title: LP_2-5_5d_13_TRBZ_10008_Liver

description: LP_2-5_5d_13_TRBZ_10008_Liver_(HT_Rat230_PM)_A07: 1470 rats were used in this study: 6 chemicals, 4 timepoints, and 6 dose groups (including control). 10 animals per group and 5 extra control animals. Timepoints were 5d, 2w, 4w, and 13 weeks. Doses varied with compound (Tribromobenzene: 0, 2-5,5,10,25,75; Bromobenzene: 0, 25, 100, 200, 300, 400; Tetrachlorophenol: 0, 10, 25, 50, 100, 200; Mehtylenebis(N,N-dimethyl)benzenamine: 0, 50, 200, 375, 500, 750; Nitrosodiphenylamine: 0, 250, 1000, 2000, 3000, 4000; Hydrazobenzene: 0, 5, 20, 80, 200, 300). Animals were dosed through gavage or diet. Two of the protocols had female rats and the rest were male rats (see protocols). F344 and Sprague Dawley rats were used.

tag: bioanalyzer results


title: brain_SMC6_replicate2

status: Public on Apr 22 2013

type: RNA

city: Neuherberg

first: Martin

last: Irmler

state: Bayern

address: Ingolstaedter Landstrasse 1

department: Institute of Experimental Genetics

country: Germany

institute: Helmholtz Zentrum München GmbH

description:
replicate 2
SAMPLE 22

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol using HiScan

data_processing: The data were normalised using cubic spline normalisation with Illumina Genomestudio 2011.1

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: brain

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

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up with QIAGEN RNeasy midi kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with gel electrophoreses.

tag: age

value: 19 weeks

tag: mouse id

tag: genotype/variation

value: SMC6 mutant

tag: strain


title: LP_2-5_5d_16_TRBZ_10008_Liver

city: RTP

first: Longlong

last: Yang

state: NC

address: 6 Davis Dr.

country: USA

institute: CIIT Centers for Health Research

description: LP_2-5_5d_16_TRBZ_10008_Liver_(HT_Rat230_PM)_A10: 1470 rats were used in this study: 6 chemicals, 4 timepoints, and 6 dose groups (including control). 10 animals per group and 5 extra control animals. Timepoints were 5d, 2w, 4w, and 13 weeks. Doses varied with compound (Tribromobenzene: 0, 2-5,5,10,25,75; Bromobenzene: 0, 25, 100, 200, 300, 400; Tetrachlorophenol: 0, 10, 25, 50, 100, 200; Mehtylenebis(N,N-dimethyl)benzenamine: 0, 50, 200, 375, 500, 750; Nitrosodiphenylamine: 0, 250, 1000, 2000, 3000, 4000; Hydrazobenzene: 0, 5, 20, 80, 200, 300). Animals were dosed through gavage or diet. Two of the protocols had female rats and the rest were male rats (see protocols). F344 and Sprague Dawley rats were used.

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: RMA normalization with Partek software program

organism: Rattus norvegicus

label_protocol: standard Affymetrix protocol

extract_protocol: Extraction Method: Qiagen

treatment_protocol: in vivo Treatment: 1,2,4-Tribromobenzene, Treatment Repeat: 7, Units of Treatment Repeat: Days/Week, Treatment Duration: 5, Units of Duration: days, Treatment Time: 1, Units of Treatment Time: exposure/day, Vehicle for Chemical: Corn Oil, Amount of Vehicle: 5, Route of Exposure: Gavage, Units of Amount of Vehicle: ml/kg, Dose or Concentration: 2.5, Units of Dose or Concentration: mg/kg

tag: array type

tag: amount to core

tag: units of amount

value: ul

tag: ratio

tag: rna integrity number

value: Excellent

tag: sample preservation

value: Frozen

tag: strain or line

value: Spague Dawley Crl:CD(SD)

tag: ncbi taxonomy id

tag: individual

tag: developmental state

value: Adult

tag: sacrifice method

value: Pentobarbital, Exsanguinated

tag: Sex

value: Male

tag: units of age

value: weeks

tag: tissue

value: Liver

tag: tissue harvest methods

value: Slices from each of the lobes were pooled together for microarray analysis


title: brain_SMC6_replicate3

description:
replicate 3
SAMPLE 23

tag: age

tag: mouse id

tag: genotype/variation


title: brain_SMC6_replicate1

description:
replicate 1
SAMPLE 21

tag: strain


title: LP_0_2w_584_OC1_10010_Liver

description: LP_0_2w_584_OC1_10010_Liver_(HT_Rat230_PM)_C10: 1470 rats were used in this study:  6 chemicals, 4 time points, and 6 dose groups (including control).  10 animals per group and 5 extra control animals.  Timepoints were 5d, 2w, 4w, and 13 weeks.  Doses varied with compound (Tribromobenzene: 0, 2.5, 5, 10, 25, 75; Bromobenzene: 0, 25, 100, 200, 300, 400; Tetrachlorophenol: 0, 10, 25, 50, 100, 200; Methylenebis(N,N-dimethyl)benzen amine: 0, 50, 200, 375, 500, 750; Nitrosodiphenylamine: 0, 250, 1000, 2000, 3000, 4000; Hydrazobenzene: 0, 5, 20, 80, 200, 300).  Animals were dosed through gavage or diet.  Two of the protocols had female rats and the rest were male rats (see protocols).  F344 and Sprague Dawley rats were used.

treatment_protocol: in vivo Treatment: Olive Oil Control 1, Treatment Repeat: 7, Units of Treatment Repeat: Days/Week, Treatment Duration: 2, Units of Duration: Weeks, Treatment Time: 1, Units of Treatment Time: exposure/day, Vehicle for Chemical: Olive Oil, Amount of Vehicle: 5, Route of Exposure: Gavage, Units of Amount of Vehicle: ml/kg, Dose or Concentration: 0, Units of Dose or Concentration: mg/kg

tag: array type

tag: amount to core

tag: units of amount

tag: bioanalyzer results

value: Weeks


title: LP_2-5_5d_12_TRBZ_10008_Liver

description: LP_2-5_5d_12_TRBZ_10008_Liver_(HT_Rat230_PM)_A06: 1470 rats were used in this study: 6 chemicals, 4 timepoints, and 6 dose groups (including control). 10 animals per group and 5 extra control animals. Timepoints were 5d, 2w, 4w, and 13 weeks. Doses varied with compound (Tribromobenzene: 0, 2-5,5,10,25,75; Bromobenzene: 0, 25, 100, 200, 300, 400; Tetrachlorophenol: 0, 10, 25, 50, 100, 200; Mehtylenebis(N,N-dimethyl)benzenamine: 0, 50, 200, 375, 500, 750; Nitrosodiphenylamine: 0, 250, 1000, 2000, 3000, 4000; Hydrazobenzene: 0, 5, 20, 80, 200, 300). Animals were dosed through gavage or diet. Two of the protocols had female rats and the rest were male rats (see protocols). F344 and Sprague Dawley rats were used.

tag: ratio

tag: rna integrity number

tag: sample preservation

tag: strain or line


title: LP_10_5d_36_TRBZ_10008_Liver

description: LP_10_5d_36_TRBZ_10008_Liver_(HT_Rat230_PM)_B08: 1470 rats were used in this study: 6 chemicals, 4 timepoints, and 6 dose groups (including control). 10 animals per group and 5 extra control animals. Timepoints were 5d, 2w, 4w, and 13 weeks. Doses varied with compound (Tribromobenzene: 0, 2-5,5,10,25,75; Bromobenzene: 0, 25, 100, 200, 300, 400; Tetrachlorophenol: 0, 10, 25, 50, 100, 200; Mehtylenebis(N,N-dimethyl)benzenamine: 0, 50, 200, 375, 500, 750; Nitrosodiphenylamine: 0, 250, 1000, 2000, 3000, 4000; Hydrazobenzene: 0, 5, 20, 80, 200, 300). Animals were dosed through gavage or diet. Two of the protocols had female rats and the rest were male rats (see protocols). F344 and Sprague Dawley rats were used.

treatment_protocol: in vivo Treatment: 1,2,4-Tribromobenzene, Treatment Repeat: 7, Units of Treatment Repeat: Days/Week, Treatment Duration: 5, Units of Duration: days, Treatment Time: 1, Units of Treatment Time: exposure/day, Vehicle for Chemical: Corn Oil, Amount of Vehicle: 5, Route of Exposure: Gavage, Units of Amount of Vehicle: ml/kg, Dose or Concentration: 10, Units of Dose or Concentration: mg/kg

tag: ncbi taxonomy id

tag: individual

tag: developmental state

tag: sacrifice method


title: brain_wt_replicate4

description:
replicate 4
SAMPLE 20

value: wildtype


title: T lymphocytes not treated with IFN-β, individual 1

city: Haifa

first: Noa

last: Henig

address: Efron st.

department: Faculty of Medicine

country: Israel

institute: Technion Israel Institute of Technology

hyb_protocol: Biotinylated cRNAs was purified, fragmented, and subsequently hybridized to an Illumina BeadChip according to the Direct Hybridization assay (Illumina Inc.). The hybridized chip was stained with streptavidin-Cy3 (AmershamTM)

scan_protocol: Illumina Beadarray reader

data_processing: The scanned images were imported into GenomeStudio (Illumina Inc.) for extraction and quality control. The un-normalized set was analyzed using ANOVA. Quantile normalization data was uploaded as well at GEO's request

organism: Homo sapiens

source_name: T lymphocytes treated with TNF-α, not treated with IFN-β

label_protocol: The RNA was amplified into cRNA and biotinylated by in vitro transcription using the Illumina TotalPrep RNA Amplification Kit (Ambion, Applied Biosystems) according to the manufacturer's protocol

growth_protocol: T cells were grown in RPMI 1640 medium containing 10% fetal calf serum, 2mM L-glutamine and 100 U/ml Penicillin-Streptomycin, monocytes medium contained also 1% MEM non-essential amino acids solution and 1mM sodium pyruvate. Cells were incubated in 5% CO2 at 37°.

extract_protocol: RNA was extracted using HighPure RNA isolation kit, Roche Applied Science

treatment_protocol: Monocytes and T cells were isolated from healthy volunteers using EasySep negative selection magnetic beads and negative selection CD3+ RosetteSep respectively, both from StemCell technologies. Cells were treated with TNF-α (10ng/ml) for 2h and then IFN-β1a (100 U/ml) was added for 16h.

tag: cell type

value: T lymphocytes

tag: donor

tag: treated

value: No


title: LP_75_4w_176_TRBZ_10008_Liver

description: LP_75_4w_176_TRBZ_10008_Liver_(HT_Rat230_PM)_H07: 1470 rats were used in this study: 6 chemicals, 4 timepoints, and 6 dose groups (including control). 10 animals per group and 5 extra control animals. Timepoints were 5d, 2w, 4w, and 13 weeks. Doses varied with compound (Tribromobenzene: 0, 2-5,5,10,25,75; Bromobenzene: 0, 25, 100, 200, 300, 400; Tetrachlorophenol: 0, 10, 25, 50, 100, 200; Mehtylenebis(N,N-dimethyl)benzenamine: 0, 50, 200, 375, 500, 750; Nitrosodiphenylamine: 0, 250, 1000, 2000, 3000, 4000; Hydrazobenzene: 0, 5, 20, 80, 200, 300). Animals were dosed through gavage or diet. Two of the protocols had female rats and the rest were male rats (see protocols). F344 and Sprague Dawley rats were used.

treatment_protocol: in vivo Treatment: 1,2,4-Tribromobenzene, Treatment Repeat: 7, Units of Treatment Repeat: Days/Week, Treatment Duration: 4, Units of Duration: Weeks, Treatment Time: 1, Units of Treatment Time: exposure/day, Vehicle for Chemical: Corn Oil, Amount of Vehicle: 5, Route of Exposure: Gavage, Units of Amount of Vehicle: ml/kg, Dose or Concentration: 75, Units of Dose or Concentration: mg/kg

tag: Sex

tag: age

tag: units of age

tag: tissue

tag: tissue harvest methods


title: brain_wt_replicate3

description:
replicate 3
SAMPLE 19

tag: mouse id

tag: genotype/variation

tag: strain


title: LP_0_5d_1_CC1_10008_Liver

description: LP_0_5d_1_CC1_10008_Liver_(HT_Rat230_PM)_A01: 1470 rats were used in this study: 6 chemicals, 4 timepoints, and 6 dose groups (including control). 10 animals per group and 5 extra control animals. Timepoints were 5d, 2w, 4w, and 13 weeks. Doses varied with compound (Tribromobenzene: 0, 2-5,5,10,25,75; Bromobenzene: 0, 25, 100, 200, 300, 400; Tetrachlorophenol: 0, 10, 25, 50, 100, 200; Mehtylenebis(N,N-dimethyl)benzenamine: 0, 50, 200, 375, 500, 750; Nitrosodiphenylamine: 0, 250, 1000, 2000, 3000, 4000; Hydrazobenzene: 0, 5, 20, 80, 200, 300). Animals were dosed through gavage or diet. Two of the protocols had female rats and the rest were male rats (see protocols). F344 and Sprague Dawley rats were used.

treatment_protocol: in vivo Treatment: Corn Oil Control 1, Treatment Repeat: 7, Units of Treatment Repeat: Days/Week, Treatment Duration: 5, Units of Duration: days, Treatment Time: 1, Units of Treatment Time: exposure/day, Vehicle for Chemical: Corn Oil, Amount of Vehicle: 5, Route of Exposure: Gavage, Units of Amount of Vehicle: ml/kg, Dose or Concentration: 0, Units of Dose or Concentration: mg/kg

tag: array type

tag: amount to core

tag: units of amount

tag: ratio

tag: rna integrity number

tag: bioanalyzer results

value: excellent

tag: sample preservation


title: LP_10_5d_31_TRBZ_10008_Liver

description: LP_10_5d_31_TRBZ_10008_Liver_(HT_Rat230_PM)_B04: 1470 rats were used in this study: 6 chemicals, 4 timepoints, and 6 dose groups (including control). 10 animals per group and 5 extra control animals. Timepoints were 5d, 2w, 4w, and 13 weeks. Doses varied with compound (Tribromobenzene: 0, 2-5,5,10,25,75; Bromobenzene: 0, 25, 100, 200, 300, 400; Tetrachlorophenol: 0, 10, 25, 50, 100, 200; Mehtylenebis(N,N-dimethyl)benzenamine: 0, 50, 200, 375, 500, 750; Nitrosodiphenylamine: 0, 250, 1000, 2000, 3000, 4000; Hydrazobenzene: 0, 5, 20, 80, 200, 300). Animals were dosed through gavage or diet. Two of the protocols had female rats and the rest were male rats (see protocols). F344 and Sprague Dawley rats were used.

value: Good

tag: strain or line

tag: ncbi taxonomy id

tag: individual

tag: developmental state

tag: sacrifice method


title: LP_0_5d_5_CC1_10008_Liver

description: LP_0_5d_5_CC1_10008_Liver_(HT_Rat230_PM)_A04: 1470 rats were used in this study: 6 chemicals, 4 timepoints, and 6 dose groups (including control). 10 animals per group and 5 extra control animals. Timepoints were 5d, 2w, 4w, and 13 weeks. Doses varied with compound (Tribromobenzene: 0, 2-5,5,10,25,75; Bromobenzene: 0, 25, 100, 200, 300, 400; Tetrachlorophenol: 0, 10, 25, 50, 100, 200; Mehtylenebis(N,N-dimethyl)benzenamine: 0, 50, 200, 375, 500, 750; Nitrosodiphenylamine: 0, 250, 1000, 2000, 3000, 4000; Hydrazobenzene: 0, 5, 20, 80, 200, 300). Animals were dosed through gavage or diet. Two of the protocols had female rats and the rest were male rats (see protocols). F344 and Sprague Dawley rats were used.

tag: Sex

tag: units of age

tag: tissue


title: LP_10_5d_35_TRBZ_10008_Liver

description: LP_10_5d_35_TRBZ_10008_Liver_(HT_Rat230_PM)_B07: 1470 rats were used in this study: 6 chemicals, 4 timepoints, and 6 dose groups (including control). 10 animals per group and 5 extra control animals. Timepoints were 5d, 2w, 4w, and 13 weeks. Doses varied with compound (Tribromobenzene: 0, 2-5,5,10,25,75; Bromobenzene: 0, 25, 100, 200, 300, 400; Tetrachlorophenol: 0, 10, 25, 50, 100, 200; Mehtylenebis(N,N-dimethyl)benzenamine: 0, 50, 200, 375, 500, 750; Nitrosodiphenylamine: 0, 250, 1000, 2000, 3000, 4000; Hydrazobenzene: 0, 5, 20, 80, 200, 300). Animals were dosed through gavage or diet. Two of the protocols had female rats and the rest were male rats (see protocols). F344 and Sprague Dawley rats were used.

tag: tissue harvest methods


title: Subject A, before Yoga intervention, replicate 1

city: Oslo

first: Leonardo

middle: A.

last: Meza-Zepeda

address: Ullernchausseen 70

department: Dept. of Tumor Biology

country: Norway

institute: The Norwegian Radium Hospital

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation in J-Express

source_name: Peripheral blood lymphocytes

extract_protocol: Blood was collected in tubes containing EDTA as anticoagulent (Greiner Bio-One), immediately loaded onto LeukoLOCK RNA isolation system (Ambion) and processed according to the manufacturer’s recommendations

treatment_protocol: Participants took part in the following routine 4 days in a row from 6:30 am to 8:30 am: The first two days they practiced SK&P which includes gentle stretches (yoga postures), specific breathing exercises (pranayamas and SK), ending with a meditative experience. The sessions were led by an experienced instructor in SK&P in a standard format. For the next two days, at the same time period, participants went for a nature walk for 60 min and then listened to classical or relaxing jazz music in silence for 60 min in the same room where they had the SK&P practice. Immediately before and right after the interventions, 20 ml of blood was collected by venous puncture from each participant.

tag: gender

value: Blood

value: Subject A

tag: treatment

value: before Yoga intervention


title: LP_75_4w_172_TRBZ_10008_Liver

description: LP_75_4w_172_TRBZ_10008_Liver_(HT_Rat230_PM)_H04: 1470 rats were used in this study: 6 chemicals, 4 timepoints, and 6 dose groups (including control). 10 animals per group and 5 extra control animals. Timepoints were 5d, 2w, 4w, and 13 weeks. Doses varied with compound (Tribromobenzene: 0, 2-5,5,10,25,75; Bromobenzene: 0, 25, 100, 200, 300, 400; Tetrachlorophenol: 0, 10, 25, 50, 100, 200; Mehtylenebis(N,N-dimethyl)benzenamine: 0, 50, 200, 375, 500, 750; Nitrosodiphenylamine: 0, 250, 1000, 2000, 3000, 4000; Hydrazobenzene: 0, 5, 20, 80, 200, 300). Animals were dosed through gavage or diet. Two of the protocols had female rats and the rest were male rats (see protocols). F344 and Sprague Dawley rats were used.

tag: array type

tag: amount to core

value: ul

value: Excellent

value: Frozen

tag: age


title: LP_0_5d_6_CC1_10008_Liver

description: LP_0_5d_6_CC1_10008_Liver_(HT_Rat230_PM)_A05: 1470 rats were used in this study: 6 chemicals, 4 timepoints, and 6 dose groups (including control). 10 animals per group and 5 extra control animals. Timepoints were 5d, 2w, 4w, and 13 weeks. Doses varied with compound (Tribromobenzene: 0, 2-5,5,10,25,75; Bromobenzene: 0, 25, 100, 200, 300, 400; Tetrachlorophenol: 0, 10, 25, 50, 100, 200; Mehtylenebis(N,N-dimethyl)benzenamine: 0, 50, 200, 375, 500, 750; Nitrosodiphenylamine: 0, 250, 1000, 2000, 3000, 4000; Hydrazobenzene: 0, 5, 20, 80, 200, 300). Animals were dosed through gavage or diet. Two of the protocols had female rats and the rest were male rats (see protocols). F344 and Sprague Dawley rats were used.

tag: units of amount

tag: ratio

tag: rna integrity number

value: Spague Dawley Crl:CD(SD)

value: Adult

value: Pentobarbital, Exsanguinated


title: LP_75_4w_171_TRBZ_10008_Liver

description: LP_75_4w_171_TRBZ_10008_Liver_(HT_Rat230_PM)_H03: 1470 rats were used in this study: 6 chemicals, 4 timepoints, and 6 dose groups (including control). 10 animals per group and 5 extra control animals. Timepoints were 5d, 2w, 4w, and 13 weeks. Doses varied with compound (Tribromobenzene: 0, 2-5,5,10,25,75; Bromobenzene: 0, 25, 100, 200, 300, 400; Tetrachlorophenol: 0, 10, 25, 50, 100, 200; Mehtylenebis(N,N-dimethyl)benzenamine: 0, 50, 200, 375, 500, 750; Nitrosodiphenylamine: 0, 250, 1000, 2000, 3000, 4000; Hydrazobenzene: 0, 5, 20, 80, 200, 300). Animals were dosed through gavage or diet. Two of the protocols had female rats and the rest were male rats (see protocols). F344 and Sprague Dawley rats were used.

tag: bioanalyzer results

tag: sample preservation

tag: strain or line

value: Male

value: weeks

value: Liver


title: LP_10_5d_34_TRBZ_10008_Liver

description: LP_10_5d_34_TRBZ_10008_Liver_(HT_Rat230_PM)_B06: 1470 rats were used in this study: 6 chemicals, 4 timepoints, and 6 dose groups (including control). 10 animals per group and 5 extra control animals. Timepoints were 5d, 2w, 4w, and 13 weeks. Doses varied with compound (Tribromobenzene: 0, 2-5,5,10,25,75; Bromobenzene: 0, 25, 100, 200, 300, 400; Tetrachlorophenol: 0, 10, 25, 50, 100, 200; Mehtylenebis(N,N-dimethyl)benzenamine: 0, 50, 200, 375, 500, 750; Nitrosodiphenylamine: 0, 250, 1000, 2000, 3000, 4000; Hydrazobenzene: 0, 5, 20, 80, 200, 300). Animals were dosed through gavage or diet. Two of the protocols had female rats and the rest were male rats (see protocols). F344 and Sprague Dawley rats were used.

tag: ncbi taxonomy id

tag: individual

tag: developmental state

value: Slices from each of the lobes were pooled together for microarray analysis


title: LP_10_5d_32_TRBZ_10008_Liver

description: LP_10_5d_32_TRBZ_10008_Liver_(HT_Rat230_PM)_B05: 1470 rats were used in this study: 6 chemicals, 4 timepoints, and 6 dose groups (including control). 10 animals per group and 5 extra control animals. Timepoints were 5d, 2w, 4w, and 13 weeks. Doses varied with compound (Tribromobenzene: 0, 2-5,5,10,25,75; Bromobenzene: 0, 25, 100, 200, 300, 400; Tetrachlorophenol: 0, 10, 25, 50, 100, 200; Mehtylenebis(N,N-dimethyl)benzenamine: 0, 50, 200, 375, 500, 750; Nitrosodiphenylamine: 0, 250, 1000, 2000, 3000, 4000; Hydrazobenzene: 0, 5, 20, 80, 200, 300). Animals were dosed through gavage or diet. Two of the protocols had female rats and the rest were male rats (see protocols). F344 and Sprague Dawley rats were used.

tag: sacrifice method

tag: Sex

tag: units of age


title: LP_5_4w_146_TRBZ_10008_Liver

description: LP_5_4w_146_TRBZ_10008_Liver_(HT_Rat230_PM)_G04: 1470 rats were used in this study: 6 chemicals, 4 timepoints, and 6 dose groups (including control). 10 animals per group and 5 extra control animals. Timepoints were 5d, 2w, 4w, and 13 weeks. Doses varied with compound (Tribromobenzene: 0, 2-5,5,10,25,75; Bromobenzene: 0, 25, 100, 200, 300, 400; Tetrachlorophenol: 0, 10, 25, 50, 100, 200; Mehtylenebis(N,N-dimethyl)benzenamine: 0, 50, 200, 375, 500, 750; Nitrosodiphenylamine: 0, 250, 1000, 2000, 3000, 4000; Hydrazobenzene: 0, 5, 20, 80, 200, 300). Animals were dosed through gavage or diet. Two of the protocols had female rats and the rest were male rats (see protocols). F344 and Sprague Dawley rats were used.

treatment_protocol: in vivo Treatment: 1,2,4-Tribromobenzene, Treatment Repeat: 7, Units of Treatment Repeat: Days/Week, Treatment Duration: 4, Units of Duration: Weeks, Treatment Time: 1, Units of Treatment Time: exposure/day, Vehicle for Chemical: Corn Oil, Amount of Vehicle: 5, Route of Exposure: Gavage, Units of Amount of Vehicle: ml/kg, Dose or Concentration: 5, Units of Dose or Concentration: mg/kg

tag: tissue

tag: tissue harvest methods


title: LP_0_5d_2_CC1_10008_Liver

description: LP_0_5d_2_CC1_10008_Liver_(HT_Rat230_PM)_A02: 1470 rats were used in this study: 6 chemicals, 4 timepoints, and 6 dose groups (including control). 10 animals per group and 5 extra control animals. Timepoints were 5d, 2w, 4w, and 13 weeks. Doses varied with compound (Tribromobenzene: 0, 2-5,5,10,25,75; Bromobenzene: 0, 25, 100, 200, 300, 400; Tetrachlorophenol: 0, 10, 25, 50, 100, 200; Mehtylenebis(N,N-dimethyl)benzenamine: 0, 50, 200, 375, 500, 750; Nitrosodiphenylamine: 0, 250, 1000, 2000, 3000, 4000; Hydrazobenzene: 0, 5, 20, 80, 200, 300). Animals were dosed through gavage or diet. Two of the protocols had female rats and the rest were male rats (see protocols). F344 and Sprague Dawley rats were used.

tag: array type


title: spleen_SMC6_replicate2

description:
replicate 2
SAMPLE 14

source_name: spleen

value: 12 weeks

tag: mouse id

tag: genotype/variation

value: SMC6 mutant

tag: strain


title: LP_5_4w_143_TRBZ_10008_Liver

description: LP_5_4w_143_TRBZ_10008_Liver_(HT_Rat230_PM)_G02: 1470 rats were used in this study: 6 chemicals, 4 timepoints, and 6 dose groups (including control). 10 animals per group and 5 extra control animals. Timepoints were 5d, 2w, 4w, and 13 weeks. Doses varied with compound (Tribromobenzene: 0, 2-5,5,10,25,75; Bromobenzene: 0, 25, 100, 200, 300, 400; Tetrachlorophenol: 0, 10, 25, 50, 100, 200; Mehtylenebis(N,N-dimethyl)benzenamine: 0, 50, 200, 375, 500, 750; Nitrosodiphenylamine: 0, 250, 1000, 2000, 3000, 4000; Hydrazobenzene: 0, 5, 20, 80, 200, 300). Animals were dosed through gavage or diet. Two of the protocols had female rats and the rest were male rats (see protocols). F344 and Sprague Dawley rats were used.

tag: amount to core

tag: units of amount

tag: ratio

tag: age


title: brain_wt_replicate1

description:
replicate 1
SAMPLE 17

value: 19 weeks

value: wildtype


title: LP_75_4w_174_TRBZ_10008_Liver

description: LP_75_4w_174_TRBZ_10008_Liver_(HT_Rat230_PM)_H06: 1470 rats were used in this study: 6 chemicals, 4 timepoints, and 6 dose groups (including control). 10 animals per group and 5 extra control animals. Timepoints were 5d, 2w, 4w, and 13 weeks. Doses varied with compound (Tribromobenzene: 0, 2-5,5,10,25,75; Bromobenzene: 0, 25, 100, 200, 300, 400; Tetrachlorophenol: 0, 10, 25, 50, 100, 200; Mehtylenebis(N,N-dimethyl)benzenamine: 0, 50, 200, 375, 500, 750; Nitrosodiphenylamine: 0, 250, 1000, 2000, 3000, 4000; Hydrazobenzene: 0, 5, 20, 80, 200, 300). Animals were dosed through gavage or diet. Two of the protocols had female rats and the rest were male rats (see protocols). F344 and Sprague Dawley rats were used.

tag: rna integrity number

tag: bioanalyzer results

tag: sample preservation

tag: strain or line


title: brain_wt_replicate2

description:
replicate 2
SAMPLE 18


title: LP_75_4w_173_TRBZ_10008_Liver

description: LP_75_4w_173_TRBZ_10008_Liver_(HT_Rat230_PM)_H05: 1470 rats were used in this study: 6 chemicals, 4 timepoints, and 6 dose groups (including control). 10 animals per group and 5 extra control animals. Timepoints were 5d, 2w, 4w, and 13 weeks. Doses varied with compound (Tribromobenzene: 0, 2-5,5,10,25,75; Bromobenzene: 0, 25, 100, 200, 300, 400; Tetrachlorophenol: 0, 10, 25, 50, 100, 200; Mehtylenebis(N,N-dimethyl)benzenamine: 0, 50, 200, 375, 500, 750; Nitrosodiphenylamine: 0, 250, 1000, 2000, 3000, 4000; Hydrazobenzene: 0, 5, 20, 80, 200, 300). Animals were dosed through gavage or diet. Two of the protocols had female rats and the rest were male rats (see protocols). F344 and Sprague Dawley rats were used.

tag: ncbi taxonomy id

tag: individual

tag: developmental state

tag: sacrifice method


title: LP_0_5d_4_CC1_10008_Liver

description: LP_0_5d_4_CC1_10008_Liver_(HT_Rat230_PM)_A03: 1470 rats were used in this study: 6 chemicals, 4 timepoints, and 6 dose groups (including control). 10 animals per group and 5 extra control animals. Timepoints were 5d, 2w, 4w, and 13 weeks. Doses varied with compound (Tribromobenzene: 0, 2-5,5,10,25,75; Bromobenzene: 0, 25, 100, 200, 300, 400; Tetrachlorophenol: 0, 10, 25, 50, 100, 200; Mehtylenebis(N,N-dimethyl)benzenamine: 0, 50, 200, 375, 500, 750; Nitrosodiphenylamine: 0, 250, 1000, 2000, 3000, 4000; Hydrazobenzene: 0, 5, 20, 80, 200, 300). Animals were dosed through gavage or diet. Two of the protocols had female rats and the rest were male rats (see protocols). F344 and Sprague Dawley rats were used.

value: excellent

tag: Sex

tag: units of age

tag: tissue

tag: tissue harvest methods


title: LP_5_4w_144_TRBZ_10008_Liver

description: LP_5_4w_144_TRBZ_10008_Liver_(HT_Rat230_PM)_G03: 1470 rats were used in this study: 6 chemicals, 4 timepoints, and 6 dose groups (including control). 10 animals per group and 5 extra control animals. Timepoints were 5d, 2w, 4w, and 13 weeks. Doses varied with compound (Tribromobenzene: 0, 2-5,5,10,25,75; Bromobenzene: 0, 25, 100, 200, 300, 400; Tetrachlorophenol: 0, 10, 25, 50, 100, 200; Mehtylenebis(N,N-dimethyl)benzenamine: 0, 50, 200, 375, 500, 750; Nitrosodiphenylamine: 0, 250, 1000, 2000, 3000, 4000; Hydrazobenzene: 0, 5, 20, 80, 200, 300). Animals were dosed through gavage or diet. Two of the protocols had female rats and the rest were male rats (see protocols). F344 and Sprague Dawley rats were used.

tag: array type


title: spleen_SMC6_replicate3

description:
replicate 3
SAMPLE 15

tag: mouse id

tag: genotype/variation

tag: strain


title: spleen_SMC6_replicate1

description:
replicate 1
SAMPLE 13

tag: age


title: spleen_SMC6_replicate4

description:
replicate 4
SAMPLE 16


title: spleen_wt_replicate4

description:
replicate 4
SAMPLE 12


title: LP_5_4w_142_TRBZ_10008_Liver

description: LP_5_4w_142_TRBZ_10008_Liver_(HT_Rat230_PM)_G01: 1470 rats were used in this study: 6 chemicals, 4 timepoints, and 6 dose groups (including control). 10 animals per group and 5 extra control animals. Timepoints were 5d, 2w, 4w, and 13 weeks. Doses varied with compound (Tribromobenzene: 0, 2-5,5,10,25,75; Bromobenzene: 0, 25, 100, 200, 300, 400; Tetrachlorophenol: 0, 10, 25, 50, 100, 200; Mehtylenebis(N,N-dimethyl)benzenamine: 0, 50, 200, 375, 500, 750; Nitrosodiphenylamine: 0, 250, 1000, 2000, 3000, 4000; Hydrazobenzene: 0, 5, 20, 80, 200, 300). Animals were dosed through gavage or diet. Two of the protocols had female rats and the rest were male rats (see protocols). F344 and Sprague Dawley rats were used.

tag: amount to core

tag: units of amount

tag: ratio

tag: rna integrity number

value: Good


title: LP_5_4w_141_TRBZ_10008_Liver

description: LP_5_4w_141_TRBZ_10008_Liver_(HT_Rat230_PM)_F12: 1470 rats were used in this study: 6 chemicals, 4 timepoints, and 6 dose groups (including control). 10 animals per group and 5 extra control animals. Timepoints were 5d, 2w, 4w, and 13 weeks. Doses varied with compound (Tribromobenzene: 0, 2-5,5,10,25,75; Bromobenzene: 0, 25, 100, 200, 300, 400; Tetrachlorophenol: 0, 10, 25, 50, 100, 200; Mehtylenebis(N,N-dimethyl)benzenamine: 0, 50, 200, 375, 500, 750; Nitrosodiphenylamine: 0, 250, 1000, 2000, 3000, 4000; Hydrazobenzene: 0, 5, 20, 80, 200, 300). Animals were dosed through gavage or diet. Two of the protocols had female rats and the rest were male rats (see protocols). F344 and Sprague Dawley rats were used.

tag: bioanalyzer results

tag: sample preservation

tag: strain or line

tag: ncbi taxonomy id


title: spleen_wt_replicate3

description:
replicate 3
SAMPLE 11


title: LP_25_4w_166_TRBZ_10008_Liver

description: LP_25_4w_166_TRBZ_10008_Liver_(HT_Rat230_PM)_H02: 1470 rats were used in this study: 6 chemicals, 4 timepoints, and 6 dose groups (including control). 10 animals per group and 5 extra control animals. Timepoints were 5d, 2w, 4w, and 13 weeks. Doses varied with compound (Tribromobenzene: 0, 2-5,5,10,25,75; Bromobenzene: 0, 25, 100, 200, 300, 400; Tetrachlorophenol: 0, 10, 25, 50, 100, 200; Mehtylenebis(N,N-dimethyl)benzenamine: 0, 50, 200, 375, 500, 750; Nitrosodiphenylamine: 0, 250, 1000, 2000, 3000, 4000; Hydrazobenzene: 0, 5, 20, 80, 200, 300). Animals were dosed through gavage or diet. Two of the protocols had female rats and the rest were male rats (see protocols). F344 and Sprague Dawley rats were used.

treatment_protocol: in vivo Treatment: 1,2,4-Tribromobenzene, Treatment Repeat: 7, Units of Treatment Repeat: Days/Week, Treatment Duration: 4, Units of Duration: Weeks, Treatment Time: 1, Units of Treatment Time: exposure/day, Vehicle for Chemical: Corn Oil, Amount of Vehicle: 5, Route of Exposure: Gavage, Units of Amount of Vehicle: ml/kg, Dose or Concentration: 25, Units of Dose or Concentration: mg/kg

tag: individual

tag: developmental state

tag: sacrifice method

tag: Sex


title: LP_25_4w_164_TRBZ_10008_Liver

description: LP_25_4w_164_TRBZ_10008_Liver_(HT_Rat230_PM)_G12: 1470 rats were used in this study: 6 chemicals, 4 timepoints, and 6 dose groups (including control). 10 animals per group and 5 extra control animals. Timepoints were 5d, 2w, 4w, and 13 weeks. Doses varied with compound (Tribromobenzene: 0, 2-5,5,10,25,75; Bromobenzene: 0, 25, 100, 200, 300, 400; Tetrachlorophenol: 0, 10, 25, 50, 100, 200; Mehtylenebis(N,N-dimethyl)benzenamine: 0, 50, 200, 375, 500, 750; Nitrosodiphenylamine: 0, 250, 1000, 2000, 3000, 4000; Hydrazobenzene: 0, 5, 20, 80, 200, 300). Animals were dosed through gavage or diet. Two of the protocols had female rats and the rest were male rats (see protocols). F344 and Sprague Dawley rats were used.

tag: array type

tag: units of age

tag: tissue

tag: tissue harvest methods


title: LP_25_4w_165_TRBZ_10008_Liver

description: LP_25_4w_165_TRBZ_10008_Liver_(HT_Rat230_PM)_H01: 1470 rats were used in this study: 6 chemicals, 4 timepoints, and 6 dose groups (including control). 10 animals per group and 5 extra control animals. Timepoints were 5d, 2w, 4w, and 13 weeks. Doses varied with compound (Tribromobenzene: 0, 2-5,5,10,25,75; Bromobenzene: 0, 25, 100, 200, 300, 400; Tetrachlorophenol: 0, 10, 25, 50, 100, 200; Mehtylenebis(N,N-dimethyl)benzenamine: 0, 50, 200, 375, 500, 750; Nitrosodiphenylamine: 0, 250, 1000, 2000, 3000, 4000; Hydrazobenzene: 0, 5, 20, 80, 200, 300). Animals were dosed through gavage or diet. Two of the protocols had female rats and the rest were male rats (see protocols). F344 and Sprague Dawley rats were used.

tag: age


title: LP_25_4w_162_TRBZ_10008_Liver

description: LP_25_4w_162_TRBZ_10008_Liver_(HT_Rat230_PM)_G10: 1470 rats were used in this study: 6 chemicals, 4 timepoints, and 6 dose groups (including control). 10 animals per group and 5 extra control animals. Timepoints were 5d, 2w, 4w, and 13 weeks. Doses varied with compound (Tribromobenzene: 0, 2-5,5,10,25,75; Bromobenzene: 0, 25, 100, 200, 300, 400; Tetrachlorophenol: 0, 10, 25, 50, 100, 200; Mehtylenebis(N,N-dimethyl)benzenamine: 0, 50, 200, 375, 500, 750; Nitrosodiphenylamine: 0, 250, 1000, 2000, 3000, 4000; Hydrazobenzene: 0, 5, 20, 80, 200, 300). Animals were dosed through gavage or diet. Two of the protocols had female rats and the rest were male rats (see protocols). F344 and Sprague Dawley rats were used.

tag: amount to core


title: spleen_wt_replicate2

description:
replicate 2
SAMPLE 10

tag: mouse id

tag: genotype/variation

tag: strain


title: LP_25_4w_163_TRBZ_10008_Liver

description: LP_25_4w_163_TRBZ_10008_Liver_(HT_Rat230_PM)_G11: 1470 rats were used in this study: 6 chemicals, 4 timepoints, and 6 dose groups (including control). 10 animals per group and 5 extra control animals. Timepoints were 5d, 2w, 4w, and 13 weeks. Doses varied with compound (Tribromobenzene: 0, 2-5,5,10,25,75; Bromobenzene: 0, 25, 100, 200, 300, 400; Tetrachlorophenol: 0, 10, 25, 50, 100, 200; Mehtylenebis(N,N-dimethyl)benzenamine: 0, 50, 200, 375, 500, 750; Nitrosodiphenylamine: 0, 250, 1000, 2000, 3000, 4000; Hydrazobenzene: 0, 5, 20, 80, 200, 300). Animals were dosed through gavage or diet. Two of the protocols had female rats and the rest were male rats (see protocols). F344 and Sprague Dawley rats were used.

tag: units of amount

tag: ratio

tag: rna integrity number

tag: bioanalyzer results


title: spleen_wt_replicate1

description:
replicate 1
SAMPLE 9


title: LP_2-5_4w_135_TRBZ_10008_Liver

description: LP_2-5_4w_135_TRBZ_10008_Liver_(HT_Rat230_PM)_F11: 1470 rats were used in this study: 6 chemicals, 4 timepoints, and 6 dose groups (including control). 10 animals per group and 5 extra control animals. Timepoints were 5d, 2w, 4w, and 13 weeks. Doses varied with compound (Tribromobenzene: 0, 2-5,5,10,25,75; Bromobenzene: 0, 25, 100, 200, 300, 400; Tetrachlorophenol: 0, 10, 25, 50, 100, 200; Mehtylenebis(N,N-dimethyl)benzenamine: 0, 50, 200, 375, 500, 750; Nitrosodiphenylamine: 0, 250, 1000, 2000, 3000, 4000; Hydrazobenzene: 0, 5, 20, 80, 200, 300). Animals were dosed through gavage or diet. Two of the protocols had female rats and the rest were male rats (see protocols). F344 and Sprague Dawley rats were used.

treatment_protocol: in vivo Treatment: 1,2,4-Tribromobenzene, Treatment Repeat: 7, Units of Treatment Repeat: Days/Week, Treatment Duration: 4, Units of Duration: Weeks, Treatment Time: 1, Units of Treatment Time: exposure/day, Vehicle for Chemical: Corn Oil, Amount of Vehicle: 5, Route of Exposure: Gavage, Units of Amount of Vehicle: ml/kg, Dose or Concentration: 2.5, Units of Dose or Concentration: mg/kg

tag: sample preservation

tag: strain or line

tag: ncbi taxonomy id

tag: individual


title: LP_10_4w_153_TRBZ_10008_Liver

description: LP_10_4w_153_TRBZ_10008_Liver_(HT_Rat230_PM)_G06: 1470 rats were used in this study: 6 chemicals, 4 timepoints, and 6 dose groups (including control). 10 animals per group and 5 extra control animals. Timepoints were 5d, 2w, 4w, and 13 weeks. Doses varied with compound (Tribromobenzene: 0, 2-5,5,10,25,75; Bromobenzene: 0, 25, 100, 200, 300, 400; Tetrachlorophenol: 0, 10, 25, 50, 100, 200; Mehtylenebis(N,N-dimethyl)benzenamine: 0, 50, 200, 375, 500, 750; Nitrosodiphenylamine: 0, 250, 1000, 2000, 3000, 4000; Hydrazobenzene: 0, 5, 20, 80, 200, 300). Animals were dosed through gavage or diet. Two of the protocols had female rats and the rest were male rats (see protocols). F344 and Sprague Dawley rats were used.

treatment_protocol: in vivo Treatment: 1,2,4-Tribromobenzene, Treatment Repeat: 7, Units of Treatment Repeat: Days/Week, Treatment Duration: 4, Units of Duration: Weeks, Treatment Time: 1, Units of Treatment Time: exposure/day, Vehicle for Chemical: Corn Oil, Amount of Vehicle: 5, Route of Exposure: Gavage, Units of Amount of Vehicle: ml/kg, Dose or Concentration: 10, Units of Dose or Concentration: mg/kg

tag: array type

tag: developmental state

tag: sacrifice method

tag: Sex


title: testis_SMC6_replicate3

description:
replicate 3
SAMPLE 7

source_name: testis

tag: age


title: LP_2-5_4w_134_TRBZ_10008_Liver

description: LP_2-5_4w_134_TRBZ_10008_Liver_(HT_Rat230_PM)_F10: 1470 rats were used in this study: 6 chemicals, 4 timepoints, and 6 dose groups (including control). 10 animals per group and 5 extra control animals. Timepoints were 5d, 2w, 4w, and 13 weeks. Doses varied with compound (Tribromobenzene: 0, 2-5,5,10,25,75; Bromobenzene: 0, 25, 100, 200, 300, 400; Tetrachlorophenol: 0, 10, 25, 50, 100, 200; Mehtylenebis(N,N-dimethyl)benzenamine: 0, 50, 200, 375, 500, 750; Nitrosodiphenylamine: 0, 250, 1000, 2000, 3000, 4000; Hydrazobenzene: 0, 5, 20, 80, 200, 300). Animals were dosed through gavage or diet. Two of the protocols had female rats and the rest were male rats (see protocols). F344 and Sprague Dawley rats were used.

tag: amount to core

tag: units of age

tag: tissue

tag: tissue harvest methods


title: LP_2-5_4w_131_TRBZ_10008_Liver

description: LP_2-5_4w_131_TRBZ_10008_Liver_(HT_Rat230_PM)_F07: 1470 rats were used in this study: 6 chemicals, 4 timepoints, and 6 dose groups (including control). 10 animals per group and 5 extra control animals. Timepoints were 5d, 2w, 4w, and 13 weeks. Doses varied with compound (Tribromobenzene: 0, 2-5,5,10,25,75; Bromobenzene: 0, 25, 100, 200, 300, 400; Tetrachlorophenol: 0, 10, 25, 50, 100, 200; Mehtylenebis(N,N-dimethyl)benzenamine: 0, 50, 200, 375, 500, 750; Nitrosodiphenylamine: 0, 250, 1000, 2000, 3000, 4000; Hydrazobenzene: 0, 5, 20, 80, 200, 300). Animals were dosed through gavage or diet. Two of the protocols had female rats and the rest were male rats (see protocols). F344 and Sprague Dawley rats were used.

tag: units of amount


title: testis_SMC6_replicate2

description:
replicate 2
SAMPLE 6

tag: mouse id

tag: genotype/variation

tag: strain


title: testis_SMC6_replicate4

description:
replicate 4
SAMPLE 8


title: testis_wt_replicate2

description:
replicate 2
SAMPLE 2


title: LP_2-5_4w_132_TRBZ_10008_Liver

description: LP_2-5_4w_132_TRBZ_10008_Liver_(HT_Rat230_PM)_F08: 1470 rats were used in this study: 6 chemicals, 4 timepoints, and 6 dose groups (including control). 10 animals per group and 5 extra control animals. Timepoints were 5d, 2w, 4w, and 13 weeks. Doses varied with compound (Tribromobenzene: 0, 2-5,5,10,25,75; Bromobenzene: 0, 25, 100, 200, 300, 400; Tetrachlorophenol: 0, 10, 25, 50, 100, 200; Mehtylenebis(N,N-dimethyl)benzenamine: 0, 50, 200, 375, 500, 750; Nitrosodiphenylamine: 0, 250, 1000, 2000, 3000, 4000; Hydrazobenzene: 0, 5, 20, 80, 200, 300). Animals were dosed through gavage or diet. Two of the protocols had female rats and the rest were male rats (see protocols). F344 and Sprague Dawley rats were used.

tag: ratio

tag: bioanalyzer results

tag: sample preservation


title: testis_SMC6_replicate1

description:
replicate 1
SAMPLE 5


title: LP_10_4w_152_TRBZ_10008_Liver

description: LP_10_4w_152_TRBZ_10008_Liver_(HT_Rat230_PM)_G05: 1470 rats were used in this study: 6 chemicals, 4 timepoints, and 6 dose groups (including control). 10 animals per group and 5 extra control animals. Timepoints were 5d, 2w, 4w, and 13 weeks. Doses varied with compound (Tribromobenzene: 0, 2-5,5,10,25,75; Bromobenzene: 0, 25, 100, 200, 300, 400; Tetrachlorophenol: 0, 10, 25, 50, 100, 200; Mehtylenebis(N,N-dimethyl)benzenamine: 0, 50, 200, 375, 500, 750; Nitrosodiphenylamine: 0, 250, 1000, 2000, 3000, 4000; Hydrazobenzene: 0, 5, 20, 80, 200, 300). Animals were dosed through gavage or diet. Two of the protocols had female rats and the rest were male rats (see protocols). F344 and Sprague Dawley rats were used.

tag: rna integrity number

tag: strain or line

tag: ncbi taxonomy id

tag: individual


title: testis_wt_replicate4

description:
replicate 4
SAMPLE 4


title: MIN6 clone4 cells at 40-50 passages  [MG_U74Bv2]

city: Suita

first: Eiji

last: Yamato

address: 2-2 Yamadaoka

country: Japan

institute: Osaka University

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on murine genome U74 version 2 GeneChip array.

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

data_processing: The data were analyzed with Affymetrix Genechip 5.1 software using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: MIN6 clone4 cells at 40-50 passages

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

growth_protocol: MIN6 cells were maintained in Dulbecco's modified Eagle's medium containing 25 mM glucose, 13% heat-inactivated fetal bovine serum, 0.1 mM 2-mercaptoethanol, 100 units/ml penicillin, and 0.05 mg/ml streptomycin in humidified 5% CO2 at 37°C.

extract_protocol: Total RNA was extracted from MIN6 cells using Trizol reagent (Invitrogen, Carlsbad, CA) and subjected to double-strand cDNA synthesis using the Superscript Choice system (Invitrogen) and the T7-(dT)24 reverse transcription primer (Amersham Biosciences, Piscataway, NJ).

tag: cell line

value: MIN6 insulinoma

tag: cell line population

value: subclone 4

tag: passages


title: LP_2-5_4w_133_TRBZ_10008_Liver

description: LP_2-5_4w_133_TRBZ_10008_Liver_(HT_Rat230_PM)_F09: 1470 rats were used in this study: 6 chemicals, 4 timepoints, and 6 dose groups (including control). 10 animals per group and 5 extra control animals. Timepoints were 5d, 2w, 4w, and 13 weeks. Doses varied with compound (Tribromobenzene: 0, 2-5,5,10,25,75; Bromobenzene: 0, 25, 100, 200, 300, 400; Tetrachlorophenol: 0, 10, 25, 50, 100, 200; Mehtylenebis(N,N-dimethyl)benzenamine: 0, 50, 200, 375, 500, 750; Nitrosodiphenylamine: 0, 250, 1000, 2000, 3000, 4000; Hydrazobenzene: 0, 5, 20, 80, 200, 300). Animals were dosed through gavage or diet. Two of the protocols had female rats and the rest were male rats (see protocols). F344 and Sprague Dawley rats were used.

tag: array type

tag: amount to core

value: ul

value: Excellent

tag: developmental state

tag: sacrifice method

tag: Sex

tag: age

tag: units of age


title: LP_10_4w_156_TRBZ_10008_Liver

description: LP_10_4w_156_TRBZ_10008_Liver_(HT_Rat230_PM)_G09: 1470 rats were used in this study: 6 chemicals, 4 timepoints, and 6 dose groups (including control). 10 animals per group and 5 extra control animals. Timepoints were 5d, 2w, 4w, and 13 weeks. Doses varied with compound (Tribromobenzene: 0, 2-5,5,10,25,75; Bromobenzene: 0, 25, 100, 200, 300, 400; Tetrachlorophenol: 0, 10, 25, 50, 100, 200; Mehtylenebis(N,N-dimethyl)benzenamine: 0, 50, 200, 375, 500, 750; Nitrosodiphenylamine: 0, 250, 1000, 2000, 3000, 4000; Hydrazobenzene: 0, 5, 20, 80, 200, 300). Animals were dosed through gavage or diet. Two of the protocols had female rats and the rest were male rats (see protocols). F344 and Sprague Dawley rats were used.

tag: units of amount

tag: ratio

value: Frozen

value: Spague Dawley Crl:CD(SD)

tag: tissue

tag: tissue harvest methods


title: LP_10_4w_154_TRBZ_10008_Liver

description: LP_10_4w_154_TRBZ_10008_Liver_(HT_Rat230_PM)_G07: 1470 rats were used in this study: 6 chemicals, 4 timepoints, and 6 dose groups (including control). 10 animals per group and 5 extra control animals. Timepoints were 5d, 2w, 4w, and 13 weeks. Doses varied with compound (Tribromobenzene: 0, 2-5,5,10,25,75; Bromobenzene: 0, 25, 100, 200, 300, 400; Tetrachlorophenol: 0, 10, 25, 50, 100, 200; Mehtylenebis(N,N-dimethyl)benzenamine: 0, 50, 200, 375, 500, 750; Nitrosodiphenylamine: 0, 250, 1000, 2000, 3000, 4000; Hydrazobenzene: 0, 5, 20, 80, 200, 300). Animals were dosed through gavage or diet. Two of the protocols had female rats and the rest were male rats (see protocols). F344 and Sprague Dawley rats were used.

tag: rna integrity number

tag: bioanalyzer results

tag: sample preservation

tag: strain or line

value: Adult

value: Pentobarbital, Exsanguinated


title: testis_wt_replicate3

description:
replicate 3
SAMPLE 3

tag: mouse id

tag: genotype/variation

tag: strain


title: LP_0_4w_123_CC1_10008_Liver

description: LP_0_4w_123_CC1_10008_Liver_(HT_Rat230_PM)_F04: 1470 rats were used in this study: 6 chemicals, 4 timepoints, and 6 dose groups (including control). 10 animals per group and 5 extra control animals. Timepoints were 5d, 2w, 4w, and 13 weeks. Doses varied with compound (Tribromobenzene: 0, 2-5,5,10,25,75; Bromobenzene: 0, 25, 100, 200, 300, 400; Tetrachlorophenol: 0, 10, 25, 50, 100, 200; Mehtylenebis(N,N-dimethyl)benzenamine: 0, 50, 200, 375, 500, 750; Nitrosodiphenylamine: 0, 250, 1000, 2000, 3000, 4000; Hydrazobenzene: 0, 5, 20, 80, 200, 300). Animals were dosed through gavage or diet. Two of the protocols had female rats and the rest were male rats (see protocols). F344 and Sprague Dawley rats were used.

treatment_protocol: in vivo Treatment: Corn Oil Control 1, Treatment Repeat: 7, Units of Treatment Repeat: Days/Week, Treatment Duration: 4, Units of Duration: Weeks, Treatment Time: 1, Units of Treatment Time: exposure/day, Vehicle for Chemical: Corn Oil, Amount of Vehicle: 5, Route of Exposure: Gavage, Units of Amount of Vehicle: ml/kg, Dose or Concentration: 0, Units of Dose or Concentration: mg/kg

tag: array type

tag: amount to core

tag: ncbi taxonomy id

tag: individual

value: Male

value: weeks


title: testis_wt_replicate1

description:
replicate 1
SAMPLE 1

tag: age


title: parental MIN6 cells at 35-40 passages  [MG_U74Bv2]

source_name: parental MIN6 cells at 35-40 passages

tag: cell line

tag: cell line population

value: parental

tag: passages


title: LP_10_4w_155_TRBZ_10008_Liver

description: LP_10_4w_155_TRBZ_10008_Liver_(HT_Rat230_PM)_G08: 1470 rats were used in this study: 6 chemicals, 4 timepoints, and 6 dose groups (including control). 10 animals per group and 5 extra control animals. Timepoints were 5d, 2w, 4w, and 13 weeks. Doses varied with compound (Tribromobenzene: 0, 2-5,5,10,25,75; Bromobenzene: 0, 25, 100, 200, 300, 400; Tetrachlorophenol: 0, 10, 25, 50, 100, 200; Mehtylenebis(N,N-dimethyl)benzenamine: 0, 50, 200, 375, 500, 750; Nitrosodiphenylamine: 0, 250, 1000, 2000, 3000, 4000; Hydrazobenzene: 0, 5, 20, 80, 200, 300). Animals were dosed through gavage or diet. Two of the protocols had female rats and the rest were male rats (see protocols). F344 and Sprague Dawley rats were used.

tag: units of amount

tag: ratio

tag: developmental state

tag: sacrifice method

tag: Sex

tag: units of age

tag: tissue

value: Liver

value: Slices from each of the lobes were pooled together for microarray analysis


title: LP_0_4w_124_CC1_10008_Liver

description: LP_0_4w_124_CC1_10008_Liver_(HT_Rat230_PM)_F05: 1470 rats were used in this study: 6 chemicals, 4 timepoints, and 6 dose groups (including control). 10 animals per group and 5 extra control animals. Timepoints were 5d, 2w, 4w, and 13 weeks. Doses varied with compound (Tribromobenzene: 0, 2-5,5,10,25,75; Bromobenzene: 0, 25, 100, 200, 300, 400; Tetrachlorophenol: 0, 10, 25, 50, 100, 200; Mehtylenebis(N,N-dimethyl)benzenamine: 0, 50, 200, 375, 500, 750; Nitrosodiphenylamine: 0, 250, 1000, 2000, 3000, 4000; Hydrazobenzene: 0, 5, 20, 80, 200, 300). Animals were dosed through gavage or diet. Two of the protocols had female rats and the rest were male rats (see protocols). F344 and Sprague Dawley rats were used.

tag: bioanalyzer results

tag: sample preservation

tag: strain or line

tag: tissue harvest methods


title: MIN6 clone4 cells at 17-20 passages  [MG_U74Bv2]

source_name: MIN6 clone4 cells at 17-20 passages


title: SG isolated from flies that express RNAi against H1 using Tub-Gal4_b

city: Bronx

first: Sandeep

middle: Nagaraj

last: Wontakal

state: NY

address: 1300 Morris Park Ave Chanin 402

department: Cell Biology

institute: Albert Einstein College of Medicine

description:
SGH1b
Salivary glands from transgenic flies expressing RNAi against H1 using a Tub-Gal4 driver, were harvested and RNA was isolated.

hyb_protocol: Standard Affymetrix guidelines.

scan_protocol: Samples were scanned by the AECOM microarray facility as suggested by Affymetrix.

data_processing: The raw data (CEL files) from each microarray was normalized by RMA methods in GeneSpring GX software. The transformed signal intensities were averaged for biological replicates, and the mean value was used to compute the fold expression change.

organism: Drosophila melanogaster

source_name: Salivary Gland

label_protocol: Labeling was performed as suggested by Affymetrix by the AECOM microarray facility.

growth_protocol: Flies were crossed at 18o and knockdown was achieved by incubating at 29o from the embryo stage.  Kc cells were grown at 25o in Scheidner's media containing 10% FBS.

extract_protocol: RNA was isolated with Trizol reagent according to manufacturer's protocol.

treatment_protocol: Kc cells were treated with 20mg of dsRNA targeted against GFP or H1 for 1 hour without serum on day 0, 2, and 4.  Cells were washed and fresh Scheidner's media was added.  RNA was subsequently isolated on day 6.  Transgenic flies used for isolation of salivary glands were described in X Lu et al. Genes Dev 2009.

value: Salivary Gland

tag: RNAi against

value: linker histone H1


title: LP_0_4w_126_CC1_10008_Liver

description: LP_0_4w_126_CC1_10008_Liver_(HT_Rat230_PM)_F06: 1470 rats were used in this study: 6 chemicals, 4 timepoints, and 6 dose groups (including control). 10 animals per group and 5 extra control animals. Timepoints were 5d, 2w, 4w, and 13 weeks. Doses varied with compound (Tribromobenzene: 0, 2-5,5,10,25,75; Bromobenzene: 0, 25, 100, 200, 300, 400; Tetrachlorophenol: 0, 10, 25, 50, 100, 200; Mehtylenebis(N,N-dimethyl)benzenamine: 0, 50, 200, 375, 500, 750; Nitrosodiphenylamine: 0, 250, 1000, 2000, 3000, 4000; Hydrazobenzene: 0, 5, 20, 80, 200, 300). Animals were dosed through gavage or diet. Two of the protocols had female rats and the rest were male rats (see protocols). F344 and Sprague Dawley rats were used.

tag: array type

tag: amount to core

tag: rna integrity number

tag: ncbi taxonomy id

tag: individual


title: SG isolated from flies that express RNAi against H1 using Tub-Gal4_c

description:
SGH1c
Salivary glands from transgenic flies expressing RNAi against H1 using a Tub-Gal4 driver, were harvested and RNA was isolated.


title: parental MIN6 cells at 17-20 passages  [MG_U74Bv2]

source_name: parental MIN6 cells at 17-20 passages

tag: cell line

tag: cell line population

tag: passages


title: LP_0_4w_122_CC1_10008_Liver

description: LP_0_4w_122_CC1_10008_Liver_(HT_Rat230_PM)_F03: 1470 rats were used in this study: 6 chemicals, 4 timepoints, and 6 dose groups (including control). 10 animals per group and 5 extra control animals. Timepoints were 5d, 2w, 4w, and 13 weeks. Doses varied with compound (Tribromobenzene: 0, 2-5,5,10,25,75; Bromobenzene: 0, 25, 100, 200, 300, 400; Tetrachlorophenol: 0, 10, 25, 50, 100, 200; Mehtylenebis(N,N-dimethyl)benzenamine: 0, 50, 200, 375, 500, 750; Nitrosodiphenylamine: 0, 250, 1000, 2000, 3000, 4000; Hydrazobenzene: 0, 5, 20, 80, 200, 300). Animals were dosed through gavage or diet. Two of the protocols had female rats and the rest were male rats (see protocols). F344 and Sprague Dawley rats were used.

tag: units of amount

tag: ratio

tag: developmental state

tag: sacrifice method

tag: age


title: LP_0_4w_121_CC1_10008_Liver

description: LP_0_4w_121_CC1_10008_Liver_(HT_Rat230_PM)_F02: 1470 rats were used in this study: 6 chemicals, 4 timepoints, and 6 dose groups (including control). 10 animals per group and 5 extra control animals. Timepoints were 5d, 2w, 4w, and 13 weeks. Doses varied with compound (Tribromobenzene: 0, 2-5,5,10,25,75; Bromobenzene: 0, 25, 100, 200, 300, 400; Tetrachlorophenol: 0, 10, 25, 50, 100, 200; Mehtylenebis(N,N-dimethyl)benzenamine: 0, 50, 200, 375, 500, 750; Nitrosodiphenylamine: 0, 250, 1000, 2000, 3000, 4000; Hydrazobenzene: 0, 5, 20, 80, 200, 300). Animals were dosed through gavage or diet. Two of the protocols had female rats and the rest were male rats (see protocols). F344 and Sprague Dawley rats were used.

tag: bioanalyzer results

tag: sample preservation

tag: Sex

tag: units of age

tag: tissue


title: SG isolated from flies that express RNAi against Nautilus using Tub-Gal4_c

description:
SGNautc
Salivary glands from transgenic flies expressing RNAi against Nautilus using a Tub-Gal4 driver, were harvested and RNA was isolated.

tag: RNAi against

value: control (Nautilus)


title: SG isolated from flies that express RNAi against Nautilus using Tub-Gal4_a

description:
SGNauta
Salivary glands from transgenic flies expressing RNAi against Nautilus using a Tub-Gal4 driver, were harvested and RNA was isolated.


title: LP_75_2w_116_TRBZ_10008_Liver

description: LP_75_2w_116_TRBZ_10008_Liver_(HT_Rat230_PM)_F01: 1470 rats were used in this study: 6 chemicals, 4 timepoints, and 6 dose groups (including control). 10 animals per group and 5 extra control animals. Timepoints were 5d, 2w, 4w, and 13 weeks. Doses varied with compound (Tribromobenzene: 0, 2-5,5,10,25,75; Bromobenzene: 0, 25, 100, 200, 300, 400; Tetrachlorophenol: 0, 10, 25, 50, 100, 200; Mehtylenebis(N,N-dimethyl)benzenamine: 0, 50, 200, 375, 500, 750; Nitrosodiphenylamine: 0, 250, 1000, 2000, 3000, 4000; Hydrazobenzene: 0, 5, 20, 80, 200, 300). Animals were dosed through gavage or diet. Two of the protocols had female rats and the rest were male rats (see protocols). F344 and Sprague Dawley rats were used.

treatment_protocol: in vivo Treatment: 1,2,4-Tribromobenzene, Treatment Repeat: 7, Units of Treatment Repeat: Days/Week, Treatment Duration: 2, Units of Duration: Weeks, Treatment Time: 1, Units of Treatment Time: exposure/day, Vehicle for Chemical: Corn Oil, Amount of Vehicle: 5, Route of Exposure: Gavage, Units of Amount of Vehicle: ml/kg, Dose or Concentration: 75, Units of Dose or Concentration: mg/kg

tag: array type

tag: amount to core

tag: rna integrity number

tag: strain or line

tag: tissue harvest methods


title: mlk-1 fasted 2

city: Kyoto

first: Eisuke

last: Nishida

address: Kitashirakawa, Sakyo-ku

department: Department of Cell and Developmental Biology

institute: Graduate School of Biostudies, Kyoto University

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

data_processing: genespring GX

organism: Caenorhabditis elegans

source_name: 4 day adult mlk-1 Fasting

label_protocol: 3` IVT

growth_protocol: 2day adult are grown with or without food (OP50-1) for 2 days

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

tag: genotype/variation

tag: treatment

value: fast


title: mlk-1 fasted 1

treatment_protocol: 2day adult are grown with or without food (OP50-1) for 2 days


title: Kc cells using RNAi against H1_a

description:
KcH1a
Cells were treated with RNAi targeting H1 on day 0, 2, and 4.  RNA was collected on day 6.

source_name: Kc Cells

tag: cell type

value: Kc Cells


title: LP_75_2w_115_TRBZ_10008_Liver

description: LP_75_2w_115_TRBZ_10008_Liver_(HT_Rat230_PM)_E12: 1470 rats were used in this study: 6 chemicals, 4 timepoints, and 6 dose groups (including control). 10 animals per group and 5 extra control animals. Timepoints were 5d, 2w, 4w, and 13 weeks. Doses varied with compound (Tribromobenzene: 0, 2-5,5,10,25,75; Bromobenzene: 0, 25, 100, 200, 300, 400; Tetrachlorophenol: 0, 10, 25, 50, 100, 200; Mehtylenebis(N,N-dimethyl)benzenamine: 0, 50, 200, 375, 500, 750; Nitrosodiphenylamine: 0, 250, 1000, 2000, 3000, 4000; Hydrazobenzene: 0, 5, 20, 80, 200, 300). Animals were dosed through gavage or diet. Two of the protocols had female rats and the rest were male rats (see protocols). F344 and Sprague Dawley rats were used.

tag: units of amount

tag: ratio

tag: ncbi taxonomy id

tag: individual

tag: developmental state


title: Kc cells using RNAi against H1_b

description:
KcH1b
Cells were treated with RNAi targeting H1 on day 0, 2, and 4.  RNA was collected on day 6.


title: LP_75_2w_114_TRBZ_10008_Liver

description: LP_75_2w_114_TRBZ_10008_Liver_(HT_Rat230_PM)_E11: 1470 rats were used in this study: 6 chemicals, 4 timepoints, and 6 dose groups (including control). 10 animals per group and 5 extra control animals. Timepoints were 5d, 2w, 4w, and 13 weeks. Doses varied with compound (Tribromobenzene: 0, 2-5,5,10,25,75; Bromobenzene: 0, 25, 100, 200, 300, 400; Tetrachlorophenol: 0, 10, 25, 50, 100, 200; Mehtylenebis(N,N-dimethyl)benzenamine: 0, 50, 200, 375, 500, 750; Nitrosodiphenylamine: 0, 250, 1000, 2000, 3000, 4000; Hydrazobenzene: 0, 5, 20, 80, 200, 300). Animals were dosed through gavage or diet. Two of the protocols had female rats and the rest were male rats (see protocols). F344 and Sprague Dawley rats were used.

tag: bioanalyzer results

value: Good

tag: sample preservation

tag: sacrifice method

tag: Sex


title: Kc cells using RNAi against GFP_b

description:
KcGFPb
Cells were treated with RNAi targeting GFP on day 0, 2, and 4.  RNA was collected on day 6.

tag: RNAi against

value: control (GFP)


title: mlk-1 fed 1

source_name: 4 day adult mlk-1 Fed

value: fed


title: SG isolated from flies that express RNAi against Nautilus using Tub-Gal4_b

description:
SGNautb
Salivary glands from transgenic flies expressing RNAi against Nautilus using a Tub-Gal4 driver, were harvested and RNA was isolated.

tag: tissue


title: mek-1 fasted 3

source_name: 4 day adult mek-1 Fasting


title: SG isolated from flies that express RNAi against H1 using Tub-Gal4_a

description:
SGH1a
Salivary glands from transgenic flies expressing RNAi against H1 using a Tub-Gal4 driver, were harvested and RNA was isolated.


title: Kc cells using RNAi against GFP_a

description:
KcGFPa
Cells were treated with RNAi targeting GFP on day 0, 2, and 4.  RNA was collected on day 6.


title: LP_75_2w_111_TRBZ_10008_Liver

description: LP_75_2w_111_TRBZ_10008_Liver_(HT_Rat230_PM)_E09: 1470 rats were used in this study: 6 chemicals, 4 timepoints, and 6 dose groups (including control). 10 animals per group and 5 extra control animals. Timepoints were 5d, 2w, 4w, and 13 weeks. Doses varied with compound (Tribromobenzene: 0, 2-5,5,10,25,75; Bromobenzene: 0, 25, 100, 200, 300, 400; Tetrachlorophenol: 0, 10, 25, 50, 100, 200; Mehtylenebis(N,N-dimethyl)benzenamine: 0, 50, 200, 375, 500, 750; Nitrosodiphenylamine: 0, 250, 1000, 2000, 3000, 4000; Hydrazobenzene: 0, 5, 20, 80, 200, 300). Animals were dosed through gavage or diet. Two of the protocols had female rats and the rest were male rats (see protocols). F344 and Sprague Dawley rats were used.

tag: array type

tag: amount to core

value: ul

value: Excellent

value: Frozen

tag: units of age


title: mek-1 fasted 2

tag: genotype/variation


title: MCF12A_Dox_2

city: Los Angeles

first: William

middle: Juster

last: Sullivan

state: California

address: 354-06 BSRB, 615 Charles E. Young Drive S

department: Biological Chemistry

institute: University of California, Los Angeles

hyb_protocol: Labeled cRNA was mixed with hybridization mix according to the Affymetrix protocol and hybridized in an Affymetrix GeneChip hybridization oven 645 at 45C for 16 hours with rotation at 60 rpm.

scan_protocol: Scanning was performed on an Affymetrix 7G scanner with target intensity 500.

data_processing: Data was processed with R/Bioconductor via the RMA method.

source_name: MCF12A breast epithelial cell line, Dox

label_protocol: Labeling was performed with the Ambion MessageAmp Premier kit (cat#: 4383452).

growth_protocol: MCF12A breast epithelial cells were grown in 10 cm culture plates in DMEM/F12 supplemented with 5% horse serum, 1% penicillin/streptomycin, 10μg/mL insulin, 0.5 μg/mL hydrocortisone, 20 ng/mL EGF, and 10 μg/mL cholera toxin.

extract_protocol: Total RNA was extracted using the Qiagen RNeasy kit using the manufacturer's guidelines.

treatment_protocol: Cells were treated with doxycycline (dissolved in water) at 1 μg/mL or with vehicle for 4 days. Media, with appropriate treatment, was refreshed after 2 days.

tag: cell line

value: breast epithelial cell line

tag: treatment

value: doxycycline (1 ug/mL)


title: mek-1 fasted 1


title: LP_75_2w_112_TRBZ_10008_Liver

description: LP_75_2w_112_TRBZ_10008_Liver_(HT_Rat230_PM)_E10: 1470 rats were used in this study: 6 chemicals, 4 timepoints, and 6 dose groups (including control). 10 animals per group and 5 extra control animals. Timepoints were 5d, 2w, 4w, and 13 weeks. Doses varied with compound (Tribromobenzene: 0, 2-5,5,10,25,75; Bromobenzene: 0, 25, 100, 200, 300, 400; Tetrachlorophenol: 0, 10, 25, 50, 100, 200; Mehtylenebis(N,N-dimethyl)benzenamine: 0, 50, 200, 375, 500, 750; Nitrosodiphenylamine: 0, 250, 1000, 2000, 3000, 4000; Hydrazobenzene: 0, 5, 20, 80, 200, 300). Animals were dosed through gavage or diet. Two of the protocols had female rats and the rest were male rats (see protocols). F344 and Sprague Dawley rats were used.

tag: units of amount

tag: rna integrity number

tag: strain or line

value: Spague Dawley Crl:CD(SD)

value: Adult

value: Pentobarbital, Exsanguinated

value: Male

value: weeks

tag: tissue harvest methods


title: MCF12A_Dox_3

tag: cell type


title: LP_5_2w_84_TRBZ_10008_Liver

description: LP_5_2w_84_TRBZ_10008_Liver_(HT_Rat230_PM)_D07: 1470 rats were used in this study: 6 chemicals, 4 timepoints, and 6 dose groups (including control). 10 animals per group and 5 extra control animals. Timepoints were 5d, 2w, 4w, and 13 weeks. Doses varied with compound (Tribromobenzene: 0, 2-5,5,10,25,75; Bromobenzene: 0, 25, 100, 200, 300, 400; Tetrachlorophenol: 0, 10, 25, 50, 100, 200; Mehtylenebis(N,N-dimethyl)benzenamine: 0, 50, 200, 375, 500, 750; Nitrosodiphenylamine: 0, 250, 1000, 2000, 3000, 4000; Hydrazobenzene: 0, 5, 20, 80, 200, 300). Animals were dosed through gavage or diet. Two of the protocols had female rats and the rest were male rats (see protocols). F344 and Sprague Dawley rats were used.

treatment_protocol: in vivo Treatment: 1,2,4-Tribromobenzene, Treatment Repeat: 7, Units of Treatment Repeat: Days/Week, Treatment Duration: 2, Units of Duration: Weeks, Treatment Time: 1, Units of Treatment Time: exposure/day, Vehicle for Chemical: Corn Oil, Amount of Vehicle: 5, Route of Exposure: Gavage, Units of Amount of Vehicle: ml/kg, Dose or Concentration: 5, Units of Dose or Concentration: mg/kg

tag: ratio

tag: bioanalyzer results

tag: ncbi taxonomy id

tag: individual

tag: developmental state

value: Liver

value: Slices from each of the lobes were pooled together for microarray analysis


title: mlk-1 fed 2


title: mek-1 fed 3

source_name: 4 day adult mek-1 Fed


title: MCF12A_control_3

source_name: MCF12A breast epithelial cell line, vehicle

value: vehicle


title: LP_5_2w_83_TRBZ_10008_Liver

description: LP_5_2w_83_TRBZ_10008_Liver_(HT_Rat230_PM)_D06: 1470 rats were used in this study: 6 chemicals, 4 timepoints, and 6 dose groups (including control). 10 animals per group and 5 extra control animals. Timepoints were 5d, 2w, 4w, and 13 weeks. Doses varied with compound (Tribromobenzene: 0, 2-5,5,10,25,75; Bromobenzene: 0, 25, 100, 200, 300, 400; Tetrachlorophenol: 0, 10, 25, 50, 100, 200; Mehtylenebis(N,N-dimethyl)benzenamine: 0, 50, 200, 375, 500, 750; Nitrosodiphenylamine: 0, 250, 1000, 2000, 3000, 4000; Hydrazobenzene: 0, 5, 20, 80, 200, 300). Animals were dosed through gavage or diet. Two of the protocols had female rats and the rest were male rats (see protocols). F344 and Sprague Dawley rats were used.

tag: sample preservation

tag: sacrifice method

tag: Sex

tag: tissue


title: mek-1 fed 1

tag: genotype/variation


title: mek-1 fed 2


title: LP_5_2w_85_TRBZ_10008_Liver

description: LP_5_2w_85_TRBZ_10008_Liver_(HT_Rat230_PM)_D08: 1470 rats were used in this study: 6 chemicals, 4 timepoints, and 6 dose groups (including control). 10 animals per group and 5 extra control animals. Timepoints were 5d, 2w, 4w, and 13 weeks. Doses varied with compound (Tribromobenzene: 0, 2-5,5,10,25,75; Bromobenzene: 0, 25, 100, 200, 300, 400; Tetrachlorophenol: 0, 10, 25, 50, 100, 200; Mehtylenebis(N,N-dimethyl)benzenamine: 0, 50, 200, 375, 500, 750; Nitrosodiphenylamine: 0, 250, 1000, 2000, 3000, 4000; Hydrazobenzene: 0, 5, 20, 80, 200, 300). Animals were dosed through gavage or diet. Two of the protocols had female rats and the rest were male rats (see protocols). F344 and Sprague Dawley rats were used.

tag: array type

tag: amount to core

tag: units of age


title: LP_5_2w_86_TRBZ_10008_Liver

description: LP_5_2w_86_TRBZ_10008_Liver_(HT_Rat230_PM)_D09: 1470 rats were used in this study: 6 chemicals, 4 timepoints, and 6 dose groups (including control). 10 animals per group and 5 extra control animals. Timepoints were 5d, 2w, 4w, and 13 weeks. Doses varied with compound (Tribromobenzene: 0, 2-5,5,10,25,75; Bromobenzene: 0, 25, 100, 200, 300, 400; Tetrachlorophenol: 0, 10, 25, 50, 100, 200; Mehtylenebis(N,N-dimethyl)benzenamine: 0, 50, 200, 375, 500, 750; Nitrosodiphenylamine: 0, 250, 1000, 2000, 3000, 4000; Hydrazobenzene: 0, 5, 20, 80, 200, 300). Animals were dosed through gavage or diet. Two of the protocols had female rats and the rest were male rats (see protocols). F344 and Sprague Dawley rats were used.

tag: units of amount


title: LP_5_2w_81_TRBZ_10008_Liver

description: LP_5_2w_81_TRBZ_10008_Liver_(HT_Rat230_PM)_D05: 1470 rats were used in this study: 6 chemicals, 4 timepoints, and 6 dose groups (including control). 10 animals per group and 5 extra control animals. Timepoints were 5d, 2w, 4w, and 13 weeks. Doses varied with compound (Tribromobenzene: 0, 2-5,5,10,25,75; Bromobenzene: 0, 25, 100, 200, 300, 400; Tetrachlorophenol: 0, 10, 25, 50, 100, 200; Mehtylenebis(N,N-dimethyl)benzenamine: 0, 50, 200, 375, 500, 750; Nitrosodiphenylamine: 0, 250, 1000, 2000, 3000, 4000; Hydrazobenzene: 0, 5, 20, 80, 200, 300). Animals were dosed through gavage or diet. Two of the protocols had female rats and the rest were male rats (see protocols). F344 and Sprague Dawley rats were used.

tag: rna integrity number

tag: strain or line


title: LP_25_2w_105_TRBZ_10008_Liver

description: LP_25_2w_105_TRBZ_10008_Liver_(HT_Rat230_PM)_E08: 1470 rats were used in this study: 6 chemicals, 4 timepoints, and 6 dose groups (including control). 10 animals per group and 5 extra control animals. Timepoints were 5d, 2w, 4w, and 13 weeks. Doses varied with compound (Tribromobenzene: 0, 2-5,5,10,25,75; Bromobenzene: 0, 25, 100, 200, 300, 400; Tetrachlorophenol: 0, 10, 25, 50, 100, 200; Mehtylenebis(N,N-dimethyl)benzenamine: 0, 50, 200, 375, 500, 750; Nitrosodiphenylamine: 0, 250, 1000, 2000, 3000, 4000; Hydrazobenzene: 0, 5, 20, 80, 200, 300). Animals were dosed through gavage or diet. Two of the protocols had female rats and the rest were male rats (see protocols). F344 and Sprague Dawley rats were used.

treatment_protocol: in vivo Treatment: 1,2,4-Tribromobenzene, Treatment Repeat: 7, Units of Treatment Repeat: Days/Week, Treatment Duration: 2, Units of Duration: Weeks, Treatment Time: 1, Units of Treatment Time: exposure/day, Vehicle for Chemical: Corn Oil, Amount of Vehicle: 5, Route of Exposure: Gavage, Units of Amount of Vehicle: ml/kg, Dose or Concentration: 25, Units of Dose or Concentration: mg/kg

tag: tissue harvest methods


title: parental MIN6 cells at 35-40 passages  [MG_U74Cv2]

tag: cell line

value: MIN6 insulinoma

tag: cell line population

value: parental

tag: passages


title: MIN6 clone4 cells at 40-50 passages  [MG_U74Cv2]

value: subclone 4


title: MIN6 clone4 cells at 17-20 passages  [MG_U74Cv2]


title: MCF12A_Dox_1

tag: cell type

tag: treatment


title: DMNT-treated MEFs, biological rep3

city: Philadelphia

first: Russell

middle: C

last: Addis

state: PA

address: 3400 Civic Center Blvd, Bldg 421, SCTR 9-196

department: Cell and Developmental Biology

institute: University of Pennsylvania

description:
Gene expression data from iCMs generated from MEFs
DMNT3

hyb_protocol: The labeling, hybridization, and scanning procedures were performed by the University of Pennsylvania Molecular Profiling facility

data_processing: Initial data analysis was performed using Affymetrix Microarray Suite 5.0 and further analyzed using PartekGS software.

source_name: zeocin-selected iCMs

growth_protocol: MEFs were grown in DMEM with 10% fetal bovine serum and 1X Glutamax.

extract_protocol: Putative iCMs were enriched by selecting for zeocin resistance driven by the TroponinT-GCaMP5-Zeo reporter and collected in Trizol at Day 21 post-transduction (7 days after initiation of zeocin selection, 300 μg/mL).  Non-transduced MEFs were cultured and collected at Day 21.  Samples were collected in triplicate from independent biological replicates and total RNA was prepared by the University of Pennsylvania Molecular Profiling Facility.

treatment_protocol: MEFs were plated into poly-L-lysine-coated 6 well dishes at 75,000 cells/well on Day -2, with 500 μL (≥ 2.5x105 IFU) each of rtTA lentivirus (FUdeltaGW-rtTA, Addgene plasmid 19780) and TroponinT-GCaMP-Zeo reporter lentivirus per well with 2 mL MEF medium. The following day (Day -1), culture medium was replaced with 2 mL fresh MEF medium and cells were transduced with 500 μL (≥ 2.5x105 IFU) of each tetO-transcription factor lentivirus. The next day (Day 0), medium was switched to 3 mL/well Reprogramming Medium consisting of AGM (Lonza CC-3186) without EGF, supplemented with 2 μg/mL doxycycline (Sigma).

tag: transcription factor treatment

value: MYOCD, MEF2C, NKX2.5, TBX5


title: LP_25_2w_103_TRBZ_10008_Liver

description: LP_25_2w_103_TRBZ_10008_Liver_(HT_Rat230_PM)_E06: 1470 rats were used in this study: 6 chemicals, 4 timepoints, and 6 dose groups (including control). 10 animals per group and 5 extra control animals. Timepoints were 5d, 2w, 4w, and 13 weeks. Doses varied with compound (Tribromobenzene: 0, 2-5,5,10,25,75; Bromobenzene: 0, 25, 100, 200, 300, 400; Tetrachlorophenol: 0, 10, 25, 50, 100, 200; Mehtylenebis(N,N-dimethyl)benzenamine: 0, 50, 200, 375, 500, 750; Nitrosodiphenylamine: 0, 250, 1000, 2000, 3000, 4000; Hydrazobenzene: 0, 5, 20, 80, 200, 300). Animals were dosed through gavage or diet. Two of the protocols had female rats and the rest were male rats (see protocols). F344 and Sprague Dawley rats were used.

value: ul

tag: ratio

tag: bioanalyzer results

value: Good

tag: sample preservation

tag: ncbi taxonomy id

tag: individual

tag: developmental state

tag: sacrifice method


title: DMNT-treated MEFs, biological rep1

description:
Gene expression data from iCMs generated from MEFs
DMNT1

scan_protocol: The labeling, hybridization, and scanning procedures were performed by the University of Pennsylvania Molecular Profiling facility


title: LP_25_2w_102_TRBZ_10008_Liver

description: LP_25_2w_102_TRBZ_10008_Liver_(HT_Rat230_PM)_E05: 1470 rats were used in this study: 6 chemicals, 4 timepoints, and 6 dose groups (including control). 10 animals per group and 5 extra control animals. Timepoints were 5d, 2w, 4w, and 13 weeks. Doses varied with compound (Tribromobenzene: 0, 2-5,5,10,25,75; Bromobenzene: 0, 25, 100, 200, 300, 400; Tetrachlorophenol: 0, 10, 25, 50, 100, 200; Mehtylenebis(N,N-dimethyl)benzenamine: 0, 50, 200, 375, 500, 750; Nitrosodiphenylamine: 0, 250, 1000, 2000, 3000, 4000; Hydrazobenzene: 0, 5, 20, 80, 200, 300). Animals were dosed through gavage or diet. Two of the protocols had female rats and the rest were male rats (see protocols). F344 and Sprague Dawley rats were used.

tag: array type

tag: amount to core

tag: units of amount

value: Excellent

value: Frozen

tag: Sex

tag: units of age

tag: tissue


title: LP_25_2w_104_TRBZ_10008_Liver

description: LP_25_2w_104_TRBZ_10008_Liver_(HT_Rat230_PM)_E07: 1470 rats were used in this study: 6 chemicals, 4 timepoints, and 6 dose groups (including control). 10 animals per group and 5 extra control animals. Timepoints were 5d, 2w, 4w, and 13 weeks. Doses varied with compound (Tribromobenzene: 0, 2-5,5,10,25,75; Bromobenzene: 0, 25, 100, 200, 300, 400; Tetrachlorophenol: 0, 10, 25, 50, 100, 200; Mehtylenebis(N,N-dimethyl)benzenamine: 0, 50, 200, 375, 500, 750; Nitrosodiphenylamine: 0, 250, 1000, 2000, 3000, 4000; Hydrazobenzene: 0, 5, 20, 80, 200, 300). Animals were dosed through gavage or diet. Two of the protocols had female rats and the rest were male rats (see protocols). F344 and Sprague Dawley rats were used.

tag: rna integrity number

tag: strain or line

tag: tissue harvest methods


title: parental MIN6 cells at 17-20 passages  [MG_U74Cv2]

tag: cell line

tag: cell line population

tag: passages


title: HNGMT-treated MEFs, biological rep3

description:
Gene expression data from iCMs generated from MEFs
HNGMT3

label_protocol: The labeling, hybridization, and scanning procedures were performed by the University of Pennsylvania Molecular Profiling facility

tag: transcription factor treatment

value: Hand2, NKX2.5, GATA4, MEF2C, TBX5


title: MIN6 clone4 cells at 17-20 passages  [MG_U74Av2]


title: MIN6 clone4 cells at 40-50 passages  [MG_U74Av2]


title: MCF12A_control_2

tag: cell type

value: breast epithelial cell line

tag: treatment


title: LP_25_2w_101_TRBZ_10008_Liver

description: LP_25_2w_101_TRBZ_10008_Liver_(HT_Rat230_PM)_E04: 1470 rats were used in this study: 6 chemicals, 4 timepoints, and 6 dose groups (including control). 10 animals per group and 5 extra control animals. Timepoints were 5d, 2w, 4w, and 13 weeks. Doses varied with compound (Tribromobenzene: 0, 2-5,5,10,25,75; Bromobenzene: 0, 25, 100, 200, 300, 400; Tetrachlorophenol: 0, 10, 25, 50, 100, 200; Mehtylenebis(N,N-dimethyl)benzenamine: 0, 50, 200, 375, 500, 750; Nitrosodiphenylamine: 0, 250, 1000, 2000, 3000, 4000; Hydrazobenzene: 0, 5, 20, 80, 200, 300). Animals were dosed through gavage or diet. Two of the protocols had female rats and the rest were male rats (see protocols). F344 and Sprague Dawley rats were used.

tag: ratio

tag: bioanalyzer results

tag: sample preservation

value: Spague Dawley Crl:CD(SD)

tag: ncbi taxonomy id

tag: individual

tag: developmental state

value: Adult


title: MCF12A_control_1


title: DMNT-treated MEFs, biological rep2

description:
Gene expression data from iCMs generated from MEFs
DMNT2


title: DMNT-treated MEFs, biological rep4

description:
Gene expression data from iCMs generated from MEFs
DMNT4


title: DMT-treated MEFs, biological rep4

description:
Gene expression data from iCMs generated from MEFs
DMT

value: MYOCD, MEF2C, TBX5


title: BJ LTSTERas, treated with DMSO, 4 hour, rep2

city: Clayton

first: Wei

last: Shi

state: Victoria

address: Wellington Rd

country: Australia

institute: Monash University

description: BJ LTSTERas DMSO 4hr replicate 2

hyb_protocol: Full-length cRNA (20μg) was fragmented to 35-200bp lengths by incubation with cRNA fragmentation reagent for 35 minutes at 94°C. Fragmented cRNA (15μg) was added to a hybridisation mix according to Affymetrix instructions and hybridized to Affymetrix HG U133 plus 2.0 probe arrays at 45°C in an Affymetrix Hybridisation oven 640 with 60rpm rotation for 16 hours. Array washes and three-stage streptavidin phycoerythrin (SAPE) staining was performed according the manufacturer’s instructions on a GeneChip fluidics station 450 (Affymetrix, Santa Clara, CA, USA).

scan_protocol: HG U133 plus 2.0 arrays were individually scanned using an Affymetrix GeneChip 3000 scanner with GeneChip Operating Software (GCOS, Affymetrix, Santa Clara, CA, USA).

data_processing: Intensities from the Affymetrix arrays were background corrected, normalised and summarised using the GC-Robust Multi-Array Analysis (GC-RMA) algorithm. Probe sets were defined by the default Affymetrix HG U133 plus 2.0 chip definition file. Box-plots of expression intensities and RNA degradation plots confirmed good consistent quality of the samples and the hybridisations. Differential expression analysis of the normalized log2-expression values was performed using the Bioconductor software package limma. All the arrays were analysed together using a linear model. Empirical Bayes moderated t-tests were used to assess differential expression between the BJ and BJLTSTERas fibroblasts and between untreated and treated cells. Specifically, baseline differences between the cell lines were identified by comparing untreated BJ and to BJ LTSTERas fibroblasts at Time 0hr. Probe sets responding to DMSO or vorinostat were identified by comparing each of the 4, 12, or 24 hour time points back to untreated cells, and this was done separately for BJ and BJ LTSTERas fibroblasts. For all comparisons, probe sets were considered to be significantly differentially expressed if the fold-change exceeded 1.5 (i.e. 50% difference in expression) and the false discovery rate (FDR) was less than 0.05. Probe sets responding differently to vorinostat treatment in BJ LTSTERas fibroblasts as compared to BJ cells (i.e. contrast genes), were identified using empirical Bayes moderated F-tests. F-tests allowed us to combine information across the three treatment time points, looking for probe-sets with differing responses at any of the times. First we used an F-test to find probe sets whose gene expression changes (from 0 hour to any of 4, 12 or 24 hours vorinostat treatment) was different in BJ fibroblasts compared to BJ LTSTERas fibroblasts. This test is analogous to testing for interaction in a two-way ANOVA. Second, we subtracted from this list any probe set whose expression response to vorinostat could not be distinguished from that to DMSO (the vehicle control). To do this, we used an F-test to find probe sets whose response to vorinostat relative to DMSO was different between BJ fibroblasts and BJ LTSTERas fibroblasts at any of the paired time points. Only probe sets detected by both the above F-tests were retained in the contrast list. The final contrast list contained therefore only bona fide vorinostat-responding genes. For all F-tests, probe sets were considered statistically significant if the FDR was less than 0.05 and at least one comparison involved in the test achieved a 1.5 fold change.

source_name: BJ LTSTERas_treated with DMSO_4 hr

label_protocol: Biotin labelled cRNA was synthesised from cDNA using a GeneChip IVT labelling kit (Affymetrix, Santa Clara, CA, USA) in a total reaction volume of 40μL. cRNA was purified and concentrated using the GeneChip sample cleanup module.

growth_protocol: BJ and BJ LTSTERas cells (kindly provided by Prof. William Hahn, Dan Farber Cancer Institute, Boston, MA) were grown in media containing 4 parts HEPES buffered DMEM, pH 7.4 (SAFC Biosciences, Brooklyn, Australia) to 1 part Medium 199 (Sigma, St Louis, MO, USA), supplemented with 15% (v/v) Fetal Bovine Serum (FBS, Commonwealth Serum Laboratories, Parkville, Australia), 1x GlutaMAX (Invitrogen, Carlsbad, CA, USA), 100U/mL penicillin and 100μg/mL streptomycin (Life Technologies, Inc. Grand Island, NY, USA).  All cells were maintained at 37°C in a humidified incubator containing 5% CO2.

extract_protocol: Total RNA (2μg) was prepared for hybridisation to Affymetrix GeneChip Human Genome U133 Plus 2.0 Arrays according to manufacturer recommendations. Poly-A RNA controls from Bacillus subtilis (lys, phe, thr and dap) were diluted in Poly-A control dilution buffer (serial dilutions of 1:20, 1:50 and 1:25) and 2μL of the third serial dilution was spiked into each RNA sample prior to cDNA synthesis. RNA was reverse transcribed using a one-cycle cDNA synthesis kit (Affymetrix, Santa Clara, CA, USA) and all annealing, amplification and incubation steps were performed in accordance with manufacturer instructions. Double stranded cDNA was purified using a GeneChip sample cleanup module according to manufacturers instructions (Affymetrix, Santa Clara, CA, USA) and cDNA was eluted from columns with 14μL cDNA elution buffer.

treatment_protocol: Vorinostat (100mM) stock solution was made in dimethyl sulphoxide (DMSO, Sigma, St Louis, MO, USA) and stored at -20°C.  Cells were incubated with vorinostat and DMSO for 0-24 hours.

value: tumorigenic BJ (human foreskin) fibroblasts

tag: treated with

value: DMSO

tag: time

value: 4 hour


title: BJ LTSTERas, treated with DMSO, 24 hour, rep3

description: BJ LTSTERas DMSO 24hr replicate 3

source_name: BJ LTSTERas_treated with DMSO_24 hr

value: 24 hour


title: parental MIN6 cells at 35-40 passages  [MG_U74Av2]

value: MIN6 insulinoma


title: HNGMT-treated MEFs, biological rep2

description:
Gene expression data from iCMs generated from MEFs
HNGMT2


title: BJ LTSTERas, treated with DMSO, 24 hour, rep1

description: BJ LTSTERas DMSO 24hr


title: BJ LTSTERas, treated with DMSO, 4 hour, rep3

description: BJ LTSTERas DMSO 4hr replicate 3


title: LP_2-5_2w_76_TRBZ_10008_Liver

description: LP_2-5_2w_76_TRBZ_10008_Liver_(HT_Rat230_PM)_D04: 1470 rats were used in this study: 6 chemicals, 4 timepoints, and 6 dose groups (including control). 10 animals per group and 5 extra control animals. Timepoints were 5d, 2w, 4w, and 13 weeks. Doses varied with compound (Tribromobenzene: 0, 2-5,5,10,25,75; Bromobenzene: 0, 25, 100, 200, 300, 400; Tetrachlorophenol: 0, 10, 25, 50, 100, 200; Mehtylenebis(N,N-dimethyl)benzenamine: 0, 50, 200, 375, 500, 750; Nitrosodiphenylamine: 0, 250, 1000, 2000, 3000, 4000; Hydrazobenzene: 0, 5, 20, 80, 200, 300). Animals were dosed through gavage or diet. Two of the protocols had female rats and the rest were male rats (see protocols). F344 and Sprague Dawley rats were used.

treatment_protocol: in vivo Treatment: 1,2,4-Tribromobenzene, Treatment Repeat: 7, Units of Treatment Repeat: Days/Week, Treatment Duration: 2, Units of Duration: Weeks, Treatment Time: 1, Units of Treatment Time: exposure/day, Vehicle for Chemical: Corn Oil, Amount of Vehicle: 5, Route of Exposure: Gavage, Units of Amount of Vehicle: ml/kg, Dose or Concentration: 2.5, Units of Dose or Concentration: mg/kg

tag: array type

tag: amount to core

tag: units of amount

tag: rna integrity number

tag: sacrifice method

value: Pentobarbital, Exsanguinated

tag: Sex

value: Male

tag: units of age

value: weeks

tag: tissue

value: Liver

value: Slices from each of the lobes were pooled together for microarray analysis


title: HGMT-treated MEFs, biological rep3

description:
Gene expression data from iCMs generated from MEFs
HGMT3

tag: transcription factor treatment

value: Hand2, GATA4, MEF2C, TBX5


title: HNGMT-treated MEFs, biological rep1

description:
Gene expression data from iCMs generated from MEFs
HNGMT1


title: BJ LTSTERas, treated with DMSO, 4 hour, rep1

description: BJ LTSTERas DMSO 4hr

tag: cell type


title: parental MIN6 cells at 17-20 passages  [MG_U74Av2]

tag: cell line

tag: cell line population

value: parental

tag: passages


title: HGMT-treated MEFs, biological rep2

description:
Gene expression data from iCMs generated from MEFs
HGMT2


title: LP_2-5_2w_72_TRBZ_10008_Liver

description: LP_2-5_2w_72_TRBZ_10008_Liver_(HT_Rat230_PM)_D01: 1470 rats were used in this study: 6 chemicals, 4 timepoints, and 6 dose groups (including control). 10 animals per group and 5 extra control animals. Timepoints were 5d, 2w, 4w, and 13 weeks. Doses varied with compound (Tribromobenzene: 0, 2-5,5,10,25,75; Bromobenzene: 0, 25, 100, 200, 300, 400; Tetrachlorophenol: 0, 10, 25, 50, 100, 200; Mehtylenebis(N,N-dimethyl)benzenamine: 0, 50, 200, 375, 500, 750; Nitrosodiphenylamine: 0, 250, 1000, 2000, 3000, 4000; Hydrazobenzene: 0, 5, 20, 80, 200, 300). Animals were dosed through gavage or diet. Two of the protocols had female rats and the rest were male rats (see protocols). F344 and Sprague Dawley rats were used.

value: ul

tag: ratio

tag: bioanalyzer results

value: Good

tag: sample preservation

value: Frozen

tag: strain or line

tag: ncbi taxonomy id

tag: individual

tag: tissue harvest methods


title: LP_2-5_2w_75_TRBZ_10008_Liver

description: LP_2-5_2w_75_TRBZ_10008_Liver_(HT_Rat230_PM)_D03: 1470 rats were used in this study: 6 chemicals, 4 timepoints, and 6 dose groups (including control). 10 animals per group and 5 extra control animals. Timepoints were 5d, 2w, 4w, and 13 weeks. Doses varied with compound (Tribromobenzene: 0, 2-5,5,10,25,75; Bromobenzene: 0, 25, 100, 200, 300, 400; Tetrachlorophenol: 0, 10, 25, 50, 100, 200; Mehtylenebis(N,N-dimethyl)benzenamine: 0, 50, 200, 375, 500, 750; Nitrosodiphenylamine: 0, 250, 1000, 2000, 3000, 4000; Hydrazobenzene: 0, 5, 20, 80, 200, 300). Animals were dosed through gavage or diet. Two of the protocols had female rats and the rest were male rats (see protocols). F344 and Sprague Dawley rats were used.

tag: array type

tag: amount to core

tag: units of amount

tag: rna integrity number

value: Spague Dawley Crl:CD(SD)

tag: developmental state

value: Adult


title: BJ LTSTERas, treated with DMSO, 12 hour, rep1

description: BJ LTSTERas DMSO 12hr

source_name: BJ LTSTERas_treated with DMSO_12 hr

value: tumorigenic BJ (human foreskin) fibroblasts

tag: treated with

tag: time

value: 12 hour


title: NGMT-treated MEFs, biological rep6

description:
Gene expression data from iCMs generated from MEFs
NGMT3

tag: transcription factor treatment

value: NKX2.5, GATA4, MEF2C, TBX5


title: BJ LTSTERas, treated with DMSO, 24 hour, rep2

description: BJ LTSTERas DMSO 24hr replicate 2

tag: cell type

value: DMSO

value: 24 hour


title: HGMT-treated MEFs, biological rep1

description:
Gene expression data from iCMs generated from MEFs
HGMT1


title: BJ LTSTERas, treated with DMSO, 12 hour, rep3

description: BJ LTSTERas DMSO 12hr replicate 3 scan 2


title: NGMT-treated MEFs, biological rep5

description:
Gene expression data from iCMs generated from MEFs
NGMT2


title: LP_2-5_2w_74_TRBZ_10008_Liver

description: LP_2-5_2w_74_TRBZ_10008_Liver_(HT_Rat230_PM)_D02: 1470 rats were used in this study: 6 chemicals, 4 timepoints, and 6 dose groups (including control). 10 animals per group and 5 extra control animals. Timepoints were 5d, 2w, 4w, and 13 weeks. Doses varied with compound (Tribromobenzene: 0, 2-5,5,10,25,75; Bromobenzene: 0, 25, 100, 200, 300, 400; Tetrachlorophenol: 0, 10, 25, 50, 100, 200; Mehtylenebis(N,N-dimethyl)benzenamine: 0, 50, 200, 375, 500, 750; Nitrosodiphenylamine: 0, 250, 1000, 2000, 3000, 4000; Hydrazobenzene: 0, 5, 20, 80, 200, 300). Animals were dosed through gavage or diet. Two of the protocols had female rats and the rest were male rats (see protocols). F344 and Sprague Dawley rats were used.

value: Excellent

tag: sacrifice method

value: Pentobarbital, Exsanguinated

tag: Sex

tag: units of age

tag: tissue


title: BJ LTSTERas, treated with vorinostat, 4 hour, rep1

description: BJ LTSTERas 25uM SAHA 4hr

source_name: BJ LTSTERas_treated with vorinostat_4 hr

value: Vorinostat (25uM)

value: 4 hour


title: NGMT-treated MEFs, biological rep4

description:
Gene expression data from iCMs generated from MEFs
NGMT1


title: LP_10_2w_93_TRBZ_10008_Liver

description: LP_10_2w_93_TRBZ_10008_Liver_(HT_Rat230_PM)_D11: 1470 rats were used in this study: 6 chemicals, 4 timepoints, and 6 dose groups (including control). 10 animals per group and 5 extra control animals. Timepoints were 5d, 2w, 4w, and 13 weeks. Doses varied with compound (Tribromobenzene: 0, 2-5,5,10,25,75; Bromobenzene: 0, 25, 100, 200, 300, 400; Tetrachlorophenol: 0, 10, 25, 50, 100, 200; Mehtylenebis(N,N-dimethyl)benzenamine: 0, 50, 200, 375, 500, 750; Nitrosodiphenylamine: 0, 250, 1000, 2000, 3000, 4000; Hydrazobenzene: 0, 5, 20, 80, 200, 300). Animals were dosed through gavage or diet. Two of the protocols had female rats and the rest were male rats (see protocols). F344 and Sprague Dawley rats were used.

treatment_protocol: in vivo Treatment: 1,2,4-Tribromobenzene, Treatment Repeat: 7, Units of Treatment Repeat: Days/Week, Treatment Duration: 2, Units of Duration: Weeks, Treatment Time: 1, Units of Treatment Time: exposure/day, Vehicle for Chemical: Corn Oil, Amount of Vehicle: 5, Route of Exposure: Gavage, Units of Amount of Vehicle: ml/kg, Dose or Concentration: 10, Units of Dose or Concentration: mg/kg

tag: ratio

tag: bioanalyzer results

tag: sample preservation

tag: strain or line

value: Male

value: weeks

value: Liver

value: Slices from each of the lobes were pooled together for microarray analysis


title: LP_10_2w_96_TRBZ_10008_Liver

description: LP_10_2w_96_TRBZ_10008_Liver_(HT_Rat230_PM)_E03: 1470 rats were used in this study: 6 chemicals, 4 timepoints, and 6 dose groups (including control). 10 animals per group and 5 extra control animals. Timepoints were 5d, 2w, 4w, and 13 weeks. Doses varied with compound (Tribromobenzene: 0, 2-5,5,10,25,75; Bromobenzene: 0, 25, 100, 200, 300, 400; Tetrachlorophenol: 0, 10, 25, 50, 100, 200; Mehtylenebis(N,N-dimethyl)benzenamine: 0, 50, 200, 375, 500, 750; Nitrosodiphenylamine: 0, 250, 1000, 2000, 3000, 4000; Hydrazobenzene: 0, 5, 20, 80, 200, 300). Animals were dosed through gavage or diet. Two of the protocols had female rats and the rest were male rats (see protocols). F344 and Sprague Dawley rats were used.

tag: array type

value: ul

value: Good

tag: ncbi taxonomy id

tag: individual

tag: tissue harvest methods


title: LP_2-5_2w_71_TRBZ_10008_Liver

description: LP_2-5_2w_71_TRBZ_10008_Liver_(HT_Rat230_PM)_C12: 1470 rats were used in this study: 6 chemicals, 4 timepoints, and 6 dose groups (including control). 10 animals per group and 5 extra control animals. Timepoints were 5d, 2w, 4w, and 13 weeks. Doses varied with compound (Tribromobenzene: 0, 2-5,5,10,25,75; Bromobenzene: 0, 25, 100, 200, 300, 400; Tetrachlorophenol: 0, 10, 25, 50, 100, 200; Mehtylenebis(N,N-dimethyl)benzenamine: 0, 50, 200, 375, 500, 750; Nitrosodiphenylamine: 0, 250, 1000, 2000, 3000, 4000; Hydrazobenzene: 0, 5, 20, 80, 200, 300). Animals were dosed through gavage or diet. Two of the protocols had female rats and the rest were male rats (see protocols). F344 and Sprague Dawley rats were used.

tag: amount to core

tag: units of amount

tag: rna integrity number

value: Frozen

value: Spague Dawley Crl:CD(SD)

tag: developmental state


title: BJ LTSTERas, treated with DMSO, 12 hour, rep2

description: BJ LTSTERas DMSO 12hr replicate 2

tag: cell type

value: tumorigenic BJ (human foreskin) fibroblasts

tag: treated with

tag: time


title: LP_10_2w_94_TRBZ_10008_Liver

description: LP_10_2w_94_TRBZ_10008_Liver_(HT_Rat230_PM)_E01: 1470 rats were used in this study: 6 chemicals, 4 timepoints, and 6 dose groups (including control). 10 animals per group and 5 extra control animals. Timepoints were 5d, 2w, 4w, and 13 weeks. Doses varied with compound (Tribromobenzene: 0, 2-5,5,10,25,75; Bromobenzene: 0, 25, 100, 200, 300, 400; Tetrachlorophenol: 0, 10, 25, 50, 100, 200; Mehtylenebis(N,N-dimethyl)benzenamine: 0, 50, 200, 375, 500, 750; Nitrosodiphenylamine: 0, 250, 1000, 2000, 3000, 4000; Hydrazobenzene: 0, 5, 20, 80, 200, 300). Animals were dosed through gavage or diet. Two of the protocols had female rats and the rest were male rats (see protocols). F344 and Sprague Dawley rats were used.

value: Adult

tag: sacrifice method

tag: Sex

tag: units of age


title: BJ LTSTERas, treated with vorinostat, 4 hour, rep3

description: BJ LTSTERas 25uM SAHA 4hr replicate 3


title: GMT-treated MEFs, biological rep4

description:
Gene expression data from iCMs generated from MEFs
GMT2

tag: transcription factor treatment

value: GATA4, MEF2C, TBX5


title: BJ LTSTERas, treated with vorinostat, 4 hour, rep2

description: BJ LTSTERas 25uM SAHA 4hr replicate 2


title: LP_10_2w_95_TRBZ_10008_Liver

description: LP_10_2w_95_TRBZ_10008_Liver_(HT_Rat230_PM)_E02: 1470 rats were used in this study: 6 chemicals, 4 timepoints, and 6 dose groups (including control). 10 animals per group and 5 extra control animals. Timepoints were 5d, 2w, 4w, and 13 weeks. Doses varied with compound (Tribromobenzene: 0, 2-5,5,10,25,75; Bromobenzene: 0, 25, 100, 200, 300, 400; Tetrachlorophenol: 0, 10, 25, 50, 100, 200; Mehtylenebis(N,N-dimethyl)benzenamine: 0, 50, 200, 375, 500, 750; Nitrosodiphenylamine: 0, 250, 1000, 2000, 3000, 4000; Hydrazobenzene: 0, 5, 20, 80, 200, 300). Animals were dosed through gavage or diet. Two of the protocols had female rats and the rest were male rats (see protocols). F344 and Sprague Dawley rats were used.

tag: ratio

tag: bioanalyzer results

tag: sample preservation

tag: tissue


title: GMT-treated MEFs, biological rep5

description:
Gene expression data from iCMs generated from MEFs
GMT3


title: GMT-treated MEFs, biological rep3

description:
Gene expression data from iCMs generated from MEFs
GMT1


title: BJ LTSTERas, treated with vorinostat, 24 hour, rep3

description: BJ LTSTERas 25uM SAHA 24hr replicate 3 scan 2

source_name: BJ LTSTERas_treated with vorinostat_24 hr


title: LP_10_2w_92_TRBZ_10008_Liver

description: LP_10_2w_92_TRBZ_10008_Liver_(HT_Rat230_PM)_D10: 1470 rats were used in this study: 6 chemicals, 4 timepoints, and 6 dose groups (including control). 10 animals per group and 5 extra control animals. Timepoints were 5d, 2w, 4w, and 13 weeks. Doses varied with compound (Tribromobenzene: 0, 2-5,5,10,25,75; Bromobenzene: 0, 25, 100, 200, 300, 400; Tetrachlorophenol: 0, 10, 25, 50, 100, 200; Mehtylenebis(N,N-dimethyl)benzenamine: 0, 50, 200, 375, 500, 750; Nitrosodiphenylamine: 0, 250, 1000, 2000, 3000, 4000; Hydrazobenzene: 0, 5, 20, 80, 200, 300). Animals were dosed through gavage or diet. Two of the protocols had female rats and the rest were male rats (see protocols). F344 and Sprague Dawley rats were used.

tag: array type

tag: strain or line

tag: ncbi taxonomy id

tag: individual


title: BJ LTSTERas, treated with vorinostat, 24 hour, rep1

description: BJ LTSTERas 25uM SAHA 24hr


title: DMT-treated MEFs, biological rep3

description:
Gene expression data from iCMs generated from MEFs
DMT3

value: MYOCD, MEF2C, TBX5


title: genomic DNA from CD14 B-cells_C213 (BeadChip)

type: genomic

city: Cambridge

first: Thomas

middle: A

last: Down

address: Tennis Court Road

department: WT/CRUK Gurdon Institute

country: United Kingdom

institute: University of Cambridge

description:
Sample name: C213
normal CD14 cells

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: GenomeStudio softwarre

label: Cy5 and Cy3

molecule: genomic DNA

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted using the Qiagen DNeasy kit.

tag: individual identifier

tag: monozygotic twin relationship

value: MZ twin of C22

value: CD14 cells


title: genomic DNA from CD14 B-cells_C212 (BeadChip)

description:
Sample name: C212
normal CD14 cells

tag: cell type


title: genomic DNA from CD14 B-cells_C211 (BeadChip)

description:
Sample name: C211
normal CD14 cells


title: LP_0_2w_65_CC1_10008_Liver

description: LP_0_2w_65_CC1_10008_Liver_(HT_Rat230_PM)_C10: 1470 rats were used in this study: 6 chemicals, 4 timepoints, and 6 dose groups (including control). 10 animals per group and 5 extra control animals. Timepoints were 5d, 2w, 4w, and 13 weeks. Doses varied with compound (Tribromobenzene: 0, 2-5,5,10,25,75; Bromobenzene: 0, 25, 100, 200, 300, 400; Tetrachlorophenol: 0, 10, 25, 50, 100, 200; Mehtylenebis(N,N-dimethyl)benzenamine: 0, 50, 200, 375, 500, 750; Nitrosodiphenylamine: 0, 250, 1000, 2000, 3000, 4000; Hydrazobenzene: 0, 5, 20, 80, 200, 300). Animals were dosed through gavage or diet. Two of the protocols had female rats and the rest were male rats (see protocols). F344 and Sprague Dawley rats were used.

treatment_protocol: in vivo Treatment: Corn Oil Control 1, Treatment Repeat: 7, Units of Treatment Repeat: Days/Week, Treatment Duration: 2, Units of Duration: Weeks, Treatment Time: 1, Units of Treatment Time: exposure/day, Vehicle for Chemical: Corn Oil, Amount of Vehicle: 5, Route of Exposure: Gavage, Units of Amount of Vehicle: ml/kg, Dose or Concentration: 0, Units of Dose or Concentration: mg/kg

tag: amount to core

tag: units of amount

tag: rna integrity number

value: Excellent

tag: developmental state

value: Pentobarbital, Exsanguinated

tag: tissue harvest methods


title: BJ LTSTERas, treated with vorinostat, 12 hour, rep1

description: BJ LTSTERas 25uM SAHA 12hr

source_name: BJ LTSTERas_treated with vorinostat_12 hr

tag: treated with

value: Vorinostat (25uM)

tag: time

value: 12 hour


title: genomic DNA from CD14 B-cells_C222 (BeadChip)

description:
Sample name: C222
normal CD14 cells

value: MZ twin of C21


title: genomic DNA from CD14 B-cells_C221 (BeadChip)

description:
Sample name: C221
normal CD14 cells


title: genomic DNA from CD14 B-cells_C121 (BeadChip)

description:
Sample name: C121
normal CD14 cells

value: MZ twin of C11


title: LP_0_2w_64_CC1_10008_Liver

description: LP_0_2w_64_CC1_10008_Liver_(HT_Rat230_PM)_C09: 1470 rats were used in this study: 6 chemicals, 4 timepoints, and 6 dose groups (including control). 10 animals per group and 5 extra control animals. Timepoints were 5d, 2w, 4w, and 13 weeks. Doses varied with compound (Tribromobenzene: 0, 2-5,5,10,25,75; Bromobenzene: 0, 25, 100, 200, 300, 400; Tetrachlorophenol: 0, 10, 25, 50, 100, 200; Mehtylenebis(N,N-dimethyl)benzenamine: 0, 50, 200, 375, 500, 750; Nitrosodiphenylamine: 0, 250, 1000, 2000, 3000, 4000; Hydrazobenzene: 0, 5, 20, 80, 200, 300). Animals were dosed through gavage or diet. Two of the protocols had female rats and the rest were male rats (see protocols). F344 and Sprague Dawley rats were used.

tag: ratio

tag: bioanalyzer results

tag: sacrifice method

tag: Sex

value: Male

tag: units of age

value: weeks

value: Liver

value: Slices from each of the lobes were pooled together for microarray analysis


title: NGMT-treated MEFs, biological rep3

description:
Gene expression data from iCMs generated from MEFs
MEF9

tag: transcription factor treatment

value: NKX2.5, GATA4, MEF2C, TBX5


title: LP_0_2w_66_CC1_10008_Liver

description: LP_0_2w_66_CC1_10008_Liver_(HT_Rat230_PM)_C11: 1470 rats were used in this study: 6 chemicals, 4 timepoints, and 6 dose groups (including control). 10 animals per group and 5 extra control animals. Timepoints were 5d, 2w, 4w, and 13 weeks. Doses varied with compound (Tribromobenzene: 0, 2-5,5,10,25,75; Bromobenzene: 0, 25, 100, 200, 300, 400; Tetrachlorophenol: 0, 10, 25, 50, 100, 200; Mehtylenebis(N,N-dimethyl)benzenamine: 0, 50, 200, 375, 500, 750; Nitrosodiphenylamine: 0, 250, 1000, 2000, 3000, 4000; Hydrazobenzene: 0, 5, 20, 80, 200, 300). Animals were dosed through gavage or diet. Two of the protocols had female rats and the rest were male rats (see protocols). F344 and Sprague Dawley rats were used.

tag: array type

value: ul

tag: sample preservation

value: Frozen

tag: strain or line

value: Spague Dawley Crl:CD(SD)

tag: ncbi taxonomy id

tag: individual

tag: tissue


title: NGMT-treated MEFs, biological rep1

description:
Gene expression data from iCMs generated from MEFs
MEF7