title: det2 samples rep2

city: Valencia

first: David

last: Alabadi

state: Valencia

address: Av de los Naranjos s/n, Campus UPV, Edificio 8E

department: Biologia del Desarrollo

country: Spain

institute: Instituto de Biologia Molecular y Celular de Plantas (CSIC-UPV)

description: det2 seedlings labelled with Cy3 (replica 2), compared to WT seedlings labelled with Cy5 (replica 2)

hyb_protocol: DNA onto slides was rehydrated by placing the slide upside-down over a water bath at 60°C for 10 s, and snap dry onto a heat block at 65°C. Rehydratation was repeated 3 times. DNA was immobilized by UV light by exposing the slides DNA-side-up to 65 mJ in a UV cross-linker (Stratagene). Slides were then washed twice in 0.1% SDS and 4 times in water, 2 min each wash at RT, and finally dipped in 96% ethanol for 1 min and dried by centrifugation at 2000 rpm 1 min at RT. Slides were prehybridized for 30 min at 42°C with 100 µL of prehybridization solution (6x SSC (Sigma), 1% BSA (Sigma) and 0.5% SDS (Sigma)), under a 60x22 mm coverslip LifterSlip (Erie Scientific) in a microarray hybridization chamber (ArrayIt Hybridization Cassette, Telechem). Slides were rinsed 5 times in H2O in a slide rack at RT and dried by centrifugation at 2000 rpm 1 min at RT. Slides were hybridized immediately.  Both coupled aa-aRNA (Cy3 and Cy5) were mixed and fragmented in the presence of 20 µg of tRNA (Ambion) and 20 µg of poly(A) (Roche) using the RNA fragmentation Reagent (Ambion) as described by the manufacturer, in a final volume of 10 µL. Fragmented aa-aRNA was used directly in the hybridization mix, which contains 50 µL deionized formamide (Sigma), 30 µL 20x SSC, 5 µL 100x Denhardt´s solution (Sigma), and 5 µL 10% SDS in a final volume of 100 µL. Hybridization mixture was denatured at 95 °C for 5 min, spun briefly, and applied by capillarity between a pre-treated slide (see above) and a 60x42 mm coverslip LifterSlip. Slides were incubated o/n at 37°C in a microarray hybridization chamber (ArrayIt Hybridization Cassette, Telechem). Slides were washed sequentially once in 1x SSC 0.1% SDS 5 min at 30°C; once in 0.2x SSC 0.1% SDS 5 min at 30°C; twice in 0.1x SSC 2 min each at 30°C; and finally 0.01x SSC 10 sec at RT. Slides were dried by centrifugation at 2000 rpm 1 min at RT.

scan_protocol: Hybridized microarray slides were scanned at 532-nm for the Cy3 and 635-nm for the Cy5 dyes, with a GenePix 4000B scanner (Axon Molecular Devices, Sunnyvale CA), at 10-mm resolution and 100% laser power.

data_processing: Spot intensities were quantified using GenePix Pro 6.0 microarray-analysis software (Axon Molecular Devices, Sunnyvale CA). Spots with a net intensity in both channels lower than the median signal background plus twice standard deviations were removed as low signal spots.  Data were normalized by median global intensity using the GenePix Pro 6.0 software.

organism: Arabidopsis thaliana

source_name: untreated WT seedlings

label_protocol: RNA was amplified using the MessageAmp II aRNA Amplification kit (Ambion), basically as described by the manufacturer. 5-(3-aminoallyl)-UTP (aa-UTP) (Ambion) was incorporated into the amplified RNA (aRNA) at ratio 1:1 with UTP. After purification 7.5 µg of aminoallyl-aRNA (aa-aRNA) were used in a coupling reaction with either fluorescent Cy3 or Cy5 as reactive N-hydroxyl succinimidal dyes (NHS-dyes) (Amersham Pharmacia Biotech, Piscataway, NJ). For this, each aliquot of Cy3 or Cy5 were dissolved in 20 µL of DMSO and used in four coupling reactions. aa-aRNA was dissolved in 15 µL of freshly-made 0.1 M NaCO3 pH 9.0, and mixed with 5 µl of either Cy-3 or Cy-5 dye. Coupling was allowed for 1 h at RT in the dark. Reaction was stopped with 35 µL of 100 mM sodium acetate pH 5.2 and incubated 5 min in the dark. Fluorescent aa-aRNA was purified using a MegaClear purification column (Ambion) as described by the manufacturer. Coupled aa-aRNA (250-300 pmol Cy dye in 5-7 µg aa-aRNA) was dried in a speedvac and dissolved in 2.5 µL of filtered water.

growth_protocol: Wild type Col-0 and det2-1 mutant seeds were surface sterilized and sown on sterile filter papers, placed on half-strength MS media plus 1% sucrose and stratified for 4 days at 4ºC in darkness. Germination of all seeds was induced by placing plates at 20ºC and under white fluorescent light (150 mmol m-2 s-1) for 8 h. Next, filter papers with seeds were transferred to treatment plates that were wrapped in aluminum foil and kept in the dark at the same temperature fora total of 7 days.

extract_protocol: Total RNA was extracted from frozen, whole etiolated seedlings, using the RNeasy Plant Mini Kit (Qiagen, Hilden, Germany).

treatment_protocol: Treatment plates contained either 1 mM PAC, 1 mM PAC+1 mM EBR, or 50 mM GA3.

tag: sample type

value: 7-day-old dark-grown seedlings

tag: age

value: 7 d

value: seedling

tag: genetic background

tag: genotype

value: wild type

value: untreated

source_name: untreated det2-1 seedlings


title: PAC samples rep2

status: Public on Aug 02 2012

type: RNA

description: WT mock-treated seedlings labelled with Cy5 (replica 2), compared with WT PAC-treated seedlings labelled with Cy3 (replica 2)

molecule: total RNA

source_name: WT mock treated seedlings

tag: tissue

tag: treatment

value: mock

source_name: WT PAC-treated seedlings

value: PAC


title: det2+GA3 samples rep2

description: det2 seedlings labelled with Cy3 (replica 2), compared to GA3-treated det2 seedlings labelled with Cy5 (replica 2)

source_name: GA3-treated det2 seedlings


title: MCF7 with negative control siRNA, biological Rep6

city: St Lucia

first: Michael

middle: Andrew

last: Pearen

state: Queensland

address: The University of Queensland

country: Australia

institute: Institute for Molecular Bioscience

description: Replicate 6

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Affymetrix GeneChip Scanner 3000 7G

data_processing:
Exon level data was processed using GeneSpring GX version 11.5.1 using the RMA16 normalization algorithm
probe group file: HuEx-1_0-st-v2.r2.pgf

label: biotin

organism: Homo sapiens

source_name: MCF7 breast cancer cell line

label_protocol: Standard Affymetrix protocol

growth_protocol: MCF-7 cells were maintained in DMEM nutrient mixture F-12 plus 10% FBS.  cells lines were maintained at 37°C and 5% CO2.

extract_protocol: Total RNA was extracted using  Trizol Reagent (Invitrogen). RNA was further purified by using RNeasy RNA mini-purification columns (Qiagen).

treatment_protocol: Cells were transfected with siRNA directed against PRMT6 or negative control siRNA (Ambion Silencer Select negative control).

tag: cell line

value: negative control siRNA


title: MCF7 with negative control siRNA, biological Rep2

description: Replicate 2


title: MCF7 with siRNA against PRMT6, biological Rep6

description: Replicate 6

value: siRNA against PRMT6


title: MCF7 with negative control siRNA, biological Rep5

description: Replicate 5


title: PAC+EBR samples rep1

description: WT seedlings treated with PAC+EBR labelled with Cy5 (replica 1), compared with WT PAC-treated seedlings labelled with Cy3 (replica 1)

source_name: WT seedlings treated with PAC+EBR

value: PAC + EBR


title: day 90, CEA424-Tag mouse 3

city: Bonn

first: Joachim

middle: L

last: Schultze

address: Carl-Troll-Str. 31

department: LIMES Institute

country: Germany

institute: University of Bonn

description: tumor with normal tissue

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using vsn normalisation using R Statistical language and packages from the Bioconductor project

organism: Mus musculus

source_name: antrum/stomach

label_protocol: Biotinylated cRNA was prepared with the  Illumina® TotalPrep™ RNA Amplification Kit (Applied Biosystems, Darmstadt, Germany).

extract_protocol: RNA was extracted with Nucleospin extraction kit  according to the manufacturer´s protocol ((Machery&Nagel, Düren, Germany). Quality control was performed with denaturing gel electrophoresis and UV measurement.

value: stomach antrum tumor with normal tissue

value: CEA424-SV40 -T antigen transgenic


title: day 90, CEA424-Tag mouse 1

description: tumor with normal tissue


title: det2+GA3 samples rep1

description: det2 seedlings labelled with Cy5 (replica 1), compared to GA3-treated det2 seedlings labelled with Cy3 (replica 1)


title: MCF7 with negative control siRNA, biological Rep4

description: Replicate 4


title: day 90, CEA424-Tag mouse 2

description: tumor with normal tissue


title: PAC+EBR samples rep2

description: WT seedlings treated with PAC+EBR labelled with Cy5 (replica 2), compared with WT PAC-treated seedlings labelled with Cy3 (replica 2)


title: day 60, CEA424-Tag mouse 2

description: tumor with normal tissue


title: det2 samples rep1

description: det2 seedlings labelled with Cy5 (replica 1), compared to WT seedlings labelled with Cy3 (replica 1)


title: day 60, CEA424-Tag mouse 1

description: tumor with normal tissue


title: PAC samples rep1

description: WT mock-treated seedlings labelled with Cy5 (replica 1), compared with WT PAC-treated seedlings labelled with Cy3 (replica 1)


title: day 60, CEA424-Tag mouse 3

description: tumor with normal tissue


title: MCF7 with negative control siRNA, biological Rep1

description: Replicate 1


title: MCF7 with negative control siRNA, biological Rep3

description: Replicate 3


title: MCF7 with siRNA against PRMT6, biological Rep2

description: Replicate 2


title: NNI-9 rep1

city: Singapore

first: Edwin

last: Sandanaraj

address: 11 Jalan Tan Tock Seng

department: Research

country: Singapore

institute: NNI

description:
Date: Feb 1, 2011
AFG1133-7

hyb_protocol: Affymetrix standard hybridization protocol

scan_protocol: Affymetrix scanning protocol

data_processing: The data were processed using mas5 normalized scaled and log2 scaleded in R2.14

source_name: Primary neurosphere

label_protocol: Affymetrix standard labelling protocol

growth_protocol: Graded brain tumor specimens were obtained with informed consent, as part of a study protocol approved by the SingHealth Centralised Institutional Review Board A. GPC lines were described in our previous work.5 Briefly, cells were seeded as free-floating spheres at a density of 2,500 cells per cm2 in chemically defined serum-free growth medium containing basic fibroblast growth factor (bFGF; 20 ng/ml; PeproTech, New Jersey), epidermal growth factor (EGF; 20 ng/ml; PeproTech), heparin (5 ug/ml; Sigma-Aldrich, St Louis), and serumfree supplement (B27; 1x; Gibco, Grand Island, NY) in a 3:1 mix of Dulbecco's modified Eagle's medium (DMEM; Sigma-Aldrich) and Ham's F-12 Nutrient Mixture (F-12; Gibco). Neurospheres were mechanically triturated with a flame-drawn glass Pasteur pipette twice weekly and re-seeded in fresh culture medium

extract_protocol: Total RNA was isolated from tumor neurospheres using TRI Reagent (Molecular Research Center, Cincinnati, OH). Thereafter, RNA samples were hybridized to Affymetrix GeneChip® Human Genome U133 Plus 2.0 Array using 3' IVT express kit (Affymetrix Inc, Santa Clara, California).

value: brain tumor

tag: histology

value: Glioblastoma multiforme

tag: grade

value: IV


title: MCF7 with siRNA against PRMT6, biological Rep4

description: Replicate 4


title: MCF7 with siRNA against PRMT6, biological Rep3

description: Replicate 3


title: day 30, CEA424-Tag mouse 3

description: tumor with normal tissue


title: day 30, CEA424-Tag mouse 1

description: tumor with normal tissue


title: Serie L, HepG2 exposed to EtOH for 48h, biological rep 1

city: Maastricht

first: Christina

last: Magkoufopoulou

address: Universiteitssingel 50

department: Health Risk Analysis and Toxicology

country: Netherlands

institute: Maastricht University

hyb_protocol: 12.5µg of cRNA were hybridized for 16 hr on 45°C on GeneChip Human Genome U133 Plus 2.0 Array, using Affymetrix® GeneChip® Fluidics Station 450 and the GeneChip Hybridization, Wash and Stain Kit

scan_protocol: Arrays were scanned using genechip scanner 3000 7G

data_processing: Obtained data sets were re-annotated to the MBNI Custom CDF-files (http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/genomic_curated_CDF.asp) (Dai et al., 2005) and RMA normalized (Irizarry et al., 2003) using the NuGOExpressionFileCreator, an enhanced version of the standard ExpressionFileCreator module that is present in GenePattern (De Groot et al., 2008). The resulting 17,788 probe sets represent 17,726 unique genes and 62 internal controls

source_name: hepatocellular carcinoma cell line

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 250ng total RNA using the 3’ IVT express kit

growth_protocol: HepG2 cells were cultured in 6-well plates in the presence of minimal essential medium (MEM) supplemented with 1% non-essential amino acids, 1% sodium-pyruvate, 2% penicillin/streptomycin and 10% fetal bovine serum (FBS) (all from Gibco BRL, Breda, The Netherlands). The cells were incubated at 37 C and 5% CO2.

extract_protocol: Trizol extraction was performed using the miRNAeasy kit from qiagen accoding to the manufacturer’s protocol

treatment_protocol: When the HepG2 cells were 80% confluent, the medium was replaced with fresh medium containing either compound or solvent (0.5% DMSO, 0.5% EtOH or PBS)

tag: compound, dose

value: EtOH

tag: time


title: MCF7 with siRNA against PRMT6, biological Rep1

description: Replicate 1


title: control mouse 2

description: control tissue

value: 2-6 months

value: normal stomach antrum


title: day 30, CEA424-Tag mouse 2

description: tumor with normal tissue


title: Serie L, HepG2 exposed to EtOH for 48h, biological rep 2


title: Serie L, HepG2 exposed to EtOH for 48h, biological rep 3


title: control mouse 1

description: control tissue


title: Serie K, HepG2 exposed to CP for 48h, biological rep 3

value: CP


title: Serie L, HepG2 exposed to Prog for 48h, biological rep 2

value: Prog


title: Serie L, HepG2 exposed to PCP for 48h, biological rep 3

value: PCP


title: Serie K, HepG2 exposed to PBS for 48h, biological rep 2

value: PBS


title: Serie L, HepG2 exposed to Prog for 48h, biological rep 3


title: Serie L, HepG2 exposed to PCP for 48h, biological rep 1


title: Serie L, HepG2 exposed to Prog for 48h, biological rep 1


title: Serie K, HepG2 exposed to CP for 48h, biological rep 2


title: Mock_cells_rep1

city: Trieste

first: Danilo

last: Licastro

department: Genomica Funzionale

country: Italy

institute: CBM

hyb_protocol: The biotinylated cRNA targets are were cleaned up, fragmented, and hybridized to GeneChip expression arrays according to standard Affymetrix protocols.GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with R/Bioconductor version 2.10 using Affy package default analysis settings. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: pLenti transduced cell lines Mock (empty vector)

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from total RNA using GeneChip IVT Labeling Kit.

extract_protocol: RNA Isolation was performed using the Tripure Isolation Reagent (Roche).Quality control was performed with Agilent Bioanalyser.

tag: cell type

value: human gastric tubular adenocarcinoma

tag: tissue origin

value: stomach (70 year-old female)


title: Serie L, HepG2 exposed to PCP for 48h, biological rep 2


title: control mouse 3

description: control tissue

value: wild type


title: Serie K, HepG2 exposed to PBS for 48h, biological rep 3


title: MCF7 with siRNA against PRMT6, biological Rep5

description: Replicate 5

value: siRNA against PRMT6


title: Serie K, HepG2 exposed to CP for 48h, biological rep 1


title: Serie K, HepG2 exposed to cisPt for 48h, biological rep 3

value: cisPt


title: Serie I, HepG2 exposed to DMSO for 48h, biological rep 2

value: DMSO


title: Serie J, HepG2 exposed to DMSO for 48h, biological rep 3


title: Serie K, HepG2 exposed to cisPt for 48h, biological rep 1


title: Serie I, HepG2 exposed to DMSO for 48h, biological rep 3


title: Serie K, HepG2 exposed to PBS for 48h, biological rep 1


title: Serie J, HepG2 exposed to Sim for 48h, biological rep 3

value: Sim


title: Serie K, HepG2 exposed to cisPt for 48h, biological rep 2


title: Ex1_cells_rep1

source_name: pLenti transduced cell lines overexpressing CDH1a


title: Serie I, HepG2 exposed to DMSO for 48h, biological rep 1


title: Serie I, HepG2 exposed to NBZ for 48h, biological rep 2

value: NBZ


title: Serie I, HepG2 exposed to NBZ for 48h, biological rep 1


title: Serie I, HepG2 exposed to Sim for 48h, biological rep 1


title: Serie J, HepG2 exposed to CCl4 for 48h, biological rep 3


title: Serie I, HepG2 exposed to CCl4 for 48h, biological rep 1


title: Serie J, HepG2 exposed to Anis for 48h, biological rep 3

value: Anis


title: Serie J, HepG2 exposed to BDCM for 48h, biological rep 3

value: BDCM


title: Serie I, HepG2 exposed to DEN for 48h, biological rep 2

value: DEN


title: Serie I, HepG2 exposed to Anis for 48h, biological rep 1


title: Serie I, HepG2 exposed to Anis for 48h, biological rep 2


title: Serie I, HepG2 exposed to MOCA for 48h, biological rep 1

value: MOCA


title: Serie I, HepG2 exposed to CCl4 for 48h, biological rep 2


title: Serie I, HepG2 exposed to DEN for 48h, biological rep 1


title: Serie I, HepG2 exposed to BDCM for 48h, biological rep 1


title: Serie J, HepG2 exposed to NBZ for 48h, biological rep 3


title: Serie I, HepG2 exposed to MOCA for 48h, biological rep 2


title: Serie I, HepG2 exposed to IQ for 48h, biological rep 3

value: IQ


title: Serie I, HepG2 exposed to MOCA for 48h, biological rep 3


title: Serie I, HepG2 exposed to BDCM for 48h, biological rep 2


title: Serie J, HepG2 exposed to DEN for 48h, biological rep 3


title: Serie I, HepG2 exposed to Sim for 48h, biological rep 2


title: Serie I, HepG2 exposed to IQ for 48h, biological rep 1


title: Serie I, HepG2 exposed to IQ for 48h, biological rep 2


title: Serie I, HepG2 exposed to HCH for 48h, biological rep 1

value: HCH


title: Serie I, HepG2 exposed to HCH for 48h, biological rep 2


title: Serie I, HepG2 exposed to EuG for 48h, biological rep 3

value: EuG


title: Serie I, HepG2 exposed to EthylB for 48h, biological rep 3

value: EthylB


title: Serie I, HepG2 exposed to HCH for 48h, biological rep 3


title: Serie I, HepG2 exposed to EuG for 48h, biological rep 2


title: Serie I, HepG2 exposed to EuG for 48h, biological rep 1


title: Serie I, HepG2 exposed to EthylB for 48h, biological rep 2


title: Serie I, HepG2 exposed to ENU for 48h, biological rep 3

value: ENU


title: Serie I, HepG2 exposed to ENU for 48h, biological rep 2


title: Serie I, HepG2 exposed to EthylB for 48h, biological rep 1


title: Serie I, HepG2 exposed to Cb for 48h, biological rep 1

value: Cb


title: Serie I, HepG2 exposed to Cb for 48h, biological rep 2


title: Serie I, HepG2 exposed to DDT for 48h, biological rep 2

value: DDT


title: Serie I, HepG2 exposed to ENU for 48h, biological rep 1


title: Serie I, HepG2 exposed to Cb for 48h, biological rep 3


title: Serie I, HepG2 exposed to CAP for 48h, biological rep 1

value: CAP


title: Serie I, HepG2 exposed to ASK for 48h, biological rep 1

value: ASK


title: Serie I, HepG2 exposed to DDT for 48h, biological rep 1


title: Serie I, HepG2 exposed to COU for 48h, biological rep 2

value: COU


title: Serie I, HepG2 exposed to CAP for 48h, biological rep 2


title: Serie I, HepG2 exposed to COU for 48h, biological rep 3


title: Serie I, HepG2 exposed to ASK for 48h, biological rep 3


title: Serie I, HepG2 exposed to DDT for 48h, biological rep 3


title: Serie I, HepG2 exposed to COU for 48h, biological rep 1


title: Serie I, HepG2 exposed to CAP for 48h, biological rep 3


title: Serie I, HepG2 exposed to BZ for 48h, biological rep 1

value: BZ


title: Serie I, HepG2 exposed to BZ for 48h, biological rep 2


title: Serie I, HepG2 exposed to BZ for 48h, biological rep 3


title: Serie I, HepG2 exposed to ABP for 48h, biological rep 2

value: ABP


title: Serie I, HepG2 exposed to ASK for 48h, biological rep 2


title: Serie I, HepG2 exposed to ABP for 48h, biological rep 3


title: Serie H, HepG2 exposed to VitC for 48h, biological rep 2

value: VitC


title: Serie H, HepG2 exposed to VitC for 48h, biological rep 3


title: Serie H, HepG2 exposed to PBS for 48h, biological rep 3

value: PBS


title: Serie I, HepG2 exposed to 2-Cl for 48h, biological rep 3


title: Serie I, HepG2 exposed to 2-Cl for 48h, biological rep 2


title: Serie I, HepG2 exposed to 2-Cl for 48h, biological rep 1


title: Serie H, HepG2 exposed to PBS for 48h, biological rep 2


title: Serie I, HepG2 exposed to ABP for 48h, biological rep 1


title: Serie G, HepG2 exposed to DMSO for 48h, biological rep 2

value: DMSO


title: Serie G, HepG2 exposed to Phenol for 48h, biological rep 2

value: Phenol


title: Serie F, HepG2 exposed to TBTO for 48h, biological rep 2

value: TBTO


title: Serie H, HepG2 exposed to PBS for 48h, biological rep 1


title: Serie H, HepG2 exposed to VitC for 48h, biological rep 1


title: Serie F, HepG2 exposed to TBTO for 48h, biological rep 1


title: Serie G, HepG2 exposed to Phenol for 48h, biological rep 3


title: Serie F, HepG2 exposed to Resor for 48h, biological rep 3

value: Resor


title: Serie F, HepG2 exposed to Resor for 48h, biological rep 1


title: Serie G, HepG2 exposed to DMSO for 48h, biological rep 3


title: Serie F, HepG2 exposed to Phen for 48h, biological rep 3

value: Phen


title: Serie F, HepG2 exposed to Resor for 48h, biological rep 2


title: Serie G, HepG2 exposed to DMSO for 48h, biological rep 1


title: Serie F, HepG2 exposed to Phen for 48h, biological rep 2


title: Serie F, HepG2 exposed to TBTO for 48h, biological rep 3


title: Serie F, HepG2 exposed to Paracres for 48h, biological rep 3

value: Paracres


title: Serie F, HepG2 exposed to Paracres for 48h, biological rep 1


title: Serie F, HepG2 exposed to Paracres for 48h, biological rep 2


title: Serie F, HepG2 exposed to Ethyl for 48h, biological rep 3

value: Ethyl


title: Serie F, HepG2 exposed to Ethyl for 48h, biological rep 2


title: Serie E, HepG2 exposed to DMSO for 48h, biological rep 2


title: Serie F, HepG2 exposed to DES for 48h, biological rep 1

value: DES


title: Serie E, HepG2 exposed to DMSO for 48h, biological rep 3


title: Serie F, HepG2 exposed to DES for 48h, biological rep 3


title: Serie F, HepG2 exposed to Phen for 48h, biological rep 1


title: Serie E, HepG2 exposed to DMBA for 48h, biological rep 1

value: DMBA


title: Serie E, HepG2 exposed to 4AAF for 48h, biological rep 3


title: Serie D, HepG2 exposed to DMSO for 48h, biological rep 3


title: Serie E, HepG2 exposed to Sulfi for 48h, biological rep 2

value: Sulfi


title: Serie E, HepG2 exposed to Cur for 48h, biological rep 2

value: Cur


title: Serie D, HepG2 exposed to DMSO for 48h, biological rep 1


title: Serie E, HepG2 exposed to 4AAF for 48h, biological rep 2


title: Serie E, HepG2 exposed to Sulfi for 48h, biological rep 1


title: Serie E, HepG2 exposed to Cur for 48h, biological rep 3


title: Serie E, HepG2 exposed to Cur for 48h, biological rep 1


title: Serie F, HepG2 exposed to Ethyl for 48h, biological rep 1


title: Serie E, HepG2 exposed to DMBA for 48h, biological rep 2


title: Serie E, HepG2 exposed to DMBA for 48h, biological rep 3


title: Serie D, HepG2 exposed to WY for 48h, biological rep 3

value: WY


title: Serie D, HepG2 exposed to DMSO for 48h, biological rep 2


title: Serie E, HepG2 exposed to 4AAF for 48h, biological rep 1


title: Serie D, HepG2 exposed to WY for 48h, biological rep 2


title: Serie E, HepG2 exposed to Sulfi for 48h, biological rep 3


title: Serie D, HepG2 exposed to WY for 48h, biological rep 1


title: Serie D, HepG2 exposed to Res for 48h, biological rep 1

value: Res


title: Serie D, HepG2 exposed to PhB for 48h, biological rep 1

value: PhB


title: Serie F, HepG2 exposed to DES for 48h, biological rep 2


title: Serie G, HepG2 exposed to Phenol for 48h, biological rep 1


title: Serie D, HepG2 exposed to Res for 48h, biological rep 3


title: Serie D, HepG2 exposed to PhB for 48h, biological rep 3


title: Serie D, HepG2 exposed to PhB for 48h, biological rep 2


title: Serie D, HepG2 exposed to NPD for 48h, biological rep 3

value: NPD


title: Serie D, HepG2 exposed to Res for 48h, biological rep 2


title: Serie D, HepG2 exposed to NPD for 48h, biological rep 2


title: Serie D, HepG2 exposed to MMC for 48h, biological rep 3

value: MMC


title: Serie D, HepG2 exposed to NPD for 48h, biological rep 1


title: Serie D, HepG2 exposed to DMN for 48h, biological rep 3

value: DMN


title: Serie D, HepG2 exposed to DEPH for 48h, biological rep 3

value: DEPH


title: Serie D, HepG2 exposed to DMN for 48h, biological rep 2


title: Serie D, HepG2 exposed to DEPH for 48h, biological rep 1


title: Serie D, HepG2 exposed to DMN for 48h, biological rep 1


title: Serie D, HepG2 exposed to DEPH for 48h, biological rep 2


title: Serie D, HepG2 exposed to 2AAF for 48h, biological rep 3


title: Serie D, HepG2 exposed to ANAC for 48h, biological rep 3

value: ANAC


title: Serie D, HepG2 exposed to 2CMP for 48h, biological rep 3


title: Serie D, HepG2 exposed to 2CMP for 48h, biological rep 1


title: Serie D, HepG2 exposed to 2AAF for 48h, biological rep 2


title: Serie D, HepG2 exposed to MMC for 48h, biological rep 1


title: Serie D, HepG2 exposed to 2CMP for 48h, biological rep 2


title: Serie D, HepG2 exposed to ANAC for 48h, biological rep 1


title: Serie C, HepG2 exposed to Diclo for 48h, biological rep 3

value: Diclo


title: Serie D, HepG2 exposed to MMC for 48h, biological rep 2


title: Serie D, HepG2 exposed to ANAC for 48h, biological rep 2


title: Serie C, HepG2 exposed to Diclo for 48h, biological rep 2


title: Serie B, HepG2 exposed to DMSO for 48h, biological rep 3

value: DMSO


title: Serie C, HepG2 exposed to APAP for 48h, biological rep 2

value: APAP


title: Serie C, HepG2 exposed to Diclo for 48h, biological rep 1


title: Serie C, HepG2 exposed to APAP for 48h, biological rep 1


title: Serie C, HepG2 exposed to APAP for 48h, biological rep 3


title: Serie B, HepG2 exposed to DMSO for 48h, biological rep 1


title: Serie B, HepG2 exposed to DMSO for 48h, biological rep 2


title: Serie B, HepG2 exposed to Que for 48h, biological rep 3

value: Que


title: Serie E, HepG2 exposed to DMSO for 48h, biological rep 1


title: Serie D, HepG2 exposed to 2AAF for 48h, biological rep 1


title: Serie B, HepG2 exposed to ampC for 48h, biological rep 3

value: ampC


title: Serie A, HepG2 exposed to E2 for 48h, biological rep 3


title: Serie B, HepG2 exposed to 8HQ for 48h, biological rep 1


title: Serie A, HepG2 exposed to E2 for 48h, biological rep 2


title: Serie B, HepG2 exposed to Que for 48h, biological rep 2


title: Serie A, HepG2 exposed to E2 for 48h, biological rep 1


title: Serie B, HepG2 exposed to ampC for 48h, biological rep 1


title: Serie B, HepG2 exposed to ampC for 48h, biological rep 2


title: Serie B, HepG2 exposed to 8HQ for 48h, biological rep 3


title: Serie A, HepG2 exposed to TCDD for 48h, biological rep 3

value: TCDD


title: Serie A, HepG2 exposed to TCDD for 48h, biological rep 1


title: Serie A, HepG2 exposed to CsA for 48h, biological rep 1

value: CsA


title: Serie A, HepG2 exposed to AFB1 for 48h, biological rep 3


title: Serie A, HepG2 exposed to TCDD for 48h, biological rep 2


title: Serie B, HepG2 exposed to Que for 48h, biological rep 1


title: Serie A, HepG2 exposed to CsA for 48h, biological rep 2


title: Serie B, HepG2 exposed to 8HQ for 48h, biological rep 2


title: Serie A, HepG2 exposed to CsA for 48h, biological rep 3


title: Serie A, HepG2 exposed to BaP for 48h, biological rep 2

value: BaP


title: Serie K, HepG2 exposed to EtOH for 24h, biological rep 1

value: EtOH


title: Serie K, HepG2 exposed to EtOH for 24h, biological rep 2


title: Serie A, HepG2 exposed to AFB1 for 48h, biological rep 1


title: Serie K, HepG2 exposed to Prog for 24h, biological rep 3

value: Prog


title: Serie K, HepG2 exposed to EtOH for 24h, biological rep 3


title: Serie K, HepG2 exposed to PCP for 24h, biological rep 2

value: PCP


title: Serie A, HepG2 exposed to BaP for 48h, biological rep 3


title: Serie A, HepG2 exposed to AFB1 for 48h, biological rep 2


title: Serie A, HepG2 exposed to BaP for 48h, biological rep 1


title: Serie K, HepG2 exposed to Prog for 24h, biological rep 1


title: Serie K, HepG2 exposed to Prog for 24h, biological rep 2


title: Serie J, HepG2 exposed to PBS for 24h, biological rep 3

value: PBS


title: Serie K, HepG2 exposed to PCP for 24h, biological rep 1


title: Serie J, HepG2 exposed to CP for 24h, biological rep 3

value: CP


title: Serie J, HepG2 exposed to PBS for 24h, biological rep 2


title: Serie J, HepG2 exposed to CP for 24h, biological rep 2


title: Serie K, HepG2 exposed to PCP for 24h, biological rep 3


title: Serie J, HepG2 exposed to CP for 24h, biological rep 1


title: Serie J, HepG2 exposed to cisPt for 24h, biological rep 3

value: cisPt


title: Serie I, HepG2 exposed to Sim for 24h, biological rep 3

value: Sim


title: Serie J, HepG2 exposed to PBS for 24h, biological rep 1


title: Serie H, HepG2 exposed to DMSO for 24h, biological rep 2


title: Serie H, HepG2 exposed to DMSO for 24h, biological rep 3


title: Serie H, HepG2 exposed to DMSO for 24h, biological rep 1


title: Serie H, HepG2 exposed to Sim for 24h, biological rep 1


title: Serie H, HepG2 exposed to Sim for 24h, biological rep 2


title: Serie H, HepG2 exposed to BDCM for 24h, biological rep 2

value: BDCM


title: Serie J, HepG2 exposed to cisPt for 24h, biological rep 1


title: Serie H, HepG2 exposed to NBZ for 24h, biological rep 2

value: NBZ


title: Serie H, HepG2 exposed to BDCM for 24h, biological rep 1


title: Serie I, HepG2 exposed to BDCM for 24h, biological rep 3


title: Serie H, HepG2 exposed to CCl4 for 24h, biological rep 1


title: Serie I, HepG2 exposed to Anis for 24h, biological rep 3

value: Anis


title: Serie H, HepG2 exposed to NBZ for 24h, biological rep 1


title: Serie J, HepG2 exposed to cisPt for 24h, biological rep 2


title: Serie H, HepG2 exposed to DEN for 24h, biological rep 2

value: DEN


title: Serie I, HepG2 exposed to DEN for 24h, biological rep 3


title: Serie H, HepG2 exposed to DEN for 24h, biological rep 1


title: Serie H, HepG2 exposed to MOCA for 24h, biological rep 2

value: MOCA


title: Serie H, HepG2 exposed to MOCA for 24h, biological rep 3


title: Serie H, HepG2 exposed to Anis for 24h, biological rep 2


title: Serie H, HepG2 exposed to IQ for 24h, biological rep 3

value: IQ


title: Serie H, HepG2 exposed to MOCA for 24h, biological rep 1


title: Serie I, HepG2 exposed to NBZ for 24h, biological rep 3


title: Serie I, HepG2 exposed to DMSO for 24h, biological rep 3

value: DMSO


title: Serie H, HepG2 exposed to IQ for 24h, biological rep 2


title: Serie H, HepG2 exposed to HCH for 24h, biological rep 2

value: HCH


title: Serie H, HepG2 exposed to Anis for 24h, biological rep 1


title: Serie H, HepG2 exposed to HCH for 24h, biological rep 1


title: Serie H, HepG2 exposed to EthylB for 24h, biological rep 3

value: EthylB


title: Serie H, HepG2 exposed to EuG for 24h, biological rep 2

value: EuG


title: Serie H, HepG2 exposed to EuG for 24h, biological rep 1


title: Serie H, HepG2 exposed to IQ for 24h, biological rep 1


title: Serie H, HepG2 exposed to HCH for 24h, biological rep 3


title: Serie H, HepG2 exposed to EuG for 24h, biological rep 3


title: Serie H, HepG2 exposed to EthylB for 24h, biological rep 1


title: Serie H, HepG2 exposed to ENU for 24h, biological rep 3

value: ENU


title: Serie H, HepG2 exposed to EthylB for 24h, biological rep 2


title: Serie H, HepG2 exposed to DDT for 24h, biological rep 3

value: DDT


title: Serie H, HepG2 exposed to ENU for 24h, biological rep 2


title: Serie H, HepG2 exposed to Cb for 24h, biological rep 3

value: Cb


title: Serie H, HepG2 exposed to COU for 24h, biological rep 1

value: COU


title: Serie H, HepG2 exposed to COU for 24h, biological rep 2


title: Serie H, HepG2 exposed to ENU for 24h, biological rep 1


title: Serie H, HepG2 exposed to DDT for 24h, biological rep 2


title: Serie H, HepG2 exposed to DDT for 24h, biological rep 1


title: Serie H, HepG2 exposed to Cb for 24h, biological rep 1


title: Serie H, HepG2 exposed to CAP for 24h, biological rep 2

value: CAP


title: Serie H, HepG2 exposed to CAP for 24h, biological rep 3


title: Serie I, HepG2 exposed to CCl4 for 24h, biological rep 3


title: Serie H, HepG2 exposed to CAP for 24h, biological rep 1


title: Serie H, HepG2 exposed to BZ for 24h, biological rep 3

value: BZ


title: Serie H, HepG2 exposed to COU for 24h, biological rep 3


title: Serie H, HepG2 exposed to BZ for 24h, biological rep 2


title: Serie H, HepG2 exposed to ABP for 24h, biological rep 2

value: ABP


title: Serie H, HepG2 exposed to ASK for 24h, biological rep 1

value: ASK


title: Serie H, HepG2 exposed to BZ for 24h, biological rep 1


title: Serie H, HepG2 exposed to ABP for 24h, biological rep 1


title: Serie H, HepG2 exposed to ASK for 24h, biological rep 2


title: Serie H, HepG2 exposed to ABP for 24h, biological rep 3


title: Serie G, HepG2 exposed to PBS for 24h, biological rep 2

value: PBS


title: Serie H, HepG2 exposed to CCl4 for 24h, biological rep 2


title: Serie H, HepG2 exposed to ASK for 24h, biological rep 3


title: Serie H, HepG2 exposed to 2-Cl for 24h, biological rep 1


title: Serie G, HepG2 exposed to VitC for 24h, biological rep 1

value: VitC


title: Serie G, HepG2 exposed to PBS for 24h, biological rep 3


title: Serie F, HepG2 exposed to DMSO for 24h, biological rep 1


title: Serie G, HepG2 exposed to PBS for 24h, biological rep 1


title: Serie G, HepG2 exposed to VitC for 24h, biological rep 2


title: Serie G, HepG2 exposed to VitC for 24h, biological rep 3


title: Serie E, HepG2 exposed to Resor for 24h, biological rep 3

value: Resor


title: Serie H, HepG2 exposed to 2-Cl for 24h, biological rep 3


title: Serie F, HepG2 exposed to Phenol for 24h, biological rep 3

value: Phenol


title: Serie H, HepG2 exposed to 2-Cl for 24h, biological rep 2


title: Serie E, HepG2 exposed to Resor for 24h, biological rep 2


title: Serie F, HepG2 exposed to Phenol for 24h, biological rep 1


title: Serie E, HepG2 exposed to TBTO for 24h, biological rep 1

value: TBTO


title: Serie F, HepG2 exposed to DMSO for 24h, biological rep 2

value: DMSO


title: Serie E, HepG2 exposed to TBTO for 24h, biological rep 2


title: Serie F, HepG2 exposed to DMSO for 24h, biological rep 3


title: Serie E, HepG2 exposed to Resor for 24h, biological rep 1


title: Serie E, HepG2 exposed to TBTO for 24h, biological rep 3


title: Serie E, HepG2 exposed to Phen for 24h, biological rep 3

value: Phen


title: Serie F, HepG2 exposed to Phenol for 24h, biological rep 2


title: Serie E, HepG2 exposed to Phen for 24h, biological rep 1


title: Serie E, HepG2 exposed to Ethyl for 24h, biological rep 3

value: Ethyl


title: Serie E, HepG2 exposed to Phen for 24h, biological rep 2


title: Serie E, HepG2 exposed to Paracres for 24h, biological rep 1

value: Paracres


title: Serie E, HepG2 exposed to Paracres for 24h, biological rep 2


title: Serie D, HepG2 exposed to Sulfi for 24h, biological rep 3

value: Sulfi


title: Serie D, HepG2 exposed to DMSO for 24h, biological rep 1


title: Serie E, HepG2 exposed to DES for 24h, biological rep 3

value: DES


title: Serie E, HepG2 exposed to Ethyl for 24h, biological rep 2


title: Serie E, HepG2 exposed to DES for 24h, biological rep 2


title: Serie D, HepG2 exposed to DMBA for 24h, biological rep 1

value: DMBA


title: Serie E, HepG2 exposed to Paracres for 24h, biological rep 3


title: Serie D, HepG2 exposed to Cur for 24h, biological rep 3

value: Cur


title: Serie D, HepG2 exposed to Cur for 24h, biological rep 2


title: Serie E, HepG2 exposed to Ethyl for 24h, biological rep 1


title: Serie D, HepG2 exposed to DMBA for 24h, biological rep 2


title: Serie D, HepG2 exposed to DMSO for 24h, biological rep 2


title: Serie D, HepG2 exposed to 4AAF for 24h, biological rep 2


title: Serie D, HepG2 exposed to Sulfi for 24h, biological rep 2


title: Serie C, HepG2 exposed to Diclo for 24h, biological rep 2

value: Diclo


title: Serie D, HepG2 exposed to Cur for 24h, biological rep 1


title: Serie D, HepG2 exposed to DMBA for 24h, biological rep 3


title: Serie C, HepG2 exposed to Diclo for 24h, biological rep 3


title: Serie E, HepG2 exposed to DES for 24h, biological rep 1


title: Serie D, HepG2 exposed to DMSO for 24h, biological rep 3


title: Serie C, HepG2 exposed to Diclo for 24h, biological rep 1


title: Serie D, HepG2 exposed to 4AAF for 24h, biological rep 3


title: Serie D, HepG2 exposed to Sulfi for 24h, biological rep 1


title: Serie D, HepG2 exposed to 4AAF for 24h, biological rep 1


title: Serie B, HepG2 exposed to DMSO for 24h, biological rep 1


title: Serie C, HepG2 exposed to APAP for 24h, biological rep 3

value: APAP


title: Serie B, HepG2 exposed to WY for 24h, biological rep 2

value: WY


title: Serie B, HepG2 exposed to Res for 24h, biological rep 1

value: Res


title: Serie B, HepG2 exposed to PhB for 24h, biological rep 3

value: PhB


title: Serie B, HepG2 exposed to NPD for 24h, biological rep 3

value: NPD


title: Serie B, HepG2 exposed to DMSO for 24h, biological rep 3


title: Serie B, HepG2 exposed to WY for 24h, biological rep 1


title: Serie B, HepG2 exposed to DMN for 24h, biological rep 3

value: DMN


title: Serie B, HepG2 exposed to DMSO for 24h, biological rep 2


title: Serie B, HepG2 exposed to DMN for 24h, biological rep 1


title: Serie C, HepG2 exposed to APAP for 24h, biological rep 2


title: Serie B, HepG2 exposed to ANAC for 24h, biological rep 3

value: ANAC


title: Serie B, HepG2 exposed to WY for 24h, biological rep 3


title: Serie B, HepG2 exposed to Res for 24h, biological rep 2


title: Serie B, HepG2 exposed to NPD for 24h, biological rep 2


title: Serie B, HepG2 exposed to NPD for 24h, biological rep 1


title: Serie B, HepG2 exposed to MMC for 24h, biological rep 2

value: MMC


title: Serie H, HepG2 exposed to Cb for 24h, biological rep 2

value: Cb


title: Serie B, HepG2 exposed to DEPH for 24h, biological rep 3

value: DEPH


title: Serie B, HepG2 exposed to PhB for 24h, biological rep 1


title: Serie B, HepG2 exposed to PhB for 24h, biological rep 2


title: Serie B, HepG2 exposed to DEPH for 24h, biological rep 1


title: Serie B, HepG2 exposed to ANAC for 24h, biological rep 2


title: Serie B, HepG2 exposed to MMC for 24h, biological rep 3


title: Serie B, HepG2 exposed to MMC for 24h, biological rep 1


title: Serie B, HepG2 exposed to Res for 24h, biological rep 3


title: Serie B, HepG2 exposed to DMN for 24h, biological rep 2


title: Serie C, HepG2 exposed to APAP for 24h, biological rep 1


title: Serie B, HepG2 exposed to 2CMP for 24h, biological rep 3


title: Serie B, HepG2 exposed to 2AAF for 24h, biological rep 3


title: Serie B, HepG2 exposed to ANAC for 24h, biological rep 1


title: Serie B, HepG2 exposed to 2CMP for 24h, biological rep 2


title: Serie B, HepG2 exposed to 2CMP for 24h, biological rep 1


title: Serie B, HepG2 exposed to 2AAF for 24h, biological rep 1


title: Serie B, HepG2 exposed to 2AAF for 24h, biological rep 2


title: Serie B, HepG2 exposed to ampC for 24h, biological rep 3

value: ampC


title: Serie B, HepG2 exposed to Que for 24h, biological rep 3

value: Que


title: Serie B, HepG2 exposed to ampC for 24h, biological rep 2


title: Serie B, HepG2 exposed to Que for 24h, biological rep 1


title: Serie B, HepG2 exposed to Que for 24h, biological rep 2


title: Serie B, HepG2 exposed to 8HQ for 24h, biological rep 2


title: Serie B, HepG2 exposed to ampC for 24h, biological rep 1


title: Serie B, HepG2 exposed to 8HQ for 24h, biological rep 3


title: Serie B, HepG2 exposed to 8HQ for 24h, biological rep 1


title: Serie A, HepG2 exposed to TCDD for 24h, biological rep 1

value: TCDD


title: Serie A, HepG2 exposed to CsA for 24h, biological rep 3

value: CsA


title: Serie A, HepG2 exposed to TCDD for 24h, biological rep 2


title: Serie A, HepG2 exposed to CsA for 24h, biological rep 2


title: Serie A, HepG2 exposed to TCDD for 24h, biological rep 3


title: Serie A, HepG2 exposed to AFB1 for 24h, biological rep 1


title: Serie A, HepG2 exposed to E2 for 24h, biological rep 2


title: Serie A, HepG2 exposed to AFB1 for 24h, biological rep 3


title: Serie A, HepG2 exposed to AFB1 for 24h, biological rep 2


title: Serie A, HepG2 exposed to BaP for 24h, biological rep 3

value: BaP


title: Serie A, HepG2 exposed to CsA for 24h, biological rep 1


title: Serie A, HepG2 exposed to BaP for 24h, biological rep 2


title: Serie A, HepG2 exposed to E2 for 24h, biological rep 3


title: Serie A, HepG2 exposed to E2 for 24h, biological rep 1


title: Serie A, HepG2 exposed to BaP for 24h, biological rep 1


title: Serie G, HepG2 exposed to VitC for 12h, biological rep 3

value: VitC


title: Serie G, HepG2 exposed to PBS for 12h, biological rep 3

value: PBS


title: Serie G, HepG2 exposed to PBS for 12h, biological rep 1


title: Serie F, HepG2 exposed to Phenol for 12h, biological rep 2

value: Phenol


title: Serie G, HepG2 exposed to VitC for 12h, biological rep 1


title: Serie F, HepG2 exposed to DMSO for 12h, biological rep 2

value: DMSO


title: Serie F, HepG2 exposed to Phenol for 12h, biological rep 1


title: Serie G, HepG2 exposed to VitC for 12h, biological rep 2


title: Serie F, HepG2 exposed to Phenol for 12h, biological rep 3


title: Serie E, HepG2 exposed to ETOH for 12h, biological rep 2

value: ETOH


title: Serie F, HepG2 exposed to DMSO for 12h, biological rep 1


title: Serie E, HepG2 exposed to ETOH for 12h, biological rep 3


title: Serie F, HepG2 exposed to DMSO for 12h, biological rep 3


title: Serie E, HepG2 exposed to ETOH for 12h, biological rep 1


title: Serie E, HepG2 exposed to TBTO for 12h, biological rep 3

value: TBTO


title: Serie G, HepG2 exposed to PBS for 12h, biological rep 2


title: Serie E, HepG2 exposed to TBTO for 12h, biological rep 2


title: Serie E, HepG2 exposed to TBTO for 12h, biological rep 1


title: Serie E, HepG2 exposed to Resor for 12h, biological rep 3

value: Resor


title: Serie E, HepG2 exposed to Paracres for 12h, biological rep 1

value: Paracres


title: Serie E, HepG2 exposed to Resor for 12h, biological rep 1


title: Serie E, HepG2 exposed to Paracres for 12h, biological rep 2


title: Serie E, HepG2 exposed to Paracres for 12h, biological rep 3


title: Serie E, HepG2 exposed to Resor for 12h, biological rep 2


title: Serie E, HepG2 exposed to Ethyl for 12h, biological rep 3

value: Ethyl


title: Serie E, HepG2 exposed to Phen for 12h, biological rep 1

value: Phen


title: Serie E, HepG2 exposed to Ethyl for 12h, biological rep 2


title: Serie E, HepG2 exposed to Phen for 12h, biological rep 3


title: Serie E, HepG2 exposed to Phen for 12h, biological rep 2


title: Serie E, HepG2 exposed to Ethyl for 12h, biological rep 1


title: Serie E, HepG2 exposed to DES for 12h, biological rep 2

value: DES


title: Serie D, HepG2 exposed to DMSO for 12h, biological rep 2


title: ovarian tumor clear cell line stably transfected with hfut1 vs. non-transfected cell line rep1

city: Shenyang

first: Ziwei

last: Feng

address: Sanhao street

country: China

institute: China Medical University

description: Comparison between before and after hfut1 gene transfection into ovarian tumor clear cell line

hyb_protocol: Labeled DNA dissolved in 30ul hybridization solution (3 × SSC, 0.2%SDS, 5× Denhart 's, 25% formamide), are hybridized at 42 ℃ overnight. Washed in  0.2% SDS and 2 × SSC of about 42 ℃ for 5 min, and then washed in 0.2 × SSC at room temperature for 5 min. Air-dry glass can be used for scanning.

scan_protocol: After hybridization and washing, the processed slides were scanned with LuxScan 10KA, double channel laser scanner.

data_processing: Using GenePix Pro 4 image analysis software (Axon Instruments) for microarray image analysis, transfer image signal into digital signal. And the chip data was analyzed by Lowess normalization; finally using the t-test method combined with 2 -fold change criteria to determine the difference of gene expression.

label_protocol: After having passed RNA measurement on the Nanodrop ND-1000 and denaturing gel electrophoresis, first, double-stranded cDNA were synthesized with primer T7-Oligo-dT and cDNA Synthesis Kit (Promega, USA), then purified with PCR NucleoSpin Extract II Kit (MN). Second, cRNA were transcripted from cDNA with T7 RiboMAX Express Large Scale RNA Production System (Promega), then purified with RNA Clean-up Kit (MN). Third, reverse transcription with M-MLV reverse transcriptase, 200 u/ µ L (Invitrogen) and 9 Random Primer, then purified with PCR NucleoSpin Extract II Kit (MN). Finally,  label the cDNA with KLENOW enzyme, then purified the labeled productions with PCR NucleoSpin Extract II Kit (MN).Experiments on this sample was analyzed by fluorescence exchange to reduce the experimental error.

growth_protocol: RMG-1 and RMG-1-hFUT cells were cultured in high glucose DMEM containing 10% FBS at 37℃ under a 5 % CO2 in humidified air.

extract_protocol: Total RNAs are harvested using TRIzol (Invitrogen) and purified with the RNA clean-up (NucleoSpin) according to manufacturer’s instructions.

value: ovarian cancer clear cell line RMG-I-H

source_name: ovarian tumor clear cell line with low expression of lewis y antigen

value: ovarian cancer clear cell line RMG-I


title: Serie D, HepG2 exposed to DMSO for 12h, biological rep 3


title: ovarian tumor clear cell line stably transfected with hfut1 vs. non-transfected cell line rep2


title: Serie D, HepG2 exposed to TPA for 12h, biological rep 2

value: TPA


title: Serie D, HepG2 exposed to DMSO for 12h, biological rep 1


title: Serie D, HepG2 exposed to TPA for 12h, biological rep 3


title: Serie E, HepG2 exposed to DES for 12h, biological rep 1


title: Serie D, HepG2 exposed to Sulfi for 12h, biological rep 3

value: Sulfi


title: Serie D, HepG2 exposed to TPA for 12h, biological rep 1


title: Serie D, HepG2 exposed to Sulfi for 12h, biological rep 2


title: Serie D, HepG2 exposed to DMBA for 12h, biological rep 2

value: DMBA


title: RFP;TTP-GFP+, technical replicate 1

city: Tampa

first: John

middle: Lamoine

last: Cleveland

state: FL

address: 12902 USF Magnolia Drive

country: USA

institute: H. Lee Moffitt Cancer Center

description: Gene expression data of retrovirally infected ex vivo lymphoma cells

hyb_protocol: 20 μg biotin-labeled cRNA was fragmented and hybridized to Affymetrix GeneChip MOE430 2.0 microarrays overnight in the Affy 640 hybridization oven with a speed of 60 rpm for 16 hr. Microarrays were washed and stained using the Affymetrix Fluidics Station FS400.

scan_protocol: GeneChip arrays were scanned using a GeneChip Scanner 3000 (Affymetrix). The probe set intensities were quantified using the GeneChip Operating Software (GCOS). All hybridized chips met standard quality control criteria.

data_processing: The data were analyzed using GeneSpring GX version 11 based on GCRMA analysis default settings.

source_name: RFP;TTP-GFP+

label_protocol: cRNA was synthesized using an IVT labeling kit (Affymetrix), with the cRNA product purified using a GeneChip Sample Cleanup Module (Affymetrix).

extract_protocol: Sequential retrovirally infected ex vivo Eμ-Myc lymphoma cells were separated by FACS based on RFP and GFP expression. RNA was prepared using the NucleoSpin RNA II kit (Macherey-Nagel).

tag: source tissue type

value: Ex vivo Eμ-Myc lymphoma

tag: sequentially infected with

value: MSCV-I-dsRed2 (RFP) and MSCV-TTP-I-GFP

tag: genotype/variation

value: MSCV-I-dsRed2+; MSCV-TTP-I-GFP+

tag: facs sorted for

value: dsRed2+ and TTP-GFP+


title: Serie D, HepG2 exposed to DMBA for 12h, biological rep 3


title: Serie D, HepG2 exposed to Sulfi for 12h, biological rep 1


title: RFP;TTP-GFP+, technical replicate 3


title: ZT22 whole skin telogen P22 KO-1

city: Irvine

first: mikhail

middle: viktorovich

last: geyfman

state: CA

address: 839 Medical Sciences Court 250 Sprague Hall

department: Medicine

institute: university of California Irvine

description: ZT22 KO whole skin P22-1

hyb_protocol: 2ug of the labeled, fragmented single-stranded cDNA is hybridized at 45oC with rotation for 17 hours (Affymetrix GeneChip Hybridization Oven 640) to probe sets present on an Affymetrix GeneChip 1.0ST array.  The GeneChip arrays were washed and then stained with streptavidin-phycoerythrin on an Affymetrix Fluidics Station 450 (Fluidics protocol FS450_007).

scan_protocol: Arrays were scanned using GeneChip Scanner 3000 7G and Command Console Software v. 3.2.3 to produce .CEL intensity files.

data_processing: The probe cell intensity files (*.CEL) were analyzed in Affymetrix Expression Console software v1.1.1 using the PLIER algorithm to generate probe level summarization files (*.CHP).  The settings used were algorithm-PLIER v2.0; quantification scale-Linear; quantification type-signal and detection p-value; background-PM-GCBG; normalization method-sketch-quantile.

source_name: whole back skin

label_protocol: The Ambion WT expression kit (Life Technologies, Carlsbad, CA) was used to prepare RNA samples for whole transcriptome microarray analysis.  Briefly, random hexamers that are tagged with a T7 promoter are used in first strand synthesis of cDNA.   Then using the T7 promoter, second strand synthesis is performed and the double stranded cDNA is subsequently used as a template in an in vitro transcription reaction to generate many copies of antisense cRNA.  10ug of antisense cRNA is input into a second cycle cDNA reaction using reverse transcriptase and random hexamers to produce single stranded DNA in the sense orientation.  The single-stranded DNA is fragmented to an average length of 70 bases and then labeled using a recombinant terminal deoxynucleotidyl transferase (TdT) and an Affymetrix proprietary DNA labeling reagent that is covalently linked to biotin.

growth_protocol: Mice were housed in 12 light : 12 dark light conditions and fed with standard mouse chow ad libidum

extract_protocol: Isolated total RNA samples were processed as recommended by Affymetrix, Inc.  (Affymetrix GeneChip Whole Transcript Sense Target Labeling Assay Manual, Affymetrix, Inc., Santa Clara, CA).  In brief, total RNA was initially isolated using TRIzol Reagent (Gibco BRL Life Technologies, Rockville, MD), and then put through an RNeasy spin column (Qiagen, Chatsworth, CA) for further clean up.  Eluted total RNAs were quantified by NanoDrop (ThermoScientific, Wilmington, DE) and the concentrations of sample aliquots were adjusted to 100ng/ul.  Total RNA samples were assessed for quality prior to performing target preparation/processing steps by loading approximately 25-250ng of each sample onto a RNA 6000 Nano LabChip and evaluated on an Agilent Biolanalyzer 2100 (Agilent Technologies, Palo Alto, CA).

tag: strain background

value: KO (both copies of Bmal1 allele deleted)

value: postnatal day (P) 22

tag: growth phase

value: telogen

tag: sample collection (zt)


title: RFP;TTP-GFP+, technical replicate 2


title: ZT22 whole skin telogen P22 KO-2

description: ZT22 KO whole skin P22-2

tag: age


title: ZT46 whole skin anagen P30

description: ZT46 Anagen

tag: strain

value: postnatal day (P) 30

tag: gender

value: male

value: whole back skin

value: anagen


title: ZT22 whole skin telogen P22 het-1

description: ZT22 het whole skin P22-1

value: het (one Bmal1 mutant allele and one wt allele)


title: RFP;TTP-GFP-, technical replicate 1

source_name: RFP;TTP-GFP-

value: MSCV-I-dsRed2+; MSCV-TTP-I-GFP-

value: dsRed2+ and TTP-GFP-


title: Serie D, HepG2 exposed to DMBA for 12h, biological rep 1

tag: cell line


title: RFP;TTP-GFP-, technical replicate 2


title: RFP;TTP-GFP-, technical replicate 3


title: ZT50 whole skin anagen P30

description: ZT50 Anagen


title: ZT38 whole skin anagen P30

description: ZT38 Anagen


title: Eμ-Myc;Eµ-TTP-1 lymphoma, biological replicate 5

description: Eu-Myc;Eu-TTP-1 lymphoma, rep 5

source_name: Eμ-Myc;Eµ-TTP-1 lymphoma

extract_protocol: Lymphoma aliquots collected from Eμ-Myc and Eμ-Myc;Eµ-TTP-1 transgenic mice were homogenized and RNA was prepared using the NucleoSpin RNA II kit (Macherey-Nagel).

value: Eμ-Myc + ;Eµ-TTP-1 +

tag: tissue type

value: lymphoma


title: Serie D, HepG2 exposed to Cur for 12h, biological rep 2

value: Cur


title: Serie D, HepG2 exposed to Cur for 12h, biological rep 3


title: Serie B, HepG2 exposed to DEPH for 24h, biological rep 2

value: DEPH


title: ZT22 whole skin telogen P22 het-2

description: ZT22 het whole skin P22-2


title: Eμ-Myc;Eµ-TTP-1 lymphoma, biological replicate 4

description: Eu-Myc;Eu-TTP-1 lymphoma, rep 4


title: ZT26 whole skin anagen P30

description: ZT26 Anagen


title: ZT42 whole skin anagen P30

description: ZT42 Anagen


title: ZT34 whole skin anagen P30

description: ZT34 Anagen


title: ZT30 whole skin anagen P30

description: ZT30 Anagen


title: ZT22 whole skin anagen P30

description: ZT22 Anagen


title: Eμ-Myc;Eµ-TTP-1 lymphoma, biological replicate 3

description: Eu-Myc;Eu-TTP-1 lymphoma, rep 3


title: Eμ-Myc;Eµ-TTP-1 lymphoma, biological replicate 2

description: Eu-Myc;Eu-TTP-1 lymphoma, rep 2


title: ZT18 whole skin anagen P30

description: ZT18 Anagen


title: Serie D, HepG2 exposed to 4AAF for 12h, biological rep 3


title: Serie D, HepG2 exposed to Cur for 12h, biological rep 1


title: ZT14 whole skin anagen P30

description: ZT14 Anagen


title: ZT10 whole skin anagen P30

description: ZT10 Anagen


title: ZT2 whole skin anagen P30

description: ZT2 Anagen


title: ZT50 whole skin telogen P46

description: ZT50 Telogen

hyb_protocol: 2ug of the labeled, fragmented single-stranded cDNA is hybridized at 45C with rotation for 17 hours (Affymetrix GeneChip Hybridization Oven 640) to probe sets present on an Affymetrix GeneChip 1.0ST array.  The GeneChip arrays were washed and then stained with streptavidin-phycoerythrin on an Affymetrix Fluidics Station 450 (Fluidics protocol FS450_007).

value: postnatal day (P) 46

tag: tissue

tag: sample collection


title: Eμ-Myc;Eµ-TTP-1 lymphoma, biological replicate 1

description: Eu-Myc;Eu-TTP-1 lymphoma, rep 1


title: Eμ-Myc lymphoma, biological replicate 3

description: Eu-Myc lymphoma, rep 3

source_name: Eμ-Myc lymphoma

value: Eμ-Myc + ;Eµ-TTP-1 -


title: Eμ-Myc lymphoma, biological replicate 4

description: Eu-Myc lymphoma, rep 4


title: Serie D, HepG2 exposed to 4AAF for 12h, biological rep 1

tag: compound, dose

tag: time


title: ZT6 whole skin anagen P30

description: ZT6 Anagen

tag: tissue origin


title: ZT46 whole skin telogen P46

description: ZT46 Telogen


title: ZT38 whole skin telogen P46

description: ZT38 Telogen


title: Serie C, HepG2 exposed to PBS for 12h, biological rep 2

value: PBS


title: Serie D, HepG2 exposed to 4AAF for 12h, biological rep 2


title: ZT22 whole skin telogen P46

description: ZT22 Telogen


title: ZT34 whole skin telogen P46

description: ZT34 Telogen


title: ZT26 whole skin telogen P46

description: ZT26 Telogen


title: Eμ-Myc lymphoma, biological replicate 2

description: Eu-Myc lymphoma, rep 2


title: Serie C, HepG2 exposed to PBS for 12h, biological rep 1


title: Serie C, HepG2 exposed to PBS for 12h, biological rep 3


title: ZT18 whole skin telogen P46

description: ZT18 Telogen


title: Eμ-Myc lymphoma, biological replicate 1

description: Eu-Myc lymphoma, rep 1


title: ZT14 whole skin telogen P46

description: ZT14 Telogen


title: ZT42 whole skin telogen P46

description: ZT42 Telogen


title: Serie E, HepG2 exposed to DES for 12h, biological rep 3

value: DES


title: ZT30 whole skin telogen P46

description: ZT30 Telogen


title: Eμ-Myc;Eµ-TTP-1 bone marrow B220+, biological replicate 3

description: Gene expression data of bone marrow B220+ cells from 4-6 weeks old Eμ-Myc;Eµ-TTP-1 littermates.

source_name: Eμ-Myc;Eµ-TTP-1 bone marrow B220+

extract_protocol: B cells were isolated from bone marrow by MACS using CD45R (B220) MicroBeads (Miltenyi Biotec). RNA was prepared using the NucleoSpin RNA II kit (Macherey-Nagel).

value: precancerous Eμ-Myc;Eµ-TTP-1 transgenic

tag: cell type

value: bone marrow B220+


title: Serie C, HepG2 exposed to Dman for 12h, biological rep 2

value: Dman


title: Serie C, HepG2 exposed to Dman for 12h, biological rep 3


title: ZT10 whole skin telogen P46

description: ZT10 Telogen

value: male

value: telogen


title: Eμ-Myc;Eµ-TTP-1 bone marrow B220+, biological replicate 2


title: Serie C, HepG2 exposed to Dman for 12h, biological rep 1


title: Serie C, HepG2 exposed to Diclo for 12h, biological rep 2

value: Diclo


title: Lung ShhCre Control 2

city: Philadelphia

first: Shanru

last: Li

state: PA

address: 3400 Civic Center Blvd, Bldg 421

institute: University of Pennsylvania

hyb_protocol: cDNAs  were added to Affymetrix hybridization cocktails, heated at 99ºC for 2 min and hybridized for 16 h at 45ºC to  GeneChips (Affymetrix Inc., Santa Clara CA). The microarrays were then washed at low (6X SSPE) and high (100mM MES, 0.1M NaCl) stringency and stained with streptavidin-phycoerythrin. Fluorescence was amplified by adding biotinylated anti-streptavidin and an additional aliquot of streptavidin-phycoerythrin stain.

scan_protocol: A confocal scanner was used to collect fluorescence signal after excitation at 570 nm.

data_processing:
Affymetrix Command Console was used to quantitate expression levels for targeted genes; default values provided by Affymetrix were applied to all analysis parameters. Probes for each targeted gene were averaged and inter-array normalization performed using the RMA algorithm .
3 independent biological replicates for each condition were assayed on microarrays.  Significance Analysis of Microarrays (SAM v3.0, www-stat.stanford.edu/~tibs/SAM/) was used to generate lists of statistically significant differentially expressed genes in pairwise comparisons of replicate averages between conditions.

label: Biotin

source_name: ShhCre-Lung

label_protocol: 100ng of total RNA was converted to first-strand cDNA using reverse transcriptase primed by a poly(T) oligomer that incorporated the T7 RNA polymerase promoter.  Second-strand cDNA synthesis was followed by in vitro transcription (Affymetrix One-Cycle Target Labeling Kit) for linear amplification and biotinylation of each transcript.

extract_protocol: RNA was extracted using Rneasy mini kit (Qiagene)

tag: developmental stage

value: lung

tag: mouse background


title: ZT6 whole skin telogen P46

description: ZT6 Telogen

value: whole back skin


title: Eμ-Myc;Eµ-TTP-1 bone marrow B220+, biological replicate 1

tag: genotype/variation


title: Lung ShhCre Control 3


title: Lung Shh-cre:Foxp1flox/flox:Foxp4flox/flox(Mut3)


title: ZT2 whole skin telogen P46

description: ZT2 Telogen


title: Eμ-Myc bone marrow B220+, biological replicate 2

source_name: Eμ-Myc bone marrow B220+

tag: strain background

value: precancerous Eμ-Myc transgenic


title: Eμ-Myc bone marrow B220+, biological replicate 3


title: Serie C, HepG2 exposed to Diclo for 12h, biological rep 3


title: Sox9egfpneg_p23-3

city: La Jolla

first: Brandon

last: Taylor

address: Sanford Consortium for Regenerative Medicine, 2880 Torrey Pines Scenic Dr., Room 3101

department: Pediatrics and Cellular & Molecular Medicine

institute: University of California, San Diego

description: Gene expression data from pancreatic Sox9- cells at p23

hyb_protocol: After labeling the resulting fragmented, biotin-tagged cDNA (2.2 μg) was placed into a hybridization cocktail (220 μL), with 200 μL actually hybridized at 45°C with rotation for 18 hours (Affymetrix GeneChip Hybridization Oven 640) to probe sets present on an Affymetrix Mouse Gene 1.0 ST array. The GeneChip arrays were washed and then stained (SAPE, streptavidin-phycoerythrin) on an Affymetrix Fluidics Station 450 using the FS450_0004 fluidics protocol.

scan_protocol: Gene chips were scanned on an Affymetrix GeneChip 3000 Scanner 7G.

data_processing: The results were quantified and analyzed using Expression Console ver.1.1 software (Affymetrix, Inc.) using the PLIER Algorithm default values (Quantification Scale: Linear; Quantification Type: Signal and Detection P-Value; Background: PM-GCBG; Normalization Method: Sketch-Quantile).

source_name: GFP- cells from Sox9-EGFP Mus Musculus pancreas at p23

label_protocol: Biotinylated cDNA were prepared according to the NuGEN FL-Ovation cDNA Biotin Module V2 protocol after fragmentation of 3.75 ug of the amplified cDNA (NuGEN Technologies, San Carlos CA).

growth_protocol: All animal experiments described herein were approved by the University of California, Irvine and San Diego Institutional Animal Care and Use Committees. Sox9-EGFP or Ngn3-EGFP males were crossed with CD1 (Charles River) wild-type females and embryos were harvested at e10.5 or e15.5.  Alternatively, pancreata were harvested from Sox9-EGFP pups at p23. For timed matings, noon on the day of vaginal plug appearance was designated e0.5.

extract_protocol: Total RNA isolation was performed with the Qiagen Micro RNA kit according to the manufacturer's instructions.  The optional on column DNAse digestion was performed. Using the NuGEN Ovation RNA Amplification System V2 (NuGEN Technologies, San Carlos, CA) first strand cDNA was synthesized from the poly(A)+ mRNA present within the isolated total RNA (20 ng total RNA starting material used in each sample reaction). Fragmentation of the mRNA within the resulting cDNA/mRNA complexes created priming sites for DNA polymerase to synthesize DNA complementary to the first strand cDNAs. The resulting double stranded (ds) cDNAs have a unique DNA/RNA heteroduplex at one end. These ds DNA templates were used to perform linear isothermal DNA amplification (SPIA, NuGEN Technologies, San Carlos, CA).

treatment_protocol: Pancreata from e10.5, e15.5, or p23 pancreata were dissected and dissociated with collagenase B and trypsin, if necessary, to create single cell suspensions that were subjected to FACS.  Cells expressing high levels of GFP were collected for analysis for each population. For the Sox9-EGFPneg_p23 samples, the GFP negative cell population was also collected. Multiple animals were pooled before sorting for each population to achieve sufficient cell numbers.

tag: background strain

value: pancreas

tag: facs

value: GFP-


title: Lung Shh-cre:Foxp1flox/flox:Foxp4flox/flox(Mut1)


title: Eμ-Myc bone marrow B220+, biological replicate 1

tag: age


title: Serie C, HepG2 exposed to Diclo for 12h, biological rep 1


title: Eµ-TTP-1 bone marrow B220+, biological replicate 3

source_name: Eµ-TTP-1 bone marrow B220+

value: Eµ-TTP-1 transgenic


title: Eµ-TTP-1 bone marrow B220+, biological replicate 1


title: Lung ShhCre Control 1


title: Sox9egfpneg_p23-2


title: Sox9egfpneg_p23-1


title: Serie C, HepG2 exposed to APAP for 12h, biological rep 2

value: APAP


title: Sox9egfp_p23-1

description: Gene expression data from pancreatic Sox9+ cells at p23

source_name: GFP+ cells from Sox9-EGFP Mus Musculus pancreas at p23

value: GFP+


title: Eµ-TTP-1 bone marrow B220+, biological replicate 2


title: Serie B, HepG2 exposed to DMSO for 12h, biological rep 3

value: DMSO


title: Serie C, HepG2 exposed to APAP for 12h, biological rep 3


title: Wild Type bone marrow B220+, biological replicate 2

source_name: Wild Type bone marrow B220+

value: wild type


title: Serie B, HepG2 exposed to DMSO for 12h, biological rep 2


title: Sox9egfp_p23-2


title: Serie C, HepG2 exposed to APAP for 12h, biological rep 1


title: Sox9egfp_p23-3


title: Serie B, HepG2 exposed to DMSO for 12h, biological rep 1


title: Serie B, HepG2 exposed to WY for 12h, biological rep 3

value: WY


title: Sox9egfp_e15.5-3

description: Gene expression data from pancreatic Sox9+ cells at e15.5

source_name: GFP+ cells from Sox9-EGFP Mus Musculus pancreas at e15.5


title: Sox9egfp_e10.5-1

description: Gene expression data from pancreatic Sox9+ cells at e10.5

source_name: GFP+ cells from Sox9-EGFP Mus Musculus pancreas at e10.5


title: Sox9egfp_e15.5-2


title: Ngn3egfp_e15.5-1

description: Gene expression data from pancreatic Ngn3+ cells at e15.5

source_name: GFP+ cells from Ngn3-EGFP Mus Musculus pancreas at e15.5


title: Sox9egfp_e10.5-3


title: adenocarcinoma at 20wk, biological rep 3

city: Changsha

first: tang

middle: an

last: liu

address: xiangya road #110

institute: Key Laboratory of Carcinogenesis, Ministry of Health, China

description: Gene expression data from colorectal adenocarcinoma of the experimental group at the end of 20 weeks after intraperitoneal injection of AOM.

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45℃ on GeneChip mouse 430 2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: 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: colorectum

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA.

growth_protocol: 6-week-old male ICR mice were maintained in Central Sourth University Animal Facility according to the Institutional Animal Care Guidelines. All animals were housed in plastic cages (4 or 5 mice/cage) with free access to distilled water and a standard diet under specific-pathogen free (SPF) conditions of humidity (50±10%), lightning (12-h light/dark cycle) and temperature (24±0.5℃).

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

treatment_protocol: For AOM/DSS group of mice, a single intraperitoneal injection of AOM was given at Day 1, followed by three cycles of DSS administration (cycle 1: 2%, Day 8~14; cycle 2: 1.5%, Day 29~33; cycle 3: 1.5%, Day 50~54) in the drinking water. For control group, AOM was replaced by saline, and DSS was replaced by distilled water.

tag: strain

value: ICR

tag: agent

value: AOM/DSS

tag: time point (week end)

tag: disease state

value: colorectal adenocarcinoma


title: adenocarcinoma at 20wk, biological rep 1


title: Sox9egfp_e10.5-2

tag: tissue


title: Sox9egfp_e15.5-1


title: Serie B, HepG2 exposed to WY for 12h, biological rep 2

source_name: hepatocellular carcinoma cell line

tag: cell line


title: Serie B, HepG2 exposed to WY for 12h, biological rep 1

tag: compound, dose


title: C2i-Myog  + SB + Dox replicate I

city: Ottawa

first: Theodore

last: Perkins

state: ON

address: 501 Smyth Rd.

department: Cellular and Molecular Medicine

country: Canada

institute: Ottawa Hospital Research Institute

description:
Expresses Myog not p38
Affy3301.CEL

hyb_protocol: Affymetrix standard

scan_protocol: Affymetrix standard

data_processing: The data were analyzed with RMA as background correction, summarization & normalization method. RMA data was produced with the Expression Console software from Affymetrix.

source_name: C2C12 modified line

label_protocol: Whole transcript sense target labeling assay

growth_protocol: C2C12 derivative stable cell lines were maintained in proliferative conditions at a cell density of less than 70% confluency in DMEM containing 10% FCS.

extract_protocol: RNeasy Mini Kit (Qiagen)

treatment_protocol: Near confluence, myoblasts were induced to differentiate through serum withdrawl using a DMEM containing 1% horse serum, insulin (10 µg/mL), and transferrin (10 µg/mL) for 48 h. Where indicated, expression of exogenous Flag-tagged mouse Myog was induced at the time of differentiation through the addition of 0.2 µg/mL of Dox (Sigma). Inhibition of p38a/b MAPK signaling was established through the addition of 10 µM SB (Calbiochem) at the time of differentiation and maintained for 48 hrs. Cells were incubated Dox-treated (to control for effects of Dox – but also leads to increased Myog expression); SB treated (blocks p38 MAPK signaling); and SB and Dox treated (blocks p38 MAPK signaling will allowing expression of exogenous Flag-Myog).

value: C2i-Myog (a stable C2C12-derived cell line)

tag: protocol

value: Differentiation with SB and Dox treatment


title: adenocarcinoma at 20wk, biological rep 2


title: C2i-Myog  + SB + Dox replicate II

description:
Expresses Myog not p38
Affy3305.CEL


title: C2i-Myog + SB replicate II

description:
Does not express p38 nor Myog
Affy3304.CEL

value: Differentiation with SB treatment


title: C2i-Myog + SB replicate III

description:
Does not express p38 nor Myog
Affy3308.CEL


title: C2i-Myog + Dox replicate III

description:
Expresses p38 & Myog
Affy3307.CEL

value: Differentiation with Dox treatment


title: Wild Type bone marrow B220+, biological replicate 1

value: bone marrow B220+


title: Serie B, HepG2 exposed to Res for 12h, biological rep 3

value: Res

tag: time


title: Lung Shh-cre:Foxp1flox/flox:Foxp4flox/flox(Mut2)

value: lung


title: Ngn3egfp_e15.5-3

value: pancreas


title: high grade dysplasia at 8wk, biological rep 2

description: Gene expression data from high grade dysplasia of the experimental group at the end of 8 weeks after intraperitoneal injection of AOM.

value: high grade dysplasia


title: high grade dysplasia at 8wk, biological rep 3


title: C2i-Myog + SB replicate I

description:
Does not express p38 nor Myog
Affy3300.CEL


title: C2i-Myog  + SB + Dox replicate III

description:
Expresses Myog not p38
Affy3309.CEL


title: C2i-Myog + Dox replicate II

description:
Expresses p38 & Myog
Affy3303.CEL


title: C2i-Myog + Dox replicate I

description:
Expresses p38 & Myog
Affy3299.CEL


title: high grade dysplasia at 8wk, biological rep 1


title: C2i-Myog replicate III

description:
Expresses p38 & Myog
Affy3306.CEL

value: Control


title: C2i-Myog replicate II

description:
Expresses p38 & Myog
Affy3302.CEL


title: C2i-Myog replicate I

description:
Expresses p38 & Myog
Affy3298.CEL


title: high grade dysplasia at 6wk, biological rep 2

description: Gene expression data from high grade dysplasia of the experimental group at the end of 6 weeks after intraperitoneal injection of AOM.


title: high grade dysplasia at 6wk, biological rep 3


title: Serie B, HepG2 exposed to Res for 12h, biological rep 2


title: Serie B, HepG2 exposed to Res for 12h, biological rep 1


title: SKOV3, IFN, 6h, rep2

city: St. John's

first: Sherri

last: Christian

state: Newfoundland

address: 232 Elizabeth Ave

department: Biochemistry

institute: Memorial University of Newfoundland

description: gene expression data from SKOV3 cells treated with Inteferon-alpha for 6 hours

hyb_protocol: Hybridization was performed by The Centre for Applied Genomics (Toronto, Canada) according to the manufacturer's protocol (FS450_0007).

scan_protocol: Scanning was performed with the Affymetrix GeneChip Scanner 3000 by The Centre for Applied Genomics (Toronto, Canada) according to the manufacturer's protocol.

data_processing: Data were analyzed using Bioconducter 2.6. Pre-processing was performed with the Oligo package using rma normalization. Each cell type was analyzed independently, relative to the time-matched control.

source_name: SKOV3 cells, IFN treated 6h

label_protocol: 500 ng of RNA was used for labeling using the Ambion WT kit. Labeling was performed by The Centre for Applied Genomics (Toronto, Canada) according to the manufacturer's protocol.

growth_protocol: Cells were plated 6-well plates the day prior to treatment.

extract_protocol: Total RNA was extracted with TriZOL (Invitrogen) following the manufacturer's protocol. RNA was treated with Turbo DNA-free to remove genomic DNA contamination.

treatment_protocol: Confluent cells were treated with interferon-alpha (500 U/ml), U0126 (20uM) or both for 6 or 12 hours.

tag: treatment

value: IFN

value: SKOV3 human ovarian adenocarcinoma cell line


title: Serie B, HepG2 exposed to PhB for 12h, biological rep 1

value: PhB


title: high grade dysplasia at 6wk, biological rep 1


title: SKOV3, IFN, 6h, rep3


title: Serie B, HepG2 exposed to PhB for 12h, biological rep 2


title: SKOV3, control, 6h, rep3

description: gene expression data from SKOV3 cells, 6 hour control

source_name: SKOV3 cells, DMSO treated 6h

value: control


title: SKOV3, IFN, 6h, rep1


title: low grade dysplasia at 4wk, biological rep 3

description: Gene expression data from low grade dysplasia lesion in the colorectum of the experimental group at the end of 4 weeks after intraperitoneal injection of AOM.

value: ICR

value: low grade dysplasia lesion


title: Serie B, HepG2 exposed to NPD for 12h, biological rep 3

value: NPD


title: Serie B, HepG2 exposed to NPD for 12h, biological rep 2


title: SKOV3, control, 6h, rep2


title: low grade dysplasia at 4wk, biological rep 2

value: AOM/DSS


title: inflamed colorectal mucosa at 2wk, biological rep 3

description: Gene expression data from inflamed colorectal mucosa of the experimental group at the end of 2 weeks after intraperitoneal injection of AOM.

value: inflamed colorectal mucosa


title: low grade dysplasia at 4wk, biological rep 1


title: SKOV3, control, 6h, rep1


title: HT1080, IFN+U0126, 12h, rep3

description: gene expression data from HT1080 cells, treated with Interferon-alpha and U0126 for 12 hours

source_name: HT1080 cells, IFN+U0126 treated for 12h

value: HT1080 human fibrosarcoma cell line


title: HT1080, IFN+U0126, 12h, rep2


title: HT1080, IFN+U0126, 12h, rep1


title: HT1080, IFN+U0126, 6h, rep2

description: gene expression data from HT1080 cells, treated with Interferon-alpha and U0126 for 6 hours

source_name: HT1080 cells, IFN+U0126 treated for 6h


title: Ngn3egfp_e15.5-2

value: GFP+


title: Serie B, HepG2 exposed to NPD for 12h, biological rep 1


title: HT1080, IFN+U0126, 6h, rep1


title: HT1080, IFN+U0126, 6h, rep3


title: HT1080, U0126, 12h, rep3

description: gene expression data from HT1080 cells, treated with U0126 for 12 hours

source_name: HT1080 cells, U0126 treated for 12h


title: Serie B, HepG2 exposed to MMC for 12h, biological rep 2

value: MMC


title: Serie B, HepG2 exposed to MMC for 12h, biological rep 3


title: Serie B, HepG2 exposed to MMC for 12h, biological rep 1


title: HT1080, U0126, 6h, rep2

description: gene expression data from HT1080 cells, treated with U0126 for 6 hours

source_name: HT1080 cells, U0126 treated for 6h


title: inflamed colorectal mucosa at 2wk, biological rep 2


title: HT1080, U0126, 6h, rep1


title: inflamed colorectal mucosa at 2wk, biological rep 1


title: HT1080, U0126, 6h, rep3


title: normal colorectal mucosa, biological rep 3

description: Gene expression data from normal colorectal mucosa of the control group at the end of 2 weeks after intraperitoneal injection of saline.

value: saline/distilled water

value: normal


title: normal colorectal mucosa, biological rep 2


title: HT1080, U0126, 12h, rep2


title: Serie B, HepG2 exposed to DMN for 12h, biological rep 2

value: DMN


title: Serie B, HepG2 exposed to DMN for 12h, biological rep 3


title: Wild Type bone marrow B220+, biological replicate 3

description: Gene expression data of bone marrow B220+ cells from 4-6 weeks old Eμ-Myc;Eµ-TTP-1 littermates.

value: wild type

tag: cell type

value: bone marrow B220+


title: HT1080, IFN, 6h, rep3

description: gene expression data from HT1080 cells, treated with Interferon-alpha for 6 hours

source_name: HT1080 cells, IFN treated for 6h

value: IFN


title: HT1080, IFN, 12h, rep3

description: gene expression data from HT1080 cells, treated with Interferon-alpha for 12 hours

source_name: HT1080 cells, IFN treated for 12h


title: HT1080, IFN, 12h, rep2


title: HT1080, IFN, 12h, rep1


title: normal colorectal mucosa, biological rep1


title: HT1080, IFN, 6h, rep2


title: HT1080, U0126, 12h, rep1


title: Serie B, HepG2 exposed to DEPH for 12h, biological rep 2

value: DEPH


title: HT1080, control, 12h, rep2

description: gene expression data from HT1080 cells, 12h control

source_name: HT1080 cells, DMSO treated for 12h


title: Serie B, HepG2 exposed to DMN for 12h, biological rep 1


title: HT1080, control, 12h, rep3


title: HT1080, IFN, 6h, rep1


title: Serie B, HepG2 exposed to DEPH for 12h, biological rep 3


title: HT1080, control, 12h, rep1


title: Serie B, HepG2 exposed to DEPH for 12h, biological rep 1


title: dorsal pancreatic epithelia-e12.5-WT-4

hyb_protocol: 1.65 μg of cRNA was fragmented and hybridized to the array for 17 hr. at 65°C then washed.

scan_protocol: Arrays were scanned with the AgilentTechnologies Scanner G2505B US23502332 using protocol version GE1-v5_95_Feb07

data_processing: Mean foreground intensities were obtained for each spot and imported into the mathematical software package “R”, which is used for all data input, diagnostic plots, normalization and quality checking steps of the analysis process using scripts developed in-house by Peter White specifically for this analysis. In outline, the Cy3 (green) intensities were not background corrected (this has been shown to only introduce noise), and corrected for the scanner offset (40 was subtracted for each intensity). The dataset was filtered to remove positive control elements and any elements that had been flagged as bad. Using the negative controls on the arrays, the background threshold was determined and all values less than this value were set to the threshold value. Finally, the data was normalized using the Limma Quantile Normalization package in “R” (Smyth 2004, Bolstad et al., 2003).

source_name: dorsal pancreatic epithelia e12.5

label_protocol: Approximately 250 ng of total RNA was amplified and labeled with Cy3 using the Low RNA Input Linear Amp Kit PLUS, One-Color (Agilent Technologies, Santa Clara, CA). This labeling reaction produces 0.25 – 2.0 μg of Cy3-labeled cRNA (anti-sense), by first converting mRNA primed with an oligo (d)T-T7 primer into dsDNA with MMLV-RT and then amplifying the sample using T7 RNA Polymerase in the presence of Cy3-CTP.

growth_protocol: All animal experiments described herein were approved by the University of California, Irvine and San Diego Institutional Animal Care and Use Committees. For timed matings, noon on the day of vaginal plug appearance was designated e0.5.

extract_protocol: E12.5 dorsal pancreatic epithelia were manually microdissected and stored in 50 μl of RLT lysis buffer (QIAGEN, Valencia, CA) in the –80°C freezer. Each individual RNA sample was collected from three dorsal pancreata (i.e. three embryos) as per the manufacturer's instructions. We prepared RNA samples in ~12 μl of DEPC-treated water. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

value: Sox9-flox [mixed FVB/N x C57Bl/6J background] X Pdx1-Cre [C57Bl/6J background]

value: dorsal pancreatic epithelia

tag: developmental stage

tag: genotype

value: wild-type


title: HT1080, control, 6h, rep3

description: gene expression data from HT1080 cells, 6h control

source_name: HT1080 cells, DMSO treated for 6h

value: control


title: dorsal pancreatic epithelia-e12.5-MUT-3

value: Sox9 mutant


title: dorsal pancreatic epithelia-e12.5-MUT-4


title: HT1080, control, 6h, rep1


title: dorsal pancreatic epithelia-e12.5-MUT-2


title: Serie B, HepG2 exposed to ANAC for 12h, biological rep 3

value: ANAC


title: dorsal pancreatic epithelia-e12.5-MUT-1


title: HT1080, control, 6h, rep2


title: dorsal pancreatic epithelia-e12.5-WT-3


title: Prot6_PK31RU

city: Ann Arbor

first: Celine

middle: C

last: Berthier

state: MI

address: 1150 W. Medical Center Dr, MSRB2

institute: University of Michigan

description: Gene expression data from NZW/BXSB nephritic kidney

hyb_protocol: standard Affymetrix protocol

scan_protocol: GeneChip arrays were scanned by GeneChip Scanner 3000 7G according to the Affymetrix Expression Analysis Technical Manual.

data_processing: The data were analyzed using GenePattern pipeline: RMA method and Mouse Entrez Gene custom CDF annotation version 10 were used for the normalization; and Combat for batch correction within the NZB/W mouse model and the NZW/BXSB mouse model.

source_name: Kidney from lupus NZW/BXSB mouse (proteinuric)

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

extract_protocol: Total RNA was isolated using Trizol and manufacturer's instructions

tag: disease status

value: Kidney from nephritic mouse

value: Whole kidney


title: Serie B, HepG2 exposed to ANAC for 12h, biological rep 2


title: Serie B, HepG2 exposed to ANAC for 12h, biological rep 1


title: Prot1_PK46RU


title: Prot2_PK48RL


title: dorsal pancreatic epithelia-e12.5-WT-1


title: Nonprot4_PK30LU

description: Gene expression data from NZW/BXSB prenephritic kidney

source_name: Kidney from lupus NZW/BXSB mouse (non-proteinuric)

value: Kidney from prenephritic mouse


title: Nonprot5_KP21LL


title: Serie B, HepG2 exposed to 2CMP for 12h, biological rep 3


title: Serie B, HepG2 exposed to 2CMP for 12h, biological rep 2


title: Prot3_PK74LL


title: dorsal pancreatic epithelia-e12.5-WT-2


title: Prot4_PK74LU


title: Nonprot6_PK48LU


title: Serie B, HepG2 exposed to 2CMP for 12h, biological rep 1


title: Sick5_VO5RU

description: Gene expression data from NZM2410 nephritic kidney

source_name: Kidney from lupus NZM2410 mouse (sick)


title: Sick4_MP7RL


title: Serie B, HepG2 exposed to 2AAF for 12h, biological rep 3


title: Serie B, HepG2 exposed to 2AAF for 12h, biological rep 2


title: Nonprot1_KP21LU


title: Prot5_PK30RU


title: Sick3_MP7LL


title: Nonprot3_KP21RU


title: duodenum HRFI day 42 rep1

city: Athens

first: Samuel

middle: E

last: Aggrey

state: GA

address: 110 Cedar Street

department: Poultry Science

institute: University of Georgia

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

scan_protocol: GeneChips were scanned using the Affymetrix GeneArray Scanner 7G

data_processing: The data were analyzed with Partek Genomics Suite 6.5, with standard RMA settings.

organism: Gallus gallus

source_name: duodenum HRFI day 42 rep1

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA - Affymetrix Manual).

value: duodenum

tag: group

value: High Residual Feed Intake (HRFI)


title: duodenum HRFI day 42 rep2

source_name: duodenum HRFI day 42 rep2


title: Nonprot2_KP21RL


title: duodenum HRFI day 42 rep3

source_name: duodenum HRFI day 42 rep3


title: duodenum HRFI day 42 rep4

source_name: duodenum HRFI day 42 rep4


title: Sick2_MP6LU


title: Serie B, HepG2 exposed to PhB for 12h, biological rep 3

source_name: hepatocellular carcinoma cell line

value: PhB


title: Sick1_MP5RU


title: Serie B, HepG2 exposed to 2AAF for 12h, biological rep 1


title: duodenum HRFI day 35 rep4

source_name: duodenum HRFI day 35 rep4


title: Serie B, HepG2 exposed to Que for 12h, biological rep 3

value: Que


title: Young5_2410_5

description: Gene expression data from NZM2410 prenephritic kidney

source_name: Kidney from lupus NZM2410 mouse (young)


title: Serie B, HepG2 exposed to Que for 12h, biological rep 1


title: Young3_2410_3


title: Young4_2410_4


title: duodenum HRFI day 35 rep3

source_name: duodenum HRFI day 35 rep3


title: Young1_2410_1


title: duodenum HRFI day 35 rep1

source_name: duodenum HRFI day 35 rep1


title: Serie B, HepG2 exposed to Que for 12h, biological rep 2


title: Young2_2410_2


title: Serie A, HepG2 exposed to DMSO for 12h, biological rep 3

value: DMSO


title: Serie B, HepG2 exposed to 8HQ for 12h, biological rep 1


title: Serie B, HepG2 exposed to ampC for 12h, biological rep 3

value: ampC


title: duodenum LRFI day 42 rep3

source_name: duodenum LRFI day 42 rep3

value: Low Residual Feed Intake (LRFI)


title: Serie B, HepG2 exposed to 8HQ for 12h, biological rep 3


title: Serie B, HepG2 exposed to ampC for 12h, biological rep 1


title: duodenum LRFI day 42 rep2

source_name: duodenum LRFI day 42 rep2


title: Serie A, HepG2 exposed to DMSO for 12h, biological rep 2


title: duodenum LRFI day 42 rep4

source_name: duodenum LRFI day 42 rep4


title: duodenum LRFI day 35 rep1

source_name: duodenum LRFI day 35 rep1


title: Serie B, HepG2 exposed to ampC for 12h, biological rep 2


title: Serie B, HepG2 exposed to 8HQ for 12h, biological rep 2


title: duodenum LRFI day 35 rep3

source_name: duodenum LRFI day 35 rep3


title: duodenum LRFI day 42 rep1

source_name: duodenum LRFI day 42 rep1


title: duodenum LRFI day 35 rep4

source_name: duodenum LRFI day 35 rep4


title: duodenum LRFI day 35 rep2

source_name: duodenum LRFI day 35 rep2


title: duodenum HRFI day 35 rep2

source_name: duodenum HRFI day 35 rep2


title: Serie A, HepG2 exposed to DMSO for 12h, biological rep 1


title: Ovarian cancer clear cell line RMG-I

hyb_protocol: Hybridized with Agilent whole genome oligo microarray in Agilent’s SureHyb Hybridization Chambers.

scan_protocol: After hybridization and washing, the processed slides were scanned with the Agilent DNA microarray scanner (part number G2505B) using settings recommended by Agilent Technologies.

data_processing: The resulting text files extracted from Agilent Feature Extraction Software (version 10.5.1.1) were imported into the Agilent GeneSpring GX software (version11.0) for further analysis.

source_name: ovarian cancer clear cell line RMG-I

label_protocol: After having passed RNA measurement on the Nanodrop ND-1000 and denaturing gel electrophoresis, the samples were amplified and labeled using the Agilent Quick Amp labeling kit

extract_protocol: Total RNAs are harvested using TRIzol (Invitrogen) and the RNeasy kit (Qiagen) according to manufacturer’s instructions, including a DNase digestion step.

value: RMG-I

tag: transfection


title: Serie A, HepG2 exposed to E2 for 12h, biological rep 2


title: Ovarian cancer clear cell line RMG-I-H

source_name: ovarian cancer clear cell line RMG-I-H


title: Serie A, HepG2 exposed to E2 for 12h, biological rep 3


title: Blood 1 day AMPH Rat MT76

city: Jefferson

middle: Francis

last: Bowyer

state: AR

address: 3900 NCTR Drive

department: Neurotoxicology

institute: National Center for Toxicological Research FDA

hyb_protocol: 1.65 µg cRNA was fragmented and hybridized onto an Agilent 4x44K oligonucleotide microarray in a hybridization oven at 65°C for 17 hr using the Agilent Gene Expression Hybridization Kit (5188-5281).  The hybridized microarrays were disassembled at room temperature in Gene Expression Wash Buffer 1 (5188-5325), and then washed in Gene Expression Wash Buffer 1 at room temperature for 1 min.  This was followed by a wash for 1 min in Gene Expression Wash Buffer 2 (5188-5326) at an elevated temperature (≈31°C) and air dried.  To preserve the fluorescent signal intensity and prevent Cy3 degradation to environmental ozone, the entire procedure with the final drying step and scanning conducted was done inside a low-ozone biobubble (<1 ppb ozone).

scan_protocol: The arrays were scanned on an Axon 4000B scanner (Molecular Devices Corporation, Sunnyvale, CA)

data_processing:
Initially processing used GenePix Pro 6.0 software (Molecular Devices) and background was (determined from median dark corners) subtracted from probe/gene signals
The working microarray dataset was obtained through, background correction, logbase2 (log2) transformation, and normalization. Probes/ID REFs were filtered to include only those genes with official NCBI gene symbols. We included in our analysis each probe for genes with less than 4 probes/ID REFs. For genes with 4 or more probes/ID REFs, we used the signal intensity after for all the probes/ID REFs except for the ones with the minimum and maximum values. Raw expression data was corrected for background signal. To symmetrize the distribution of background-corrected intensity values and stabilize the variance, we transformed gene expression data using log2 transformation and applied quantile normalization (Bolstad et al., 2003).

organism: Rattus norvegicus

source_name: Blood AMPH 1 day post

label_protocol: 500 ng of total RNA was used in the Agilent Quick Amp Labeling Kit according to the manufacturer's instructions.  The cRNA was fluorescently labeled by incorporation of cyanine (Cy)3-CTP.  After purification, using the RNeasy mini kit (Qiagen), cRNA yield and Cy3 incorporation efficiency (specific activity) into the cRNA were determined using a NanoDrop® ND-1000 Spectrophotometer (NanoDrop Technologies).  All cRNAs had a yield >5 µg and a specific activity of 8–15 pmol/µg

growth_protocol: Animals used in these experiments were NCTR strain of Sprague-Dawley rat kept on a 12hour light cycle 6:00am to 6:00pm

extract_protocol: Total RNA was extracted using Tri Reagent (Molecular Research Center Inc., Cincinnati, OH) (Chomczynski and Mackey, 1995) with modifications similar to those previously described (Bowyer et al., 2007).

treatment_protocol: Tissues (trunk blood collected by decapitation and choroid plexus of the brain) were extracted from 3 month old Sprague-Dawley rats (NCTR strain) at 3 hr or 1 day after saline, environmental hyperthermia or amphetamine exposure after.

value: blood from striatum (brain region)

tag: gender

value: male

tag: age

value: 3 months

value: amphetamine toxicity

value: 1 day post

value: Sprague-Dawley


title: Blood 1 day AMPH Rat MT51

tag: strain


title: Blood 1 day AMPH Rat MT59


title: Blood 1 day AMPH Rat MT53


title: Serie A, HepG2 exposed to TCDD for 12h, biological rep 2

source_name: hepatocellular carcinoma cell line

value: TCDD


title: Serie A, HepG2 exposed to CsA for 12h, biological rep 1

value: CsA


title: Blood 1 day EIH Rat MT87

source_name: Blood EIH 1 day post

value: environmentally induced hyperthermia


title: Serie A, HepG2 exposed to TCDD for 12h, biological rep 1


title: Serie A, HepG2 exposed to CsA for 12h, biological rep 2


title: Serie A, HepG2 exposed to CsA for 12h, biological rep 3


title: Blood 1 day EIH Rat MT39


title: Abcg8 knockout testes + ezetimibe, 4413

city: Northbrook

last: Falduto

state: IL

address: 1808 Janke, Unit M

institute: GenUs BioSystems, Inc.

hyb_protocol: cRNA was fragmented to uniform size and verified on the Bioanalyzer. Applied Biosystems Mouse Genome Survey microarrays were hybridized with the cRNA target and treated for chemiluminescence detection.

scan_protocol: Arrays were imaged and processed on the AB1700 Microarray Analyzer.

data_processing: Data was analyzed with GeneSpring GX software. Intensity values were normalized to the median intensity of each array.

label: Digoxigenin

source_name: testes, Abcg8 knockout, ezetimibe

label_protocol: First and second strand cDNA was prepared from the total RNA samples. Digoxigenin-labeled cRNA target was prepared from the DNA template and verified on the Bioanalyzer.

growth_protocol: Mice were fed rodent chow. All mice were between 10-12 weeks of age.

extract_protocol: Total RNA was extracted and purified using RiboPure RNA Isolation (Ambion). Total RNA samples were quantitated by UV spectrophotometry. Quality of total RNA was assessed using an Agilent Bioanalyzer.

treatment_protocol: Mice were fed chow supplemented with 0.005% ezetimibe.

tag: strain/background

value: Abcg8 knockout

value: adult

value: 10-12 weeks

value: testes

value: ezetimibe


title: Abcg8 knockout testes + ezetimibe, 4416


title: Serie A, HepG2 exposed to E2 for 12h, biological rep 1

hyb_protocol: 12.5µg of cRNA were hybridized for 16 hr on 45°C on GeneChip Human Genome U133 Plus 2.0 Array, using Affymetrix® GeneChip® Fluidics Station 450 and the GeneChip Hybridization, Wash and Stain Kit

extract_protocol: Trizol extraction was performed using the miRNAeasy kit from qiagen accoding to the manufacturer’s protocol


title: Wild-type testes, M2

source_name: testes, wild-type

value: wild-type


title: Serie A, HepG2 exposed to TCDD for 12h, biological rep 3


title: Blood 1 day EIH Rat MT38


title: Blood 1 day Control Rat MT67

source_name: Blood Control 1 day post

value: saline


title: Blood 1 day EIH Rat MT71


title: Abcg8 knockout testes, 4574

source_name: testes, Abcg8 knockout


title: Serie A, HepG2 exposed to AFB1 for 12h, biological rep 3


title: Blood 1 day Control Rat MT66


title: Blood 1 day Control Rat MT36


title: Blood 1 day Control Rat MT33


title: Wild-type testes, M1


title: Serie A, HepG2 exposed to AFB1 for 12h, biological rep 2


title: Blood 3 hr AMPH Rat MT75

source_name: Blood AMPH 3 hr post

value: 3 hr post


title: Abcg8 knockout testes, 4573


title: Blood 3 hr AMPH Rat MT90

value: blood from striatum (brain region)


title: Blood 3 hr EIH Rat MT70

source_name: Blood EIH 3 hr post

value: male


title: pancreatic epithelia-e15.5-MUT-4

scan_protocol: Arrays were scanned with the AgilentTechnologies Scanner G2505B US23502657using protocol version GE1-v5_95_Feb07

data_processing:
Mean foreground intensities were obtained for each spot and imported into the mathematical software package “R”, which is used for all data input, diagnostic plots, normalization and quality checking steps of the analysis process using scripts developed in-house by Peter White specifically for this analysis. In outline, the Cy3 (green) intensities were not background corrected (this has been shown to only introduce noise), and corrected for the scanner offset (40 was subtracted for each intensity). The dataset was filtered to remove positive control elements and any elements that had been flagged as bad. Using the negative controls on the arrays, the background threshold was determined and all values less than this value were set to the threshold value. Finally, the data was normalized using the Limma Quantile Normalization package in “R” (Smyth 2004, Bolstad et al., 2003).
In designing the interest statistic for data analysis we borrowed ideas from the software package Focus (Cole et al. 2003). The interest statistic reflects a biologists understanding that a gene with a greater fold change (in absolute value) than other genes is potentially more interesting. Also, given two genes with the same fold changes, it is the gene with a higher expression level (and therefore higher absolute change) that is more relevant. This approach is described in greater detail elsewhere (Ogawa et al. 2004)

source_name: pancreatic epithelia e15.5

label_protocol: Approximately 250 ng of total RNA was amplified and labeled with Cy3 using the QuickAmp Labeling Kit, One-Color (Agilent Technologies, Santa Clara, CA). This labeling reaction produces 3 – 4.5 μg of Cy3-labeled cRNA (anti-sense), by first converting mRNA primed with an oligo (d)T-T7 primer into dsDNA with MMLV-RT and then amplifying the sample using T7 RNA Polymerase in the presence of Cy3-CTP.

extract_protocol: E15.5 whole pancreatic epithelia (including both dorsal and ventral pancreatic epithelia) were manually microdissected and stored in 350 μl of RLT lysis buffer (QIAGEN, Valencia, CA) in the –80°C freezer. Each individual RNA sample was collected from four pancreata (i.e. four embryos) as per the manufacturer's instructions. We prepared RNA samples in ~12 μl of DEPC-treated water. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Dams were injected with 6 mg/40 g tamoxifen in corn oil at e12.5.

value: Sox9-flox [mixed FVB/N x C57Bl/6J x CD1 background] X Rosa26-CreER [C57Bl/6J background]

value: pancreatic epithelia

value: Sox9 mutant


title: pancreatic epithelia-e15.5-MUT-2


title: Blood 3 hr AMPH Rat MT62

value: 3 months

value: amphetamine toxicity

value: Sprague-Dawley


title: Blood 3 hr AMPH Rat MT48


title: pancreatic epithelia-e15.5-MUT-3


title: pancreatic epithelia-e15.5-WT-4


title: Blood 3 hr Control Rat MT31

source_name: Blood Control 3 hr post


title: Blood 3 hr Control Rat MT65


title: pancreatic epithelia-e15.5-WT-1


title: pancreatic epithelia-e15.5-WT-3


title: Blood 3 hr EIH Rat MT69

value: environmentally induced hyperthermia


title: Blood 3 hr Control Rat MT64


title: Serie A, HepG2 exposed to AFB1 for 12h, biological rep 1

scan_protocol: Arrays were scanned using genechip scanner 3000 7G

data_processing: Obtained data sets were re-annotated to the MBNI Custom CDF-files (http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/genomic_curated_CDF.asp) (Dai et al., 2005) and RMA normalized (Irizarry et al., 2003) using the NuGOExpressionFileCreator, an enhanced version of the standard ExpressionFileCreator module that is present in GenePattern (De Groot et al., 2008). The resulting 17,788 probe sets represent 17,726 unique genes and 62 internal controls

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 250ng total RNA using the 3’ IVT express kit


title: Blood 3 hr EIH Rat MT40


title: Serie A, HepG2 exposed to BaP for 12h, biological rep 2

value: BaP


title: Serie A, HepG2 exposed to BaP for 12h, biological rep 1


title: pancreatic epithelia-e15.5-WT-2


title: pancreatic epithelia-e15.5-MUT-1


title: tumor cell line GC424  48 h after transfection with siRNA to the SV40 large T-antigen (culture 2)

description: tumor cell line after transfection with siRNA

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation using R Statistical language and packages from the Bioconductor project. The given data were normalized in a context of additional arrays, which are not displayed here.

source_name: antrum of the stomach

label_protocol: Biotinylated cRNA was prepared with the  Illumina® TotalPrep™ RNA Amplification Kit (Applied Biosystems, Darmstadt, Germany).

extract_protocol: RNA was extracted with Nucleospin extraction kit  according to the manufacturer´s protocol ((Machery&Nagel, Düren, Germany). Quality control was performed with denaturing gel electrophoresis and UV measurement.

tag: genetic background

value: 2-6 months

value: siRNA to the SV40 large T-antigen


title: Blood 3 hr Control Rat MT63

tag: tissue


title: tumor cell line GC424  48 h after transfection with siRNA to the SV40 large T-antigen (culture 1)

tag: cell line


title: tumor cell line GC424 established from the antrum of tumor bearing CEA424-Tag mice, separate culture 2, rep2

description: tumor cell line