blood HFCSD 19 weeks male 1


title: STAT5 double knocked in control 0 h rep 3


title: CA04M001_10^5_2d_4

description:
Sample name: 251486831453_1_2
A/CA/04/2009 infected with 10^5 PFU

value: 2 day


title: CA04M001_10^5_1d_3

description:
Sample name: 251486831455_1_1
A/CA/04/2009 infected with 10^5 PFU

value: 1 day


title: CA04M001_10^5_4d_1

description:
Sample name: 251486831431_1_4
A/CA/04/2009 infected with 10^5 PFU


title: Whole Blood control 27 weeks male 2

value: whole blood


title: Whole Blood HFCSD 19 weeks male 2

value: high-cholesterol high-sucrose diet HFCSD


title: CA04M001_10^5_2d_1

description:
Sample name: 251486831430_1_1
A/CA/04/2009 infected with 10^5 PFU


title: STAT5 double knocked in control 0 h rep 1


title: Whole Blood HFCD 19 weeks male 2

value: miniature pig


title: CA04M001_10^5_4d_2

description:
Sample name: 251486831454_1_3
A/CA/04/2009 infected with 10^5 PFU


title: STAT5 double knocked in control 0 h rep 4

value: STAT5 double knocked in


title: Macrosomic, rep 1

city: Columbia

first: Julia

middle: A

last: Taylor

state: MO

address: 114 Lefevre Hall

department: Biological Sciences

institute: University of Missouri

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

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: We used GCOS 1.4 software with the default setting (alpha1: 0.05, alpha2: 0.065, tau: 0.015, TGT Value: 500, Normalization factor (NF): 1.000) to generate the CHP files.

source_name: Macrosomic (M)

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

growth_protocol: Animals were the offspring of hemiovariectomized female mice. The resulting hyperovulation results in a crowded uterine horn. Embryo growth is affected, and pups born have a wide range of body weights.

extract_protocol: Tri Reagent extraction of total RNA was performed according to the manufacturer's instructions, with further cleanup on Qiagen Rneasy columns.

treatment_protocol: No treatment other than maternal hemiovariectomy prior to pregnancy.

value: 24 weeks (adult)

value: Epididymal fat pad


title: CA04M001_10^5_2d_2

description:
Sample name: 251486831450_1_3
A/CA/04/2009 infected with 10^5 PFU

value: lung


title: Macrosomic, rep 3


title: wild type control 0 h rep 3

description:
0hr, wt
control without IL-2 induction

value: control

value: 0 h


title: Whole Blood control 27 weeks male 1

value: 27 weeks


title: Whole Blood control 19 weeks male 4

description: gene expression analysis performed on a whole blood (PAXgene) preparation from a male 19 weeks control diet miniature pig.


title: Whole Blood HFCD 19 weeks male 1

value: high-cholesterol diet HFCD


title: CA04M001_10^5_7d_1

description:
Sample name: 251486831429_1_2
A/CA/04/2009 infected with 10^5 PFU

value: Female

value: 7 day


title: Macrosomic, rep 2


title: Whole Blood HFCD 19 weeks male 3

value: 19 weeks


title: CA04M001_10^5_1d_2

description:
Sample name: 251486831456_1_2
A/CA/04/2009 infected with 10^5 PFU

value: 20 week old


title: CA04M001_10^5_1d_4

description:
Sample name: 251486831453_1_1
A/CA/04/2009 infected with 10^5 PFU


title: CA04M001_10^5_2d_3

description:
Sample name: 251486831429_1_3
A/CA/04/2009 infected with 10^5 PFU

value: 2 day


title: Whole Blood control 19 weeks male 3

value: male


title: PXVE:miR169nm 24h estradiol rep3

city: Irapuato

first: Enrique

middle: Ibarra

last: Laclette

state: Guanajuato

address: Km 9.6 Libramiento Norte Carretera Irapuato-León, A.P. 629

country: Mexico

institute: Laboratorio Nacional de Genomíca (LANGEBIO), Centro de Investigación y Estudios Avanzados del IPN (CINVESTAV)

description: Biological replicate 3 of 3 (in swap)

hyb_protocol: Probes were mixed, concentrated by precipitation and resuspended in the hybridization solution (50% formamide, 5X SSC, 0.1% SDS, 0.4 μg/ l tRNA and 0.2 μg/ l Salmon Sperm DNA) for 14h. Slides were washed 5 min in each of the following solutions: a) 2x SSC, 0.1% SDS/42°C, b) 0.1x SSC/RT and two final washes with 0.05x SSC/RT carried out.

scan_protocol: Slides were scanned with an Axon GenePix 4000 B scanner at a resolution of 10 µm adjusting the laser and gain parameters to obtain similar levels of fluorescence intensity in both channels. Spot intensities were quantified using Axon GenePix Pro 6.0 image analysis software. The mean of the signals and the median of backgrounds were used for further analysis.

data_processing: Raw data were imported into the R 2.2.1 software (http://www.R-project.org). Background correction was done using the method substract whereas normalization of the signal intensities within slides was carried out using the printtiploess method (Yang et al., 2002) using the LIMMA package (Smyth et al., 2003, www.bioconductor.org).

source_name: complete 8-day-old seedlings estradiol-exposed for 24 h

label_protocol: For each transgenic line, three biological replicates were used for probe synthesis. For each sample, 1.5 μg total RNA were amplified in the presence of aminoallyl-dUTP (Ambion) using the Aminoallyl Message Amp II kit (Ambion). Resulting amplified RNA probes were further labeled with fluorescent Cy3 and Cy5 dyes (Amersham). The fluorescent dye-labeled probes were then purified using RNeasy columns (Qiagen).

growth_protocol: Arabidopsis thaliana ecotype Col-0 seeds were surface sterilized with 70% (v/v) ethanol for 7 min and 20% (v/v) bleach for 7 min. After three washes in distilled water, seeds were germinated and grown on agar plates containing 0.1X Murashige and Skook medium. Plates were placed vertically at an angle of 65˚ to allow root growth along the agar surface and to allow unimpeded growth of the hypocotyl into the air. For plant growth, we used a plant growth cabinet (Percival Scientific AR95L, Perry, IA), with a photoperiod of 16 h of light, 8 h of darkness, and temperature of 22 °C.

extract_protocol: Total RNA was isolated from whole seedlings using the RNeasy kit (Qiagen) following the manufacturer’s instructions.

treatment_protocol: Eight-day-old seedlings grown on liquid medium were exposed for 24 h to 7 mM b-estradiol or DMSO (mock treatment) prior to RNA extraction

tag: genetic background

value: Columbia 0

value: 8 days

value: whole seedling

value: 7 uM estradiol

source_name: Total RNA from pooled PXVE transgenic lines DMSO-exposed for 24h

value: Pooled PXVE transgenic lines

value: DMSO


title: IUGR_high postnatal growth, rep 3

source_name: IUGR_high postnatal growth (IH)

value: 24 weeks (adult)

value: Epididymal fat pad


title: PXVE:miR169nm 24h estradiol rep2

description: Biological replicate 2 of 3

tag: treatment


title: IUGR_high postnatal growth, rep 1

tag: gender


title: IUGR_low postnatal growth, rep 2

source_name: IUGR_low postnatal growth (IL)

tag: age


title: PXVE:miR169nm 24h estradiol rep1

description: Biological replicate 1 of 3

tag: tissue


title: Whole Blood HFCSD 10 weeks male 3

description: gene expression analysis performed on a whole blood (PAXgene) preparation from a male 10 weeks high-fat, high-cholesterol, and high-sucrose diet miniature pig.

value: whole blood

value: high-cholesterol high-sucrose diet HFCSD

value: 10 weeks

value: miniature pig


title: CA04M001_10^5_1d_1

description:
Sample name: 251486831436_1_4
A/CA/04/2009 infected with 10^5 PFU

value: Female

value: 1 day

value: lung


title: PXVE:NF-YA7SRDX  24h estradiol rep3

description: Biological replicate 3 of 3 (in swap)

tag: genotype


title: Whole Blood control 19 weeks male 2

value: control

tag: time

value: 19 weeks


title: PXVE:NF-YA7SRDX  24h estradiol rep2

description: Biological replicate 2 of 3

value: Columbia 0


title: PXVE:NF-YA10SRDX  24h estradiol rep2

description: Biological replicate 2 of 3

value: 8 days


title: Whole Blood HFCSD 10 weeks male 4

value: male


title: Whole Blood control 19 weeks male 1


title: Whole Blood HFCD 10 weeks male 4

description: gene expression analysis performed on a whole blood (PAXgene) preparation from a male 10 weeks high-fat and high-cholesterol diet miniature pig.

value: high-cholesterol diet HFCD


title: IUGR_high postnatal growth, rep 2


title: CA04M001_10^4_7d_3

description:
Sample name: 251486831451_1_4
A/CA/04/2009 infected with 10^4 PFU

value: 7 day

value: 20 week old


title: CA04M001_10^4_7d_2

description:
Sample name: 251486831457_1_2
A/CA/04/2009 infected with 10^4 PFU


title: CA04M001_10^4_4d_3

description:
Sample name: 251486831437_1_4
A/CA/04/2009 infected with 10^4 PFU

value: 4 day


title: Whole Blood HFCSD 10 weeks male 2


title: CA04M001_10^4_4d_1

description:
Sample name: 251486831450_1_1
A/CA/04/2009 infected with 10^4 PFU


title: CA04M001_10^4_7d_1

description:
Sample name: 251486831433_1_3
A/CA/04/2009 infected with 10^4 PFU


title: CA04M001_10^4_4d_2

description:
Sample name: 251486831455_1_2
A/CA/04/2009 infected with 10^4 PFU


title: PXVE:NF-YA10SRDX  24h estradiol rep3

description: Biological replicate 3 of 3 (in swap)

value: whole seedling

value: 7 uM estradiol

value: Pooled PXVE transgenic lines

value: DMSO


title: Whole Blood HFCSD 10 weeks male 1

value: whole blood

value: high-cholesterol high-sucrose diet HFCSD

value: 10 weeks

value: miniature pig


title: PXVE:NF-YA10SRDX  24h estradiol rep1

description: Biological replicate 1 of 3


title: Whole Blood HFCD 10 weeks male 3


title: IUGR_low postnatal growth, rep 3

value: 24 weeks (adult)

value: Epididymal fat pad


title: Hippocampus L26 rep2

city: Cantoblanco

first: Juan

middle: Carlos

last: Oliveros

state: Madrid

address: Darwin 3

country: Spain

institute: CNB, CSIC

description: Gene expression data from hippocampus cells (L26)

hyb_protocol: Following fragmentation, 10 µg of biotinylated cRNA were hybridized to Affymetrix chips (GeneChip Mouse Genome 430 2.0 Array). Each sample was added to a hybridization solution containing 100mM 2-(N-morpholino)ethanesulfonic acid, 1 M Na+, and 20mM of EDT

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

data_processing: GeneChip intensities were background-corrected, normalized and sumarized by RMA method, using the “Affy” package from Bioconductor.

source_name: Hippocampus, L26

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 4 µg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Experiments were performed in adult male mice from two daDREAM transgenic lines, L1 and L26, homozygous for the transgene, and wild type littermates. The genetic background in all cases was C57B6xCBA.

extract_protocol: RNA was prepared using TRIzol (Invitrogen) and the RNeasy Mini Kit (Qiagen). RNA was quantified and the RNA quality was assessed with a 2100 Bioanalyzer from Agilent Technologies

value: L26 daDREAM transgenic line

value: Hippocampus


title: CA04M001_10^4_2d_4

description:
Sample name: 251486831456_1_1
A/CA/04/2009 infected with 10^4 PFU

value: Female

value: 2 day

value: lung


title: IUGR_low postnatal growth, rep 1

value: male


title: Hippocampus L26 rep3


title: CA04M001_10^4_2d_3

description:
Sample name: 251486831454_1_1
A/CA/04/2009 infected with 10^4 PFU

value: 20 week old


title: PXVE:NF-YA2SRDX  24h estradiol rep3

description: Biological replicate 3 of 3 (in swap)

value: Columbia 0

value: 8 days

value: whole seedling


title: Hippocampus wild type rep3

description: Gene expression data from hippocampus cells (wild type)

source_name: Hippocampus, wild type

value: Wild Type


title: Whole Blood HFCD 10 weeks male 2

value: whole blood

value: high-cholesterol diet HFCD


title: Whole Blood control 10 weeks male 4

description: gene expression analysis performed on a whole blood (PAXgene) preparation from a male 10 weeks control diet miniature pig.

value: control

value: 10 weeks


title: Hippocampus wild type rep1


title: Whole Blood control 10 weeks male 2

value: miniature pig


title: PXVE:NF-YA10  24h estradiol rep2

description: Biological replicate 2 of 3

value: 7 uM estradiol

value: Pooled PXVE transgenic lines

value: DMSO


title: Hippocampus L26 rep1

value: L26 daDREAM transgenic line

value: Hippocampus


title: PXVE:NF-YA10  24h estradiol rep3

description: Biological replicate 3 of 3 (in swap)


title: CA04M001_10^4_2d_2

description:
Sample name: 251486831426_1_1
A/CA/04/2009 infected with 10^4 PFU

value: Female

value: 2 day

value: lung


title: PXVE:NF-YA7SRDX  24h estradiol rep1

description: Biological replicate 1 of 3

value: Columbia 0


title: Whole Blood control 10 weeks male 1

value: male


title: CA04M001_10^4_1d_2

description:
Sample name: 251486831434_1_3
A/CA/04/2009 infected with 10^4 PFU

value: 1 day

value: 20 week old


title: CA04M001_10^4_2d_1

description:
Sample name: 251486831435_1_1
A/CA/04/2009 infected with 10^4 PFU


title: CA04M001_10^4_1d_3

description:
Sample name: 251486831430_1_3
A/CA/04/2009 infected with 10^4 PFU


title: Whole Blood HFCD 10 weeks male 1

value: whole blood


title: PXVE:NF-YA10  24h estradiol rep1

description: Biological replicate 1 of 3

value: 8 days

value: whole seedling


title: PXVE:NF-YA7  24h estradiol rep3

description: Biological replicate 3 of 3 (in swap)


title: PXVE:NF-YA2SRDX  24h estradiol rep1

description: Biological replicate 1 of 3


title: Hippocampus wild type rep2

value: Wild Type


title: CA04M001_10^3_7d_4

description:
Sample name: 251486831426_1_3
A/CA/04/2009 infected with 10^3 PFU

value: 7 day


title: PXVE:NF-YA7  24h estradiol rep2

description: Biological replicate 2 of 3

value: 7 uM estradiol


title: CA04M001_10^4_1d_1

description:
Sample name: 251486831433_1_1
A/CA/04/2009 infected with 10^4 PFU


title: Whole Blood control 10 weeks male 3

value: control

value: 10 weeks

value: miniature pig


title: control MSN 28Q

city: Irvine

first: Leslie

last: Thompson

address: Biological Sciences III

institute: University of California, Irvine

description: Sample name: MSN4.2

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Partek Genomics Suite Version 6.6 Beta (6.12.0207) was used for data processing. Only interrogating probes were imported. No probe filtering was done. RMA background correction was done. Quantile Normalization was applied. Log Probes using Base 2. Probeset summarization Median Polish was done.
probe group file: HuGene-1_0-st-v1.r4.pgf
meta-probeset file: HuGene-1_0-st-v1.r4.mps

source_name: control MSN

label_protocol: Standard 100ng total RNA labeling protocol (Affymetrix)

growth_protocol: Differentiated human iPS-derived NSCs, with additional 56d differentiation to striatal-like cells. NSC lines were generated by collagenase treating (1mg/ml, Gibco) iPSC colonies and lifting them from the feeder layers directly into Stemline medium (Sigma) supplemented 100ng/ml basic FGF (Chemicon), 100ng/ml EGF (Chemicon), and 5?g/ml heparin (Sigma) in polyhema-coated flasks to prevent attachment. iPSC-derived NSCs were expanded as spherical aggregates and passaged weekly with a chopping technique. To generate striatal-like cells, growth medium containing EGF/FGF was removed from NSCs, and cells were plated on laminin or allowed to aggregate for 5 days in NIM (1% N2 in DMEM:F12). BDNF (20ng/ml; Peprotech 450-02) was then added for 2 days. The medium was then supplemented for 21 days with BDNF, rhShh (200ng/ml; R&D 1845-SH), and Dkk1 (100ng/ml; R&D 1096-DK-010). The rest of the differentiation was then completed in NIM with BDNF, dibutyryl cyclic AMP (dbcAMP, 0.5mM; Sigma D0260) and valproic acid (VPA, 0.5mM; Sigma P4546). Medium was half-changed twice per week or as needed. If cells were differentiated as aggregates, they were plated on day 42.

extract_protocol: Samples were identified as HD or control by genotyping. Samples were snap frozen in liquid N2. RNA was extracted using RNeasy kit (Qiagen) with DNAse treatment.

tag: cag length

tag: disease state

value: iPS-derived MSN-like


title: CA04M001_10^3_7d_3

description:
Sample name: 251486831430_1_4
A/CA/04/2009 infected with 10^3 PFU

value: Female


title: PXVE:NF-YA2SRDX  24h estradiol rep2

description: Biological replicate 2 of 3

value: Pooled PXVE transgenic lines

value: DMSO


title: CA04M001_10^4_1d_4

description:
Sample name: 251486831427_1_3
A/CA/04/2009 infected with 10^4 PFU

value: lung


title: control MSN 33Q

description: Sample name: MSN33i.8


title: CA04M001_10^3_7d_2

description:
Sample name: 251486831455_1_3
A/CA/04/2009 infected with 10^3 PFU


title: PXVE:NF-YA7  24h estradiol rep1

description: Biological replicate 1 of 3

value: Columbia 0


title: PXVE:NF-YA3  24h estradiol rep1

description: Biological replicate 1 of 3


title: PXVE:NF-YA3  24h estradiol rep3

description: Biological replicate 3 of 3 (in swap)


title: CA04M001_10^3_4d_4

description:
Sample name: 251486831432_1_2
A/CA/04/2009 infected with 10^3 PFU

value: 4 day


title: haploid ES cell line H129-1 p17 1 sort vs male somatic 129/Sv gDNA

type: genomic

city: Vienna

first: Martin

last: Leeb

address: Dr.-Bohr-Gasse 9/3

department: Max Perutz Labs

country: Austria

institute: University of Vienna

description: CNV analysis of H129 haploid ES cell line vs somatic 129/Sv male

hyb_protocol: sample processing, labelling and data processing were performed by a commercial provider; Source Bioscience

molecule: genomic DNA

source_name: gDNA from haploid ES cell line H129-1

extract_protocol: gDNA was extracted using the Quiagen Gentra Puregene Kit

treatment_protocol: ES cells were established and cultured in 2i medium

value: haploid ES cells

source_name: 129/Sv male kidney control

growth_protocol: gDNA extracted from male kidney

value: male somatic kidney


title: CA04M001_10^3_4d_3

description:
Sample name: 251486831434_1_4
A/CA/04/2009 infected with 10^3 PFU

value: 20 week old


title: CA04M001_10^3_2d_3

description:
Sample name: 251486831427_1_2
A/CA/04/2009 infected with 10^3 PFU

value: 2 day


title: PXVE:NF-YA2  24h estradiol rep3

description: Biological replicate 3 of 3 (in swap)

value: 8 days

value: whole seedling


title: PXVE:NF-YA3  24h estradiol rep2

description: Biological replicate 2 of 3

value: 7 uM estradiol


title: PXVE:NF-YA2  24h estradiol rep1

description: Biological replicate 1 of 3


title: CA04M001_10^3_4d_1

description:
Sample name: 251486831452_1_2
A/CA/04/2009 infected with 10^3 PFU


title: CA04M001_10^3_2d_1

description:
Sample name: 251486831432_1_4
A/CA/04/2009 infected with 10^3 PFU


title: HD MSN 60Q clone2

description: Sample name: MSN60i.3

source_name: HD MSN

value: HD


title: control NSC 33Q rep1

description: Sample name: HD33i.8 (1)

source_name: control NSC

value: control

value: iPS-derived NSC


title: haploid ES cell line H129-1 p12 1 sort vs male somatic 129/Sv gDNA

description: CNV analysis of H129-2 haploid ES cell line vs somatic 129/Sv male

scan_protocol: sample processing, labelling and data processing were performed by a commercial provider; Source Bioscience

source_name: gDNA from haploid ES cell line H129-2


title: PXVE:NF-YA2  24h estradiol rep2

description: Biological replicate 2 of 3


title: HD MSN 60Q clone1

description: Sample name: MSN60i.4

value: iPS-derived MSN-like


title: HD MSN 180Q

description: Sample name: MSN180i.5


title: CA04M001_10^3_2d_2

description:
Sample name: 251486831431_1_1
A/CA/04/2009 infected with 10^3 PFU

value: Female


title: HD NSC 60Q rep2

description: Sample name: HD60i.4 (2)

source_name: HD NSC


title: CA04M001_10^3_4d_2

description:
Sample name: 251486831431_1_3
A/CA/04/2009 infected with 10^3 PFU


title: control NSC 33Q rep2

description: Sample name: HD33i.8 (2)


title: HD NSC 60Q rep1

description: Sample name: HD60i.4 (1)


title: Sfrp5 KO HFD 8 weeks, biological rep7

city: Ann Arbor

first: Ormond

last: MacDougald

state: MI

address: 6458 Brehm Center, 1000 Wall Street

department: Molecular and Integrative Physiology

institute: University of Michigan

hyb_protocol: Following Labeling, 4 ug of cDNA were hybridized for 16 hr at 45C on GeneChip Gene ST 1.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix 3000 7G GeneChip Scanner with Autoloader.

data_processing: Data was analyzed using the limma, oligo and affy Bioconductor packages implemented in the R-statistical environment (Affy package v. 1.18 from bioconductor version 2.2).  RMA was used to normalize the data and fit log2 transformed expression values (Affy Expression Console version 1.1.2800.19935).

source_name: gonadal white adipose tissue_Sfrp5 KO_8 weeks of high-fat diet

label_protocol: Biotinylated cDNA were prepared according to the Nugen WT-Pico Ovation kit protocol from 10 ng total RNA (WT-Pico Ovation RNA Amplification System Manual, 2007, NuGEN). Subsequently cDNA is made double stranded fragmented and end-labeled following manufacturers standard protocol (NuGEN exon module, encore end-labeling module).

extract_protocol: RNA Stat60 extraction of total RNA was performed according to the manufacturer's instructions.

tag: genotype/variation

value: Sfrp5 KO (Q27Stop)

value: male

value: 12 weeks

tag: diet

value: 8 wks of high-fat diet

value: gonadal white adipose tissue (WAT)


title: CA04M001_10^3_1d_3

description:
Sample name: 251486831438_1_4
A/CA/04/2009 infected with 10^3 PFU

tag: strain

value: 1 day

value: lung


title: Sfrp5 KO HFD 8 weeks, biological rep8


title: HD NSC 180Q rep2

description: Sample name: HD180i.5 (2)


title: Sfrp5 KO HFD 8 weeks, biological rep5


title: Sfrp5 KO HFD 8 weeks, biological rep6


title: CA04M001_10^3_1d_4

description:
Sample name: 251486831429_1_4
A/CA/04/2009 infected with 10^3 PFU

tag: sample collection time post infection

value: 20 week old


title: CA04M001_10^3_1d_2

description:
Sample name: 251486831436_1_2
A/CA/04/2009 infected with 10^3 PFU

tag: infection


title: Wild-type HFD 8 weeks, biological rep7

source_name: gonadal white adipose tissue_wild-type_8 weeks of high-fat diet

value: wild type


title: Sfrp5 KO HFD 8 weeks, biological rep4


title: Healthy Control (Cy5)_O3 lifetime (Cy3)_Pooled 2 Seed

description: Dye-swap (Cy5/Cy3) of O3 lifetime Pooled 2 seed

hyb_protocol: Agilent: hybridization_Kit: in situ hybridization plus

scan_protocol: Scanner: Agilent Microarray scanner G2565BA

data_processing: Agilent Feature Extraction software (version 9.5.3.1)

organism: Oryza sativa

source_name: Ozone_mature seed

label_protocol: Manual: Agilent Low RNA Input Fluorescent Linear Amplification Kit

growth_protocol: Plants were grown in controlled greenhouse, OTC

extract_protocol: CTAB plus QIAGEN, Rneasy Mini

tag: cultivar

value: Koshihikari

value: seed

value: O3 for 8h

source_name: Control_mature seed

treatment_protocol: control, filtered air


title: PC12Control2

city: Minato-ku

first: Yuzuru

last: Otsuka

state: Tokyo

department: Department of Nutrition

institute: Toita Women's College

description:
KNRatPC12Cont2
Cell culture.
Gene expression after 6hr incubation.

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >9.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 microl containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturer's instructions. On completion of the fragmentation reaction, 55 microl of 2x GE hybridization buffer HI-RPM was added to the fragmentation mixture and hybridized to Agilent Whole Rat Genome microarray arrays (G4131F) for 17 hours at 65°C in a rotating Agilent hybridization oven with 10rpm. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 90% for High and 5% for Low).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1 (Agilent) using default parameters (protocol GE1-v5_95_feb07 and Grid: 014879_D_F_20090416) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: PC12 cells, 6hr, no NGF

label_protocol: Cyanine-3 (Cy3)-labeled cRNA was prepared from 100 ng RNA using the One-Color Low Input Quick Amp Labeling kit (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the Hitachi UV Spectrophotometer.

growth_protocol: PC12 cells (Riken, Saitama) derived from rat pheochromocytoma were cultured in Dulbecco’s Modified Eagle’s Medium (LOW) containing 10% Fetal Bovine Serum (Irvine Scientific)], 10% Horse Serum (GIBCO), 150IU/ml:100mg/ml penicillin/streptomycin (ICN Biomedicals) in 37C 5% CO2.

extract_protocol: RNA was prepared using the Isogen RNA Purification kit (Nipon gene, Toyama Japan) following the manufacturer's recommendations. The RNA was then treated with DNase I and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: After 24hours incubation of PC12 cells cultured in 4 ml of the medium in 60mm Tissue Culture Dishes at 2.0×10^5cells/ml, the medium was changed and NGF was added to 1ng/mL (0 ng/mL for the control group). After 6 hours incubation, the total RNA was extracted.

tag: cell line


title: Sfrp5 KO HFD 8 weeks, biological rep3


title: Sfrp5 KO HFD 8 weeks, biological rep1


title: PC12NGF1

description:
KNRatPC12NGF1
Cell culture.
Gene expression after 6hr incubation with NGF.

source_name: PC12 cells, 6hr, 1ng/mL NGF

value: nerve growth factor (NGF)


title: Healthy Control (Cy3)_O3 lifetime (Cy5)_Pooled 1 Seed

description: Dye-swap (Cy3/Cy5) of O3 lifetime Pooled 1 seed


title: HD NSC 180Q rep1

description: Sample name: HD180i.5 (1)

value: HD

tag: cell type


title: Wild-type HFD 8 weeks, biological rep4


title: Sfrp5 KO HFD 8 weeks, biological rep2


title: PC12Control3

description:
KNRatPC12Cont3
Cell culture.
Gene expression after 6hr incubation.


title: Healthy Control (Cy5)_O3 8 h (Cy3)_Pooled 2 Panicle

description: Dye-swap (Cy5/Cy3) of O3 8 h Pooled 2 panicle

source_name: Ozone_fumigated_8 h Flowering stage plant

growth_protocol: Plants were grown in controlled greenhouse

value: panicle

source_name: Control_8 h Flowering stage plant


title: PC12NGF3

description:
KNRatPC12NGF3
Cell culture.
Gene expression after 6hr incubation with NGF.


title: Healthy Control (Cy3)_O3 8 h (Cy5)_Pooled 1 Panicle

description: Dye-swap (Cy3/Cy5) of O3 8 h Pooled 1 panicle


title: Wild-type HFD 8 weeks, biological rep5


title: Wild-type HFD 8 weeks, biological rep3


title: Wild-type HFD 8 weeks, biological rep6


title: control NSC 21Q

description: Sample name: HD21i.5

value: control

value: iPS-derived NSC


title: PC12NGF2

description:
KNRatPC12NGF2
Cell culture.
Gene expression after 6hr incubation with NGF.


title: Wild-type HFD 8 weeks, biological rep1


title: HD NSC 109Q

description: Sample name: HD109i.1


title: Wild-type HFD 8 weeks, biological rep2


title: MPH_72h_D5_2

status: Public on Apr 24 2012

city: Brussels

first: Tatyana

last: Doktorova

state: Belgium

address: Laarbeeklaan 103, building G

department: FAFY

country: Belgium

institute: VUB

description: Treatment with MPH 72h

hyb_protocol: We used standard Affymetrix hybridisation rotocols

scan_protocol: We used standard Affymetrix scanning parameters

data_processing: All samples were normalized by MAS 5 algorithm

source_name: Treatment with MPH 72h

label_protocol: We used standard Affymetrix labeling protocols

growth_protocol: Hepatocytes were isolated by using a two-step collagenase perfusion technique . The viability was assessed by trypan blue exclusion and the cells (≥85% viability) were cultured as a monolayer at a density of 0.57x105 cells/cm2 in William’s E medium supplemented with 10%v/v fetal bovine serum, 292mg/ml L-glutamine, 7ng/ml glucagon and antibiotics (7.33IU/ml benzylpenicillin sodium, 50µg/ml kanamycin monosulphate, 50µg/ml streptomycin sulphate, and 10µg/ml ampicillin sodium) in an incubator at 37°C (5% CO2 and 95% air, 100% humidity). After 4 hours, the medium was renewed with serum-free culture medium, supplemented with 25µg/ml hydrocortisone hemisuccinate and 1mg/ml bovine insulin.

extract_protocol: Samples for RNA isolation were collected after 24 hours and 72 hours of exposure. Three independent biological experiments were conducted for each compound. The total RNA extraction (RNA extraction kit, Qiagen), including a DNase digestion step, was done according to the manufacturer’s instructions.

treatment_protocol: At 18-20 hours post-plating, exposure to 2-Nitrofluorene  (78 µM), Aflatoxin B (19 nM), Clonidine hydrochloride (277 µM), Methapyrilene hydrichloride (8.5 µM), Nifedipine (156 µM), 4(methylnitrosamino)-1-(3-pyridyl)-1 –butanone (625 µM), Piperonyl butoxide (13.4 µM), Wy-14,643 (250 µM) was initiated.

value: primary hepatocytes

tag: exposure time

tag: replicate


title: C(MPH)_72h_D6_3

description: Control for MPH 72h

source_name: Control for MPH 72h


title: C(MPH)_72h_D5_2

description: Control for MPH 72h


title: C(NNK)_72h_D9_3

description: Control for NNK 72h

source_name: Control for NNK 72h


title: NNK_72h_D9_3

description: Treatment with NNK 72h

source_name: Treatment with NNK 72h


title: C(MPH)_72h_D4_1

description: Control for MPH 72h


title: GFP-LKP2ox

city: Tokyo

first: Yuji

last: Miyazaki

address: 1-5-1, mejiro, Toshima-ku

department: Graduate School of Science

institute: Gakushuin University

description: Gene expression data from p35S:GFP-LKP2-overexpressing leaves

hyb_protocol: The hybridization procedure was performed according to the Agilent 60-mer oligo microarray processing protocol using the Agilent Gene Expression Hybridization Kit (Agilent Technologies). 1.65 μg Cy3-labeled fragmented cRNA in hybridization buffer was hybridized overnight (17 hours, 65 °C) to Agilent Whole Arabidopsis Genome Oligo Microarrays 4x44K V4 (G2519F) using Agilent’s recommended hybridization chamber and oven. After hybridization, microarrays were washed once with the Agilent Gene Expression Wash Buffer 1 for 1 min at room temperature followed by a second wash with preheated Agilent Gene Expression Wash Buffer 2 (37 °C) for 1 min. The last washing step was performed with acetonitrile.

scan_protocol: Fluorescence signals of the hybridized Agilent Microarrays were detected using Agilent’s Microarray Scanner System (Agilent Technologies).

data_processing: The scanned images were analyzed with Feature Extraction Software (Agilent Technologies).

label_protocol: Cy3-labeled cRNA was prepared from 100 ng of each total RNA using the Quick Amp Labeling kit (Agilent Technologies) according to the manufacturer's instructions. Dye incorporation and cRNA yield were checked with the ND-1000 Spectrophotometer (NanoDrop Technologies).

growth_protocol: Plants were grown in soil under long-day (16-h light/8-h dark) conditions at 22°C under white light (90–100 μmol m-2 sec-1).

extract_protocol: Total RNA was prepared using the RNeasy Plant mini kit (QIAGEN) following the manufacturer's instruction.

treatment_protocol: Thirty-two-day-old plants were used for analysis. Rosette leaves were harvested from transgenic Arabidopsis plants at ZT0.

tag: ecotype

tag: treatment

tag: expression

value: leaf


title: MPH_72h_D6_3

description: Treatment with MPH 72h


title: MPH_72h_D4_1

description: Treatment with MPH 72h


title: PIPB_72h_D8_2

description: Treatment with PIPB 72h

source_name: Treatment with PIPB 72h


title: NIF_72h_D8_2

description: Treatment with NIF 72h

source_name: Treatment with NIF 72h


title: PIPB_72h_D9_3

description: Treatment with PIPB 72h


title: NIF_72h_D7_1

description: Treatment with NIF 72h


title: 2NF_72h_D7_1

description: Treatment with 2NF 72h

source_name: Treatment with 2NF 72h


title: C(NNK)_72h_D7_1

description: Control for NNK 72h


title: 2NF_72h_D9_3

description: Treatment with 2NF 72h


title: NIF_72h_D9_3

description: Treatment with NIF 72h


title: NNK_72h_D7_1

description: Treatment with NNK 72h


title: NNK_72h_D8_2

description: Treatment with NNK 72h


title: PC12Control1

description:
KNRatPC12Cont1
Cell culture.
Gene expression after 6hr incubation.


title: C(2NF_PIPB_NIF)_72h_D9_3

description: Control for 2NF, PIPB and NIF 72h

source_name: Control for 2NF, PIPB and NIF 72h


title: GFPox

description: Gene expression data from p35S:GFP-overexpressing leaves

source_name: GFPox

tag: tissue


title: 2NF_72h_D8_2

description: Treatment with 2NF 72h


title: C(2NF_PIPB_NIF)_72h_D8_2

description: Control for 2NF, PIPB and NIF 72h


title: PIPB_72h_D7_1

description: Treatment with PIPB 72h


title: C(2NF_PIPB_NIF)_72h_D7_1

description: Control for 2NF, PIPB and NIF 72h


title: AFB_72h_D2_2

description: Treatment with AFB 72h

source_name: Treatment with AFB 72h


title: AFB_72h_D3_3

description: Treatment with AFB 72h


title: C(NNK)_72h_D8_2

description: Control for NNK 72h


title: CND_72h_D3_3

description: Treatment with CND 72h

source_name: Treatment with CND 72h


title: CND_72h_D2_2

description: Treatment with CND 72h


title: CND_72h_D1_1

description: Treatment with CND 72h


title: WYE_72h_D3_3

description: Treatment with WYE 72h

source_name: Treatment with WYE 72h


title: C(WYE_CND_AFB)_72h_D2_2

description: Control for WYE, CND and AFB 72h

source_name: Control for WYE, CND and AFB 72h


title: C(WYE_CND_AFB)_72h_D1_1

description: Control for WYE, CND and AFB 72h