title: Cont-preT-AGA, rep18

description:
SAMPLE_5728
Placenta sample purchased from the Research Centre for Women’s and Infants’ Health (RCWIH) BioBank (Toronto, Canada), which utilizes a systematic sampling procedure in which four tissue biopsies (one sample/quadrant) are collected and pooled per placenta. At the time of sample collection and purchase, PE was defined as the onset of systolic pressure ≥ 140 mmHg and/or diastolic pressure ≥ 90 mmHg after the 20th week of gestation, accompanied by proteinuria (greater than 300 mg protein/day, or greater ≥ 2+ by dipstick). CH: chronic maternal hypertension; systolic pressure ≥ 140 mmHg and/or sustained diastolic ≥ 90 mmHg before the 20th week of gestation. Preterm: delivery prior to 34 weeks gestation. SGA: small-for-gestational-age infant; neonatal birth weight < 10th percentile for gestational age and sex. AGA: average-for-gestational age infant.

tag: diagnosis

value: non-PE

tag: tissue

tag: maternal age

tag: maternal bmi

tag: maternal ethnicity

tag: maternal blood type

tag: previous nulliparity

tag: previous miscarriage

tag: previous hypertensive pregnancy

tag: mean uterine pi

tag: mean umbilical pi

tag: maximum systolic bp

tag: maximum diastolic bp

tag: mode proteinuria

tag: hellp diagnosis

tag: iugr diagnosis

tag: attempted vaginal delivery

tag: mode of delivery

tag: ga (week)

tag: ga (day)

tag: infant gender

value: F


title: high grade serous ovarian cancer (EOC83)

status: Public on May 10 2016

type: genomic

city: Omaha

first: Adam

middle: R.

last: Karpf

state: Nebraska

address: 985950 Nebraska Medical Center

department: Eppley Institute for Research in Cancer

country: USA

institute: University of Nebraska Medical Center

description: Female high grade serous ovarian cancer, primary tumor

hyb_protocol: Bisulfite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450K Beadchip using standard Illumina protocol

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

data_processing: Rnbeads Version 1.0.0

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

source_name: Fresh-frozen high grade serous ovarian cancer sample from patient undergoing surgical resection at Roswell Park Cancer Institute

label_protocol: Standard Illumina Protocol

extract_protocol: Isolated genomic DNA using the Puregene Tissue Kit (Qiagen), which includes RNAse treatment

tag: gender

value: Female

tag: patient age

tag: tumor type

value: ovarian cancer

tag: tumor histology

value: Predominantly serous, with focal components of mucinous, clear cell, and endometriod

tag: Stage

value: IIIC

tag: grade


title: high grade serous ovarian cancer (EOC99)

value: serous

value: IIIB


title: CY514 D7

type: RNA

city: Stanford

first: Fiona

last: Strouts

state: CA

address: Campus Drive

institute: Stanford

description: PAXGene NHP aRNA, 8ug, Epicenter amplified, Cy5 labeled, spiked with 20ng doping control labeled separately

hyb_protocol: reference URL : http://www.chem.agilent.com/Library/usermanuals/Public/G4140-90050_GeneExpression_TwoColor_6.8.pdf Hybridization method : 8 ug of Cy5-labeled amplified RNA and 5 ug of Cy3-labeled Universal Human Reference aRNA (Stratagene) were hybridized to Human Exonic Evidence Based Oligonucleotide (HEEBO) microarrays. Dye-labeled RNA was fragmented and then mixed with 250 ?l 2_ Hi-RPM Hybridization Buffer (Agilent Technologies) and hybridized to the microarrays at 65?C for 14 hours using the hybridization gasket slides and microarray hybridization chamber (Agilent Technologies).

scan_protocol: Scan Power : 100 PMT Volts : 508 Pixel Size : 10 Laser on time : 181762 Laser Power : 3.09 Scan Date : 2012-07-02 Scan Temperature : 33.50 Scan Time : 13:21:19 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

data_processing:
Extraction Software : GenePix Pro
Extraction Software Version : 5.0.0.51
Datafile type : GenePix Results 3
Image Origin : 760, 5480

molecule: total RNA

source_name: Stratagene Human Universal Reference aa aRNA, NuGEN amplified, 5ug of pooled Alexa Fluor 3 labeled

label_protocol:
Type of label : Cy3
reference URL : http://www.gelifesciences.com/webapp/wcs/stores/servlet/ProductDisplay?categoryId=11158&catalogId=10101&productId=16547&storeId=11787&langId=-1

extract_protocol: Extraction method : Human Universal Reference RNA (Stratagene)

tag: reference sample name

source_name: 8ug NHP aRNA EpiC amp Cy5 labeled, spiked with 20ng dc

label_protocol:
Type of label : Cy5
reference URL : http://www.gelifesciences.com/webapp/wcs/stores/servlet/ProductDisplay?categoryId=11158&catalogId=10101&productId=16547&storeId=11787&langId=-1

extract_protocol:
Extraction method : PreAnalytiX PAXgene Blood RNA Kit
Amplification method : Epicentre TargetAmp Aminoallyl aRNA Amp Kit

treatment_protocol:
Vaccine Route : ID
Treatment : Vaccine
Treatment group : 2
Vaccine Dose : Single
Day : 7

tag: test sample name

tag: time point (days)


title: Cont-preT-AGA, rep19

city: Toronto

first: Brian

last: Cox

state: Ontario

address: 1 King's College Circle

department: Physiology

country: Canada

institute: University of Toronto

description:
SAMPLE_6265
Placenta sample purchased from the Research Centre for Women’s and Infants’ Health (RCWIH) BioBank (Toronto, Canada), which utilizes a systematic sampling procedure in which four tissue biopsies (one sample/quadrant) are collected and pooled per placenta. At the time of sample collection and purchase, PE was defined as the onset of systolic pressure ≥ 140 mmHg and/or diastolic pressure ≥ 90 mmHg after the 20th week of gestation, accompanied by proteinuria (greater than 300 mg protein/day, or greater ≥ 2+ by dipstick). CH: chronic maternal hypertension; systolic pressure ≥ 140 mmHg and/or sustained diastolic ≥ 90 mmHg before the 20th week of gestation. Preterm: delivery prior to 34 weeks gestation. SGA: small-for-gestational-age infant; neonatal birth weight < 10th percentile for gestational age and sex. AGA: average-for-gestational age infant.

hyb_protocol: Hybridization was performed by the Princess Margaret Genomics Centre (Toronto, Canada) as per Affymetrics protocols.

scan_protocol: Scanning was performed by the Princess Margaret Genomics Centre (Toronto, Canada) as per Affymetrics protocols.

data_processing:
Data was processed, normalized, and converted into log2 values in R 3.0.1 using the Affy library from Bioconductor.
The file complete_dataset.csv contains the expression information for 14,651 genes found in common across the different array platforms analyzed. Row names contain gene symbols.

label: biotin

source_name: Human placenta from Cont-preT-AGA pregnancy

label_protocol: Biotinylated cDNA was prepared by the Princess Margaret Genomics Centre (Toronto, Canada) as per Affymetrics protocols.

extract_protocol: To control for batch affect, samples were randomized into groups of 20 for processing. A 100 mg aliquot was used to prepare an mRNA extract using Trizol followed by RNAeasy spin columns. RNA purity and integrity were determined using 28S to 18S rRNA ratio (Agilent Bioanalyzer).

treatment_protocol: Four tissue biopsies (one sample/quadrant, excluding the chorionic plate) are collected per placenta, rinsed in PBS to remove contaminating maternal blood, pooled, crushed into a powder, and snap-frozen in liquid nitrogen.

tag: diagnosis

tag: tissue

value: Placenta

tag: maternal age

tag: maternal bmi

tag: maternal ethnicity

value: Caucasian

tag: maternal blood type

value: O

tag: previous nulliparity

value: Yes

tag: previous miscarriage

value: No

tag: previous hypertensive pregnancy

tag: mean uterine pi

tag: mean umbilical pi

tag: maximum systolic bp

tag: maximum diastolic bp

tag: mode proteinuria

value: Vaginal

value: M

tag: newborn weight z-score

tag: apgar score (1 min)

tag: apgar score (5 min)

tag: nicu transfer

tag: placental weight z-score

tag: umbilical cord diameter

tag: chorioamnionitis diagnosis


title: Mutant B8_0.8%Bu_1.5h_rep3

city: Wuxi

first: Ye

last: Ni

state: Jiangsu

address: 1800 Lihu Road

department: School of Biotechnology

country: China

institute: Jiangnan University

description: Gene expression after 1.5hr under 0.8% (v/v) butanol,

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent-020097 for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

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

data_processing: Data was extracted with Agilent Feature Extraction software 10.7 (Agilent) using default parameters (protocol GE1-v1_91) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Escherichia coli

source_name: Mutant B8, 0.8%butanol,1.5h,replicate 3

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: E. coli strains harboring σ70 mutant B8 and WT were cultured overnight and inoculated (1%) into fresh medium.

extract_protocol: Total RNA was extracted using Qiagen RNeasy kit (Hilden, Germany) following manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US). Qualified total RNA was further purified by RNeasy mini kit (QIAGEN, GmBH, Germany) and RNase‐Free DNase Set (QIAGEN, GmBH, Germany).

treatment_protocol: n-Butanol (0.8%, v/v) was added at 0.8 OD660 and further incubated for 1.5 h.

tag: genotype/variation

value: σ70 mutation

tag: phenotype

value: 2% n-butanol tolerance


title: CY482 D7

scan_protocol: Scan Power : 100 PMT Volts : 518 Pixel Size : 10 Laser on time : 183056 Laser Power : 3.07 Scan Date : 2012-07-08 Scan Temperature : 31.85 Scan Time : 17:46:38 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

data_processing:
Extraction Software : GenePix Pro
Extraction Software Version : 5.0.0.51
Datafile type : GenePix Results 3
Image Origin : 520, 4330

tag: reference sample name

value: Human Universal Reference RNA (Stratagene)

treatment_protocol:
Vaccine Route : ID
Treatment : Vaccine
Treatment group : 3
Vaccine Dose : Single
Day : 7

tag: test sample name

tag: time point (days)


title: high grade serous ovarian cancer (EOC150)

tag: gender

tag: patient age

tag: tumor type

tag: tumor histology

tag: Stage

tag: grade


title: Control109_0.8%Bu_1.5h_rep3

source_name: Control, 0.8%butanol,1.5h,replicate 3

tag: strain

value: Wild type strain

value: 0.6% n-butanol tolerance


title: high grade serous ovarian cancer (EOC82)

value: Female

value: ovarian cancer

value: IV


title: Cont-Term-CH, rep11

description:
SAMPLE_5543
Placenta sample purchased from the Research Centre for Women’s and Infants’ Health (RCWIH) BioBank (Toronto, Canada), which utilizes a systematic sampling procedure in which four tissue biopsies (one sample/quadrant) are collected and pooled per placenta. At the time of sample collection and purchase, PE was defined as the onset of systolic pressure ≥ 140 mmHg and/or diastolic pressure ≥ 90 mmHg after the 20th week of gestation, accompanied by proteinuria (greater than 300 mg protein/day, or greater ≥ 2+ by dipstick). CH: chronic maternal hypertension; systolic pressure ≥ 140 mmHg and/or sustained diastolic ≥ 90 mmHg before the 20th week of gestation. Preterm: delivery prior to 34 weeks gestation. SGA: small-for-gestational-age infant; neonatal birth weight < 10th percentile for gestational age and sex. AGA: average-for-gestational age infant.

source_name: Human placenta from Cont-Term-CH pregnancy

tag: diagnosis

value: non-PE

tag: tissue

tag: maternal age

tag: maternal bmi

tag: maternal ethnicity

value: Asian

tag: maternal blood type

value: A

tag: previous nulliparity

tag: previous miscarriage

tag: previous hypertensive pregnancy

tag: mean uterine pi

tag: mean umbilical pi

tag: maximum systolic bp

tag: maximum diastolic bp

tag: mode proteinuria

tag: hellp diagnosis

tag: iugr diagnosis

tag: attempted vaginal delivery

tag: mode of delivery

tag: ga (week)

tag: ga (day)

tag: infant gender

value: F

tag: newborn weight z-score

tag: apgar score (1 min)

tag: apgar score (5 min)


title: high grade serous ovarian cancer (EOC59)

tag: gender

tag: patient age

tag: tumor type

tag: tumor histology

value: serous

tag: Stage

value: IIIC

tag: grade


title: CY483R D3

scan_protocol: Scan Power : 100 PMT Volts : 552 Pixel Size : 10 Laser on time : 187684 Laser Power : 3.07 Scan Date : 2012-07-27 Scan Temperature : 32.03 Scan Time : 14:30:14 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

data_processing:
Extraction Software : GenePix Pro
Extraction Software Version : 5.0.0.51
Datafile type : GenePix Results 3
Image Origin : 640, 6120

source_name: Stratagene Human Universal Reference aa aRNA, 5ug of pooled Cy3 labeled

tag: reference sample name

treatment_protocol:
Vaccine Route : ID
Treatment : Vaccine
Treatment group : 3
Vaccine Dose : Single
Day : 3

tag: test sample name

tag: time point (days)


title: Cont-PreT-CH, rep2

description:
SAMPLE_5534
Placenta sample purchased from the Research Centre for Women’s and Infants’ Health (RCWIH) BioBank (Toronto, Canada), which utilizes a systematic sampling procedure in which four tissue biopsies (one sample/quadrant) are collected and pooled per placenta. At the time of sample collection and purchase, PE was defined as the onset of systolic pressure ≥ 140 mmHg and/or diastolic pressure ≥ 90 mmHg after the 20th week of gestation, accompanied by proteinuria (greater than 300 mg protein/day, or greater ≥ 2+ by dipstick). CH: chronic maternal hypertension; systolic pressure ≥ 140 mmHg and/or sustained diastolic ≥ 90 mmHg before the 20th week of gestation. Preterm: delivery prior to 34 weeks gestation. SGA: small-for-gestational-age infant; neonatal birth weight < 10th percentile for gestational age and sex. AGA: average-for-gestational age infant.

source_name: Human placenta from Cont-PreT-CH pregnancy

tag: diagnosis

tag: tissue

value: Placenta

tag: maternal age

tag: maternal bmi

tag: maternal ethnicity

value: Other

tag: maternal blood type

value: B

tag: previous nulliparity

value: No

tag: previous miscarriage

value: Yes

tag: previous hypertensive pregnancy

tag: mean uterine pi

tag: mean umbilical pi

tag: maximum systolic bp

tag: maximum diastolic bp

tag: mode proteinuria

tag: hellp diagnosis

tag: iugr diagnosis

tag: attempted vaginal delivery

value: C-Section

tag: nicu transfer

tag: placental weight z-score

tag: umbilical cord diameter

tag: chorioamnionitis diagnosis


title: high grade serous ovarian cancer (EOC66)

tag: gender

tag: patient age

tag: tumor type

tag: tumor histology

tag: Stage

tag: grade


title: CY482 D-2

scan_protocol: Scan Power : 100 PMT Volts : 513 Pixel Size : 10 Laser on time : 182713 Laser Power : 3.10 Scan Date : 2012-07-05 Scan Temperature : 31.03 Scan Time : 11:33:22 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

data_processing:
Extraction Software : GenePix Pro
Extraction Software Version : 5.0.0.51
Datafile type : GenePix Results 3
Image Origin : 920, 5400

tag: reference sample name

value: Human Universal Reference RNA (Stratagene)

treatment_protocol:
Vaccine Route : ID
Treatment : Vaccine
Treatment group : 3
Vaccine Dose : Single
Day : -2

tag: test sample name

tag: time point (days)


title: high grade serous ovarian cancer (EOC5)


title: CY514 D5

scan_protocol: Scan Power : 100 PMT Volts : 500 Pixel Size : 10 Laser on time : 181746 Laser Power : 3.10 Scan Date : 2012-07-02 Scan Temperature : 33.32 Scan Time : 13:06:01 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

treatment_protocol:
Vaccine Route : ID
Treatment : Vaccine
Treatment group : 2
Vaccine Dose : Single
Day : 5


title: Mutant B8_0.8%Bu_1.5h_rep1

source_name: Mutant B8, 0.8%butanol,1.5h,replicate 1

tag: genotype/variation

value: σ70 mutation

tag: phenotype

value: 2% n-butanol tolerance


title: CY514 D3

scan_protocol: Scan Power : 100 PMT Volts : 485 Pixel Size : 10 Laser on time : 181731 Laser Power : 3.11 Scan Date : 2012-07-02 Scan Temperature : 33.07 Scan Time : 12:50:36 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

treatment_protocol:
Vaccine Route : ID
Treatment : Vaccine
Treatment group : 2
Vaccine Dose : Single
Day : 3


title: high grade serous ovarian cancer (EOC12)

value: Female

value: ovarian cancer


title: Cont-Term-CH, rep10

description:
SAMPLE_5273
Placenta sample purchased from the Research Centre for Women’s and Infants’ Health (RCWIH) BioBank (Toronto, Canada), which utilizes a systematic sampling procedure in which four tissue biopsies (one sample/quadrant) are collected and pooled per placenta. At the time of sample collection and purchase, PE was defined as the onset of systolic pressure ≥ 140 mmHg and/or diastolic pressure ≥ 90 mmHg after the 20th week of gestation, accompanied by proteinuria (greater than 300 mg protein/day, or greater ≥ 2+ by dipstick). CH: chronic maternal hypertension; systolic pressure ≥ 140 mmHg and/or sustained diastolic ≥ 90 mmHg before the 20th week of gestation. Preterm: delivery prior to 34 weeks gestation. SGA: small-for-gestational-age infant; neonatal birth weight < 10th percentile for gestational age and sex. AGA: average-for-gestational age infant.

tag: diagnosis

value: non-PE

tag: tissue

tag: maternal age

tag: maternal bmi

tag: maternal ethnicity

value: Caucasian

tag: maternal blood type

tag: previous nulliparity

tag: previous miscarriage

tag: previous hypertensive pregnancy

tag: mean uterine pi

tag: mean umbilical pi

tag: maximum systolic bp

tag: maximum diastolic bp

tag: mode proteinuria

tag: hellp diagnosis

tag: iugr diagnosis

tag: mode of delivery

tag: ga (week)

tag: ga (day)

tag: infant gender

tag: newborn weight z-score

tag: apgar score (1 min)

tag: apgar score (5 min)


title: PE-PreT-CH, rep7

description:
SAMPLE_5264
Placenta sample purchased from the Research Centre for Women’s and Infants’ Health (RCWIH) BioBank (Toronto, Canada), which utilizes a systematic sampling procedure in which four tissue biopsies (one sample/quadrant) are collected and pooled per placenta. At the time of sample collection and purchase, PE was defined as the onset of systolic pressure ≥ 140 mmHg and/or diastolic pressure ≥ 90 mmHg after the 20th week of gestation, accompanied by proteinuria (greater than 300 mg protein/day, or greater ≥ 2+ by dipstick). CH: chronic maternal hypertension; systolic pressure ≥ 140 mmHg and/or sustained diastolic ≥ 90 mmHg before the 20th week of gestation. Preterm: delivery prior to 34 weeks gestation. SGA: small-for-gestational-age infant; neonatal birth weight < 10th percentile for gestational age and sex. AGA: average-for-gestational age infant.

source_name: Human placenta from PE-PreT-CH pregnancy

tag: diagnosis

value: PE

tag: tissue

tag: maternal age

tag: maternal bmi

tag: maternal ethnicity

value: Black

tag: maternal blood type

value: O

tag: previous nulliparity

tag: attempted vaginal delivery

value: M

tag: nicu transfer

tag: placental weight z-score

tag: umbilical cord diameter

tag: chorioamnionitis diagnosis


title: PHH_WO_LD_exp3 [genomic]

city: Maastricht

first: Linda

last: Rieswijk

address: Universiteitssingel 50

department: Toxicogenomics

country: Netherlands

institute: Maastricht University

hyb_protocol: Labeling and hybridization of arrays were performed according to the manufactures’ protocol. Slides were washed using the NimbleGen wash buffer kit and scanned using the 2 µm high resolution NimbleGen MS 200 microarray scanner.

scan_protocol: Signal intensity data was extracted from the scanned images of each array using NimbleScan v2.6 software and quantile normalized on a per channel basis.

data_processing:
Log2 ratios of the intensities were computed (ratio of MeDIP signal / Input signal) and for each array, centering was performed by subtracting the global array bi-weight mean of the log2 ratios such that the computed log2 ratios were centered around 0. Detection of differential methylation was performed using the Probe Sliding Window-ANOVA algorithm (PSW-ANOVA). PSW-ANOVA was implemented in the R statistical programming environment (v2.15.3) (http://www.r-project.org) as a custom script and was provided by Roche NimbleGen in collaboration .   PSW-ANOVA (sliding window of 750 bp comprising 7 probes, and a FDR corrected p- value < 0.01) was used to identify differential methylated regions (DMR) which were statistically significantly different between the different conditions tested in the experiment i.e. Exposed versus Control. Peaks were identified in the DMR by searching for regions containing at least 8 significant consecutive probes (p<0.01).   Peaks were mapped to promoter regions (from 3 kb upstream to 1 kb downstream of the transcription start site (25)) and CpG islands of genes using the NimbleScan v2.6 software. A control corrected median log2 ratio was calculated for each peak. Log2 ratio’s > 0 indicate hypermethylation and log2 ratio’s < 0 indicate hypomethylation.
scaled, log2 (medip/Input) ratio for demethylated regions

source_name: Input DNA from PHH exposed to 0.3uM of AFB1 for 5 days followed by a 3-day washout period replicate 3

label_protocol: In order to obtain fragments ranging from 200 bp to 600 bp, genomic DNA was sonicated. Next, the fragments were cleaned up using silica columns (Zymo Research) and eluted in TE buffer. MeDIP was performed using the MagMeDIP kit (Diagenode, Liege, Belgium) according to the manufacturer’s protocol. Briefly, IP incubation mix was added to 1.2 µg sonicated DNA sample and denaturated at 95°C. 10% of this was used as reference samples. The remaining sample was immunoprecipitated overnight using antibody mix containing the 5-methylcytidine antibody and magnetic beads. Following purification using the Ipure kit (Diagenode), reference and MeDIP samples were prepared for microarray analysis by whole genome amplification (WGA) using the WGA2 kit (Sigma-Aldrich) without performing the fragmentation step. Methylation enrichment in the paired samples MeDIP/reference was derived from qPCR data by calculating the ratio positive control/negative control, applying the ΔΔCt method. The Human DNA Methylation 2.1M Deluxe Promoter Array (Roche NimbleGen) was used for analyses of DNA methylation levels.

extract_protocol: Cells were lysed in 500 µl digestion buffer (containing 0.5 M EDTA; 1 M Tris–HCl, pH 8.0; 10% SDS) and incubated for 1 hour at 55 °C. Next, 25µl of proteinase K (20mg/ml) (Ambion) was added. After incubation of 1 hour at 55 °C, the proteinase K was inactivated for 10 minutes at 80 °C. RNAse A (2 µl; 100mg/ml) (Qiagen) and collagenase (25 µl; 1%) (Sigma) treatment was performed for 1 hour at 37 °C. Thereupon, 500 µl of phenol-chloroform-isoamylalcohol (PCI; 25:24:1) (Sigma) was added. The mixture was shaked manually for 5 min, and centrifuged for 5 minutes at maximum speed. The upper phase was transferred to a new Eppendorf and the step with PCI was repeated. The upper phase was collected and precipitated using 50 µl 3M NaAc pH 5.6 and 1250 µl cold 100% ethanol for 30 min. at -80°C. After centrifugation for 30 minutes at maximum speed, the DNA pellet was washed using cold 70% ETOH, dried in a speed vac and dissolved in 50µl nuclease free water. The total amount was at least 10 µg DNA, the 260/280 ratio ranged between 1.7-1.9, and the 260/230 ratio appeared higher than 1.6. A total of 6 DNA samples were prepared.

tag: cell type

value: primary human hepatocytes

tag: fraction

value: input

value: Immunoprecipitated genomic DNA with antibody against a monoclonal antibody against 5’-methylcytidine


title: CY514 D1

scan_protocol: Scan Power : 100 PMT Volts : 507 Pixel Size : 10 Laser on time : 181711 Laser Power : 3.10 Scan Date : 2012-07-02 Scan Temperature : 32.71 Scan Time : 12:30:35 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

tag: reference sample name

treatment_protocol:
Vaccine Route : ID
Treatment : Vaccine
Treatment group : 2
Vaccine Dose : Single
Day : 1

tag: test sample name

tag: time point (days)


title: CY514 D-2

scan_protocol: Scan Power : 100 PMT Volts : 511 Pixel Size : 10 Laser on time : 181676 Laser Power : 3.07 Scan Date : 2012-07-02 Scan Temperature : 31.91 Scan Time : 11:54:59 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

treatment_protocol:
Vaccine Route : ID
Treatment : Vaccine
Treatment group : 2
Vaccine Dose : Single
Day : -2


title: PE-Term-SGA, rep9

description:
SAMPLE_4756
Placenta sample purchased from the Research Centre for Women’s and Infants’ Health (RCWIH) BioBank (Toronto, Canada), which utilizes a systematic sampling procedure in which four tissue biopsies (one sample/quadrant) are collected and pooled per placenta. At the time of sample collection and purchase, PE was defined as the onset of systolic pressure ≥ 140 mmHg and/or diastolic pressure ≥ 90 mmHg after the 20th week of gestation, accompanied by proteinuria (greater than 300 mg protein/day, or greater ≥ 2+ by dipstick). CH: chronic maternal hypertension; systolic pressure ≥ 140 mmHg and/or sustained diastolic ≥ 90 mmHg before the 20th week of gestation. Preterm: delivery prior to 34 weeks gestation. SGA: small-for-gestational-age infant; neonatal birth weight < 10th percentile for gestational age and sex. AGA: average-for-gestational age infant.

source_name: Human placenta from PE-Term-SGA pregnancy

tag: diagnosis

value: Placenta

value: A

tag: previous miscarriage

value: No

tag: previous hypertensive pregnancy

tag: mean uterine pi

tag: mean umbilical pi

tag: maximum systolic bp

tag: maximum diastolic bp

tag: mode proteinuria

tag: hellp diagnosis

tag: iugr diagnosis

tag: mode of delivery

tag: ga (week)

tag: ga (day)

tag: infant gender

tag: newborn weight z-score

tag: apgar score (1 min)

tag: apgar score (5 min)


title: PHH_WO_LD_exp2 [genomic]

source_name: Input DNA from PHH exposed to 0.3uM of AFB1 for 5 days followed by a 3-day washout period replicate 2

tag: cell type

tag: fraction


title: PE-PreT-AGA, rep9

description:
SAMPLE_4809
Placenta sample purchased from the Research Centre for Women’s and Infants’ Health (RCWIH) BioBank (Toronto, Canada), which utilizes a systematic sampling procedure in which four tissue biopsies (one sample/quadrant) are collected and pooled per placenta. At the time of sample collection and purchase, PE was defined as the onset of systolic pressure ≥ 140 mmHg and/or diastolic pressure ≥ 90 mmHg after the 20th week of gestation, accompanied by proteinuria (greater than 300 mg protein/day, or greater ≥ 2+ by dipstick). CH: chronic maternal hypertension; systolic pressure ≥ 140 mmHg and/or sustained diastolic ≥ 90 mmHg before the 20th week of gestation. Preterm: delivery prior to 34 weeks gestation. SGA: small-for-gestational-age infant; neonatal birth weight < 10th percentile for gestational age and sex. AGA: average-for-gestational age infant.

source_name: Human placenta from PE-PreT-AGA pregnancy

tag: diagnosis

tag: tissue

tag: maternal age

tag: maternal bmi

tag: maternal ethnicity

tag: maternal blood type

tag: previous nulliparity

value: Yes

tag: previous miscarriage

tag: previous hypertensive pregnancy

tag: attempted vaginal delivery

value: C-Section

value: F

tag: nicu transfer

tag: placental weight z-score

tag: umbilical cord diameter

tag: chorioamnionitis diagnosis


title: high grade serous ovarian cancer (EOC11)

tag: gender

value: Female

tag: patient age

tag: tumor type

tag: tumor histology

value: serous

tag: Stage

value: IIIB

tag: grade


title: fallopian tube epithelial cells (FTE22)

description: Epithelial layer by mechanical scraping of resected fimbriae fallopian tubes

source_name: Fresh-frozen normal fallopian tube epithelial cells

tag: cell type

value: normal fallopian tube epithelial cells


title: CY0513 D7

description: CY0513 D7 paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR

scan_protocol: Scan Power : 100 PMT Volts : 465 Pixel Size : 10 Laser on time : 201298 Laser Power : 3.52 Scan Date : 2013-03-22 Scan Temperature : 35.18 Scan Time : 16:42:14 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

data_processing:
Extraction Software : GenePix Pro
Extraction Software Version : 5.0.0.51
Datafile type : GenePix Results 3
Image Origin : 560, 4900

source_name: Strat UHR and v4 MJ doping control aa-aRNA labeled 31813

tag: reference sample name

value: Human Universal Reference RNA (Stratagene)

tag: test sample name

tag: time point (days)


title: CY514 D-11

scan_protocol: Scan Power : 100 PMT Volts : 505 Pixel Size : 10 Laser on time : 181653 Laser Power : 3.09 Scan Date : 2012-07-02 Scan Temperature : 31.61 Scan Time : 11:33:16 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

treatment_protocol:
Vaccine Route : ID
Treatment : Vaccine
Treatment group : 2
Vaccine Dose : Single
Day : -11


title: CY0513 D3

description: CY0513 D3 paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR

scan_protocol: Scan Power : 100 PMT Volts : 471 Pixel Size : 10 Laser on time : 201259 Laser Power : 3.51 Scan Date : 2013-03-22 Scan Temperature : 35.09 Scan Time : 16:03:08 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0


title: Cont-Term-CH, rep9

description:
SAMPLE_5105
Placenta sample purchased from the Research Centre for Women’s and Infants’ Health (RCWIH) BioBank (Toronto, Canada), which utilizes a systematic sampling procedure in which four tissue biopsies (one sample/quadrant) are collected and pooled per placenta. At the time of sample collection and purchase, PE was defined as the onset of systolic pressure ≥ 140 mmHg and/or diastolic pressure ≥ 90 mmHg after the 20th week of gestation, accompanied by proteinuria (greater than 300 mg protein/day, or greater ≥ 2+ by dipstick). CH: chronic maternal hypertension; systolic pressure ≥ 140 mmHg and/or sustained diastolic ≥ 90 mmHg before the 20th week of gestation. Preterm: delivery prior to 34 weeks gestation. SGA: small-for-gestational-age infant; neonatal birth weight < 10th percentile for gestational age and sex. AGA: average-for-gestational age infant.

tag: diagnosis

value: non-PE

tag: tissue

tag: maternal age

tag: maternal bmi

tag: maternal ethnicity

value: Asian

tag: maternal blood type

tag: previous nulliparity

tag: previous miscarriage

tag: mean uterine pi

tag: mean umbilical pi

tag: maximum systolic bp

tag: maximum diastolic bp

tag: mode proteinuria

tag: hellp diagnosis

tag: iugr diagnosis

tag: mode of delivery

tag: ga (week)

tag: ga (day)

tag: infant gender

tag: newborn weight z-score

tag: apgar score (1 min)

tag: apgar score (5 min)


title: CY0513 D1

description: CY0513 D1 paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR

scan_protocol: Scan Power : 100 PMT Volts : 476 Pixel Size : 10 Laser on time : 201244 Laser Power : 3.51 Scan Date : 2013-03-22 Scan Temperature : 35.02 Scan Time : 15:49:00 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

tag: reference sample name

tag: test sample name

tag: time point (days)


title: CY0513 D5

description: CY0513 D5 paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR

scan_protocol: Scan Power : 100 PMT Volts : 461 Pixel Size : 10 Laser on time : 201282 Laser Power : 3.52 Scan Date : 2013-03-22 Scan Temperature : 35.15 Scan Time : 16:27:31 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0


title: PHH_WO_LD_exp1 [genomic]

tag: cell type

tag: fraction

source_name: DNA from PHH exposed to 0.3uM of AFB1 for 5 days followed by a 3-day washout period replicate 3


title: high grade serous ovarian cancer (EOC54)

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

source_name: Fresh-frozen high grade serous ovarian cancer sample from patient undergoing surgical resection at Roswell Park Cancer Institute

tag: gender

tag: patient age

tag: tumor type

value: ovarian cancer

tag: tumor histology

tag: Stage

value: IIIC

tag: grade


title: CY0513 D-2

description: CY0513 D-2 paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR

scan_protocol: Scan Power : 100 PMT Volts : 480 Pixel Size : 10 Laser on time : 201224 Laser Power : 3.50 Scan Date : 2013-03-22 Scan Temperature : 34.93 Scan Time : 15:28:23 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0


title: fallopian tube epithelial cells (FTE21)


title: Cont-preT-AGA, rep16

description:
SAMPLE_4653
Placenta sample purchased from the Research Centre for Women’s and Infants’ Health (RCWIH) BioBank (Toronto, Canada), which utilizes a systematic sampling procedure in which four tissue biopsies (one sample/quadrant) are collected and pooled per placenta. At the time of sample collection and purchase, PE was defined as the onset of systolic pressure ≥ 140 mmHg and/or diastolic pressure ≥ 90 mmHg after the 20th week of gestation, accompanied by proteinuria (greater than 300 mg protein/day, or greater ≥ 2+ by dipstick). CH: chronic maternal hypertension; systolic pressure ≥ 140 mmHg and/or sustained diastolic ≥ 90 mmHg before the 20th week of gestation. Preterm: delivery prior to 34 weeks gestation. SGA: small-for-gestational-age infant; neonatal birth weight < 10th percentile for gestational age and sex. AGA: average-for-gestational age infant.

scan_protocol: Scanning was performed by the Princess Margaret Genomics Centre (Toronto, Canada) as per Affymetrics protocols.

tag: diagnosis

tag: tissue

tag: maternal age

tag: maternal bmi

tag: maternal ethnicity

value: Caucasian

tag: maternal blood type

value: O

tag: previous nulliparity

tag: previous miscarriage

tag: previous hypertensive pregnancy

tag: mean uterine pi

tag: mean umbilical pi

tag: maximum systolic bp

tag: maximum diastolic bp

tag: mode proteinuria

tag: hellp diagnosis

tag: iugr diagnosis

tag: attempted vaginal delivery

tag: mode of delivery

value: Vaginal

tag: ga (week)

value: M

tag: nicu transfer

tag: placental weight z-score

tag: umbilical cord diameter

tag: chorioamnionitis diagnosis


title: PE-PreT-CH, rep6

description:
SAMPLE_4744
Placenta sample purchased from the Research Centre for Women’s and Infants’ Health (RCWIH) BioBank (Toronto, Canada), which utilizes a systematic sampling procedure in which four tissue biopsies (one sample/quadrant) are collected and pooled per placenta. At the time of sample collection and purchase, PE was defined as the onset of systolic pressure ≥ 140 mmHg and/or diastolic pressure ≥ 90 mmHg after the 20th week of gestation, accompanied by proteinuria (greater than 300 mg protein/day, or greater ≥ 2+ by dipstick). CH: chronic maternal hypertension; systolic pressure ≥ 140 mmHg and/or sustained diastolic ≥ 90 mmHg before the 20th week of gestation. Preterm: delivery prior to 34 weeks gestation. SGA: small-for-gestational-age infant; neonatal birth weight < 10th percentile for gestational age and sex. AGA: average-for-gestational age infant.

tag: diagnosis

value: PE

tag: tissue

value: Placenta

tag: maternal age

tag: maternal bmi

tag: maternal ethnicity

value: Black

tag: maternal blood type

value: A

tag: previous nulliparity

value: No

tag: ga (day)

tag: infant gender

tag: newborn weight z-score

tag: apgar score (1 min)

tag: apgar score (5 min)


title: PHH_WO_control_exp2 [genomic]

source_name: Input DNA from PHH exposed to zero dose of AFB1 for 5 days followed by a 3-day washout period replicate 2

tag: cell type

value: primary human hepatocytes

tag: fraction

value: input

value: Immunoprecipitated genomic DNA with antibody against a monoclonal antibody against 5’-methylcytidine


title: PHH_WO_control_exp1 [genomic]

source_name: Input DNA from PHH exposed to zero dose of AFB1 for 5 days followed by a 3-day washout period replicate 1


title: PHH_WO_control_exp3 [genomic]

source_name: Input DNA from PHH exposed to zero dose of AFB1 for 5 days followed by a 3-day washout period replicate 3


title: fallopian tube epithelial cells (FTE11)

tag: gender

value: Female

tag: patient age

value: normal fallopian tube epithelial cells


title: Mutant B8_0.8%Bu_1.5h_rep2

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

source_name: Mutant B8, 0.8%butanol,1.5h,replicate 2

tag: genotype/variation

value: σ70 mutation

tag: phenotype

value: 2% n-butanol tolerance


title: PE-Term-SGA, rep8

description:
SAMPLE_4101
Placenta sample purchased from the Research Centre for Women’s and Infants’ Health (RCWIH) BioBank (Toronto, Canada), which utilizes a systematic sampling procedure in which four tissue biopsies (one sample/quadrant) are collected and pooled per placenta. At the time of sample collection and purchase, PE was defined as the onset of systolic pressure ≥ 140 mmHg and/or diastolic pressure ≥ 90 mmHg after the 20th week of gestation, accompanied by proteinuria (greater than 300 mg protein/day, or greater ≥ 2+ by dipstick). CH: chronic maternal hypertension; systolic pressure ≥ 140 mmHg and/or sustained diastolic ≥ 90 mmHg before the 20th week of gestation. Preterm: delivery prior to 34 weeks gestation. SGA: small-for-gestational-age infant; neonatal birth weight < 10th percentile for gestational age and sex. AGA: average-for-gestational age infant.

tag: diagnosis

tag: tissue

value: Asian

tag: previous miscarriage

tag: previous hypertensive pregnancy

tag: mean uterine pi

tag: mean umbilical pi

tag: maximum systolic bp

tag: maximum diastolic bp

tag: mode proteinuria

tag: hellp diagnosis

tag: iugr diagnosis

tag: attempted vaginal delivery

value: Yes

tag: mode of delivery

tag: ga (week)

tag: nicu transfer

tag: placental weight z-score

tag: umbilical cord diameter

tag: chorioamnionitis diagnosis


title: fallopian tube epithelial cells (FTE18)

tag: gender

tag: patient age

tag: cell type


title: CY0513 D-11

description: CY0513 D-11 paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR

scan_protocol: Scan Power : 100 PMT Volts : 466 Pixel Size : 10 Laser on time : 201209 Laser Power : 3.50 Scan Date : 2013-03-22 Scan Temperature : 34.87 Scan Time : 15:14:06 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

tag: reference sample name

value: Human Universal Reference RNA (Stratagene)

tag: test sample name

tag: time point (days)


title: PHH_5D_LD_exp3

data_processing: Log2 ratios of the intensities were computed (ratio of MeDIP signal / Input signal) and for each array, centering was performed by subtracting the global array bi-weight mean of the log2 ratios such that the computed log2 ratios were centered around 0. Detection of differential methylation was performed using the Probe Sliding Window-ANOVA algorithm (PSW-ANOVA). PSW-ANOVA was implemented in the R statistical programming environment (v2.15.3) (http://www.r-project.org) as a custom script and was provided by Roche NimbleGen in collaboration .   PSW-ANOVA (sliding window of 750 bp comprising 7 probes, and a FDR corrected p- value < 0.01) was used to identify differential methylated regions (DMR) which were statistically significantly different between the different conditions tested in the experiment i.e. Exposed versus Control. Peaks were identified in the DMR by searching for regions containing at least 8 significant consecutive probes (p<0.01).   Peaks were mapped to promoter regions (from 3 kb upstream to 1 kb downstream of the transcription start site (25)) and CpG islands of genes using the NimbleScan v2.6 software. A control corrected median log2 ratio was calculated for each peak. Log2 ratio’s > 0 indicate hypermethylation and log2 ratio’s < 0 indicate hypomethylation.

source_name: Input DNA from PHH exposed to 0.3 uM dose dose of AFB1 for 5 days

extract_protocol: Cells were lysed in 500 µl digestion buffer (containing 0.5 M EDTA; 1 M Tris–HCl, pH 8.0; 10% SDS) and incubated for 1 hour at 55 °C. Next, 25µl of proteinase K (20mg/ml) (Ambion) was added. After incubation of 1 hour at 55 °C, the proteinase K was inactivated for 10 minutes at 80 °C. RNAse A (2 µl; 100mg/ml) (Qiagen) and collagenase (25 µl; 1%) (Sigma) treatment was performed for 1 hour at 37 °C. Thereupon, 500 µl of phenol-chloroform-isoamylalcohol (PCI; 25:24:1) (Sigma) was added. The mixture was shaked manually for 5 min, and centrifuged for 5 minutes at maximum speed. The upper phase was transferred to a new Eppendorf and the step with PCI was repeated. The upper phase was collected and precipitated using 50 µl 3M NaAc pH 5.6 and 1250 µl cold 100% ethanol for 30 min. at -80°C. After centrifugation for 30 minutes at maximum speed, the DNA pellet was washed using cold 70% ETOH, dried in a speed vac and dissolved in 50µl nuclease free water. The total amount was at least 10 µg DNA, the 260/280 ratio ranged between 1.7-1.9, and the 260/230 ratio appeared higher than 1.6. A total of 9 DNA samples were prepared.

tag: sample type

source_name: Immunoprecipitated DNA from PHH exposed to 0.3 uM dose dose of AFB1 for 5 days

tag: antibody

value: antibody against a monoclonal antibody against 5'-methylcytidine


title: PHH_5D_LD_exp2


title: Cont-PreT-CH, rep1

description:
SAMPLE_4423
Placenta sample purchased from the Research Centre for Women’s and Infants’ Health (RCWIH) BioBank (Toronto, Canada), which utilizes a systematic sampling procedure in which four tissue biopsies (one sample/quadrant) are collected and pooled per placenta. At the time of sample collection and purchase, PE was defined as the onset of systolic pressure ≥ 140 mmHg and/or diastolic pressure ≥ 90 mmHg after the 20th week of gestation, accompanied by proteinuria (greater than 300 mg protein/day, or greater ≥ 2+ by dipstick). CH: chronic maternal hypertension; systolic pressure ≥ 140 mmHg and/or sustained diastolic ≥ 90 mmHg before the 20th week of gestation. Preterm: delivery prior to 34 weeks gestation. SGA: small-for-gestational-age infant; neonatal birth weight < 10th percentile for gestational age and sex. AGA: average-for-gestational age infant.

source_name: Human placenta from Cont-PreT-CH pregnancy

tag: diagnosis

value: non-PE

tag: tissue

tag: maternal age

tag: maternal bmi

tag: maternal ethnicity

tag: maternal blood type

value: B

tag: previous nulliparity

tag: previous miscarriage

tag: previous hypertensive pregnancy

tag: mean uterine pi

tag: mean umbilical pi

tag: maximum systolic bp

tag: maximum diastolic bp

tag: mode proteinuria

tag: hellp diagnosis

value: C-Section

tag: ga (day)

tag: infant gender

value: F

tag: newborn weight z-score

tag: apgar score (1 min)

tag: apgar score (5 min)


title: PHH_5D_LD_exp1

tag: cell type

tag: sample type

tag: antibody


title: CY0512 D5

description: CY0512 D5 paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR

scan_protocol: Scan Power : 100 PMT Volts : 482 Pixel Size : 10 Laser on time : 201156 Laser Power : 3.48 Scan Date : 2013-03-22 Scan Temperature : 34.60 Scan Time : 14:20:13 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

tag: reference sample name

tag: test sample name

tag: time point (days)


title: fallopian tube epithelial cells (FTE19)

tag: gender

tag: patient age


title: CY0512 D3

description: CY0512 D3 paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR

scan_protocol: Scan Power : 100 PMT Volts : 476 Pixel Size : 10 Laser on time : 201123 Laser Power : 3.48 Scan Date : 2013-03-22 Scan Temperature : 34.48 Scan Time : 13:48:30 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0


title: PE-PreT-CH, rep5

description:
SAMPLE_4687
Placenta sample purchased from the Research Centre for Women’s and Infants’ Health (RCWIH) BioBank (Toronto, Canada), which utilizes a systematic sampling procedure in which four tissue biopsies (one sample/quadrant) are collected and pooled per placenta. At the time of sample collection and purchase, PE was defined as the onset of systolic pressure ≥ 140 mmHg and/or diastolic pressure ≥ 90 mmHg after the 20th week of gestation, accompanied by proteinuria (greater than 300 mg protein/day, or greater ≥ 2+ by dipstick). CH: chronic maternal hypertension; systolic pressure ≥ 140 mmHg and/or sustained diastolic ≥ 90 mmHg before the 20th week of gestation. Preterm: delivery prior to 34 weeks gestation. SGA: small-for-gestational-age infant; neonatal birth weight < 10th percentile for gestational age and sex. AGA: average-for-gestational age infant.

tag: diagnosis

value: PE

tag: tissue

value: Placenta

tag: maternal age

tag: maternal bmi

tag: maternal ethnicity

value: Caucasian

tag: maternal blood type

value: A

tag: previous nulliparity

tag: previous miscarriage

tag: previous hypertensive pregnancy

tag: mean uterine pi

tag: mean umbilical pi

tag: maximum systolic bp

tag: iugr diagnosis

tag: attempted vaginal delivery

tag: mode of delivery

value: Vaginal

tag: ga (week)

tag: nicu transfer

tag: placental weight z-score

tag: umbilical cord diameter

tag: chorioamnionitis diagnosis


title: PE-Term-AGA, rep10

description:
SAMPLE_3423
Placenta sample purchased from the Research Centre for Women’s and Infants’ Health (RCWIH) BioBank (Toronto, Canada), which utilizes a systematic sampling procedure in which four tissue biopsies (one sample/quadrant) are collected and pooled per placenta. At the time of sample collection and purchase, PE was defined as the onset of systolic pressure ≥ 140 mmHg and/or diastolic pressure ≥ 90 mmHg after the 20th week of gestation, accompanied by proteinuria (greater than 300 mg protein/day, or greater ≥ 2+ by dipstick). CH: chronic maternal hypertension; systolic pressure ≥ 140 mmHg and/or sustained diastolic ≥ 90 mmHg before the 20th week of gestation. Preterm: delivery prior to 34 weeks gestation. SGA: small-for-gestational-age infant; neonatal birth weight < 10th percentile for gestational age and sex. AGA: average-for-gestational age infant.

source_name: Human placenta from PE-Term-AGA pregnancy

tag: diagnosis

tag: tissue

tag: maternal age

tag: maternal bmi

value: No

tag: maximum diastolic bp

tag: mode proteinuria

tag: hellp diagnosis

tag: ga (day)

tag: infant gender

value: M

tag: newborn weight z-score

tag: apgar score (1 min)

tag: apgar score (5 min)


title: Genomic DNA from adult brain

city: London

first: Denise

last: Sheer

address: Blizard Institute, 4 Newark Street

department: Neuroscience & Trauma

country: United Kingdom

institute: Barts & The London School of Medicine & Dentistry

hyb_protocol: Illumina Infinium HD Assay Methylation Protocol using the HumanMethylation450 BeadChip

scan_protocol: Illumina iScan with Autoloader2 to scan the arrays by Barts and The London Genome Centre (QMUL, UK).

data_processing:
Data was pre-processed using Illumina GenomeStudio Methylation Module v1.9.
The non_normalized.txt contains Unmethylated and methylated signal intensities

source_name: Adult brain (Biochain #B302140)

label_protocol: standard Illumina protocol

extract_protocol: DNA extraction was performed from using the QIAamp DNA mini kit (QIAgen). Bisulphite conversion of the DNA (1µg) was performed using EZ DNA methylation kit (Zymo)

treatment_protocol: Fresh frozen tissue

tag: pathology

value: Adult brain

tag: age (yrs)

tag: gender

value: male

tag: tumour location

value: Whole brain


title: Genomic DNA from foetal cerebellum

source_name: Foetal cerebellum (Biochain #B205044)

value: Foetal cerebellum

value: Cerebellum


title: PE-Term-AGA, rep9

description:
SAMPLE_3084
Placenta sample purchased from the Research Centre for Women’s and Infants’ Health (RCWIH) BioBank (Toronto, Canada), which utilizes a systematic sampling procedure in which four tissue biopsies (one sample/quadrant) are collected and pooled per placenta. At the time of sample collection and purchase, PE was defined as the onset of systolic pressure ≥ 140 mmHg and/or diastolic pressure ≥ 90 mmHg after the 20th week of gestation, accompanied by proteinuria (greater than 300 mg protein/day, or greater ≥ 2+ by dipstick). CH: chronic maternal hypertension; systolic pressure ≥ 140 mmHg and/or sustained diastolic ≥ 90 mmHg before the 20th week of gestation. Preterm: delivery prior to 34 weeks gestation. SGA: small-for-gestational-age infant; neonatal birth weight < 10th percentile for gestational age and sex. AGA: average-for-gestational age infant.

tag: maternal ethnicity

tag: maternal blood type

value: O

tag: previous nulliparity

value: Yes

tag: previous miscarriage

tag: previous hypertensive pregnancy

tag: mean uterine pi

tag: mean umbilical pi

tag: maximum systolic bp

tag: iugr diagnosis

tag: attempted vaginal delivery

tag: mode of delivery

tag: ga (week)

tag: nicu transfer

tag: placental weight z-score

tag: umbilical cord diameter

tag: chorioamnionitis diagnosis


title: CY0512 D1

description: CY0512 D1 paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR

scan_protocol: Scan Power : 100 PMT Volts : 476 Pixel Size : 10 Laser on time : 201093 Laser Power : 3.49 Scan Date : 2013-03-22 Scan Temperature : 34.32 Scan Time : 13:17:58 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

tag: reference sample name

value: Human Universal Reference RNA (Stratagene)

tag: test sample name

tag: time point (days)


title: PHH_5D_HD_exp3

scan_protocol: Signal intensity data was extracted from the scanned images of each array using NimbleScan v2.6 software and quantile normalized on a per channel basis.

source_name: Input DNA from PHH exposed to 1 uM dose dose of AFB1 for 5 days

tag: cell type

value: primary human hepatocytes

tag: sample type

value: input

source_name: Immunoprecipitated DNA PHH exposed to 1 uM dose dose of AFB1 for 5 days

tag: antibody

value: antibody against a monoclonal antibody against 5'-methylcytidine


title: Genomic DNA from foetal frontal lobe

source_name: Foetal frontal lobe (Biochain #B205045)

tag: pathology

value: Foetal frontal lobe

tag: age (yrs)

tag: gender

tag: tumour location

value: Cerebral cortex


title: CY0512 D-11

description: CY0512 D-11 paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR

scan_protocol: Scan Power : 100 PMT Volts : 466 Pixel Size : 10 Laser on time : 202845 Laser Power : 3.60 Scan Date : 2013-03-27 Scan Temperature : 33.68 Scan Time : 14:53:13 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

data_processing:
Extraction Software : GenePix Pro
Extraction Software Version : 5.0.0.51
Datafile type : GenePix Results 3
Image Origin : 440, 5000


title: CY0512 D7

description: CY0512 D7 paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR

scan_protocol: Scan Power : 100 PMT Volts : 483 Pixel Size : 10 Laser on time : 201171 Laser Power : 3.48 Scan Date : 2013-03-22 Scan Temperature : 34.63 Scan Time : 14:35:43 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0


title: PHH_5D_HD_exp2


title: Genomic DNA from pilocytic astrocytoma PA17

source_name: Paediatric pilocytic astrocytoma

value: Pilocytic astrocytoma

value: female


title: Cont-preT-AGA, rep15

description:
SAMPLE_3047
Placenta sample purchased from the Research Centre for Women’s and Infants’ Health (RCWIH) BioBank (Toronto, Canada), which utilizes a systematic sampling procedure in which four tissue biopsies (one sample/quadrant) are collected and pooled per placenta. At the time of sample collection and purchase, PE was defined as the onset of systolic pressure ≥ 140 mmHg and/or diastolic pressure ≥ 90 mmHg after the 20th week of gestation, accompanied by proteinuria (greater than 300 mg protein/day, or greater ≥ 2+ by dipstick). CH: chronic maternal hypertension; systolic pressure ≥ 140 mmHg and/or sustained diastolic ≥ 90 mmHg before the 20th week of gestation. Preterm: delivery prior to 34 weeks gestation. SGA: small-for-gestational-age infant; neonatal birth weight < 10th percentile for gestational age and sex. AGA: average-for-gestational age infant.

source_name: Human placenta from Cont-preT-AGA pregnancy

tag: diagnosis

value: non-PE

tag: tissue

value: Placenta

tag: maternal age

tag: maternal bmi

tag: maternal ethnicity

value: Caucasian

tag: maternal blood type

value: B

tag: previous nulliparity

value: No

tag: previous miscarriage

tag: previous hypertensive pregnancy

tag: mean uterine pi

tag: mean umbilical pi

tag: maximum systolic bp

tag: maximum diastolic bp

tag: mode proteinuria

tag: hellp diagnosis

tag: iugr diagnosis

tag: attempted vaginal delivery

value: C-Section

tag: ga (day)

tag: infant gender

tag: newborn weight z-score

tag: apgar score (1 min)

tag: apgar score (5 min)


title: PE-PreT-AGA, rep8

description:
SAMPLE_2759
Placenta sample purchased from the Research Centre for Women’s and Infants’ Health (RCWIH) BioBank (Toronto, Canada), which utilizes a systematic sampling procedure in which four tissue biopsies (one sample/quadrant) are collected and pooled per placenta. At the time of sample collection and purchase, PE was defined as the onset of systolic pressure ≥ 140 mmHg and/or diastolic pressure ≥ 90 mmHg after the 20th week of gestation, accompanied by proteinuria (greater than 300 mg protein/day, or greater ≥ 2+ by dipstick). CH: chronic maternal hypertension; systolic pressure ≥ 140 mmHg and/or sustained diastolic ≥ 90 mmHg before the 20th week of gestation. Preterm: delivery prior to 34 weeks gestation. SGA: small-for-gestational-age infant; neonatal birth weight < 10th percentile for gestational age and sex. AGA: average-for-gestational age infant.

source_name: Human placenta from PE-PreT-AGA pregnancy

tag: diagnosis

value: PE

tag: tissue

tag: maternal age

tag: maternal bmi

tag: maternal ethnicity

tag: maternal blood type

tag: mode of delivery

tag: ga (week)

value: M

tag: nicu transfer

tag: placental weight z-score

tag: umbilical cord diameter

tag: chorioamnionitis diagnosis


title: CY0512 D-2

description: CY0512 D-2 paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR

scan_protocol: Scan Power : 100 PMT Volts : 470 Pixel Size : 10 Laser on time : 201073 Laser Power : 3.49 Scan Date : 2013-03-22 Scan Temperature : 34.20 Scan Time : 12:57:57 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

data_processing:
Extraction Software : GenePix Pro
Extraction Software Version : 5.0.0.51
Datafile type : GenePix Results 3
Image Origin : 760, 5160

source_name: Strat UHR and v4 MJ doping control aa-aRNA labeled 31813

tag: reference sample name

tag: test sample name

tag: time point (days)


title: PHH_5D_HD_exp1

tag: cell type

tag: sample type

tag: antibody


title: Genomic DNA from neural stem cells

source_name: ReN VM neural stem cells

tag: pathology

value: ReN VM neural stem cells

tag: age (yrs)

tag: tumour location

value: neural stem cells diencephalon


title: CY0511 D7

description: CY0511 D7 paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR

scan_protocol: Scan Power : 100 PMT Volts : 471 Pixel Size : 10 Laser on time : 200592 Laser Power : 3.59 Scan Date : 2013-03-22 Scan Temperature : 35.60 Scan Time : 01:45:25 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

data_processing:
Extraction Software : GenePix Pro
Extraction Software Version : 5.0.0.51
Datafile type : GenePix Results 3
Image Origin : 520, 3520

value: Human Universal Reference RNA (Stratagene)


title: Genomic DNA from pilocytic astrocytoma PA16

tag: gender

value: Cerebellum


title: PHH_5D_control_exp2

description: T5_HD_ratios.txt, T5_LD_ratios.txt

source_name: Input DNA from PHH exposed to zero dose of AFB1 for 5 days

value: primary human hepatocytes

value: input

source_name: Immunoprecipitated DNA from PHH exposed to zero dose of AFB1 for 5 days

value: antibody against a monoclonal antibody against 5'-methylcytidine


title: PHH_5D_control_exp3

description: T5_HD_ratios.txt, T5_LD_ratios.txt

source_name: Immunoprecipitated from PHH exposed to zero dose of AFB1 for 5 days


title: Genomic DNA from pilocytic astrocytoma PA13

value: Pilocytic astrocytoma

value: male


title: PHH_5D_control_exp1

description: T5_HD_ratios.txt, T5_LD_ratios.txt


title: CY0511 D1

description: CY0511 D1 paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR

scan_protocol: Scan Power : 100 PMT Volts : 474 Pixel Size : 10 Laser on time : 200520 Laser Power : 3.60 Scan Date : 2013-03-22 Scan Temperature : 35.45 Scan Time : 00:33:34 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0


title: PE-Term-AGA, rep8

description:
SAMPLE_15897
Placenta sample purchased from the Research Centre for Women’s and Infants’ Health (RCWIH) BioBank (Toronto, Canada), which utilizes a systematic sampling procedure in which four tissue biopsies (one sample/quadrant) are collected and pooled per placenta. At the time of sample collection and purchase, PE was defined as the onset of systolic pressure ≥ 140 mmHg and/or diastolic pressure ≥ 90 mmHg after the 20th week of gestation, accompanied by proteinuria (greater than 300 mg protein/day, or greater ≥ 2+ by dipstick). CH: chronic maternal hypertension; systolic pressure ≥ 140 mmHg and/or sustained diastolic ≥ 90 mmHg before the 20th week of gestation. Preterm: delivery prior to 34 weeks gestation. SGA: small-for-gestational-age infant; neonatal birth weight < 10th percentile for gestational age and sex. AGA: average-for-gestational age infant.

tag: diagnosis

tag: tissue

tag: maternal age

tag: maternal bmi

tag: maternal ethnicity

value: Black

tag: maternal blood type

value: A

tag: previous nulliparity

tag: previous miscarriage

tag: previous hypertensive pregnancy

tag: mean uterine pi

tag: mean umbilical pi

tag: maximum systolic bp

tag: maximum diastolic bp

tag: mode proteinuria

tag: hellp diagnosis

tag: iugr diagnosis

tag: attempted vaginal delivery

tag: ga (day)

tag: infant gender

value: F

tag: newborn weight z-score

tag: apgar score (1 min)

tag: apgar score (5 min)


title: CY0511 D5

description: CY0511 D5 paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR

scan_protocol: Scan Power : 100 PMT Volts : 476 Pixel Size : 10 Laser on time : 200575 Laser Power : 3.59 Scan Date : 2013-03-22 Scan Temperature : 35.60 Scan Time : 01:29:10 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

tag: reference sample name

tag: test sample name

tag: time point (days)


title: Genomic DNA from foetal brain

source_name: Foetal brain (Biochain #B106024)

tag: pathology

value: Foetal brain

tag: age (yrs)

tag: gender

value: female

tag: tumour location

value: Whole brain


title: Genomic DNA from pilocytic astrocytoma PA15


title: Cont-Term-CH, rep7

description:
SAMPLE_15873
Placenta sample purchased from the Research Centre for Women’s and Infants’ Health (RCWIH) BioBank (Toronto, Canada), which utilizes a systematic sampling procedure in which four tissue biopsies (one sample/quadrant) are collected and pooled per placenta. At the time of sample collection and purchase, PE was defined as the onset of systolic pressure ≥ 140 mmHg and/or diastolic pressure ≥ 90 mmHg after the 20th week of gestation, accompanied by proteinuria (greater than 300 mg protein/day, or greater ≥ 2+ by dipstick). CH: chronic maternal hypertension; systolic pressure ≥ 140 mmHg and/or sustained diastolic ≥ 90 mmHg before the 20th week of gestation. Preterm: delivery prior to 34 weeks gestation. SGA: small-for-gestational-age infant; neonatal birth weight < 10th percentile for gestational age and sex. AGA: average-for-gestational age infant.

source_name: Human placenta from Cont-Term-CH pregnancy

tag: diagnosis

value: non-PE

tag: tissue

value: Placenta

tag: maternal age

tag: maternal bmi

tag: maternal ethnicity

tag: maternal blood type

value: O

tag: previous nulliparity

value: No

tag: previous miscarriage

value: Yes

tag: previous hypertensive pregnancy

tag: mean uterine pi

tag: mean umbilical pi

tag: maximum systolic bp

tag: maximum diastolic bp

tag: mode of delivery

value: Vaginal

tag: ga (week)

tag: nicu transfer

tag: placental weight z-score

tag: umbilical cord diameter

tag: chorioamnionitis diagnosis


title: CY0511 D-2

description: CY0511 D-2 paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR

scan_protocol: Scan Power : 100 PMT Volts : 486 Pixel Size : 10 Laser on time : 200503 Laser Power : 3.60 Scan Date : 2013-03-22 Scan Temperature : 35.48 Scan Time : 00:15:46 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

tag: reference sample name

value: Human Universal Reference RNA (Stratagene)

tag: test sample name

tag: time point (days)


title: CY0511 D3

description: CY0511 D3 paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR

scan_protocol: Scan Power : 100 PMT Volts : 466 Pixel Size : 10 Laser on time : 202830 Laser Power : 3.60 Scan Date : 2013-03-27 Scan Temperature : 33.35 Scan Time : 14:37:30 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0


title: Genomic DNA from pilocytic astrocytoma PA14

tag: pathology

tag: age (yrs)

tag: gender

tag: tumour location

value: Cerebellum


title: Cont-Term-CH, rep6

description:
SAMPLE_15848
Placenta sample purchased from the Research Centre for Women’s and Infants’ Health (RCWIH) BioBank (Toronto, Canada), which utilizes a systematic sampling procedure in which four tissue biopsies (one sample/quadrant) are collected and pooled per placenta. At the time of sample collection and purchase, PE was defined as the onset of systolic pressure ≥ 140 mmHg and/or diastolic pressure ≥ 90 mmHg after the 20th week of gestation, accompanied by proteinuria (greater than 300 mg protein/day, or greater ≥ 2+ by dipstick). CH: chronic maternal hypertension; systolic pressure ≥ 140 mmHg and/or sustained diastolic ≥ 90 mmHg before the 20th week of gestation. Preterm: delivery prior to 34 weeks gestation. SGA: small-for-gestational-age infant; neonatal birth weight < 10th percentile for gestational age and sex. AGA: average-for-gestational age infant.

tag: diagnosis

tag: tissue

tag: maternal age

tag: maternal bmi

tag: maternal ethnicity

value: Caucasian

tag: maternal blood type

value: B

tag: previous nulliparity

tag: previous miscarriage

tag: previous hypertensive pregnancy

tag: mean uterine pi

tag: mode proteinuria

tag: hellp diagnosis

tag: iugr diagnosis

tag: attempted vaginal delivery

tag: ga (day)

tag: infant gender

value: M

tag: newborn weight z-score

tag: apgar score (1 min)

tag: apgar score (5 min)


title: CY0511 D-11

description: CY0511 D-11 paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR

scan_protocol: Scan Power : 100 PMT Volts : 479 Pixel Size : 10 Laser on time : 200442 Laser Power : 3.61 Scan Date : 2013-03-21 Scan Temperature : 35.54 Scan Time : 23:15:59 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

tag: reference sample name

tag: test sample name

tag: time point (days)


title: Genomic DNA from pilocytic astrocytoma PA10

tag: pathology

value: Pilocytic astrocytoma

tag: age (yrs)

tag: gender

value: male

tag: tumour location


title: Genomic DNA from pilocytic astrocytoma PA11


title: CY0510 D5

description: CY0510 D5 paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR

scan_protocol: Scan Power : 100 PMT Volts : 497 Pixel Size : 10 Laser on time : 200408 Laser Power : 3.61 Scan Date : 2013-03-21 Scan Temperature : 35.24 Scan Time : 22:41:06 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0


title: Genomic DNA from pilocytic astrocytoma PA12

value: Brain stem


title: CY0510 D7

description: CY0510 D7 paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR

scan_protocol: Scan Power : 100 PMT Volts : 500 Pixel Size : 10 Laser on time : 200424 Laser Power : 3.61 Scan Date : 2013-03-21 Scan Temperature : 35.39 Scan Time : 22:57:54 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0


title: PE-PreT-AGA, rep7

description:
SAMPLE_15861
Placenta sample purchased from the Research Centre for Women’s and Infants’ Health (RCWIH) BioBank (Toronto, Canada), which utilizes a systematic sampling procedure in which four tissue biopsies (one sample/quadrant) are collected and pooled per placenta. At the time of sample collection and purchase, PE was defined as the onset of systolic pressure ≥ 140 mmHg and/or diastolic pressure ≥ 90 mmHg after the 20th week of gestation, accompanied by proteinuria (greater than 300 mg protein/day, or greater ≥ 2+ by dipstick). CH: chronic maternal hypertension; systolic pressure ≥ 140 mmHg and/or sustained diastolic ≥ 90 mmHg before the 20th week of gestation. Preterm: delivery prior to 34 weeks gestation. SGA: small-for-gestational-age infant; neonatal birth weight < 10th percentile for gestational age and sex. AGA: average-for-gestational age infant.

scan_protocol: Scanning was performed by the Princess Margaret Genomics Centre (Toronto, Canada) as per Affymetrics protocols.

tag: diagnosis

value: PE

tag: tissue

tag: maternal age

tag: maternal bmi

tag: maternal ethnicity

tag: maternal blood type

tag: previous nulliparity

tag: previous miscarriage

tag: previous hypertensive pregnancy

tag: mean uterine pi

tag: mean umbilical pi

tag: maximum systolic bp

tag: maximum diastolic bp

tag: mode of delivery

value: C-Section

tag: ga (week)

value: F

tag: nicu transfer

tag: placental weight z-score

tag: umbilical cord diameter

tag: chorioamnionitis diagnosis


title: Cont-preT-AGA, rep13

description:
SAMPLE_15479
Placenta sample purchased from the Research Centre for Women’s and Infants’ Health (RCWIH) BioBank (Toronto, Canada), which utilizes a systematic sampling procedure in which four tissue biopsies (one sample/quadrant) are collected and pooled per placenta. At the time of sample collection and purchase, PE was defined as the onset of systolic pressure ≥ 140 mmHg and/or diastolic pressure ≥ 90 mmHg after the 20th week of gestation, accompanied by proteinuria (greater than 300 mg protein/day, or greater ≥ 2+ by dipstick). CH: chronic maternal hypertension; systolic pressure ≥ 140 mmHg and/or sustained diastolic ≥ 90 mmHg before the 20th week of gestation. Preterm: delivery prior to 34 weeks gestation. SGA: small-for-gestational-age infant; neonatal birth weight < 10th percentile for gestational age and sex. AGA: average-for-gestational age infant.

tag: diagnosis

value: non-PE

tag: tissue

tag: maternal age

value: East Indian

value: A

tag: mode proteinuria

tag: hellp diagnosis

tag: iugr diagnosis

tag: attempted vaginal delivery

tag: ga (day)

tag: infant gender

tag: newborn weight z-score

tag: apgar score (1 min)

tag: apgar score (5 min)


title: CY0510 D3

description: CY0510 D3 paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR

scan_protocol: Scan Power : 100 PMT Volts : 497 Pixel Size : 10 Laser on time : 201189 Laser Power : 3.51 Scan Date : 2013-03-22 Scan Temperature : 34.78 Scan Time : 14:54:38 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

tag: reference sample name

tag: test sample name

tag: time point (days)


title: CY0510 D-2

description: CY0510 D-2 paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR

scan_protocol: Scan Power : 100 PMT Volts : 486 Pixel Size : 10 Laser on time : 200317 Laser Power : 3.57 Scan Date : 2013-03-21 Scan Temperature : 36.12 Scan Time : 18:29:02 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

data_processing:
Extraction Software : GenePix Pro
Extraction Software Version : 5.0.0.51
Datafile type : GenePix Results 3
Image Origin : 520, 4000


title: Genomic DNA from pilocytic astrocytoma PA8

scan_protocol: Illumina iScan with Autoloader2 to scan the arrays by Barts and The London Genome Centre (QMUL, UK).

tag: pathology

tag: age (yrs)

tag: gender

value: female

tag: tumour location


title: CY480 D7

description: PAXGene NHP aRNA, 8ug, Epicenter amplified, Cy5 labeled, spiked with 20ng doping control labeled separately

scan_protocol: Scan Power : 100 PMT Volts : 536 Pixel Size : 10 Laser on time : 182323 Laser Power : 3.12 Scan Date : 2012-07-03 Scan Temperature : 33.22 Scan Time : 13:14:41 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

source_name: Stratagene Human Universal Reference aa aRNA, NuGEN amplified, 5ug of pooled Alexa Fluor 3 labeled

source_name: 8ug NHP aRNA EpiC amp Cy5 labeled, spiked with 20ng dc


title: CY0510 D-11

description: CY0510 D-11 paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR

scan_protocol: Scan Power : 100 PMT Volts : 486 Pixel Size : 10 Laser on time : 200187 Laser Power : 3.60 Scan Date : 2013-03-21 Scan Temperature : 35.70 Scan Time : 16:18:48 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0


title: Genomic DNA from pilocytic astrocytoma PA6

value: Hypothalamus


title: CY480 D5

scan_protocol: Scan Power : 100 PMT Volts : 538 Pixel Size : 10 Laser on time : 181355 Laser Power : 3.10 Scan Date : 2012-06-29 Scan Temperature : 34.60 Scan Time : 16:48:34 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

data_processing:
Extraction Software : GenePix Pro
Extraction Software Version : 5.0.0.51
Datafile type : GenePix Results 3
Image Origin : 760, 4360

source_name: Stratagene Human Universal Reference aa aRNA, 5ug of pooled Cy3 labeled


title: Genomic DNA from pilocytic astrocytoma PA5

value: Cerebral cortex


title: Cont-preT-AGA, rep11

description:
SAMPLE_14941
Placenta sample purchased from the Research Centre for Women’s and Infants’ Health (RCWIH) BioBank (Toronto, Canada), which utilizes a systematic sampling procedure in which four tissue biopsies (one sample/quadrant) are collected and pooled per placenta. At the time of sample collection and purchase, PE was defined as the onset of systolic pressure ≥ 140 mmHg and/or diastolic pressure ≥ 90 mmHg after the 20th week of gestation, accompanied by proteinuria (greater than 300 mg protein/day, or greater ≥ 2+ by dipstick). CH: chronic maternal hypertension; systolic pressure ≥ 140 mmHg and/or sustained diastolic ≥ 90 mmHg before the 20th week of gestation. Preterm: delivery prior to 34 weeks gestation. SGA: small-for-gestational-age infant; neonatal birth weight < 10th percentile for gestational age and sex. AGA: average-for-gestational age infant.

tag: diagnosis

tag: tissue

value: Placenta

tag: maternal age

tag: maternal bmi

tag: maternal ethnicity

value: Black

tag: maternal blood type

value: AB

tag: previous nulliparity

value: Yes

tag: previous miscarriage

value: No

tag: previous hypertensive pregnancy

tag: mean uterine pi

tag: mean umbilical pi

tag: maximum systolic bp

tag: maximum diastolic bp

tag: mode of delivery

tag: ga (week)

tag: nicu transfer

tag: placental weight z-score

tag: umbilical cord diameter

tag: chorioamnionitis diagnosis


title: CY480 D-2

scan_protocol: Scan Power : 100 PMT Volts : 557 Pixel Size : 10 Laser on time : 181309 Laser Power : 3.09 Scan Date : 2012-06-29 Scan Temperature : 34.41 Scan Time : 16:02:56 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

tag: reference sample name

value: Human Universal Reference RNA (Stratagene)

tag: test sample name

tag: time point (days)


title: CY480 D-11

scan_protocol: Scan Power : 100 PMT Volts : 553 Pixel Size : 10 Laser on time : 181293 Laser Power : 3.10 Scan Date : 2012-06-29 Scan Temperature : 34.35 Scan Time : 15:46:31 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0


title: Cont-preT-AGA, rep14

description:
SAMPLE_16225
Placenta sample purchased from the Research Centre for Women’s and Infants’ Health (RCWIH) BioBank (Toronto, Canada), which utilizes a systematic sampling procedure in which four tissue biopsies (one sample/quadrant) are collected and pooled per placenta. At the time of sample collection and purchase, PE was defined as the onset of systolic pressure ≥ 140 mmHg and/or diastolic pressure ≥ 90 mmHg after the 20th week of gestation, accompanied by proteinuria (greater than 300 mg protein/day, or greater ≥ 2+ by dipstick). CH: chronic maternal hypertension; systolic pressure ≥ 140 mmHg and/or sustained diastolic ≥ 90 mmHg before the 20th week of gestation. Preterm: delivery prior to 34 weeks gestation. SGA: small-for-gestational-age infant; neonatal birth weight < 10th percentile for gestational age and sex. AGA: average-for-gestational age infant.

tag: diagnosis

tag: tissue

tag: maternal age

tag: maternal bmi

tag: maternal ethnicity

value: Caucasian

tag: maternal blood type

value: O

tag: mode proteinuria

tag: hellp diagnosis

tag: iugr diagnosis

tag: attempted vaginal delivery

value: Vaginal

tag: ga (day)

tag: infant gender

value: M

tag: newborn weight z-score

tag: apgar score (1 min)

tag: apgar score (5 min)


title: Genomic DNA from pilocytic astrocytoma PA7

tag: pathology

value: Pilocytic astrocytoma

tag: age (yrs)

tag: gender

value: male

tag: tumour location

value: Cerebellum


title: CY480 D1

scan_protocol: Scan Power : 100 PMT Volts : 518 Pixel Size : 10 Laser on time : 182310 Laser Power : 3.10 Scan Date : 2012-07-03 Scan Temperature : 33.01 Scan Time : 13:00:42 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

tag: reference sample name

tag: test sample name

tag: time point (days)


title: CY508 5

description: CY508 5

scan_protocol: Scan Power : 100 PMT Volts : 538 Pixel Size : 10 Laser on time : 193624 Laser Power : 3.11 Scan Date : 2012-11-06 Scan Temperature : 33.35 Scan Time : 17:07:12 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

data_processing:
Extraction Software : GenePix Pro
Extraction Software Version : 5.0.0.51
Datafile type : GenePix Results 3
Image Origin : 580, 4970

source_name: PAXGene NHP aRNA, 8ug, EpiC amplified, Cy5 lab, spiked dop control

treatment_protocol:
Vaccine Route : ID
Treatment : Vaccine
Treatment group : 1
Vaccine Dose : Double
Day : 5


title: Genomic DNA from pilocytic astrocytoma PA9


title: CY508 7

description: CY508 7

scan_protocol: Scan Power : 100 PMT Volts : 536 Pixel Size : 10 Laser on time : 193642 Laser Power : 3.10 Scan Date : 2012-11-06 Scan Temperature : 33.44 Scan Time : 17:24:28 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

treatment_protocol:
Vaccine Route : ID
Treatment : Vaccine
Treatment group : 1
Vaccine Dose : Double
Day : 7


title: CY480 D3

scan_protocol: Scan Power : 100 PMT Volts : 543 Pixel Size : 10 Laser on time : 181338 Laser Power : 3.09 Scan Date : 2012-06-29 Scan Temperature : 34.57 Scan Time : 16:32:21 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0


title: CY0510 D1

description: CY0510 D1 paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR

scan_protocol: Scan Power : 100 PMT Volts : 496 Pixel Size : 10 Laser on time : 200346 Laser Power : 3.55 Scan Date : 2013-03-21 Scan Temperature : 34.26 Scan Time : 21:38:42 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0


title: Genomic DNA from pilocytic astrocytoma PA2


title: Genomic DNA from pilocytic astrocytoma PA3


title: Genomic DNA from diffuse astrocytoma DA8

source_name: Paediatric diffuse astrocytoma

value: Diffuse astrocytoma


title: PHH_WO_LD_exp3 [mRNA]

description: BrainArray custom CDF v15.1.0

hyb_protocol: Amplified, biotinylated and fragmented targets were then hybridized on to the arrays.

scan_protocol: After hybridization, arrays were washed and stained using an Affymetrix fluidics station and scanned by use of an Affymetrix GeneArray scanner. A total of 6 RNA samples was prepared and analyzed on GeneChip arrays (treated and control samples from each time point were at least in triplicate). Normalization quality controls, including scaling factors, average intensities, present calls, background intensities, noise, and raw Q values, appeared to be within acceptable limits for all chips. Hybridization controls BioB, BioC, BioD, and CreX were called present on all chips and yielded the expected increases in intensities.

data_processing: The Arrayanalysis.org web service was used for quality control (27) and all microarrays except one were of high quality which was omitted from the analyses. CEL files were imported into R v2.15.3 (http://www.r-project.org) using the “affy” library (28) within BioConductor (v2.9) (29). Probe re-annotation, normalization and data filtering was performed as previously described (30).

label: Biotin

label_protocol: High-density oligonucleotide GeneChips from Affymetrix were used to measure gene expression levels (Human Genome U133 Plus 2.0 array (604,258 probes)). Targets for these arrays were prepared, hybridized and scanned according to the Affymetrix protocol (Affymetrix).Normalization quality controls appeared to be within acceptable limits for almost all chips.

growth_protocol: Cryopreserved primary human hepatocytes (PHH) were purchased from Life Technologies. Cells were cultured in pre-coated 24-well and 6-well plates (700,000 cells/ml) in a 2-layer collagen sandwich (A11428-02, Gibco), according to the supplier’s protocol (Invitrogen, 2012). The following culture media were used: Hepatocyte Thawing Medium (HTM) for thawing (CM7500, Gibco), Williams’ Medium E (1x, no phenol red) (A1217601, Gibco) + Cell Maintenance supplement B kit (CM4000, Gibco) for plating and incubation.

extract_protocol: Cells were cultured in triplicate in 24 wells (RNA) or 6 wells (DNA) in a collagen sandwich layer. Following 5 days of repetitive daily exposure the treatment was removed for 3 days (washout period), then cells lysates were harvested for DNA and total RNA isolation. At the end of washout, medium was removed and PHH were harvested in Qiazol (Qiagen). Total RNA was isolated using a miRNeasy Mini Kit (Qiagen) according to the manufacturer’s protocol and followed by DNase I (Qiagen) treatment. Upon purification, RNA concentrations were measured by means of a NanoDrop® ND-1000 spectrophotometer (Thermo Scientific) at 260 and 280 nm. RNA quality and integrity were assessed by using automated gel electrophoresis on an Agilent 2100 Bioanalyzer system (Agilent Technologies). Only RNA samples which showed clear 18S and 28S peaks and with an RNA integrity number (RIN) higher than 8, were used. Samples were stored at -80ºC until RNA hybridization.

treatment_protocol: After quick thawing in a water bath at 37°C, viability of the cells was checked by a Trypan blue (CAS no. 72-57-1, Sigma–Aldrich) exclusion test as instructed in the supplier’s protocol (Invitrogen, 2012). All viability scores after thawing were in agreement with those listed by the supplier. Before AFB1 treatment, cells were allowed to acclimatize for 48 hours. This is needed for the hepatocytes to restore an in vivo like cellular configuration and enzyme expression levels as optimally as possible.AFB1 doses causing minimal (IC20) cytotoxicity after 5 days of repetitive daily exposure were established by means of the MTT assay (23). Furthermore, crucial liver function enzymes such as lactate dehydrogenase (LDH) and alanine transaminase (ALT) were measured. LDH and ALT were spectrophotometrically determined on a Cobas 8000 Modular Analyser (Roche Diagnostics, Basel, Switzerland). Based on this data,  0.3 µM of AFB1, was selected for the main experiment.

tag: cell type

value: primary human hepatocytes

tag: main source

value: liver

tag: study type

value: Wash out effect

tag: assay type

value: ex vivo

tag: strain

tag: agent

value: aflatoxin B1

tag: dose

tag: dose unit

value: uM

tag: dose duration

tag: duration unit

value: days

tag: dose frequency

value: daily

tag: vehicle

value: DMSO

tag: route

value: medium


title: PHH_WO_LD_exp2 [mRNA]

description: BrainArray custom CDF v15.1.0


title: CY508 1

description: CY508 1

scan_protocol: Scan Power : 100 PMT Volts : 527 Pixel Size : 10 Laser on time : 193595 Laser Power : 3.11 Scan Date : 2012-11-06 Scan Temperature : 33.16 Scan Time : 16:37:53 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

value: Human Universal Reference RNA (Stratagene)

treatment_protocol:
Vaccine Route : ID
Treatment : Vaccine
Treatment group : 1
Vaccine Dose : Double
Day : 1


title: PHH_WO_LD_exp1 [mRNA]

description: BrainArray custom CDF v15.1.0


title: PHH_WO_LD_control_exp3 [mRNA]

description: BrainArray custom CDF v15.1.0


title: Genomic DNA from pilocytic astrocytoma PA1

tag: pathology

tag: age (yrs)

tag: gender

value: female

tag: tumour location

value: Cerebral cortex


title: Genomic DNA from diffuse astrocytoma DA7


title: Genomic DNA from diffuse astrocytoma DA10


title: Genomic DNA from diffuse astrocytoma DA9


title: PE-PreT-AGA, rep6

description:
SAMPLE_14551
Placenta sample purchased from the Research Centre for Women’s and Infants’ Health (RCWIH) BioBank (Toronto, Canada), which utilizes a systematic sampling procedure in which four tissue biopsies (one sample/quadrant) are collected and pooled per placenta. At the time of sample collection and purchase, PE was defined as the onset of systolic pressure ≥ 140 mmHg and/or diastolic pressure ≥ 90 mmHg after the 20th week of gestation, accompanied by proteinuria (greater than 300 mg protein/day, or greater ≥ 2+ by dipstick). CH: chronic maternal hypertension; systolic pressure ≥ 140 mmHg and/or sustained diastolic ≥ 90 mmHg before the 20th week of gestation. Preterm: delivery prior to 34 weeks gestation. SGA: small-for-gestational-age infant; neonatal birth weight < 10th percentile for gestational age and sex. AGA: average-for-gestational age infant.

tag: diagnosis

value: PE

tag: tissue

value: Placenta

tag: maternal age

tag: maternal bmi

tag: maternal ethnicity

value: Caucasian

tag: maternal blood type

value: O

tag: previous nulliparity

value: Yes

tag: previous miscarriage

value: No

tag: previous hypertensive pregnancy

tag: mean uterine pi

tag: mean umbilical pi

tag: maximum systolic bp

tag: maximum diastolic bp

tag: mode proteinuria

tag: hellp diagnosis

tag: iugr diagnosis

tag: attempted vaginal delivery

tag: mode of delivery

value: C-Section

tag: ga (week)

tag: ga (day)

tag: infant gender

value: M

tag: newborn weight z-score

tag: apgar score (1 min)

tag: apgar score (5 min)

tag: nicu transfer

tag: placental weight z-score

tag: umbilical cord diameter

tag: chorioamnionitis diagnosis


title: Genomic DNA from diffuse astrocytoma DA5

tag: pathology

value: Diffuse astrocytoma

tag: age (yrs)

tag: gender

value: male

tag: tumour location


title: PHH_WO_LD_control_exp2 [mRNA]

description: BrainArray custom CDF v15.1.0

tag: cell type

value: primary human hepatocytes

tag: main source

value: liver

tag: study type

value: Wash out effect

tag: assay type

value: ex vivo

tag: strain

tag: agent

tag: dose

tag: dose unit

tag: dose duration

tag: duration unit

value: days

tag: dose frequency

tag: vehicle

tag: route


title: CY508 -2

description: CY508 -2

scan_protocol: Scan Power : 100 PMT Volts : 521 Pixel Size : 10 Laser on time : 193578 Laser Power : 3.10 Scan Date : 2012-11-06 Scan Temperature : 33.01 Scan Time : 16:21:15 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

tag: reference sample name

value: Human Universal Reference RNA (Stratagene)

treatment_protocol:
Vaccine Route : ID
Treatment : Vaccine
Treatment group : 1
Vaccine Dose : Double
Day : -2

tag: test sample name

tag: time point (days)


title: CY508 -11

description: CY508 -11

scan_protocol: Scan Power : 100 PMT Volts : 535 Pixel Size : 10 Laser on time : 193565 Laser Power : 3.10 Scan Date : 2012-11-06 Scan Temperature : 32.89 Scan Time : 16:07:21 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

treatment_protocol:
Vaccine Route : ID
Treatment : Vaccine
Treatment group : 1
Vaccine Dose : Double
Day : -11


title: Genomic DNA from diffuse astrocytoma DA1

tag: pathology

tag: age (yrs)

tag: gender

value: female

tag: tumour location

value: Cerebral cortex


title: CY507 5

description: CY507 5

scan_protocol: Scan Power : 100 PMT Volts : 548 Pixel Size : 10 Laser on time : 193531 Laser Power : 3.10 Scan Date : 2012-11-06 Scan Temperature : 32.74 Scan Time : 15:34:04 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

data_processing:
Extraction Software : GenePix Pro
Extraction Software Version : 5.0.0.51
Datafile type : GenePix Results 3
Image Origin : 380, 4650


title: Genomic DNA from diffuse astrocytoma DA6


title: Cont-preT-AGA, rep9

description:
SAMPLE_14429
Placenta sample purchased from the Research Centre for Women’s and Infants’ Health (RCWIH) BioBank (Toronto, Canada), which utilizes a systematic sampling procedure in which four tissue biopsies (one sample/quadrant) are collected and pooled per placenta. At the time of sample collection and purchase, PE was defined as the onset of systolic pressure ≥ 140 mmHg and/or diastolic pressure ≥ 90 mmHg after the 20th week of gestation, accompanied by proteinuria (greater than 300 mg protein/day, or greater ≥ 2+ by dipstick). CH: chronic maternal hypertension; systolic pressure ≥ 140 mmHg and/or sustained diastolic ≥ 90 mmHg before the 20th week of gestation. Preterm: delivery prior to 34 weeks gestation. SGA: small-for-gestational-age infant; neonatal birth weight < 10th percentile for gestational age and sex. AGA: average-for-gestational age infant.

scan_protocol: Scanning was performed by the Princess Margaret Genomics Centre (Toronto, Canada) as per Affymetrics protocols.

data_processing:
Data was processed, normalized, and converted into log2 values in R 3.0.1 using the Affy library from Bioconductor.
The file complete_dataset.csv contains the expression information for 14,651 genes found in common across the different array platforms analyzed. Row names contain gene symbols.

treatment_protocol: Four tissue biopsies (one sample/quadrant, excluding the chorionic plate) are collected per placenta, rinsed in PBS to remove contaminating maternal blood, pooled, crushed into a powder, and snap-frozen in liquid nitrogen.

tag: diagnosis

value: non-PE

tag: tissue

value: Placenta

tag: maternal age

tag: maternal bmi

tag: maternal ethnicity

tag: maternal blood type

value: B

tag: previous nulliparity

tag: previous miscarriage

tag: previous hypertensive pregnancy

tag: mean uterine pi

tag: mean umbilical pi

tag: maximum systolic bp

tag: maximum diastolic bp

tag: mode proteinuria

tag: hellp diagnosis

tag: iugr diagnosis

tag: attempted vaginal delivery

tag: mode of delivery

tag: ga (week)

tag: ga (day)

tag: infant gender

tag: newborn weight z-score

tag: apgar score (1 min)

tag: apgar score (5 min)

tag: nicu transfer

tag: placental weight z-score

tag: umbilical cord diameter

tag: chorioamnionitis diagnosis


title: PHH_5D_LD_exp3

hyb_protocol: Amplified, biotinylated and fragmented targets were then hybridized on to the BrainArray custom CDF v15.1.0 array.

scan_protocol: After hybridization, arrays were washed and stained using an Affymetrix fluidics station and scanned by use of an Affymetrix GeneArray scanner. A total of 60 RNA samples was prepared and analyzed on GeneChip arrays (treated and control samples from each time point were at least in triplicate). Normalization quality controls, including scaling factors, average intensities, present calls, background intensities, noise, and raw Q values, appeared to be within acceptable limits for all chips. Hybridization controls BioB, BioC, BioD, and CreX were called present on all chips and yielded the expected increases in intensities.

extract_protocol: Cells were cultured in triplicate in 24 wells (RNA) or 6 wells (DNA) in a collagen sandwich layer. Following 5 days of repetitive daily exposure, cells lysates were harvested for DNA and total RNA isolation. At the end of treatment, medium was removed and PHH were harvested in Qiazol (Qiagen). Total RNA was isolated using a miRNeasy Mini Kit (Qiagen) according to the manufacturer’s protocol and followed by DNase I (Qiagen) treatment. Upon purification, RNA concentrations were measured by means of a NanoDrop® ND-1000 spectrophotometer (Thermo Scientific) at 260 and 280 nm. RNA quality and integrity were assessed by using automated gel electrophoresis on an Agilent 2100 Bioanalyzer system (Agilent Technologies). Only RNA samples which showed clear 18S and 28S peaks and with an RNA integrity number (RIN) higher than 8, were used. Samples were stored at -80ºC until RNA hybridization.

treatment_protocol: After quick thawing in a water bath at 37°C, viability of the cells was checked by a Trypan blue (CAS no. 72-57-1, Sigma–Aldrich) exclusion test as instructed in the supplier’s protocol (Invitrogen, 2012). All viability scores after thawing were in agreement with those listed by the supplier. Before AFB1 treatment, cells were allowed to acclimatize for 48 hours. This is needed for the hepatocytes to restore an in vivo like cellular configuration and enzyme expression levels as optimally as possible.AFB1 doses causing minimal (IC20) and moderate (IC40) cytotoxicity after 5 days of repetitive daily exposure were established by means of the MTT assay (23). Furthermore, crucial liver function enzymes such as lactate dehydrogenase (LDH) and alanine transaminase (ALT) were measured. LDH and ALT were spectrophotometrically determined on a Cobas 8000 Modular Analyser (Roche Diagnostics, Basel, Switzerland). Based on this data, two doses, 0.3 µM and 1 µM of AFB1, were selected for the main experiment.

tag: cell type

tag: study type

value: Single Dose Toxicity

tag: assay type

tag: strain

tag: compound

value: aflatoxin B1

tag: dose

tag: dose unit

value: uM

tag: dose duration

tag: duration unit

tag: dose frequency

value: daily

tag: vehicle

value: DMSO

tag: route

value: medium


title: CY508 3

description: CY508 3

scan_protocol: Scan Power : 100 PMT Volts : 515 Pixel Size : 10 Laser on time : 193609 Laser Power : 3.11 Scan Date : 2012-11-06 Scan Temperature : 33.29 Scan Time : 16:51:40 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

tag: reference sample name

treatment_protocol:
Vaccine Route : ID
Treatment : Vaccine
Treatment group : 1
Vaccine Dose : Double
Day : 3

tag: test sample name

tag: time point (days)


title: PHH_5D_LD_exp2

value: primary human hepatocytes


title: Genomic DNA from diffuse astrocytoma DA3

scan_protocol: Illumina iScan with Autoloader2 to scan the arrays by Barts and The London Genome Centre (QMUL, UK).

tag: pathology

value: Diffuse astrocytoma

tag: age (yrs)

tag: gender

tag: tumour location


title: CY507 3

description: CY507 3

scan_protocol: Scan Power : 100 PMT Volts : 539 Pixel Size : 10 Laser on time : 193425 Laser Power : 3.06 Scan Date : 2012-11-06 Scan Temperature : 31.79 Scan Time : 13:47:53 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0


title: PHH_WO_LD_control_exp1 [mRNA]

description: BrainArray custom CDF v15.1.0

tag: cell type

tag: main source

value: liver

tag: study type

value: Wash out effect

tag: assay type

tag: agent


title: Cont-preT-AGA, rep8

description:
SAMPLE_14403
Placenta sample purchased from the Research Centre for Women’s and Infants’ Health (RCWIH) BioBank (Toronto, Canada), which utilizes a systematic sampling procedure in which four tissue biopsies (one sample/quadrant) are collected and pooled per placenta. At the time of sample collection and purchase, PE was defined as the onset of systolic pressure ≥ 140 mmHg and/or diastolic pressure ≥ 90 mmHg after the 20th week of gestation, accompanied by proteinuria (greater than 300 mg protein/day, or greater ≥ 2+ by dipstick). CH: chronic maternal hypertension; systolic pressure ≥ 140 mmHg and/or sustained diastolic ≥ 90 mmHg before the 20th week of gestation. Preterm: delivery prior to 34 weeks gestation. SGA: small-for-gestational-age infant; neonatal birth weight < 10th percentile for gestational age and sex. AGA: average-for-gestational age infant.

tag: diagnosis

tag: tissue

tag: maternal age

tag: maternal bmi

tag: maternal ethnicity

value: Caucasian

tag: maternal blood type

value: A

tag: previous nulliparity

value: No

tag: previous miscarriage

tag: previous hypertensive pregnancy

tag: mean uterine pi

tag: mean umbilical pi

tag: maximum systolic bp

tag: maximum diastolic bp

tag: mode proteinuria

tag: hellp diagnosis

tag: iugr diagnosis

tag: attempted vaginal delivery

value: Yes

tag: mode of delivery

value: Vaginal

tag: ga (week)

tag: ga (day)

tag: infant gender

value: M

tag: newborn weight z-score

tag: apgar score (1 min)

tag: apgar score (5 min)

tag: nicu transfer

tag: placental weight z-score

tag: umbilical cord diameter

tag: chorioamnionitis diagnosis


title: Genomic DNA from diffuse astrocytoma DA4

tag: pathology

tag: age (yrs)

tag: gender

value: male

tag: tumour location

value: Cerebral cortex


title: Genomic DNA from pilocytic astrocytoma PA4

value: Pilocytic astrocytoma