title: HL-1-mock_rep 2

first: Ellen

last: Leich

department: Institute of Pathology

hyb_protocol: Affymetrix Hybridization Protocol : Following fragmentation, 20 micrograms of cRNA were hybridized for 16 hours at 45C on U133 plus 2.0 GeneChips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Affymetrix Scanning Protocol : Scanning was performed by the Affymetrix 3000 Scanner.

data_processing: MAS 5.0 Data Processing Protocol Calculation Method: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

source_name: mock-transfected HL-1 cells

label_protocol: Affymetrix Labeling Protocol : Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 microg mRNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: HL-1 cells were cultured at 37°C and 5% CO2 in Claycomb medium (Sigma) supplemented with 100μM norepinephrine, 4mM L-glutamine and 10% FCS.

extract_protocol: Total RNA from two CD56-140kD-transfected samples and 2 mock-transfected samples was extracted from HL-1 cells with TriPure isolation reagent (Roche, Mannheim, Germany).

treatment_protocol: Adherent HL-1 cells in 30mm dishes were transfected with 4-5µg plasmids bearing CD56-isoform cDNAs using FuGENE (Roche) according to the manufacturer’s instructions and incubated for 18 hours at 37°C and 5% CO2.

tag: cell line

value: mock-transfected

value: murine cardiomyocyte


title: ttha0198-1-sta

status: Public on Dec 01 2014

type: RNA

city: Toyonaka

first: Hiromasa

last: Ohyama

address: Machikaneyamachou 1-1

country: Japan

institute: Osaka University

hyb_protocol: 2 μg of 3’-terminal-labeled cDNA was hybridized to a TTHB8401a520105F GeneChip (Affymetrix). The array was incubated for 16 h at 50°C in a solution comprising 180 mM MES, pH 6.6, 40 mM EDTA, 0.02% Tween 20, 7% dimethyl sulfoxide, 1 mg of herring sperm DNA (Promega), 0.5 mg of bovine serum albumin, the recommended amount of Eukaryotic Hybridization Control (Affymetrix), and Control Oligo B2 for the alignment signal (Affymetrix).  Then the array was automatically washed and stained with streptavidin, biotin anti-streptavidin, and streptavidin-phycoerythrin (Invitrogen) by using a GeneChip Fluidics Station, 450XP (Affymetrix).

scan_protocol: The Probe Array was scanned with a GeneChip Scanner 3000 (Affymetrix).

data_processing: The image data was scaled to the target intensity by one-step Tukey’s biweight algorithm using GeneChip Operating software, version 1.4 (Affymetrix). Scaled probe value was calculated as Sc = 500 according to Statistical Algorithms Description Document (Affymetrix).

label: biotin

molecule: total RNA

organism: Thermus thermophilus HB8

source_name: the sample of ttha0198 gene disruptant during the stationary phase

label_protocol: 10 μg of total RNA was mixed with 750 ng of random primers (Invitrogen), incubated at 70°C for 10 min, and 25°C for 10 min.  The RNA/primer solution was reacted with SuperScript II reverse transcriptase (Invitrogen) to synthesize cDNA.  The reaction was performed in the presence of RNase inhibitor SUPERase (Ambion) and 6 base random primers (Invitrogen).  The synthesized DNA was purified by ethanol precipitation, and 3 μg of cDNA was fragmented with 35 units of DNase I (GE Healthcare) at 37°C for 10 min.  The reaction was stopped by incubation of the reaction solution at 98°C for 10 min.  3 μg of fragmented cDNA was labeled with GeneChip DNA Labeling Reagent (Affymetrix), using terminal transferase according to the manufacturer’s instructions (Affymetrix).  Gel-shift assay using NeutrAvidin (Invitrogen) as a probe confirmed that the majority of cDNA was successfully labeled with biotin.

growth_protocol: The T. thermophilus HB8 wild-type strain and disruptants were cultured in TT medium at 70°C until the cells reached to OD600 of 0.8 or to stationary phase.

extract_protocol: Collected cells were mixed with 1.4 ml of 5 mM Tris-HCl (pH 7.5) containing 5 mM EDTA, 0.25% SDS, and 50% of water-saturated phenol to the cell pellet. This mixture was incubated at 65°C for 5 min, chilled on ice for 5 min, and then centrifuged at 4°C.  Aqueous phase (0.2 ml) was collected and mixed with 0.75 ml of TRIZOL LS (Invitrogen, Carlsbad, CA), and incubated at room temperature for 5 min.  Then, 0.2 ml of chloroform was added, and the mixture was vortexed for 10 sec.  After centrifugation, aqueous phase was collected, mixed with 0.5 ml of chloroform, and vortexed for 10 min.   The aqueous phase was collected and mixed with 0.5 ml of isopropanol to precipitate RNA.  After incubation at -20°C for 60 min and centrifugation, aqueous phase was removed.  The pellet was dissolved in 0.2 ml of nuclease-free water, and further purified through the ethanol precipitation, and then resuspended in 0.2 ml of water.  The obtained RNA solution was treated with DNase I (Ambion, Austin, TX) at 37°C for 20 min in a 25 μl reaction mixture. The reaction was terminated by the addition of 1 μl of 0.5 M EDTA, followed by incubation at 70°C for 5 min.  Thereafter, the RNA was precipitated with ethanol in the presence of 1% glycogen and 1 M NH4OAc.

treatment_protocol: In the case of TTHA0137, TTHA0540 and TTHA1817, an equal volume of hot medium was added to the culture.  In the other disruptants, cultures were added to an equal volume of 100% ethanol and stored at -80°C.

tag: genotype

tag: growth phase

value: stationary


title: liver_female wt_rep1

city: Ann Arbor

first: Malcolm

last: Low

state: MI

address: 1000 Wall Street

country: USA

institute: University of Michigan

hyb_protocol: Following fragmentation, 16 ug of aRNA were hybridized for 16 hr at 45C on GeneChip Mouse 430 2.0 Arrays. 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 affy bioconductor package implemented in the R-statistical environment version 2.12.2. RMA was used to normalize the data and fit log2 transformed expression values.

organism: Mus musculus

source_name: liver

label_protocol: Biotinylated aRNA were prepared according to the Affymetrix GeneChip 3’ IVT Express kit protocol from 250 ng total RNA (Affymetrix GeneChip 3’ IVT Express kit Instruction Manual, P/N 702646 Rev. 5).

growth_protocol: Mice were housed in a temperature-controlled environment with a 12:12 hour light:dark cycle and free access to food and water. At 16 weeks of age, mice were euthanized and liver tissue was collected and stored at -80.

extract_protocol: RNA was extracted using the Trizol reagent (Invitrogen) from 100 mg of liver tissue according to the manufacturer's instructions. Quality of RNA was checked with the Agilent 2100 BioAnalyzer.

tag: Sex

value: female

value: sst +/+

tag: tissue

value: liver

tag: genetic background


title: ttha1046-2-sta

description: cultures were added to an equal volume of 100% ethanol and stored at -80°C.

source_name: the sample of ttha1046 gene disruptant during the stationary phase


title: HL-1-mock_rep 1

city: Wuerzburg

country: Germany

institute: University of Wuerzburg

tag: genotype/variation

tag: cell type


title: ttha1046-1-sta


title: ttha0252-1-log

source_name: the sample of ttha0252 gene disruptant during the log phase

value: log


title: ttha0198-2-log

source_name: the sample of ttha0198 gene disruptant during the log phase


title: ttha0198-3-log


title: HL-1-CD56-140kd_rep 2

source_name: CD56(140kD)-transfected HL-1 cells


title: HL-1-CD56-140kd_rep 1


title: ttha0252-2-log


title: ttha0198-3-sta


title: ttha0137-3-sta

source_name: the sample of ttha0137 gene disruptant during the stationary phase


title: KO mice Islet sample No.2

city: Salamanca

first: Alberto

last: Fernández-Medarde

state: Salamanca

address: Campus Miguel de Unamuno

country: Spain

institute: Instituto de Biología Molecular y Celular del Cáncer-IBMCC

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: The RMA function provided by the package Affy from R/Bioconductor was applied to the raw expression data.

source_name: RasGrf1 Islets 2

label_protocol: standard Affymetrix protocol

growth_protocol: Animals of the same sex were housed in type IIL individually ventilated cages, in a temperature- and humidity-controlled room with a 12h light/dark cycle, with food (Teklad 2014, Harlan Laboratories) and water available ad libitum.  All testing was completed during the light phase.

extract_protocol: Manually selected pancreatic islets from collagenase-P digests of WT and RasGrf1 KO mice pancreases were used for RNA extraction using the TRIZOL protocol. Trizol extraction of total RNA was performed according to the manufacturer's instructions. Further RNA purification was performed usin Rneasy mini kit from Qiagen.

value: pancreatic islets

value: RasGrf1 KO


title: ttha0198-2-sta


title: ttha0137-2-sta


title: ttha0198-1-log


title: ttha0137-3-log

description: An equal volume of hot medium was added to the culture, when the culture was harvested.

source_name: the sample of ttha0137 gene disruptant during the log phase


title: WT mice Islet sample No.3

source_name: Control Islets 3

value: wild type


title: ttha0137-2-log


title: ttha0137-1-sta


title: WT mice Islet sample No.2

source_name: Control Islets 2


title: KO mice Islet sample No.3

source_name: RasGrf1 Islets 3


title: wild-type-oyama-3

source_name: the control sample at log phase of other gene disruptants

value: wildtype


title: wild-type-sta-2

source_name: the control sample at stationary phase of all gene disruptants


title: wild-type-sta-3


title: ttha0137-1-log


title: wild-type-oyama-2


title: wild-type-oyama-1


title: wild-type-dilution-3

source_name: the control sample at log phase of ttha0137, ttha0540 and ttha1817 disruptants


title: wild-type-sta-1


title: WT mice Islet sample No.1

source_name: Control Islets 1


title: wild-type-dilution-1


title: wild-type-dilution-2


title: R.5386.shp53.4hr.2

city: 3601 Spruce Street

first: Yan

last: Zhou

state: PA

address: 333 Cottman Ave

department: Bioinformatics

institute: Fox Chase Cancer Center

description: Gene expression of GM05386,R72, shp53

hyb_protocol: 1.65 ug of Cy-3 labeled cRNA targets is hybridized onto Agilent 4x44k whole genome arrays for 17 hours at 65º C and washed according to Agilent procedure.

scan_protocol: The hybridized slides are scanned at 5µm resolution on Agilent scanner (Agilent)  G2505B.

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.3 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

organism: Homo sapiens

source_name: GM05386,R72,shp53,4hr, 5 Gy, replicate 2

label_protocol: 500 ng total RNA was amplified and labeled using Agilent QuickAmp labeling kit following the manufacturer protocol.

growth_protocol: Cells grown in DMEM plus 10% fetal bovine serum and antibiotics

extract_protocol: Total RNA was isolated from purified mouse thymocytes using TRIzol reagent (Invitrogen, Carlsbad, CA) and further purified by the RNeasy kit (Qiagen, Valencia, CA) according to manufacturer’s instructions.

treatment_protocol: Untreated or gamma irradiated, 5 Gray

value: Normal Human Fibroblast

tag: time

tag: treatment

value: 5 Gy


title: R.5386.shp53.2hr.3

description: Gene expression of GM05386,R72, shp53

source_name: GM05386,R72,shp53,2hr, 5 Gy, replicate 3


title: KO mice Islet sample No.1

source_name: RasGrf1 Islets 1


title: R.5386.shp53.4hr.1

description: Gene expression of GM05386,R72, shp53

source_name: GM05386,R72,shp53,4hr, 5 Gy, replicate 1


title: R.5386.shp53.2hr.1

description: Gene expression of GM05386,R72, shp53

source_name: GM05386,R72,shp53,2hr, 5 Gy, replicate 1


title: R.5386.shp53.UT.3

description: Gene expression of GM05386, R72, shp53

source_name: GM05386,R72,shp53,0hr, untreated, replicate 3

value: untreated


title: R.5386.shp53.2hr.2

description: Gene expression of GM05386,R72, shp53

source_name: GM05386,R72,shp53,2hr, 5 Gy, replicate 2


title: R.5386.shp53.UT.1

description: Gene expression of GM05386, R72, shp53

source_name: GM05386,R72,shp53,0hr, untreated, replicate 1


title: Prostate_Tumor_HSPH0089

city: Boston

first: Kathryn

last: Penney

address: 181 Longwood Ave

department: Medicine

institute: Brigham and Women's Hospital

hyb_protocol: Not provided

scan_protocol: Not provided

data_processing: For the expression profiles generated, we regressed out technical variables including mRNA concentration, age of the block, batch (96-well plate), percent of the probes on the array detectable above the background, log transformed average background signal, and the median of the perfect match probes for each probe intensity of the raw data. The residuals were then shifted to have the original mean expression values and normalized using the RMA method. We mapped gene names to Affymetrix transcript cluster IDs using the NetAffx annotations as implemented in Bioconductor annotation package pd.hugene.1.0.st.v1; this resulted in 20,254 unique named genes.  As gene names were used in the final analysis, this is what we have included in the sample tables.

source_name: FFPE prostate tumor

label_protocol: Not provided

extract_protocol: Not provided


title: R.5386.shp53.4hr.3

description: Gene expression of GM05386,R72, shp53

source_name: GM05386,R72,shp53,4hr, 5 Gy, replicate 3


title: R.6555.4hr.3

description: Gene expression of GM06555,R72

source_name: GM06555,R72,4hr, 5 Gy, replicate 3


title: R.6555.2hr.1

description: Gene expression of GM06555,R72

source_name: GM06555,R72,2hr, 5 Gy, replicate 1


title: R.6555.4hr.2

description: Gene expression of GM06555,R72

source_name: GM06555,R72,4hr, 5 Gy, replicate 2


title: R.6555.2hr.2

description: Gene expression of GM06555,R72

source_name: GM06555,R72,2hr, 5 Gy, replicate 2


title: R.6555.UT.1

description: Gene expression of GM06555, R72

source_name: GM06555,R72,0hr, untreated, replicate 1


title: R.6555.4hr.1

description: Gene expression of GM06555,R72

source_name: GM06555,R72,4hr, 5 Gy, replicate 1


title: R.6555.UT.2

description: Gene expression of GM06555, R72

source_name: GM06555,R72,0hr, untreated, replicate 2


title: R.6555.2hr.3

description: Gene expression of GM06555,R72

source_name: GM06555,R72,2hr, 5 Gy, replicate 3


title: R.5386.shp53.UT.2

description: Gene expression of GM05386, R72, shp53

source_name: GM05386,R72,shp53,0hr, untreated, replicate 2


title: R.5386.4hr.2

description: Gene expression of GM05386,R72

source_name: GM05386,R72,4hr, 5 Gy, replicate 2


title: HDFa fibroblast_2 µM indomethacin_48h_rep3

city: Gdańsk

first: Magdalena

last: Gabig-Cimińska

address: Wita Stwosza 59

department: of Medical Biology and Genetics

country: Poland

institute: University of Gdańsk

description:
48h2IndoHDFa_3
replicate 3

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized using quantile normalization with Illumina GenomeStudio software package  (gene expression module version 1.9.0).

source_name: fibroblasts

label_protocol: Biotinylated cRNA was prepared with the Ambion TotalPrepAmp Kit for Illumina arrays

growth_protocol: Fibroblasts were cultured from cryo-preserved cells in Dulbecco’s modified Eagle’s medium containing 10% fetal bovine serum and 1% antibiotic/antimycotic solution at 37 oC in a humidified atmosphere of 5% CO2. 10E5 cells were seeded in 6-well plates and grown to a confluence of approximately 80 %.

extract_protocol: Total RNA was extracted from cells using the High Pure RNA Isolation Kit in accordance with the prescribed protocol, quantified with Quant iT RiboGreen Assay Kit

treatment_protocol: The medium was replaced by fresh medium non-supplemented, containing dimethyl sulfooxide (DMSO) added to a final concentration of 0.05%, or to 2 or 10 µM indomethacin, 5 or 25 µM nimesulide, with 0.05% DMSO. The experimental treatment was carried out for 1h, 24 h and 48 h period.

value: HDFa


title: R.5386.4hr.3

description: Gene expression of GM05386,R72

source_name: GM05386,R72,4hr, 5 Gy, replicate 3


title: R.6555.UT.3

description: Gene expression of GM06555, R72

source_name: GM06555,R72,0hr, untreated, replicate 3


title: R.5386.4hr.1

description: Gene expression of GM05386,R72

source_name: GM05386,R72,4hr, 5 Gy, replicate 1


title: Prostate_Tumor_HSPH0090


title: HDFa fibroblast_K_0.05%DMSO_48h_rep3

description:
48hKHDFa_3
replicate 3


title: HDFa fibroblast_25 µM nimesulide_24h_rep3

description:
24h25NimHDFa_3
replicate 3


title: MPSII fibroblast_K_0.05%DMSO_24h_rep3

description:
24hKMPSII_3
replicate 3

value: MPS II


title: HDFa fibroblast_10 µM indomethacin_48h_rep3

description:
48h10IndoHDFa_3
replicate 3


title: HDFa fibroblast_5 µM nimesulide_48h_rep3

description:
48h5NimHDFa_3
replicate 3


title: R.5386.2hr.3

description: Gene expression of GM05386,R72

source_name: GM05386,R72,2hr, 5 Gy, replicate 3


title: HDFa fibroblast_5 µM nimesulide_24h_rep3

description:
24h5NimHDFa_3
replicate 3


title: MPSII fibroblast_25 µM nimesulide_24h_rep3

description:
24h25NimMPSII_3
replicate 3


title: HDFa fibroblast_K_0.05%DMSO_24h_rep3

description:
24hKHDFa_3
replicate 3


title: HDFa fibroblast_10 µM indomethacin_24h_rep3

description:
24h10IndoHDFa_3
replicate 3


title: HDFa fibroblast_K_0.05%DMSO_48h_rep2

description:
48hKHDFa_2
replicate 2


title: HDFa fibroblast_25 µM nimesulide_48h_rep3

description:
48h25NimHDFa_3
replicate 3


title: R.5386.2hr.2

description: Gene expression of GM05386,R72

source_name: GM05386,R72,2hr, 5 Gy, replicate 2


title: HDFa fibroblast_2 µM indomethacin_24h_rep3

description:
24h2IndoHDFa_3
replicate 3


title: HDFa fibroblast_25 µM nimesulide_48h_rep2

description:
48h25NimHDFa_2
replicate 2


title: R.5386.UT.3

description: Gene expression of GM05386, R72

source_name: GM05386,R72,0hr, untreated, replicate 3


title: R.5386.2hr.1

description: Gene expression of GM05386,R72

source_name: GM05386,R72,2hr, 5 Gy, replicate 1


title: HDFa fibroblast_2 µM indomethacin_48h_rep2

description:
48h2IndoHDFa_2
replicate 2


title: HDFa fibroblast_5 µM nimesulide_48h_rep2

description:
48h5NimHDFa_2
replicate 2


title: MPSII fibroblast_25 µM nimesulide_24h_rep2

description:
24h25NimMPSII_2
replicate 2


title: R.5386.UT.2

description: Gene expression of GM05386, R72

source_name: GM05386,R72,0hr, untreated, replicate 2


title: HDFa fibroblast_5 µM nimesulide_24h_rep2

description:
24h5NimHDFa_2
replicate 2


title: R.5386.UT.1

description: Gene expression of GM05386, R72

source_name: GM05386,R72,0hr, untreated, replicate 1


title: MPSII fibroblast_K_0.05%DMSO_24h_rep2

description:
24hKMPSII_2
replicate 2


title: HDFa fibroblast_10 µM indomethacin_24h_rep2

description:
24h10IndoHDFa_2
replicate 2


title: HDFa fibroblast_10 µM indomethacin_48h_rep2

description:
48h10IndoHDFa_2
replicate 2


title: P.6113.shp53.4hr.2

description: Gene expression of GM06113,P72, shp53

source_name: GM06113,P72,shp53,4hr, 5 Gy, replicate 2


title: P.6113.shp53.4hr.3

description: Gene expression of GM06113,P72, shp53

source_name: GM06113,P72,shp53,4hr, 5 Gy, replicate 3


title: HDFa fibroblast_25 µM nimesulide_24h_rep2

description:
24h25NimHDFa_2
replicate 2


title: HDFa fibroblast_2 µM indomethacin_24h_rep2

description:
24h2IndoHDFa_2
replicate 2


title: P.6113.shp53.2hr.3

description: Gene expression of GM06113,P72, shp53

source_name: GM06113,P72,shp53,2hr, 5 Gy, replicate 3


title: HDFa fibroblast_25 µM nimesulide_48h_rep1

description:
48h25NimHDFa_1
replicate 1


title: P.6113.shp53.4hr.1

description: Gene expression of GM06113,P72, shp53

source_name: GM06113,P72,shp53,4hr, 5 Gy, replicate 1


title: MPSII fibroblast_25 µM nimesulide_24h_rep1

description:
24h25NimMPSII_1
replicate 1


title: HDFa fibroblast_5 µM nimesulide_48h_rep1

description:
48h5NimHDFa_1
replicate 1


title: P.6113.shp53.2hr.2

description: Gene expression of GM06113,P72, shp53

source_name: GM06113,P72,shp53,2hr, 5 Gy, replicate 2


title: HDFa fibroblast_K_0.05%DMSO_48h_rep1

description:
48hKHDFa_1
replicate 1


title: HDFa fibroblast_K_0.05%DMSO_24h_rep2

description:
24hKHDFa_2
replicate 2


title: HDFa fibroblast_2 µM indomethacin_48h_rep1

description:
48h2IndoHDFa_1
replicate 1


title: MPSII fibroblast_K_0.05%DMSO_24h_rep1

description:
24hKMPSII_1
replicate 1


title: HDFa fibroblast_25 µM nimesulide_24h_rep1

description:
24h25NimHDFa_1
replicate 1


title: HDFa fibroblast_K_0.05%DMSO_24h_rep1

description:
24hKHDFa_1
replicate 1


title: P.6113.shp53.2hr.1

description: Gene expression of GM06113,P72, shp53

source_name: GM06113,P72,shp53,2hr, 5 Gy, replicate 1


title: HDFa fibroblast_10 µM indomethacin_48h_rep1

description:
48h10IndoHDFa_1
replicate 1


title: HDFa fibroblast_10 µM indomethacin_24h_rep1

description:
24h10IndoHDFa_1
replicate 1


title: P.6113.shp53.UT.2

description: Gene expression of GM06113, P72, shp53

source_name: GM06113,P72,shp53,0hr, untreated, replicate 2


title: HDFa fibroblast_5 µM nimesulide_24h_rep1

description:
24h5NimHDFa_1
replicate 1

source_name: fibroblasts


title: HDFa fibroblast_2 µM indomethacin_24h_rep1

description:
24h2IndoHDFa_1
replicate 1


title: P.6113.shp53.UT.1

description: Gene expression of GM06113, P72, shp53

source_name: GM06113,P72,shp53,0hr, untreated, replicate 1


title: P.6113.2hr.3

description: Gene expression of GM06113,P72

source_name: GM06113,P72,2hr, 5 Gy, replicate 3


title: RPMI 2650 cells exposed to low concentration welding fume 6h with 4h post-exposure incubation replicate 3

city: Iowa City

first: Aditya

last: Stanam

state: Iowa

address: 500 Newton Road

department: Pathology

institute: University of Iowa

description:
ATCC #CCL-30 RPMI 2650 nasal septal squamous cell carcinoma cells/monolayer ~8 x 10^6 exposed to low concentration welding fumes 6h followed by 4 hour post-exposure incubation sample 3
Sample name: 21_low 6-4h-3
Biological replicate 3
Samples 01-12 were hybridized together on one chip, and samples 13-24 were hybridized together on a different chip.

hyb_protocol: Standard Illumina Hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: The data was quantile normalized in GenomeStudio.

source_name: RPMI 2650 cells exposed to low concentration of welding fume for 6h with 4h post-exposure incubation

label_protocol: Biotinylated cRNA were prepared with the Ambion TotalPrep RNA Amplification Kit for Illumina arrays.

growth_protocol: RPMI 2650 cells were cultured in modified Eagle's medium supplemented with 10% fetal bovine serum (Hyclone, Logan, UT), pencillin 100 U/mL (Gibco), and streptomycin 100 µg/mL (Gibco).

extract_protocol: RNA was extracted using RNeasy® Plus Mini Kit (Qiagen) in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: RPMI 2650 cell monolayers were either unexposed (incubator-resting) or exposed to particle-free clean air or welding fumes at two different concentrations (85 µg/m3 - low; 760 µg/m3 - high) for 6h and subjected to post-exposure incubation for zero hours (or) four hours before isolating RNA.

value: ATCC #CCL-30 RPMI 2650

value: nasal septal squamous cell carcinoma cell line


title: P.6113.shp53.UT.3

description: Gene expression of GM06113, P72, shp53

source_name: GM06113,P72,shp53,0hr, untreated, replicate 3


title: RPMI 2650 cells exposed to high concentration welding fume 6h with 4h post-exposure incubation replicate 2

description:
ATCC #CCL-30 RPMI 2650 nasal septal squamous cell carcinoma cells/monolayer ~8 x 10^6 exposed to high concentration welding fumes 6h followed by 4 hour post-exposure incubation sample 2
Sample name: 23_high 6-4h-2
Biological replicate 2
Samples 01-12 were hybridized together on one chip, and samples 13-24 were hybridized together on a different chip.

source_name: RPMI 2650 cells exposed to high concentration of welding fume for 6h with 4h post-exposure incubation


title: RPMI 2650 cells exposed to high concentration welding fume 6h with 4h post-exposure incubation replicate 3

description:
ATCC #CCL-30 RPMI 2650 nasal septal squamous cell carcinoma cells/monolayer ~8 x 10^6 exposed to high concentration welding fumes 6h followed by 4 hour post-exposure incubation sample 3
Sample name: 24_high 6-4h-3
Biological replicate 3
Samples 01-12 were hybridized together on one chip, and samples 13-24 were hybridized together on a different chip.


title: RPMI 2650 cells exposed to particle-free clean air 6h with 4h post-exposure incubation replicate 3

description:
ATCC #CCL-30 RPMI 2650 nasal septal squamous cell carcinoma cells/monolayer ~8 x 10^6 exposed to clean air 6h followed by 4 hour post-exposure incubation sample 3
Sample name: 18_clean 6-4h-3
Biological replicate 3
Samples 01-12 were hybridized together on one chip, and samples 13-24 were hybridized together on a different chip.

source_name: RPMI 2650 cells exposed to particle-free clean air for 6h with 4h post-exposure incubation


title: P.6113.2hr.1

description: Gene expression of GM06113,P72

source_name: GM06113,P72,2hr, 5 Gy, replicate 1


title: P.6113.4hr.2

description: Gene expression of GM06113,P72

source_name: GM06113,P72,4hr, 5 Gy, replicate 2


title: RPMI 2650 cells exposed to low concentration welding fume 6h with 4h post-exposure incubation replicate 2

description:
ATCC #CCL-30 RPMI 2650 nasal septal squamous cell carcinoma cells/monolayer ~8 x 10^6 exposed to low concentration welding fumes 6h followed by 4 hour post-exposure incubation sample 2
Sample name: 20_low 6-4h-2
Biological replicate 2
Samples 01-12 were hybridized together on one chip, and samples 13-24 were hybridized together on a different chip.


title: RPMI 2650 cells exposed to high concentration welding fume 6h replicate 3

description:
ATCC #CCL-30 RPMI 2650 nasal septal squamous cell carcinoma cells/monolayer ~8 x 10^6 exposed to high concentration welding fumes 6h sample 3
Sample name: 12_high 6h-3
Biological replicate 3
Samples 01-12 were hybridized together on one chip, and samples 13-24 were hybridized together on a different chip.

source_name: RPMI 2650 cells exposed to high concentration of welding fume for 6h with 0h post-exposure incubation


title: P.6113.2hr.2

description: Gene expression of GM06113,P72

source_name: GM06113,P72,2hr, 5 Gy, replicate 2


title: RPMI 2650 cells unexposed-replicate 5

description:
ATCC #CCL-30 RPMI 2650 nasal septal squamous cell carcinoma cells/monolayer ~8 x 10^6 sample 5
Sample name: 14_incubator control-2
Biological replicate 5
Samples 01-12 were hybridized together on one chip, and samples 13-24 were hybridized together on a different chip.

source_name: Unexposed (i.e., incubator-resting) RPMI 2650 cells

value: unexposed


title: P.6113.4hr.3

description: Gene expression of GM06113,P72

source_name: GM06113,P72,4hr, 5 Gy, replicate 3


title: RPMI 2650 cells unexposed-replicate 4

description:
ATCC #CCL-30 RPMI 2650 nasal septal squamous cell carcinoma cells/monolayer ~8 x 10^6 sample 4
Sample name: 13_incubator control-1
Biological replicate 4
Samples 01-12 were hybridized together on one chip, and samples 13-24 were hybridized together on a different chip.


title: RPMI 2650 cells exposed to low concentration welding fume 6h with 4h post-exposure incubation replicate 1

description:
ATCC #CCL-30 RPMI 2650 nasal septal squamous cell carcinoma cells/monolayer ~8 x 10^6 exposed to low concentration welding fumes 6h followed by 4 hour post-exposure incubation sample 1
Sample name: 19_low 6-4h-1
Biological replicate 1
Samples 01-12 were hybridized together on one chip, and samples 13-24 were hybridized together on a different chip.


title: RPMI 2650 cells exposed to particle-free clean air 6h with 4h post-exposure incubation replicate 2

description:
ATCC #CCL-30 RPMI 2650 nasal septal squamous cell carcinoma cells/monolayer ~8 x 10^6 exposed to clean air 6h followed by 4 hour post-exposure incubation sample 2
Sample name: 17_clean 6-4h-2
Biological replicate 2
Samples 01-12 were hybridized together on one chip, and samples 13-24 were hybridized together on a different chip.


title: RPMI 2650 cells exposed to high concentration welding fume 6h with 4h post-exposure incubation replicate 1

description:
ATCC #CCL-30 RPMI 2650 nasal septal squamous cell carcinoma cells/monolayer ~8 x 10^6 exposed to high concentration welding fumes 6h followed by 4 hour post-exposure incubation sample 1
Sample name: 22_high 6-4h-1
Biological replicate 1
Samples 01-12 were hybridized together on one chip, and samples 13-24 were hybridized together on a different chip.


title: P.6113.UT.3

description: Gene expression of GM06113, P72

source_name: GM06113,P72,0hr, untreated, replicate 3


title: RPMI 2650 cells exposed to particle-free clean air 6h with 4h post-exposure incubation replicate 1

description:
ATCC #CCL-30 RPMI 2650 nasal septal squamous cell carcinoma cells/monolayer ~8 x 10^6 exposed to clean air 6h followed by 4 hour post-exposure incubation sample 1
Sample name: 16_clean 6-4h-1
Biological replicate 1
Samples 01-12 were hybridized together on one chip, and samples 13-24 were hybridized together on a different chip.


title: RPMI 2650 cells exposed to low concentration welding fume 6h replicate 1

description:
ATCC #CCL-30 RPMI 2650 nasal septal squamous cell carcinoma cells/monolayer ~8 x 10^6 exposed to low concentration welding fumes 6h sample 1
Sample name: 07_low 6h-1
Biological replicate 1
Samples 01-12 were hybridized together on one chip, and samples 13-24 were hybridized together on a different chip.

source_name: RPMI 2650 cells exposed to low concentration of welding fume for 6h with 0h post-exposure incubation


title: P.6113.4hr.1

description: Gene expression of GM06113,P72

source_name: GM06113,P72,4hr, 5 Gy, replicate 1


title: RPMI 2650 cells unexposed-replicate 6

description:
ATCC #CCL-30 RPMI 2650 nasal septal squamous cell carcinoma cells/monolayer ~8 x 10^6 sample 6
Sample name: 15_incubator control-3
Biological replicate 6
Samples 01-12 were hybridized together on one chip, and samples 13-24 were hybridized together on a different chip.


title: RPMI 2650 cells exposed to high concentration welding fume 6h replicate 1

description:
ATCC #CCL-30 RPMI 2650 nasal septal squamous cell carcinoma cells/monolayer ~8 x 10^6 exposed to high concentration welding fumes 6h sample 1
Sample name: 10_high 6h-1
Biological replicate 1
Samples 01-12 were hybridized together on one chip, and samples 13-24 were hybridized together on a different chip.


title: RPMI 2650 cells exposed to low concentration welding fume 6h replicate 3

description:
ATCC #CCL-30 RPMI 2650 nasal septal squamous cell carcinoma cells/monolayer ~8 x 10^6 exposed to low concentration welding fumes 6h sample 3
Sample name: 09_low 6h-3
Biological replicate 3
Samples 01-12 were hybridized together on one chip, and samples 13-24 were hybridized together on a different chip.


title: RPMI 2650 cells exposed to high concentration welding fume 6h replicate 2

description:
ATCC #CCL-30 RPMI 2650 nasal septal squamous cell carcinoma cells/monolayer ~8 x 10^6 exposed to high concentration welding fumes 6h sample 2
Sample name: 11_high 6h-2
Biological replicate 2
Samples 01-12 were hybridized together on one chip, and samples 13-24 were hybridized together on a different chip.


title: RPMI 2650 cells exposed to low concentration welding fume 6h replicate 2

description:
ATCC #CCL-30 RPMI 2650 nasal septal squamous cell carcinoma cells/monolayer ~8 x 10^6 exposed to low concentration welding fumes 6h sample 2
Sample name: 08_low 6h-2
Biological replicate 2
Samples 01-12 were hybridized together on one chip, and samples 13-24 were hybridized together on a different chip.


title: RPMI 2650 cells exposed to particle-free clean air 6h replicate 3

description:
ATCC #CCL-30 RPMI 2650 nasal septal squamous cell carcinoma cells/monolayer ~8 x 10^6 exposed to clean air 6h sample 3
Sample name: 06_clean 6h-3
Biological replicate 3
Samples 01-12 were hybridized together on one chip, and samples 13-24 were hybridized together on a different chip.

source_name: RPMI 2650 cells exposed to particle-free clean air for 6h with 0h post-exposure incubation

value: exposed to clean air 6h


title: P.6113.UT.2

description: Gene expression of GM06113, P72

source_name: GM06113,P72,0hr, untreated, replicate 2


title: RPMI 2650 cells exposed to particle-free clean air 6h replicate 2

description:
ATCC #CCL-30 RPMI 2650 nasal septal squamous cell carcinoma cells/monolayer ~8 x 10^6 exposed to clean air 6h sample 2
Sample name: 05_clean 6h-2
Biological replicate 2
Samples 01-12 were hybridized together on one chip, and samples 13-24 were hybridized together on a different chip.


title: first visit [GG2_0370]

city: Decatur

first: Aliza

middle: P.

last: Wingo

state: GA

address: 1670 Clairmont Rd

department: Psychiatry

institute: Atlanta VAMC/Emory University

hyb_protocol: Illumina's BeadArray protocol

scan_protocol: Illumina's BeadArray protocol and GenomeStudio (Gene expression module)

data_processing: The raw log2 transformed probes were normalized by ANOVA fitting technical effects of date of hybridization and RIN score. The reason why there are so many missing probes in the normalized dataset is because they are below the expression threshold and so not included in the normalization process.

source_name: whole peripheral blood

label_protocol: Illumina BeadArray protocol

extract_protocol: Total RNA was extracted from whole peripheral blood using Tempus Spin RNA Isolation kit. Quality control was performed using Agilent's Bioanalyzer.

tag: age

tag: body mass index

tag: ethnicity

value: CAU

tag: gad7 score

tag: hybridization batch

value: D

tag: rin


title: P.6113.UT.1

description: Gene expression of GM06113, P72

source_name: GM06113,P72,0hr, untreated, replicate 1


title: RPMI 2650 cells exposed to particle-free clean air 6h replicate 1

description:
ATCC #CCL-30 RPMI 2650 nasal septal squamous cell carcinoma cells/monolayer ~8 x 10^6 exposed to clean air 6h sample 1
Sample name: 04_clean 6h-1
Biological replicate 1
Samples 01-12 were hybridized together on one chip, and samples 13-24 were hybridized together on a different chip.


title: RPMI 2650 cells unexposed-replicate 3

description:
ATCC #CCL-30 RPMI 2650 nasal septal squamous cell carcinoma cells/monolayer ~8 x 10^6 sample 3
Sample name: 03_incubator control-3
Biological replicate 3
Samples 01-12 were hybridized together on one chip, and samples 13-24 were hybridized together on a different chip.


title: first visit [GG2_0364]


title: first visit [GG2_0367]

tag: anxiety case/control

value: case


title: first visit [GG2_0371]


title: first visit [GG2_0365]


title: first visit [GG2_0369]


title: P.1603.4hr.3

description: Gene expression of GM01603,P72

source_name: GM01603,P72,4hr, 5 Gy, replicate 3

tag: cell line


title: P.1603.2hr.3

description: Gene expression of GM01603,P72

source_name: GM01603,P72,2hr, 5 Gy, replicate 3


title: P.1603.2hr.2

description: Gene expression of GM01603,P72

source_name: GM01603,P72,2hr, 5 Gy, replicate 2


title: P.1603.4hr.2

description: Gene expression of GM01603,P72

source_name: GM01603,P72,4hr, 5 Gy, replicate 2


title: first visit [GG2_0362]

value: AFR


title: first visit [GG2_0368]


title: first visit [GG2_0363]

value: control


title: first visit [GG2_0360]


title: RPMI 2650 cells unexposed-replicate 1

description:
ATCC #CCL-30 RPMI 2650 nasal septal squamous cell carcinoma cells/monolayer ~8 x 10^6 sample 1
Sample name: 01_incubator control-1
Biological replicate 1
Samples 01-12 were hybridized together on one chip, and samples 13-24 were hybridized together on a different chip.


title: P.1603.4hr.1

description: Gene expression of GM01603,P72

source_name: GM01603,P72,4hr, 5 Gy, replicate 1


title: first visit [GG2_0358]


title: P.1603.UT.3

description: Gene expression of GM01603, P72

source_name: GM01603,P72,0hr, untreated, replicate 3


title: first visit [GG2_0361]


title: RPMI 2650 cells unexposed-replicate 2

description:
ATCC #CCL-30 RPMI 2650 nasal septal squamous cell carcinoma cells/monolayer ~8 x 10^6 sample 2
Sample name: 02_incubator control-2
Biological replicate 2
Samples 01-12 were hybridized together on one chip, and samples 13-24 were hybridized together on a different chip.


title: first visit [GG2_0357]


title: first visit [GG2_0359]


title: first visit [GG2_0366]


title: first visit [GG2_0348]


title: first visit [GG2_0354]

value: CAH


title: first visit [GG2_0353]


title: first visit [GG2_0356]


title: first visit [GG2_0346]


title: first visit [GG2_0355]


title: first visit [GG2_0347]


title: first visit [GG2_0349]


title: first visit [GG2_0352]


title: P.1603.UT.2

description: Gene expression of GM01603, P72

source_name: GM01603,P72,0hr, untreated, replicate 2


title: first visit [GG2_0345]


title: first visit [GG2_0344]


title: first visit [GG2_0351]


title: BEAS2B - CeO2-NP - 10 hours - repl.3

city: Mol

first: Sylvie

last: Remy

state: Antwerp

address: Boeretang 200

country: Belgium

institute: VITO

description: BEAS-2B - CzO2

hyb_protocol: Equal amounts of the exposed and negative control labeled cRNA samples were competitively hybridized onto the arrays in a fully automatic HS 4800 Pro hybridization station (Tecan, Grödig/Salzburg, Austria) for 17 hours.

scan_protocol: The arrays were scanned on an Agilent scanner (G2565BA, Agilent Technologies). Images were quantified using Agilent Feature Extraction Software (version 10.5.1.1).

data_processing: Raw data feature extraction files were generated using Agilent protocol GE2-107_Sep09. Changes in gene expression relative to solvent control (fold-change (FC)) were obtained by calculating the ratio between rProcessedSignal (exposed sample) and gProcessedSignal (solvent control sample).  Data were filtered with regards to reliability of the feature. Reliable features were defined as features 1) of which the intensity was higher than the feature noise level, 2) of which the intensity was below the feature saturation level, 3) that were not a population outlier, 4) that were uniform spots, and 5) that were not a control feature. For each microarray, the data used for further statistical analysis contained the log2 transformed FC of reliable features only. Missing values in the data table files correspond to features of which the signal is not reliable. A feature was flagged as not reliable if:            gProcessedSignal<2*gProcessedSigError;  And/Or          rProcessedSignal<2*rProcessedSigError;  And/Or          gIsSaturated ~= 0;  And/Or          rIsSaturated ~= 0;  And/Or          gIsFeatNonUnifOL ~= 0;  And/Or          rIsFeatNonUnifOL ~= 0;  And/Or          ControlType ~= 0;

source_name: BEAS2B, vehicle control, 10 hours

label_protocol: 1 μg of total RNA was used in the Agilent LIRAK PLUS, two-colour Low RNA input Linear Amplification method, according to the manufacturer’s instructions.  cRNAs showing a yield >825 ng and a specific activity of 8-20 pmol/μg cRNA were selected for further processing.

growth_protocol:
BEAS-2B cells were grown in T-75 culture flasks precoated with a mixture of 10 µg/ml human plasma fibronectin (Invitrogen, Paisley, UK), 30 µg/ml PureColTM (Advance Biomatrix, USA), and 10µg/ml bovine serum albumin (Sigma–Aldrich Chemie Gmbh, Steinheim, Germany) dissolved in growth medium (BEGM, Lonza). The mixture was added at a ratio of 0.2 ml/cm2 surface area.
The cells were kept in a humidified atmosphere at 37 °C and 5% CO2. Before reaching 80% confluence, cells were subcultured using 0.25 % trypsin/0.53 mM versene (EDTA) solution (LGC Promochem) containing 0.5% polyvinylpyrrolidone (Sigma–Aldrich Chemie Gmbh). Medium was refreshed every 2–3 days and cells were subcultured weekly (3000 cells/cm2).
A549 cells were grown in T-75 culture flasks in medium containing 89%RPMI 1640 medium with GlutaMAX and 25mM HEPES, 10% fetal bovine serum and 1% penicillin-streptomysin.
The cells were kept in a humidified atmosphere at 37 °C and 5% CO2. Before reaching 90% confluence, cells were subcultured using 500 mg/l trypsin/200 mg/l versene solution.

extract_protocol: After exposure time, the supernatants was removed and the cells were lysed with 99% RLT lysis buffer (Qiagen, Hilden, Germany) and 1% 2-mercaptoethanol (Sigma–Aldrich Chemie Gmbh). Total RNA was isolated using mini RNeasy RNA isolation kits, according to the manufacturer’s specifications (Qiagen).

treatment_protocol:
BEAS-2B cells were seeded in six-well plates (6×105 cells suspended in 4 ml growth medium per well) 48 hours before exposure to the test substance.  Cells were exposed for 3, 6, 10, and 24 hours to the selected nanoparticles to a concentration yielding 20% cell viability reduction (IC20). This concentration was derived from concentration-response relationships after 24 hours of exposure determined using the neutral red uptake assay.
A549 cells were seeded in six-well plates (6×105 cells suspended in 4 ml growth medium per well) and incubated overnight before exposure to the test substance.
The cells were exposed to a non-cytotoxic NP concentration.

source_name: BEAS2B, nanoparticle, 10 hours


title: P.1603.UT.1

description: Gene expression of GM01603, P72

source_name: GM01603,P72,0hr, untreated, replicate 1


title: BEAS2B - CeO2-NP - 10 hours - repl.2

description: BEAS-2B - CzO2


title: BEAS2B - CeO2-NP - 3 hours - repl.3

description: BEAS-2B - CzO2

source_name: BEAS2B, vehicle control, 3 hours

source_name: BEAS2B, nanoparticle, 3 hours


title: BEAS2B - CeO2-NP - 24 hours - repl.3

description: BEAS-2B - CzO2

source_name: BEAS2B, vehicle control, 24 hours

source_name: BEAS2B, nanoparticle, 24 hours


title: first visit [GG2_0342]


title: BEAS2B - CeO2-NP - 6 hours - repl.3

description: BEAS-2B - CzO2

source_name: BEAS2B, vehicle control, 6 hours

source_name: BEAS2B, nanoparticle, 6 hours


title: first visit [GG2_0343]

source_name: whole peripheral blood


title: first visit [GG2_0340]


title: first visit [GG2_0339]


title: P.1603.2hr.1

description: Gene expression of GM01603,P72

source_name: GM01603,P72,2hr, 5 Gy, replicate 1


title: first visit [GG2_0338]


title: BEAS2B - CeO2-NP - 3 hours - repl.2

description: BEAS-2B - CzO2


title: BEAS2B - CeO2-NP - 6 hours - repl.2

description: BEAS-2B - CzO2


title: first visit [GG2_0333]


title: first visit [GG2_0332]


title: first visit [GG2_0335]


title: first visit [GG2_0337]


title: BEAS2B - CeO2-NP - 24 hours - repl.2

description: BEAS-2B - CzO2


title: first visit [GG2_0341]


title: first visit [GG2_0336]


title: BEAS2B - CeO2-NP - 10 hours - repl.1

description: BEAS-2B - CzO2


title: BEAS2B - CeO2-NP - 24 hours - repl.1

description: BEAS-2B - CzO2


title: first visit [GG2_0331]


title: first visit [GG2_0329]


title: first visit [GG2_0328]

value: ASN


title: BEAS2B - CeO2-NP - 6 hours - repl.1

description: BEAS-2B - CzO2


title: first visit [GG2_0326]


title: Prostate_Tumor_HSPH0041

source_name: FFPE prostate tumor


title: first visit [GG2_0325]


title: first visit [GG2_0330]


title: first visit [GG2_0321]


title: first visit [GG2_0323]


title: first visit [GG2_0324]


title: BEAS2B - CoO-NP - 6 hours - repl.3

description: BEAS-2B - CoO


title: BEAS2B - CoO-NP - 10 hours - repl.3

description: BEAS-2B - CoO


title: first visit [GG2_0327]


title: BEAS2B - CoO-NP - 24 hours - repl.3

description: BEAS-2B - CoO


title: BEAS2B - CoO-NP - 6 hours - repl.2

description: BEAS-2B - CoO


title: first visit [GG2_0322]


title: BEAS2B - CoO-NP - 3 hours - repl.2

description: BEAS-2B - CoO


title: BEAS2B - CoO-NP - 10 hours - repl.2

description: BEAS-2B - CoO


title: BEAS2B - CeO2-NP - 3 hours - repl.1

description: BEAS-2B - CzO2


title: first visit [GG2_0320]


title: first visit [GG2_0311]


title: first visit [GG2_0315]


title: first visit [GG2_0318]


title: first visit [GG2_0319]


title: BEAS2B - CoO-NP - 3 hours - repl.3

description: BEAS-2B - CoO


title: first visit [GG2_0316]


title: first visit [GG2_0317]


title: BEAS2B - CoO-NP - 10 hours - repl.1

description: BEAS-2B - CoO


title: BEAS2B - CoO-NP - 24 hours - repl.2

description: BEAS-2B - CoO


title: first visit [GG2_0314]


title: first visit [GG2_0309]


title: first visit [GG2_0310]


title: first visit [GG2_0308]


title: first visit [GG2_0312]


title: first visit [GG2_0313]


title: first visit [GG2_0305]


title: BEAS2B - CoO-NP - 24 hours - repl.1

description: BEAS-2B - CoO


title: first visit [GG2_0302]


title: first visit [GG2_0299]


title: BEAS2B - CoO-NP - 3 hours - repl.1

description: BEAS-2B - CoO


title: first visit [GG2_0303]


title: first visit [GG2_0304]


title: first visit [GG2_0306]


title: BEAS2B - CoO-NP - 6 hours - repl.1

description: BEAS-2B - CoO


title: first visit [GG2_0300]


title: first visit [GG2_0297]


title: first visit [GG2_0296]


title: first visit [GG2_0295]


title: A549 - CeO2-NP - 24 hours - repl.3

description: A549 - CzO2

source_name: A549, vehicle control, 24 hours

source_name: A549, nanoparticle, 24 hours


title: A549 - CeO2-NP - 3 hours - repl.3

description: A549 - CzO2

source_name: A549, vehicle control, 3 hours

source_name: A549, nanoparticle, 3 hours


title: first visit [GG2_0350]


title: first visit [GG2_0298]


title: first visit [GG2_0294]


title: A549 - CeO2-NP - 6 hours - repl.3

description: A549 - CzO2

source_name: A549, vehicle control, 6 hours

source_name: A549, nanoparticle, 6 hours


title: first visit [GG2_0301]


title: A549 - CeO2-NP - 10 hours - repl.3

description: A549 - CzO2

source_name: A549, vehicle control, 10 hours

source_name: A549, nanoparticle, 10 hours


title: Prostate_Tumor_HSPH0027


title: A549 - CeO2-NP - 24 hours - repl.2

description: A549 - CzO2


title: first visit [GG2_0293]


title: first visit [GG2_0291]


title: first visit [GG2_0292]


title: A549 - CeO2-NP - 3 hours - repl.2

description: A549 - CzO2


title: first visit [GG2_0290]


title: first visit [GG2_0289]


title: A549 - CeO2-NP - 10 hours - repl.2

description: A549 - CzO2


title: first visit [GG2_0288]

value: C


title: A549 - CeO2-NP - 24 hours - repl.1

description: A549 - CzO2


title: first visit [GG2_0287]


title: first visit [GG2_0286]


title: first visit [GG2_0285]


title: first visit [GG2_0284]


title: first visit [GG2_0280]


title: first visit [GG2_0281]


title: first visit [GG2_0276]


title: A549 - CeO2-NP - 10 hours - repl.1

description: A549 - CzO2


title: A549 - CeO2-NP - 6 hours - repl.2

description: A549 - CzO2


title: first visit [GG2_0274]


title: first visit [GG2_0283]


title: first visit [GG2_0279]


title: A549 - CeO2-NP - 3 hours - repl.1

description: A549 - CzO2


title: first visit [GG2_0272]


title: first visit [GG2_0273]

value: B


title: first visit [GG2_0278]


title: first visit [GG2_0282]


title: A549 - CeO2-NP - 6 hours - repl.1

description: A549 - CzO2


title: first visit [GG2_0277]


title: A549 - CoO-NP - 24 hours - repl.3

description: A549 - CoO


title: A549 - CoO-NP - 3 hours - repl.3

description: A549 - CoO


title: A549 - CoO-NP - 10 hours - repl.3

description: A549 - CoO


title: first visit [GG2_0271]


title: first visit [GG2_0275]


title: A549 - CoO-NP - 6 hours - repl.3

description: A549 - CoO


title: first visit [GG2_0270]


title: Prostate_Tumor_HSPH0010


title: first visit [GG2_0269]


title: first visit [GG2_0263]


title: first visit [GG2_0267]


title: A549 - CoO-NP - 24 hours - repl.2

description: A549 - CoO


title: first visit [GG2_0268]


title: A549 - CoO-NP - 10 hours - repl.2

description: A549 - CoO


title: first visit [GG2_0266]


title: HCC of STAM mice 2-2

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

institute: Toray Industries,Inc.

hyb_protocol: Hybridized for 16 h at 37 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: 3D-Gene Scanner ((Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction(Toray Industries Inc., Tokyo, Japan).

data_processing: The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots’ signal intensities of 95% confidence intervals. Measurements of both duplicate spots with the signal intensities greater than 2 standard deviations (SD) of the background signal intensity were considered to be valid. A relative expression level of a given miRNA was calculated by comparing the signal intensities of the averaged valid spots with their mean value throughout the microarray experiments.

source_name: HCC of STAM mice

label_protocol: Extracted total RNA was labeled with Hy5 using the miRCURY LNA Array miR labeling kit (Exiqon, Vedbaek, Denmark)

growth_protocol: STAM mice,  a NASH-HCC model, were injected with STZ and fed with high-fat diet.

extract_protocol: RNA samples were extracted from cells using miRNesy mini kit (Qiagen).

treatment_protocol: STAM mice develop HCC at 18 weeks of age.

tag: strain background

tag: strain

value: STAM (NASH-HCC model)

value: Hepatocellular carcinoma (HCC)


title: A549 - CoO-NP - 6 hours - repl.2

description: A549 - CoO


title: first visit [GG2_0262]


title: A549 - CoO-NP - 10 hours - repl.1

description: A549 - CoO


title: first visit [GG2_0260]


title: first visit [GG2_0261]


title: first visit [GG2_0259]


title: first visit [GG2_0264]


title: first visit [GG2_0251]


title: first visit [GG2_0265]


title: first visit [GG2_0254]


title: first visit [GG2_0255]


title: first visit [GG2_0258]


title: A549 - CoO-NP - 6 hours - repl.1

description: A549 - CoO


title: A549 - CoO-NP - 24 hours - repl.1

description: A549 - CoO


title: first visit [GG2_0257]


title: first visit [GG2_0252]


title: A549 - CoO-NP - 3 hours - repl.2

description: A549 - CoO


title: HCC of STAM mice 2-1


title: first visit [GG2_0256]


title: Non-tumor liver of STAM mice 2

source_name: Non-tumor liver of STAM mice

value: non-tumor liver


title: HCC of STAM mice 1


title: first visit [GG2_0249]


title: first visit [GG2_0253]


title: A549 - CoO-NP - 3 hours - repl.1

description: A549 - CoO


title: first visit [GG2_0248]


title: first visit [GG2_0247]


title: first visit [GG2_0245]


title: first visit [GG2_0246]


title: Non-tumor liver of STAM mice 1


title: normal mouse liver

description: Control

source_name: normal mouse liver

value: normal liver


title: first visit [GG2_0244]


title: first visit [GG2_0241]


title: first visit [GG2_0235]


title: first visit [GG2_0238]


title: first visit [GG2_0242]


title: first visit [GG2_0240]


title: first visit [GG2_0237]


title: first visit [GG2_0250]


title: first visit [GG2_0243]


title: first visit [GG2_0239]


title: first visit [GG2_0230]


title: first visit [GG2_0229]


title: first visit [GG2_0231]


title: first visit [GG2_0227]


title: first visit [GG2_0225]


title: first visit [GG2_0228]


title: first visit [GG2_0221]


title: first visit [GG2_0217]


title: first visit [GG2_0234]


title: first visit [GG2_0222]


title: first visit [GG2_0223]


title: first visit [GG2_0232]


title: first visit [GG2_0218]


title: first visit [GG2_0226]


title: first visit [GG2_0224]


title: first visit [GG2_0215]


title: first visit [GG2_0214]


title: first visit [GG2_0216]


title: first visit [GG2_0233]


title: first visit [GG2_0211]


title: first visit [GG2_0212]


title: first visit [GG2_0213]


title: first visit [GG2_0210]


title: first visit [GG2_0220]


title: first visit [GG2_0206]


title: first visit [GG2_0208]


title: first visit [GG2_0209]


title: first visit [GG2_0205]


title: first visit [GG2_0207]


title: first visit [GG2_0203]


title: first visit [GG2_0204]


title: first visit [GG2_0201]


title: first visit [GG2_0196]


title: first visit [GG2_0195]


title: first visit [GG2_0193]


title: first visit [GG2_0189]


title: first visit [GG2_0199]


title: first visit [GG2_0185]


title: first visit [GG2_0192]


title: first visit [GG2_0184]


title: first visit [GG2_0190]


title: first visit [GG2_0202]


title: first visit [GG2_0191]


title: first visit [GG2_0183]


title: first visit [GG2_0186]


title: first visit [GG2_0182]


title: first visit [GG2_0180]


title: first visit [GG2_0181]


title: first visit [GG2_0197]


title: first visit [GG2_0179]


title: first visit [GG2_0187]


title: first visit [GG2_0177]


title: first visit [GG2_0198]


title: first visit [GG2_0175]


title: first visit [GG2_0173]


title: first visit [GG2_0174]


title: first visit [GG2_0178]


title: first visit [GG2_0172]


title: first visit [GG2_0188]


title: first visit [GG2_0194]


title: first visit [GG2_0171]


title: first visit [GG2_0176]


title: first visit [GG2_0164]


title: first visit [GG2_0166]


title: first visit [GG2_0167]


title: Uninfected Control_FK25

city: San Antonio

first: Mahesh

last: Mohan

state: Texas

address: 8715 West Military Road

department: Host Pathogen Interaction Program

institute: Southwest National Primate Research Center

description: Control

data_processing:
TLDA-SDS run files from twelve SIV-infected and four uninfected control macaques were loaded onto Applied Biosystems Relative Quantification (RQ) Manager Software v1.2.2 and analyzed using automatic baseline settings and a manual threshold of 0.2.
The results from the RQ manager analysis containing five columns (well, sample, detector, task and CT values) were saved as a tab-delimited text file which was later imported and analyzed using the DataAssist version 3.01 software (Lifetech Corp), a data analysis tool designed to compare samples using the deltadelta CT method for relative quantification of gene expression.
MiRNA expression data was analyzed using global normalization method.
In all experiments, the CT upper limit was set to 33 meaning that all miRNA detectors with a CT value greater than or equal to 33 were excluded.
Multiple comparisons correction using Benjamini-Hochberg method for false discovery rate was simultaneously applied to all 768 miRNA target probes (card A and B combined).
DataAssist software automatically performs global normalization including all deltadeltaCT based fold-change calculations from the uploaded raw threshold cycle values.
Fold Change worksheet reports test/control (i.e., Chronic SIV infected/uninfected control) ratios.

label: FAM

organism: Macaca mulatta

source_name: Intact Colon

label_protocol: microRNA profiling was performed using the TaqMan® Array Human MicroRNA A+B Cards Set v3.0 (Life Tech) following the manufacturer’s instructions. Reverse transcription was first performed from 350 ng of total RNA using the microRNA reverse transcription kit. 2.5 µL of cDNA was preamplified using the TaqMan® PreAmp Master Mix kit. Preamplified products were first diluted and then loaded onto to TLDA plates. TLDA plates were run on the ABI 7900 HT Fast PCR system following the manufacturer’s recommended thermal cycling conditions.

extract_protocol: Total RNA (small and large) was extracted using the miRNeasy Mini kit (Qiagen). On-column DNase digestion was also performed to eliminate contaminating genomic DNA.

treatment_protocol: 12 animals were infected intravenously with 100 TCID50 SIVmac251 and 5 remained uninfected

tag: infection

value: Uninfected Control

tag: time (days post siv infection [dpi])

value: colon


title: first visit [GG2_0170]


title: first visit [GG2_0161]


title: first visit [GG2_0157]


title: Chronic SIV_HG58

description: Test

value: Chronic SIV

value: 286 dpi

tag: tissue


title: Uninfected Control_EL66

description: Control


title: Uninfected Control_EH70

description: Control


title: Uninfected Control_EH80

description: Control


title: first visit [GG2_0165]


title: first visit [GG2_0168]


title: first visit [GG2_0158]

value: CAU


title: first visit [GG2_0155]

tag: Sex

value: M


title: first visit [GG2_0160]


title: first visit [GG2_0159]


title: first visit [GG2_0149]

value: F

value: case


title: first visit [GG2_0162]


title: first visit [GG2_0163]


title: first visit [GG2_0150]

value: AFR


title: first visit [GG2_0148]


title: first visit [GG2_0169]


title: first visit [GG2_0152]

value: control


title: first visit [GG2_0153]


title: Chronic SIV_HG45

description: Test

value: 281 dpi


title: first visit [GG2_0154]


title: first visit [GG2_0151]


title: first visit [GG2_0147]

value: ASN


title: Chronic SIV_DV42

description: Test

value: 226 dpi


title: Chronic SIV_GK31

description: Test

value: 180 dpi


title: Chronic SIV_GA19

description: Test


title: Chronic SIV_HB31

description: Test


title: Chronic SIV_HI68

description: Test

value: 158 dpi


title: Chronic SIV_HB48

description: Test


title: first visit [GG2_0145]

value: B


title: Chronic SIV_CP47

description: Test

value: 151 dpi


title: Chronic SIV_GH25

description: Test

value: 148 dpi


title: first visit [GG2_0146]


title: Chronic SIV_FE53

description: Test

value: 140 dpi

value: colon


title: first visit [GG2_0144]


title: first visit [GG2_0137]


title: first visit [GG2_0143]


title: first visit [GG2_0136]


title: first visit [GG2_0140]


title: first visit [GG2_0138]


title: first visit [GG2_0141]


title: first visit [GG2_0139]


title: PXB0327-0085 controls-IFN [tissue]

description:
tissue PXB0327-0085
Uninfected, untreated control mice

source_name: controls-IFN

growth_protocol: Mice were inoculated with serum samples from HCV or HBV carriers via the tail vein. Mice were sacrificed by diethyl ether anesthesia. Human hepatocytes from mouse livers were finely dissected and stored in liquid nitrogen after submergence in RNA later solution.

treatment_protocol: Interferon-alpha (7,000IU/g body weight) was administered at week 8 six hours prior to sacrifice in 5 HBV-infected and 5 HCV-infected mice.

tag: experiment model

value: human hepatocyte chimeric mice

tag: inoculated with

value: none (control)

tag: injected with

value: human hepatocytes from mouse liver

value: Day 0


title: first visit [GG2_0142]

tag: age

value: F

value: CAU


title: PXB0327-0095 controls-IFN [tissue]

description:
tissue PXB0327-0095
Uninfected, untreated control mice

value: Interferon-alpha (7,000IU/g body weight)

tag: time


title: PXB0327-0016 controls-IFN [tissue]

description:
tissue PXB0327-0016
Uninfected, untreated control mice


title: Chronic SIV_FT11

description: Test

value: Chronic SIV

value: 145 dpi


title: PXB0327-0111 controls-IFN [tissue]

description:
tissue PXB0327-0111
Uninfected, untreated control mice


title: PXB0327-0098 controls-IFN [tissue]

description:
tissue PXB0327-0098
Uninfected, untreated control mice


title: first visit [GG2_0135]

tag: body mass index

tag: ethnicity

value: case


title: first visit [GG2_0133]

tag: gad7 score

tag: hybridization batch


title: PXB304-31 HBV IFN 8W [tissue]

description:
tissue PXB304-31 8W
HBV-infected mice were injected with interferon alpha and euthanized 8 weeks after infection

source_name: HBV IFN 8W

value: serum samples from HBV carriers

value: Week 8


title: PXB303-26 HBV IFN 8W [tissue]

description:
tissue PXB303-26 8W
HBV-infected mice were injected with interferon alpha and euthanized 8 weeks after infection


title: PXB303-11 HBV IFN 8W [tissue]

description:
tissue PXB303-11 8W
HBV-infected mice were injected with interferon alpha and euthanized 8 weeks after infection


title: PXB0327-0076 controls-IFN [tissue]

description:
tissue PXB0327-0076
Uninfected, untreated control mice


title: first visit [GG2_0134]

source_name: whole peripheral blood

value: M

value: B

tag: rin


title: PXB305-48 HBV IFN 8W [tissue]

description:
tissue PXB305-48 8W
HBV-infected mice were injected with interferon alpha and euthanized 8 weeks after infection


title: PXB304-77 HBV IFN 8W [tissue]

description:
tissue PXB304-77 8W
HBV-infected mice were injected with interferon alpha and euthanized 8 weeks after infection


title: PXB304-60 HBV non-treat 8W [tissue]

description:
tissue PXB304-60 8W
HBV-infected mice were euthanized 8 weeks after infection

source_name: HBV non-treat 8W


title: PXB304-49 HBV non-treat 8W [tissue]

description:
tissue PXB304-49 8W
HBV-infected mice were euthanized 8 weeks after infection


title: first visit [GG2_0131]

tag: anxiety case/control

value: control


title: PXB304-26 HBV non-treat 8W [tissue]

description:
tissue PXB304-26 8W
HBV-infected mice were euthanized 8 weeks after infection


title: first visit [GG2_0124]


title: PXB303-51 HBV non-treat 8W [tissue]

description:
tissue PXB303-51 8W
HBV-infected mice were euthanized 8 weeks after infection


title: first visit [GG2_0132]


title: first visit [GG2_0125]


title: first visit [GG2_0127]


title: first visit [GG2_0122]


title: first visit [GG2_0126]


title: first visit [GG2_0130]


title: first visit [GG2_0123]


title: PXB303-45 HBV non-treat 8W [tissue]

description:
tissue PXB303-45 8W
HBV-infected mice were euthanized 8 weeks after infection


title: PXB302-83 HCV IFN 8W [tissue]

description:
tissue PXB302-83 8W
HCV-infected mice were injected with interferon alpha and euthanized 8 weeks after infection

source_name: HCV IFN 8W

value: serum samples from HCV carriers


title: first visit [GG2_0129]

value: ASN


title: first visit [GG2_0128]

value: AFR


title: first visit [GG2_0119]


title: first visit [GG2_0121]


title: PXB302-71 HCV IFN 8W [tissue]

description:
tissue PXB302-71 8W
HCV-infected mice were injected with interferon alpha and euthanized 8 weeks after infection

value: human hepatocyte chimeric mice


title: first visit [GG2_0118]


title: PXB302-53 HCV IFN 8W [tissue]

description:
tissue PXB302-53 8W
HCV-infected mice were injected with interferon alpha and euthanized 8 weeks after infection

value: human hepatocytes from mouse liver


title: PXB0282-0049 HCV day10

description:
PXB282-49
HCV-infected mice were euthanized 10 days after infection

source_name: HCV day10

value: Day 10


title: PXB0282-0052 HCV day10

description:
PXB282-52
HCV-infected mice were euthanized 10 days after infection


title: PXB0282-0003 HBV day10

description:
PXB282-3
HBV-infected mice were euthanized 10 days after infection

source_name: HBV day10


title: PXB0282-0007 HBV day10

description:
PXB282-7
HBV-infected mice were euthanized 10 days after infection


title: first visit [GG2_0114]

value: F


title: first visit [GG2_0116]

value: CAU


title: PXB302-30 HCV IFN 8W [tissue]

description:
tissue PXB302-30 8W
HCV-infected mice were injected with interferon alpha and euthanized 8 weeks after infection

value: Interferon-alpha (7,000IU/g body weight)


title: PXB302-67 HCV non-treat 8W  [tissue]

description:
tissue PXB302-67 8W
HCV-infected mice were euthanized 8 weeks after infection

source_name: HCV non-treat 8W


title: PXB0282-0033 HCV day10

description:
PXB282-33
HCV-infected mice were euthanized 10 days after infection


title: PXB302-15 HCV IFN 8W [tissue]

description:
tissue PXB302-15 8W
HCV-infected mice were injected with interferon alpha and euthanized 8 weeks after infection


title: PXB302-80 HCV non-treat 8W [tissue]

description:
tissue PXB302-80 8W
HCV-infected mice were euthanized 8 weeks after infection


title: first visit [GG2_0112]


title: first visit [GG2_0113]


title: PXB303-32 HCV non-treat 8W [tissue]

description:
tissue PXB303-32 8W
HCV-infected mice were euthanized 8 weeks after infection


title: first visit [GG2_0111]


title: PXB 175-006 HCV 8w

description:
PXB 175-006
HCV-infected mice were euthanized 8 weeks after infection

source_name: HCV 8w


title: PXB 175-010 HCV 8w

description:
PXB 175-010
HCV-infected mice were euthanized 8 weeks after infection


title: PXB 175-002 HCV 8w

description:
PXB 175-002
HCV-infected mice were euthanized 8 weeks after infection


title: PXB 0282-0029 HBV 8w

description:
PXB 0282-0029
HBV-infected mice were euthanized 8 weeks after infection

source_name: HBV 8w


title: first visit [GG2_0115]


title: PXB303-8 HCV non-treat 8W [tissue]

description:
tissue PXB303-8 8W
HCV-infected mice were euthanized 8 weeks after infection


title: PXB0327-0111 controls-IFN

extract_protocol: RNA samples were extracted from serum using 3D-Gene RNA extraction reagent from liquid sampl (Toray Industries Inc., Tokyo, Japan).

value: none (control)

value: serum


title: first visit [GG2_0117]


title: PXB303-28 HCV non-treat 8W [tissue]

description:
tissue PXB303-28 8W
HCV-infected mice were euthanized 8 weeks after infection


title: first visit [GG2_0109]


title: first visit [GG2_0110]


title: first visit [GG2_0108]

value: case


title: PXB0327-0098 controls-IFN


title: PXB0327-0016 controls-IFN


title: PXB 0282-0022 HBV 8w

description:
PXB 0282-0022
HBV-infected mice were euthanized 8 weeks after infection

value: serum samples from HBV carriers


title: first visit [GG2_0107]


title: PXB 0282-0005 HBV 8w

description:
PXB 0282-0005
HBV-infected mice were euthanized 8 weeks after infection

value: Week 8


title: PXB 0282-0001 HBV 6w

description:
PXB 0282-0001
HBV-infected mice were euthanized 6 weeks after infection

source_name: HBV 6w

value: Week 6


title: PXB0327-0095 controls-IFN


title: PXB 0282-0015 HBV 6w

description:
PXB 0282-0015
HBV-infected mice were euthanized 6 weeks after infection


title: PXB0327-0076 controls-IFN


title: PXB304-77 HBV IFN 8W

description: Serum was collected 8 weeks after HBV infection following injection with interferon alpha

source_name: HBV IFN 8W_serum


title: PXB305-48 HBV IFN 8W


title: PXB304-31 HBV IFN 8W


title: PXB 282-25 HBV day10

description:
PXB 282-25
HBV-infected mice were euthanized 10 days after infection


title: PXB 282-34 HCV day10

description:
PXB 282-34
HCV-infected mice were euthanized 10 days after infection


title: PXB 282-48 HCV day10

description:
PXB 282-48
HCV-infected mice were euthanized 10 days after infection


title: first visit [GG2_0105]

value: B


title: PXB303-11 HBV IFN 8W


title: PXB 0282-0004 HBV 8w

description:
PXB 0282-0004
HBV-infected mice were euthanized 8 weeks after infection


title: PXB 282-26 HBV day10

description:
PXB 282-26
HBV-infected mice were euthanized 10 days after infection


title: first visit [GG2_0104]

value: control


title: first visit [GG2_0106]

value: M


title: first visit [GG2_0100]


title: first visit [GG2_0103]


title: first visit [GG2_0102]


title: first visit [GG2_0099]


title: PXB0327-0085 controls-IFN


title: PXB 282-30 HBV day10

description:
PXB 282-30
HBV-infected mice were euthanized 10 days after infection

value: serum samples from HCV carriers


title: first visit [GG2_0098]


title: PXB 264-5 control

description:
PXB 264-5
Uninfected, untreated control mice

source_name: control

value: Day 0


title: PXB304-49 HBV non-treat 8W

description: Serum was collected 8 weeks after HBV infection

source_name: HBV non-treat 8W_serum

value: human hepatocyte chimeric mice


title: first visit [GG2_0101]


title: PXB 264-4 control

description:
PXB 264-4
Uninfected, untreated control mice

value: human hepatocytes from mouse liver


title: PXB303-26 HBV non-treat 8W


title: PXB304-60 HBV non-treat 8W


title: first visit [GG2_0097]


title: PXB 201-014 control

description:
PXB 201-014
Uninfected, untreated control mice


title: first visit [GG2_0096]

value: O


title: PXB303-51 HBV non-treat 8W


title: PXB 201-012 control

description:
PXB 201-012
Uninfected, untreated control mice


title: PXB 201-006 control

description:
PXB 201-006
Uninfected, untreated control mice


title: PXB302-83 HCV IFN 8W

description: Serum was collected 8 weeks after HCV infection following injection with interferon alpha

source_name: HCV IFN 8W_serum


title: PXB303-45 HBV non-treat 8W


title: first visit [GG2_0095]

value: F


title: first visit [GG2_0093]

value: ASN


title: first visit [GG2_0094]

value: CAU


title: PXB 282-53 control

description:
PXB 282-53
Uninfected, untreated control mice

value: none (control)


title: PXB302-53 HCV IFN 8W

value: Interferon-alpha (7,000IU/g body weight)

value: serum


title: PXB302-30 HCV IFN 8W


title: PXB302-71 HCV IFN 8W


title: PXB302-15 HCV IFN 8W


title: PXB 303-51 HBV day10

description: Serum was collected 10 days after HBV infection

source_name: HBV day10_serum

value: serum samples from HBV carriers

value: Day 10


title: PXB 304-26 HBV day0

description: Serum collected from mice at day 0 prior to HBV infection

source_name: HBV day0_serum


title: PXB 304-26 HBV day10


title: first visit [GG2_0092]


title: first visit [GG2_0090]

value: case


title: PXB 303-51 HBV day0


title: first visit [GG2_0091]

value: AFR


title: PXB303-28 HCV non-treat 8W

description: Serum was collected 8 weeks after HCV infection

source_name: HCV non-treat 8W_serum

value: Week 8


title: first visit [GG2_0089]

value: A


title: first visit [GG2_0088]

value: M


title: PXB303-26 HBV IFN 8W

description: Serum was collected 8 weeks after HBV infection following injection with interferon alpha


title: PXB 303-45 HBV day10


title: PXB 303-45 HBV day0

value: Day 0


title: first visit [GG2_0087]


title: PXB303-8 HCV non-treat 8W

value: human hepatocyte chimeric mice

value: serum samples from HCV carriers


title: PXB 303-26 HBV day10


title: PXB302-80 HCV non-treat 8W


title: PXB302-67 HCV non-treat 8W


title: first visit [GG2_0086]


title: PXB303-32 HCV non-treat 8W


title: PXB 303-26 HBV day0


title: PXB 303-11 HBV day10


title: first visit [GG2_0083]

value: O


title: PXB 303-11 HBV day0


title: first visit [GG2_0082]

value: control


title: PXB 303-32 HCV day10

description: Serum was collected 10 days after HCV infection

source_name: HCV day10_serum


title: PXB 303-32 HCV day0

description: Serum collected from mice at day 0 prior to HCV infection

source_name: HCV day0_serum


title: first visit [GG2_0081]

source_name: whole peripheral blood


title: first visit [GG2_0079]

value: F


title: first visit [GG2_0085]

value: CAU


title: first visit [GG2_0077]


title: PXB 302-70 HCV day10


title: PXB 302-15 HCV day10


title: PXB 302-15 HCV day0


title: PXB 302-70 HCV day0


title: PXB 302-8 HCV day10


title: first visit [GG2_0080]


title: Neonates_Diofenolan-2_rep2

city: Okazaki

first: Kenji

last: Toyota

address: 5-1 Higashiyama

institute: National Institute for Basic Biology

description: Gene expression after 48hr  in Diofenolan treated neonate

hyb_protocol: 165 µg of Cyanine3-labeled cRNA were hybridized to the custom 4x44k D. magna microarray using the protocols of Agilent Technologies. After 17 h incubation with rotation, the microarrays were washed with Gene Expression Wash Buffer Kit (Agilent Technologies) according to the manufacturer’s protocols.

scan_protocol: DNA microarrays were scanned using a GenePix 4000B scanner (Molecular Devices, Sunnyvale, CA, USA) at 5 µm resolution. The signal intensity of the spots was digitized using the microarray imager software (Combimatrix Molecular Diagnostics, Irvine, CA, USA).

data_processing: Data files generated by Agilent Feature Extraction Software were imported into Subio Platform (Subio Inc., Tokyo) for further data processing.

organism: Daphnia magna

source_name: Neonates, Diofenolan-2, replicate 2

label_protocol: 500 ng of total RNA were prepared for microarray hybridization using the Quick Amp Labeling Kit and One-color RNA Spike-in kit (Agilent Technologies), and purified using the RNeasy Micro Kit (Qiagen) following the manufacturer’s protocol. The quality of Cyanine3-labeled complementary RNA (cRNA) was analyzed using the Agilent 2100 Bioanalyzer (Agilent Technologies).

extract_protocol: At least 20 individuals were used for one set of samples for each chemical concentration and controls. Harvested daphnids were briefly washed and homogenized using the physcotron NS-310E (Nichion, Tokyo, Japan). Total RNA was purified with TRIZOL reagent (Invitrogen, Tokyo, Japan), and purified using the RNeasy Micro Kit (Qiagen, Valencia, CA, USA) according to the manufacturer’s protocols. The quality of total RNA was analyzed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). Three experiments were conducted independently (biological triplicates).

value: whole body

tag: treatment

value: Diofenolan


title: first visit [GG2_0156]

value: B


title: first visit [GG2_0078]


title: Neonates_Diofenolan-1_rep1

source_name: Neonates, Diofenolan-1, replicate 1


title: Neonates_Diofenolan-4_rep4

source_name: Neonates, Diofenolan-4, replicate 4


title: first visit [GG2_0074]


title: HepG2 cells treated with 5-Aza-CdR

description: HepG2 5AZA

growth_protocol: HepG2 cells were clutured with DMEM supplemented with 10% FBS.

treatment_protocol: HepG2 cells were treated with 1uM of 5-aza-2'-deoxycytidine for 24h and/or 1uM of suberoylanilide hydroxamic acid for 4 days.

tag: cell line

tag: cell type

value: liver cancer cells

tag: treated with


title: Neonates_Diofenolan-3_rep3

source_name: Neonates, Diofenolan-3, replicate 3

tag: tissue


title: first visit [GG2_0073]

tag: Sex


title: Neonates_DMF-4_rep4 (Diofenolan)

description: Gene expression after 48hr  in DMF treated neonate

source_name: Neonates, DMF-4, replicate 4

value: DMF


title: first visit [GG2_0072]


title: first visit [GG2_0071]

value: case


title: first visit [GG2_0075]


title: Neonates_DMF-1_rep1 (Diofenolan)

source_name: Neonates, DMF-1, replicate 1


title: Neonates_DMF-2_rep2 (Diofenolan)

source_name: Neonates, DMF-2, replicate 2


title: Neonates_DMF-3_rep3 (Diofenolan)

source_name: Neonates, DMF-3, replicate 3


title: PXB 302-8 HCV day0

tag: experiment model

value: serum


title: first visit [GG2_0070]


title: untreated HepG2 cells

description: HepG2 Control

value: none (control)


title: HepG2 cells treated with SAHA and 5-Aza-CdR

description: HepG2 SAHA 5-Aza

value: SAHA and 5-Aza-CdR


title: first visit [GG2_0069]

value: M

value: AFR


title: first visit [GG2_0068]


title: first visit [GG2_0067]


title: first visit [GG2_0064]

value: A


title: first visit [GG2_0063]


title: first visit [GG2_0065]

value: ASN


title: first visit [GG2_0060]

value: O


title: first visit [GG2_0066]

value: control


title: first visit [GG2_0059]

value: F


title: first visit [GG2_0061]

value: CAU


title: NSCLC tumor, biological rep 43

city: Pittsburgh

first: Marjorie

last: Romkes

address: 5117 Centre Avenue

department: Medicine - Hematology/Oncology

institute: University of Pittsburgh

description:
Lung tissue samples obtained from the University of Pittsburgh Lung Cancer SPORE Tissue Bank.
PLS43

data_processing: The data were normalized using quantile normalization withIllumina Genome Studio

source_name: NSCLC tumor

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

extract_protocol: RNA was extracted withQiazol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent 2100 Bioanalyzer.

tag: tnm 7th ed stage

value: IIA

tag: 7th ed. tnm classification

tag: gender

value: female

tag: adjuvant chemotherapy

value: no

tag: intraoperative brachtherapy

tag: dead/alive as of 6/11

tag: overall survival (months) as of 6/11

tag: smoking status at enrollment

value: former

tag: packyear

tag: number of years quit


title: NSCLC tumor, biological rep 44

description:
Lung tissue samples obtained from the University of Pittsburgh Lung Cancer SPORE Tissue Bank.
PLS44

value: IB

tag: age

value: male

value: yes


title: first visit [GG2_0062]

tag: body mass index

tag: ethnicity

tag: gad7 score

tag: hybridization batch

tag: rin


title: NSCLC tumor, biological rep 36

description:
Lung tissue samples obtained from the University of Pittsburgh Lung Cancer SPORE Tissue Bank.
PLS36

value: active


title: NSCLC tumor, biological rep 45

description:
Lung tissue samples obtained from the University of Pittsburgh Lung Cancer SPORE Tissue Bank.
PLS45


title: NSCLC tumor, biological rep 38

description:
Lung tissue samples obtained from the University of Pittsburgh Lung Cancer SPORE Tissue Bank.
PLS38


title: NSCLC tumor, biological rep 41

description:
Lung tissue samples obtained from the University of Pittsburgh Lung Cancer SPORE Tissue Bank.
PLS41


title: first visit [GG2_0057]

tag: Sex


title: first visit [GG2_0056]

tag: anxiety case/control


title: NSCLC tumor, biological rep 46

description:
Lung tissue samples obtained from the University of Pittsburgh Lung Cancer SPORE Tissue Bank.
PLS46

tag: tnm 7th ed stage

tag: 7th ed. tnm classification


title: first visit [GG2_0055]

value: case


title: NSCLC tumor, biological rep 42

description:
Lung tissue samples obtained from the University of Pittsburgh Lung Cancer SPORE Tissue Bank.
PLS42

tag: gender

tag: adjuvant chemotherapy


title: NSCLC tumor, biological rep 40

description:
Lung tissue samples obtained from the University of Pittsburgh Lung Cancer SPORE Tissue Bank.
PLS40

tag: intraoperative brachtherapy

tag: dead/alive as of 6/11


title: NSCLC tumor, biological rep 34

description:
Lung tissue samples obtained from the University of Pittsburgh Lung Cancer SPORE Tissue Bank.
PLS34

tag: overall survival (months) as of 6/11

tag: smoking status at enrollment


title: NSCLC tumor, biological rep 35

description:
Lung tissue samples obtained from the University of Pittsburgh Lung Cancer SPORE Tissue Bank.
PLS35

tag: packyear

tag: number of years quit


title: NSCLC tumor, biological rep 39

description:
Lung tissue samples obtained from the University of Pittsburgh Lung Cancer SPORE Tissue Bank.
PLS39

tag: age


title: NSCLC tumor, biological rep 33

description:
Lung tissue samples obtained from the University of Pittsburgh Lung Cancer SPORE Tissue Bank.
PLS33


title: first visit [GG2_0054]

tag: body mass index

tag: ethnicity


title: NSCLC tumor, biological rep 37

description:
Lung tissue samples obtained from the University of Pittsburgh Lung Cancer SPORE Tissue Bank.
PLS37


title: NSCLC tumor, biological rep 32

description:
Lung tissue samples obtained from the University of Pittsburgh Lung Cancer SPORE Tissue Bank.
PLS32


title: first visit [GG2_0050]

value: M

tag: gad7 score

tag: hybridization batch


title: first visit [GG2_0052]

tag: Sex

value: AFR

tag: rin


title: first visit [GG2_0046]

tag: anxiety case/control


title: NSCLC tumor, biological rep 28

description:
Lung tissue samples obtained from the University of Pittsburgh Lung Cancer SPORE Tissue Bank.
PLS28

tag: tnm 7th ed stage

tag: 7th ed. tnm classification


title: first visit [GG2_0048]


title: first visit [GG2_0051]

value: A


title: first visit [GG2_0045]

value: ASN


title: first visit [GG2_0043]

value: O


title: first visit [GG2_0047]


title: first visit [GG2_0044]


title: first visit [GG2_0042]


title: NSCLC tumor, biological rep 24

description:
Lung tissue samples obtained from the University of Pittsburgh Lung Cancer SPORE Tissue Bank.
PLS24

tag: gender

tag: adjuvant chemotherapy


title: first visit [GG2_0049]

value: CAH


title: first visit [GG2_0039]

value: F


title: first visit [GG2_0040]

value: CAU

value: control


title: first visit [GG2_0038]


title: NSCLC tumor, biological rep 21

description:
Lung tissue samples obtained from the University of Pittsburgh Lung Cancer SPORE Tissue Bank.
PLS21

value: female

tag: intraoperative brachtherapy

tag: dead/alive as of 6/11

value: non-smoker


title: NSCLC tumor, biological rep 23

description:
Lung tissue samples obtained from the University of Pittsburgh Lung Cancer SPORE Tissue Bank.
PLS23

value: no

tag: overall survival (months) as of 6/11

tag: smoking status at enrollment

value: former


title: NSCLC tumor, biological rep 26

description:
Lung tissue samples obtained from the University of Pittsburgh Lung Cancer SPORE Tissue Bank.
PLS26

value: IB

tag: packyear

tag: number of years quit


title: NSCLC tumor, biological rep 31

description:
Lung tissue samples obtained from the University of Pittsburgh Lung Cancer SPORE Tissue Bank.
PLS31

tag: age

value: yes


title: NSCLC tumor, biological rep 29

description:
Lung tissue samples obtained from the University of Pittsburgh Lung Cancer SPORE Tissue Bank.
PLS29

value: male

value: active


title: NSCLC tumor, biological rep 22

description:
Lung tissue samples obtained from the University of Pittsburgh Lung Cancer SPORE Tissue Bank.
PLS22


title: NSCLC tumor, biological rep 25

description:
Lung tissue samples obtained from the University of Pittsburgh Lung Cancer SPORE Tissue Bank.
PLS25


title: NSCLC tumor, biological rep 19

description:
Lung tissue samples obtained from the University of Pittsburgh Lung Cancer SPORE Tissue Bank.
PLS19


title: NSCLC tumor, biological rep 20

description:
Lung tissue samples obtained from the University of Pittsburgh Lung Cancer SPORE Tissue Bank.
PLS20


title: NSCLC tumor, biological rep 27

description:
Lung tissue samples obtained from the University of Pittsburgh Lung Cancer SPORE Tissue Bank.
PLS27


title: NSCLC tumor, biological rep 18

description:
Lung tissue samples obtained from the University of Pittsburgh Lung Cancer SPORE Tissue Bank.
PLS18


title: first visit [GG2_0037]

value: M

tag: body mass index

tag: ethnicity


title: first visit [GG2_0053]

tag: gad7 score

value: case

tag: hybridization batch


title: first visit [GG2_0036]

tag: Sex

tag: rin


title: first visit [GG2_0034]


title: NSCLC tumor, biological rep 17

description:
Lung tissue samples obtained from the University of Pittsburgh Lung Cancer SPORE Tissue Bank.
PLS17

tag: tnm 7th ed stage


title: first visit [GG2_0031]

tag: anxiety case/control


title: NSCLC tumor, biological rep 14

description:
Lung tissue samples obtained from the University of Pittsburgh Lung Cancer SPORE Tissue Bank.
PLS14

tag: 7th ed. tnm classification

tag: gender


title: NSCLC tumor, biological rep 15

description:
Lung tissue samples obtained from the University of Pittsburgh Lung Cancer SPORE Tissue Bank.
PLS15

tag: adjuvant chemotherapy

tag: intraoperative brachtherapy


title: first visit [GG2_0032]

value: AFR


title: NSCLC tumor, biological rep 13

description:
Lung tissue samples obtained from the University of Pittsburgh Lung Cancer SPORE Tissue Bank.
PLS13

tag: dead/alive as of 6/11

tag: overall survival (months) as of 6/11


title: NSCLC tumor, biological rep 12

description:
Lung tissue samples obtained from the University of Pittsburgh Lung Cancer SPORE Tissue Bank.
PLS12

value: IIB

tag: smoking status at enrollment

tag: packyear


title: first visit [GG2_0035]

tag: age

value: O


title: first visit [GG2_0029]

tag: body mass index

value: A


title: NSCLC tumor, biological rep 11

description:
Lung tissue samples obtained from the University of Pittsburgh Lung Cancer SPORE Tissue Bank.
PLS11

tag: number of years quit


title: NSCLC tumor, biological rep 10

description:
Lung tissue samples obtained from the University of Pittsburgh Lung Cancer SPORE Tissue Bank.
PLS10


title: NSCLC tumor, biological rep 16

description:
Lung tissue samples obtained from the University of Pittsburgh Lung Cancer SPORE Tissue Bank.
PLS16


title: first visit [GG2_0026]

value: F

tag: ethnicity

tag: gad7 score


title: first visit [GG2_0030]

tag: Sex

value: CAU

tag: hybridization batch


title: first visit [GG2_0025]

tag: rin


title: NSCLC tumor, biological rep 9

description:
Lung tissue samples obtained from the University of Pittsburgh Lung Cancer SPORE Tissue Bank.
PLS9

tag: tnm 7th ed stage


title: NSCLC tumor, biological rep 6

description:
Lung tissue samples obtained from the University of Pittsburgh Lung Cancer SPORE Tissue Bank.
PLS6

tag: 7th ed. tnm classification


title: first visit [GG2_0024]

tag: anxiety case/control

value: control


title: first visit [GG2_0033]

value: ASN


title: NSCLC tumor, biological rep 7

description:
Lung tissue samples obtained from the University of Pittsburgh Lung Cancer SPORE Tissue Bank.
PLS7

tag: gender

value: female

tag: adjuvant chemotherapy

value: non-smoker


title: first visit [GG2_0027]

value: CAH


title: NSCLC tumor, biological rep 8

description:
Lung tissue samples obtained from the University of Pittsburgh Lung Cancer SPORE Tissue Bank.
PLS8

value: IB

tag: intraoperative brachtherapy

value: no

tag: dead/alive as of 6/11

value: former


title: NSCLC tumor, biological rep 5

description:
Lung tissue samples obtained from the University of Pittsburgh Lung Cancer SPORE Tissue Bank.
PLS5

value: male

value: yes

tag: overall survival (months) as of 6/11

tag: smoking status at enrollment


title: first visit [GG2_0028]

tag: age

value: M


title: first visit [GG2_0022]

tag: body mass index


title: NSCLC tumor, biological rep 3

description:
Lung tissue samples obtained from the University of Pittsburgh Lung Cancer SPORE Tissue Bank.
PLS3

value: active

tag: packyear

tag: number of years quit


title: first visit [GG2_0023]

tag: ethnicity

value: AFR

tag: gad7 score

value: case


title: NSCLC tumor, biological rep 4

description:
Lung tissue samples obtained from the University of Pittsburgh Lung Cancer SPORE Tissue Bank.
PLS4


title: NSCLC tumor, biological rep 2

description:
Lung tissue samples obtained from the University of Pittsburgh Lung Cancer SPORE Tissue Bank.
PLS2


title: NSCLC tumor, biological rep 1

description:
Lung tissue samples obtained from the University of Pittsburgh Lung Cancer SPORE Tissue Bank.
PLS1

value: IIA


title: first visit [GG2_0021]

tag: Sex

value: F

tag: hybridization batch

value: O


title: first visit [GG2_0020]

value: CAU

value: control

tag: rin


title: first visit [GG2_0018]


title: first visit [GG2_0015]

value: A


title: first visit [GG2_0013]


title: PXB0327-0085 controls-IFN

description:
tissue PXB0327-0085
Uninfected, untreated control mice

source_name: controls-IFN

label_protocol: Amino Allyl aRNA was synthesis by Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion#1753). CyeDye Coupling and fragmentation were performed as the protocol supplied by TORAY Industries, Inc..

tag: experiment model

value: human hepatocyte chimeric mice

tag: inoculated with

value: none (control)

tag: injected with

value: Interferon-alpha (7,000IU/g body weight)

tag: time

value: Day 0

tag: tissue

value: human hepatocytes from mouse liver


title: first visit [GG2_0011]

tag: anxiety case/control


title: first visit [GG2_0017]


title: PXB0327-0098 controls-IFN

description:
tissue PXB0327-0098
Uninfected, untreated control mice


title: PXB0327-0095 controls-IFN

description:
tissue PXB0327-0095
Uninfected, untreated control mice


title: PXB0327-0111 controls-IFN

description:
tissue PXB0327-0111
Uninfected, untreated control mice


title: NSCLC tumor, biological rep 30

description:
Lung tissue samples obtained from the University of Pittsburgh Lung Cancer SPORE Tissue Bank.
PLS30

tag: tnm 7th ed stage

value: IB

tag: 7th ed. tnm classification

tag: gender

value: female

tag: adjuvant chemotherapy

value: no

tag: intraoperative brachtherapy

tag: dead/alive as of 6/11

tag: overall survival (months) as of 6/11

value: former


title: first visit [GG2_0019]

tag: age

value: M

tag: body mass index

tag: ethnicity

value: ASN

tag: gad7 score


title: PXB304-31 HBV IFN 8W

description:
tissue PXB304-31 8W
HBV-infected mice were injected with interferon alpha and euthanized 8 weeks after infection

source_name: HBV IFN 8W

tag: experiment model

value: serum samples from HBV carriers

value: Week 8


title: PXB305-48 HBV IFN 8W

description:
tissue PXB305-48 8W
HBV-infected mice were injected with interferon alpha and euthanized 8 weeks after infection

tag: inoculated with


title: PXB0327-0016 controls-IFN

description:
tissue PXB0327-0016
Uninfected, untreated control mice

tag: injected with


title: first visit [GG2_0009]

tag: Sex

value: F

value: AFR

tag: hybridization batch

value: O

tag: rin


title: first visit [GG2_0012]

tag: anxiety case/control

value: control


title: PXB304-77 HBV IFN 8W

description:
tissue PXB304-77 8W
HBV-infected mice were injected with interferon alpha and euthanized 8 weeks after infection

value: human hepatocyte chimeric mice

tag: time

tag: tissue


title: first visit [GG2_0014]

value: CAU

value: case

value: A


title: first visit [GG2_0010]


title: first visit [GG2_0008]


title: first visit [GG2_0006]


title: PXB0327-0076 controls-IFN

description:
tissue PXB0327-0076
Uninfected, untreated control mice

value: none (control)

value: Interferon-alpha (7,000IU/g body weight)

value: Day 0

value: human hepatocytes from mouse liver


title: first visit [GG2_0005]


title: PXB304-60 HBV non-treat 8W

description:
tissue PXB304-60 8W
HBV-infected mice were euthanized 8 weeks after infection

source_name: HBV non-treat 8W


title: first visit [GG2_0007]


title: PXB304-49 HBV non-treat 8W

description:
tissue PXB304-49 8W
HBV-infected mice were euthanized 8 weeks after infection


title: first visit [GG2_0004]


title: PXB304-26 HBV non-treat 8W

description:
tissue PXB304-26 8W
HBV-infected mice were euthanized 8 weeks after infection


title: first visit [GG2_0001]


title: PXB303-11 HBV IFN 8W

description:
tissue PXB303-11 8W
HBV-infected mice were injected with interferon alpha and euthanized 8 weeks after infection


title: PXB302-53 HCV IFN 8W

description:
tissue PXB302-53 8W
HCV-infected mice were injected with interferon alpha and euthanized 8 weeks after infection

source_name: HCV IFN 8W

value: serum samples from HCV carriers


title: PXB303-26 HBV IFN 8W

description:
tissue PXB303-26 8W
HBV-infected mice were injected with interferon alpha and euthanized 8 weeks after infection


title: first visit [GG2_0003]


title: PXB302-71 HCV IFN 8W

description:
tissue PXB302-71 8W
HCV-infected mice were injected with interferon alpha and euthanized 8 weeks after infection


title: PXB303-51 HBV non-treat 8W

description:
tissue PXB303-51 8W
HBV-infected mice were euthanized 8 weeks after infection


title: first visit [GG1_000210]

value: Z


title: first visit [GG1_000209]


title: first visit [GG1_000208]


title: PXB302-30 HCV IFN 8W

description:
tissue PXB302-30 8W
HCV-infected mice were injected with interferon alpha and euthanized 8 weeks after infection


title: PXB302-83 HCV IFN 8W

description:
tissue PXB302-83 8W
HCV-infected mice were injected with interferon alpha and euthanized 8 weeks after infection


title: first visit [GG2_0002]


title: PXB303-8 HCV non-treat 8W

description:
tissue PXB303-8 8W
HCV-infected mice were euthanized 8 weeks after infection

source_name: HCV non-treat 8W


title: PXB303-45 HBV non-treat 8W

description:
tissue PXB303-45 8W
HBV-infected mice were euthanized 8 weeks after infection


title: first visit [GG1_000205]


title: PXB303-32 HCV non-treat 8W

description:
tissue PXB303-32 8W
HCV-infected mice were euthanized 8 weeks after infection


title: first visit [GG1_000203]


title: first visit [GG1_000211]


title: PXB302-15 HCV IFN 8W

description:
tissue PXB302-15 8W
HCV-infected mice were injected with interferon alpha and euthanized 8 weeks after infection


title: first visit [GG1_000206]


title: PXB0282-0033 HCV day10

description:
PXB282-33
HCV-infected mice were euthanized 10 days after infection

source_name: HCV day10

value: Day 10


title: PXB303-28 HCV non-treat 8W

description:
tissue PXB303-28 8W
HCV-infected mice were euthanized 8 weeks after infection


title: PXB302-80 HCV non-treat 8W

description:
tissue PXB302-80 8W
HCV-infected mice were euthanized 8 weeks after infection


title: PXB302-67 HCV non-treat 8W

description:
tissue PXB302-67 8W
HCV-infected mice were euthanized 8 weeks after infection


title: first visit [GG1_000201]

value: M


title: PXB0282-0049 HCV day10

description:
PXB282-49
HCV-infected mice were euthanized 10 days after infection


title: HT1080_QUE_DMSO_r3

city: Research Triangle Park

first: Rebecca

middle: A

last: Clewell

state: NC

address: 6 Davis Drive

department: Institute for Chemical Safety Sciences

institute: The Hamner Institutes for Health Sciences

description: Sample 142

hyb_protocol: Samples were loaded onto a HT HG-U133+ PM GeneChip™ array plate and run on the GeneTitan® according to manufacturer’s protocol (Applied Biosystems, Carlsbad, CA).

scan_protocol: GeneChips were scanned using the Affymetrix GeneTitan system.

data_processing: Analysis of gene expression data was performed using Partek software (Partek Inc., St. Louis, MO) utlising GC-RMA normalisation. A 1-way ANOVA with interactions was performed to compare gene expression between the treated and control cells. Probability values were adjusted for multiple comparisons using a false discovery rate of 5%

label_protocol: RNA samples were prepared for microarray hybridization using the GeneAtlas™ 3’ IVT Express Kit according to manufacturer’s protocol (Applied Biosystems, Carlsbad, CA).  Briefly, total RNA was reverse transcribed to synthesize first-strand cDNA. The cDNA was then converted into a double-stranded DNA template for transcription. Amplified cRNA (aRNA) was transcribed in vitro, with incorporation of a biotin-congugated nucleotide.  The aRNA was then purified to remove unincorporated NTPs, salts, enzymes, and inorganic phosphate, and samples were fragmented to prepare the biotin-labeled aRNA samples for hybridization onto Affymetrix® GeneChip™

growth_protocol: HT1080 cells were grown under the conditions recommended by ATCC:  Eagle’s Minimum Essential media (EMEM) supplemented with 10% (v/v) heat-inactivated fetal bovine serum (FBS), 100 mg/L streptomycin and 100 U/mL of penicillin G at 37 °C in a humidified atmosphere of 95% air and 5% CO2

extract_protocol: total RNA was collected from the treated cells using the Qiaxtractor and the Qiagen VX reagent pack according to the manufacturer’s protocol (Qiagen, Valencia, CA).  A DNase 1 incubation was performed on all samples to remove any possible contamination of the RNA samples with cellular DNA (Qiagen)

treatment_protocol: Cells were plated in complete media containing 10% heat-inactivated FBS and allowed to attach overnight. Stock solutions of chemicals were prepared in DMSO at 1,000-fold higher concentrations than the final target doses.  Stock solutions were aliquoted and stored at -20C for up to 1 week. Dosing solutions were prepared immediately prior to treatment of the cells by diluting stock solutions 1:200 in complete media.  24 hrs after seeding the cells, the media in each well was supplemented with the dosing solutions (1:5 v/v), for a final chemical dilution of 1:1000 (0.1% vehicle). Cells were maintained in original complete media throughout the course of the experiment.  Immediately following treatment, media was removed and the cells were washed with PBS and prepared for subsequent analyses

tag: cell line

tag: cell type

value: human fibrosarcoma cells

tag: treated with

value: DMSO (vehicle) for 24hrs


title: first visit [GG1_000204]


title: PXB0282-0052 HCV day10

description:
PXB282-52
HCV-infected mice were euthanized 10 days after infection


title: HT1080_QUE_DMSO_r4-nf

description: Sample 143


title: PXB0282-0007 HBV day10

description:
PXB282-7
HBV-infected mice were euthanized 10 days after infection

source_name: HBV day10

value: serum samples from HBV carriers


title: HT1080_QUE_DMSO_r6

description: Sample 145


title: HT1080_QUE_DMSO_r1

description: Sample 140


title: first visit [GG1_000199]

source_name: whole peripheral blood


title: HT1080_QUE_DMSO_r5

description: Sample 144


title: HT1080_QUE_100_r5

description: Sample 137

value: quercetin (QUE) for 24hrs


title: HT1080_QUE_100_r6-nf

description: Sample 138


title: HT1080_QUE_100_r6

description: Sample 139


title: HT1080_QUE_DMSO_r2

description: Sample 141


title: first visit [GG1_000202]

value: F

value: control


title: first visit [GG1_000198]

value: CAU


title: PXB0282-0003 HBV day10

description:
PXB282-3
HBV-infected mice were euthanized 10 days after infection

value: human hepatocyte chimeric mice


title: PXB 175-010 HCV 8w

description:
PXB 175-010
HCV-infected mice were euthanized 8 weeks after infection

source_name: HCV 8w

value: Week 8


title: HT1080_QUE_100_r4-nf

description: Sample 136


title: first visit [GG1_000196]


title: first visit [GG1_000195]


title: PXB 0282-0029 HBV 8w

description:
PXB 0282-0029
HBV-infected mice were euthanized 8 weeks after infection

source_name: HBV 8w


title: PXB 0282-0005 HBV 8w

description:
PXB 0282-0005
HBV-infected mice were euthanized 8 weeks after infection


title: first visit [GG1_000197]


title: PXB 175-006 HCV 8w

description:
PXB 175-006
HCV-infected mice were euthanized 8 weeks after infection


title: PXB 175-002 HCV 8w

description:
PXB 175-002
HCV-infected mice were euthanized 8 weeks after infection


title: HT1080_QUE_100_r2

description: Sample 134


title: first visit [GG1_000193]

value: ASN


title: HT1080_QUE_100_r3

description: Sample 135


title: HT1080_QUE_80_r5

description: Sample 131


title: HT1080_QUE_80_r6

description: Sample 132


title: first visit [GG1_000194]


title: PXB 0282-0022 HBV 8w

description:
PXB 0282-0022
HBV-infected mice were euthanized 8 weeks after infection


title: first visit [GG1_000192]

value: case


title: MW1-css2-10 vs. MW1-Bl6

city: Utrecht

first: Marian

last: Groot Koerkamp

state: Utrecht

address: Heidelberglaan 25

department: Research

country: Netherlands

institute: Princess Maxima Center for Pediatric Oncology

hyb_protocol: Tecan HS4800 hybridization

scan_protocol: Scanning of slides using Agilent G256BA scanner Imagene feature extraction

data_processing: Normalization was done using print-tip LOESS as described in (Yang et al. 2002), for all gene probes using no background substraction and a span of 0.4. Probes flagged as absent, or with a (nearly) saturated signal (i.e., > 2^15) in either channel were not considered for the estimation of the LOESS curve. Signals were corrected for dye bias using intrinsic gene-specific dye biases estimated from the hybset itself, as described in Margaritis, Lijnzaad et al., Mol. Sys. Biol. 2009

label_protocol: robot amplification and labeling v1.0

extract_protocol: RNA isolation using Trizol v1.0 (tissue sections)

tag: strain

value: P14 hypocampus


title: PXB 0282-0004 HBV 8w

description:
PXB 0282-0004
HBV-infected mice were euthanized 8 weeks after infection

value: human hepatocytes from mouse liver


title: first visit [GG1_000190]

tag: age


title: PXB 282-48 HCV day10

description:
PXB 282-48
HCV-infected mice were euthanized 10 days after infection

value: serum samples from HCV carriers


title: first visit [GG1_000189]

tag: body mass index

value: AFR

value: Z