title: HepaRG_6h_C30D1B1G5

description: Chemical signature/dose response study


title: HepaRG_6h_C34D3B3G5

status: Public on Mar 25 2016

type: RNA

city: MASON

first: Jay

middle: Patrick

last: Tiesman

state: OH

address: PO BOX 8006

department: Global Biotechnology

country: USA

institute: Procter & Gamble

description: Chemical signature/dose response study

hyb_protocol: GeneChip targets were hybridized on Affymetrix U219-96 plates using the GeneTitan single-channel instrument and protocols provided by Affymetrix.

scan_protocol: GeneTitan plates were scanned on a GeneTitan single-channel instrument using protocols provided by Affymetrix.

data_processing: Data was processed using the PLIER algorithm implemented from the Affymetrix Command Console Software.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: HepaRG Hepatocytes

label_protocol: 500 ng of total RNA was converted to Affymetrix GeneChip targets using the Affymetrix IVT-Express kit and protocols provided by Affymetrix.

growth_protocol: HepaRG human hepatoma cells were purchased from Biopredic International (Rennes, France). Differentiated HepaRG cells were grown following suppliers’ protocol (Biopredic) in Williams E medium (Invitrogen), supplemented with 2mM Glutamax (Invitrogen), 10% ADD670 supplement (Biopredic International) and maintained at 37°C in an atmosphere of 5% CO2.

extract_protocol: Cells were extracted in QIAgen RLT buffer and total RNA was extracted using the Agencourt RNAdvance Tissue protocol implemented on a Beckman FXp robot using methods provided by Beckman Coulter.

treatment_protocol: Cells in collagen coated 24 well plates (BD, Franklin Lakes, NJ) were treated with 3 concentrations of chemical or DMSO vehicle for 6 h.

tag: chemical treatment

value: Imidacloprid

tag: dose

value: 10 uM

tag: replicate

tag: gender

value: Female

tag: cell line

value: HepaRG


title: HepaRG_6h_DMSOS52B2G5

description: Chemical signature/dose response study

value: DMSO


title: HepaRG_6h_C31D2B1G5

description: Chemical signature/dose response study

value: ANIT


title: HepaRG_6h_C29D1B2G5

description: Chemical signature/dose response study

value: Methotrexate


title: HepaRG_6h_C33D1B2G5

description: Chemical signature/dose response study

value: Nicotine


title: HepaRG_6h_C33D2B1G5

description: Chemical signature/dose response study


title: HepaRG_6h_DMSOS51B1G5

description: Chemical signature/dose response study


title: HepaRG_6h_C5D1B5G5

description: Chemical signature/dose response study

value: Clofibrate

value: 1 mM


title: HepaRG_6h_C34D1B2G5

description: Chemical signature/dose response study


title: HepaRG_6h_DMSOS53B1G5

description: Chemical signature/dose response study


title: HepaRG_6h_C25D3B1G4

description: Chemical signature/dose response study

value: Amoxicillin


title: HepaRG_6h_DMSOS52B3G5

description: Chemical signature/dose response study


title: HepaRG_6h_C34D2B2G5

description: Chemical signature/dose response study


title: HepaRG_6h_C30D2B2G5

description: Chemical signature/dose response study

value: Vinblastine


title: HepaRG_6h_C30D3B3G5

description: Chemical signature/dose response study

value: 10 nM


title: HepaRG_6h_C32D2B3G5

description: Chemical signature/dose response study

value: Griseofulvin

value: 1 uM


title: HepaRG_6h_C32D2B2G5

description: Chemical signature/dose response study


title: HepaRG_6h_C29D1B3G5

description: Chemical signature/dose response study


title: HepaRG_6h_DMSOS42B1G4

description: Chemical signature/dose response study


title: HepaRG_6h_C29D1B1G5

description: Chemical signature/dose response study


title: HepaRG_6h_C31D1B1G5

description: Chemical signature/dose response study


title: HepaRG_6h_C4D1B1G1

description: Chemical signature/dose response study

value: Tamoxifen


title: HepaRG_6h_C31D2B2G5

description: Chemical signature/dose response study


title: HepaRG_6h_C30D3B1G5

description: Chemical signature/dose response study


title: HepaRG_6h_C32D1B1G5

description: Chemical signature/dose response study


title: HepaRG_6h_C34D2B3G5

description: Chemical signature/dose response study


title: HepaRG_6h_C33D2B3G5

description: Chemical signature/dose response study


title: HepaRG_6h_C5D2B6G5

description: Chemical signature/dose response study


title: HepaRG_6h_C29D2B1G5

description: Chemical signature/dose response study


title: HepaRG_6h_C5D3B5G5

description: Chemical signature/dose response study


title: HepaRG_6h_DMSOS53B3G5

description: Chemical signature/dose response study


title: HepaRG_6h_C31D3B2G5

description: Chemical signature/dose response study


title: HepaRG_6h_DMSOS53B2G5

description: Chemical signature/dose response study


title: HepaRG_6h_C34D1B3G5

description: Chemical signature/dose response study


title: HepaRG_6h_C30D1B3G5

description: Chemical signature/dose response study


title: HepaRG_6h_C34D1B1G5

description: Chemical signature/dose response study


title: HepaRG_6h_DMSOS52B1G5

description: Chemical signature/dose response study


title: HepaRG_6h_C33D3B2G5

description: Chemical signature/dose response study


title: HepaRG_6h_C29D2B2G5

description: Chemical signature/dose response study


title: HepaRG_6h_C5D3B6G5

description: Chemical signature/dose response study


title: HepaRG_6h_C13D2B1G2

description: Chemical signature/dose response study

value: Thyroxine


title: HepaRG_6h_C31D3B1G5

description: Chemical signature/dose response study


title: HepaRG_6h_C9D2B1G2

description: Chemical signature/dose response study

value: Flutamide


title: HepaRG_6h_C19D2B3G3

description: Chemical signature/dose response study

value: Progesterone

value: 10 uM


title: HepaRG_6h_C18D3B3G3

description: Chemical signature/dose response study

value: Chenodeoxychobe Acid

value: Female

value: HepaRG


title: HepaRG_6h_C20D1B3G3

description: Chemical signature/dose response study


title: HepaRG_6h_DMSOS13B1G1

description: Chemical signature/dose response study

value: DMSO


title: HepaRG_6h_C21D1B3G3

description: Chemical signature/dose response study

value: Ketoconazole


title: HepaRG_6h_C5D2B5G5

description: Chemical signature/dose response study

value: Clofibrate


title: HepaRG_6h_C23D3B3G4

description: Chemical signature/dose response study

value: Vorinostat


title: HepaRG_6h_C2D3B3G1

description: Chemical signature/dose response study

value: Genistein


title: HepaRG_6h_C7D1B3G1

description: Chemical signature/dose response study

value: Troglitazone


title: HepaRG_6h_C17D1B3G3

description: Chemical signature/dose response study

value: Farnesol


title: HepaRG_6h_C27D1B3G4

description: Chemical signature/dose response study

value: Metformin


title: HepaRG_6h_DMSOS41B3G4

description: Chemical signature/dose response study


title: HepaRG_6h_C32D1B3G5

description: Chemical signature/dose response study

value: Griseofulvin


title: HepaRG_6h_DMSOS11B3G1

description: Chemical signature/dose response study


title: HepaRG_6h_C29D3B3G5

description: Chemical signature/dose response study

value: Methotrexate

value: 1 uM


title: HepaRG_6h_C27D3B3G4

description: Chemical signature/dose response study


title: HepaRG_6h_C7D3B3G1

description: Chemical signature/dose response study


title: HepaRG_6h_C14D2B3G2

description: Chemical signature/dose response study

value: Tetrachlorodibenzo p dioxin

value: 10 nM


title: HepaRG_6h_C33D3B3G5

description: Chemical signature/dose response study

value: Nicotine


title: HepaRG_6h_C4D2B3G1

description: Chemical signature/dose response study

value: Tamoxifen


title: HepaRG_6h_C6D1B3G1

description: Chemical signature/dose response study

value: Dehydrorepiandrosterone

value: 10 uM

value: Female


title: HepaRG_6h_C22D2B3G4

description: Chemical signature/dose response study

value: Valproic Acid

value: HepaRG


title: HepaRG_6h_C8D1B3G2

description: Chemical signature/dose response study

value: DHP


title: HepaRG_6h_C20D2B3G3

description: Chemical signature/dose response study


title: HepaRG_6h_C3D2B1G1

description: Chemical signature/dose response study

value: Ethenyl Estradiol


title: HepaRG_6h_C23D2B3G4

description: Chemical signature/dose response study

value: Vorinostat


title: HepaRG_6h_C3D2B3G1

description: Chemical signature/dose response study


title: HepaRG_6h_C24D2B3G4

description: Chemical signature/dose response study

value: Desferrioxamine


title: HepaRG_6h_C25D3B3G4

description: Chemical signature/dose response study

value: Amoxicillin


title: HepaRG_6h_C25D1B3G4

description: Chemical signature/dose response study

value: 1 mM


title: HepaRG_6h_DMSOS22B3G2

description: Chemical signature/dose response study

value: DMSO


title: HepaRG_6h_C23D1B3G4

description: Chemical signature/dose response study


title: HepaRG_6h_C15D2B3G2

description: Chemical signature/dose response study

value: Dihydroxyvitamin 3


title: HepaRG_6h_C18D2B3G3

description: Chemical signature/dose response study

value: Chenodeoxychobe Acid


title: HepaRG_6h_C26D1B3G4

description: Chemical signature/dose response study

value: 6 Aminonicotinamide


title: HepaRG_6h_C12D3B3G2

description: Chemical signature/dose response study

value: Retinoic Acid

value: 10 nM


title: HepaRG_6h_C13D2B3G2

description: Chemical signature/dose response study

value: Thyroxine


title: HepaRG_6h_C1D1B1G1

description: Chemical signature/dose response study

value: Bisphenol A


title: HepaRG_6h_C3D3B3G1

description: Chemical signature/dose response study

value: Female


title: HepaRG_6h_DMSOS21B3G2

description: Chemical signature/dose response study


title: HepaRG_6h_C17D2B3G3

description: Chemical signature/dose response study

value: Farnesol

value: 10 uM


title: HepaRG_6h_C8D3B3G2

description: Chemical signature/dose response study

value: DHP

value: HepaRG


title: HepaRG_6h_C1D1B3G1

description: Chemical signature/dose response study


title: HepaRG_6h_C4D3B3G1

description: Chemical signature/dose response study

value: Tamoxifen


title: HepaRG_6h_C25D2B3G4

description: Chemical signature/dose response study


title: HepaRG_6h_C5D3B3G1

description: Chemical signature/dose response study

value: Clofibrate


title: HepaRG_6h_DMSOS33B3G3

description: Chemical signature/dose response study


title: HepaRG_6h_C9D1B3G2

description: Chemical signature/dose response study

value: Flutamide


title: HepaRG_6h_C14D3B3G2

description: Chemical signature/dose response study

value: Tetrachlorodibenzo p dioxin

value: 1 nM


title: HepaRG_6h_C21D3B3G3

description: Chemical signature/dose response study

value: Ketoconazole

value: 1 uM


title: HepaRG_6h_C22D3B3G4

description: Chemical signature/dose response study

value: Valproic Acid


title: HepaRG_6h_C28D3B3G4

description: Chemical signature/dose response study

value: Phenformin


title: HepaRG_6h_DMSOS42B3G4

description: Chemical signature/dose response study

value: DMSO


title: HepaRG_6h_C2D3B1G1

description: Chemical signature/dose response study

value: Genistein


title: HepaRG_6h_C19D1B3G3

description: Chemical signature/dose response study

value: Progesterone


title: HepaRG_6h_C11D2B3G2

description: Chemical signature/dose response study

value: Phenobarbital

value: Female


title: HepaRG_6h_DMSOS12B3G1

description: Chemical signature/dose response study


title: HepaRG_6h_C12D2B3G2

description: Chemical signature/dose response study

value: Retinoic Acid


title: HepaRG_6h_C17D3B3G3

description: Chemical signature/dose response study

value: Farnesol


title: HepaRG_6h_C22D1B3G4

description: Chemical signature/dose response study

value: 1 mM

value: HepaRG


title: HepaRG_6h_C8D2B3G2

description: Chemical signature/dose response study

value: DHP

value: 10 uM


title: HepaRG_6h_C21D2B3G3

description: Chemical signature/dose response study


title: HepaRG_6h_C3D1B3G1

description: Chemical signature/dose response study

value: Ethenyl Estradiol


title: HepaRG_6h_C28D1B3G4

description: Chemical signature/dose response study


title: HepaRG_6h_C16D2B3G3

description: Chemical signature/dose response study

value: Clobetasol


title: HepaRG_6h_C9D3B3G2

description: Chemical signature/dose response study

value: Flutamide


title: HepaRG_6h_C11D3B3G2

description: Chemical signature/dose response study

value: 1 uM


title: HepaRG_6h_C16D1B3G3

description: Chemical signature/dose response study


title: HepaRG_6h_C26D3B3G4

description: Chemical signature/dose response study

value: 6 Aminonicotinamide


title: HepaRG_6h_DMSOS23B3G2

description: Chemical signature/dose response study


title: HepaRG_6h_C2D2B3G1

description: Chemical signature/dose response study


title: HepaRG_6h_C27D2B3G4

description: Chemical signature/dose response study

value: Metformin


title: HepaRG_6h_C10D3B3G2

description: Chemical signature/dose response study

value: Trenbolone

value: 1 nM


title: HepaRG_6h_C24D1B3G4

description: Chemical signature/dose response study

value: Desferrioxamine


title: HepaRG_6h_C10D1B3G2

description: Chemical signature/dose response study


title: HepaRG_6h_C15D1B3G3

description: Chemical signature/dose response study

value: Dihydroxyvitamin 3


title: HepaRG_6h_C13D3B3G2

description: Chemical signature/dose response study

value: Thyroxine

value: 10 nM

value: Female


title: HepaRG_6h_C1D2B3G1

description: Chemical signature/dose response study

value: Bisphenol A


title: HepaRG_6h_DMSOS43B3G4

description: Chemical signature/dose response study

value: DMSO

value: HepaRG


title: HepaRG_6h_C16D3B3G3

description: Chemical signature/dose response study


title: HepaRG_6h_C11D1B3G2

description: Chemical signature/dose response study

value: Phenobarbital


title: HepaRG_6h_C9D2B3G2

description: Chemical signature/dose response study

value: 10 uM


title: HepaRG_6h_C7D2B3G1

description: Chemical signature/dose response study

value: Troglitazone


title: HepaRG_6h_C13D1B3G2

description: Chemical signature/dose response study


title: HepaRG_6h_C5D1B3G1

description: Chemical signature/dose response study

value: Clofibrate

value: 1 mM


title: HepaRG_6h_C5D2B3G1

description: Chemical signature/dose response study


title: HepaRG_6h_C18D1B3G3

description: Chemical signature/dose response study

value: Chenodeoxychobe Acid


title: HepaRG_6h_C2D2B1G1

description: Chemical signature/dose response study

value: Genistein


title: HepaRG_6h_C26D2B1G4

description: Chemical signature/dose response study

value: 6 Aminonicotinamide


title: HepaRG_6h_C1D3B3G1

description: Chemical signature/dose response study

value: 1 uM


title: HepaRG_6h_C4D1B3G1

description: Chemical signature/dose response study

value: Tamoxifen


title: HepaRG_6h_DMSOS13B3G1

description: Chemical signature/dose response study


title: HepaRG_6h_DMSOS32B3G3

description: Chemical signature/dose response study


title: HepaRG_6h_C24D3B3G4

description: Chemical signature/dose response study

value: Desferrioxamine


title: HepaRG_6h_C20D3B3G3

description: Chemical signature/dose response study

value: 1 nM


title: HepaRG_6h_C10D2B3G2

description: Chemical signature/dose response study

value: Trenbolone

value: 10 nM


title: HepaRG_6h_DMSOS31B3G3

description: Chemical signature/dose response study

value: Female


title: HepaRG_6h_C26D2B3G4

description: Chemical signature/dose response study


title: HepaRG_6h_C19D3B3G3

description: Chemical signature/dose response study

value: Progesterone


title: HepaRG_6h_C22D1B2G4

description: Chemical signature/dose response study

value: Valproic Acid

value: HepaRG


title: HepaRG_6h_C21D2B2G3

description: Chemical signature/dose response study

value: Ketoconazole

value: 10 uM


title: HepaRG_6h_C28D2B3G4

description: Chemical signature/dose response study

value: Phenformin


title: HepaRG_6h_C11D3B2G2

description: Chemical signature/dose response study

value: Phenobarbital


title: HepaRG_6h_C12D1B3G2

description: Chemical signature/dose response study

value: Retinoic Acid


title: HepaRG_6h_C15D3B3G3

description: Chemical signature/dose response study

value: Dihydroxyvitamin 3


title: HepaRG_6h_C14D1B3G2

description: Chemical signature/dose response study

value: Tetrachlorodibenzo p dioxin


title: HepaRG_6h_DMSOS33B2G3

description: Chemical signature/dose response study

value: DMSO


title: HepaRG_6h_C5D3B1G1

description: Chemical signature/dose response study

value: Clofibrate


title: HepaRG_6h_C6D2B3G1

description: Chemical signature/dose response study

value: Dehydrorepiandrosterone

value: 1 uM


title: HepaRG_6h_C2D1B3G1

description: Chemical signature/dose response study

value: Genistein


title: HepaRG_6h_DMSOS32B2G3

description: Chemical signature/dose response study


title: HepaRG_6h_C10D3B2G2

description: Chemical signature/dose response study

value: Trenbolone

value: 1 nM


title: HepaRG_6h_C27D3B2G4

description: Chemical signature/dose response study

value: Metformin

value: Female


title: HepaRG_6h_C6D3B2G1

description: Chemical signature/dose response study

value: HepaRG


title: HepaRG_6h_C24D1B2G4

description: Chemical signature/dose response study

value: Desferrioxamine


title: HepaRG_6h_C28D1B2G4

description: Chemical signature/dose response study


title: HepaRG_6h_C9D2B2G2

description: Chemical signature/dose response study

value: Flutamide

value: 10 uM


title: HepaRG_6h_DMSOS43B2G4

description: Chemical signature/dose response study


title: HepaRG_6h_C20D1B2G3

description: Chemical signature/dose response study


title: HepaRG_6h_C10D1B2G2

description: Chemical signature/dose response study


title: HepaRG_6h_C25D2B2G4

description: Chemical signature/dose response study

value: Amoxicillin


title: HepaRG_6h_C1D2B2G1

description: Chemical signature/dose response study

value: Bisphenol A


title: HepaRG_6h_C8D2B2G2

description: Chemical signature/dose response study

value: DHP


title: HepaRG_6h_C6D1B2G1

description: Chemical signature/dose response study


title: HepaRG_6h_C28D2B2G4

description: Chemical signature/dose response study

value: Phenformin


title: HepaRG_6h_C10D2B1G2

description: Chemical signature/dose response study

value: 10 nM


title: HepaRG_6h_C15D2B1G2

description: Chemical signature/dose response study

value: Dihydroxyvitamin 3


title: HepaRG_6h_C19D2B2G3

description: Chemical signature/dose response study

value: Progesterone


title: HepaRG_6h_C10D2B2G2

description: Chemical signature/dose response study


title: HepaRG_6h_C5D1B2G1

description: Chemical signature/dose response study

value: Clofibrate

value: 1 mM


title: HepaRG_6h_C18D3B2G3

description: Chemical signature/dose response study

value: Chenodeoxychobe Acid

value: 1 uM


title: HepaRG_6h_C20D2B2G3

description: Chemical signature/dose response study


title: HepaRG_6h_C21D3B2G3

description: Chemical signature/dose response study

value: Ketoconazole


title: HepaRG_6h_C8D3B2G2

description: Chemical signature/dose response study

value: Female


title: HepaRG_6h_C17D2B2G3

description: Chemical signature/dose response study

value: Farnesol

value: HepaRG


title: HepaRG_6h_C26D3B2G4

description: Chemical signature/dose response study

value: 6 Aminonicotinamide


title: HepaRG_6h_C15D1B2G3

description: Chemical signature/dose response study

value: 1 nM


title: HepaRG_6h_C24D3B2G4

description: Chemical signature/dose response study

value: Desferrioxamine


title: HepaRG_6h_DMSOS11B2G1

description: Chemical signature/dose response study

value: DMSO


title: HepaRG_6h_C12D3B2G2

description: Chemical signature/dose response study

value: Retinoic Acid


title: HepaRG_6h_C6D1B1G1

description: Chemical signature/dose response study

value: Dehydrorepiandrosterone

value: 10 uM


title: HepaRG_6h_C9D3B2G2

description: Chemical signature/dose response study

value: Flutamide


title: EBR_180 min_2

city: Taipei

first: Hsueh-Fen

last: Juan

address: No. 1, Sec. 4, Roosevelt Road

department: institute of molecular and cellular biology

country: Taiwan

institute: National Taiwan university

description: Gene expression after 180 min in EBR-treated Arabidopsis thaliana

hyb_protocol: RNA processing and hybridization were performed using miRBASE V14 arrays (Agilent Technologies, Palo Alto, CA, USA) according to the manufacturer’s protocol (this release contains 161 Arabidopsis thaliana miRNA genes).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Arabidopsis thaliana

source_name: Seedlings were cultured under exogenous 10 nM EBR treatments for 180 minutes

label_protocol: 100 ng total RNAs of each sample were prepared for labeling with Cyanine 3-pCp using the One-Color RNA Amplification kit (Agilent) according to the manufacturer's instructions.

growth_protocol: Seedlings were grown in 1/2 MS medium with 1.5% sucrose. After stratification, seeds were transferred into 50 ml flasks with 10 ml liquid medium and incubated for seven days at 50 rpm and 22 °C under continuous light conditions.

extract_protocol: Total RNAs were extracted from complete frozen seedlings using TRIzol® Reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's recommendations, and RNA purity was confirmed by spectrophotometry (A260/A280 ratio) and capillary electrophoresis (Agilent 2100 Bioanalyzer, Agilent Technologies, Palo Alto, CA, USA).

treatment_protocol: Seedlings were then treated with medium containing 10 nM EBR or DMSO (mock) solution for 0.5 hours and 3 hours, respectively.

tag: tissue

value: seedlings

tag: treatment

value: 10 nM EBR

tag: time

value: 180 min


title: DMSO_180 min_2

description: Gene expression after 180 min in DMSO-treated Arabidopsis thaliana

source_name: Seedlings were cultured under exogenous DMSO (mock) treatments for 180 minutes

value: DMSO (mock)


title: HepaRG_6h_C27D1B2G4

description: Chemical signature/dose response study

value: Metformin


title: EBR_30 min_2

description: Gene expression after 30 min in EBR-treated Arabidopsis thaliana

source_name: Seedlings were cultured under exogenous 10 nM EBR treatments for 30 minutes

value: 30 min


title: B11_(Mm35b_P01R_v02)

type: genomic

city: Toronto

first: Arturas

last: Petronis

address: 250 College St Rm606

country: Canada

institute: Centre for Addiction and Mental Health

description:
Sample name: 60_7-3
Enterocytes extracted using Warm Chelating method

hyb_protocol: 7 ug ofDNA was hybridized on GeneChip Human Tiling 2.0R Array (B array; Hs35b_P02R) or Mouse Tiling 2.0R Array (A array; Mm35b_P01R) as indicated in ChIP protocol

scan_protocol: Arrays were scanned on an Affymetrix GeneChip Scanner 3000 Targeted Genotyping System (GCS 3000 TF system)

data_processing:
Array Data were quantile normalized and log2 transformed. A probe's center defines a 200bp window. The Tiling array intensities were extracted using R2.15.2 and the bioconductor package "AffyTiling". Probe sequences were re-mapped to Hg19 for human and Mm10 for mouse using mrfast2.6.1.0 with maximum edit distance 0. Probe intensities were then smoothed using a pseudomedian filter with a bandwidth of 401 bp.
*.smooth.txt.gz: tab-delimited text files containing post-processed probe intensities, with columns: chromosome, start, intensity

molecule: genomic DNA

organism: Mus musculus

source_name: enterocytes

label_protocol: GeneChip Double-stranded DNA Terminal Labeling kit (Affymetrix)

extract_protocol: DNA was extracted with standard phenol chloroform and ethanol preicpitation method

treatment_protocol: Enterocytes were extracted from jejunum surgical samples. For each sample, the remaining tissue also extracted and is referred to as jejunum lacking enterocytes

value: mTAG enrichment protocol

tag: strain

tag: sample source

value: Toronto Centre for Phenogenomics

tag: age

tag: Sex

value: M

tag: relative lactase mrna expression

tag: cell type

value: enterocytes


title: HepaRG_6h_C12D2B2G2

description: Chemical signature/dose response study

value: Female

value: HepaRG


title: DMSO_30 min_2

description: Gene expression after 30 min in DMSO-treated Arabidopsis thaliana

source_name: Seedlings were cultured under exogenous DMSO (mock) treatments for 30 minutes


title: HepaRG_6h_C11D1B2G2

description: Chemical signature/dose response study

value: Phenobarbital


title: HepaRG_6h_C9D1B2G2

description: Chemical signature/dose response study


title: EBR_180 min_1


title: HepaRG_6h_C3D2B2G1

description: Chemical signature/dose response study

value: Ethenyl Estradiol


title: DMSO_30 min_1


title: HepaRG_6h_C7D1B2G1

description: Chemical signature/dose response study

value: Troglitazone


title: HepaRG_6h_C22D3B2G4

description: Chemical signature/dose response study

value: Valproic Acid

value: 10 uM


title: HepaRG_6h_DMSOS12B2G1

description: Chemical signature/dose response study

value: DMSO


title: HepaRG_6h_C14D1B2G2

description: Chemical signature/dose response study

value: Tetrachlorodibenzo p dioxin


title: HepaRG_6h_DMSOS23B1G2

description: Chemical signature/dose response study


title: HepaRG_6h_DMSOS42B2G4

description: Chemical signature/dose response study


title: HepaRG_6h_C4D1B2G1

description: Chemical signature/dose response study

value: Tamoxifen


title: HepaRG_6h_C25D3B2G4

description: Chemical signature/dose response study

value: Amoxicillin


title: HepaRG_6h_C6D3B3G1

description: Chemical signature/dose response study

value: Dehydrorepiandrosterone


title: HepaRG_6h_C13D3B2G2

description: Chemical signature/dose response study

value: Thyroxine

value: 10 nM


title: HepaRG_6h_C20D3B2G3

description: Chemical signature/dose response study

value: 1 nM


title: B10_(Mm35b_P01R_v02)

description:
Sample name: 60_7-2
Enterocytes extracted using Warm Chelating method

value: mTAG enrichment protocol

value: Toronto Centre for Phenogenomics

value: M


title: EBR_30 min_1

value: seedlings

value: 10 nM EBR

value: 30 min


title: B8_(Mm35b_P01R_v02)

description:
Sample name: 60_2-2-4
Enterocytes extracted using Warm Chelating method

value: enterocytes


title: HepaRG_6h_C24D2B2G4

description: Chemical signature/dose response study

value: Desferrioxamine

value: Female

value: HepaRG


title: HepaRG_6h_C26D2B2G4

description: Chemical signature/dose response study

value: 6 Aminonicotinamide


title: HepaRG_6h_C19D1B2G3

description: Chemical signature/dose response study

value: Progesterone


title: HepaRG_6h_C7D2B2G1

description: Chemical signature/dose response study

value: Troglitazone

value: 10 uM


title: B7_(Mm35b_P01R_v02)

description:
Sample name: 60_2-2-3
Enterocytes extracted using Warm Chelating method


title: DMSO_180 min_1

value: DMSO (mock)

value: 180 min


title: B5_(Mm35b_P01R_v02)

description:
Sample name: 60_2-2-1
Enterocytes extracted using Warm Chelating method


title: B3_(Mm35b_P01R_v02)

description:
Sample name: 60_2-1-7
Enterocytes extracted using Warm Chelating method


title: B1_(Mm35b_P01R_v02)

description:
Sample name: 60_2-1-5
Enterocytes extracted using Warm Chelating method


title: A11_(Mm35b_P01R_v02)

description:
Sample name: 60_2-1-3
Enterocytes extracted using Warm Chelating method


title: HepaRG_6h_C11D2B2G2

description: Chemical signature/dose response study

value: Phenobarbital


title: A12_(Mm35b_P01R_v02)

description:
Sample name: 60_2-1-4
Enterocytes extracted using Warm Chelating method

value: mTAG enrichment protocol


title: HepaRG_6h_C23D3B2G4

description: Chemical signature/dose response study

value: Vorinostat

value: 1 uM


title: B6_(Mm35b_P01R_v02)

description:
Sample name: 60_2-2-2
Enterocytes extracted using Warm Chelating method

value: Toronto Centre for Phenogenomics

value: M


title: HepaRG_6h_C25D1B2G4

description: Chemical signature/dose response study

value: Amoxicillin

value: 1 mM


title: HepaRG_6h_C2D2B2G1

description: Chemical signature/dose response study

value: Genistein


title: A10_(Mm35b_P01R_v02)

description:
Sample name: 60_2-1-2
Enterocytes extracted using Warm Chelating method

value: enterocytes


title: HepaRG_6h_C4D3B1G1

description: Chemical signature/dose response study

value: Tamoxifen

value: Female

value: HepaRG


title: HepaRG_6h_C28D3B2G4

description: Chemical signature/dose response study

value: Phenformin


title: A9_(Mm35b_P01R_v02)

description:
Sample name: 60_2-1-1
Enterocytes extracted using Warm Chelating method


title: B2_(Mm35b_P01R_v02)

description:
Sample name: 60_2-1-6
Enterocytes extracted using Warm Chelating method


title: HepaRG_6h_C12D1B2G2

description: Chemical signature/dose response study

value: Retinoic Acid


title: HepaRG_6h_C21D1B2G3

description: Chemical signature/dose response study

value: Ketoconazole


title: HepaRG_6h_C17D3B2G3

description: Chemical signature/dose response study

value: Farnesol


title: B4_(Mm35b_P01R_v02)

description:
Sample name: 60_2-1-8
Enterocytes extracted using Warm Chelating method


title: C11_(Mm35b_P01R_v02)

description:
Sample name: 6_9-7
Enterocytes extracted using Warm Chelating method


title: C9_(Mm35b_P01R_v02)

description:
Sample name: 6_9-5
Enterocytes extracted using Warm Chelating method


title: C8_(Mm35b_P01R_v02)

description:
Sample name: 6_9-4
Enterocytes extracted using Warm Chelating method


title: C7_(Mm35b_P01R_v02)

description:
Sample name: 6_9-3
Enterocytes extracted using Warm Chelating method


title: HepaRG_6h_C7D1B1G1

description: Chemical signature/dose response study

value: Troglitazone


title: HepaRG_6h_C19D3B2G3

description: Chemical signature/dose response study

value: Progesterone


title: HepaRG_6h_C4D3B2G1

description: Chemical signature/dose response study


title: C6_(Mm35b_P01R_v02)

description:
Sample name: 6_9-2
Enterocytes extracted using Warm Chelating method

value: mTAG enrichment protocol


title: HepaRG_6h_C27D2B2G4

description: Chemical signature/dose response study

value: Metformin

value: 1 uM


title: HepaRG_6h_C16D3B2G3

description: Chemical signature/dose response study

value: Clobetasol


title: C5_(Mm35b_P01R_v02)

description:
Sample name: 6_8-7
Enterocytes extracted using Warm Chelating method

value: Toronto Centre for Phenogenomics

value: M


title: HepaRG_6h_C3D1B2G1

description: Chemical signature/dose response study

value: Ethenyl Estradiol


title: HepaRG_6h_DMSOS31B2G3

description: Chemical signature/dose response study

value: DMSO


title: C3_(Mm35b_P01R_v02)

description:
Sample name: 6_8-5
Enterocytes extracted using Warm Chelating method

value: enterocytes


title: C4_(Mm35b_P01R_v02)

description:
Sample name: 6_8-6
Enterocytes extracted using Warm Chelating method


title: C2_(Mm35b_P01R_v02)

description:
Sample name: 6_8-4
Enterocytes extracted using Warm Chelating method


title: B12_(Mm35b_P01R_v02)

description:
Sample name: 6_8-2
Enterocytes extracted using Warm Chelating method


title: HepaRG_6h_C2D1B2G1

description: Chemical signature/dose response study

value: Genistein

value: Female


title: A8_(Mm35b_P01R_v02)

description:
Sample name: 6_2-2-4
Enterocytes extracted using Warm Chelating method


title: HepaRG_6h_C1D3B2G1

description: Chemical signature/dose response study

value: Bisphenol A

value: HepaRG


title: S026 [ISExWRS-2+IVM] (2277)

city: Glasgow

first: Victoria

last: Gillan

address: bearsden road

country: United Kingdom

institute: University of Glasgow

description: Backcross between MHco3(ISE) and MHco4(WRS). Progeny from the crosses of MHco4(WRS) with MHco3(ISE) underwent four rounds of back-crossing to MHco3(ISE), with IVM selection, to produce a fourth backcross generation: MHco3/10.BC4. Harvested from sheep treated with IVM at 0.2 mg/Kg seven days prior to euthanasia

hyb_protocol: Performed by LC Sciences http://www.lcsciences.com/discovery/applications/transcriptomics/mirna-profiling/mirna/

scan_protocol: Axon GenePix 4000B Microarray Scanner

organism: Haemonchus contortus

source_name: Whole organism

extract_protocol: Whole worm total RNA was extracted using trizol (Invitrogen)

tag: sample type

value: Mixed sex adult

tag: genotype/variation

value: Progeny from the crosses of MHco4(WRS) with MHco3(ISE) underwent four rounds of back-crossing to MHco3(ISE), with IVM selection, to produce a fourth backcross generation:MHco3/10.BC4. Harvested from sheep treated with IVM at 0.2 mg/Kg seven days prior to euthanasia


title: S027 [ISExWRS-3+IVM] (2313)

data_processing: Performed by LC Sciences http://www.lcsciences.com/discovery/applications/transcriptomics/mirna-profiling/mirna/

value: Backcross between MHco3(ISE) and MHco4(WRS)


title: S025 [ISExWRS-1+IVM] (2353)

label_protocol: Performed by LC Sciences http://www.lcsciences.com/discovery/applications/transcriptomics/mirna-profiling/mirna/


title: S024 [ISExWRS-3] (2567)

description: Backcross between MHco3(ISE) and MHco4(WRS). Progeny from the crosses of MHco4(WRS) with MHco3(ISE) underwent four rounds of back-crossing to MHco3(ISE), with IVM selection, to produce a fourth backcross generation: MHco3/10.BC4. Harvested from untreated sheep

value: Progeny from the crosses of MHco4(WRS) with MHco3(ISE) underwent four rounds of back-crossing to MHco3(ISE), with IVM selection, to produce a fourth backcross generation:MHco3/10.BC4.


title: S023 [ISExWRS-2] (2253)


title: S022 [ISExWRS-1] (2427)

description: Backcross between MHco3(ISE) and MHco4(WRS). Progeny from the crosses of MHco4(WRS) with MHco3(ISE) underwent four rounds of back-crossing to MHco3(ISE), with IVM selection, to produce a fourth backcross generation: MHco3/10.BC4.


title: C1_(Mm35b_P01R_v02)

description:
Sample name: 6_8-3
Enterocytes extracted using Warm Chelating method

value: mTAG enrichment protocol


title: HepaRG_6h_DMSOS41B2G4

description: Chemical signature/dose response study


title: HepaRG_6h_C2D3B2G1

description: Chemical signature/dose response study


title: High dose PM2.5 group

city: Guangzhou

first: Jianjun

last: Wu

address: Xinzao Town, Panyu District

department: School of Public Health

country: China

institute: Guangzhou Medical University

description: 16HBE cell treated with high dose PM2.5 (500 μg/mL, experimental group)

hyb_protocol: According manufacturer's instructions, hybridization was carried out for the antisense RNA labeled with Cy5, including pre-hybridization, hybridization and hybridization washing.

scan_protocol: The slides were scanned using the Axon GenePix 4000B microarray scanner (Axon Instruments, Foster City, CA).

data_processing: Scanned images were then imported into GenePix® Pro Microarray Image Analysis Software for analysis. Expressed data were normalized using the Median normalization. Fold changes for differential expression were set as ≥ 2 and p ≤ 0.05. Finally, cluster analyses were used to classify lncRNAs based on their distinguishable expression in different samples.

source_name: 16HBE cell treated with hign dose PM2.5 (500 μg/mL)

label_protocol: The antisense RNA was generated using Amino Allyl messageAmp II kit (Life Technologies) and labeled with Cy5. Labeling efficiency can be calculated by the concentration of CyDye and RNA measured by K5500 micro-spectrophotometer. For good microarray result, labeling efficiency should be between 1.0~3.6.

extract_protocol: Total RNA was isolated using TRIzol (Life Technologies) according to manufacturer’s instructions.RNA quality and quantity was measured by using Agilent 2200 Bioanalyzer.

treatment_protocol: 16HBE cell in control group was treated with PBS and 16HBE cells in experimental group were treated with low dose PM2.5 (125 μg/mL) and high dose PM2.5 (500 μg/mL).


title: HepaRG_6h_C23D1B2G4

description: Chemical signature/dose response study

value: Vorinostat


title: HepaRG_6h_C26D1B2G4

description: Chemical signature/dose response study

value: 6 Aminonicotinamide

value: 1 mM


title: control group

description: 16HBE cell treated with PBS(control group)

source_name: 16HBE cell treated with PBS


title: HepaRG_6h_C8D1B2G2

description: Chemical signature/dose response study

value: DHP

value: 1 uM


title: HepaRG_6h_C5D2B2G1

description: Chemical signature/dose response study

value: Clofibrate


title: Low dose PM2.5 group

description: 16HBE cell treated with low dose PM2.5 (125 μg/mL,experimental group)

source_name: 16HBE cell treated with low dose PM2.5 (125 μg/mL)


title: HepaRG_6h_C22D2B2G4

description: Chemical signature/dose response study

value: Valproic Acid


title: lasalocid_rep2

city: Yokohama

first: Yukio

last: Kurihara

state: Kanagawa

address: 1-7-22 Suehiro-cho, Tsurumi-ku

department: CSRS

country: Japan

institute: Riken

description: gene expression in seedlings treated with 1 uM lasalocid sodium

hyb_protocol: 1.65 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 55 ml containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ml of 2x GE Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Arabidopsis Genome Oligo Microarrays (G2519F) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 021169_D_F_20131126) to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: seedlings

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 1ug RNA using the Quick-Amp Labeling kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Seeds of Arabidopsis thaliana ecotype Col-0 were sterilized with sodium hypochlorite solution, and incubated in water in the dark at 4˚C for 4 days. Subsequently, the seeds were sown onto germination medium comprised of MS salt mixture, Gamborg’s vitamin mixture, 1 % (w/v) sucrose and 0.8 % (w/v) agar (pH 5.8) followed by incubation at 22˚C in the dark for 3 days. The 3-day-old seedlings were put into a liquid medium (MS salt mixture and 1 % (w/v) sucrose, pH 5.8) with or without 1 M lasalocid sodium, and then incubated at 22˚C in the dark for 24 h. After the incubation, the samples were harvested and frozen in liquid nitrogen immediately.

extract_protocol: Total RNA was extracted using Plant RNeasy mini kit (Qiagen) and digested with DNase I (Takara bio.).

treatment_protocol: 0 or 1 uM lasalocid sodium

tag: genotype

value: wild type

tag: agent

value: 1 uM lasalocid sodium

tag: ecotype

tag: protocol

value: 4 days old plants grown in dark chamber


title: lasalocid_rep1


title: HepaRG_6h_C23D2B2G4

description: Chemical signature/dose response study

tag: chemical treatment

tag: dose

value: 10 uM

tag: replicate

tag: gender

value: Female


title: control_rep2

description: gene expression in seedlings treated with ０ uM lasalocid sodium


title: HepaRG_6h_C15D2B2G2

description: Chemical signature/dose response study

value: Dihydroxyvitamin 3

value: 10 nM

tag: cell line

value: HepaRG


title: HepaRG_6h_DMSOS21B2G2

description: Chemical signature/dose response study

value: DMSO


title: S021 [ISExCAVR-3+IVM] (633J)

description: Backcross between MHco3(ISE) and MHco10(CAVR). Progeny from the crosses of MHco10(CAVR) with MHco3(ISE) underwent four rounds of back-crossing to MHco3(ISE), with IVM selection, to produce a fourth backcross generation: MHco3/10.BC4. Harvested from sheep treated with IVM at 0.2 mg/Kg seven days prior to euthanasia

value: Mixed sex adult

tag: strain

value: Progeny from the crosses of MHco10(CAVR) with MHco3(ISE) underwent four rounds of back-crossing to MHco3(ISE), with IVM selection, to produce a fourth backcross generation:MHco3/10.BC4. Harvested from sheep treated with IVM at 0.2 mg/Kg seven days prior to euthanasia


title: control_rep1

description: gene expression in seedlings treated with 0 uM lasalocid sodium


title: HepaRG_6h_C14D3B2G2

description: Chemical signature/dose response study

value: Tetrachlorodibenzo p dioxin

value: 1 nM


title: lasalocid_rep3


title: HepaRG_6h_C1D1B2G1

description: Chemical signature/dose response study

value: Bisphenol A


title: control_rep3


title: S020 [ISExCAVR-2+IVM] (2319)

value: Backcross between MHco3(ISE) and MHco10(CAVR)


title: HepaRG_6h_DMSOS23B2G2

description: Chemical signature/dose response study


title: HepaRG_6h_C3D3B2G1

description: Chemical signature/dose response study

value: Ethenyl Estradiol


title: S017 [ISExCAVR-2] (2290)

description: Backcross between MHco3(ISE) and MHco10(CAVR). Progeny from the crosses of MHco10(CAVR) with MHco3(ISE) underwent four rounds of back-crossing to MHco3(ISE), with IVM selection, to produce a fourth backcross generation: MHco3/10.BC4. Harvested from untreated sheep

value: Progeny from the crosses of MHco10(CAVR) with MHco3(ISE) underwent four rounds of back-crossing to MHco3(ISE), with IVM selection, to produce a fourth backcross generation:MHco3/10.BC4. Harvested from untreated sheep


title: S016 [ISExCAVR-1] (2428)


title: S015 WRS-3+IVM (01533)

description: White River Strain (WRS) Haemonchus contortus MHco4 is resistant to IVM and benzimidazole anthelmintics harvested from sheep treated with IVM at 0.2 mg/Kg seven days prior to euthanasia

value: White River Strain (WRS)


title: S018 [ISExCAVR-3] (2270)


title: S013 WRS-1+IVM (01511)

value: resistant to IVM and benzimidazole anthelmintics harvested from sheep treated with IVM at 0.2 mg/Kg seven days prior to euthanasia


title: S019 [ISExCAVR-1+IVM] (2267)


title: HepaRG_6h_C16D1B2G3

description: Chemical signature/dose response study

value: Clobetasol


title: HepaRG_6h_C16D2B2G3

description: Chemical signature/dose response study

value: 10 uM


title: HepaRG_6h_C6D2B2G1

description: Chemical signature/dose response study

value: Dehydrorepiandrosterone

value: 1 uM

value: Female


title: HepaRG_6h_C17D1B2G3

description: Chemical signature/dose response study

value: Farnesol

value: HepaRG


title: HepaRG_6h_C13D2B2G2

description: Chemical signature/dose response study

value: Thyroxine


title: S012 WRS-3 (01578)

description: White River Strain (WRS) Haemonchus contortus MHco4 is resistant to IVM and benzimidazole anthelmintics harvested from untreated sheep

value: Mixed sex adult


title: S010 WRS-1 (01522)

value: resistant to IVM and benzimidazole anthelmintics harvested from untreated sheep


title: S011 WRS-2 (01554)


title: S08 CAVR-2 + IVM (1588)

description: Chiswick Avermectin Resistant (CAVR) Haemonchus contortus MHco10 is highly resistant to IVM but susceptible to benzimidazoles and levamisole harvested from sheep treated with IVM at 0.2 mg/Kg seven days prior to euthanasia

value: Chiswick Avermectin Resistant (CAVR)


title: S09 CAVR-3 + IVM (652J)

value: highly resistant to IVM but susceptible to benzimidazoles and levamisole harvested from sheep treated with IVM at 0.2 mg/Kg seven days prior to euthanasia


title: HepaRG_6h_C18D2B2G3

description: Chemical signature/dose response study

value: Chenodeoxychobe Acid


title: HepaRG_6h_C15D3B2G3

description: Chemical signature/dose response study

value: Dihydroxyvitamin 3


title: HepaRG_6h_DMSOS13B2G1

description: Chemical signature/dose response study

value: DMSO


title: HepaRG_6h_C5D3B2G1

description: Chemical signature/dose response study

value: Clofibrate


title: S014 WRS-2+IVM (01513)

value: White River Strain (WRS)

value: resistant to IVM and benzimidazole anthelmintics harvested from sheep treated with IVM at 0.2 mg/Kg seven days prior to euthanasia


title: HepaRG_6h_C18D1B2G3

description: Chemical signature/dose response study


title: HepaRG_6h_C7D2B1G1

description: Chemical signature/dose response study

value: Troglitazone

value: 10 uM


title: HepaRG_6h_C28D1B1G4

description: Chemical signature/dose response study

value: Phenformin


title: S06 CAVR-3 (1584)

description: Chiswick Avermectin Resistant (CAVR) Haemonchus contortus MHco10 is highly resistant to IVM but susceptible to benzimidazoles and levamisole harvested from untreated sheep


title: HepaRG_6h_C14D2B2G2

description: Chemical signature/dose response study

value: Tetrachlorodibenzo p dioxin

value: 10 nM

value: Female


title: S05 CAVR-2 (1574)

value: highly resistant to IVM but susceptible to benzimidazoles and levamisole harvested from untreated sheep


title: S07 CAVR-1 + IVM (1575)

value: Mixed sex adult


title: S04 CAVR-1 (1539)


title: S03 ISE-3 (1589)

description: Haemonchus contortus MHco3(ISE) susceptible to all broad-spectrum anthelmintics


title: S02 ISE-2 (653J)

value: susceptible to all broad-spectrum anthelmintics


title: S01 ISE-1 (1517)


title: HepaRG_6h_DMSOS22B1G2

description: Chemical signature/dose response study

value: HepaRG


title: HepaRG_6h_DMSOS21B1G2

description: Chemical signature/dose response study


title: dKD MCF10A sample 1

city: Omaha

first: Mayumi

last: Naramura

state: NE

address: 985950 Nebraska Medical Center

department: Eppley Institute

institute: University of Nebraska Medical Center

description: Sample name: KD1_20090326

hyb_protocol: Samples were hybridized with GeneChip Human Genome U133 Plus 2.0 Arrays (Affymetrix) at the UNMC Microarray Core Facility.

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix) at the UNMC Microarray Core Facility.

data_processing: Raw data were processed with the GenePattern (Broad Institute).

label_protocol: Samples were labeled without amplification at the UNMC Microarray Core Facility.

growth_protocol: MCF10A cells were grown in DFCI-1 media

extract_protocol: RNA was isolated using TriReagent (Life Technologies)

treatment_protocol: Cells were harvested under normal growth condition

value: mammary epithelial cell line MCF10A

value: Cbl, Cbl-b shRNA


title: HepaRG_6h_C20D2B1G3

description: Chemical signature/dose response study


title: HepaRG_6h_C25D1B1G4

description: Chemical signature/dose response study

value: Amoxicillin

value: 1 mM


title: HepaRG_6h_C16D2B1G3

description: Chemical signature/dose response study

value: Clobetasol


title: dKD MCF10A sample 2

description: Sample name: KD2_20090326


title: Control MCF10A sample 2

description: Sample name: CTRL2_20090326

value: control


title: Control MCF10A sample 1

description: Sample name: CTRL1_20090326


title: HepaRG_6h_C3D3B1G1

description: Chemical signature/dose response study

value: Ethenyl Estradiol


title: Luminal A Sample152 rep1

status: Public on Mar 24 2016

city: PARIS

first: Fatima

last: Mechta-Grigoriou

address: 26 rue d'Ulm

department: INSERM U830

country: France

institute: Institut Curie

hyb_protocol: See manufacturer protocol.

scan_protocol: See manufacturer protocol.

data_processing: The data were first normalized by using GC-RMA (R version 2.14.1). A linear mixed model using Restricted Maximum Likelihood (REML using name package) was then applied. The model included the different experimental batches and the sample type as fixed effects, and treated technical variation as random effects. No interaction terms were included. This model was used to derive significance for differential expression between different tumor types and for correction of batch and hybridization effects. For further analysis, technical replicates were averaged. We choose to discard probe-sets with noise-level signal from the analysis: specifically, we considered as not expressed and therefore discarded, all the probe-sets with a log2 intensity of less than 4 in 95% or more of tissue samples.

label: Biotin

source_name: Human Luminal A Tumor Sample

label_protocol: After RNA quality and quantity controls, 2 µg of total RNA were amplified and labeled according to the Affymetrix one cycle synthesis target preparation protocol to hybridize Affymetrix U133 plus 2.0 chips, as described by the company.

extract_protocol: Total RNA was extracted and purified from tumor samples by using the Rneasy Mini Kit (Qiagen) and then, the RNA clean up kit (Macherey Nagel) according to the manufacturers’ instructions

tag: diagnosis

value: Breast cancer

tag: tumor subtype

value: Luminal A

tag: batch

tag: hybridation


title: Luminal B Sample153 rep1

source_name: Human Luminal B Tumor Sample

value: Luminal B


title: Luminal A Sample149 rep1


title: HepaRG_6h_C5D2B1G1

description: Chemical signature/dose response study

value: Clofibrate


title: Luminal B Sample147 rep1


title: Luminal A Sample151 rep1


title: Luminal A Sample148 rep1


title: Luminal B Sample154 rep1


title: Luminal B Sample155 rep1


title: Luminal B Sample143 rep1


title: Luminal B Sample146 rep1


title: Luminal B Sample150 rep1


title: Luminal A Sample139 rep1


title: Luminal A Sample141 rep1


title: Luminal A Sample142 rep1


title: Luminal B Sample144 rep1


title: Luminal A Sample137 rep1


title: Luminal A Sample138 rep1


title: Luminal A Sample145 rep1


title: Luminal A Sample140 rep1


title: Luminal B Sample129 rep1


title: Luminal B Sample131 rep1


title: Luminal B Sample128 rep1


title: Luminal A Sample130 rep1


title: Luminal B Sample132 rep1


title: Luminal B Sample136 rep1


title: Luminal A Sample126 rep1


title: Luminal B Sample124 rep1


title: Luminal B Sample135 rep1


title: Luminal A Sample125 rep1


title: Luminal A Sample133 rep1


title: Luminal B Sample110 rep1


title: Luminal A Sample120 rep1


title: Luminal A Sample121 rep1


title: Luminal A Sample134 rep1


title: Luminal B Sample123 rep1


title: Luminal B Sample127 rep1


title: Luminal B Sample115 rep1


title: Luminal B Sample119 rep1


title: Luminal B Sample118 rep1


title: Luminal A Sample116 rep1


title: Luminal A Sample122 rep1


title: Luminal A Sample111 rep1


title: Luminal B Sample113 rep1


title: Luminal A Sample117 rep1


title: Luminal A Sample112 rep1


title: Luminal B Sample114 rep1


title: Luminal B Sample109 rep1


title: Luminal A Sample108 rep1


title: HepaRG_6h_C13D1B2G2

description: Chemical signature/dose response study

value: Thyroxine

value: 1 uM


title: Luminal A Sample107 rep1


title: Luminal A Sample98 rep1


title: Luminal B Sample106 rep1


title: Luminal B Sample100 rep1


title: Luminal B Sample105 rep1


title: Luminal A Sample101 rep1


title: Normal Sample94 rep1

source_name: Human Normal

value: None (normal)


title: Normal Sample92 rep1


title: Luminal B Sample103 rep1


title: Luminal B Sample99 rep1


title: Luminal A Sample104 rep1


title: Normal Sample96 rep1


title: Normal Sample95 rep1


title: Normal Sample91 rep1


title: Luminal B Sample102 rep1


title: Normal Sample89 rep1


title: CellLine Sample82 rep1

source_name: Human CellLine

tag: cell origin

value: Breast carcinoma


title: CellLine Sample80 rep1


title: CellLine Sample85 rep1

value: Breast mammary gland


title: Normal Sample88 rep1


title: CellLine Sample84 rep1


title: CellLine Sample81 rep1


title: Luminal A Sample97 rep1


title: Normal Sample86 rep1


title: Normal Sample90 rep1


title: CellLine Sample79 rep1


title: Normal Sample93 rep1


title: Normal Sample87 rep1


title: CellLine Sample83 rep1

value: Hs 578T


title: CellLine Sample77 rep1


title: CellLine Sample75 rep1


title: Her2 Sample68 rep1

source_name: Human Her2 Tumor Sample


title: Her2 Sample70 rep1


title: Her2 Sample69 rep1


title: CellLine Sample72 rep1


title: Her2 Sample71 rep1


title: Basal Sample63 rep1

source_name: Human Basal Tumor Sample

value: Basal


title: CellLine Sample78 rep1


title: Basal Sample62 rep1


title: CellLine Sample74 rep1


title: CellLine Sample76 rep1


title: Basal Sample67 rep1-2


title: Basal Sample59 rep1


title: Basal Sample61 rep1


title: Basal Sample65 rep1


title: Basal Sample52 rep1


title: Her2 Sample58 rep1


title: Basal Sample66 rep1


title: Her2 Sample50 rep1


title: Her2 Sample49 rep1


title: Basal Sample64 rep1


title: Basal Sample60 rep1-2


title: Her2 Sample57 rep1


title: Her2 Sample54 rep1


title: Basal Sample55 rep1-2


title: CellLine Sample73 rep1


title: Basal Sample56 rep1


title: Her2 Sample51 rep1-2


title: Basal Sample48 rep1


title: Basal Sample53 rep1


title: Her2 Sample46 rep1


title: Her2 Sample44 rep1


title: Basal Sample37 rep1-2


title: Her2 Sample43 rep1-2


title: Basal Sample41 rep1


title: Her2 Sample40 rep1


title: Her2 Sample39 rep1-2


title: Basal Sample47 rep1


title: Basal Sample35 rep1-2


title: Her2 Sample34 rep1-2


title: Basal Sample45 rep1


title: Basal Sample36 rep1-2


title: Her2 Sample22 rep1


title: Her2 Sample20 rep1


title: Basal Sample23 rep1-2


title: Basal Sample29 rep1-2


title: Her2 Sample33 rep1


title: Her2 Sample24 rep1-2


title: Basal Sample31 rep1


title: Basal Sample19 rep1-2


title: Basal Sample27 rep1


title: Basal Sample28 rep1


title: Basal Sample30 rep1


title: Basal Sample26 rep1


title: Basal Sample32 rep1


title: Basal Sample25 rep1


title: Her2 Sample38 rep1


title: Basal Sample16 rep1-2


title: Her2 Sample21 rep1-2


title: Her2 Sample13 rep1


title: Her2 Sample15 rep1


title: Her2 Sample17 rep1


title: Her2 Sample12 rep1-2


title: Basal Sample18 rep1


title: Basal Sample11 rep1


title: Her2 Sample14 rep1


title: Basal Sample10 rep1-2


title: Basal Sample7 rep1


title: Her2 Sample6 rep1-2


title: Her2 Sample3 rep1


title: Basal Sample4 rep1-2


title: Basal Sample8 rep1-2


title: Basal Sample9 rep1


title: Her2 Sample5 rep1-2


title: Basal Sample1 rep1


title: alveolar macrophage, early-COPD 020

city: New York

first: Yael

last: Strulovici-Barel

state: NY

address: 1300 York Avenue

department: Department of Genetic Medicine

institute: Weill Cornell Medical College

description: alveolar macrophage, early-COPD 020

hyb_protocol: Following fragmentation, 15 microg of cRNA were hybridized for 16 hr at 45C on GeneChip HG-U133 Plus 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.

source_name: alveolar macrophages obtained by bronchoscopy and bronchoalveolar lavage

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 microg total RNA (Expression Analysis Technical Manual, 701022 Rev.2, Affymetrix).

extract_protocol: Trizol extraction and RNAeasy clean-up of total RNA was performed according to the manufacturer's instructions.

tag: Age

tag: Sex

value: M

tag: Ethnic group

value: black

tag: Smoking status

value: early-COPD, 26 pack-years


title: alveolar macrophage, early-COPD 058

description: alveolar macrophage, early-COPD 058

value: early-COPD, 18 pack-years


title: Basal Sample2 rep1-2


title: alveolar macrophage, early-COPD 071

description: alveolar macrophage, early-COPD 071

value: early-COPD, 52 pack-years


title: pfr1 HA Immuniopricitation Replicate 1

city: Calgary

first: Gordon

last: Chua

state: Alberta

address: 2500 University Drive NW

department: Biological Sciences

institute: University of Calgary

description: pfr1HA IP

hyb_protocol: Hybridization was performed according to the manufactruer's instruction (Agilent Technology). Microarray was washed in 6X SSPE/0.005% sodium N-lauroylsarcosine at room temperature for 5 min followed by a second wash in pre-heated 42°C 0.6X SSPE for 2 min.

scan_protocol: Microarrays were scanned on an GenePix 4200A instrument with GenePix 3.0 software

data_processing: The raw data was lowess normalized and the average log2 ratios with the corresponding t-test p values from the dye-swap experiments were obtained using the R Bioconductor Limma package.

molecule: polyA RNA

organism: Schizosaccharomyces pombe

source_name: pfr1 HA IP

label_protocol: 2 ug of mRNA were converted into cDNA using 140 nmol of Oligo-dT(25) anchored primer (Sigma), 20 nmol of aminoallyl dUTP dNTP (Sigma) mixture, and 200 units of SuperScript II reverse transcriptase (Invitrogen). 1 ug of cDNA each from overexpression or deletion strain and empty vector control strain was labeled with Cy3 or Cy5 (GE Healthcare) and were combined for QIAquick purification (QIAGEN).

growth_protocol: S. pombe yeast cells were inoculated in EMM+AU or EMM+AL minimal media with no thiamine or YES+ALU with glucose or glycerol media and cultured for 20-24hr.

extract_protocol: Total RNA was extracted using hot phenol-chloroform method, followed by mRNA isolation using gravity-flow Oligo-dT cellulose beads.

tag: genotype/variation

value: pfr1 HA

tag: antibody

value: anti-HA F-7 antibody; Santa Cruz Biotech.; sc-7392; E0610

source_name: pfr1 HA refrence

value: strain MBY1343 (ura4-D18)

tag: sample type

value: input reference


title: pfr1 deletion glycerol Replicate 1

description: pfr1 del glycerol-rep1

source_name: wild type glycerol

value: wild type

source_name: pfr1 del glycerol

value: strain 972

value: pfr1 del


title: alveolar macrophage, early-COPD 089

description: alveolar macrophage, early-COPD 089

value: early-COPD, 15 pack-years


title: pfr1 deletion Replicate1

description: pfr1 del-rep1

source_name: pfr1 del

source_name: wild type


title: alveolar macrophage, early-COPD 079

description: alveolar macrophage, early-COPD 079

value: hispanic

value: early-COPD, 25 pack-years


title: pfr1 Overexpression Replicate 1

description: pfr1 OE-rep1

source_name: empty vector

value: empty vector

source_name: pfr1 overexpression strain

value: strain JK25 (leu1 - 32)

value: pfr1 overexpression


title: alveolar macrophage, early-COPD 066

description: alveolar macrophage, early-COPD 066

value: F

value: black

value: early-COPD, 60 pack-years


title: alveolar macrophage, early-COPD 018

description: alveolar macrophage, early-COPD 018

value: early-COPD, 30 pack-years


title: pfr1 deletion Replicate2

description: pfr1 del-rep2


title: alveolar macrophage, early-COPD 008

description: alveolar macrophage, early-COPD 008

value: M

value: early-COPD, 70 pack-years


title: alveolar macrophage, early-COPD 102

description: alveolar macrophage, early-COPD 102


title: pfr1 Overexpression Replicate 2

description: pfr1 OE-rep2


title: pfr1 Overexpression Replicate 3

description: pfr1 OE-rep3


title: alveolar macrophage, early-COPD 087

description: alveolar macrophage, early-COPD 087


title: pfr1 deletion glycerol Replicate 2

description: pfr1 del glycerol-rep2


title: pfr1 Overexpression Replicate 4

description: pfr1 OE-rep4


title: alveolar macrophage, early-COPD 076

description: alveolar macrophage, early-COPD 076

value: early-COPD, 62 pack-years


title: SAMPLE8 Poor

hyb_protocol: Following fragmentation, 5.5 ug of cDNA were hybridized for 17 hours at 45°C on Human Gene 1.1ST array plates. GeneChips were washed and stained in the Affymetrix® GeneTitan device.

scan_protocol: GeneChip were scanned by Affymetrix® GeneTitan.

data_processing: The data were analyzed with Partek Genomics Suite version 6.6. Normalization was performed using RMA background correction with pre-background adjustment for GC content. Exons were summarized to genes using average method. Only probes with a log2 intensity greater than 5.6 in at least 10% of all samples were kept for further analysis.

source_name: triple negative breat tumor_poor response

label_protocol: 100ng of total RNA was amplified by the Ambion® WT expression kit (ref 4411974) to generate cDNA sense target. Then products were labeled (biotinylated) using Affymetrix WT terminal labelling kit (ref 901524)

extract_protocol: Qiazol extraction followed Qiagen miRNeasy protocol

treatment_protocol: All patients received epirubicin (75 mg/m2)-cyclophosphamide (750 mg/m2) intravenously every 3 weeks for four cycles followed by docetaxel (100 mg/m2) every 3 weeks for four cycles. We selected only patients with complete therapeutic response.

value: female

tag: tissue

value: Triple Negative Breast tumors

tag: clinical response

value: Poor (absent or minor)


title: SAMPLE10 Poor

tag: gender


title: SAMPLE9 Poor


title: SAMPLE5 Poor


title: SAMPLE6 Good

source_name: triple negative breat tumor_good response

value: Good (major or complete)


title: SAMPLE4 Poor


title: SAMPLE7 Poor


title: SAMPLE3 Poor


title: 7_after

description: Gene expression of patient 7 after neoadjuvant chemotherapy

data_processing: The data were analyzed with Partek Genomics Suite version 6.6. Normalization was performed using RMA bacground correction with pre-background adjustment for GC content.

label_protocol: 100ng of total RNA was amplified by the  Ambion® WT expression kit (ref 4411974) to generate cDNA sense target. Then products were labeled (biotinylated) using  Affymetrix WT terminal labelling kit (ref 901524)

treatment_protocol: All patients received epirubicin (75 mg/m2)–cyclophosphamide (750 mg/m2) intravenously every 3 weeks for four cycles followed by docetaxel (100 mg/m2) every 3 weeks for four cycles. We selected patients for who both biopsy and tumorectomy tissues were available. Surgery (lumpectomy or modified radical mastectomy associated to axillary clearance) was performed 21–45 days after cycle 8, according to initial and post-chemotherapy assessment

value: breast cancer tissue

tag: patient

tag: time point

value: after neoadjuvant chemotherapy


title: SAMPLE1 Poor


title: SAMPLE2 Good


title: 3_after

description: Gene expression of patient 3 after neoadjuvant chemotherapy


title: 7_before

description: Gene expression of patient 7 before neoadjuvant chemotherapy

value: before neoadjuvant chemotherapy


title: 4_before

description: Gene expression of patient 4 before neoadjuvant chemotherapy


title: 6_before

description: Gene expression of patient 6 before neoadjuvant chemotherapy


title: 3_before

description: Gene expression of patient 3 before neoadjuvant chemotherapy


title: 5_before

description: Gene expression of patient 5 before neoadjuvant chemotherapy


title: 5_after

description: Gene expression of patient 5 after neoadjuvant chemotherapy


title: 4_after

description: Gene expression of patient 4 after neoadjuvant chemotherapy


title: 6_after

description: Gene expression of patient 6 after neoadjuvant chemotherapy


title: 1_after

description: Gene expression of patient 1 after neoadjuvant chemotherapy


title: Basal Sample42 rep1

tag: diagnosis

value: Breast cancer

value: Basal


title: 2_before

description: Gene expression of patient 2 before neoadjuvant chemotherapy


title: VEE strain ZGH868

city: Livermore

first: Kevin

last: McLoughlin

state: CA

address: PO Box 808

department: Global Security

institute: Lawrence Livermore National Laboratory

hyb_protocol: DNA samples were prepared for hybridization using the NimbleGen Hybridization Kit LS (Roche). Three µg of labeled DNA was hybridized to each array, incubating for 40-45 hours at 42°C. Arrays were washed using the NimbleGen Wash Buffer Kit (Roche).

scan_protocol: The fluorescent signal on the array was scanned using a 2 µm Roche MS200 fluorescent scanner.

data_processing: Array feature intensities were generated using the NimbleScan software available from Roche NimbleGen. We used custom analysis software to call alleles at each locus. The software fits a linear model of strand and allele effects to the logs of the raw intensity values from all probes for the locus, and calls the allele as the one with the largest coefficient in the fitted model.

organism: Venezuelan equine encephalitis virus

source_name: VEE strain ZGH868

label_protocol: Fluorescent labeling of samples was performed using the NimbleGen One-Color DNA Labeling Kit (Roche). One µg VEEV cDNA was added to Cy-3 labeled random primers, followed by isothermal amplification at 37°C using Klenow polymerase.  Labeled DNA was purified via isopropanol precipitation and resuspended in water for microarray hybridization.

extract_protocol: Viral genomic RNA was extracted and purified using the Direct-zol RNA MiniPrep kit (Zymo Research, Irvine, CA) according to the manufacturer’s instructions. cDNA was synthesized from extracted RNA via reverse transcription using SuperScript III. Random hexamers and oligo dT primers were used for priming.

tag: strain

value: VEE strain ZGH868


title: VEE strain ZGH734

source_name: VEE strain ZGH734

value: VEE strain ZGH734


title: 1_before

description: Gene expression of patient 1 before neoadjuvant chemotherapy


title: 2_after

description: Gene expression of patient 2 after neoadjuvant chemotherapy


title: VEE strain ZPC10

source_name: VEE strain ZPC10

value: VEE strain ZPC10


title: VEE strain V198

source_name: VEE strain V198

value: VEE strain V198


title: VEE strain ZPC820

source_name: VEE strain ZPC820

value: VEE strain ZPC820


title: VEE strain ZPC727 v2

source_name: VEE strain ZPC727 v2

value: VEE strain ZPC727 v2


title: VEE strain V202

source_name: VEE strain V202

value: VEE strain V202


title: VEE strain PMCHo5

source_name: VEE strain PMCHo5

value: VEE strain PMCHo5


title: VEE strain V-263E

source_name: VEE strain V-263E

value: VEE strain V-263E


title: VEE strain TrD

source_name: VEE strain TrD

value: VEE strain TrD


title: VEE strain SH3

source_name: VEE strain SH3

value: VEE strain SH3


title: VEE strain PHO1275

source_name: VEE strain PHO1275

value: VEE strain PHO1275


title: Mucambo virus strain PE407660

organism: Mucambo virus

source_name: Mucambo virus strain PE407660

value: Mucambo virus strain PE407660


title: VEE strain V178

source_name: VEE strain V178

value: VEE strain V178


title: VEE strain Piura

source_name: VEE strain Piura

value: VEE strain Piura


title: Brain tissue extract from mouse infected with VEE strain TC83 - replicate 3

source_name: VEE strain TC83

value: VEE strain TC83

tag: host organism

value: mus musculus

tag: host tissue

value: brain


title: VEE strain P676Ag

source_name: VEE strain P676Ag

value: VEE strain P676Ag


title: VEE strain Pan34958

source_name: VEE strain Pan34958

value: VEE strain Pan34958


title: VEE strain SH5

source_name: VEE strain SH5

value: VEE strain SH5


title: VEE strain PHO127

source_name: VEE strain PHO127

value: VEE strain PHO127


title: VEE strain R16880

source_name: VEE strain R16880

value: VEE strain R16880


title: Brain tissue extract from mouse infected with VEE strain TC83 - replicate 2


title: Mucambo virus strain PC254

source_name: Mucambo virus strain PC254

value: Mucambo virus strain PC254


title: VEE strain MX10-H91

source_name: VEE strain MX10-H91

value: VEE strain MX10-H91


title: VEE strain MX09-M64

source_name: VEE strain MX09-M64

value: VEE strain MX09-M64


title: VEE strain MX09-Eq03

source_name: VEE strain MX09-Eq03

value: VEE strain MX09-Eq03


title: Brain tissue extract from mouse infected with VEE strain TC83 - replicate 1


title: VEE strain MX08-H50

source_name: VEE strain MX08-H50

value: VEE strain MX08-H50


title: VEE strain MX03-H2

source_name: VEE strain MX03-H2

value: VEE strain MX03-H2


title: VEE strain MAC10

source_name: VEE strain MAC10

value: VEE strain MAC10


title: VEE strain MX03-H1

source_name: VEE strain MX03-H1

value: VEE strain MX03-H1


title: VEE strain MX01-32

source_name: VEE strain MX01-32

value: VEE strain MX01-32


title: VEE strain FSL2314

source_name: VEE strain FSL2314

value: VEE strain FSL2314


title: VEE strain MenaII

source_name: VEE strain MenaII

value: VEE strain MenaII


title: VEE strain CoAn9004

source_name: VEE strain CoAn9004

value: VEE strain CoAn9004


title: VEE strain CoAn5384

source_name: VEE strain CoAn5384

value: VEE strain CoAn5384


title: VEE strain IQT1724

source_name: VEE strain IQT1724

value: VEE strain IQT1724


title: VEE strain GML903843

source_name: VEE strain GML903843

value: VEE strain GML903843


title: VEE strain IC 12.225

source_name: VEE strain IC 12.225

value: VEE strain IC 12.225


title: VEE strain FVB0258

source_name: VEE strain FVB0258

value: VEE strain FVB0258


title: Mucambo virus strain FSL0190

source_name: Mucambo virus strain FSL0190

value: Mucambo virus strain FSL0190


title: Cabassou virus strain CABV AR508

organism: Cabassou virus

source_name: Cabassou virus strain CABV AR508

value: Cabassou virus strain CABV AR508


title: VEE strain FPI3700

source_name: VEE strain FPI3700

value: VEE strain FPI3700


title: VEE strain FSE507

source_name: VEE strain FSE507

value: VEE strain FSE507


title: VEE strain CoAn9145

source_name: VEE strain CoAn9145

value: VEE strain CoAn9145


title: VEE strain INH9813

source_name: VEE strain INH9813

value: VEE strain INH9813


title: VEE strain FSL2649

source_name: VEE strain FSL2649

value: VEE strain FSL2649


title: VEE strain 9813

source_name: VEE strain 9813

value: VEE strain 9813


title: VEE strain 99SMM304-1

source_name: VEE strain 99SMM304-1

value: VEE strain 99SMM304-1


title: VEE strain E541-73

source_name: VEE strain E541-73

value: VEE strain E541-73


title: VEE strain FVB0204

source_name: VEE strain FVB0204

value: VEE strain FVB0204


title: Pixuna virus strain BeAr 35645

organism: Pixuna virus

source_name: Pixuna virus strain BeAr 35645

value: Pixuna virus strain BeAr 35645


title: Mucambo virus strain BeAn8

source_name: Mucambo virus strain BeAn8

value: Mucambo virus strain BeAn8


title: FXS Neurons (47)

city: Jerusalem

first: Nissim

last: Benvenisty

state: Israel

address: Edmond Safra Campus Givat Ram

department: Genetics

country: Israel

institute: Hebrew University

hyb_protocol: GeneChip scanner 3000 7G, GeneChip Operating Software v1.4

scan_protocol: standard affymetrix protocol

data_processing: Affymetrix Expression Console (v. 1.3; RMA)

source_name: neurons differentiated from human iPSCs

label_protocol: Affymetrix protocol, 11 µg cRNA

extract_protocol: 200 ng total RNA, Affymetrix protocol

treatment_protocol: Total RNA was extracted using PerfectPure RNA Cultured Cell Kit (5 PRIME)

value: Male

tag: cell type

value: neural differentiation

value: wild type


title: VEE strain BT2607

source_name: VEE strain BT2607

value: VEE strain BT2607


title: FXS iPS C

source_name: human iPSCs from fibroblasts with FXS

value: induced pluripotent stem cells

value: Fragile X syndrome (FXS)


title: VEE strain 980267

source_name: VEE strain 980267

value: VEE strain 980267


title: WT Neurons (28)

source_name: neurons differentiated from human iPSCs with FXS


title: FXS iPS B


title: VEE strain 980408

source_name: VEE strain 980408

value: VEE strain 980408


title: VEE strain MX08-H53

source_name: VEE strain MX08-H53

value: VEE strain MX08-H53


title: VEE strain 97Co42_1

source_name: VEE strain 97Co42

value: VEE strain 97Co42


title: FXS iPS A


title: VEE strain 980027

source_name: VEE strain 980027

value: VEE strain 980027


title: VEE strain 903104

source_name: VEE strain 903104

value: VEE strain 903104


title: VEE strain 98-007

source_name: VEE strain 98-007

value: VEE strain 98-007


title: WT Neurons


title: VEE strain V209A

source_name: VEE strain V209A

value: VEE strain V209A


title: VEE strain 980019

source_name: VEE strain 980019

value: VEE strain 980019


title: VEE strain 78U202

source_name: VEE strain 78U202

value: VEE strain 78U202


title: VEE strain 92Co59

source_name: VEE strain 92Co59

value: VEE strain 92Co59


title: VEE strain 97Co42_2


title: VEE strain 98-003

source_name: VEE strain 98-003

value: VEE strain 98-003


title: VEE strain 76V2561

source_name: VEE strain 76V2561

value: VEE strain 76V2561


title: VEE strain 75D143

source_name: VEE strain 75D143

value: VEE strain 75D143


title: VEE strain 80U76

source_name: VEE strain 80U76

value: VEE strain 80U76


title: WT iPS (28)

source_name: human iPSCs from fibroblasts

value: Male

value: induced pluripotent stem cells

value: wild type


title: VEE strain 8138_1

source_name: VEE strain 8138

value: VEE strain 8138


title: WT iPS (29)


title: WT Fibs (BJ)

source_name: human fibroblasts

tag: cell line

value: BJ

value: fibroblasts


title: FXS Fibs B

source_name: human fibroblasts with FXS

value: Fragile X syndrome (FXS)


title: VEE strain 72U23

source_name: VEE strain 72U23

value: VEE strain 72U23


title: VEE strain 71U382

source_name: VEE strain 71U382

value: VEE strain 71U382


title: VEE strain 70U74

source_name: VEE strain 70U74

value: VEE strain 70U74


title: VEE strain 73U151

source_name: VEE strain 73U151

value: VEE strain 73U151


title: WT Fibs (FS)

value: FS


title: PHH from Donor 1 (D6), treated with CITCO

city: Stuttgart

first: Ulrich

middle: M.

last: Zanger

address: Auerbachstr. 112

country: Germany

institute: Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology

description: Gene expression data from PHH treated with CITCO

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Human Gene 1.0ST Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip® scanner 7G (Affymetrix).

data_processing: After visual inspection of the obtained GeneChip images, the Affymetrix Expression Console (Affymetrix) was used for quality control of microarrays and pre-processing of expression data  via robust multi-array average (RMA; Gene Level - Default).

source_name: primary human hepatocytes

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

growth_protocol: After the treatment for 24h with the indicated agonists the cells were lysed.

extract_protocol: Total RNA was isolated using Rneasy kit from Qiagen according to the manufacture´s conditions. All (24) used RNA samples had an RNA integrity number (RIN) > 9 (determined with the Bioanalyzer 2100 from Agilent Technologies) to ensure high quality of RNA.

treatment_protocol: Hepatocytes were isolated and seeded at a density of 4x105 viable cells/well onto BioCoat Collagen I Cellware 12-well culture plates in William’s E Medium, supplemented with 10% FBS, 100 U/ml Pen/Strep, 2 mM L-glutamine,32 mU/ml human insulin, 1 mM sodium pyruvate, 1 x nonessential amino acids, 15 mM HEPES, and 0.8 µg/ml hydrocortisone. After 24 h fully attached cells were adapted for another 12 h to William’s E Medium, supplemented with 10% FBS, 100 U/ml Pen/Strep, 2 mM L-glutamine,32 mU/ml human insulin, 0.1  µM dexamethasone and 0.1% DMSO. Cells were treated for 24 hours in fresh medium with 1µM CITCO, 10 µM rifampicin, 50 µM WY14,643 or vehicle  (0.1% dimethylsulfoxide (DMSO).

value: female

tag: age


title: PHH from Donor 1 (D5), treated with CITCO

value: male


title: PHH from Donor 1 (D6), treated with DMSO

description: Gene expression data from PHH treated with DMSO


title: VEE strain 70U1134

source_name: VEE strain 70U1134

value: VEE strain 70U1134


title: VEE strain 71U384

source_name: VEE strain 71U384

value: VEE strain 71U384


title: VEE strain 8138_2


title: PHH from Donor 1 (D6), treated with Rifampicin

description: Gene expression data from PHH treated with Rifampicin


title: VEE strain 68U217

source_name: VEE strain 68U217

value: VEE strain 68U217


title: VEE strain 68U200

source_name: VEE strain 68U200

value: VEE strain 68U200


title: FXS Fibs A

value: Male


title: VEE strain 68U315

source_name: VEE strain 68U315

value: VEE strain 68U315


title: VEE strain 69Z1

source_name: VEE strain 69Z1

value: VEE strain 69Z1


title: PHH from Donor 1 (D5), treated with Rifampicin


title: VEE strain 68U201

source_name: VEE strain 68U201

value: VEE strain 68U201


title: VEE strain 6803

source_name: VEE strain 6803

value: VEE strain 6803


title: PHH from Donor 1 (D5), treated with WY14,643

description: Gene expression data from PHH treated with WY14,643


title: VEE strain Beck Wycoff

source_name: VEE strain Beck Wycoff

value: VEE strain Beck Wycoff


title: PHH from Donor 1 (D4), treated with CITCO


title: PHH from Donor 1 (D4), treated with WY14,643


title: PHH from Donor 1 (D4), treated with Rifampicin


title: HP_day3_rep1_Cy3 [13209954]

city: Huntsville

first: Leland

middle: J.

last: Cseke

state: AL

address: 301 Sparkman Dr.

institute: The University of Alabama Huntsville

description: 954 HP Cy3 Mean (locBGC)

hyb_protocol: All microarray slides were checked using a dissecting microscope for uniformity of spots. Slides were prehybridized for 30 min on a slow rotary shaker in 5X SSC, 0.1% SDS, and 1% BSA, and rinsed 20 times in ddH2O.  DNA was denatured by incubating slides in 95°C ddH2O for 1 min, followed by washing in 100% ice-cold ethanol for 15 s.  Slides were dried by centrifugation (4°C, 2500 rpm, 2 min) and stored at 4°C.  Hybridization was performed within 1 h of prehybridization. Targets were resuspended in 55 µl hybridization solution (50% formamide, 5X SSC, 0.1% SDS, and 0.1% BSA) and centrifuged at 14,000 × g for 1 min before denaturation at 45°C for 5-10 min.  Hybridization was performed in Corning hybridization chambers (Corning Inc., Acton, MA) with Lifter slips (Erie Scientific Co., Portsmouth, NH) and incubated in a 43°C water bath in a hybridization oven for 36 h. Slides were rinsed in wash solution I (1X SSC, 0.2% SDS), prewarmed to 45°C, to remove the lifter slips.  Slides were washed once in wash solution I for 15 min at 45°C with gentle agitation, once in wash solution II (0.1X SSC, 0.2% SDS) for 10 min, and twice in wash solution III (0.1X SSC) for 2 min each.  Finally, slides were immersed in ddH2O for 10 seconds, 100% ethanol for 10 seconds, then dried by centrifugation (4°C, 2500 rpm, 2 min) and stored in darkness at room temperature.

scan_protocol: Slides were scanned using a VersArray ChipReader™ scanner (BioRad, Hercules, CA) at 5 µm resolution. Cy3 and Cy5 images were aligned and spots flagged using VersArray Analyzer 5.0 (BioRad, CA).

data_processing:
For the analysis in the associated paper, local background subtraction and exclusion of flagged spots was performed.  Signal intensity was then log(2) transformed and normalized by the LOWESS algorithm with a smoothing parameter of 0.2, using GeneGazer software (Bio-Rad, CA). Spots having intensities below 20 in both channels were excluded.
local background subtraction for each sample and channel are included the sample data table.

organism: Populus maximowiczii x Populus nigra

source_name: Poplar HP cells_day3

label_protocol: RNA (13.5 µg of each sample) was reverse transcribed using a SuperscriptTM Indirect cDNA Labeling System (Invitrogen, Carlsbad, CA), with oligo-dT primers.  cDNA was purified using S.N.A.P. Columns (Invitrogen, Carlsbad, CA) and resuspended in 10 µl Coupling Buffer following the manufacturer’s instructions.  Individual aliquots of Cy3 and Cy5 (RPN 5661, GE Healthcare, Piscataway, NJ) were resuspended in 5 µl DMSO, mixed with 5 µl of the cDNA in Coupling Buffer and incubated at room temperature for 1 h in the dark. The labeled cDNAs were purified using S.N.A.P. purification columns, and the yield and dye incorporation were evaluated using a NanoDrop ND-1000 Spectrophotometer (NanoDrop Technologies, Wilmington, DE). Targets were prepared by combining 40 pmol of each labeled sample in an amber microfuge tube.  This was flash frozen in liquid nitrogen and dried in a vacuum centrifuge before storage at -20°C.

growth_protocol: Liquid cultures of both the HP and control cell lines were maintained on a weekly subculture routine and harvested as described (Page et al., 2012). Over long term, solid cultures (callus) of the two lines were also maintained (on a monthly subculture routine) and used to restart the liquid cultures if they were lost due to contamination etc. All cultures, except the NT (non-transgenic) cells were grown in Murashige and Skoog (1962) medium (solid or liquid) containing 3% sucrose and 0.5 mg.L-1 2,4-D under 12 h light cycle (80-100 μE.m-2.sec-1 at 25±1 C.   • Page, A.F., Minocha, R., and Minocha, S.C. (2012). Living with high putrescine: expression of ornithine and arginine biosynthetic pathway genes in high and low putrescine producing poplar cells Amino Acids 42:295-308.

extract_protocol: The cells from liquid cultures were collected by vacuum filtration on Miracloth, washed quickly with de-ionized water, and weighed. Total RNA was extracted as described by Page and Minocha (2004), and treated with the TURBO DNA-free kit (Ambion Inc, Austin, TX) to remove genomic DNA contamination.    • Page, A.F., and Minocha, S.C. (2004).  Analysis of gene expression in transgenic plants. In: Transgenic Plants: methods and Protocols--Pena, L., ed.: Humana Press. 291-312.

treatment_protocol: The HP and the control cell lines of Populus nigra × maximowiczii used here have been described previously (Bhatnagar et al., 2001; 2002). The former expresses a mODC cDNA while the latter expresses the bacterial GUS gene (that serves as a control); both cell lines also express the neomycin phosphotransferase (NPTII) selectable marker. All transgenes are constitutively expressed under the control of a modified 35S CaMV promoter. This strategy has allowed us to treat both lines identically for maintenance of stocks during their culture history; e.g. growth in the presence of kanamycin.  • Bhatnagar, P., Glasheen, B.M., Bains, S.K., Long, S.L., Minocha, R., Walter, C., and Minocha, S.C. (2001). Transgenic manipulation of the metabolism of polyamines in poplar cells. Plant Physiol. 125:2139-2153.  • Bhatnagar, P., Minocha, R., and Minocha, S.C. (2002). Transgenic manipulation of the metabolism of polyamines in poplar cells: the catabolism of putrescine. Plant Physiol. 128:1455-1469.

value: high putrescine producing (HP) cell line

tag: vector

value: mODC (ornithine decarboxylase transgene)

value: 3 days of growth


title: VEE strain 67U225

source_name: VEE strain 67U225

value: VEE strain 67U225


title: PHH from Donor 1 (D4), treated with DMSO


title: PHH from Donor 1 (D5), treated with DMSO


title: Control_day3_rep1_Cy5 [13209954]

description: 954 cont Cy5 Mean (locBGC)

source_name: Poplar control cells_day3

value: control cell line

value: GUS


title: VEE strain 67U208

source_name: VEE strain 67U208

value: VEE strain 67U208


title: FXS Neurons (52)

source_name: neurons differentiated from human iPSCs with FXS

value: neural differentiation

value: Fragile X syndrome (FXS)


title: PHH from Donor 1 (D3), treated with WY14,643

value: male


title: Control_day3_rep1_Cy3 [13209953]

description: 953 cont Cy3 Mean (locBGC)


title: VEE strain 67U222

source_name: VEE strain 67U222

value: VEE strain 67U222


title: PHH from Donor 1 (D3), treated with CITCO

value: female


title: HP_day3_rep1_Cy5 [13209953]

description: 953 HP Cy5 Mean (locBGC)


title: PHH from Donor 1 (D3), treated with Rifampicin


title: HP_day3_rep2_Cy3 [13214391]

description: 391 HP Cy3 Mean (locBGC)


title: PHH from Donor 1 (D2), treated with WY14,643


title: VEE strain 65U206

source_name: VEE strain 65U206

value: VEE strain 65U206


title: VEE strain 6119

source_name: VEE strain 6119

value: VEE strain 6119


title: VEE strain 67U201

source_name: VEE strain 67U201

value: VEE strain 67U201


title: VEE strain 63A216

source_name: VEE strain 63A216

value: VEE strain 63A216


title: VEE strain 622-41

source_name: VEE strain 622-41

value: VEE strain 622-41


title: Control_day3_rep2_Cy5 [13214391]

description: 391 cont Cy5 Mean (locBGC)


title: Control_day3_rep2_Cy3 [13214390]

description: 390 cont Cy3 Mean (locBGC)


title: HP_day3_rep3_Cy3 [13214386]

description: 386 HP Cy3 Mean (locBGC)

value: high putrescine producing (HP) cell line


title: VEE strain 485029

source_name: VEE strain 485029

value: VEE strain 485029


title: HP_day3_rep2_Cy5 [13214390]

description: 390 HP Cy5 Mean (locBGC)

value: mODC (ornithine decarboxylase transgene)

value: 3 days of growth


title: PHH from Donor 1 (D1), treated with WY14,643

source_name: primary human hepatocytes


title: PHH from Donor 1 (D2), treated with CITCO


title: PHH from Donor 1 (D2), treated with DMSO


title: VEE strain 484551

source_name: VEE strain 484551

value: VEE strain 484551


title: HP_day3_rep3_Cy5 [13214385]

description: 385 HP Cy5 Mean (locBGC)


title: PHH from Donor 1 (D1), treated with Rifampicin


title: PHH from Donor 1 (D1), treated with CITCO


title: VEE strain 4840

source_name: VEE strain 4840

value: VEE strain 4840


title: PHH from Donor 1 (D2), treated with Rifampicin


title: Control_day3_rep3_Cy5 [13214386]

description: 386 cont Cy5 Mean (locBGC)

value: control cell line

value: GUS


title: VEE strain 474590_2

source_name: VEE strain 474590

value: VEE strain 474590


title: VEE strain 481460

source_name: VEE strain 481460

value: VEE strain 481460


title: VEE strain 79U13

source_name: VEE strain 79U13

value: VEE strain 79U13


title: VEE strain 474590_1


title: Control_day3_rep3_Cy3 [13214385]

description: 385 cont Cy3 Mean (locBGC)


title: FXS Fibs C

source_name: human fibroblasts with FXS

value: Male

value: fibroblasts

value: Fragile X syndrome (FXS)


title: VEE strain 3880

source_name: VEE strain 3880

value: VEE strain 3880


title: HP_day5_rep3_Cy5 [13214383]

description: 383 HP Cy5 Mean (locBGC)

source_name: Poplar HP cells_day5

value: 5 days of growth


title: VEE strain 980517

source_name: VEE strain 980517

value: VEE strain 980517


title: VEE strain 369680

source_name: VEE strain 369680

value: VEE strain 369680


title: PHH from Donor 1 (D6), treated with WY14,643

value: female


title: Wild_Bern_muscle_week4

city: Davis

first: Heather

last: Knych

state: California

address: 620 W.  Health Sciencse Drive

department: CAHFS

institute: University of California Davis

description: Gene expression data from horse muscle after administartion of escalating doses of clenbuterol drug (0.8 µg/kg, BID x 3 days; 1.6 µg/kg, BID x 3 days; 2.4 µg/kg, BID x 3 days; 3.2 µg/kg, BID for 21 days); week 4 time point.

hyb_protocol: Following fragmentation 10ug of cRNA were hypridized for 16 hr at 45C on Equus caballus Gene 1.0 ST Array [transcript (gene) version] represents the equine gene 1.ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400

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

data_processing: Expression data was normalized, background corrected and summarized using the RMA algorithm implemented in the Affymetrix Expression Console.  Data visualization and filtering was performed in Transcriptome Analysis console version 3.0

organism: Equus caballus

source_name: Horse received escalating doses of clenbuterol drug_collected at week4

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

extract_protocol: Muscle biopsy samples were placed in 600 µl of lysis buffer, contaning 2-β- mercaptoethanol (Qiagen Inc, Valencia, CA).  The tissue sample was then transferred to MagNa Green Beads tubes (Roche Diagnostics, Mannhein, Germany).  Homogenization was performed using a MagNaLyse (Roche Diagnostics, Mannhein, Germany) at 6000 rpm for 30 sec followed by a 1.0 min cool down period.  Homogenization intervals were continued until pieces of muscle were no longer visible (≤3 times).  Total RNA was purified using an miRNeasy Mini kit (RNeasy Mini, Qiagen Inc, Valencia, CA) and following the manufacturer’s instructions. Total RNA integrity was assessed using the Experion Automated Electrophoresis System (Bio-rad, Hercules, CA).  Only RNA samples with RIN ≥ 8 and 260/280 ratios between 1.7 and 2.1 were used (Denisov et al 2008) (Fleige et al 2006)

treatment_protocol: Five of the horses received 0.8 µg/kg clenbuterol PO BID for 30 days and an additional 4 horses received 0.8 µg/kg, BID x 3 days; 1.6 µg/kg, BID x 3 days; 2.4 µg/kg, BID x 3 days; 3.2 µg/kg, BID for 21 days

tag: breed

value: Thoroughbred horse

tag: treated with

value: week 4

value: muscle


title: Control_day5_rep3_Cy5 [13214382]

description: 382 Cont Cy5 Mean (locBGC)

source_name: Poplar control cells_day5

tag: genotype/variation


title: HP_day5_rep2_Cy3 [13210257]

description: 257 HP Cy3Mean (locBGC)

value: high putrescine producing (HP) cell line

value: mODC (ornithine decarboxylase transgene)


title: Control_day5_rep2_Cy5 [13210257]

description: 257 cont Cy5 Mean (locBGC)

value: control cell line

value: GUS


title: VEE strain 369676

source_name: VEE strain 369676

value: VEE strain 369676


title: VEE strain 369678

source_name: VEE strain 369678

value: VEE strain 369678


title: VEE strain 369673

source_name: VEE strain 369673

value: VEE strain 369673


title: Differentiating ES cells sh Ctrl replicate 3

city: La Tronche

first: Sophie

last: Rousseaux

address: Bd de la Chantourne

department: IAB

institute: INSERM-UGA

hyb_protocol: Hybridization, staining and detection of cRNAs on Illumina Mouse WG-6 v2 Expression BeadChips were performed according to the manufacturer’s protocol.

scan_protocol: The Illumina I-Scan system was used to scan Expression BeadChips, according to Illumina recommendations.

data_processing: The data were normalised using quantile normalisation.

source_name: Embryonic Stem Cells

label_protocol: The starting amount of total RNA used for the reactions was 200 nanograms per sample. The Illumina Total Prep RNA Amplification Kit (Applied Biosystems / Ambion, Austin, USA) was used to generate biotinylated, amplified cRNA according to the manufacturer recommendations.

growth_protocol: Generation of stable Atad2 knock-down ESC: Non-targeting or Atad2 targeting oligonucleotides were cloned into the lentiviral vector pLKO.1-puroycin (Addgene) for shRNA expression and packaged. 46C-Atad2-tagged ESCs were transduced with lentiviral particles for 24 hours and further cultured for an additional 5 days in the presence of puromycin (2g/ml) for selection. Stable pooled cells were analyzed for Atad2 depletion by western blot using Ha antibody or by RT-qPCR.

extract_protocol: 0.5-1 μg RNA was reverse transcribed with the SuperScriptTM III First-Strand Synthesis SuperMix (Invitrogen). Total RNA quantification was performed using the Nanodrop ND-1000 spectrophotometer (Thermo Fisher Scientific Incorporation, Waltham, USA). Integrity of the extracted RNAs was assessed with the Bioanalyzer 2100 and the RNA6000 Nano kit (Agilent Technologies Incorporation, Santa Clara, USA). A RNA integrity number (RIN) greater or equal to 7.00 was achieved for all samples.

treatment_protocol: ES cells were cultured for three days in the absence of LIF to induce differentiation.

value: embryonic stem cells

tag: differentiation stage

value: Day3 LIF-

tag: sh treatment

value: Sh control


title: HP_day5_rep3_Cy3 [13214382]

description: 382 HP Cy3 Mean (locBGC)

value: 5 days of growth


title: Differentiating ES cells sh Ctrl replicate 1


title: Differentiating ES cells sh Atad2 replicate 2

value: Sh Atad2


title: VEE strain 335733

source_name: VEE strain 335733

value: VEE strain 335733


title: Control_day5_rep3_Cy3 [13214383]

description: 383 cont Cy3 Mean (locBGC)


title: My_Crafty_Life_muscle_week4

value: escalating doses of clenbuterol drug (0.8 µg/kg, BID x 3 days; 1.6 µg/kg, BID x 3 days; 2.4 µg/kg, BID x 3 days; 3.2 µg/kg, BID for 21 days)

tag: tissue


title: Control_day5_rep2_Cy3 [13210256]

description: 256 cont Cy3 Mean (locBGC)


title: HP_day5_rep2_Cy5 [13210256]

description: 256 HP Cy5 Mean (locBGC)


title: Bull_Roar_muscle_week4

value: Thoroughbred horse


title: Global_Captiva_muscle_week4

value: week 4


title: Differentiating ES cells sh Atad2 replicate 1


title: VEE strain 312714

source_name: VEE strain 312714

value: VEE strain 312714


title: Differentiating ES cells sh Ctrl replicate 2


title: VEE strain 334250

source_name: VEE strain 334250

value: VEE strain 334250


title: Differentiating ES cells sh Atad2 replicate 3


title: HP_day5_rep1_Cy3 [13210255]

description: 255 HP Cy3 Mean (locBGC)

value: high putrescine producing (HP) cell line

value: mODC (ornithine decarboxylase transgene)


title: Wild_Bern_muscle_baseline

description: Gene expression data from horse muscle before administration escalting doses of clenbuterol drug (0.8 µg/kg, BID x 3 days; 1.6 µg/kg, BID x 3 days; 2.4 µg/kg, BID x 3 days; 3.2 µg/kg, BID for 21 days); baseline2 time point

source_name: Horse before receiving escalating doses of clenbuterol drug

value: baseline before receiving escalating doses of clenbuterol drug

value: muscle


title: My_Crafty_Life_muscle_baseline


title: Global_Captiva_muscle_baseline


title: VEE strain 309752

source_name: VEE strain 309752

value: VEE strain 309752


title: Control_day5_rep1_Cy5 [13210255]

description: 255 cont Cy5 Mean (locBGC)

value: control cell line

value: GUS


title: VEE strain 309506

source_name: VEE strain 309506

value: VEE strain 309506


title: Bull_Roar_muscle_baseline


title: Control_day5_rep1_Cy3 [13210254]

description: 254 cont Cy3 Mean (locBGC)


title: Simon_muscle_week2

description: Gene expression data from horse muscle after administration a low dose of clenbuterol drug (0.8 µg/kg orally twice a day for 30 days);week 2 time point.

source_name: Horse received low dose of clenbuterol_collected at week2.

value: week 2


title: Sparrow_muscle_week2

value: low dose of clenbuterol drug (0.8 µg/kg orally twice a day for 30 days)


title: VEE strain 25716

source_name: VEE strain 25716

value: VEE strain 25716


title: VEE strain 63Z1

source_name: VEE strain 63Z1

value: VEE strain 63Z1


title: Boy_muscle_week2


title: VEE strain 25717

source_name: VEE strain 25717

value: VEE strain 25717


title: VEE strain 307537

source_name: VEE strain 307537

value: VEE strain 307537


title: Angel_muscle_week2

value: Thoroughbred horse


title: Sparrow_muscle_baseline

description: Gene expression data from horse muscle before administration of low dose of clenbuterol (0.8 µg/kg orally twice a day for 30 days); baseline1 time point

source_name: Horse before receiving low dose of clenbuterol

value: baseline before receiving low dose of clenbuterol drug


title: VEE strain 254934

source_name: VEE strain 254934

value: VEE strain 254934


title: MBZ_36hE_n3

city: Tsu

first: Yuhei

last: Nishimura

state: Mie

address: 2-174 Edobashi

department: Integrative Pharmacology

institute: Mie University Graduate School of Medicine

description: Gene expression in zebrafish eye treated with 0.3 uM MBZ for 36 h

hyb_protocol: 1500 ng of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 uL containing fragmentation buffer and blocking agent according to the manufacture's protocol. After the fragmentation, 55 uL of hybridization buffer was added to the fragmentation mixture. For each reaction 100 uL was hybridized to an Agilent Zebrafish DNA Oligo Microarray (GPL6457) for 17 hours at 65°C in a rotating hybridization chamber. After the hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1, 1 minute with 37°C GE Wash buffer 2.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565BA) using one color scan setting for 4x44k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software 8.0 (Agilent). The data was normalized using Agi4x44PreProcess package in Bioconductor. Features flagged in gIsSaturated, gIsFeatNonUnifOL, gIsPosAndSignif and gIsWellAboveBG were excluded from further analysis.

organism: Danio rerio

source_name: eye

label_protocol: Three hundred nanograms of total RNA from each eye depot were converted into labeled cRNA using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent).

growth_protocol: Zebrafish were raised at 28.5 ± 0.5°C with a 14 h/10 h light/dark cycle.

extract_protocol: Zebrafish was stored in RNA-later (Applied Biosystems, Foster City, CA, USA).  The eyes of zebrafish were collected by surgical extraction under a microscope. Total RNA was then extracted using an RNeasy Plus Micro Kit (Qiagen, Valencia, CA, USA), qualified by an Agilent Bioanalyzer 2100 (Agilent, Santa Clara, CA, USA) and quantified using a spectrophotometer (NanoDrop ND-100, Wilmington, DE, USA).

treatment_protocol: Zebrafish (AB line) at 48 hpf were treated with 0.3 uM of MBZ or BBC for 12, 24 or 36 hours.

value: eye

value: 84 hpf

tag: treatment

value: 0.3 uM MBZ for 36 h


title: VEE strain 255058

source_name: VEE strain 255058

value: VEE strain 255058


title: MBZ_24hE_n4

description: Gene expression in zebrafish eye treated with 0.3 uM MBZ for 24 h

value: 72 hpf

value: 0.3 uM MBZ for 24 h


title: VEE strain 255010

source_name: VEE strain 255010

value: VEE strain 255010


title: Roxy_muscle_week2

value: muscle


title: VEE strain 249443_1

source_name: VEE strain 249443

value: VEE strain 249443


title: VEE strain 255005

source_name: VEE strain 255005

value: VEE strain 255005


title: PHH from Donor 1 (D3), treated with DMSO

source_name: primary human hepatocytes

tag: gender

value: female


title: MBZ_36hE_n2


title: MBZ_36hE_n4


title: MBZ_36hE_n1


title: VEE strain 249443_2


title: MBZ_24hE_n2


title: VEE strain 251641

source_name: VEE strain 251641

value: VEE strain 251641


title: HP_day5_rep1_Cy5 [13210254]

description: 254 HP Cy5 Mean (locBGC)

source_name: Poplar HP cells_day5

value: high putrescine producing (HP) cell line

value: mODC (ornithine decarboxylase transgene)

tag: time point

value: 5 days of growth


title: Simon_muscle_baseline

value: Thoroughbred horse

value: baseline before receiving low dose of clenbuterol drug


title: Roxy_muscle_baseline


title: Boy_muscle_baseline


title: MBZ_24hE_n1

value: eye


title: VEE strain 66U91

source_name: VEE strain 66U91

value: VEE strain 66U91


title: MBZ_12hE_n4

description: Gene expression in zebrafish eye treated with 0.3 uM MBZ for 12 h

value: 60 hpf

value: 0.3 uM MBZ for 12 h


title: VEE strain 247186

source_name: VEE strain 247186

value: VEE strain 247186


title: VEE strain 247168

source_name: VEE strain 247168

value: VEE strain 247168


title: MBZ_12hE_n3


title: MBZ_12hE_n1


title: VEE strain 243937

source_name: VEE strain 243937

value: VEE strain 243937


title: BBC_24hE_n2

description: Gene expression in zebrafish eye treated with 0.3 uM BBC for 24 h

value: 72 hpf

value: 0.3 uM BBC for 24 h