title: PE-PreT-SGA, rep13

description:
SAMPLE_6171
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.

value: PE

tag: tissue

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: attempted vaginal delivery

tag: apgar score (1 min)

tag: apgar score (5 min)

tag: nicu transfer


title: Cont-Ter-AGA, rep7

status: Public on May 10 2016

type: RNA

city: Toronto

first: Brian

last: Cox

state: Ontario

address: 1 King's College Circle

department: Physiology

country: Canada

institute: University of Toronto

description:
SAMPLE_14259
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

molecule: total RNA

organism: Homo sapiens

source_name: Human placenta from Cont-Ter-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

value: non-PE

value: Placenta

tag: maternal age

tag: maternal bmi

tag: maternal ethnicity

tag: maternal blood type

value: A

tag: previous nulliparity

value: No

tag: previous miscarriage

value: Yes

tag: iugr diagnosis

tag: mode of delivery

value: C-Section

tag: ga (week)

tag: ga (day)

tag: infant gender

value: F

tag: newborn weight z-score

tag: placental weight z-score

tag: umbilical cord diameter

tag: chorioamnionitis diagnosis


title: Cont-Term-CH, rep5

description:
SAMPLE_14869
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: tissue

value: Caucasian

value: AB

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: attempted vaginal delivery

value: M

tag: apgar score (1 min)

tag: apgar score (5 min)

tag: nicu transfer


title: Cont-PreT-CH, rep3

description:
SAMPLE_6613
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: maternal age

tag: maternal bmi

tag: maternal ethnicity

value: Asian

tag: maternal blood type

value: B

tag: previous nulliparity

tag: previous miscarriage

tag: iugr diagnosis

tag: mode of delivery

tag: ga (week)

tag: ga (day)

tag: infant gender


title: Cont-Ter-AGA, rep6

description:
SAMPLE_14230
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: tissue

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: newborn weight z-score

tag: placental weight z-score

tag: umbilical cord diameter

tag: chorioamnionitis diagnosis


title: PE-PreT-CH, rep8

description:
SAMPLE_5947
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

tag: maternal age

tag: maternal bmi

tag: maternal ethnicity

value: Black

tag: maternal blood type

value: O

tag: previous nulliparity

tag: previous miscarriage

tag: iugr diagnosis

tag: attempted vaginal delivery

tag: apgar score (1 min)

tag: apgar score (5 min)

tag: nicu transfer


title: Cont-Ter-AGA, rep10

description:
SAMPLE_15568
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: tissue

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: mode of delivery

tag: ga (week)

tag: ga (day)

tag: infant gender


title: PE-PreT-SGA, rep12

description:
SAMPLE_15449
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-SGA pregnancy

tag: diagnosis

tag: maternal age

tag: maternal bmi

tag: maternal ethnicity

tag: maternal blood type

tag: previous nulliparity

tag: previous miscarriage

tag: iugr diagnosis

tag: newborn weight z-score

tag: placental weight z-score

tag: umbilical cord diameter

tag: chorioamnionitis diagnosis


title: PE-PreT-SGA, rep6

description:
SAMPLE_14416
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: tissue

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: attempted vaginal delivery

tag: apgar score (1 min)

tag: apgar score (5 min)

tag: nicu transfer


title: PE-PreT-SGA, rep10

description:
SAMPLE_15123
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: maternal age

tag: maternal bmi

tag: maternal ethnicity

value: East Indian

tag: maternal blood type

tag: previous nulliparity

tag: previous miscarriage

tag: iugr diagnosis

tag: mode of delivery

tag: ga (week)

tag: ga (day)

tag: infant gender


title: PE-PreT-SGA, rep7

description:
SAMPLE_14732
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: tissue

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: newborn weight z-score

tag: placental weight z-score

tag: umbilical cord diameter

tag: chorioamnionitis diagnosis


title: PE-PreT-CH, rep4

description:
SAMPLE_15080
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: maternal age

tag: maternal bmi

tag: maternal ethnicity

tag: maternal blood type

tag: previous nulliparity

tag: previous miscarriage

tag: iugr diagnosis

tag: attempted vaginal delivery

tag: apgar score (1 min)

tag: apgar score (5 min)

tag: nicu transfer


title: PE-Term-CH, rep3

description:
SAMPLE_6842
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-CH pregnancy

tag: tissue

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: mode of delivery

tag: ga (week)

tag: ga (day)

tag: infant gender


title: PE-Term-CH, rep2

description:
SAMPLE_4520
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: maternal age

tag: maternal bmi

tag: maternal ethnicity

tag: maternal blood type

tag: previous nulliparity

tag: previous miscarriage

tag: iugr diagnosis

value: Vaginal

tag: newborn weight z-score

tag: placental weight z-score

tag: umbilical cord diameter

tag: chorioamnionitis diagnosis


title: PE-Term-SGA, rep6

description:
SAMPLE_14392
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

value: PE

tag: tissue

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: attempted vaginal delivery

tag: apgar score (1 min)

tag: apgar score (5 min)

tag: nicu transfer


title: Cont-Ter-AGA, rep8

description:
SAMPLE_14967
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: maternal age

tag: maternal bmi

tag: maternal ethnicity

tag: maternal blood type

tag: previous nulliparity

tag: previous miscarriage

tag: iugr diagnosis

tag: mode of delivery

tag: ga (week)

tag: ga (day)

tag: infant gender


title: Cont-Ter-AGA, rep5

description:
SAMPLE_14061
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: tissue

value: Placenta

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: newborn weight z-score

tag: placental weight z-score

tag: umbilical cord diameter

tag: chorioamnionitis diagnosis


title: Cont-PreT-CH, rep5

description:
SAMPLE_6996
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: maternal age

tag: maternal bmi

tag: maternal ethnicity

tag: maternal blood type

value: A

tag: previous nulliparity

tag: previous miscarriage

tag: iugr diagnosis

tag: attempted vaginal delivery

tag: apgar score (1 min)

tag: apgar score (5 min)

tag: nicu transfer


title: PE-Term-SGA, rep5

description:
SAMPLE_13760
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: tissue

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: mode of delivery

tag: ga (week)

tag: ga (day)

tag: infant gender


title: Cont-Term-CH, rep3

description:
SAMPLE_13299
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: maternal age

tag: maternal bmi

tag: maternal ethnicity

tag: maternal blood type

tag: previous nulliparity

tag: previous miscarriage

value: Yes

tag: iugr diagnosis

tag: newborn weight z-score

tag: placental weight z-score

tag: umbilical cord diameter

tag: chorioamnionitis diagnosis


title: PE-PreT-SGA, rep4

description:
SAMPLE_12138
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: tissue

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: attempted vaginal delivery

value: C-Section

tag: apgar score (1 min)

tag: apgar score (5 min)

tag: nicu transfer


title: PE-Term-SGA, rep4

description:
SAMPLE_12673
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: maternal age

tag: maternal bmi

tag: maternal ethnicity

tag: maternal blood type

tag: previous nulliparity

tag: previous miscarriage

tag: iugr diagnosis

tag: mode of delivery

tag: ga (week)

tag: ga (day)

tag: infant gender


title: PE-PreT-SGA, rep5

description:
SAMPLE_12880
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: tissue

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: F

tag: newborn weight z-score

tag: placental weight z-score

tag: umbilical cord diameter

tag: chorioamnionitis diagnosis


title: PE-PreT-SGA, rep2

description:
SAMPLE_11387
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: maternal age

tag: maternal bmi

tag: maternal ethnicity

value: Caucasian

tag: maternal blood type

tag: previous nulliparity

tag: previous miscarriage

tag: iugr diagnosis

tag: attempted vaginal delivery

tag: apgar score (1 min)

tag: apgar score (5 min)

tag: nicu transfer


title: Cont-Ter-AGA, rep3

description:
SAMPLE_12747
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: tissue

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: mode of delivery

tag: ga (week)

tag: ga (day)

tag: infant gender


title: PE-PreT-CH, rep3

description:
SAMPLE_13810
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: maternal age

tag: maternal bmi

tag: maternal ethnicity

tag: maternal blood type

tag: previous nulliparity

tag: previous miscarriage

tag: iugr diagnosis

tag: newborn weight z-score

tag: placental weight z-score

tag: umbilical cord diameter

tag: chorioamnionitis diagnosis


title: PE-PreT-SGA, rep3

description:
SAMPLE_11857
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: tissue

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: attempted vaginal delivery

tag: apgar score (1 min)

tag: apgar score (5 min)

tag: nicu transfer


title: PE-Term-SGA, rep2

description:
SAMPLE_10683
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: maternal age

tag: maternal bmi

tag: maternal ethnicity

tag: maternal blood type

tag: previous nulliparity

tag: previous miscarriage

tag: iugr diagnosis

tag: mode of delivery

tag: ga (week)

tag: ga (day)

tag: infant gender


title: Cont-Ter-AGA, rep4

description:
SAMPLE_13287
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: tissue

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: newborn weight z-score

tag: placental weight z-score

tag: umbilical cord diameter

tag: chorioamnionitis diagnosis


title: PE-PreT-CH, rep2

description:
SAMPLE_10646
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: maternal age

tag: maternal bmi

tag: maternal ethnicity

value: Other

tag: maternal blood type

tag: previous nulliparity

tag: previous miscarriage

tag: iugr diagnosis

tag: attempted vaginal delivery

tag: apgar score (1 min)

tag: apgar score (5 min)

tag: nicu transfer


title: Cont-Ter-AGA, rep1

description:
SAMPLE_10625
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: tissue

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: mode of delivery

tag: ga (week)

tag: ga (day)

tag: infant gender

value: M


title: Cont-Ter-AGA, rep2

description:
SAMPLE_11128
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: maternal age

tag: maternal bmi

tag: maternal ethnicity

tag: maternal blood type

tag: previous nulliparity

tag: previous miscarriage

tag: iugr diagnosis

tag: newborn weight z-score

tag: placental weight z-score

tag: umbilical cord diameter

tag: chorioamnionitis diagnosis


title: PE-PreT-CH, rep1

description:
SAMPLE_10170
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: tissue

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: attempted vaginal delivery

tag: apgar score (1 min)

tag: apgar score (5 min)

tag: nicu transfer


title: PE-PreT-SGA, rep1

description:
SAMPLE_10914
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: maternal age

tag: maternal bmi

tag: maternal ethnicity

tag: maternal blood type

value: AB

tag: previous nulliparity

tag: previous miscarriage

tag: iugr diagnosis

tag: mode of delivery

tag: ga (week)

tag: ga (day)

tag: infant gender


title: PE-Term-SGA, rep1

description:
SAMPLE_10021
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: tissue

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: newborn weight z-score

tag: placental weight z-score

tag: umbilical cord diameter

tag: chorioamnionitis diagnosis


title: PE-Term-SGA, rep3

description:
SAMPLE_11391
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: maternal age

tag: maternal bmi

tag: maternal ethnicity

tag: maternal blood type

tag: previous nulliparity

tag: previous miscarriage

tag: iugr diagnosis

tag: attempted vaginal delivery

tag: apgar score (1 min)

tag: apgar score (5 min)

tag: nicu transfer


title: Cont-Term-CH, rep1

description:
SAMPLE_10084
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: tissue

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: mode of delivery

tag: ga (week)

tag: ga (day)

tag: infant gender


title: 071310_166592843_031

status: Public on May 14 2015

city: Cambridge

first: Jadwiga

last: Bienkowska

state: MA

address: 45 Fayette Str Apt 3

country: USA

institute: BiogenIdec

hyb_protocol: standard Affymetrix protcol

scan_protocol: HTAPS scanner was used

data_processing: Data was normalized using  gcrma using R package for each set separately (Controls and SLE were normalized as one set).

source_name: SLE

label_protocol: NuGEN Ovation

growth_protocol: Whole Blood samples in collected fom PAXgene tubes

extract_protocol: The RNA was extracted with Trizol reagent (Life Technologies) and cleaned up with RNA easy (Qiagen) according to the manufacturer’s protocols.

value: whole blood

tag: time-point

value: baseline

tag: disease

value: SLE (Systemic LUPUS Erythomatosus)


title: 071310_165620333_085


title: 072010_155534213_141


title: 071310_166590323_044


title: 071910_165619913_020


title: 072010_166594143_046


title: 071310_155534223_095


title: 071310_166592733_086


title: 071910_164130513_132


title: 071310_162824333_084


title: 072010_166590223_050


title: 072010_155533613_017


title: 072010_270303013_183


title: 071910_164130313_016


title: 071910_166594853_139


title: 071910_166588343_049


title: 072010_166590633_125


title: 071910_166590543_040


title: 071910_164129813_061


title: 072010_164129943_025


title: 071910_162825513_009


title: 071910_164130433_137


title: 072010_166593943_024


title: 071310_166593543_094


title: 071910_162825533_101


title: 071310_165620013_083


title: 071310_166481233_082


title: 072010_165620143_114


title: 071910_162825113_084


title: 071310_164131023_047


title: 071910_166588553_036


title: 072010_166594053_029


title: 072010_270300813_173


title: 071310_162825233_062


title: 072010_166593833_126


title: 071910_166589843_038


title: 072010_166592443_146


title: 072010_166481243_147


title: 071310_166590553_024


title: 072010_166592053_012


title: 072010_166479753_027


title: 071310_155534123_058


title: 071310_164131123_041


title: 071310_166588843_051


title: 072010_166594333_139


title: 072010_166588743_132


title: 071310_166481253_037


title: 071310_166594743_006


title: 071310_166589643_005


title: 071910_166594543_058


title: 071910_155534143_141


title: 071910_164129433_018


title: 071910_165619743_100


title: 071910_166478133_111


title: 071910_164130013_124


title: 072010_166477813_045


title: 032310_BDP069_063

source_name: Control

value: Control


title: 072010_164130123_043


title: 032310_BDP058_056


title: 071910_162824723_147


title: 032310_BDP066_061


title: 032310_BDP054_055


title: 032310_BDP071_065


title: 071910_166593233_022


title: 032310_BDP063_059


title: 032310_BDP065_060


title: 071910_166593243_015


title: 032310_BDP070_064


title: 032310_BDP043_054


title: 032310_BDP060_057


title: 071910_166590843_152


title: 032310_BDP020_051


title: 032310_BDP039_053


title: 032310_BDP068_062


title: 032310_BDP022_052


title: 032310_BDP008_049


title: 032310_270629091_009


title: 032310_270629051_016


title: 032310_270628991_005


title: 032310_270629071_019


title: 032310_296438041_008


title: E13 embryo_rep4

status: Public on May 01 2014

city: Paris

first: Matthias

last: Groszer

address: 17, rue du Fer à Moulin

department: Developmental Neuroscience

country: France

institute: INSERM U839

description:
E13_62_WT
E13 replicate4

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Illumina BeadArray Reader used to capture images with default setting.

data_processing: Illumina GenomeStudiov2011.1 were used to obtain raw signal intensities.  Background substracted signal intensity for the detected probes (Detection Pval<0.05) were used for analysis.   Probes detected in one array and not in other were not considered during analysis.  Further, outlier probes were removed and data were quantile normalized (Bolstad BM et al., 2003)

organism: Mus musculus

source_name: Mouse embryonic cortex_E13 stage_replicate4

label_protocol: Biotinylated cRNA were prepared by using Illumina TotalPrep-96 RNA Amplification kit from Ambion # 4393543

extract_protocol: Total RNA was extracted from FACS isolated BPs by using mirVanaTM kit (Ambion) following manufacturer's protocol

tag: developmental stage

value: Brain cortex

tag: cell type

value: Basal progenitors


title: E16 embryo_rep2

description:
E16_16_WT
E16 replicate2

source_name: Mouse embryonic cortex_E16 stage_replicate2


title: E16 embryo_rep4

description:
E16_92_WT
E16 replicate4

source_name: Mouse embryonic cortex_E16 stage_replicate4


title: E16 embryo_rep5

description:
E16_101_WT
E16 replicate5

source_name: Mouse embryonic cortex_E16 stage_replicate5


title: E13 embryo_rep6

description:
E13_66_WT
E13 replicate6

source_name: Mouse embryonic cortex_E13 stage_replicate6


title: E16 embryo_rep3

description:
E16_79_WT
E16 replicate3

source_name: Mouse embryonic cortex_E16 stage_replicate3


title: E13 embryo_rep3

description:
E13_55_WT
E13 replicate3

source_name: Mouse embryonic cortex_E13 stage_replicate3


title: Day 12 set1

status: Public on Feb 03 2014

city: Delhi

first: Vivek

middle: T

last: Natarajan

state: Delhi

address: Mathura Road

country: India

institute: CSIR-IGIB

description: pigmented

hyb_protocol: hybridization performed as per manufacturer's instructions (illumina)

scan_protocol: scanning performed as per manufacturer's instructions (illumina)

data_processing: Data was processed using bead studio module with average normalization after background subtration

source_name: B16 melanoma cells

label_protocol: labelling was performed as per instructions by manufacturer's using the Illumina total prep RNA labelling kit from Ambion

extract_protocol: Total RNA was isolated from cells using trizol method, isopropanol precipitated RNA was column purified using Qiagen RNA purification kit

treatment_protocol: B16 cells were grown in DMEM supplemented with 10% vol/vol Fetal calf serum, for the set up of the experiment cells were seeded at 100 cells/cm2 and harvested after indicated days (4,8 and 12), on day 12 cells were plated at 10,000 cells /cm2 and harvested on days 16 and 20

tag: growth

value: cells grown in High density 10000 cells per cm2

tag: cell line

tag: time

value: Day 12

tag: treatment

value: pigmented


title: E16 embryo_rep1

description:
E16_12_WT
E16 replicate1

source_name: Mouse embryonic cortex_E16 stage_replicate1

tag: tissue


title: E13 embryo_rep2

description:
E13_41_WT
E13 replicate2

source_name: Mouse embryonic cortex_E13 stage_replicate2


title: PBT036 3

status: Public on Jan 29 2014

city: Duarte

first: Charles

middle: David

last: Warden

state: CA

address: 1500 East Duarte Rd

department: Department of Molecular and Cellular Biology

institute: City of Hope

description: Gene expression data, continuous culture as indicated in 'characteristics'

hyb_protocol: The chips were hybridized by Affymetrix Hybridization Oven 640 and washed by Affymetrix Fluidics Station 450 according to manufacturer's protocols.

scan_protocol: The chips were scanned by Affymetrix scanner 3000 7G using manufacturer's default settings.

data_processing: Raw Affymetrix intensity measurements of all probe sets were background-corrected, normalized, and summarized into gene level expression measurements using RMA method implemented in Partek Genomic Suite V6.0.

label: Biotin

source_name: PBT036, IL13Ra2-pos, replicate 3

label_protocol: One-Cycle target labeling was performed using 5ug of total RNA according to Affymetrix's Eukaryotic Target Labeling protocol.

growth_protocol: Low-passage primary glioma tumor sphere lines were grown in neural stem cell media, and established glioma cell line U251T was grown in serum containing media.

extract_protocol: TRIzol reagent (Invitrogen, Carlsbad, CA) was used for RNA isolation from cell lines, according to manufacturer’s protocol

treatment_protocol: RNA was harvested from cell lines growing in above-mentioned growth protocol conditions

tag: passage

value: Low

value: cultured in neurosphere media supplemented with EGF and FGF


title: E13 embryo_rep1

description:
E13_36_WT
E13 replicate1

source_name: Mouse embryonic cortex_E13 stage_replicate1


title: E13 embryo_rep5

description:
E13_63_WT
E13 replicate5

source_name: Mouse embryonic cortex_E13 stage_replicate5


title: Day 16 set1

description: depigmented

growth_protocol: B16 cells were grown in DMEM supplemented with 10% vol/vol Fetal calf serum,

value: cells grown in Low density 100 cells per cm2

value: Day 16

value: depigmented


title: Day 16 set2

description: depigmented


title: U251T 2

source_name: U251T, IL13Ra2-pos, replicate 2

value: cultured in neurosphere media


title: Day 4 set1

description: pigmented

value: Day 4


title: Day 8 set1

description: pigmented

value: Day 8


title: Day 8 set2

description: pigmented


title: Day 20 set1

description: depigmented

value: Day 20


title: Day 12 set2

description: pigmented


title: U251T 1

source_name: U251T, IL13Ra2-pos, replicate 1


title: Day 4 set2

description: pigmented


title: Day 0 set2

description: depigmented

value: Day 0


title: PBT036 2

source_name: PBT036, IL13Ra2-pos, replicate 2


title: PBT030 2

source_name: PBT030, IL13Ra2-pos, replicate 2


title: PBT030 3

source_name: PBT030, IL13Ra2-pos, replicate 3


title: PBT009 2

source_name: PBT009, IL13Ra2-neg, replicate 2


title: PBT022 3

source_name: PBT022, IL13Ra2-neg, replicate 3


title: PBT022 2

source_name: PBT022, IL13Ra2-neg, replicate 2


title: PBT009 3

source_name: PBT009, IL13Ra2-neg, replicate 3


title: PBT017-4 2

source_name: PBT017-4, IL13Ra2-pos, replicate 2

value: Tumor passaged 4 times in mice


title: PBT030 1

source_name: PBT030, IL13Ra2-pos, replicate 1


title: PBT017-4 3

source_name: PBT017-4, IL13Ra2-pos, replicate 3


title: PBT008 2

source_name: PBT008, IL13Ra2-neg, replicate 2


title: PBT015 2

source_name: PBT015, IL13Ra2-pos, replicate 2


title: PBT015 3

source_name: PBT015, IL13Ra2-pos, replicate 3


title: PBT036 1

source_name: PBT036, IL13Ra2-pos, replicate 1


title: PBT022 1

source_name: PBT022, IL13Ra2-neg, replicate 1


title: PBT017-4 1

source_name: PBT017-4, IL13Ra2-pos, replicate 1


title: PBT015 1

source_name: PBT015, IL13Ra2-pos, replicate 1


title: PBT009 1

source_name: PBT009, IL13Ra2-neg, replicate 1


title: PBT008 1

source_name: PBT008, IL13Ra2-neg, replicate 1


title: PBT003 2

source_name: PBT003, IL13Ra2-neg, replicate 2


title: PBT003 3

source_name: PBT003, IL13Ra2-neg, replicate 3


title: PBT008 3

source_name: PBT008, IL13Ra2-neg, replicate 3


title: PBT003 1

source_name: PBT003, IL13Ra2-neg, replicate 1


title: mutant1 [expression]

status: Public on Jun 08 2013

description: SAMPLE 4

source_name: HCT116 mutant derived cell line with altered DNA methylation

label_protocol: WT Target Labeling Assay was performed using 100ng of total RNA accorind to Affymetrix's 100 ng Total RNA Labeling Protocol.

growth_protocol: Cells were cultured in McCoy's 5A medium supplemented with 10% FBS and antibiotics.

extract_protocol: RNA was extracted with the RNeasy kit (Qiagen)

tag: genotype/variation

value: mutant with altered DNA methylation


title: parental3 [expression]

description: SAMPLE 3

source_name: HCT116 cell line

value: parental


title: mutant3 [expression]

description: SAMPLE 6


title: mutant2 [expression]

description: SAMPLE 5


title: parental2 [expression]

description: SAMPLE 2


title: parental1 [expression]

description: SAMPLE 1


title: MIRA

type: genomic

description: embryonic stem cell line

hyb_protocol: The labeled DNA was precipitated with 0.1 volume 5M NaCl and 1 volume isopropanol, and hybridized in 45 ul of buffer containing 20% formamide, 1.2 M betaine, 0.1 ug/ul herring sperm DNA and 10 ug of human COT1 DNA (Invitrogen). Arrays were hybridized in Maui hybridization stations for 16-18 h at 42C, and then washed in Wash I, Wash II, Wash III according to manufacturer's protocols (http://www.nimblegen.com/)

scan_protocol: Arrays were scanned on an Roche NimbleGen MS200 scanner per manufacturer's protocol (http://www.nimblegen.com/).

data_processing: NimbleScan 2.6.0.0

molecule: genomic DNA

source_name: HES-2_MIRA enriched DNA

label_protocol: 1 µg methylation DNA was directly labeled by Klenow (Roche NimbleGen) random priming with Cy3 nonamers per manufacturer's protocol (http://www.nimblegen.com/).

growth_protocol: Matrigel (BD)/mTesR1 (STEMCELL technologies) standard protocol

extract_protocol: HES-2 (ES02) human embryonic stem cells were adapted from mitotically inactive MEF feeders to matrigel substrate (BD Biosciences) and mTesR1 medium (STEMCELL Technologiesaccording to manufacturer's protocol.  Adaptation was for 4 passages and the final passage number was p72.  DNA was extracted from Tra 1-60+ cells isolated by flow cytometry and prepared for MIRA-chip analysis.  500 ng of sonicated and fragmented DNA was enriched for methylated DNA using the MethylCollector Ultra Kit (Active Motif). Eluted DNA was puriﬁed with MinElute reaction cleanup kit (Qiagen). MIRA-enriched and 10 ng of sonicated input DNA was subsequently ampliﬁed using the Whole Genome Ampliﬁcation kit2 (Sigma).

value: embryonic stem cell line HES-2

tag: sample type

value: MIRA enriched sample

source_name: HES-2_INPUT DNA

value: input DNA