title: B5/B6

city: Hannover

first: Frank

last: Stahl

address: Callinstr. 3

department: Institut für Technische Chemie

institute: Universität Hannover

description: Gene expression of cells from run 1 to run 6 and a control samples, that consists of a pool of all RNAs from run 1-6, from brewery B was analyzed. Run 2 was used as alignment control.

hyb_protocol: The differently labeled cDNAs (Fluorescein and Biotin) of both samples are hybridized (42°C, overnight) simultaneously in one experiment to the same array according to the slide manufacturer´s recommendations.

scan_protocol: The microarrays were scanned by the Axon 4000B scanner; image intensity data were extracted and analysed with GenePix® Pro 6.0 software.

data_processing: Data from different scans of Dye-swap experiment were extracted by GenePix Pro 6.0 software, normalized by the median of the background intensities and united. An outliertest has been applied in order to find outliers amongst the gene replicats. Subsequently, a t-test (1% and 5% probability of error) has been used in order to find regulated genes.

organism: Saccharomyces pastorianus

source_name: yeast cells harvested by the end of fermentation from brewery B cylindro-conical vessel

label_protocol: The indirect labeling by the tyramide-signal-amplification method was used to increase the Cy3/Cy5 signals of microarray detection. 6 µg of the total RNA were reverse transcribed and thereby the cDNA was labeled with Fluorescein-dCTP/ Biotin-dCTP.

growth_protocol: Beer brewery process, industrial serial repitching

extract_protocol: The isolation of RNA was done by disruption of the cells under liquid nitrogen using mortar and pistil and then the Qiagen RNeasy Midi Kit with some modifications within the manufacturers´ protocol and the Qiagen RNase-Free DNase Set were applied.

treatment_protocol: successive runs varied from 1 to 6

value: HEBRU

tag: run

tag: pool

value: The RNA of 3 corresponding runs was pooled in an equimolar manner.


title: GLBRCE1_ACSH_Exp_rep327_1

status: Public on Jul 18 2014

type: RNA

city: Madison

first: Robert

middle: C

last: Landick

state: WI

address: 1550 Linden Dr

department: Great Lakes Bioenergy Research Center

country: USA

institute: University of Wisconsin - Madison

hyb_protocol: hybridization protocol was conducted according to the manufacturer’s instructions (Roche NimbleGen)

scan_protocol: Hybridized arrays were scanned with a NimbleGen MS 200 microarray scanner, and the probe signal intensities were determined using NimbleScan v 2.6 (Roche NimbleGen).

data_processing: Probe signal intensities were preprocessed using robust multichip averaging (RMA) in the program ArrayStar (DNASTAR), and the resulting gene expression signals were quantile-normalized across all samples using the normalize.quantiles function in the Bioconductor package for R.

molecule: total RNA

organism: Escherichia coli

source_name: GLBRCE1, ACSH, Exp

label_protocol: cDNA labeling protocol was conducted according to the manufacturer’s instructions (Roche NimbleGen)

growth_protocol: Fermentations were carried out in 3 L bioreactors (Applikon Biotechnology) containing 2.45 L of ACSH or SynH media, and cultures were diluted into ACSH or SynH with initial OD at 0.2, grown anaerobically overnight, and then inoculated into bioreactors to a starting OD600 of 0.2

extract_protocol: RNA was obtained from cells pellets by lysozyme treatment and phenol-chloroform extraction, analyzed by agarose gel electrophoresis to confirm integrity, quantified using a Nanodrop spectrophotometer (Thermo Scientific), and stored at -80°C

treatment_protocol: Cells (10 ml) for transcriptomic analysis were collected into tubes containing 1.25 ml ice-cold 5% (vol/vol) unbuffered phenol in ethanol (EP) and pelleted by centrifugation (10,000 g, 4°C, 3 min). To remove residual traces of hydrolysate, cell pellets were twice resuspended in ice-cold GMM plus 0.125 volume of EP, repelleted, then flash frozen in dry ice-ethanol, and stored at -80°C.

tag: strain

tag: medium

value: ACSH

tag: growth phase

value: Exp

tag: biological replicate

tag: technical replicate


title: B6/BK

country: Germany

value: The RNA of all 6 pooled run samples was pooled in an equimolar manner.


title: GLBRCE1_ACSH_Trans_rep320_1

source_name: GLBRCE1, ACSH, Trans

value: Trans


title: GLBRCE1_ACSH_Trans_rep318_2


title: IF001_290_trachea_PBS_d1_2_A

city: Seattle

first: Michael

last: Katze

state: WA

address: Rosen Building 960 Republican St.

department: Microbiology

institute: University of Washington

description: We designed two versions of oligonucleotide microarray using Agilent eArray Web portal (https://earray.chem.agilent.com/earray) to profile both Ensembl annotated transcripts and intergenic transcripts derived from ferret RNA-seq data. In both cases, the longest isoform of each locus was selected for probe design with the ‘Design with 3’ Bias’ checked, and probe length was set to 60nt.  For first version of microarray (design ID: 048471) 36,950 probes were selected to target Ensembl annotated genes and intergenic transcripts uncovered from mRNA-seq data, which was intended to work with conventional experimental protocols using polyA priming for cDNA synthesis. For the second version (design ID: 048472) 64,238 probes were selected to target Ensembl annotated genes, intergenic transcripts uncovered from both mRNA-seq and Total RNA-seq data, which was intended to work with experimental protocols using random priming for cDNA synthesis to capture both polyA and non-polyA transcripts.

hyb_protocol: The Agilent One-Color Microarray-Based Gene Expression Analysis Protocol was followed for hybridization and array washing. Two hundred fifty ng of each RNA sample was hybridized to both Agilent 8X60K (Design ID 048471) and Agilent 4X180K (Design ID 048472) arrays.

scan_protocol: Dry slides were scanned on an Agilent DNA microarray scanner (Model G2505B) using the XDR setting.

data_processing: Raw images were analyzed using the Agilent Feature Extraction software (version 9.5.3.1) and the GE1-v5_95_Feb07 extraction protocol. All arrays were required to pass Agilent QC flags.  The whole ferret expression data was re-processed together using Bioconductor package ‘limma’. The ‘normexp’ method was for background correction, and the ‘quantile’ method was used for normalizing intensities across all arrays. The log2 fold changes were calculated for each infection condition relative to matched mock samples, and used for further analysis.

organism: Mustela putorius furo

source_name: Study#, animal#, trachea, infection, day 1, biological replicate, technical replicate

label_protocol: The Agilent One-Color Microarray-Based Gene Expression Analysis Protocol was followed for the Cy3-cDNA probe preparation, followed by RNeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

extract_protocol: All Trizol lysates were processed simultaneously: they were phase-separated, and RNA was isolated from the aqueous phase (diluted 2 fold with RLT buffer) using Qiagen RNeasy Mini columns and the manufacturer’s recommended protocol (Qiagen Inc., Valencia, CA). RNA quality was assessed on an Agilent 2100 Bioanalyzer using the nanochip format, and only intact RNA was used for microarray analyses.

treatment_protocol: Specific lobes of the lung as well as trachea tissue from each animal were harvested and briefly rinsed in cold (4ºC) PBS. Following the RNALater (Ambion) protocol, tissue was cut into small chunks (<0.5cm in any single dimension) and placed immediately into a 10-20 volumes (w/v) (e.g. 100mg/ml) RNALater. After a 4ºC incubation for overnight, samples were stored at -80ºC until processing. Tissue was removed from RNALater, washed in a small volume of Trizol, homogenized in 10-20 volumes (w/v) Trizol and stored at -80°C until RNA isolation.

tag: tissue

value: trachea

tag: gender

value: Female

tag: age

value: 4-8 month-old

tag: infection

value: PBS


title: BK/B1


title: GLBRCE1_SynH_LT_Stat2_rep327_1

source_name: GLBRCE1, SynH_LT, Stat2


title: GLBRCE1_ACSH_Exp_rep318_1


title: GLBRCE1_SynH_LT_Stat2_rep320_1


title: GLBRCE1_ACSH_Exp_rep320_1


title: GLBRCE1_SynH_LT_Stat2_rep318_1


title: B4/B5


title: B2/B3


title: GLBRCE1_ACSH_Trans_rep318_1


title: GLBRCE1_SynH_LT_Stat1_rep320_1

source_name: GLBRCE1, SynH_LT, Stat1


title: B1/B2


title: B3/B4


title: GLBRCE1_SynH_LT_Trans_rep327_1

source_name: GLBRCE1, SynH_LT, Trans


title: AK/A1

description: Gene expression of cells from run 1 to run 6 and a control samples, that consists of a pool of all RNAs from run 1-6, from brewery A was analyzed. Run 2 was used as alignment control.

source_name: yeast cells harvested by the end of fermentation from brewery A cylindro-conical vessel


title: A6/AK


title: A5/A6


title: GLBRCE1_SynH_LT_Trans_rep320_1


title: A4/A5


title: A3/A4


title: A1/A2


title: GLBRCE1_SynH_LT_Exp_rep320_1

source_name: GLBRCE1, SynH_LT, Exp


title: GLBRCE1_SynH_LT_Stat1_rep327_1


title: GLBRCE1_SynH_LT_Stat1_rep318_1


title: GLBRCE1_SynH_Stat1_rep327_1

source_name: GLBRCE1, SynH, Stat1

value: SynH


title: GLBRCE1_SynH_Stat1_rep320_1


title: GLBRCE1_SynH_Stat2_rep327_1

source_name: GLBRCE1, SynH, Stat2


title: GLBRCE1_SynH_Trans_rep327_1

source_name: GLBRCE1, SynH, Trans


title: A2/A3


title: GLBRCE1_SynH_LT_Exp_rep318_1


title: GLBRCE1_SynH_Stat1_rep318_1


title: GLBRCE1_SynH_Trans_rep320_1


title: GLBRCE1_SynH_Trans_rep318_1


title: GLBRCE1_SynH_LT_Trans_rep318_1


title: GLBRCE1_SynH_LT_Exp_rep327_1


title: GLBRCE1_SynH_Exp_rep318_1

source_name: GLBRCE1, SynH, Exp


title: GLBRCE1_SynH_Exp_rep327_1


title: GLBRCE1_SynH_Exp_rep320_1


title: GLBRCE1_SynH_Exp_rep318_2


title: S18/SP_0_15h_rep1

city: Guangzhou

first: jiao

last: ji

state: Guangdong

address: 651 Dongfeng Road East

department: State Key Laboratory of Oncology in Southern China

country: China

institute: Sun Yat-Sen University Cancer Center

description: sample name: C

hyb_protocol: The Hy3TM-labeled samples were hybridized on the miRCURY LNA microRNA Array, 7th generation REV - hsa, mmu & rno (Exiqon) according to array manual

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 6.0 software (Axon) for grid alignment and data extraction. Replicated miRNAs were averaged and miRNAs that intensities>=50 in all samples were chosen for calculating normalization factor. Expressed data were normalized using the Median normalization. After normalization, differentially expressed miRNAs with statistical significance were identified through Volcano Plot filtering

organism: Homo sapiens

label_protocol: The miRCURY™ Hy3™/Hy5™ Power labeling kit (Exiqon, Vedbaek, Denmark) was used according to the manufacturer’s guideline for miRNA labelling

growth_protocol:
The cells were cultivated in DMEM medium supplemented with 10% fetal bovine serum in a 5% CO2 humidified atmosphere at 37°C.
The S18 cell line was kind gifts from Dr. Chaonan Qian (Sun Yat-sen University Cancer Center, China). All cell lines were passaged less than six month.

extract_protocol: Total RNA was isolated using TRIzol (Invitrogen) and miRNeasy mini kit (QIAGEN) according to manufacturer’s instructions, which efficiently recovered all RNA species, including miRNAs. RNA quality and quantity was measured by using nanodrop spectrophotometer (ND-1000, Nanodrop Technologies) and RNA Integrity was determined by gel electrophoresis.

treatment_protocol: The CNE-2-S-18-SP cells were harvested and resuspended at a concentration of 1 × 106 cells/ml. Hoechst 33342 was then added to a final concentration of 5 μg/ml and incubated for 90 min at 37°C in the dark with interval mixing. After washing twice with PBS, the cells were sorted by flow cytometry analysis (EPICS ALTRA Flow Cytosorter, Beckman Coulter). Then the sorting CNE-2-S-18-SP cells were cultured in 6-well plates with either DMSO or 10μmol/L DC120, and allowed to reach logarithmic growth phase.

tag: cell line

tag: cell type

value: nasopharyngeal carcinoma cells

tag: treated with

value: DMSO for 15hrs


title: S18/SP_10uM_15h_rep1

description: sample name: T

value: 10μmol/L DC120 for 15h


title: control 5 (saline-treated at P7)

city: London

first: Morgan

middle: L

last: Kleiber

state: Ontario

address: Biological and Geological Sciences Building

department: Biology

country: Canada

institute: University of Western Ontario

hyb_protocol: 5.5 ug of single-stranded cDNA was hybridized for 16 hours at 45 degrees C to Mouse GeneChip 1.0 ST arrays.  Liquid handling steps were performed by a GeneChip Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 using Command Console v1.1

data_processing: The data were analyzed with Partek Genomics Suite software v6.6.  Probes  were quantile-normalized using the GeneChip-Robust Multiarray Averaging and log2 transformed. All other settings were left as default.

label: biotin

organism: Mus musculus

source_name: brain, total RNA pooled from 3 saline-treated males

label_protocol: Single-stranded cDNA was synthesized using 200 ng of total RNA using Ambion WE Expression Kit for Affymetrix GeneChip Whole Transcript WT Expression Arrays and labelled using the Affymetrix GeneChip WT Terminal Labeling kit.

growth_protocol: Mice were raised from P0-P7 by their biological mother in standard housing conditions (14/10-hour light/dark cycle, 40-60% humidity,21°C to 24°C temperature).  Mice were sacrificed at postnatal day 7.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions and cleaned using RNeasy Mini kit (QIAGEN).  RNA quality and quantity was analyzed by Agilent 2100 Bioanalyzer and a NanoDrop ND-1000 spectrophotometer.  Equal ug of total brain RNA were pooled from three male mice (from different litters) to minimize expression differences due to litter effects.

treatment_protocol: Mice were injected subcutaneously with 20% ethanol in 0.15M saline (or 0.15M saline alone as a control) at postnatal day 7.  Dosages represented two 2.5 g/kg ethanol doses spaced two hours.  During treatment, the mother was removed from the cage and replaced following the completion of all injections.  To avoid litter effects, mice were sex and weight-matched within litters (ie, control and ethanol-treated mice were parented by the same dam).  At postntatal day 7, mice were sacrificed by CO2 asphyxiation and whole brain tissue were dissected using RNAse-free tools.  Brains were snap-frozen in liquid nitrogen and stored at -80 degrees C until RNA isolation.

tag: treatment

value: control

tag: Sex

value: male (3 pooled)

value: postnatal day 7

value: brain


title: ethanol 2 (ethanol-treated at P7)

source_name: brain, total RNA pooled from 3 ethanol-treated males

value: ethanol


title: ethanol 4 (ethanol-treated at P7)


title: mouse treated, biological rep2

city: Göttingen

first: Holger

middle: M

last: Reichardt

address: Humboldtallee 34

department: Cellular and Molecular Immunology

institute: University of Göttingen Medical School

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on the GeneChip Array Mouse Gene 1.0 ST. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneArray Scanner 3000.

data_processing:
Microarray data were analyzed with Affymetrix GeneChip Command Console Software (Affymetrix). The advanced analysis was done with R (version 2.9) with package limma.
Data preprocessing steps included RMA via usage of the R packages affy and probe summarization via the brainarray-cdf file.

source_name: stomach

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

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

treatment_protocol: Female wildtype Balb/c mice aged 8-12 weeks received dex at a concentration of 50 mg/l for three days via the drining water. Control mice were left untreated. Dex was changed once on day 2.

value: 50 mg/l dex

tag: time

value: 3 days

value: Balb/c


title: mouse treated, biological rep1


title: mouse treated, biological rep3


title: control 3 (saline-treated at P7)


title: control 6 (saline-treated at P7)


title: control 1 (saline-treated at P7)


title: mouse control, biological rep3


title: intestine-shYAP/TAZ

city: Kyoto

first: Masamichi

last: Imajo

address: Yoshidakonoe-cho, Sakyo-ku,

country: Japan

institute: Kyoto University

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hr at 45C on Mouse Gene 1.0 ST Array (Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Hybridized arrays were scanned using an Affymetrix GeneChip Scanner 3000.

data_processing: Images from scanned chips were processed by using the Affymetrix-GeneChip Command Console (AGCC) software. The CEL files created by AGCC were imported into GeneSpring GX 11.5.1 (Agilent Technologies) microarray analysis software. Prior to analysis, gene expression data were filtered to exclude probe sets with signals present at background noise levels.

source_name: The intestinal epithelilum, transfected with plasmids expressing shRNAs for YAP and TAZ.

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol using WT Terminal Labeling and Hybridization Kit.

growth_protocol: Mice transfected with siRNAs or expression plasmids for shRNAs were fed under standard conditions.

extract_protocol: Total RNAs were extracted from isolated mouse intestinal epithelial cells by using RNeasy Mini Kit (QIAGEN).

treatment_protocol: The mouse small intestine was transfected with a control siRNA, siRNAs against YAP/TAZ, or expression plasmids for either a control shRNA or YAP/TAZ shRNAs. After transfection, mice were fed for four days under standard conditions.

value: intestinal epithelium

value: male

value: 8 week-old

value: ICR

value: shYAP/TAZ


title: mouse control, biological rep2


title: intestine-siYAP/TAZ-3

source_name: The intestinal epithelilum, transfected with siRNAs for YAP and TAZ.

value: siYAP/TAZ


title: mouse control, biological rep1


title: intestine-siGFP-1

source_name: The intestinal epithelilum, transfected with an siRNA for GFP.

value: siGFP


title: intestine-siYAP/TAZ-1


title: Irinotecan Resistant to 8uM, Irinotecan 8uM

city: Seoul

first: Hae Yong

last: Yoo

address: 50 Ilwon-Dong, Gangnam-Gu

country: South Korea

institute: Sungkyunkwan University

description: Gene expression data from Irinotecan resistant cell line, Irinotecan 8uM culture

hyb_protocol: Fragmented end-labeled cDNA was  hybridized to the GeneChip® Mouse Gene 1.0 ST arrays for 16 hours at 45 “C and 60 rpm as described in the Gene Chip Whole Transcript (WT) Sense Target Labeling Assay Manual (Affymetrix).

scan_protocol: After hybridization, the chips were stained and washed in a Genechip Fluidics Station 450(Affymetrix) and scanned by using a Genechip Array scanner 3000 7G (Affymetrix).

data_processing: Expression data were generated by Affymetrix Expression Console software version1.1. For the normalization, RMA (Robust Multi-Average) algorithm implemented in Affymetrix Expression Console software was used.

source_name: colorectal cancer cell line LoVo, Irinotecan resistant

label_protocol: 300 ng of total RNA from each sample was converted to double-strand cDNA Using a random hexamer incorporating a T7 promoter, amplified RNA( cRNA) was generated from the double-stranded cDNA template though an IVT( in-vitro transcription) reaction and purified with the Affymetrix sample cleanup module. cDNA was regenerated through a random-primed reverse transcription using a dNTP mix containing dUTP. The cDNA was then fragmented by UDG and APE 1 restriction endonucleases and end-labeled by terminal transferase reaction incorporating a biotinylated dideoxynucleotide.

growth_protocol: LoVo cells were maintained at RPMI 1640 supplemented 10% FBS.

extract_protocol: Total RNA was purified using RNeasy mini kit (Qiagen)

treatment_protocol: Cell lines were cultured in RPMI 1640 supplemented with 10% heat-inactivated fetal bovine serum (Hyclone), penicillin-streptomycin, sodium pyruvate, L-glutamine, at 37℃ in 5 % CO2 and 95% air. Irinotecan drug was treated 24 hours before purification of the total RNA. Irinotecan was purchased from Sigma.

value: LoVo


title: intestine-siYAP/TAZ-2


title: IF001_290_lung_PBS_d1_2_A

source_name: Study#, animal#, lung, infection, day 1, biological replicate, technical replicate

value: lung

value: Female

value: 4-8 month-old

value: PBS


title: intestine-shLacZ

description: control-for-shYAP/TAZ

source_name: The intestinal epithelilum, transfected with a plasmid expressing an shRNA for LacZ.

value: shLacZ


title: IF001_292_trachea_1918_d1_1_A

source_name: Study#, animal#, trachea, infection, day 1, biological replicate, technical replicate

value: trachea


title: IF001_292_trachea_1918_d1_1_B


title: IF001_292_lung_1918_d1_1_B


title: Irinotecan Resistant to 8uM, Irinotecan free

description: Gene expression data from Irinotecan resistant cell line, Irinotecan free culture


title: intestine-siGFP-2


title: intestine-siGFP-3


title: IF001_290_trachea_PBS_d1_2_B


title: IF001_290_lung_PBS_d1_2_B


title: LoVo parental cells

description: Gene expression data from parental LoVo cells

source_name: colorectal cancer cell line LoVo, parental cells


title: IF001_290_trachea_PBS_d1_2_A


title: K-media (JUG 22)

status: Public on Jul 17 2014

city: Montreal

first: Sylvie

last: Rocheleau

state: Quebec

address: 6100 Royalmount Avenue

institute: National Research Council Canada

hyb_protocol: Labeled (Cy3/Cy5) cRNA samples were hybridized to C. elegans whole genome microarrays (Version 2) obtained from Agilent Technologies (Santa Clara, CA).

scan_protocol: Arrays were scanned using the ScanArray Express microarray analysis system (perkin Elmer).

data_processing: The data were extracted from scan images using the ImaGene software (BioDiscovery).  Microarray data were normalized using the Lowess algorithm and Log2 transformed (GeneSpring, Agilent).

organism: Caenorhabditis elegans

source_name: 3-days synchronized adults

label_protocol: Purified total RNA was transcribed to cRNA using the two-color microarray-based gene expression analysis kit from Agilent Technologies (Santa Clara, CA).

growth_protocol: The C. elegans strain N2 (wild type) was kindly obtained from the Richard Roy laboratory (McGill University, Montreal, QC, Canada). The strain was maintained at 20 ± 1°C on nematode growth medium (NGM) plates containing a lawn of Escherichia coli OP50 as a food source. The C. elegans culture was age synchronized by adding a 1% sodium hypochlorite/sodium hydroxide solution to 3-day old adults (Freeman et al. 1998) and by mixing using a syringe equipped with 22G and 25G gauge needles. Lysed adults were then removed by successive rinsing with K-medium and centrifugation at 3000 rpm for 10 min.

extract_protocol: Total RNA was extracted using phenol/chloroform (99%; Ambion, Carlsbad, CA), precipitated in isopropanol (Sigma-Aldrich, St-Louis, MO), and purified using the RNeasy purification kit (Qiagen Sciences, Valencia, CA). RNA quantity and integrity were verified using a NanoDrop 1000 spectrophotometer (Thermo Scientific, Wilmington, DE) and a Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA), respectively.

treatment_protocol: Three-day synchronized cultures were exposed to juglone concentrations of 0.2, 2 or 20 uM for 24 h without extra feeding at 20°C in darkness. C. elegans cultures were then centrifuged at 3000 rpm for 15 min and quickly frozen in TRIzol reagent (Ambion, Carlsbad, CA).

value: K-media

tag: concentration

value: 0 uM


title: K-media (JUG 14)


title: K-media (JUG 19)


title: K-media (JUG 21)


title: K-media (JUG 17)


title: K-media (JUG 18)


title: Juglone 20 (JUG 12)

value: Juglone

value: 20 uM


title: K-media (JUG 24)


title: Juglone 20 (JUG 11)


title: K-media (JUG 23)


title: K-media (JUG 16)


title: K-media (JUG 20)


title: Juglone 20 (JUG 10)


title: Juglone 2 (JUG 05)

value: 2 uM


title: Juglone 2 (JUG 07)


title: Juglone 2 (JUG 08)


title: Juglone 20 (JUG 09)


title: Juglone 2 (JUG 06)


title: Juglone 0.2 (JUG 02)


title: K-media (JUG 15)


title: Rutile Bulk 1 mg/L (R Bulk 08)

data_processing: The data were extracted from scan images using the ImaGene software (BioDiscovery).  Microarray data were normalized using the Lowess algorithm and the ratio were calculated by dividing the treatment (Anatase/Rutile) by the negative control (H2O) and adjusted for dye-swaps (GeneSpring, Agilent).

treatment_protocol: Three-day synchronized cultures were exposed to sub-lethal bulk or nano-TiO2 concentrations of 0.01, 0.1, 1, and 10 mg/L for 24 h without extra feeding at 20°C in darkness. C. elegans cultures were then centrifuged at 3000 rpm for 15 min and quickly frozen in TRIzol reagent (Ambion, Carlsbad, CA).

value: 0 mg/L

value: Rutile Bulk

value: 1 mg/L


title: Rutile Bulk 0.1 mg/L (R Bulk 05)


title: Juglone 0.2 (JUG 04)


title: Juglone 0.2 (JUG 01)


title: Rutile Bulk 1 mg/L (R Bulk 07)


title: K-media (JUG 13)


title: Rutile Bulk 1 mg/L (R Bulk 09)


title: Juglone 0.2 (JUG 03)


title: Rutile Bulk 0.01 mg/L (R Bulk 02)


title: Rutile Bulk 0.01 mg/L (R Bulk 01)


title: Rutile Bulk 0.1 mg/L (R Bulk 04)


title: Rutile Bulk 0.1 mg/L (R Bulk 06)


title: Rutile Bulk 0.01 mg/L (R Bulk 03)


title: Rutile Nano 1 mg/L (R Nano 09)

value: Rutile Nano


title: Rutile Nano 0.1 mg/L (R Nano 04)


title: Anatase Bulk 1 mg/L (A Bulk 09)

value: Anatase Bulk


title: Rutile Nano 1 mg/L (R Nano 08)


title: Rutile Nano 0.01 mg/L (R Nano 02)


title: Rutile Nano 0.01 mg/L (R Nano 03)


title: Anatase Bulk 0.1 mg/L (A Bulk 05)


title: Anatase Bulk 1 mg/L (A Bulk 08)


title: Rutile Nano 0.1 mg/L (R Nano 06)


title: Anatase Bulk 0.01 mg/L (A Bulk 03)


title: Rutile Nano 1 mg/L (R Nano 07)


title: Anatase Nano 1 mg/L (A Nano 08)

value: Anatase Nano


title: Anatase Bulk 0.1 mg/L (A Bulk 06)


title: Anatase Nano 1 mg/L (A Nano 09)


title: Rutile Nano 0.01 mg/L (R Nano 01)


title: Anatase Nano 0.1 mg/L (A Nano 06)


title: Anatase Bulk 1 mg/L (A Bulk 07)


title: Anatase Bulk 0.1 mg/L (A Bulk 04)


title: Anatase Bulk 0.01 mg/L (A Bulk 02)


title: Anatase Nano 1 mg/L (A Nano 07)


title: Anatase Bulk 0.01 mg/L (A Bulk 01)


title: Anatase Nano 0.1 mg/L (A Nano 05)


title: Anatase Nano 0.01 mg/L (A Nano 02)


title: No treatment (H2O 02)


title: Rutile Nano 0.1 mg/L (R Nano 05)


title: No treatment (H2O 01)


title: Anatase Nano 0.1 mg/L (A Nano 04)


title: Anatase Nano 0.01 mg/L (A Nano 01)


title: embryo implant site, biological rep 1 [mouse array]

city: Nashville

first: Bibhash

last: Paria

state: TN

address: 2215 B. Garland Avenue

institute: Vanderbilt

description: Gene expression data from periimplantation hampster uterus

hyb_protocol: EukGE-WS2v4. 6 of 15  A3 wash. Draining    30°C. fluidics station 1

scan_protocol: Pixel size: 3. Filter: 570. Number of scans: 2. Scanner Type: HP

data_processing: The data were analyzed with Partek Genomics Suite 6.6 software using gene expression analysis default analysis settings and RMA (Robust Multi-chip Average) as the normalization method

organism: Mesocricetus auratus

source_name: hamster uterus day 5 of pregnancy

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol. Solution Type: SAPE:  1/3/03   Goat IgG: 2/7/03   Bio Anti-Streptavidin:  2/25/03; Solution Lot: SAPE:  83C1-1   Goat IgG: 22K9071   Bio Anti-Streptavidin:  PO113

growth_protocol: Primary tissues were obtained from pregnant syrian golden hamsters

extract_protocol: Trizol extraction of total RNA was performed per manufacturer's instructions

treatment_protocol: no treatment

value: uterus:embryo implantation site


title: embryo implant site, biological rep 2 [mouse array]


title: Myoblast Short, biological rep1

city: Dallas

first: Kimberly

last: Batten

state: TX

address: 5323 Harry Hines Blvd

department: Cell biology

institute: UT Southwestern Medical Center

description: Whole-transcript expression data from normal human myoblasts with short telomere

hyb_protocol: Arrays were hybridized, washed, and stained using the GeneChip® Hybridization, Wash and Stain Kit following the manufacturer's protocol

scan_protocol: Arrays were scanned on an Affymetrix GCS 3000

data_processing: CEL files were processed using RMA methodology using the oligo package and differential expression determined using limma with p-value correction by eBayes. All analysis was perfomred using R/Bioconductor.

label: DNA Labeling Reagent, Ambion

source_name: normal myoblasts with short (6 kb) telomeres

label_protocol: Target cDNA was generated using the Ambion WT Expression Kit. Fragmentation and labeling of sense cDNA with the Affymetrix GeneChip® WT Terminal Labeling and Controls Kit was performed using the manufacturer's protocols.

growth_protocol: Cells were cultured in 0.1% gelatin coated dishes in Low Co2, using adequate growth media. Dishes were splited when reaching 50% confluency

extract_protocol: Rneasy plus  Kit (Qiagen) of 300k cell pellet

treatment_protocol: Cell were infected with a floxed hTERT casette to provide telomere extension, then excision of the hTERT was planned at different time point and cells were cultured to provide different telomere length at similar PD's  (measured by TRF)

tag: telomere length

value: 6 kb

value: normal human myoblast


title: IF001_292_lung_1918_d1_1_A

value: lung

value: Female

value: 4-8 month-old


title: Anatase Nano 0.01 mg/L (A Nano 03)

tag: strain


title: Myoblast Short, biological rep3


title: embryo implant site, biological rep 3 [mouse array]


title: interimplant site, biological rep 3 [mouse array]


title: Myoblast Short, biological rep2


title: interimplant site, biological rep 2 [mouse array]


title: interimplant site, biological rep 1 [mouse array]


title: Myoblast Long, biological rep3

description: Whole-transcript expression data from normal human myoblasts with long telomere

source_name: normal myoblasts with long (15 kb) telomeres

value: 15 kb


title: Myoblast Long, biological rep1


title: 105 [expression array]

city: Malmö

first: Joao

last: Fadista

address: Jan Waldenströms gata 35

country: Sweden

institute: Lund University Diabetes Centre

description: Gene expression data from human pancreatic islets

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized onto the GeneChip® Human Gene 1.0 ST whole transcript based assay overnight in the GeneChip® Hybridization oven 6400 using standard procedures. The arrays were washed and stained in a GeneChip® Fluidics Station 450.

scan_protocol: Scanning was carried out with the GeneChip® Scanner 3000 and image analysis was performed using GeneChip® Operating Software.

data_processing:
The array data was summarized and normalized with Robust Multi-array Analysis (RMA) method using the oligo package from bioconductor. Batch correction using COMBAT function from SVA package from bioconductor. Annotation using annotate package from bioconductor and hugene10sttranscriptcluster.db annotation data.
The probesets were filtered as following (resulting a subest of 18883 ID_REFs out of a possible 33297): probsets that match uniquely to a gene in the latest hg19 human genome assembly, only probesets (or genes) that are on the autosomes, one probeset at random (if more than one probeset matches a gene) in order to have only 1 probeset to gene.

source_name: pancreatic islets

label_protocol: Briefly, 100-200 ng total RNA was processed as indicated by GeneChip® Expression 3’-Amplification Reagents Onecycle cDNA synthesis kit instructions (Affymetrix Inc, Santa Clara, CA, USA) was used to produce double-stranded cDNA. This was used as a template to generate biotintargeted cRNA following the manufacturer’s specifications.

extract_protocol: Total RNA was isolated with the AllPrep DNA/RNA Mini Kit (Qiagen, Hilden, Germany). RNA quality and concentration were measured using an Agilent 2100 bioanalyzer (Bio-Rad, Hercules, CA, USA) and a Nanodrop ND-1000 (NanoDrop Technologies, Wilmington, DE, USA).

treatment_protocol: The islets were cultured in CMRL 1066 (ICN Biomedicals, Costa Mesa, CA, USA) supplemented with 10 mM/l HEPES, 2 mM/l L-glutamine, 50 µg/ml gentamicin, 0.25 µg/ml Fungizone (GIBCO, BRL, Gaithersburg, MD, USA), 20 µg/ml ciprofloxacin (Bayer Healthcare, Leverkusen, Germany), and 10 mM/l nicotinamide at 37 °C (5% CO2) for 1-9 days prior to RNA preparation.

tag: bmi

value: male

tag: year of birth

value: pancreatic islets


title: 110 [expression array]


title: 107 [expression array]


title: Myoblast Long, biological rep2


title: 106 [expression array]


title: 102 [expression array]


title: 103 [expression array]


title: 101 [expression array]

value: female


title: 108 [expression array]


title: 109 [expression array]


title: 104 [expression array]


title: 100 [expression array]


title: 89 [expression array]


title: 87 [expression array]


title: 82 [expression array]


title: 90 [expression array]


title: 80 [expression array]


title: 86 [expression array]


title: 79 [expression array]


title: 85 [expression array]


title: 91 [expression array]


title: 78 [expression array]


title: 84 [expression array]


title: 88 [expression array]


title: 70 [expression array]


title: 75 [expression array]


title: 77 [expression array]


title: 81 [expression array]


title: 73 [expression array]


title: 71 [expression array]


title: 66 [expression array]


title: 72 [expression array]


title: 65 [expression array]


title: 76 [expression array]


title: 67 [expression array]


title: 64 [expression array]


title: E13-Vip2/Cip2

type: genomic

city: Pullman

middle: K

last: Skinner

address: Abelson 507

department: SBS

institute: WSU

description:
Sample name: 65815205
E13 Vinclozolin (Vip) sample 2 is compared to E13 Control (Cip) sample 2

hyb_protocol: Three different comparative (amplified MeDIP vs. amplified MeDIP) hybridization experiments included in three sub-arrays were performed by Nimblegen.  Each comparative hybridization experiment contained one biological replicate of a germ cell whole genome amplified-MeDIP-DNA sample from each lineage treatment (control or vinclozolin lineages).

scan_protocol: Roche Nimblegen’s Rat DNA Methylation 3x720K CpG Island Plus RefSeq Promoter Array was used, which contains three identical sub-arrays, with 713,670 probes per sub-array, scanning a total of 15,287 promoters (3,880 bp upstream and 970 bp downstream from each transcription start site).

data_processing:
For each comparative hybridization experiment, raw data from both the Cy3 and Cy5 channels were imported into R (R Development Core Team (2010), R: A language for statistical computing, R Foundation for Statistical Computing, Vienna, Austria. ISBN 3-900051-07-0, URL http://www.R-project.org), checked for quality and converted to MA values (M = Cy5-Cy3; A = (Cy5+Cy3)/2). The following normalization procedure was conducted within each array.  Probes were separated into groups by GC content and each group was separately normalized between Cy3 and Cy5 using the loess normalization procedure. Normalization curves were generated specific to each GC group.  The arrays were then normalized across arrays using the A quantile normalization procedure.  Following normalization, each probe within each array was normalized and M values were replaced with the median value of all probe normalized M values across all arrays within a 600 bp window. If the number of probes present in the window was less than 3, no value was assigned to that probe. Each probe’s A values were likewise normalized using the same procedure. Following normalization, each probe’s M value represented the median intensity difference between vinclozolin lineage and control lineage samples within a 600 bp window. Significance was assigned to probe differences between vinclozolin lineage and control lineage samples by calculating the median value of the intensity differences as compared to a normal distribution scaled to the experimental mean and standard deviation of the normalized M. A Z-score and P-value were computed for each probe from that distribution. The statistical analysis was performed in pairs of comparative IP hybridizations between vinclozolin lineage (V) and control lineage (C). V1-C1 and V2-C2 gave 715 sites; V1-C1 and V3-C3 gave 633 sites; V2-C2 and V3-C3 gave 807 sites (multiple sites exist within a specific DMR).  In order to assure the reproducibility of the candidate DMR obtained, only the candidate DMR showing significant changes in all three of the paired comparisons were chosen as having a significant change in DNA methylation between the vinclozolin lineage and control lineage samples. This is a very stringent approach to select for differences, since it only considers those differences found in all paired analyses.
Nimblescan software-generated Cy3/Cy5 expression ratios are presented in the processed data files, but R-code data processing of raw data as described was used as the basis for conlusions in this study.

molecule: genomic DNA

organism: Rattus norvegicus

source_name: MeDIP ChIP DNA from F3 Vinclozolin (Vip) germ cells

label_protocol: Samples from experimental groups were labeled with Cy3 and MeDIP DNA samples from the control groups were labeled with Cy5

growth_protocol: The F0 generation pregnant females were exposed to a vehicle (dimethylsulfoxide DMSO) as control or to vinclozolin, during days 8 to 14 as described in the Methods. The F1 generation offspring were bred to generate the F2 generation and the F2 generation offspring were bred to generate the F3 generation offspring, as previously described.  The timed pregnant F2 generation females were used to isolate the F3 generation control and vinclozolin lineage fetal gonads at the E13 and E16 time points. The F3 generation E13 PGC and E16 prospermatogonia were isolated.

extract_protocol: DNA was isolated using the TrizolTM (Invitrogen) method as per the manufacturer protocol, from the same germ cell TrizolTM preparations that were used for RNA isolations.  Therefore, three independent DNA TrizolTM fractions from germ cells per group were used to obtain three different biological replicates of DNA samples from each of the two treatment groups. Each of these DNA samples were then used for methylated DNA immunoprecipitation (MeDIP).

treatment_protocol: Vinclozolin

value: Sprague-Dawley

tag: generation

value: Vinclozolin (Vip)

value: germ cells

tag: ip antibody

value: anti-5-methylCytidine monoclonal antibody (Diagenode)

source_name: MeDIP ChIP DNA from F3 vehicle dimethylsulfoxide DMSO as control (Cip) germ cells

treatment_protocol: Control

value: control


title: 63 [expression array]

tag: tissue


title: E16-Vip2/Cip1

description:
Sample name: 65815105
E16 Vinclozolin (Vip) sample 2 is compared to E16 Control (Cip) sample 1


title: 60 [expression array]

tag: gender


title: 62 [expression array]

tag: age


title: E13-Vip1/Cip1

description:
Sample name: 65814905
E13 Vinclozolin (Vip) sample 1 is compared to E13 Control (Cip) sample 1


title: E16-Vip2/Cip2

description:
Sample name: 65814705
E16 Vinclozolin (Vip) sample 2 is compared to E16 Control (Cip) sample 2


title: 58 [expression array]


title: 59 [expression array]


title: 57 [expression array]


title: Zebrafish_Control2_Cy5-Trained2_Cy3

city: Wageningen

first: ansa

last: fiaz

address: De Elst 1

country: Netherlands

institute: Wageningen University

description:
US22502677_252643710224_S01_GE2_105_Dec08_1_4
control caudal fins (labeled with Cy5) and trained caudal fins (labeled with Cy3) samples hybridized together on one array
biological replicates

hyb_protocol: Samples were hybridized on two  4x44k Zebrafish Agilent microarray slides  and placed in a hybridization chamber at 10 rpm for maximum 17 hours at 65°C.  After hybridization, slides were washed and mounted.

scan_protocol: Slides were scanned on a Agilent Technologies Scanner G2505C US22502677

data_processing: Data was extracted with Agilent Feature Extraction Software (Version 10.5.1.1) and standard settings were used for background subtraction and normalization.

organism: Danio rerio

source_name: control pooled caudal fins

label_protocol: 100 ng of pooled RNA of caudal fins of control fish was labeled with Cy5 and Cy3 and 100 ng of pooled RNA of caudal fins of trained fish was labeled with Cy3 and C5.  Labeling of total RNA was performed  according to the manufacturer's protocol (Two-color Microarray-based gene expression analysis, version 6.0, low input quick amp labeling, Agilent Technologies, Palo Alto, USA). Subsequently, equal amounts of labeled RNA of the pooled control samples were mixed with equal amounts of labeled RNA of the pooled trained samples including dye-swap (control-Cy3 with trained-Cy5 and control-Cy5 with trained-Cy3 with the following combinations: C2-T2, C3-T3).

extract_protocol: For each sample (C2-C3 and T2-T3),  total RNA was isolated from pooled caudal fins of 15 individual fish with the Qiagen Rneasy kit according to the manufacturer's protocol (Qiagen, Hilden, Germany).

treatment_protocol: Wildtype zebrafish were subjected to swim-training from 5 until 10 dpf (each day in sessions of three hours from 8:30-18:30). Each sampled fish was divided in three parts (head, body and caudal fin) and each part was immediately frozen in liquid nitrogen and stored at -80°C until further use.

value: 10 days post fertilization

value: caudal fins

value: wildtype zebrafish

source_name: trained pooled caudal fins of zebrafish larvae


title: E16-Vip1/Cip1

description:
Sample name: 65815005
E16 Vinclozolin (Vip) sample 1 is compared to E16 Control (Cip) sample 1


title: 54 [expression array]


title: Zebrafish_Control3_Cy5-Trained3_Cy3

description:
US22502677_252643710612_S01_GE2_105_Dec08_1_2
control caudal fins (labeled with Cy5) and trained caudal fins (labeled with Cy3) samples hybridized together on one array
biological replicates


title: Zebrafish_Control3_Cy3-Trained3_Cy5

description:
US22502677_252643710224_S01_GE2_105_Dec08_1_3
control caudal fins (labeled with Cy3) and trained caudal fins (labeled with Cy5) samples hybridized together on one array
biological replicates


title: 55 [expression array]


title: 53 [expression array]


title: Zebrafish_Control2_Cy3-Trained2_Cy5

description:
US22502677_252643710224_S01_GE2_105_Dec08_1_2
control caudal fins (labeled with Cy3) and trained caudal fins (labeled with Cy5) samples hybridized together on one array
biological replicates


title: 56 [expression array]


title: 52 [expression array]


title: 50 [expression array]


title: Zebrafish_Control2_Cy3-Trained2_Cy5_TR

description:
US22502677_252643710612_S01_GE2_105_Dec08_1_3
control caudal fins (labeled with Cy3) and trained caudal fins (labeled with Cy5) samples hybridized together on one array
technical replicate


title: 49 [expression array]


title: E13-Vip2/Cip1

description:
Sample name: 65814805
E13 Vinclozolin (Vip) sample 2 is compared to E13 Control (Cip) sample 1


title: Zebrafish_Control2_Cy5-Trained2_Cy3_TR

description:
US22502677_252643710612_S01_GE2_105_Dec08_1_4
control caudal fins (labeled with Cy5) and trained caudal fins (labeled with Cy3) samples hybridized together on one array
technical replicate


title: 51 [expression array]


title: 48 [expression array]


title: 46 [expression array]


title: 45 [expression array]


title: COE_1.CEL

city: New York

first: Lionel

last: Christiaen

state: NY

address: 1009 Silver Center 100 Washington Square East

institute: NYU

hyb_protocol: Single-stranded cDNA were amplified from 500pg of total RNA using the Ovation® Pico WTA System (NuGen, San Carlos, CA), fragmented, and biotin labeled using Encore™ Biotin Module (NuGen) according to the instructions of the manufacturer. QC for concentration and size of the resulting product was performed using a RNA 6000 Nano LabChip and associated kit (Agilent, Santa Clara, CA). Preparation of the target cDNA and microarray hybridization were performed according to NuGen instructions using GeneChip® Hybridization Control Kit and GeneChip® Hybridization, Wash, and Stain Kit (Affymetrix, Santa Clara, CA). Target cDNA were hybridized to the Ciona intestinalis custom-design Affymetrix GeneChip® (Christiaen et al., 2008) for 16 hours at 45°C in a GeneChip® Hybridization Oven (Affymetrix). Washes and staining were performed in a Genechip Fluidics station using the FS450_001 fluidics protocols for expression arrays and microarrays were finally scanned using a GeneArray Scanner, all from Affymetrix.

data_processing: Raw expression values (.CEL files) for each probe and biological replicate were used, together with previously obtain raw data(Christiaen et al., 2008; Woznica et al., 2012), for normalization and computation of probe set expression estimates using the robust multi-chip analysis (RMA) algorithm (Irizarry et al., 2003). To determine whether we could normalize data from this microarray experiment with a previous one, we performed the following tests: we took the Pearson correlation of expression values for each gene across conditions, which were common to both experiments. To determine the effects of normalizing the experiments together, we normalized each experiment separately, then together, then took the Pearson correlation of each gene's expression value under the separate normalizations with its expression value under the combined normalization. We also identified which genes exhibited significant changes in expression due to changes in normalization, and verified using a training set of validated genes to ensure that normalizing the two data sets together did not adversely affect the signal. LIMMA was used to combine probe-level expression data into estimates of differential expression for probesets, and to compute corresponding p-values (p) using a moderated t-statistic (Smyth, 2004). We used the Benjamini and Hochberg method (BH) to control the false discovery rate. We searched gene models for matches to probe sequences and discarded expression data for those probes mapping to more than one gene model. For Aniseed IDs with multiple probeset matches, we selected a single most representative probeset by using the probeset with the lowest p-value in the COE-COE::WRPW comparison.

organism: Ciona intestinalis

source_name: FACS-purified cell populations_21 hpf

label_protocol: To sort cells from the B7.5 lineage we used samples electroporated with Mesp>GFP and MyoD(905)>Venus, as described(Christiaen et al., 2008). For each of them, between 1000 and 5000 sorted cells were directly collected in the lysis buffer of the RNAqueous®-Micro Kit (Ambion, Carlsbad, CA) and kept on ice for RNA extraction following the instructions of the manufacturer. RNA samples were stored at -80°C before quality control (QC). QC was performed on Agilent Bioanalyzer 2100 with RNA 6000 Pico Chips and associated kit (Agilent, Santa Clara, CA). Only samples with concentration above 100pg/µL and RNA integrity number above 7 were further considered for microarray hybridization.

growth_protocol: Animals were kept in tanks under constant light in order to avoid spawning. Gametes from several animals were separately collected for in vitro cross-fertilization. Zygotes were then dechorionated and electroporated as previously described.

treatment_protocol: Zygotes were then dechorionated and electroporated as previously described (Christiaen et al., 2009a, c).

value: 21 hpf larvae

tag: genotype/variation

value: FoxF>COE

value: TVC-specific misexpression of COE


title: Y96-T1

city: Washington

first: Jeffrey

last: Bethony

state: DC

address: 2300 Eye St. NW.

department: Microbiology, Immunology, and Tropical Medicine

institute: George Washington University

hyb_protocol: Labeled total RNA samples were dried completely by using speed-vac, and then hybrized with probes on array slides, accorkding to the manufacture. The hybridization lasted for 20 hours inside 55'C hybridization oven (Agilent). After hybridization, arrays were washed with Gene Expression Wash Buffer 1 (Agilent) at room temperature, and then wahsed with Wash Buffer 2 (Agilent) at 37'C. The washed array were dried and processed to scanning step immediately.

scan_protocol: Slides was scanned immediated after washing step on Agilent G2565CA Microarray Scanner System. (Scan Area is 61x21.6 mm; Scan resolution is 3um; Color channel is Green; Green PMT is 100%)

data_processing: The feature intensities were transferred to digital data and Log2 transformed by using Feature Extraction (V.10.7) software on default setting. (Protocol is miRNA_107_Sep09, Grid is 031181_D_F_20111226). For data analysis, inter-sample variance was normalized by using 90 percentile normalization strategies on GeneSpringGX 12.0.

source_name: liver. CCA patient

label_protocol: 250ng Total RNA from each FFPE case was labeled with Cyanine 3-pCp by using Agilent miRNA labeling kits according to the manufacturer's instructions. Labeled samples were desalted by using MicroBioSpin 6 Columns (Bio-Rad).

extract_protocol: Total RNA was isolated from FFPE sections using the miRNeasy FFPE kit (Qiagen) according to manufacturer’s protocol. Briefly, 320 µL Deparaffinization Solution (Qiagen) was added followed by brief vortexing, centrifugation and incubation. Buffer PKD was added, samples centrifuged and proteinase K added. Digestion was performed at 56◦C for 15 minutes and 80◦C for 15 minutes in order to partially reverse formaldehyde modification. The lower phase was removed and DNase digestion performed at room temperature for 15 minutes. 500 µL RBC buffer was then added, followed by 100% Ethanol (Acros Chemical) and transferred to the RNeasy MiniElute column. The column was washed twice with RPE, followed by drying and then eluted with 30 µL RNase-free water

treatment_protocol: Formalin Fixed Paraffin Embedded (FFPE) biopsy samples from four cases of histologically proven nasopharyngeal carcinoma.2 x 20 µm slices from each case were prepared for RNA purification.

value: FFPE tissue

tag: sample type

value: Tumor

tag: histology

value: Papillary carcinomas


title: Y96-N1

value: Normal

value: Non-CCA tissue.Papillary carcinomas


title: LC-whole-1.CEL

scan_protocol: ly scanned using a GeneArray Scanner, all from Affymetrix.

source_name: FACS-purified cell populations_control embryos and larvae_midtailbud

extract_protocol: To sort cells from the B7.5 lineage we used samples electroporated with Mesp>GFP and MyoD(905)>Venus, as described(Christiaen et al., 2008). For each of them, between 1000 and 5000 sorted cells were directly collected in the lysis buffer of the RNAqueous®-Micro Kit (Ambion, Carlsbad, CA) and kept on ice for RNA extraction following the instructions of the manufacturer. RNA samples were stored at -80°C before quality control (QC). QC was performed on Agilent Bioanalyzer 2100 with RNA 6000 Pico Chips and associated kit (Agilent, Santa Clara, CA). Only samples with concentration above 100pg/µL and RNA integrity number above 7 were further considered for microarray hybridization.

value: embryos and larvae at midtailbud stage


title: COE_2.CEL


title: 22hpf3.CEL

source_name: FACS-purified cell populations_control embryos and larvae_22 hpf

value: embryos and larvae at 22 hpf


title: LC-whole-3.CEL


title: 44 [expression array]

value: female

value: pancreatic islets


title: Y93-T1


title: Y93-N1


title: 43 [expression array]


title: 4565A

source_name: liver. non-cancer healthy patient with gastric bypass surgery

value: Healthy


title: 42 [expression array]

value: male


title: 22hpf1.CEL

value: control


title: LC-whole-2.CEL


title: 39 [expression array]


title: 22hpf2.CEL


title: 26hpf3.CEL

source_name: FACS-purified cell populations_control embryos and larvae_26 hpf

value: embryos and larvae at 26 hpf


title: 26hpf2.CEL


title: 38 [expression array]


title: 26hpf1.CEL


title: Y89-T


title: 3967A


title: Y89-Nerc

value: Necrotic


title: 20hpf4.CEL

source_name: FACS-purified cell populations_control embryos and larvae_20 hpf

value: embryos and larvae at 20 hpf


title: Y88-T1


title: Y89-N


title: 36 [expression array]


title: 37 [expression array]


title: 20hpf1.CEL


title: 35 [expression array]


title: Y88-N2


title: 20hpf2.CEL


title: 20hpf3.CEL


title: 34 [expression array]


title: 24hpf3.CEL

source_name: FACS-purified cell populations_control embryos and larvae_24 hpf

value: embryos and larvae at 24 hpf


title: Y83-T1


title: 40 [expression array]


title: Y83-N1


title: B83-T1

value: Well-differentiated


title: 24hpf1.CEL


title: 24hpf2.CEL


title: 33 [expression array]


title: 3869A

value: FFPE tissue


title: B83-N1

value: Non-CCA tissue. Well-differentiated


title: 31 [expression array]


title: 3563A


title: B70-N1


title: 3564A


title: B79-N1


title: B70-T1

value: Tumor


title: B79-T1


title: Y62-T1

value: Papillary carcinomas


title: 28hpf1.CEL

source_name: FACS-purified cell populations_control embryos and larvae_28 hpf

value: embryos and larvae at 28 hpf


title: 28hpf3.CEL


title: Y56-T1


title: Y62-N1

value: Normal

value: Non-CCA tissue.Papillary carcinomas


title: 28hpf2.CEL


title: Y56-N1


title: 25 [expression array]

value: female


title: 26 [expression array]

value: pancreatic islets


title: 22 [expression array]


title: B40-T1


title: 16hpf2.CEL

source_name: FACS-purified cell populations_control embryos and larvae_16 hpf

value: embryos and larvae at 16 hpf


title: 20 [expression array]

value: male


title: 24 [expression array]


title: 32 [expression array]


title: 10hpf2.CEL

source_name: FACS-purified cell populations_control embryos and larvae_10 hpf

value: embryos and larvae at 10 hpf

value: control


title: 12hpf1.CEL

source_name: FACS-purified cell populations_control embryos and larvae_12 hpf

value: embryos and larvae at 12 hpf


title: B40-N1


title: 23 [expression array]

source_name: pancreatic islets


title: 12hpf4.CEL


title: 16 [expression array]


title: 16hpf3.CEL


title: LC-MV-2.CEL

value: 21 hpf larvae


title: 16hpf1.CEL


title: 10hpf1.CEL


title: 10hpf3.CEL


title: 12hpf2.CEL


title: 30 [expression array]


title: 10 [expression array]


title: 12 [expression array]


title: 15 [expression array]


title: 12hpf3.CEL


title: LC-MV-3.CEL


title: 10hpf4.CEL


title: 3707A

value: Healthy


title: 21 [expression array]


title: 13 [expression array]


title: LC-MV-1.CEL


title: Y42-T1

value: Well-differentiated


title: B99-N1

value: FFPE tissue


title: 14 [expression array]


title: 19 [expression array]


title: B90-T1


title: LC-LG-3.CEL

description: late gastrula

source_name: FACS-purified cell populations_control embryos and larvae collected every two hours from 8 to 28 hpf


title: 9 [expression array]


title: 3578A


title: B90-N1

value: Non-CCA tissue. Well-differentiated


title: 8 [expression array]


title: 3575A


title: LC-FW-1.CEL


title: LC-LG-1.CEL

description: late gastrula

value: embryos and larvae collected every two hours from 8 to 28 hpf


title: 4 [expression array]


title: LC-FW-2.CEL


title: 7 [expression array]


title: Y70-T1

value: Tumor

value: Moderately-differentiated


title: 3641A


title: Y42-N1

value: Normal


title: Y70-N1


title: B99-T1


title: 2 [expression array]


title: LC-LG-2.CEL

description: late gastrula


title: 3 [expression array]


title: LC-FV-1.CEL


title: LC-FV-3.CEL


title: B91-T1


title: interimplant site, biological rep 2 [human array]

source_name: hamster uterus day 5 of pregnancy


city: Durham

first: Hui

last: Wang

state: NC

address: 380 Research Drive

institute: Duke University

description: gene expression data from CD133-negative D456MG cells infected with vector control

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Human Genome U133 Plus 2.0 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: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.

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

growth_protocol: CD133-negative D456MG cells were cultured in the proper media

extract_protocol: Total RNA was prepared using the mirVanaTM miRNA Isolation Kit (Ambion)

treatment_protocol: CD133-negative D456MG cells were infected with lenti-virus, sorted by GFP marker after 48 hours, and collected

tag: cell line

value: CD133-negative D456MG

tag: tumor stage

value: Glioblastoma Grade IV


title: B91-Nec1

value: Necrotic


title: 3377A


title: interimplant site, biological rep 1 [human array]

description: Gene expression data from periimplantation hampster uterus


title: 14hpf3.CEL

source_name: FACS-purified cell populations_control embryos and larvae_14 hpf

value: embryos and larvae at 14 hpf


title: 1 [expression array]

value: male

value: pancreatic islets


title: LC-FV-2.CEL


title: 14hpf1.CEL

value: control


title: LC-wt-2.CEL

value: FACS-sorted B7.5 lineage at 10hpf

value: wild type


title: 3337A

value: Healthy


title: LC-wt-1.CEL


title: 3356A


title: 14hpf2.CEL


title: 3325A


title: interimplant site, biological rep 3 [human array]


title: Platelet_HPR_rep4

city: Beijing

first: Jing

address: 167 Beilishi Road

department: State Key Laboratory of Cardiovascular Disease

institute: Fuwai Hospital, National Center for Cardiovascular Diseases

description: microRNA expression in platelets

hyb_protocol: Each slide was hybridized with 100ng Cy3-labeled RNA using miRNA Complete Labeling and Hyb Kit in hybridization Oven at 55℃，20rpm for 20 hours according to the manufacturer’s instructions, hybridization section. After hybridization, slides were washed in staining dishes with Gene Expression Wash Buffer Kit.

scan_protocol: Slides were scanned by Agilent Microarray Scanner and Feature Extraction software 10.7 with default settings.

data_processing: Raw data were normalized by Quantile algorithm, Gene Spring Software 11.0.

source_name: Platelet, high platelet reactivity, replicate 4

label_protocol: miRNA molecular in total RNA was labeled by miRNA Complete Labeling and Hyb Kit followed the manufacturer’s instructions, labeling section.

extract_protocol: Leukocyte-depleted platelets were lysed in Lysis/Binding buffer and total platelet RNA was harvested with the mirVana miRNA Isolation Kit (Applied Biosystems, Foster City, CA) according to the manufacturer’s instructions. Total RNA was eluted in 80ul elution solution and stored at -80°C until further processing.

treatment_protocol: Venous blood was drawn into acid citrate dextrose (ACD) tubes (BD Vacutainer) through a 21-gauge needle and centrifuged at 180g for 20min to obtain platelet suspension. Platelets were pelleted at 1000g for 15min and then resuspended in 1ml Beads buffer. For platelets purification, 40ul human CD45 MicroBeads reagent (Miltenyi Biotec, Bergisch Gladbach, Germany) was added and incubated for 45 min at 4°C with gentle mixing. Leukocyte-depleted platelets were collected by depleting CD45-positive cells using magnetic separating unit.

value: blood

tag: cell type

value: Platelet

value: female

tag: age (years)


description: gene expression data from CD133-negative D456MG cells with miR-33a over-expression


title: embryo implant site, biological rep 1 [human array]

value: uterus:embryo implantation site


title: Platelet_HPR_rep3

description: microRNA expression in platelets

source_name: Platelet, high platelet reactivity, replicate 3


title: Platelet_HPR_rep2

description: microRNA expression in platelets

source_name: Platelet, high platelet reactivity, replicate 2


title: embryo implant site, biological rep 2 [human array]


title: Platelet_HPR_rep1

description: microRNA expression in platelets

source_name: Platelet, high platelet reactivity, replicate 1


title: LC-wt-3.CEL

source_name: FACS-purified cell populations_21 hpf


title: LC-EV-3.CEL

source_name: FACS-purified cell populations_mid-tailbud (MTB1)

value: mid-tailbud (MTB1)


title: LC-EV-1.CEL


title: Platelet_LPR_rep3

description: microRNA expression in platelets

source_name: Platelet, low platelet reactivity, replicate 3


title: Platelet_LPR_rep4

description: microRNA expression in platelets

source_name: Platelet, low platelet reactivity, replicate 4


title: Liver, indole-3-carbinol 4

city: Research Triangle Park

last: Wyde

address: 111 T.W. Alexander Drive

institute: National Institute of Environmental Health Sciences

hyb_protocol: Labeled cRNA was fragmented and hybridized to the Affymetrix Rat Genome 230 2.0 Array as described in the Affymetrix GeneChip protocol. Chip hybridization, washing, and staining were performed according to the Affymetrix recommended protocol EukGE-Ws2v5.

scan_protocol: Chips were scanned using an Affymetrix GeneChip Scanner 3000 and the acquired data further processed by the Affymetrix GeneChip Operating Software (GCOS) version 1.2.

data_processing: Normalized expression of probe level data was calculated using the Robust Multiarray Average function (RMA) implemented in Bioconductor's affy-package.

label: Biotin

source_name: Liver, indole-3-carbinol

label_protocol: Total RNA (5 ug) was used to synthesize double strand cDNA using Affymetrix 3' Amplification One Cycle cDNA Synthesis reagents which served as template to synthesize biotin-labeled antisense cRNA using the IVT Labeling Kit.

extract_protocol: Liver tissues were homogenized for 45 seconds in lysis buffer using OmniTip plastic disposable probes.  Samples were then centrifuged, RNA etracted from supernatant using Qiagen RNeasy Midi Kit and RNA QC performed using UV analysis (NanoDrop 1000) and gel electrophoresis (FlashGel RNA cassette system).

treatment_protocol: At collection, tissues were immediately frozen in liquid nitrogen.

value: Harlan Sprague-Dawley

value: Liver

tag: compound

tag: dose

value: 300 mg/kg

tag: time

value: 5 days/week, 13 weeks

tag: vehicle

value: Corn oil

tag: route

value: Gavage

tag: Sex

value: Female


title: LC-FW-3.CEL

value: 21 hpf larvae


title: Liver, indole-3-carbinol 5

tag: strain


title: 08hpf1.CEL

source_name: FACS-purified cell populations_control embryos and larvae_8 hpf

tag: tissue

value: embryos and larvae at 8 hpf

value: control


title: 08hpf2.CEL


title: 08hpf3.CEL


title: Liver, indole-3-carbinol 2


title: Liver, indole-3-carbinol 3


title: 18hpf4.CEL

source_name: FACS-purified cell populations_control embryos and larvae_18 hpf

value: embryos and larvae at 18 hpf


title: Platelet_LPR_rep2

description: microRNA expression in platelets

source_name: Platelet, low platelet reactivity, replicate 2

tag: gender

value: male


title: 18hpf2.CEL


title: Liver, vehicle control 5

source_name: Liver, vehicle control

value: 0 mg/kg


title: 18hpf1.CEL


title: Platelet_LPR_rep1

description: microRNA expression in platelets

source_name: Platelet, low platelet reactivity, replicate 1

value: blood

value: Platelet


title: 18hpf3.CEL


title: Liver, vehicle control 3


title: Liver, vehicle control 4


title: Liver, indole-3-carbinol 1


title: Liver, vehicle control 2


title: 6 [expression array]

source_name: pancreatic islets

tag: age

tag: bmi

tag: year of birth

value: pancreatic islets


title: LC-dnFGFR-3.CEL

tag: genotype/variation

value: Mesp>dnFGFR


title: Liver, vehicle control 1

value: Harlan Sprague-Dawley


title: lacZ_5.CEL

value: control FoxF>NLS::lacZ


title: lacZ_4.CEL


title: lacZ_2.CEL


title: LC-dnFGFR-2.CEL


title: COEWRPW_4.CEL

value: FoxF>COE

value: TVC-specific misexpression of dominant repressor COE::WRPW


title: COEWRPW_3.CEL


title: LC-dnFGFR-1.CEL


title: treated-cy5-untreated-cy3_rep5

first: Liang

last: Zhang

address: Xingnan Road 521

department: Translational Medicine Research Center

institute: Guangdong Women and Children Hospital

hyb_protocol: Microarray hybridization was performed on Agilent SurePrint G3 Human GE 8x60K Microarray Kit (Agilent Technologies, Santa Clara, CA). The arrays were washed consecutively by using Gene Expression Wash Buffer Kit (Agilent Technologies) after hybridization.

scan_protocol: Fluorescence images of the hybridized arrays were generated using the Agilent DNA Microarray Scanner, and the data of obtained images were extracted with Agilent Feature Extraction software.

data_processing: Agilent Feature Extraction Software was used for normalization. Normalization was by LOWESS method, averaging replicate probes.

source_name: Primary RMECs_treated

label_protocol: The derivated cDNA of CoCl2-treated cells labeled with Cy5 and the cDNA of untreated cells labeled with Cy3 were combined. To assess and minimize the effects of dye bias on fluorescent hybridization signals, dye-swap assays were performed.

growth_protocol: Primary RMECs was isolated and maintained in DMEM media complemented with 10% FBS. Specific antibodies against von Willebrand factor (vWF) and CD31 were used to validate expression and localization of endothelial cell markers. Immunocytochemical staining and confocal immunofluorescence microscopy were performed as described in our previous report.

extract_protocol: Total RNA extracted from cultured RMECs was reverse transcribed to cDNA, amplified by using the MessageAmpTM Ⅱ aRNA amplification Kit (life technologies, ) according to the manufacturer’s recommendations.

treatment_protocol: When RMECs grew up to 70-80% confluence, CoCl2 (Sigma, St. Louis, Mo., USA) was added to the media at various concentrations of 100 μM, 150 μM, 200 μM, 250 μM, 300 μM, 350 μM for 12 h, 24 h, 48 h, 72 h, 96 h, respectively. Growth curve was plotted according to MTT date. According to growth curve, we selected 150 μM CoCl2 treatment for 72 h in cultured cells for following microarray assays.  cultured cells without CoCl2 treatment acted as control.

tag: developmental stage

value: fetus (20-28 weeks)

value: eye

value: retinal microvascular endothelial cells (RMECs)

tag: treated condition

source_name: Primary RMECs_control


title: treated-cy5-untreated-cy3_rep3

tag: cell type


title: treated-cy5-untreated-cy3_rep4


title: COEWRPW_1.CEL

value: 21 hpf larvae


title: treated-cy5-untreated-cy3_rep1


title: GC-Vip2/GC-Cip2

description:
Sample name: 62940505
Vinclozolin sample 2 verses control sample 2 (array two) is compared to vinclozolin sample 3 verses control sample 3 (array three)

hyb_protocol: Roche Nimblegen's Rat DNA Methylation 3x720K CpG Island Plus RefSeq Promoter Array was used, which contains three identical sub-arrays, with 713,670 probes per sub-array, scanning a total of 15,287 promoters (3,880 bp upstream and 970 bp downstream from transcription start site). Probe sizes range from 50–75 mer in length with a median probe spacing of 100 bp. Three different comparative (amplified MeDIP vs. amplified MeDIP) hybridizations experiments (3 sub-arrays) were performed, each encompassing DNA samples from 24 animals (3 treatment and 3 control groups).

scan_protocol: Scanning and image acquisition was performed in-house by Nimblegen Inc.

data_processing:
For each comparative hybridization experiment, raw data from both the Cy3 and Cy5 channels were imported into R (R Development Core Team (2010), R: A language for statistical computing, R Foundation for Statistical Computing, Vienna, Austria. ISBN 3-900051-07-0, URL http://www.R-project.org), checked for quality and converted to MA values (M = Cy5−Cy3; A = (Cy5+Cy3)/2). The following normalization procedure was conducted. Within each array, probes were separated into groups by GC content and each group was separately normalized, between Cy3 and Cy5 using the loess normalization procedure. This allowed for GC groups to receive a normalization curve specific to that group. After each array had its CG groups normalized within the array, the arrays were then normalized across arrays using the A quantile normalization procedure.Following normalization each probe within each array was subjected to a smoothing procedure, whereby the probe's normalized M values were replaced with the median value of all probe normalized M values across all arrays within a 600 bp window. If the number of probes present in the window was less than 3, no value was assigned to that probe. Each probe's A values were likewise smoothened using the same procedure. Following normalization and smoothing each probe's M value represents the median intensity difference between vinclozolin generation and control generation of a 600 bp window. Significance was assigned to probe differences between treatment-generation samples and control generation samples by calculating the median value of the intensity differences as compared to a normal distribution scaled to the experimental mean and standard deviation of the normalized M. A Z-score and P-value were computed for each probe from that distribution. The statistical analysis was performed in pairs of comparative IP hybridizations between treatment lineage (T) and control lineage (C). T1-C1 and T2-C2 gave 333 sites; T1-C1 and T3-C3 gave 327 sites; T2-C2 and T3-C3 gave 340 sites. In order to assure the reproducibility of the candidates obtained, only the candidates showing significant changes in all three of the paired comparisons were chosen as having a significant change in DNA methylation between the experimental group and controls. This is a very stringent approach to select for changes, since it only considers those changes repeated in all paired analyses.Clustered Regions of interest were then determined by combining consecutive probes within 600 bases of each other, and based on whether their mean M values were positive or negative, with significance p-values less than 10−5. The statistically significant differential DNA methylated regions were identified and P-value associated with each region presented. Each region of interest was then annotated for gene and CpG content. This list was further reduced to those regions with an average intensity value exceeding 9.5 (log scale) and a CpG density ≥1 CpG/100 bp.
Nimblescan software-generated Cy3/Cy5 expression ratios are presented in the processed data files, but R-code data processing of raw data as described was used as the basis for conlusions in this study.  Value definitions for processed data files: #ClusterID= ID and chrolosomal location for cluster of probes showing a significant difference (p<1.0E-5) between red and green channel hybridization (treated vs. control),  #Chromosome= Chromosome number, #cSTART= Cluster start site,  #cSTOP= Cluster stop site,  #meanM= mean log2 intensity ratio (treated vs. control) across all microarray chips for this treatment/control group,  #meanA= mean log2 hybridization intensity (both red and green channel) across all microarray chips for this treatment/control group,  #minP= p-value for difference between treated and control intensity as calculated by indicated R-code from raw data files. P-value must be p<1.0E-5 or less for inclusion,  #nProbes= number of consecutive probes with p<1.0E-5 included in cluster,  #CG= CG content of cluster,  #CpG= CpG content of cluster, and #CpGdensity= number of CpGs per hundred base pairs.

source_name: MeDIP ChIP DNA from F3 Vinclozolin (Vip) granulosa cells

label_protocol: MeDIP DNA samples from experimental groups were labeled with Cy3 and MeDIP DNA samples from the control groups were labeled with Cy5.

growth_protocol: F0 generation grestrating female rats were exposed to various enviormental compounds during fetal gonadal sex determination. The offspring of the F0 generation were the F1 generation. The F1 generation offspring were bred to other F1 animals of the same treatment group to generate an F2 generation and then F2 generation animals bred similarly to generate the F3 generation animals. No sibling or cousin breedings were performed so as to avoid inbreeding. Note that only the original F0 generation pregnant females were injected with the treatment compounds.

extract_protocol: F3 generation rats from both vinclozolin-treated and control lineages were treated with Pregnant Mare Serum Gonadotropin (Sigma cat, St. Louis, MO)(30 IU PMSG injected IP) at five to six months of age. Two days later animals were sacrificed and ovaries removed. The ovarian bursa and its adherent fat was removed from each ovary and the ovaries processed for granulosa cell collection [104]. The ovaries were suspended in the base medium used for all procedures was Ham's F-12 (Thermo Scientific). Following sequential 30 minute incubations at 37 °C in 6 mM EGTA in F-12 (to decrease Ca2+ - mediated cell adhesion) and then 0.5 M sucrose in F-12 (to increase osmotic pressure within follicles), ovaries were returned to F-12. Granulosa cells were released into the medium from antral follicles using 30-gauge needles and gentle pressure. Oocytes were removed by aspiration under a dissecting microscope. Granulosa cells from each rat were collected into 1.5 mL tubes, allowed to settle for 10 minutes and supernatant removed. 1.0 mL of Trizol™ (Invitrogen) was added to each sample, and then samples were stored at −70° until the time of RNA and DNA isolation. DNA was collected from the same granulosa cell Trizol™ preparations that were used for RNA isolation. The DNA Trizol™ fractions from four animals of the same treatment group were pooled to create three different pooled DNA samples from each of the two treatment groups. These DNA samples were then used for methylated DNA immunoprecipitation (MeDIP). MeDIP was performed as follows: 6 µg of genomic DNA was subjected to series of three 20 pulse sonications at 20% amplitude and the appropriate fragment size (200–1000 bp) was verified through 2% agarose gels; the sonicated genomic DNA was resuspended in 350 µl TE and denatured for 10 min at 95°C and then immediately placed on ice for 5 min; 100 µl of 5× IP buffer (50 mM Na-phosphate pH7, 700 mM NaCl, 0.25% Triton X-100) was added to the sonicated and denatured DNA. An overnight incubation of the DNA was performed with 5 µg of antibody anti-5-methylCytidine monoclonal from Diagenode S.A (Denville, NJ) at 4°C on a rotating platform. Protein A/G beads from Santa Cruz (Santa Cruz, CA) were prewashed on PBS-BSA 0.1% and resuspended in 40 µl 1× IP buffer. Beads were then added to the DNA-antibody complex and incubated 2 h at 4°C on a rotating platform. Beads bound to DNA-antibody complex were washed 3 times with 1 ml 1× IP buffer; washes included incubation for 5 min at 4°C on a rotating platform and then centrifugation at 6000 rpm for 2 min. Beads-DNA-antibody complex were then resuspended in 250 µl digestion buffer (50 mM Tris HCl pH 8, 10 mM EDTA, 0.5% SDS) and 3.5 µl of proteinase K (20 mg/ml) was added to each sample and then incubated overnight at 55°C on a rotating platform. DNA purification was performed first with phenol and then with chloroform:isoamyl alcohol. Two washes were then performed with 70% ethanol, 1 M NaCl and glycogen. MeDIP selected DNA was then resuspended in 30 µl TE buffer. Whole-genome amplification was then performed with the WGA2 kit (Sigma-Aldrich #WGA2) on each MeDIP sample to be used in the microarray comparative hybridization analysis.

value: Sprague-Dawley

tag: generation

tag: treatment

value: Vinclozolin (Vip)

value: granulosa cells

tag: ip antibody

value: anti-5-methylCytidine monoclonal antibody (Diagenode)

source_name: MeDIP ChIP DNA from F3 Control (Cip) Granulosa cells


title: COEWRPW_2.CEL


title: GC-Vip3/GC-Cip3

description:
Sample name: 62940405
Vinclozolin sample 1 verses control sample 1 (array one) is compared vinclozolin sample 3 verses control sample 3 (array three)

value: control


title: untreated-cy5-treated-cy3_rep5


title: treated-cy5-untreated-cy3_rep2


title: untreated-cy5-treated-cy3_rep3


title: lacZ_1.CEL


title: untreated-cy5-treated-cy3_rep4


title: GC-Vip1/GC-Cip1

description:
Sample name: 62940305
Vinclozolin sample 1 verses control sample 1 (array one) is compared vinclozolin sample 2 verses control sample 2 (array two)


title: 5 [expression array]

description: Gene expression data from human pancreatic islets

value: female


title: untreated-cy5-treated-cy3_rep2


title: untreated-cy5-treated-cy3_rep1


title: KBD PBMCs Replicate 97

status: Public on Jul 16 2014

city: Xi'an

first: Xi

address: No.76 Yanta West Road

institute: Xi‘an Jiaotong University Health Science Center

description: Biological replicate 97 of 100. KBD peripheral blood mononuclear cells cells, harvested after several passages.

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential

scan_protocol: The microarray slides were scanned using Gene-Pix 4000B (Axon Instruments Inc., Foster City, California, USA), which used a 532nm laser for Cy3 measurement and a 635nm laser for Cy5 measurement.

data_processing: Sixteen-bit TIFF images produced by the Axon scanner were analyzed using the GenePixPro 3.0 software package (Axon Instruments Inc.). Data were normalized using the Global normalization method.

source_name: KBD PBMCs

label_protocol: 10 µg of total RNA were primed with 2 µl of 100 µM T16N2 DNA primer at 70°C for 10 min, then reversed transcribed at 42°C for 1 h in the presence of 400 U SuperScript II RTase (Invitrogen), and 100 µM each dATP, dTTP, dGTP, with 25 µM dCTP, 25 µM Cy3-labe

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

value: peripheral blood mononuclear cells (PBMCs)

value: Female

tag: Stage

value: Ⅰ


title: KBD PBMCs Replicate 87

description: Biological replicate 87 of 100. KBD peripheral blood mononuclear cells cells, harvested after several passages.

value: Male

value: Ⅱ


title: KBD PBMCs Replicate 91

description: Biological replicate 91 of 100. KBD peripheral blood mononuclear cells cells, harvested after several passages.


title: KBD PBMCs Replicate 90

description: Biological replicate 90 of 100. KBD peripheral blood mononuclear cells cells, harvested after several passages.


title: KBD PBMCs Replicate 92

description: Biological replicate 92 of 100. KBD peripheral blood mononuclear cells cells, harvested after several passages.


title: KBD PBMCs Replicate 88

description: Biological replicate 88 of 100. KBD peripheral blood mononuclear cells cells, harvested after several passages.


title: KBD PBMCs Replicate 94

description: Biological replicate 94 of 100. KBD peripheral blood mononuclear cells cells, harvested after several passages.


title: KBD PBMCs Replicate 93

description: Biological replicate 93 of 100. KBD peripheral blood mononuclear cells cells, harvested after several passages.


title: COE_4.CEL

value: FoxF>COE

value: TVC-specific misexpression of COE


title: KBD PBMCs Replicate 89

description: Biological replicate 89 of 100. KBD peripheral blood mononuclear cells cells, harvested after several passages.


title: KBD PBMCs Replicate 98

description: Biological replicate 98 of 100. KBD peripheral blood mononuclear cells cells, harvested after several passages.


title: KBD PBMCs Replicate 99

description: Biological replicate 99 of 100. KBD peripheral blood mononuclear cells cells, harvested after several passages.


title: KBD PBMCs Replicate 100

description: Biological replicate 100 of 100. KBD peripheral blood mononuclear cells cells, harvested after several passages.


title: KBD PBMCs Replicate 86

description: Biological replicate 86 of 100. KBD peripheral blood mononuclear cells cells, harvested after several passages.


title: genomic DNA of U2Os cells infected with pRS-CK2 vector 5

city: Bruxelles

first: Matthieu

last: Defrance

address: CP614 route de Lennik 808

country: Belgium

institute: Université Libre de Bruxelles

description: osteosarcoma

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation27 Beadchip using standard Illumina protocol.

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

data_processing: GenomeStudio software v2010.2, Methylation module v1.7.0

label: Cy5 and Cy3

source_name: Bone

label_protocol: Standard Illumina protocol

growth_protocol: U2Os cells were maintained in Dubelcco’s modified Eagle’s medium (DMEM, Gibco BRL) supplemented with 10% fetal bovine serum and grown at 37°C under 5% CO2. They are splited three times a week with a 1/4 dilution.

extract_protocol: Genomic DNA was extracted and purified from cells using Qiagen QiaAMP Kit according to standard instructions. The recommended RNase treatment was performed.

treatment_protocol: After retroviral infection, cells were maitained 6 days in presence of 1µg/ml of puromycin


title: KBD PBMCs Replicate 96

description: Biological replicate 96 of 100. KBD peripheral blood mononuclear cells cells, harvested after several passages.


title: genomic DNA of U2Os cells infected with pRS-CK2 vector 6

description: osteosarcoma


title: genomic DNA of U2OS cells infected with pRS empty vector 3

description: osteosarcoma


title: KBD PBMCs Replicate 95

description: Biological replicate 95 of 100. KBD peripheral blood mononuclear cells cells, harvested after several passages.


title: genomic DNA of U2Os cells infected with pRS-CK2 vector 4

description: osteosarcoma


title: COE_3.CEL

source_name: FACS-purified cell populations_21 hpf


title: genomic DNA of U2OS cells infected with pRS empty vector 1

description: osteosarcoma


title: genomic DNA of U2OS cells infected with pRS empty vector 2

description: osteosarcoma


title: KBD PBMCs Replicate 78

description: Biological replicate 78 of 100. KBD peripheral blood mononuclear cells cells, harvested after several passages.


title: KBD PBMCs Replicate 84

description: Biological replicate 84 of 100. KBD peripheral blood mononuclear cells cells, harvested after several passages.


title: KBD PBMCs Replicate 82

description: Biological replicate 82 of 100. KBD peripheral blood mononuclear cells cells, harvested after several passages.


title: KBD PBMCs Replicate 79

description: Biological replicate 79 of 100. KBD peripheral blood mononuclear cells cells, harvested after several passages.


title: KBD PBMCs Replicate 75

description: Biological replicate 75 of 100. KBD peripheral blood mononuclear cells cells, harvested after several passages.


title: KBD PBMCs Replicate 73

description: Biological replicate 73 of 100. KBD peripheral blood mononuclear cells cells, harvested after several passages.


title: KBD PBMCs Replicate 72

description: Biological replicate 72 of 100. KBD peripheral blood mononuclear cells cells, harvested after several passages.


title: KBD PBMCs Replicate 76

description: Biological replicate 76 of 100. KBD peripheral blood mononuclear cells cells, harvested after several passages.


title: KBD PBMCs Replicate 70

description: Biological replicate 70 of 100. KBD peripheral blood mononuclear cells cells, harvested after several passages.


title: KBD PBMCs Replicate 80

description: Biological replicate 80 of 100. KBD peripheral blood mononuclear cells cells, harvested after several passages.


title: KBD PBMCs Replicate 83

description: Biological replicate 83 of 100. KBD peripheral blood mononuclear cells cells, harvested after several passages.


title: KBD PBMCs Replicate 81

description: Biological replicate 81 of 100. KBD peripheral blood mononuclear cells cells, harvested after several passages.


title: KBD PBMCs Replicate 74

description: Biological replicate 74 of 100. KBD peripheral blood mononuclear cells cells, harvested after several passages.


title: KBD PBMCs Replicate 71

description: Biological replicate 71 of 100. KBD peripheral blood mononuclear cells cells, harvested after several passages.


title: KBD PBMCs Replicate 68

description: Biological replicate 68 of 100. KBD peripheral blood mononuclear cells cells, harvested after several passages.


title: KBD PBMCs Replicate 85

description: Biological replicate 85 of 100. KBD peripheral blood mononuclear cells cells, harvested after several passages.


title: KBD PBMCs Replicate 69

description: Biological replicate 69 of 100. KBD peripheral blood mononuclear cells cells, harvested after several passages.


title: embryo implant site, biological rep 3 [human array]

description: Gene expression data from periimplantation hampster uterus

source_name: hamster uterus day 5 of pregnancy

value: uterus:embryo implantation site


title: KBD PBMCs Replicate 67

description: Biological replicate 67 of 100. KBD peripheral blood mononuclear cells cells, harvested after several passages.


title: LC-EV-2.CEL

source_name: FACS-purified cell populations_mid-tailbud (MTB1)

value: mid-tailbud (MTB1)


title: Zebrafish Control Cy5-Trained Cy3

description: control (labeled with Cy5) and trained (labeled with Cy3) samples hybridized together on one array

hyb_protocol: Control-Cy3 with Trained-Cy5 and Control-Cy5 with Trained-Cy3 were hybridized on 4x44k Zebrafish Agilent microarrays  and placed in a hybridization chamber at 10 rpm for maximum 17 hours at 65°C.  After hybridization, slides were washed and mounted.

scan_protocol: Slides were scanned on a  Agilent Scanner 22502677

data_processing: Data was extracted with Agilent Feature Extraction Software (Version 10.5.1.1) and used for background subtraction and normalization.

source_name: control pooled whole zebrafish larvae

label_protocol: Equal amounts RNA (400 ng) of 10 individual fish was pooled (trained/control). Subsequently, 100 ng of pooled RNA (control/trained) was labeled with Cy5 and Cy3. Equal amounts of labeled RNA of the pooled control samples were mixed with the labeled RNA of the trained samples (Control-Cy3 with Trained-Cy5 and Control-Cy5 with Trained-Cy3).  Labeling of total RNA was performed  according to the manufacturer's protocol (Two-color Microarray-based gene expression analysis, version 6.0, low input quick amp labeling, Agilent Technologies, Palo Alto, USA).

extract_protocol: Total RNA from each individual fish was isolated with the Qiagen Rneasy kit according to the manufacturer's protocol (Qiagen, Hilden, Germany)

treatment_protocol: Wildtype zebrafish were subjected to swim-training from 5 until 10 dpf (each day in sessions of three hours from 8:30-18:30). Fish were sampled at 10 dpf, at the end of the day, and frozen in liquid nitrogen and stored at -80°C until further use.

value: 10 days post fertilization

value: whole zebrafish larva

value: wild type zebrafish

tag: genetic background

value: Wageningen wild type X Tubingen wildtype (Zod2)

source_name: trained pooled whole zebrafish larvae

value: swim training


title: Zebrafish Control Cy3-Trained Cy5

description: control (labeled with Cy3) and trained (labeled with Cy5) samples hybridized together on one array


title: KBD PBMCs Replicate 66

description: Biological replicate 66 of 100. KBD peripheral blood mononuclear cells cells, harvested after several passages.


title: KBD PBMCs Replicate 64

description: Biological replicate 64 of 100. KBD peripheral blood mononuclear cells cells, harvested after several passages.


title: KBD PBMCs Replicate 65

description: Biological replicate 65 of 100. KBD peripheral blood mononuclear cells cells, harvested after several passages.


title: KBD PBMCs Replicate 63

description: Biological replicate 63 of 100. KBD peripheral blood mononuclear cells cells, harvested after several passages.


title: KBD PBMCs Replicate 62

description: Biological replicate 62 of 100. KBD peripheral blood mononuclear cells cells, harvested after several passages.


title: KBD PBMCs Replicate 61

description: Biological replicate 61 of 100. KBD peripheral blood mononuclear cells cells, harvested after several passages.


title: KBD PBMCs Replicate 77

description: Biological replicate 77 of 100. KBD peripheral blood mononuclear cells cells, harvested after several passages.


title: KBD PBMCs Replicate 60

description: Biological replicate 60 of 100. KBD peripheral blood mononuclear cells cells, harvested after several passages.


title: KBD PBMCs Replicate 59

description: Biological replicate 59 of 100. KBD peripheral blood mononuclear cells cells, harvested after several passages.


title: KBD PBMCs Replicate 57

description: Biological replicate 57 of 100. KBD peripheral blood mononuclear cells cells, harvested after several passages.


title: KBD PBMCs Replicate 58

description: Biological replicate 58 of 100. KBD peripheral blood mononuclear cells cells, harvested after several passages.


title: KBD PBMCs Replicate 54

description: Biological replicate 54 of 100. KBD peripheral blood mononuclear cells cells, harvested after several passages.


title: KBD PBMCs Replicate 56

description: Biological replicate 56 of 100. KBD peripheral blood mononuclear cells cells, harvested after several passages.


title: KBD PBMCs Replicate 55

description: Biological replicate 55 of 100. KBD peripheral blood mononuclear cells cells, harvested after several passages.


title: KBD PBMCs Replicate 53

description: Biological replicate 53 of 100. KBD peripheral blood mononuclear cells cells, harvested after several passages.


title: KBD PBMCs Replicate 50

description: Biological replicate 50 of 100. KBD peripheral blood mononuclear cells cells, harvested after several passages.


title: KBD PBMCs Replicate 46

description: Biological replicate 46 of 100. KBD peripheral blood mononuclear cells cells, harvested after several passages.


title: KBD PBMCs Replicate 37

description: Biological replicate 37 of 100. KBD peripheral blood mononuclear cells cells, harvested after several passages.


title: KBD PBMCs Replicate 51

description: Biological replicate 51 of 100. KBD peripheral blood mononuclear cells cells, harvested after several passages.


title: KBD PBMCs Replicate 39

description: Biological replicate 39 of 100. KBD peripheral blood mononuclear cells cells, harvested after several passages.


title: KBD PBMCs Replicate 42

description: Biological replicate 42 of 100. KBD peripheral blood mononuclear cells cells, harvested after several passages.


title: KBD PBMCs Replicate 47

description: Biological replicate 47 of 100. KBD peripheral blood mononuclear cells cells, harvested after several passages.


title: KBD PBMCs Replicate 41

description: Biological replicate 41 of 100. KBD peripheral blood mononuclear cells cells, harvested after several passages.


title: KBD PBMCs Replicate 43

description: Biological replicate 43 of 100. KBD peripheral blood mononuclear cells cells, harvested after several passages.


title: KBD PBMCs Replicate 32

description: Biological replicate 32 of 100. KBD peripheral blood mononuclear cells cells, harvested after several passages.


title: KBD PBMCs Replicate 40

description: Biological replicate 40 of 100. KBD peripheral blood mononuclear cells cells, harvested after several passages.


title: KBD PBMCs Replicate 33

description: Biological replicate 33 of 100. KBD peripheral blood mononuclear cells cells, harvested after several passages.


title: KBD PBMCs Replicate 45

description: Biological replicate 45 of 100. KBD peripheral blood mononuclear cells cells, harvested after several passages.


title: KBD PBMCs Replicate 38

description: Biological replicate 38 of 100. KBD peripheral blood mononuclear cells cells, harvested after several passages.


title: KBD PBMCs Replicate 44

description: Biological replicate 44 of 100. KBD peripheral blood mononuclear cells cells, harvested after several passages.


title: KBD PBMCs Replicate 31

description: Biological replicate 31 of 100. KBD peripheral blood mononuclear cells cells, harvested after several passages.


title: KBD PBMCs Replicate 34

description: Biological replicate 34 of 100. KBD peripheral blood mononuclear cells cells, harvested after several passages.


title: KBD PBMCs Replicate 35

description: Biological replicate 35 of 100. KBD peripheral blood mononuclear cells cells, harvested after several passages.


title: KBD PBMCs Replicate 36

description: Biological replicate 36 of 100. KBD peripheral blood mononuclear cells cells, harvested after several passages.


title: KBD PBMCs Replicate 52

description: Biological replicate 52 of 100. KBD peripheral blood mononuclear cells cells, harvested after several passages.


title: KBD PBMCs Replicate 48

description: Biological replicate 48 of 100. KBD peripheral blood mononuclear cells cells, harvested after several passages.


title: KBD PBMCs Replicate 49

description: Biological replicate 49 of 100. KBD peripheral blood mononuclear cells cells, harvested after several passages.


title: KBD PBMCs Replicate 30

description: Biological replicate 30 of 100. KBD peripheral blood mononuclear cells cells, harvested after several passages.


title: KBD PBMCs Replicate 29

description: Biological replicate 29 of 100. KBD peripheral blood mononuclear cells cells, harvested after several passages.


title: KBD PBMCs Replicate 28

description: Biological replicate 28 of 100. KBD peripheral blood mononuclear cells cells, harvested after several passages.


title: KBD PBMCs Replicate 27

description: Biological replicate 27 of 100. KBD peripheral blood mononuclear cells cells, harvested after several passages.


title: KBD PBMCs Replicate 20

description: Biological replicate 20 of 100. KBD peripheral blood mononuclear cells cells, harvested after several passages.


title: KBD PBMCs Replicate 24

description: Biological replicate 24 of 100. KBD peripheral blood mononuclear cells cells, harvested after several passages.


title: KBD PBMCs Replicate 19

description: Biological replicate 19 of 100. KBD peripheral blood mononuclear cells cells, harvested after several passages.


title: KBD PBMCs Replicate 26

description: Biological replicate 26 of 100. KBD peripheral blood mononuclear cells cells, harvested after several passages.


title: KBD PBMCs Replicate 25

description: Biological replicate 25 of 100. KBD peripheral blood mononuclear cells cells, harvested after several passages.


title: KBD PBMCs Replicate 18

description: Biological replicate 18 of 100. KBD peripheral blood mononuclear cells cells, harvested after several passages.


title: KBD PBMCs Replicate 23

description: Biological replicate 23 of 100. KBD peripheral blood mononuclear cells cells, harvested after several passages.


title: KBD PBMCs Replicate 21

description: Biological replicate 21 of 100. KBD peripheral blood mononuclear cells cells, harvested after several passages.


title: KBD PBMCs Replicate 22

description: Biological replicate 22 of 100. KBD peripheral blood mononuclear cells cells, harvested after several passages.


title: Patient 3 NLUM

type: protein

city: Daejeon

first: Myung-Shin

last: Lee

address: Yongdu-dong, Jung-gu

department: Microbiology and Immunology

institute: Eulji University School of Medicine

description: 3pairs of BC/normal mucosa were analyzed by antibody arrary with 656 antibodies

hyb_protocol: Biotin labeled extract was hybridized with antibody-spotted slide for 2hr at room temperature. After hybridization, slide was washed with 1X wash buffer (Fullmoon Bio) and de-ionized water. Detection Buffer including Cy3-Streptavidin (fullmoon Bio) was treated for 20min at room temperature. And slide was washed with 1X wash buffer (Fullmoon Bio) and de-ionized water.

scan_protocol: Scanned on an Axon 4000B scanner.

data_processing: GenePix Software (v 6.1) was used for data extraction and Genowiz software (v 4.0.5.6) was used for global normalization.

molecule: protein

source_name: normal urothelial mucosa

label_protocol: 50ug of Tissue extract was labeled with Biotin and label buffer (Fullmoon Bio).

extract_protocol: 10~40mg of tissues were washed with cold 1X PBS. And tissue samples were homogenized with Extracting buffer (Fullmoon Bio). Debris was removed from tissue extract with centrifuge.

treatment_protocol: Primary high grade non-muscle invasive bladder cancer tissues were obtained from TURBT. Adjacent normal mucosa tissues were used as controls

value: bladder

value: normal urothelial mucosa


title: Patient 2 BC

source_name: primary bladder cancer

value: bladder cancer


title: Patient 2 NLUM


title: KBD PBMCs Replicate 16

description: Biological replicate 16 of 100. KBD peripheral blood mononuclear cells cells, harvested after several passages.

value: peripheral blood mononuclear cells (PBMCs)


title: KBD PBMCs Replicate 15

description: Biological replicate 15 of 100. KBD peripheral blood mononuclear cells cells, harvested after several passages.

value: Female


title: KBD PBMCs Replicate 17

description: Biological replicate 17 of 100. KBD peripheral blood mononuclear cells cells, harvested after several passages.

value: Ⅰ


title: Patient 1 NLUM

value: Male


title: Patient 1 BC


title: KBD PBMCs Replicate 14

description: Biological replicate 14 of 100. KBD peripheral blood mononuclear cells cells, harvested after several passages.