title: LP_10_4w_654_TTCP10_10010_Liver

description: LP_10_4w_654_TTCP10_10010_Liver_(HT_Rat230_PM)_F10: 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.

tag: rna integrity number

value: Frozen

tag: sacrifice method

tag: Sex


title: LP_10_4w_652_TTCP10_10010_Liver

status: Public on Apr 22 2013

type: RNA

city: RTP

first: Longlong

last: Yang

state: NC

address: 6 Davis Dr.

country: USA

institute: CIIT Centers for Health Research

description: LP_10_4w_652_TTCP10_10010_Liver_(HT_Rat230_PM)_F08: 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.

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: RMA normalization with Partek software program

label: biotin

molecule: total RNA

organism: Rattus norvegicus

label_protocol: standard Affymetrix protocol

extract_protocol: Extraction Method: Qiagen

treatment_protocol: in vivo Treatment: 2,3,4,6-Tetrachlorophenol, 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: Olive 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: amount to core

tag: units of amount

value: ul

tag: ratio

tag: bioanalyzer results

value: Excellent

tag: sample preservation

tag: strain or line

value: Spague Dawley Crl:CD(SD)

tag: ncbi taxonomy id

tag: individual

tag: developmental state

value: Adult

value: Pentobarbital, Exsanguinated

value: Male

tag: age

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: Subject C, before Control 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

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

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

organism: Homo sapiens

source_name: Peripheral blood lymphocytes

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

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 C

tag: treatment

value: before Control intervention


title: Subject C, after Yoga intervention, replicate 2

value: after Yoga intervention


title: Subject C, after Control intervention, replicate 1

value: after Control intervention


title: Subject D, before Yoga intervention, replicate 1

value: Subject D

value: before Yoga intervention


title: LP_10_4w_653_TTCP10_10010_Liver

description: LP_10_4w_653_TTCP10_10010_Liver_(HT_Rat230_PM)_F09: 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.

tag: rna integrity number

value: Frozen

tag: sacrifice method

tag: Sex


title: Subject C, before Yoga intervention, replicate 1


title: LP_0_4w_645_OC1_10010_Liver

description: LP_0_4w_645_OC1_10010_Liver_(HT_Rat230_PM)_F06: 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: 4, 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

value: ul


title: LP_10_4w_651_TTCP10_10010_Liver

description: LP_10_4w_651_TTCP10_10010_Liver_(HT_Rat230_PM)_F07: 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.

tag: ratio

tag: bioanalyzer results

value: Excellent

tag: sample preservation


title: LP_100_4w_686_TTCP100_10010_Liver

description: LP_100_4w_686_TTCP100_10010_Liver_(HT_Rat230_PM)_H02: 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: 2,3,4,6-Tetrachlorophenol, 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: Olive Oil, Amount of Vehicle: 5, Route of Exposure: Gavage, Units of Amount of Vehicle: ml/kg, Dose or Concentration: 100, Units of Dose or Concentration: mg/kg

value: Good

tag: strain or line

value: Spague Dawley Crl:CD(SD)

tag: ncbi taxonomy id

tag: individual


title: Subject B, after Control intervention, replicate 1

value: Subject B


title: Subject C, after Yoga intervention, replicate 1

value: Male


title: LP_100_4w_683_TTCP100_10010_Liver

description: LP_100_4w_683_TTCP100_10010_Liver_(HT_Rat230_PM)_G12: 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.

tag: developmental state

value: Adult

value: Pentobarbital, Exsanguinated

tag: age

tag: units of age

value: Weeks


title: LP_100_4w_684_TTCP100_10010_Liver

description: LP_100_4w_684_TTCP100_10010_Liver_(HT_Rat230_PM)_H01: 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.

tag: tissue

value: Liver

tag: tissue harvest methods

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


title: LP_100_4w_681_TTCP100_10010_Liver

description: LP_100_4w_681_TTCP100_10010_Liver_(HT_Rat230_PM)_G10: 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.

tag: rna integrity number


title: LP_0_4w_641_OC1_10010_Liver

description: LP_0_4w_641_OC1_10010_Liver_(HT_Rat230_PM)_F02: 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.

tag: sacrifice method


title: Subject B, before Control intervention, replicate 2

tag: gender

value: Blood

tag: treatment

value: before Control intervention


title: Subject C, before Yoga intervention, replicate 2

value: Subject C


title: Subject B, before Control intervention, replicate 1


title: LP_100_4w_682_TTCP100_10010_Liver

description: LP_100_4w_682_TTCP100_10010_Liver_(HT_Rat230_PM)_G11: 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.

tag: array type

tag: amount to core

tag: Sex


title: LP_0_4w_643_OC1_10010_Liver

description: LP_0_4w_643_OC1_10010_Liver_(HT_Rat230_PM)_F04: 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.

tag: units of amount

tag: ratio

tag: bioanalyzer results


title: LP_50_2w_614_TTCP50_10010_Liver

description: LP_50_2w_614_TTCP50_10010_Liver_(HT_Rat230_PM)_E02: 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: 2,3,4,6-Tetrachlorophenol, 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: 50, Units of Dose or Concentration: mg/kg

tag: sample preservation

tag: strain or line

tag: ncbi taxonomy id


title: LP_50_2w_613_TTCP50_10010_Liver

description: LP_50_2w_613_TTCP50_10010_Liver_(HT_Rat230_PM)_E01: 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.

tag: individual

tag: developmental state

tag: age


title: LP_0_4w_644_OC1_10010_Liver

description: LP_0_4w_644_OC1_10010_Liver_(HT_Rat230_PM)_F05: 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.

tag: units of age

tag: tissue

tag: tissue harvest methods


title: LP_25_2w_605_TTCP25_10010_Liver

description: LP_25_2w_605_TTCP25_10010_Liver_(HT_Rat230_PM)_D08: 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: 2,3,4,6-Tetrachlorophenol, 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: 25, Units of Dose or Concentration: mg/kg

tag: rna integrity number

tag: sacrifice method


title: LP_50_2w_615_TTCP50_10010_Liver

description: LP_50_2w_615_TTCP50_10010_Liver_(HT_Rat230_PM)_E03: 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.

tag: array type


title: LP_25_2w_606_TTCP25_10010_Liver

description: LP_25_2w_606_TTCP25_10010_Liver_(HT_Rat230_PM)_D09: 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.

tag: amount to core


title: LP_50_2w_612_TTCP50_10010_Liver

description: LP_50_2w_612_TTCP50_10010_Liver_(HT_Rat230_PM)_D11: 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.

tag: Sex


title: Subject B, after Control intervention, replicate 2

tag: gender

tag: treatment

value: after Control intervention


title: LP_25_2w_604_TTCP25_10010_Liver

description: LP_25_2w_604_TTCP25_10010_Liver_(HT_Rat230_PM)_D07: 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.

tag: units of amount

tag: ratio

tag: bioanalyzer results


title: LP_50_2w_611_TTCP50_10010_Liver

description: LP_50_2w_611_TTCP50_10010_Liver_(HT_Rat230_PM)_D10: 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.

tag: sample preservation

tag: strain or line

tag: ncbi taxonomy id


title: LP_200_2w_635_TTCP200_10010_Liver

description: LP_200_2w_635_TTCP200_10010_Liver_(HT_Rat230_PM)_F01: 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: 2,3,4,6-Tetrachlorophenol, 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: 200, Units of Dose or Concentration: mg/kg

tag: individual

tag: developmental state

tag: age


title: LP_10_2w_594_TTCP10_10010_Liver

description: LP_10_2w_594_TTCP10_10010_Liver_(HT_Rat230_PM)_D03: 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: 2,3,4,6-Tetrachlorophenol, 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: 10, Units of Dose or Concentration: mg/kg

tag: units of age

tag: tissue

tag: tissue harvest methods


title: LP_10_2w_593_TTCP10_10010_Liver

description: LP_10_2w_593_TTCP10_10010_Liver_(HT_Rat230_PM)_D02: 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.

tag: array type

tag: rna integrity number

tag: sacrifice method


title: Subject A, after Yoga intervention, replicate 2

tag: gender

value: Subject A

value: after Yoga intervention


title: LP_25_2w_602_TTCP25_10010_Liver

description: LP_25_2w_602_TTCP25_10010_Liver_(HT_Rat230_PM)_D05: 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.

tag: amount to core

value: ul

value: Frozen

tag: Sex


title: LP_200_2w_634_TTCP200_10010_Liver

description: LP_200_2w_634_TTCP200_10010_Liver_(HT_Rat230_PM)_E12: 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.

tag: units of amount

tag: ratio

value: Excellent


title: LP_200_2w_632_TTCP200_10010_Liver

description: LP_200_2w_632_TTCP200_10010_Liver_(HT_Rat230_PM)_E10: 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.

tag: bioanalyzer results

tag: sample preservation

value: Spague Dawley Crl:CD(SD)


title: Subject A, before Control intervention, replicate 2

tag: treatment


title: LP_25_2w_603_TTCP25_10010_Liver

description: LP_25_2w_603_TTCP25_10010_Liver_(HT_Rat230_PM)_D06: 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.

tag: strain or line

tag: ncbi taxonomy id

tag: individual


title: Subject A, before Control intervention, replicate 1


title: Subject B, after Yoga intervention, replicate 2

value: Subject B


title: Subject A, after Control intervention, replicate 2

value: Male


title: Subject B, before Yoga intervention, replicate 1

value: before Yoga intervention


title: LP_200_2w_633_TTCP200_10010_Liver

description: LP_200_2w_633_TTCP200_10010_Liver_(HT_Rat230_PM)_E11: 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.

tag: developmental state

value: Adult

value: Pentobarbital, Exsanguinated

tag: age

tag: units of age


title: Subject A, after Control intervention, replicate 1

tag: tissue


title: LP_10_2w_591_TTCP10_10010_Liver

description: LP_10_2w_591_TTCP10_10010_Liver_(HT_Rat230_PM)_C12: 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.

tag: array type

tag: rna integrity number

value: Weeks

value: Liver

tag: tissue harvest methods


title: LP_100_2w_625_TTCP100_10010_Liver

description: LP_100_2w_625_TTCP100_10010_Liver_(HT_Rat230_PM)_E08: 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: 2,3,4,6-Tetrachlorophenol, 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: 100, Units of Dose or Concentration: mg/kg

tag: amount to core

tag: sacrifice method

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


title: LP_200_2w_631_TTCP200_10010_Liver

description: LP_200_2w_631_TTCP200_10010_Liver_(HT_Rat230_PM)_E09: 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.

tag: units of amount

value: Good

tag: Sex


title: LP_100_2w_623_TTCP100_10010_Liver

description: LP_100_2w_623_TTCP100_10010_Liver_(HT_Rat230_PM)_E06: 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.

tag: ratio

tag: bioanalyzer results


title: Subject A, before Yoga intervention, replicate 2

tag: gender

value: Blood

tag: treatment


title: LP_100_2w_624_TTCP100_10010_Liver

description: LP_100_2w_624_TTCP100_10010_Liver_(HT_Rat230_PM)_E07: 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.

tag: sample preservation

tag: strain or line

tag: ncbi taxonomy id


title: LP_10_2w_598_TTCP10_10010_Liver

description: LP_10_2w_598_TTCP10_10010_Liver_(HT_Rat230_PM)_D04: 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.

tag: individual

tag: developmental state

tag: age


title: Subject A, after Yoga intervention, replicate 1

tag: tissue


title: LP_0_4w_642_OC1_10010_Liver

description: LP_0_4w_642_OC1_10010_Liver_(HT_Rat230_PM)_F03: 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.

tag: array type

tag: rna integrity number

tag: units of age


title: Subject B, before Yoga intervention, replicate 2


title: LP_10_2w_592_TTCP10_10010_Liver

description: LP_10_2w_592_TTCP10_10010_Liver_(HT_Rat230_PM)_D01: 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.

tag: amount to core

tag: sacrifice method

tag: tissue harvest methods


title: LP_100_2w_622_TTCP100_10010_Liver

description: LP_100_2w_622_TTCP100_10010_Liver_(HT_Rat230_PM)_E05: 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.

tag: units of amount

tag: ratio

tag: Sex


title: LP_25_4w_663_TTCP25_10010_Liver

description: LP_25_4w_663_TTCP25_10010_Liver_(HT_Rat230_PM)_G02: 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: 2,3,4,6-Tetrachlorophenol, 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: Olive 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: bioanalyzer results


title: LP_100_2w_621_TTCP100_10010_Liver

description: LP_100_2w_621_TTCP100_10010_Liver_(HT_Rat230_PM)_E04: 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.

tag: sample preservation


title: LP_0_2w_586_OC1_10010_Liver

description: LP_0_2w_586_OC1_10010_Liver_(HT_Rat230_PM)_C11: 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: strain or line


title: Monocytes not treated with IFN-β, individual 3

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

source_name: monocytes 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: Monocytes

tag: donor

tag: treated

value: No


title: LP_75_13w_236_TRBZ_10008_Liver

description: LP_75_13w_236_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.

treatment_protocol: in vivo Treatment: 1,2,4-Tribromobenzene, Treatment Repeat: 7, Units of Treatment Repeat: Days/Week, Treatment Duration: 13, 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: ncbi taxonomy id

tag: individual

tag: developmental state

tag: age

value: weeks


title: LP_0_2w_582_OC1_10010_Liver

description: LP_0_2w_582_OC1_10010_Liver_(HT_Rat230_PM)_C08: 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.

tag: array type

value: ul

tag: rna integrity number

tag: units of age

tag: tissue


title: LP_75_13w_232_TRBZ_10008_Liver

description: LP_75_13w_232_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: amount to core

tag: units of amount

value: Frozen

tag: sacrifice method

tag: tissue harvest methods


title: LP_0_2w_583_OC1_10010_Liver

description: LP_0_2w_583_OC1_10010_Liver_(HT_Rat230_PM)_C09: 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.

tag: ratio

tag: bioanalyzer results

value: Excellent

tag: sample preservation

tag: Sex


title: LP_5_13w_205_TRBZ_10008_Liver

description: LP_5_13w_205_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.

treatment_protocol: in vivo Treatment: 1,2,4-Tribromobenzene, Treatment Repeat: 7, Units of Treatment Repeat: Days/Week, Treatment Duration: 13, 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: strain or line

value: Spague Dawley Crl:CD(SD)


title: LP_75_13w_234_TRBZ_10008_Liver

description: LP_75_13w_234_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.

tag: ncbi taxonomy id


title: T lymphocytes not treated with IFN-β, individual 3

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

tag: cell type

value: T lymphocytes

tag: donor

tag: treated


title: Monocytes treated with IFN-β, individual 3

source_name: monocytes treated with TNF-α and also with IFN-β

value: Yes


title: LP_75_13w_235_TRBZ_10008_Liver

description: LP_75_13w_235_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: individual

tag: developmental state

value: Male

tag: age


title: LP_5_13w_206_TRBZ_10008_Liver

description: LP_5_13w_206_TRBZ_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: amount to core

tag: rna integrity number

value: Adult

tag: units of age

tag: tissue


title: Monocytes treated with IFN-β, individual 2


title: LP_25_13w_226_TRBZ_10008_Liver

description: LP_25_13w_226_TRBZ_10008_Liver_(HT_Rat230_PM)_C05: 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: 13, 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: units of amount

tag: ratio

tag: sacrifice method

value: Pentobarbital, Exsanguinated

tag: tissue harvest methods


title: LP_5_13w_204_TRBZ_10008_Liver

description: LP_5_13w_204_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: bioanalyzer results

tag: sample preservation

tag: strain or line

tag: Sex


title: Monocytes not treated with IFN-β, individual 2

tag: cell type

tag: donor

tag: treated


title: LP_5_13w_201_TRBZ_10008_Liver

description: LP_5_13w_201_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: array type

tag: ncbi taxonomy id

tag: individual

tag: developmental state


title: LP_0_2w_581_OC1_10010_Liver

description: LP_0_2w_581_OC1_10010_Liver_(HT_Rat230_PM)_C07: 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.

tag: amount to core

tag: age

tag: units of age

value: Weeks


title: LP_5_13w_203_TRBZ_10008_Liver

description: LP_5_13w_203_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.

tag: units of amount

tag: ratio

tag: tissue

value: Liver


title: LP_25_13w_224_TRBZ_10008_Liver

description: LP_25_13w_224_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: rna integrity number

tag: bioanalyzer results

tag: sacrifice method

tag: tissue harvest methods

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


title: T lymphocytes treated with IFN-β, individual 3

source_name: T lymphocytes treated with TNF-α and also with IFN-β

tag: cell type


title: LP_25_13w_223_TRBZ_10008_Liver

description: LP_25_13w_223_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: sample preservation

tag: strain or line

tag: Sex


title: LP_75_13w_231_TRBZ_10008_Liver

description: LP_75_13w_231_TRBZ_10008_Liver_(HT_Rat230_PM)_C07: 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: Good

tag: ncbi taxonomy id


title: T lymphocytes treated with IFN-β, individual 2

tag: donor

tag: treated


title: Monocytes treated with IFN-β, individual 1


title: T lymphocytes not treated with IFN-β, individual 2


title: Monocytes not treated with IFN-β, individual 1


title: mouse miRNA array diabetic_2

city: Delhi

first: Malabika

last: Datta

address: Mall Road

country: India

institute: Institute of Genomics and Integrative Biology

description: miRNA expression in diabetic skeletal muscle

hyb_protocol: The hybridization mixture (10X GE blocking agent (4.5µl) and 2X Hi-RPM hybridization buffer (22.5µl)) along with the labelled miRNA sample was heated for 5 min at 100 °C and immediately cooled on ice. Each 45 µL sample was hybridized onto a microarray at 55 °C for 20 h. Slides were then washed for 5 min in GE wash buffer 1 at RT and again for 5 min in GE wash buffer 2 at 37 °C, followed by an acetonitrile wash for 1 min at RT to dry the slides completely.

scan_protocol: Slides were scanned on a microarray scanner (G2565BA, Agilent) at 100 and 5% XDR settings. Agilent Feature Extraction software version 9.3.5 was used to extract the raw data.

data_processing:
From raw data, gBG Sub Signal from four control and treated samples was taken for further analysis. Then median of all signals was taken and this was used as an input file for normalization by using R method. After normalization by R method, we obtained output file in which we applied Z-score statistical test.
Given below is the algorithm used to generate normalized data provided in the VALUE column.
Algorithm used in R for data normalization
Step1:  x<- read.table("input_file.txt",header=T,row.names=1,sep="\t")
Step 2: log_x<-log(x,base=2)
Step3: attach(log_x )
Step4:
cnt<-(1/8)*(sort(Signal_1)+sort(Signal_2)+sort(Signal_3)+sort(Signal_4)+
sort(Signal_5)+sort(Signal_6)++sort(Signal_7)+sort(Signal_8))
Step5: value_1<-c(rank(Signal_1))
Step6: value_2<-c(rank(Signal_2))
Step7: value_3<-c(rank(Signal_3))
Step8: value_4<-c(rank(Signal_4))
Step9: value_5<-c(rank(Signal_5))
Step10: value_6<-c(rank(Signal_6))
Step11: value_7<-c(rank(Signal_7))
Step12: value_8<-c(rank(Signal_8))
Step13:
final<-cbind(value_1,value_2,value_3,value_4,value_5,value_6,value_7,val
ue_8)
boxplot(final)
Step14: write.table(final,"f//priyanka/R method/result.txt")
Step15: write.table(final,"result.txt")

organism: Mus musculus

source_name: skeletal muscle

label_protocol: Briefly, 100 ng of total RNA was dephosphorylated with calf intestine alkaline phosphatase for 30 min at 37°C. Denaturation was performed by adding DMSO and incubating at 100°C for 7 min and immediately transferred to a ice water bath. Ligation was performed with pCp-Cy3 at 16 °C for 2 h. The labeled samples were dried completely in a vacuum concentrator and resuspended in 18 ul of nuclease free water.

extract_protocol: Total miRNA from tissue sample was isolated from control and diabetic skeletal muscle using Ambion miRNA isolation kit as per manufacture's instruction

tag: group

value: diabetic

tag: strain

value: C57BL/KsJ db+


title: mouse miRNA array diabetic_4


title: LP_25_13w_221_TRBZ_10008_Liver

description: LP_25_13w_221_TRBZ_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: amount to core

tag: units of amount

tag: individual

tag: developmental state

tag: age

tag: units of age


title: mouse miRNA array diabetic_1


title: LP_25_13w_222_TRBZ_10008_Liver

description: LP_25_13w_222_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: ratio

tag: rna integrity number

tag: bioanalyzer results

tag: sacrifice method

tag: tissue

tag: tissue harvest methods


title: mouse miRNA array diabetic_3


title: LP_2-5_13w_194_TRBZ_10008_Liver

description: LP_2-5_13w_194_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.

treatment_protocol: in vivo Treatment: 1,2,4-Tribromobenzene, Treatment Repeat: 7, Units of Treatment Repeat: Days/Week, Treatment Duration: 13, 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: sample preservation

tag: strain or line

tag: ncbi taxonomy id

tag: Sex


title: LP_10_13w_214_TRBZ_10008_Liver

description: LP_10_13w_214_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.

treatment_protocol: in vivo Treatment: 1,2,4-Tribromobenzene, Treatment Repeat: 7, Units of Treatment Repeat: Days/Week, Treatment Duration: 13, 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: amount to core


title: LP_2-5_13w_192_TRBZ_10008_Liver

description: LP_2-5_13w_192_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: units of amount


title: LP_0_13w_184_CC1_10008_Liver

description: LP_0_13w_184_CC1_10008_Liver_(HT_Rat230_PM)_H11: 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: 13, 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: individual


title: LP_2-5_13w_193_TRBZ_10008_Liver

description: LP_2-5_13w_193_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: developmental state


title: T lymphocytes treated with IFN-β, individual 1

tag: cell type

tag: donor

tag: treated


title: mouse miRNA array control_4

description: miRNA expression in control skeletal muscle

tag: group

value: control

tag: strain

value: C57BL/KsJ db/db


title: LP_10_13w_216_TRBZ_10008_Liver

description: LP_10_13w_216_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.

value: ul

tag: ratio

tag: rna integrity number

tag: bioanalyzer results

tag: sacrifice method

tag: age

tag: units of age

value: weeks


title: mouse miRNA array control_3


title: LP_0_13w_186_CC1_10008_Liver

description: LP_0_13w_186_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: array type

tag: sample preservation

value: Frozen

tag: strain or line

tag: ncbi taxonomy id

tag: tissue

tag: tissue harvest methods


title: LP_10_13w_213_TRBZ_10008_Liver

description: LP_10_13w_213_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: amount to core

tag: units of amount

value: Spague Dawley Crl:CD(SD)

tag: individual

tag: developmental state

tag: Sex


title: LP_2-5_13w_195_TRBZ_10008_Liver

description: LP_2-5_13w_195_TRBZ_10008_Liver_(HT_Rat230_PM)_C05: 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

value: Excellent


title: mouse miRNA array control_2

tag: group

tag: strain


title: LP_10_13w_212_TRBZ_10008_Liver

description: LP_10_13w_212_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: rna integrity number

tag: bioanalyzer results

tag: sacrifice method


title: LP_2-5_13w_196_TRBZ_10008_Liver

description: LP_2-5_13w_196_TRBZ_10008_Liver_(HT_Rat230_PM)_C07: 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: age

tag: units of age


title: LP_0_13w_183_CC1_10008_Liver

description: LP_0_13w_183_CC1_10008_Liver_(HT_Rat230_PM)_H10: 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: strain or line

tag: ncbi taxonomy id


title: LP_0_13w_181_CC1_10008_Liver

description: LP_0_13w_181_CC1_10008_Liver_(HT_Rat230_PM)_H08: 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: tissue

tag: tissue harvest methods


title: LP_75_5d_56_TRBZ_10008_Liver

description: LP_75_5d_56_TRBZ_10008_Liver_(HT_Rat230_PM)_C06: 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: 75, Units of Dose or Concentration: mg/kg

tag: units of amount

tag: individual

tag: developmental state


title: LP_0_13w_182_CC1_10008_Liver

description: LP_0_13w_182_CC1_10008_Liver_(HT_Rat230_PM)_H09: 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: Sex


title: LP_10_13w_215_TRBZ_10008_Liver

description: LP_10_13w_215_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: rna integrity number


title: mouse miRNA array control_1

tag: group

tag: strain


title: LP_75_5d_54_TRBZ_10008_Liver

description: LP_75_5d_54_TRBZ_10008_Liver_(HT_Rat230_PM)_C04: 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: bioanalyzer results

tag: sacrifice method


title: LP_75_5d_52_TRBZ_10008_Liver

description: LP_75_5d_52_TRBZ_10008_Liver_(HT_Rat230_PM)_C03: 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: units of age


title: Subject B, after Yoga intervention, replicate 1

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 B

tag: treatment

value: after Yoga intervention


title: LP_75_5d_55_TRBZ_10008_Liver

description: LP_75_5d_55_TRBZ_10008_Liver_(HT_Rat230_PM)_C05: 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: strain or line

tag: ncbi taxonomy id

value: Adult

value: Pentobarbital, Exsanguinated

value: Male

tag: tissue


title: LP_5_5d_24_TRBZ_10008_Liver

description: LP_5_5d_24_TRBZ_10008_Liver_(HT_Rat230_PM)_B01: 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: 5, Units of Dose or Concentration: mg/kg

tag: units of amount

tag: individual

tag: developmental state

value: Liver

tag: tissue harvest methods

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


title: LP_25_5d_46_TRBZ_10008_Liver

description: LP_25_5d_46_TRBZ_10008_Liver_(HT_Rat230_PM)_C01: 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: 25, Units of Dose or Concentration: mg/kg

tag: ratio

tag: rna integrity number

tag: Sex


title: LP_5_5d_22_TRBZ_10008_Liver

description: LP_5_5d_22_TRBZ_10008_Liver_(HT_Rat230_PM)_A12: 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: bioanalyzer results


title: IMR-90-ING4_N214D.1

city: Madrid

first: Gema

last: Moreno-Bueno

state: Madrid

address: Arturo Duperier

department: Biochemistry

country: Spain

institute: IIB

hyb_protocol: The arrays hybridization was performed using In Situ Hybridization Kit Plus (Agilent technologies) according to Peinado et al, Cancer Research 2008.

scan_protocol: After hybridization and washing, the slides were scanned in an Axon GenePix Scanner (Axon Instruments), according to manufacturer's protocol.

data_processing: Differentially expressed genes in wild-type ING4 versus vector were identified with GEPAS (Gene Expression Pattern Analysis Suite, http://gepas3.bioinfo.cipf.es) selecting genes with a fold difference of at least two in all of the samples and standard deviation lower than 0,5.  This subset was further analyzed in the arrays from ING4N214D-infected cells.  Functional enrichment analysis was performed using the FatiGO application (http://babelomics.bioinfo.cipf.es).

source_name: primary human diploid fibroblasts

label_protocol: 1mg from tRNA was labelled and array hybridized using the Low RNA Linear Amplification Kit (Agilent) following manufacturer’s protocol.

growth_protocol: IMR-90 primary human diploid fibroblasts were obtained from the American Type Culture Collection (ATCC, Manassas, VA, USA) and used at a population doubling level (PDL) lower than 30.

extract_protocol: Total RNA was prepared using Tri Reagent (Sigma) from asynchronously growing cells. RNA was used for cDNA síntesis using M/MLV reverse transcriptase (Promega, Madison, WI, USA).

tag: cell line

tag: cell type

value: fibroblasts

tag: genotype/variation

value: N214D mutant

value: vector-infected cells


title: LP_25_5d_45_TRBZ_10008_Liver

description: LP_25_5d_45_TRBZ_10008_Liver_(HT_Rat230_PM)_B12: 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: sample preservation

tag: sacrifice method

tag: units of age


title: LP_2-5_5d_15_TRBZ_10008_Liver

description: LP_2-5_5d_15_TRBZ_10008_Liver_(HT_Rat230_PM)_A09: 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: 2.5, Units of Dose or Concentration: mg/kg

tag: amount to core

value: ul

tag: strain or line

tag: ncbi taxonomy id


title: IMR-90-ING4_N214D.2


title: brain_SMC6_replicate4

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 4
SAMPLE 24

scan_protocol: Standard Illumina scanning protocol using HiScan

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

source_name: brain

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

value: SMC6 mutant

tag: strain


title: LP_25_5d_44_TRBZ_10008_Liver

description: LP_25_5d_44_TRBZ_10008_Liver_(HT_Rat230_PM)_B11: 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: individual

tag: developmental state

value: weeks

tag: tissue

tag: tissue harvest methods


title: IMR-90-ING4wt2

tag: cell line

tag: cell type

value: wild-type ING4


title: LP_5_5d_25_TRBZ_10008_Liver

description: LP_5_5d_25_TRBZ_10008_Liver_(HT_Rat230_PM)_B02: 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: rna integrity number

tag: bioanalyzer results

tag: sample preservation

tag: Sex


title: LP_25_5d_42_TRBZ_10008_Liver

description: LP_25_5d_42_TRBZ_10008_Liver_(HT_Rat230_PM)_B10: 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

value: Excellent

tag: strain or line

tag: ncbi taxonomy id

tag: sacrifice method

tag: units of age


title: LP_75_5d_51_TRBZ_10008_Liver

description: LP_75_5d_51_TRBZ_10008_Liver_(HT_Rat230_PM)_C02: 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: Adult


title: LP_2-5_5d_14_TRBZ_10008_Liver

description: LP_2-5_5d_14_TRBZ_10008_Liver_(HT_Rat230_PM)_A08: 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: individual

tag: developmental state

value: Pentobarbital, Exsanguinated


title: IMR-90-ING4wt1

tag: genotype/variation


title: LP_5_5d_26_TRBZ_10008_Liver

description: LP_5_5d_26_TRBZ_10008_Liver_(HT_Rat230_PM)_B03: 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: Male

tag: tissue

tag: tissue harvest methods


title: LP_5_5d_21_TRBZ_10008_Liver

description: LP_5_5d_21_TRBZ_10008_Liver_(HT_Rat230_PM)_A11: 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: Liver


title: LP_25_5d_41_TRBZ_10008_Liver

description: LP_25_5d_41_TRBZ_10008_Liver_(HT_Rat230_PM)_B09: 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

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