title: 0GyF7/ reference male mouse1

status: Public on Nov 16 2016

description: 0GyF7 Cy5

data_processing:
Agilent Genomic Workbench Software (v 7.0.) was used and performed FuzzyZero correction.  Agilent Feature Extraction Software (version 10.7.1.1) also performed the following normalization.
The log ratio i is the measure of differential expression between the red and green channels for every probe i:  LogRatio = Log2 (ProcessedSignalr/ProcessedSignalg)  where ProcessedSignalr and ProcessedSignalg are signals post dye normalization and post surrogate processing in the red and green channels, respectively.  The dye-normalized signal is calculated by multiplying the background-subtracted signal by the dye normalization factor: DyeNormSignal = (BGSubSignal/MultDetrendSignal) x DNF  DNF: LinearDyeNormFactor  The linear dye normalization method assumes that dye bias is not intensity-dependent and therefore takes a global approach to dye normalization.  A linear dye normalization factor is computed per channel by setting the geometric mean of signal intensity of the normalization features equal to 1000.


title: 0GyGM/ reference male mouse1

status: Public on Nov 17 2016

type: genomic

city: Rokkasho-mura,Kamikita-gun,

first: Keiji

last: OGURA

state: Aomori

address: Takahoko, Hacchasawa,

department: Department of Radiobiology

country: Japan

institute: Institute for Environmental Science

description: 0GyGM Cy5

hyb_protocol: Oligonucleotide Array-Based CGH for Genomic DNA Analysis, protocol version 4.0.8.

scan_protocol: Scanned on an Agilent G2565BA scanner. Images were quantified using Agilent Feature Extraction Software (version 10.7.1.1).

data_processing:
Agilent Genomic Workbench Software (v 7.0.) was used and performed FuzzyZero correction. Agilent Feature Extraction Software (version 10.7.1.1) also performed the following normalization.
The log ratio i is the measure of differential expression between the red and green channels for every probe i: LogRatio = Log2 (ProcessedSignalr/ProcessedSignalg) where ProcessedSignalr and ProcessedSignalg are signals post dye normalization and post surrogate processing in the red and green channels, respectively. The dye-normalized signal is calculated by multiplying the background-subtracted signal by the dye normalization factor: DyeNormSignal = (BGSubSignal/MultDetrendSignal) x DNF DNF: LinearDyeNormFactor The linear dye normalization method assumes that dye bias is not intensity-dependent and therefore takes a global approach to dye normalization. A linear dye normalization factor is computed per channel by setting the geometric mean of signal intensity of the normalization features equal to 1000.

molecule: genomic DNA

organism: Mus musculus

extract_protocol: PI-50a (Kurabo Industries LTD.) tissue DNA extraction protocol.

tag: strain/background

tag: gender

value: male

tag: tissue

value: tail

tag: treatment

tag: generation

value: parent

source_name: reference male mouse1

tag: sample type

value: reference


title: reference male mouse1/ 0GyGM

description: 0GyGM Cy3

label_protocol: Oligonucleotide Array-Based CGH for Genomic DNA Analysis, protocol version 4.0.8.


title: reference male mouse1/ 0GyGF

description: 0GyGF Cy3

value: female


title: reference male mouse1/ 0GyF4

description: 0GyF4 Cy3

value: progeny


title: reference male mouse1/ 0GyF7

description: 0GyF7 Cy3


title: 0GyF5/ reference male mouse1

description: 0GyF5 Cy5


title: reference male mouse1/ 0GyF5

description: 0GyF5 Cy3


title: 0GyG3/ reference male mouse1

description: 0GyG3 Cy5


title: reference male mouse1/ 0GyG1

description: 0GyG1 Cy3


title: reference male mouse1/ 0GyG4

description: 0GyG4 Cy3


title: 0GyF3/ reference male mouse1

description: 0GyF3 Cy5


title: 0GyF6/ reference male mouse1

description: 0GyF6 Cy5


title: 0GyF4/ reference male mouse1

description: 0GyF4 Cy5


title: reference male mouse1/ 0GyF2

description: 0GyF2 Cy3


title: 0GyF1/ reference male mouse1

description: 0GyF1 Cy5


title: reference male mouse1/ 0GyF1

description: 0GyF1 Cy3


title: reference male mouse1/ 0GyG3

description: 0GyG3 Cy3


title: reference male mouse1/ 0GyF3

description: 0GyF3 Cy3


title: reference male mouse1/ 0GyF6

description: 0GyF6 Cy3


title: reference male mouse1/ 0GyFF

description: 0GyFF Cy3


title: 0GyF2/ reference male mouse1

description: 0GyF2 Cy5


title: 0GyE5/ reference male mouse1

description: 0GyE5 Cy5

hyb_protocol: Oligonucleotide Array-Based CGH for Genomic DNA Analysis, protocol version 4.0.8

tag: strain

tag: mouse status

value: reference male mouse


title: 0GyG6/ reference male mouse1

description: 0GyG6 Cy5


title: 0GyE4/ reference male mouse1

description: 0GyE4 Cy5

label_protocol: Oligonucleotide Array-Based CGH for Genomic DNA Analysis, protocol version 4.0.8


title: 0GyE6/ reference male mouse1

description: 0GyE6 Cy5


title: reference male mouse1/ 0GyFM

description: 0GyFM Cy3


title: 0GyFM/ reference male mouse1

description: 0GyFM Cy5


title: 0GyE2/ reference male mouse1

description: 0GyE2 Cy5


title: 0GyD7/ reference male mouse1

description: 0GyD7 Cy5


title: 0GyFF/ reference male mouse1

description: 0GyFF Cy5


title: reference male mouse1/ 0GyEF

description: 0GyEF Cy3

value: non-irradiated female (0mGyEF)


title: reference male mouse1/ 0GyD8

description: 0GyD8 Cy3


title: 0GyEF/ reference male mouse1

description: 0GyEF Cy5


title: 0GyE3/ reference male mouse1

description: 0GyE3 Cy5


title: 0GyEM/ reference male mouse1

description: 0GyEM Cy5

value: non-irradiated male (0mGyEM)


title: reference male mouse1/ 0GyE5

description: 0GyE5 Cy3


title: reference male mouse1/ 0GyE1

description: 0GyE1 Cy3


title: reference male mouse1/ 0GyE4

description: 0GyE4 Cy3


title: reference male mouse1/ 0GyD5

description: 0GyD5 Cy3


title: 0GyD4/ reference male mouse1

description: 0GyD4 Cy5


title: reference male mouse1/ 0GyEM

description: 0GyEM Cy3


title: 0GyD8/ reference male mouse1

description: 0GyD8 Cy5


title: 0GyD5/ reference male mouse1

description: 0GyD5 Cy5


title: reference male mouse1/ 0GyE2

description: 0GyE2 Cy3


title: reference male mouse1/ 0GyD4

description: 0GyD4 Cy3


title: reference male mouse1/ 0GyD7

description: 0GyD7 Cy3


title: reference male mouse1/ 0GyE6

description: 0GyE6 Cy3


title: 0GyD6/ reference male mouse1

description: 0GyD6 Cy5


title: reference male mouse1/ 0GyD6

description: 0GyD6 Cy3


title: 0GyD2/ reference male mouse1

description: 0GyD2 Cy5


title: reference male mouse1/ 0GyD2

description: 0GyD2 Cy3


title: 0GyD3/ reference male mouse1

description: 0GyD3 Cy5


title: reference male mouse1/ 0GyD3

description: 0GyD3 Cy3


title: reference male mouse1/ 0GyC5

status: Public on Nov 03 2016

description: 0GyC5 Cy3

data_processing:
Agilent Genomic Workbench Software (v 7.0.) was used and performed FuzzyZero correction. Agilent Feature Extraction Software (version 10.7.1.1) also performed the following normalization.
The log ratio i is the measure of differential expression between the red and green channels for every probe i: LogRatio = Log2 (ProcessedSignalr/ProcessedSignalg) where ProcessedSignalr and ProcessedSignalg are signals post dye normalization and post surrogate processing in the red and green channels, respectively. The dye-normalized signal is calculated by multiplying the background-subtracted signal by the dye normalization factor: DyeNormSignal = (BGSubSignal/MultDetrendSignal) x DNF DNF: LinearDyeNormFactor The linear dye normalization method assumes that dye bias is not intensity-dependent and therefore takes a global approach to dye normalization. A linear dye normalization factor is computed per channel by setting the geometric mean of signal intensity of the normalization features equal to 1000.
A linear dye normalization factor is computed per channel by setting the geometric mean of signal intensity of the normalization features equal to 1000:


title: 0GyC6/ reference male mouse1

description: 0GyC6 Cy5


title: reference male mouse1/ 0GyDF

description: 0GyDF Cy3

value: non-irradiated female (0mGyDF)


title: 0GyDM/ reference male mouse1

description: 0GyDM Cy5

value: non-irradiated male (0mGyDM)


title: reference male mouse1/ 0GyDM

description: 0GyDM Cy3


title: reference male mouse1/ 0GyD1

description: 0GyD1 Cy3


title: reference male mouse1/ 0GyC4

description: 0GyC4 Cy3


title: 0GyDF/ reference male mouse1

description: 0GyDF Cy5


title: 0GyC3/ reference male mouse1

description: 0GyC3 Cy5


title: reference male mouse1/ 0GyC3

description: 0GyC3 Cy3


title: 0GyC2/ reference male mouse1

description: 0GyC2 Cy5


title: 0GyCM/ reference male mouse1

description: 0GyCM Cy5

value: non-irradiated male (0mGyCM)


title: 0GyB6/ reference male mouse1

description: 0GyB6 Cy5


title: reference male mouse1/ 0GyB6

description: 0GyB6 Cy3


title: 0GyCF/ reference male mouse1

description: 0GyCF Cy5

value: non-irradiated female (0mGyCF)


title: reference male mouse1/ 0GyC2

description: 0GyC2 Cy3


title: reference male mouse1/ 0GyCF

description: 0GyCF Cy3


title: 0GyE1/ reference male mouse1

description: 0GyE1 Cy5


title: 0GyC4/ reference male mouse1

description: 0GyC4 Cy5


title: 0GyD1/ reference male mouse1

description: 0GyD1 Cy5


title: reference male mouse1/ 0GyB4

description: 0GyB4 Cy3


title: reference male mouse1/ 0GyCM

description: 0GyCM Cy3


title: 0GyB5/ reference male mouse1

description: 0GyB5 Cy5


title: reference male mouse1/ 0GyB2

description: 0GyB2 Cy3


title: 0GyB4/ reference male mouse1

description: 0GyB4 Cy5


title: reference male mouse1/ 0GyB1

description: 0GyB1 Cy3


title: 0GyB1/ reference male mouse1

description: 0GyB1 Cy5


title: Doxorubicin + sAcvR2B-Fc 5 (Muscle)

status: Public on Sep 25 2016

type: RNA

city: Jyväskylä

first: Juha

middle: J

last: Hulmi

address: Rautpohjankatu 8a Viv

department: Biology of Physical Activity

country: Finland

institute: University of Jyväskylä

description: replicate 5

hyb_protocol: Standard Illumina hybridization protocol. Conducted at the Functional Genomics Unit at Biomedicum Helsinki, University of Helsinki, Finland.

scan_protocol: Standard Illumina scanning protocol. Conducted at the Functional Genomics Unit at Biomedicum Helsinki, University of Helsinki, Finland.

data_processing: The data were normalized with quantiles normalization and data quality was assessed using Chipster software (IT Center for Science, Espoo, Finland)

label: biotin

molecule: total RNA

source_name: m. tibialis anterior

label_protocol: Biotinylated cRNA were  prepared with TargetAmp™- Nano Labeling Kit for Illumina® Expression BeadChip®, P/N TAN07924, Lit.#269, 5/2013, EPILIT269.  Rev. A (Epicentre).

extract_protocol: Total RNA was extracted from the tibialis anterior (TA)  muscle with TRIsure reagent (BIO-38032, Bioline, Luckenwalde, Germany) and further purified with NucleoSpin® RNA II columns (#740955.50, Macherey-Nagel, Germany) according to the manufacturer’s protocols.

value: muscle

tag: Sex

tag: age

value: 8-10 weeks

value: doxorubicin + sAcvR2B-Fc


title: 0GyB2/ reference male mouse1

description: 0GyB2 Cy5


title: Doxorubicin + sAcvR2B-Fc 4 (Muscle)

description: replicate 4


title: Doxorubicin + sAcvR2B-Fc 3 (Muscle)

description: replicate 3


title: 0GyB3/ reference male mouse1

description: 0GyB3 Cy5


title: Doxorubicin + sAcvR2B-Fc 2 (Muscle)

description: replicate 2


title: Doxorubicin 4 (Muscle)

description: replicate 4

value: doxorubicin


title: reference male mouse1/ 0GyBM

description: 0GyBM Cy3

value: non-irradiated male (0mGyBM)


title: Doxorubicin + sAcvR2B-Fc 1 (Muscle)

description: replicate 1

value: male


title: Doxorubicin 5 (Muscle)

description: replicate 5


title: Doxorubicin 3 (Muscle)

description: replicate 3


title: 0GyBF/ reference male mouse1

description: 0GyBF Cy5

value: non-irradiated female (0mGyBF)

value: tail


title: reference male mouse1/ 0GyA3

description: 0GyA3 Cy3


title: 0GyBM/ reference male mouse1

description: 0GyBM Cy5


title: reference male mouse1/ 0GyAF

description: 0GyAF Cy3

value: non-irradiated female (0mGyFM)


title: reference male mouse1/ 0GyA1

description: 0GyA1 Cy3

value: progeny


title: Control (PBS) 5 (Muscle)

description: replicate 5

value: PBS


title: 0GyA3/ reference male mouse1

description: 0GyA3 Cy5

value: reference male mouse


title: Doxorubicin 1 (Muscle)

description: replicate 1


title: reference male mouse1/ 0GyBF

description: 0GyBF Cy3


title: reference male mouse1/ 0GyE3

description: 0GyE3 Cy3


title: Doxorubicin 2 (Muscle)

description: replicate 2


title: Control (PBS) 1 (Muscle)

description: replicate 1


title: PE-PreT-CH, rep11

status: Public on May 10 2016

city: Toronto

first: Brian

last: Cox

state: Ontario

address: 1 King's College Circle

department: Physiology

country: Canada

institute: University of Toronto

description:
SAMPLE_8319
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.

organism: Homo sapiens

source_name: Human placenta from PE-PreT-CH 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: PE

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: 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

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: Control (PBS) 2 (Muscle)

description: replicate 2

tag: strain

tag: tissue

value: muscle

tag: Sex

tag: age

value: 8-10 weeks

tag: treatment


title: reference male mouse1/ 0GyA2

description: 0GyA2 Cy3

tag: mouse status


title: PE-Term-CH, rep5

description:
SAMPLE_7971
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: diagnosis

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


title: Control (PBS) 4 (Muscle)

description: replicate 4

tag: strain

tag: tissue

tag: Sex

value: male

tag: age

tag: treatment


title: 0GyA2/ reference male mouse1

description: 0GyA2 Cy5

tag: mouse status

value: progeny

value: tail


title: 0GyAM/ reference male mouse1

description: 0GyAM Cy5

value: non-irradiated male (0mGyAM)

value: reference male mouse


title: Cont-preT-AGA, rep24

description:
SAMPLE_7668
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

value: Placenta

tag: maternal age

tag: maternal bmi

tag: maternal ethnicity

tag: maternal blood type

tag: previous nulliparity

tag: previous miscarriage

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: PE-PreT-CH, rep9

description:
SAMPLE_6776
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: A

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: F


title: PE-Term-CH, rep4

description:
SAMPLE_7646
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 age

tag: maternal bmi

tag: maternal ethnicity

value: East Indian

tag: maternal blood type

tag: previous nulliparity

value: No

tag: previous miscarriage

value: Yes

value: C-Section

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-AGA, rep10

description:
SAMPLE_6987
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

value: B

tag: previous hypertensive pregnancy

tag: mean uterine pi

tag: mean umbilical pi

tag: maximum systolic bp

tag: maximum diastolic bp

tag: mode proteinuria

tag: nicu transfer

tag: placental weight z-score

tag: umbilical cord diameter

tag: chorioamnionitis diagnosis


title: PE-PreT-AGA, rep12

description:
SAMPLE_7387
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 age

tag: maternal bmi

tag: maternal ethnicity

value: Asian

tag: maternal blood type

tag: previous nulliparity

tag: previous miscarriage

tag: hellp diagnosis

tag: iugr diagnosis

tag: attempted vaginal delivery

tag: mode of delivery

tag: ga (week)

tag: ga (day)


title: Cont-preT-AGA, rep12

description:
SAMPLE_15039
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: Caucasian

value: O

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

tag: infant gender

value: M

tag: newborn weight z-score

tag: apgar score (1 min)

tag: apgar score (5 min)


title: 0GyAF/ reference male mouse1

description: 0GyAF Cy5

tag: strain

tag: mouse status

value: non-irradiated female (0mGyFM)

value: tail


title: PE-Term-AGA, rep7

description:
SAMPLE_14284
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: maternal age

tag: maternal bmi

tag: maternal ethnicity

tag: maternal blood type

tag: previous nulliparity

tag: previous miscarriage

tag: hellp diagnosis

tag: iugr diagnosis

tag: attempted vaginal delivery

tag: mode of delivery

tag: nicu transfer

tag: placental weight z-score

tag: umbilical cord diameter

tag: chorioamnionitis diagnosis


title: reference male mouse1/ 0GyAM

description: 0GyAM Cy3

value: reference male mouse

tag: tissue

value: non-irradiated male (0mGyAM)


title: reference male mouse1/ 0GyB5

description: 0GyB5 Cy3

tag: strain

value: progeny


title: 0GyC5/ reference male mouse1

description: 0GyC5 Cy5

tag: mouse status


title: reference male mouse1/ 0GyC6

description: 0GyC6 Cy3


title: PE-PreT-AGA, rep18

description:
SAMPLE_9801
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

value: Placenta

tag: maternal age

tag: previous hypertensive pregnancy

tag: mean uterine pi

tag: mean umbilical pi

tag: maximum systolic bp

tag: maximum diastolic bp

tag: mode proteinuria

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: Cont-preT-AGA, rep17

description:
SAMPLE_5157
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: non-PE

tag: tissue

tag: maternal bmi

tag: maternal ethnicity

tag: maternal blood type

tag: previous nulliparity

tag: previous miscarriage

tag: hellp diagnosis

tag: iugr diagnosis

tag: attempted vaginal delivery

tag: mode of delivery

tag: nicu transfer

tag: placental weight z-score

tag: umbilical cord diameter

tag: chorioamnionitis diagnosis


title: PE-PreT-AGA, rep1

description:
SAMPLE_10986
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

value: A

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: ga (week)

tag: ga (day)

tag: infant gender

value: F

tag: newborn weight z-score


title: Cont-preT-AGA, rep1

description:
SAMPLE_11405
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: maternal bmi

tag: maternal ethnicity

tag: maternal blood type

tag: previous nulliparity

tag: previous miscarriage

tag: hellp diagnosis

tag: iugr diagnosis

tag: attempted vaginal delivery

value: Yes

tag: mode of delivery

value: C-Section

tag: apgar score (1 min)

tag: apgar score (5 min)


title: PE-Term-AGA, rep2

description:
SAMPLE_11118
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

value: Caucasian

tag: previous hypertensive pregnancy

tag: mean uterine pi

tag: mean umbilical pi

tag: maximum systolic bp

tag: maximum diastolic bp

tag: mode proteinuria

tag: nicu transfer

tag: placental weight z-score

tag: umbilical cord diameter

tag: chorioamnionitis diagnosis


title: Cecum_SAHC.AC_pod2_rep3

status: Public on Jul 30 2015

city: Chicago

first: John

middle: C

last: Alverdy

state: IL

address: 5841 South Maryland Avenue

department: Surgery

country: USA

institute: University of Chicago

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized using quantile normalization with Illumina Beadstudio software by the University of Chicago Genomics Core (900 E. 57th Street, Room # 1230C, Chicago, IL 60637). Functional analysis of differentially expressed genes using Ingenuity pathway analysis and DAVID software.

source_name: Cecum, SAHC + AC

label_protocol: Standard Illumina labeling protocol

growth_protocol: Four pathogen community consisting of Candida albicans, Enterococcus faecalis, multi-drug resistant Klebsiella oxytoca, and multi-drug resistant Serratia marcescens was isolated from the stool of a critically ill patient who was exposed to numerous antibiotics over the course of his sepsis. Each pathogen were grown overnight on TSB agar. Colonies were suspended in liquid TSB medium for 1hr and then adjusted to a final OD600 of 0.2. All four pathogens were then combined together in equal volumes. Bacterial suspension was centrifuged at 6,000 rpm for 10min, the excess TSB removed and the remaining pellet was re-suspended in the same volume of 10% glycerol. The resulting microbial suspension was used for cecal injections.

extract_protocol: The cecum, left lobe of the liver, and spleen were isolated from mice and stored in RNAprotect cell reagent (Qiagen, 76526). RNA extraction was performed using the RNeasy Plus Mini Kit (Qiagen, 74134). In order to maximize the yield of RNA extraction, chloroform extraction technique was utilized on the liver samples.

tag: organ

value: Cecum

tag: treatment

value: SAHC + AC

tag: pod

tag: status

value: Septic

tag: mouse


title: PE-Term-AGA, rep3

description:
SAMPLE_11641
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 bmi

tag: maternal ethnicity

tag: maternal blood type

value: O

tag: previous nulliparity

tag: previous miscarriage

tag: hellp diagnosis

tag: iugr diagnosis

tag: attempted vaginal delivery

tag: mode of delivery

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)


title: Cont-preT-AGA, rep6

description:
SAMPLE_13487
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

value: B

tag: previous hypertensive pregnancy

tag: mean uterine pi

tag: mean umbilical pi

tag: maximum systolic bp

tag: maximum diastolic bp

tag: mode proteinuria

tag: nicu transfer

tag: placental weight z-score

tag: umbilical cord diameter

tag: chorioamnionitis diagnosis


title: Control (PBS) 3 (Muscle)

description: replicate 3

tag: strain

tag: tissue

value: muscle

tag: Sex

value: male

tag: age

value: 8-10 weeks

tag: treatment

value: PBS


title: healthy people, biological rep3

status: Public on Jul 23 2015

city: Changchun

first: Bo

middle: Fan

last: Meng

address: Xiantai Street 126 of Changchun of Jilin Province

country: China

institute: the Department of Cardiology, China–Japan Union Hospital, Jilin University,

description:
the total RNA was extracted from the leucocyte of peripheral blood
healthy people 3_3
Identical RMA signals in GSM1830992 and GSM2561554.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45℃ on HG-U133_Plus_2. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using Genechip Scanner 3000

data_processing: The data were analyzed with robust multichip average method and present or absent calls of each probe set were determined by MAS5 method with affy package in R. The differentially genes between coronary heart disease and healthy groups were identified by performing moderated t-statistic in limma package, and the raw p values were adjusted by the FDR method.

source_name: the peripheral blood of healthy people

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 ug total RNA

growth_protocol: the peripheral blood were stored in 4℃ before extracting the total RNA

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

treatment_protocol: Two milliliter peripheral blood from each subject was collected into BD Vacutainer Single-use Containers for human venous blood specimen collection

value: peripheral blood

tag: ethnicity

value: Chinese

value: 52 years

tag: disease state

value: control


title: 0GyC1/ reference male mouse1

description: 0GyC1 Cy5

tag: mouse status

value: progeny

value: tail

value: reference male mouse


title: reference male mouse1/ 0GyB3

description: 0GyB3 Cy3


title: PE-PreT-AGA, rep3

description:
SAMPLE_11486
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

value: Placenta

tag: maternal age

tag: maternal bmi

tag: maternal ethnicity

value: Black

tag: maternal blood type

tag: previous nulliparity

value: No

tag: previous miscarriage

value: Yes

tag: previous hypertensive pregnancy

tag: mean uterine pi

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

tag: newborn weight z-score

tag: apgar score (1 min)

tag: apgar score (5 min)


title: reference male mouse1/ 0GyC1

description: 0GyC1 Cy3

tag: strain

tag: mouse status

tag: tissue


title: healthy people, biological rep1

description:
the total RNA was extracted from the leucocyte of peripheral blood
healthy people 3_1
Identical RMA signals in GSM1830990 and GSM2561552.

tag: ethnicity

tag: age

value: 59 years

tag: disease state


title: healthy people, biological rep2

description:
the total RNA was extracted from the leucocyte of peripheral blood
healthy people 3_2
Identical RMA signals in GSM1830991 and GSM2561553.

value: 50 years


title: PE-Term-AGA, rep1

description:
SAMPLE_10134
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

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

value: Vaginal

value: M

tag: nicu transfer

tag: placental weight z-score

tag: umbilical cord diameter

tag: chorioamnionitis diagnosis


title: 0GyA1/ reference male mouse1

description: 0GyA1 Cy5

tag: strain

tag: mouse status

tag: tissue


title: BreastPrimaryTumor_treatmentFS_timePtTS_patient_1222

status: Public on Jun 12 2015

city: San Francisco

first: Mark

last: Magbanua

state: CA

address: 1450 3rd Street, PO Box 589001

department: HemOnc

institute: UCSF/Helen Diller Familiy Comprehensive Cancer Center

hyb_protocol: Labeled cDNA was hybridized to a microarray slide at 63° C for 12-16 h.

scan_protocol: Slides were then washed and immediately scanned with Axon Imager 4000b (Axon Instruments, Foster City, Ca), using GenePixPro3 software.

data_processing: printTipLoess normalized, background subtracted VALUE data obtained from log2 of processed Red signal/processed Green signal. Experimental bias (hybridization batch) was removed by fitting linear models & taking residuals. Statistical packages marray and limma in the R environment was used.

source_name: Breast Tumor biopsy after chemotherapy (TS)

label_protocol: One microgram of total target RNA from randomized samples, side by side with 1 µg of universal human reference RNA (Stratagene #740000), was linearly amplified through two rounds of modified in vitro transcription. Randomized amplified RNAs were converted to aminoallyl-modified cDNA and coupled to N-hydroxysuccinimidyl esters of Cy3 or Cy5 (Amersham Biosciences, Piscataway, NJ),

extract_protocol: One 5-µm tissue section (usually after 15 30-µm sections) of each biopsy and the first and the last section of each remaining tumor were hematoxylin and eosin stained to monitor the tumor cell percentage of the tissue. Only specimens with ≥ 50% of tumor cells were included in further analysis.A #10 scalpel blade was used to scrape tissue from the pathologic area of interest. Tissue was homogenized [Polytron 1200C, Brinkmann, Westbury, NY, at setting 4 for 30 sec] with 600µl of RNA lysis buffer plus 1% 2-mercaptoethanol, and RNA was isolated using RNEasy columns (Qiagen, Valencia, Ca).

treatment_protocol: Patients with invasive breast cancer greater than 3 cm and/or at least one tumor-positive axillary lymph node were eligible for the study. Patients were treated with an anthracycline-based chemotherapy followed by taxane in the I-SPY TRIAL (CALGB150007/150012/ACRIN 6657)..

tag: patient

value: Breast

tag: treatment

value: FS

tag: biopsy time

value: TS

tag: recurrence_yes is 1

tag: hr-positive_yes is 1

tag: her2-positive_yes is 1

tag: pcr_yes is 1

tag: rcb class

tag: rcb index

tag: reference

value: Stratagene Reference Pooled RNA


title: BreastPrimaryTumor_treatmentFS_timePtTS_patient_1203

source_name: universal human reference RNA (Stratagene #740000)


title: BreastPrimaryTumor_treatmentFS_timePtTS_patient_1231


title: BreastPrimaryTumor_treatmentFS_timePtTS_patient_1206


title: BreastPrimaryTumor_treatmentFS_timePtTS_patient_1225


title: BreastPrimaryTumor_treatmentFS_timePtTS_patient_1194


title: BreastPrimaryTumor_treatmentFS_timePtTS_patient_1221


title: BreastPrimaryTumor_treatmentFS_timePtTS_patient_1230


title: BreastPrimaryTumor_treatmentFS_timePtTS_patient_1199


title: Spleen_SAHC.AC_pod7_rep3

source_name: Spleen, SAHC + AC

tag: organ

value: Spleen

value: SAHC + AC

tag: pod

tag: status

value: Healthy

tag: mouse


title: BreastPrimaryTumor_treatmentFS_timePtTS_patient_1197


title: BreastPrimaryTumor_treatmentFS_timePtTS_patient_1200


title: BreastPrimaryTumor_treatmentFS_timePtTS_patient_1192


title: BreastPrimaryTumor_treatmentFS_timePtTS_patient_1188


title: BreastPrimaryTumor_treatmentFS_timePtTS_patient_1191


title: BreastPrimaryTumor_treatmentFS_timePtTS_patient_1226


title: BreastPrimaryTumor_treatmentFS_timePtTS_patient_1181


title: BreastPrimaryTumor_treatmentFS_timePtTS_patient_1219


title: BreastPrimaryTumor_treatmentFS_timePtTS_patient_1193


title: BreastPrimaryTumor_treatmentFS_timePtTS_patient_1173


title: BreastPrimaryTumor_treatmentFS_timePtTS_patient_1164


title: BreastPrimaryTumor_treatmentFS_timePtTS_patient_1169


title: BreastPrimaryTumor_treatmentFS_timePtTS_patient_1175


title: BreastPrimaryTumor_treatmentFS_timePtTS_patient_1160


title: BreastPrimaryTumor_treatmentFS_timePtTS_patient_1183


title: BreastPrimaryTumor_treatmentFS_timePtTS_patient_1159


title: BreastPrimaryTumor_treatmentFS_timePtTS_patient_1170


title: BreastPrimaryTumor_treatmentFS_timePtTS_patient_1179


title: BreastPrimaryTumor_treatmentFS_timePtTS_patient_1146


title: BreastPrimaryTumor_treatmentFS_timePtTS_patient_1185


title: BreastPrimaryTumor_treatmentFS_timePtTS_patient_1143


title: BreastPrimaryTumor_treatmentFS_timePtTS_patient_1154


title: BreastPrimaryTumor_treatmentFS_timePtTS_patient_1115


title: BreastPrimaryTumor_treatmentFS_timePtTS_patient_1121


title: BreastPrimaryTumor_treatmentFS_timePtTS_patient_1139


title: BreastPrimaryTumor_treatmentFS_timePtTS_patient_1110


title: BreastPrimaryTumor_treatmentFS_timePtTS_patient_1112


title: BreastPrimaryTumor_treatmentFS_timePtTS_patient_1129


title: BreastPrimaryTumor_treatmentFS_timePtTS_patient_1167


title: BreastPrimaryTumor_treatmentFS_timePtTS_patient_1111


title: BreastPrimaryTumor_treatmentFS_timePtTS_patient_1149


title: BreastPrimaryTumor_treatmentFS_timePtTS_patient_1091


title: BreastPrimaryTumor_treatmentFS_timePtTS_patient_1095


title: BreastPrimaryTumor_treatmentFS_timePtTS_patient_1062


title: BreastPrimaryTumor_treatmentFS_timePtTS_patient_1104


title: BreastPrimaryTumor_treatmentFS_timePtTS_patient_1063


title: BreastPrimaryTumor_treatmentFS_timePtTS_patient_1069


title: BreastPrimaryTumor_treatmentFS_timePtTS_patient_1054


title: BreastPrimaryTumor_treatmentFS_timePtTS_patient_1040


title: BreastPrimaryTumor_treatmentFS_timePtTS_patient_1055


title: BreastPrimaryTumor_treatmentFS_timePtTS_patient_1084


title: BreastPrimaryTumor_treatmentFS_timePtTS_patient_1009


title: BreastPrimaryTumor_treatmentFS_timePtTS_patient_1049


title: BreastPrimaryTumor_treatmentFS_timePtTS_patient_1061


title: BreastPrimaryTumor_treatmentFS_timePtTS_patient_1044


title: BreastPrimaryTumor_treatmentFS_timePtTS_patient_1016


title: BreastPrimaryTumor_treatmentFS_timePtTS_patient_1039


title: BreastPrimaryTumor_treatmentFS_timePtTS_patient_1008


title: BreastPrimaryTumor_treatmentFS_timePtTS_patient_1032


title: BreastPrimaryTumor_treatmentF3_timePtT2_patient_1127

source_name: 24-72 hours after initiation of treatment Breast tumor biopsy (T2)


title: BreastPrimaryTumor_treatmentFS_timePtTS_patient_1004


title: BreastPrimaryTumor_treatmentFS_timePtTS_patient_1005


title: BreastPrimaryTumor_treatmentF3_timePtT2_patient_1114


title: BreastPrimaryTumor_treatmentF3_timePtT2_patient_1101


title: BreastPrimaryTumor_treatmentFS_timePtTS_patient_1002


title: BreastPrimaryTumor_treatmentF3_timePtT2_patient_1086


title: BreastPrimaryTumor_treatmentF3_timePtT2_patient_1132


title: BreastPrimaryTumor_treatmentFS_timePtTS_patient_1003


title: BreastPrimaryTumor_treatmentF3_timePtT2_patient_1110


title: BreastPrimaryTumor_treatmentF4_timePtT2_patient_1125


title: BreastPrimaryTumor_treatmentF3_timePtT2_patient_1100


title: BreastPrimaryTumor_treatmentF3_timePtT2_patient_1084


title: BreastPrimaryTumor_treatmentF3_timePtT2_patient_1095


title: BreastPrimaryTumor_treatmentF3_timePtT2_patient_1063


title: BreastPrimaryTumor_treatmentF3_timePtT2_patient_1081


title: BreastPrimaryTumor_treatmentF3_timePtT2_patient_1058


title: BreastPrimaryTumor_treatmentF3_timePtT2_patient_1059


title: BreastPrimaryTumor_treatmentF3_timePtT2_patient_1069


title: BreastPrimaryTumor_treatmentF3_timePtT2_patient_1049


title: BreastPrimaryTumor_treatmentF3_timePtT2_patient_1054


title: BreastPrimaryTumor_treatmentF3_timePtT2_patient_1044


title: BreastPrimaryTumor_treatmentF3_timePtT2_patient_1043


title: BreastPrimaryTumor_treatmentF3_timePtT2_patient_1042


title: BreastPrimaryTumor_treatmentF3_timePtT2_patient_1057


title: BreastPrimaryTumor_treatmentF3_timePtT2_patient_1041


title: BreastPrimaryTumor_treatmentF3_timePtT2_patient_1077


title: BreastPrimaryTumor_treatmentF3_timePtT2_patient_1078


title: BreastPrimaryTumor_treatmentF3_timePtT2_patient_1039


title: BreastPrimaryTumor_treatmentF3_timePtT2_patient_1037


title: BreastPrimaryTumor_treatmentF3_timePtT2_patient_1045


title: BreastPrimaryTumor_treatmentF3_timePtT2_patient_1022


title: BreastPrimaryTumor_treatmentF3_timePtT2_patient_1012


title: BreastPrimaryTumor_treatmentF3_timePtT2_patient_1017


title: BreastPrimaryTumor_treatmentF3_timePtT2_patient_1004


title: BreastPrimaryTumor_treatmentF3_timePtT2_patient_1016


title: BreastPrimaryTumor_treatmentF2_timePtT1_patient_1094

source_name: pretreatment Breast Tumor biopsy (T1)


title: BreastPrimaryTumor_treatmentF3_timePtT2_patient_1034


title: BreastPrimaryTumor_treatmentF4_timePtT2_patient_1026


title: BreastPrimaryTumor_treatmentF2_timePtT1_patient_1221


title: BreastPrimaryTumor_treatmentF2_timePtT1_patient_1228


title: BreastPrimaryTumor_treatmentF1_timePtT1_patient_1060


title: BreastPrimaryTumor_treatmentF4_timePtT2_patient_1051


title: BreastPrimaryTumor_treatmentF3_timePtT2_patient_1027


title: BreastPrimaryTumor_treatmentF1_timePtT1_patient_1194


title: BreastPrimaryTumor_treatmentF3_timePtT2_patient_1029


title: BreastPrimaryTumor_treatmentF3_timePtT2_patient_1032


title: BreastPrimaryTumor_treatmentF1_timePtT1_patient_1200


title: BreastPrimaryTumor_treatmentF3_timePtT2_patient_1031


title: BreastPrimaryTumor_treatmentF4_timePtT2_patient_1009


title: BreastPrimaryTumor_treatmentF3_timePtT2_patient_1036


title: BreastPrimaryTumor_treatmentF2_timePtT1_patient_1081


title: BreastPrimaryTumor_treatmentF1_timePtT1_patient_1219


title: BreastPrimaryTumor_treatmentF4_timePtT2_patient_1001


title: BreastPrimaryTumor_treatmentF3_timePtT2_patient_1033


title: BreastPrimaryTumor_treatmentF2_timePtT1_patient_1184


title: BreastPrimaryTumor_treatmentF1_timePtT1_patient_1193


title: BreastPrimaryTumor_treatmentF1_timePtT1_patient_1199


title: BreastPrimaryTumor_treatmentF1_timePtT1_patient_1222


title: BreastPrimaryTumor_treatmentF1_timePtT1_patient_1223


title: BreastPrimaryTumor_treatmentF1_timePtT1_patient_1218


title: BreastPrimaryTumor_treatmentF1_timePtT1_patient_1209


title: BreastPrimaryTumor_treatmentF1_timePtT1_patient_1232


title: BreastPrimaryTumor_treatmentF1_timePtT1_patient_1216


title: BreastPrimaryTumor_treatmentF1_timePtT1_patient_1236


title: BreastPrimaryTumor_treatmentF1_timePtT1_patient_1220


title: BreastPrimaryTumor_treatmentF1_timePtT1_patient_1211


title: BreastPrimaryTumor_treatmentF2_timePtT1_patient_1187


title: BreastPrimaryTumor_treatmentF1_timePtT1_patient_1237


title: BreastPrimaryTumor_treatmentF1_timePtT1_patient_1205


title: BreastPrimaryTumor_treatmentF1_timePtT1_patient_1226


title: BreastPrimaryTumor_treatmentF1_timePtT1_patient_1231


title: BreastPrimaryTumor_treatmentF1_timePtT1_patient_1213


title: BreastPrimaryTumor_treatmentF1_timePtT1_patient_1225


title: BreastPrimaryTumor_treatmentF1_timePtT1_patient_1203


title: BreastPrimaryTumor_treatmentF1_timePtT1_patient_1130


title: BreastPrimaryTumor_treatmentF1_timePtT1_patient_1227


title: BreastPrimaryTumor_treatmentF2_timePtT1_patient_1202


title: BreastPrimaryTumor_treatmentF1_timePtT1_patient_1169


title: BreastPrimaryTumor_treatmentF1_timePtT1_patient_1239


title: BreastPrimaryTumor_treatmentF1_timePtT1_patient_1179


title: BreastPrimaryTumor_treatmentF1_timePtT1_patient_1191


title: BreastPrimaryTumor_treatmentF1_timePtT1_patient_1074


title: BreastPrimaryTumor_treatmentF1_timePtT1_patient_1208


title: BreastPrimaryTumor_treatmentF1_timePtT1_patient_1142


title: BreastPrimaryTumor_treatmentF1_timePtT1_patient_1192


title: BreastPrimaryTumor_treatmentF1_timePtT1_patient_1206


title: BreastPrimaryTumor_treatmentF3_timePtT2_patient_1038


title: BreastPrimaryTumor_treatmentF1_timePtT1_patient_1087


title: BreastPrimaryTumor_treatmentF3_timePtT2_patient_1035


title: BreastPrimaryTumor_treatmentF1_timePtT1_patient_1215


title: BreastPrimaryTumor_treatmentF1_timePtT1_patient_1146


title: BreastPrimaryTumor_treatmentF1_timePtT1_patient_1122


title: BreastPrimaryTumor_treatmentF1_timePtT1_patient_1164


title: BreastPrimaryTumor_treatmentF1_timePtT1_patient_1155


title: BreastPrimaryTumor_treatmentF1_timePtT1_patient_1162


title: BreastPrimaryTumor_treatmentF1_timePtT1_patient_1150


title: BreastPrimaryTumor_treatmentF1_timePtT1_patient_1161


title: BreastPrimaryTumor_treatmentF1_timePtT1_patient_1152


title: BreastPrimaryTumor_treatmentF1_timePtT1_patient_1148


title: BreastPrimaryTumor_treatmentF1_timePtT1_patient_1163


title: BreastPrimaryTumor_treatmentF1_timePtT1_patient_1173


title: BreastPrimaryTumor_treatmentF1_timePtT1_patient_1151


title: BreastPrimaryTumor_treatmentF1_timePtT1_patient_1160


title: BreastPrimaryTumor_treatmentF1_timePtT1_patient_1176


title: BreastPrimaryTumor_treatmentF1_timePtT1_patient_1175


title: BreastPrimaryTumor_treatmentF1_timePtT1_patient_1165


title: BreastPrimaryTumor_treatmentF1_timePtT1_patient_1154


title: BreastPrimaryTumor_treatmentF1_timePtT1_patient_1144


title: BreastPrimaryTumor_treatmentF1_timePtT1_patient_1123


title: BreastPrimaryTumor_treatmentF1_timePtT1_patient_1147


title: BreastPrimaryTumor_treatmentF1_timePtT1_patient_1166


title: BreastPrimaryTumor_treatmentF1_timePtT1_patient_1158


title: BreastPrimaryTumor_treatmentF1_timePtT1_patient_1139


title: BreastPrimaryTumor_treatmentF1_timePtT1_patient_1138


title: BreastPrimaryTumor_treatmentF1_timePtT1_patient_1149


title: BreastPrimaryTumor_treatmentF1_timePtT1_patient_1136


title: BreastPrimaryTumor_treatmentF1_timePtT1_patient_1113


title: BreastPrimaryTumor_treatmentF1_timePtT1_patient_1109


title: BreastPrimaryTumor_treatmentF1_timePtT1_patient_1065


title: BreastPrimaryTumor_treatmentF1_timePtT1_patient_1121


title: BreastPrimaryTumor_treatmentF1_timePtT1_patient_1073


title: BreastPrimaryTumor_treatmentF1_timePtT1_patient_1135


title: BreastPrimaryTumor_treatmentF1_timePtT1_patient_1118


title: BreastPrimaryTumor_treatmentF1_timePtT1_patient_1134


title: BreastPrimaryTumor_treatmentF1_timePtT1_patient_1082


title: BreastPrimaryTumor_treatmentF1_timePtT1_patient_1126


title: BreastPrimaryTumor_treatmentF1_timePtT1_patient_1106


title: BreastPrimaryTumor_treatmentF1_timePtT1_patient_1088


title: BreastPrimaryTumor_treatmentF1_timePtT1_patient_1099


title: BreastPrimaryTumor_treatmentF1_timePtT1_patient_1132


title: BreastPrimaryTumor_treatmentF1_timePtT1_patient_1075


title: BreastPrimaryTumor_treatmentF1_timePtT1_patient_1083


title: BreastPrimaryTumor_treatmentF1_timePtT1_patient_1069


title: BreastPrimaryTumor_treatmentF1_timePtT1_patient_1145


title: BreastPrimaryTumor_treatmentF1_timePtT1_patient_1058


title: BreastPrimaryTumor_treatmentF1_timePtT1_patient_1129


title: BreastPrimaryTumor_treatmentF1_timePtT1_patient_1114


title: BreastPrimaryTumor_treatmentF1_timePtT1_patient_1100


title: BreastPrimaryTumor_treatmentF2_timePtT1_patient_1086


title: BreastPrimaryTumor_treatmentF1_timePtT1_patient_1128


title: BreastPrimaryTumor_treatmentF1_timePtT1_patient_1062


title: BreastPrimaryTumor_treatmentF1_timePtT1_patient_1055


title: BreastPrimaryTumor_treatmentF1_timePtT1_patient_1111


title: BreastPrimaryTumor_treatmentF1_timePtT1_patient_1127


title: BreastPrimaryTumor_treatmentF1_timePtT1_patient_1041


title: BreastPrimaryTumor_treatmentF1_timePtT1_patient_1044


title: BreastPrimaryTumor_treatmentF1_timePtT1_patient_1042


title: BreastPrimaryTumor_treatmentF1_timePtT1_patient_1110


title: BreastPrimaryTumor_treatmentF1_timePtT1_patient_1054


title: BreastPrimaryTumor_treatmentF1_timePtT1_patient_1038


title: BreastPrimaryTumor_treatmentF1_timePtT1_patient_1078


title: BreastPrimaryTumor_treatmentF1_timePtT1_patient_1085


title: BreastPrimaryTumor_treatmentF1_timePtT1_patient_1095


title: BreastPrimaryTumor_treatmentF1_timePtT1_patient_1051


title: BreastPrimaryTumor_treatmentF1_timePtT1_patient_1048


title: BreastPrimaryTumor_treatmentF1_timePtT1_patient_1045


title: BreastPrimaryTumor_treatmentF1_timePtT1_patient_1057


title: BreastPrimaryTumor_treatmentF1_timePtT1_patient_1046


title: BreastPrimaryTumor_treatmentF1_timePtT1_patient_1061


title: BreastPrimaryTumor_treatmentF1_timePtT1_patient_1043


title: BreastPrimaryTumor_treatmentF1_timePtT1_patient_1047


title: BreastPrimaryTumor_treatmentF1_timePtT1_patient_1049


title: BreastPrimaryTumor_treatmentF1_timePtT1_patient_1034


title: BreastPrimaryTumor_treatmentF1_timePtT1_patient_1064


title: BreastPrimaryTumor_treatmentF1_timePtT1_patient_1032


title: BreastPrimaryTumor_treatmentF1_timePtT1_patient_1035


title: BreastPrimaryTumor_treatmentF1_timePtT1_patient_1026


title: BreastPrimaryTumor_treatmentF1_timePtT1_patient_1077


title: BreastPrimaryTumor_treatmentF1_timePtT1_patient_1033


title: BreastPrimaryTumor_treatmentF2_timePtT1_patient_1004


title: BreastPrimaryTumor_treatmentF1_timePtT1_patient_1016


title: BreastPrimaryTumor_treatmentF1_timePtT1_patient_1017


title: DamID Fibroblast replicate 132

status: Public on Dec 16 2014

city: Baltimore

first: Karen

last: Reddy

state: MD

address: 855 North Wolfe Street

department: Center for Epigenetics/Biological Chemistry

institute: Johns Hopkins University

description:
fibroblast_DamID_log2ratio_chr11_chr12.bedgraph
DamID-chip fibroblasts (LmnB1/Dam)

hyb_protocol: Labeled samples were hybed on 2007-08-17_MM8_Economy_03 arrays using standard protocol found in Chapter 4, NimbleGen Arrays User's Guide, Version 1.0

scan_protocol: Arrays were scanned on an MS200_2 scanner using standard manafacturer protocol.

data_processing:
Data was processed using Nimblegen standard procedures for DEVA 1.0.2 to create .pair and Dam-LmnB1/Dam-only Log2 ratio files
DEVA 1.0.2 processed files, Dam-LmnB1/Dam-only Log2 ratio files were lifted over to mm9. Duplicates were quantile normalized and averaged together. Processed files are in UCSC compatible bedgraph format

source_name: Dam-LmnB1 data from fibroblasts

label_protocol: 1 ug of sample DNA was labeled with Cy3 or Cy5 dye as described by Chapter 3, NimbleGen Arrays User's Guide, Version 1.0

growth_protocol: Cells were cultured in dishes in DMEM-Hi glucose medium

extract_protocol: gDNA was extracted using the QIAamp DNA Mini Kit. DamID was performed as described in Vogel et al, Nature Protocols, 2007 and previously described in Zullo et al, Cell, 2013  QIAamp DNA Mini Kit

treatment_protocol: Cells were infected with Dam-LmnB1 retroviral vectors in the presence of polybrene. NIH3T3 fibroblasts are an established cell line.

tag: cell line

value: NIH3T3 Fibroblasts

tag: strain

tag: damid construct

source_name: Dam-only data from fibroblasts

treatment_protocol: Cells were infected with Dam-only retroviral vectors in the presence of polybrene. NIH3T3 fibroblasts are an established cell line.

value: Dam-only


title: DamID Fibroblast replicate 882


title: 1926tube

status: Public on Mar 19 2014

type: SRA

city: Seattle

first: Stephen

last: Tapscott

state: WASHINGTON

address: 1100 Fairview N. Ave

department: Human Biology

institute: Fred Hutch Cancer Research Center

library_source: transcriptomic

data_processing:
Base calls and quality scores were generated using Illumina's Real-Time Analysis software v1.8.7.  Binary base call files were converted to text formatted qseq files via OLB 1.9.0, which were then filtered and converted to fastq format by CASAVA 1.7, using the default Chastity threshold of 0.6.
Read counts for the genes are collected by Bioconductor Biostrings and IRanges packages.  Reads that are mapped ambiguously to M locations are counted as 1/M at each occurrence.
Genome_build: hg19
Supplementary_files_format_and_content: read counts

Raw data not provided due to patient privacy concerns.

molecule: polyA RNA

source_name: cultured myotube from control individual

growth_protocol: Human primary myoblasts cell lines were received from the University of Rochester biorepository (http://www.urmc.rochester.edu/fields-center/). Myoblasts were cultured in DMEM/F-10 media (#31550 GIBCO, Grand Island, NY) in the presence of 20% heat inactivated fetal bovine serum (FBS #10270 GIBCO), 1% penicillin/streptomycin (#15140 GIBCO) and was supplemented with 10ng/ml rhFGF (#G5071 Promega, Madison, Wisconsin) and 1μM dexamethasone (#D2915 SIGMA, St. Louis, Missouri).

extract_protocol:
Samples for RNA sequencing were harvested in QIAzol lysis reagent (#79306 Qiagen N.V., The Netherlands). RNA was isolated by miRNeasy Mini Kit (#217004 Qiagen) including DNase treatment according to the manufacturer instructions.
mRNA purification, mRNA fragmentation and cDNA synthesis were performed with the TruSeq RNA Sample Preparation Kit (Illumina) according to the manufacturer's protocol.

treatment_protocol: Myoblasts were fused at 80% confluence in DMEM/F-12 Glutamax media (#) containing 2% KnockOut serum replacement formulation (#10828 GIBCO) for 36 hours.

tag: subject

value: control individual 1

tag: cell type

value: differentiated human primary myotube cells


title: BreastPrimaryTumor_treatmentF1_timePtT1_patient_1027

tag: patient

tag: tissue

tag: treatment

tag: biopsy time


title: 2081tube

value: control individual 3


title: 2315tube

source_name: cultured myotube from FSHD1 patient

value: FSHD1 patient 1


title: 2316tube

value: FSHD1 patient 2


title: BreastPrimaryTumor_treatmentF1_timePtT1_patient_1031

tag: recurrence_yes is 1

tag: hr-positive_yes is 1

tag: her2-positive_yes is 1

tag: pcr_yes is 1


title: BreastPrimaryTumor_treatmentF1_timePtT1_patient_1024

tag: rcb class

tag: rcb index

tag: reference


title: BreastPrimaryTumor_treatmentF1_timePtT1_patient_1005


title: BreastPrimaryTumor_treatmentF1_timePtT1_patient_1002


title: BreastPrimaryTumor_treatmentF2_timePtT1_patient_1008


title: BreastPrimaryTumor_treatmentF1_timePtT1_patient_1009


title: BreastPrimaryTumor_treatmentF1_timePtT1_patient_1021


title: 2068tube

value: control individual 2


title: BreastPrimaryTumor_treatmentF1_timePtT1_patient_1028


title: BreastPrimaryTumor_treatmentF2_timePtT1_patient_1001


title: BreastPrimaryTumor_treatmentF1_timePtT1_patient_1011


title: BreastPrimaryTumor_treatmentF1_timePtT1_patient_1022


title: BreastPrimaryTumor_treatmentF1_timePtT1_patient_1012


title: BreastPrimaryTumor_treatmentF1_timePtT1_patient_1007


title: BreastPrimaryTumor_treatmentF1_timePtT1_patient_1013


title: BreastPrimaryTumor_treatmentF1_timePtT1_patient_1019


title: BreastPrimaryTumor_treatmentF1_timePtT1_patient_1107


title: primary human muscle myoblasts rep1

status: Public on Aug 29 2013

data_processing:
Probe intensities were corrected, normalized, and summarized by the Lumi package of Bioconductor (Du et al., 2008). Differentially expressed genes were identified by the LIMMA package of Bioconductor (Wettenhall and Smyth, 2004).
Data was vst transformed and quantile normalized using the Lumi package of Bioconductor (Du et al., 2008).

source_name: primary human muscle myoblasts

label_protocol: Biotinylated cRNA were prepared with the Illumina TotalPrep RNA Amplification Kit (Applied Biosystems) for Illumina arrays

growth_protocol: Cells were collected both in growth medium at a low cell density for the myoblast condition and after 72 h at complete cellular confluence in low-serum differentiation medium for the myotube condition. Cells were maintained in DMEM with 10% bovine calf serum and 1% Pen-Strep (Gibco). Low-serum differentiation media consisted of DMEM with 1% horse serum, 1% Pen-Strep and 10 ug/mL insulin and transferrin.

extract_protocol: RNA was extracted with Qiagen RNeasy kit according to manufacturer's instruction. Quality control was performed with Agilent Bioanalyzer.

value: primary human muscle myoblasts


title: primary human muscle myoblasts rep2


title: primary human muscle myotubes rep3

source_name: primary human muscle myotubes

value: primary human muscle myotubes


title: primary human muscle myotubes rep2


title: primary human muscle myoblasts rep3


title: primary human muscle myotubes rep1


title: P19_control_rep2_batch3

status: Public on Mar 26 2012

hyb_protocol: Standard Affymetrix hybridization protocol

scan_protocol: Standard Affymetrix scanning protocol

data_processing: Probe intensities were corrected, normalized, and summarized by the  simpleaffy package of Bioconductor (Wilson and Miller,2005). Differentially expressed genes were identified by the LIMMA package of Bioconductor (Wettenhall and Smyth, 2004).

source_name: control untransduced P19 cells

label_protocol: Biotinylated cRNA were prepared with the Affymetrix One-Cycle Eukaryotic Target Labeling Assay.

growth_protocol: P19 cells were maintained in MEMα as previously described (Farah et al., 2000, PUBMED ID 10648228), and MEFs derived from Myod-/-/Myf5-/- mice were maintained in DMEM with 10% FBS.

extract_protocol: Neuronally differentiated P19 cells were harvested 72 hours after infection. MEFs were harvested 36-40 hours after switching to differentiation media.

treatment_protocol: P19 cells and MEFs were infected with lentivirus in media containing polybrene (final concentration 8 µg /ml), and after 24 hours the cells were switched into fresh media. MEFs transduced with MyoD were switched to differentiation media (1% heat inactivated horse serum, 10 μg/mL insulin, 10 μg/mL transferrin) 48 hours after infection.

value: undifferentiated P19 cells


title: P19_MyoD_rep2_batch1

source_name: P19 transduced with MyoD lentivirus

value: Neuronally differentiated P19 cells


title: P19_MyoD_rep1_batch1


title: P19_control_rep1_batch3


title: MM_MyoD_rep1_batch1

source_name: MEF transduced with MyoD lentivirus

value: Neuronally differentiated MEF cells


title: MM_ND2_rep3_batch2

source_name: MEF transduced with NeuroD2 lentivirus


title: MM_control_rep2_batch1

source_name: control untransduced MEF cells

value: undifferentiated MEF cells


title: P19_control_rep2_batch1


title: MM_control_rep2_batch2


title: MM_ND2_rep1_batch2


title: P19_control_rep3_batch1


title: P19_ND2_rep1_batch3

source_name: P19 transduced with NeuroD2 lentivirus


title: MM_ND2_rep2_batch2


title: P19_ND2_rep3_batch3


title: MM_control_rep3_batch1


title: MM_control_rep3_batch2


title: MM_MyoD_rep3_batch1


title: P19_MyoD_rep3_batch1


title: P19_ND2_rep2_batch3


title: MM_control_rep1_batch1


title: MM_MyoD_rep2_batch1


title: P19_control_rep3_batch3


title: MM_control_rep1_batch2


title: P19_control_rep1_batch1


title: descending colon biopsy from crohns disease subject (PRB12506)

status: Public on Jul 19 2010

city: South San Francisco

first: Alex

last: Abbas

address: 1 DNA Way

department: Bioinformatics

institute: Genentech, Inc.

hyb_protocol: 18 hours at 60°C with constant rotation on Agilent WHG

scan_protocol: Agilent scanner according to the manufacturer’s protocol

data_processing: the data were extracted and normalized according to the default settings of Agilent Feature Extraction 7.5. LOWESS normalization, background subtraction, and ratio computation.

label_protocol: T7 RNA polymerase single round of linear amplification

extract_protocol: micro total RNA isolation from animal tissues protocol (Qiagen, Valencia, CA)

tag: current medication

value: 6MP 50mg

tag: birth date

tag: ethnicity

value: CAUCASIAN

tag: symptoms onset date

tag: diagnosis date

tag: ocp

value: unknown

tag: joint problems

value: FALSE

tag: family history

tag: aza treated

value: NO

tag: aza tolerant

tag: procedure date

tag: indictation for procedure:

tag: cdai

tag: harvey bradshaw

tag: esr

tag: crp

tag: hb

tag: wcc

tag: neutrophils

tag: albumin

tag: blood obtained

tag: ibd affected relatives

tag: nod 1007 fs:

tag: further operations:

tag: stoma ileal

tag: diagnosis oral

tag: diagnosis ileal

value: TRUE

tag: diagnosis colonic

tag: diagnosis rectal

tag: diagnosis anal perianal

tag: diagnosis vienna classifi

tag: last followup date

tag: followup oral

tag: followup ileal

tag: followup colonic

tag: followup rectal

tag: followup anal perianal

tag: followup vienna classific

tag: casenote review date

tag: behavior at diagnosis

tag: diagnosis stricture fistu

tag: diagnosis details:

tag: behavior at followup

tag: disease group

value: REMISSION

tag: smoking status

value: never

tag: smoking start date:

tag: smoking stop date:

tag: smoking amount

tag: other illnesses

tag: disease

value: crohns disease

tag: anatomic location

value: descending colon

value: SoC treated

tag: treatment response

value: responder

tag: inflammation status

value: uninflamed

source_name: Stratagene Universal Human Reference RNA (Catalog #740000)

extract_protocol: not applicable, Universal Human Reference RNA (Catalog #740000) purchased from Stratagene


title: descending colon biopsy from crohns disease subject (PRB5326)

tag: patient

tag: current medication

tag: birth date

tag: ethnicity

tag: symptoms onset date

tag: diagnosis date

tag: ocp

value: EX

tag: joint problems

tag: family history

tag: aza treated

tag: aza tolerant

tag: procedure date

tag: indictation for procedure:

tag: cdai

tag: harvey bradshaw

tag: esr

tag: crp

tag: hb

tag: wcc

tag: neutrophils

tag: albumin

tag: blood obtained

tag: ibd affected relatives

tag: nod 1007 fs:

tag: further operations:

tag: stoma ileal

tag: diagnosis oral

tag: diagnosis ileal

tag: diagnosis colonic

tag: diagnosis rectal

tag: diagnosis anal perianal

tag: diagnosis vienna classifi

tag: last followup date

tag: followup oral

tag: followup ileal

tag: followup colonic

tag: followup rectal

tag: followup anal perianal

value: Myobacterium identified in biopsies from resection 2001. Given 6 months of anti TB therapy.

tag: treatment

tag: reference

value: Stratagene Universal Human Reference RNA


title: descending colon biopsy from crohns disease subject (PRB5298)

tag: patient

tag: current medication

tag: birth date

tag: ethnicity

tag: symptoms onset date

tag: diagnosis date

tag: ocp

value: NEVER

tag: joint problems

tag: family history

tag: aza treated

tag: aza tolerant

tag: procedure date

tag: indictation for procedure:

tag: cdai

tag: harvey bradshaw

tag: esr

tag: crp

tag: hb

tag: wcc

tag: neutrophils

tag: albumin

tag: blood obtained

tag: ibd affected relatives

tag: nod 1007 fs:

tag: followup vienna classific

tag: casenote review date

tag: behavior at diagnosis

tag: diagnosis stricture fistu

tag: diagnosis details:

tag: behavior at followup

tag: disease group

value: NEW

tag: smoking status

tag: smoking start date:

tag: smoking stop date:

tag: smoking amount

tag: other illnesses

tag: disease

tag: anatomic location

value: SoC untreated

tag: treatment response

tag: inflammation status

value: inflamed


title: descending colon biopsy from crohns disease subject (PRB5329)

tag: patient

tag: current medication

value: Pentaza 1g BD, Folic acid 5mg, Codine P, Atenolol.

tag: birth date

tag: ethnicity

value: CAUCASIAN

tag: symptoms onset date

tag: diagnosis date

tag: ocp

value: unknown

tag: joint problems

value: FALSE

tag: family history

tag: aza treated

value: YES

tag: aza tolerant

tag: procedure date

tag: indictation for procedure:

tag: cdai

tag: harvey bradshaw

tag: esr

tag: crp

tag: hb

tag: wcc

tag: neutrophils

tag: albumin

tag: blood obtained

tag: ibd affected relatives

tag: nod 1007 fs:

tag: further operations:

tag: stoma ileal

tag: diagnosis oral

tag: diagnosis ileal

tag: diagnosis colonic

tag: diagnosis rectal

tag: diagnosis anal perianal

tag: diagnosis vienna classifi

tag: last followup date

tag: followup oral

tag: followup ileal

tag: followup colonic

tag: followup rectal

tag: followup anal perianal

tag: diagnosis details

value: Peri-anal abcess at diagnosis

value: ex

tag: smoking start date

tag: smoking stop date

tag: treatment

tag: reference


title: descending colon biopsy from crohns disease subject (PRB5291)

tag: patient

tag: current medication

tag: birth date

tag: ethnicity

tag: symptoms onset date

tag: diagnosis date

tag: ocp

tag: joint problems

tag: family history

tag: aza treated

value: NO

tag: aza tolerant

tag: procedure date

tag: indictation for procedure:

tag: cdai

tag: harvey bradshaw

tag: esr

tag: crp

tag: hb

tag: wcc

tag: neutrophils

tag: albumin

tag: blood obtained

tag: ibd affected relatives

tag: nod 1007 fs:

tag: further operations:

tag: stoma ileal

tag: diagnosis oral

value: TRUE

tag: followup vienna classific

tag: casenote review date

tag: behavior at diagnosis

tag: diagnosis stricture fistu

tag: diagnosis details:

tag: behavior at followup

tag: disease group

tag: smoking status

value: current

tag: smoking stop date:

tag: smoking amount

tag: other illnesses

tag: disease

value: crohns disease

tag: anatomic location

value: descending colon

tag: treatment response

tag: inflammation status


title: descending colon biopsy from crohns disease subject (PRB5351)

tag: patient

tag: current medication

value: Methotrexate 12.5mg prednisolone 10mg Folic acid

tag: birth date

tag: ethnicity

tag: symptoms onset date

tag: diagnosis date

tag: ocp

tag: joint problems

tag: family history

tag: aza treated

tag: aza tolerant

tag: procedure date

tag: indictation for procedure:

tag: cdai

tag: harvey bradshaw

tag: esr

tag: crp

tag: hb

tag: wcc

tag: neutrophils

tag: albumin

tag: blood obtained

tag: ibd affected relatives

tag: nod 1007 fs:

tag: further operations:

tag: stoma ileal

tag: diagnosis ileal

tag: diagnosis colonic

tag: diagnosis rectal

tag: diagnosis anal perianal

tag: diagnosis vienna classifi

tag: last followup date

tag: followup oral

tag: followup ileal

tag: followup colonic

tag: followup rectal

tag: followup anal perianal

value: FAILURE OF TREATMENT

value: never

tag: smoking start date:

tag: other illnesses:

tag: treatment

value: SoC treated

value: nonresponder

tag: reference

value: Stratagene Universal Human Reference RNA


title: descending colon biopsy from crohns disease subject (PRB5333)

tag: patient

tag: current medication

value: Azathioprine 100mg Omeprazole 20mg Seroxat 30mg.

tag: birth date

tag: ethnicity

value: CAUCASIAN

tag: symptoms onset date

tag: diagnosis date

tag: ocp

value: NEVER

tag: joint problems

tag: family history

tag: aza treated

tag: aza tolerant

tag: procedure date

tag: indictation for procedure:

tag: cdai

tag: harvey bradshaw

tag: esr

tag: crp

tag: hb

tag: wcc

tag: neutrophils

tag: albumin

tag: blood obtained

tag: ibd affected relatives

tag: nod 1007 fs:

tag: further operations:

tag: diagnosis oral

tag: followup vienna classific

tag: casenote review date

tag: behavior at diagnosis

tag: diagnosis stricture fistu

tag: diagnosis details:

tag: behavior at followup

tag: disease group

value: REMISSION

tag: smoking status

tag: smoking stop date:

tag: smoking amount

tag: other illnesses

value: Depression, Irritable bowel syndrome

tag: disease

tag: anatomic location

tag: treatment response

value: responder

tag: inflammation status

value: uninflamed


title: descending colon biopsy from crohns disease subject (PRB5344)

tag: patient

tag: current medication

value: AZA 100mg Budesonide 3mg Omeprazole 20mg Asacol 6d

tag: birth date

tag: ethnicity

tag: symptoms onset date

tag: diagnosis date

tag: ocp

value: unknown

tag: joint problems

value: FALSE

tag: family history

tag: aza treated

value: YES

tag: aza tolerant

tag: procedure date

tag: indictation for procedure:

tag: cdai

tag: harvey bradshaw

tag: esr

tag: crp

tag: hb

tag: wcc

tag: neutrophils

tag: albumin

tag: blood obtained

value: TRUE

tag: ibd affected relatives

tag: nod 1007 fs:

tag: further operations:

tag: stoma ileal

tag: diagnosis ileal

tag: diagnosis colonic

tag: diagnosis rectal

tag: diagnosis anal perianal

tag: diagnosis vienna classifi

tag: last followup date

tag: followup oral

tag: followup ileal

tag: followup colonic

tag: followup rectal

tag: followup anal perianal

value: ex

tag: smoking start date:

tag: smoking stop date

value: Asthma

tag: treatment

value: inflamed

tag: reference


title: descending colon biopsy from crohns disease subject (PRB12504)

tag: patient

tag: current medication

value: Azathioprine 150mg Asacol 800mg BD

tag: birth date

tag: ethnicity

tag: symptoms onset date

tag: diagnosis date

tag: ocp

tag: joint problems

tag: family history

tag: aza treated

tag: aza tolerant

tag: procedure date

tag: indictation for procedure:

tag: cdai

tag: harvey bradshaw

tag: esr

tag: crp

tag: hb

tag: wcc

tag: neutrophils

tag: albumin

tag: blood obtained

tag: ibd affected relatives

tag: nod 702

tag: nod 908

tag: dlg5 133a

tag: nod 1007 fs

tag: further operations:

tag: diagnosis oral

tag: followup vienna classific

tag: casenote review date

tag: behavior at diagnosis

tag: diagnosis stricture fistu

tag: diagnosis details:

tag: behavior at followup

tag: disease group

tag: smoking status

value: never

tag: smoking stop date:

tag: smoking amount

tag: other illnesses

value: Hayfever

tag: disease

value: crohns disease

tag: anatomic location

value: descending colon

value: SoC treated

tag: treatment response

tag: inflammation status


title: descending colon biopsy from crohns disease subject (PRB5354)

tag: patient

tag: current medication

tag: birth date

tag: ethnicity

value: CAUCASIAN

tag: symptoms onset date

tag: diagnosis date

tag: ocp

tag: joint problems

tag: family history

tag: aza treated

value: NO

tag: aza tolerant

tag: procedure date

tag: indictation for procedure:

tag: cdai

tag: harvey bradshaw

tag: esr

tag: crp

tag: hb

tag: wcc

tag: neutrophils

tag: albumin

tag: blood obtained

tag: ibd affected relatives

tag: nod 1007 fs:

tag: further operations:

tag: stoma ileal

tag: diagnosis ileal

tag: diagnosis colonic

tag: diagnosis rectal

tag: diagnosis anal perianal

tag: diagnosis vienna classifi

tag: last followup date:

tag: followup oral

tag: followup ileal

tag: followup colonic

tag: followup rectal

tag: followup anal perianal

value: FAILURE OF TREATMENT

tag: smoking start date:

tag: treatment

value: nonresponder

tag: reference

value: Stratagene Universal Human Reference RNA


title: descending colon biopsy from crohns disease subject (PRB11454)

tag: patient

tag: current medication

value: Pentaza Omeprazole Calcium Vit D

tag: birth date

tag: ethnicity

tag: symptoms onset date

tag: diagnosis date

tag: ocp

value: unknown

tag: joint problems

value: FALSE

tag: family history

tag: aza treated

tag: aza tolerant

tag: procedure date

tag: indictation for procedure:

tag: cdai

tag: harvey bradshaw

tag: esr

tag: crp

tag: hb

tag: wcc

tag: neutrophils

tag: albumin

tag: blood obtained

tag: ibd affected relatives

tag: nod 1007 fs:

tag: diagnosis oral

tag: followup vienna classific

tag: casenote review date:

tag: behavior at diagnosis:

tag: diagnosis stricture fistu

tag: diagnosis details:

tag: behavior at followup:

tag: disease group

value: REMISSION

tag: smoking status

tag: smoking stop date

tag: smoking amount

tag: other illnesses

tag: disease

tag: anatomic location

tag: treatment response

value: responder

tag: inflammation status

value: uninflamed


title: descending colon biopsy from crohns disease subject (PRB5296)

tag: patient

tag: current medication

tag: birth date

tag: ethnicity

tag: symptoms onset date

tag: diagnosis date

tag: ocp

tag: joint problems

tag: family history

tag: aza treated

tag: aza tolerant

tag: procedure date

tag: indictation for procedure:

tag: cdai

tag: harvey bradshaw

tag: esr

tag: crp

tag: hb

tag: wcc

tag: neutrophils

tag: albumin

tag: blood obtained

tag: ibd affected relatives

tag: nod 1007 fs:

tag: further operations:

tag: stoma ileal

tag: diagnosis ileal

tag: diagnosis colonic

tag: diagnosis rectal

tag: diagnosis anal perianal

value: TRUE

tag: diagnosis vienna classifi

tag: last followup date

tag: followup oral

tag: followup ileal

tag: followup colonic

tag: followup rectal

tag: followup anal perianal

tag: casenote review date

tag: behavior at diagnosis

tag: behavior at followup

value: NEW

value: current

tag: smoking start date:

tag: smoking stop date:

tag: treatment

value: SoC untreated

tag: reference


title: descending colon biopsy from crohns disease subject (PRB12502)

tag: patient

tag: current medication

value: Pentaza 4g/d Calcium/Vit D Residronate

tag: birth date

tag: ethnicity

tag: symptoms onset date

tag: diagnosis date

tag: ocp

tag: joint problems

tag: family history

tag: aza treated

value: YES

tag: aza tolerant

tag: procedure date

tag: indictation for procedure:

tag: cdai

tag: harvey bradshaw

tag: esr

tag: crp

tag: hb

tag: wcc

tag: neutrophils

tag: albumin

tag: blood obtained

tag: ibd affected relatives

tag: nod 1007 fs:

tag: further operations:

tag: stoma ileal

tag: diagnosis oral

tag: diagnosis ileal

tag: diagnosis colonic

tag: followup vienna classific

tag: diagnosis stricture fistu

tag: diagnosis details:

tag: disease group

tag: smoking status

value: ex

tag: smoking stop date

tag: smoking amount

tag: other illnesses

value: Peripheral neuropathy -IHD

tag: disease

value: crohns disease

tag: anatomic location

value: descending colon

tag: treatment response

tag: inflammation status


title: descending colon biopsy from crohns disease subject (PRB5330)

tag: patient

tag: current medication

value: Pentaza 4g daily

tag: birth date

tag: ethnicity

value: CAUCASIAN

tag: symptoms onset date

tag: diagnosis date

tag: ocp

value: NEVER

tag: joint problems

tag: family history

tag: aza treated

value: NO

tag: aza tolerant

tag: procedure date

tag: indictation for procedure:

tag: cdai

tag: harvey bradshaw

tag: esr

tag: crp

tag: hb

tag: wcc

tag: neutrophils

tag: albumin

tag: blood obtained

tag: ibd affected relatives

tag: nod 702

tag: nod 908

tag: dlg5 133a

tag: nod 1007 fs

tag: further operations:

tag: diagnosis rectal

tag: diagnosis anal perianal

tag: diagnosis vienna classifi

tag: last followup date

tag: followup oral

tag: followup ileal

tag: followup colonic

tag: followup rectal

tag: followup anal perianal

tag: casenote review date

tag: behavior at diagnosis

tag: behavior at followup

tag: smoking start date:

tag: smoking stop date:

tag: treatment

value: SoC treated

tag: reference

value: Stratagene Universal Human Reference RNA


title: descending colon biopsy from crohns disease subject (PRB12517)

tag: patient

tag: current medication

value: None 7 years

tag: birth date

tag: ethnicity

tag: symptoms onset date

tag: diagnosis date

tag: ocp

value: unknown

tag: joint problems

value: FALSE

tag: family history

tag: aza treated

tag: aza tolerant

tag: procedure date

tag: indictation for procedure:

tag: cdai

tag: harvey bradshaw

tag: esr

tag: crp

tag: hb

tag: wcc

tag: neutrophils

tag: albumin

tag: blood obtained

tag: ibd affected relatives

tag: nod 1007 fs:

tag: further operations:

tag: stoma ileal

tag: diagnosis oral

tag: diagnosis ileal

tag: diagnosis colonic

tag: followup vienna classific

tag: diagnosis stricture fistu

tag: diagnosis details:

tag: disease group

value: FAILURE OF TREATMENT

tag: smoking status

tag: smoking amount

tag: other illnesses

tag: disease

tag: anatomic location

tag: treatment response

value: nonresponder

tag: inflammation status

value: inflamed


title: descending colon biopsy from crohns disease subject (PRB5357)

tag: patient

tag: current medication

value: Pred 10mg Aza 100mg MMF 500mg BG Fosomax

tag: birth date

tag: ethnicity

tag: symptoms onset date

tag: diagnosis date

tag: ocp

tag: joint problems

value: TRUE

tag: family history

tag: aza treated

value: YES

tag: aza tolerant

tag: procedure date

tag: indictation for procedure:

tag: cdai

tag: harvey bradshaw

tag: esr

tag: crp

tag: hb

tag: wcc

tag: neutrophils

tag: albumin

tag: blood obtained

tag: ibd affected relatives

tag: nod 1007 fs:

tag: diagnosis rectal

tag: diagnosis anal perianal

tag: diagnosis vienna classifi

tag: last followup date

tag: followup oral

tag: followup ileal

tag: followup colonic

tag: followup rectal

tag: followup anal perianal

tag: casenote review date

tag: behavior at diagnosis

tag: behavior at followup

value: never

tag: smoking start date:

tag: smoking stop date:

value: Chronic active hepatitis

tag: treatment

value: uninflamed

tag: reference


title: descending colon biopsy from crohns disease subject (PRB11465)

tag: patient

tag: current medication

value: Asacol 1.2g TDS Prednisolone 5mg

tag: birth date

tag: ethnicity

value: CAUCASIAN

tag: symptoms onset date

tag: diagnosis date

tag: ocp

tag: joint problems

tag: family history

tag: aza treated

tag: aza tolerant

tag: procedure date

tag: indictation for procedure:

tag: cdai

tag: harvey bradshaw

tag: esr

tag: crp

tag: hb

tag: wcc

tag: neutrophils

tag: albumin

tag: blood obtained

tag: ibd affected relatives

tag: nod 1007 fs:

tag: further operations:

tag: stoma ileal

tag: diagnosis oral

tag: diagnosis ileal

tag: diagnosis colonic

tag: followup vienna classific

tag: diagnosis stricture fistu

tag: diagnosis details:

tag: disease group

value: REMISSION

tag: smoking status

value: ex

tag: smoking stop date

tag: smoking amount

tag: other illnesses

tag: disease

value: crohns disease

tag: anatomic location

value: descending colon

tag: treatment response

value: responder

tag: inflammation status


title: descending colon biopsy from crohns disease subject (PRB5293)

tag: patient

tag: current medication

tag: birth date

tag: ethnicity

tag: symptoms onset date

tag: diagnosis date

tag: ocp

value: NEVER

tag: joint problems

value: FALSE

tag: family history

tag: aza treated

value: NO

tag: aza tolerant

tag: procedure date

tag: indictation for procedure:

tag: cdai

tag: harvey bradshaw

tag: esr

tag: crp

tag: hb

tag: wcc

tag: neutrophils

tag: albumin

tag: blood obtained

tag: ibd affected relatives

tag: nod 1007 fs:

tag: further operations:

tag: diagnosis rectal

tag: diagnosis anal perianal

tag: diagnosis vienna classifi

tag: last followup date

tag: followup oral

tag: followup ileal

tag: followup colonic

tag: followup rectal

tag: followup anal perianal

tag: casenote review date

tag: behavior at diagnosis

tag: diagnosis details

value: Actively draining fistula at diagnosis

tag: behavior at followup

value: NEW

tag: smoking start date:

tag: treatment

value: SoC untreated

tag: reference

value: Stratagene Universal Human Reference RNA


title: descending colon biopsy from crohns disease subject (PRB12512)

tag: patient

tag: current medication

value: Azathioprine 150mg

tag: birth date

tag: ethnicity

tag: symptoms onset date

tag: diagnosis date

tag: ocp

value: unknown

tag: joint problems

tag: family history

value: TRUE

tag: aza treated

value: YES

tag: aza tolerant

tag: procedure date

tag: indictation for procedure:

tag: cdai

tag: harvey bradshaw

tag: esr

tag: crp

tag: hb

tag: wcc

tag: neutrophils

tag: albumin

tag: blood obtained

tag: ibd affected relatives

tag: nod 1007 fs:

tag: further operations:

tag: stoma ileal

tag: diagnosis oral

tag: diagnosis ileal

tag: diagnosis colonic

tag: followup vienna classific

tag: diagnosis stricture fistu

tag: diagnosis details:

tag: disease group

value: FAILURE OF TREATMENT

tag: smoking status

tag: smoking stop date

tag: smoking amount

tag: other illnesses

tag: disease

tag: anatomic location

value: SoC treated

tag: treatment response

value: nonresponder

tag: inflammation status

value: inflamed


title: descending colon biopsy from crohns disease subject (PRB12495)

tag: patient

tag: current medication

tag: birth date

tag: ethnicity

value: CAUCASIAN

tag: symptoms onset date

tag: diagnosis date

tag: ocp

tag: joint problems

tag: family history

tag: aza treated

tag: aza tolerant

tag: procedure date

tag: indictation for procedure:

tag: cdai

tag: harvey bradshaw

tag: esr

tag: crp

tag: hb

tag: wcc

tag: neutrophils

tag: albumin

tag: blood obtained

tag: ibd affected relatives

tag: nod 1007 fs:

tag: further operations:

tag: diagnosis rectal

tag: diagnosis anal perianal

tag: diagnosis vienna classifi

tag: last followup date

tag: followup oral

tag: followup ileal

tag: followup colonic

tag: followup rectal

tag: followup anal perianal

tag: casenote review date

tag: behavior at diagnosis

tag: behavior at followup

value: REMISSION

value: never

tag: smoking start date:

tag: smoking stop date:

value: crohns disease

value: descending colon

tag: treatment

value: uninflamed

tag: reference


title: descending colon biopsy from crohns disease subject (PRB5345)

tag: patient

tag: current medication

value: MST Oramorph Asacol Fosomax Diadepam B12 Folate

tag: birth date

tag: ethnicity

tag: symptoms onset date

tag: diagnosis date

tag: ocp

tag: joint problems

value: FALSE

tag: family history

tag: aza treated

value: NO

tag: aza tolerant

tag: procedure date

tag: indictation for procedure:

tag: cdai

tag: harvey bradshaw

tag: esr

tag: crp

tag: hb

tag: wcc

tag: neutrophils

tag: albumin

tag: blood obtained

tag: ibd affected relatives

tag: nod 1007 fs:

tag: further operations

value: 16/05/1995 R hemicolectomy and iliectomy

tag: stoma ileal

tag: diagnosis oral

tag: diagnosis ileal

tag: diagnosis colonic

tag: followup vienna classific

tag: diagnosis stricture fistu

tag: diagnosis details:

tag: disease group

tag: smoking status

value: current

tag: smoking start date

tag: smoking amount

tag: other illnesses

value: Osteoporosis

tag: disease

tag: anatomic location

tag: treatment response

tag: inflammation status


title: descending colon biopsy from crohns disease subject (PRB5332)

tag: patient

tag: current medication

value: Asacol 800mg TDS, Cocodamol

tag: birth date

tag: ethnicity

tag: symptoms onset date

tag: diagnosis date

tag: ocp

value: CURRENT

tag: joint problems

tag: family history

tag: aza treated

tag: aza tolerant

tag: procedure date

tag: indictation for procedure:

tag: cdai

tag: harvey bradshaw

tag: esr

tag: crp

tag: hb

tag: wcc

tag: neutrophils

tag: albumin

tag: blood obtained

tag: ibd affected relatives

tag: nod 1007 fs:

tag: further operations:

value: TRUE

tag: diagnosis rectal

tag: diagnosis anal perianal

tag: diagnosis vienna classifi

tag: last followup date

tag: followup oral

tag: followup ileal

tag: followup colonic

tag: followup rectal

tag: followup anal perianal

tag: casenote review date

tag: behavior at diagnosis

tag: behavior at followup

tag: smoking start date:

tag: smoking stop date:

tag: treatment

value: responder

tag: reference

value: Stratagene Universal Human Reference RNA


title: descending colon biopsy from crohns disease subject (PRB5328)

tag: patient

tag: current medication

value: Asacol 400mg TDS, Adcal D3, HRT.

tag: birth date

tag: ethnicity

value: CAUCASIAN

tag: symptoms onset date

tag: diagnosis date

tag: ocp

value: EX

tag: joint problems

tag: family history

tag: aza treated

tag: aza tolerant

tag: procedure date

tag: indictation for procedure:

tag: cdai

tag: harvey bradshaw

tag: esr

tag: crp

tag: hb

tag: wcc

tag: neutrophils

tag: albumin

tag: blood obtained

tag: ibd affected relatives

tag: nod 1007 fs:

tag: further operations:

tag: stoma ileal

tag: diagnosis oral

tag: diagnosis ileal

tag: diagnosis colonic

tag: followup vienna classific

tag: diagnosis stricture fistu

tag: diagnosis details:

tag: disease group

tag: smoking status

tag: smoking amount

value: unknown

tag: other illnesses

value: Reiters syndrome 14/05/1997

tag: disease

tag: anatomic location

value: SoC treated

tag: treatment response

tag: inflammation status


title: descending colon biopsy from crohns disease subject (PRB12508)

tag: patient

tag: current medication

value: Azathioprine 150mg. Salazopyrine

tag: birth date

tag: ethnicity

tag: symptoms onset date

tag: diagnosis date

tag: ocp

tag: joint problems

tag: family history

tag: aza treated

tag: aza tolerant

tag: procedure date

tag: indictation for procedure:

tag: cdai

tag: harvey bradshaw

tag: esr

tag: crp

tag: hb

tag: wcc

tag: neutrophils

tag: albumin

tag: blood obtained

tag: ibd affected relatives

tag: nod 1007 fs:

tag: diagnosis rectal

tag: diagnosis anal perianal

tag: diagnosis vienna classifi

tag: last followup date

tag: followup oral

tag: followup ileal

tag: followup colonic

tag: followup rectal

tag: followup anal perianal

tag: casenote review date

tag: behavior at diagnosis

tag: behavior at followup

value: REMISSION

value: ex

tag: smoking start date:

tag: smoking stop date

value: crohns disease

value: descending colon

tag: treatment

value: uninflamed

tag: reference


title: descending colon biopsy from crohns disease subject (PRB5327)

tag: patient

tag: current medication

value: Lamotragine, Ceppra,Ca Vit D, Fosomax, Thyroxine

tag: birth date

tag: ethnicity

tag: symptoms onset date

tag: diagnosis date

tag: ocp

value: NEVER

tag: joint problems

tag: family history

tag: aza treated

value: NO

tag: aza tolerant

value: FALSE

tag: procedure date

tag: indictation for procedure:

tag: cdai

tag: harvey bradshaw

tag: esr

tag: crp

tag: hb

tag: wcc

tag: neutrophils

tag: albumin

tag: blood obtained

tag: ibd affected relatives

tag: nod 1007 fs:

tag: further operations:

tag: stoma ileal

tag: diagnosis oral

tag: diagnosis ileal

tag: diagnosis colonic

tag: followup vienna classific

tag: diagnosis stricture fistu

tag: diagnosis details:

tag: disease group

tag: smoking status

value: never

tag: smoking stop date:

tag: smoking amount

tag: other illnesses

value: Epilepsy, L parietal bleed 06/2004, Hypothyrodism

tag: disease

tag: anatomic location

tag: treatment response

tag: inflammation status

value: inflamed


title: descending colon biopsy from crohns disease subject (PRB5331)

tag: patient

tag: current medication

value: Pentaza 1g BD

tag: birth date

tag: ethnicity

value: CAUCASIAN

tag: symptoms onset date

tag: diagnosis date

tag: ocp

tag: joint problems

tag: family history

tag: aza treated

tag: aza tolerant

tag: procedure date

tag: indictation for procedure:

tag: cdai

tag: harvey bradshaw

tag: esr

tag: crp

tag: hb

tag: wcc

tag: neutrophils

tag: albumin

tag: blood obtained

value: TRUE

tag: ibd affected relatives

tag: nod 1007 fs:

tag: further operations:

tag: diagnosis rectal

tag: diagnosis anal perianal

tag: diagnosis vienna classifi

tag: last followup date

tag: followup oral

tag: followup ileal

tag: followup colonic

tag: followup rectal

tag: followup anal perianal

tag: casenote review date

tag: behavior at diagnosis

tag: behavior at followup

tag: smoking start date:

tag: smoking stop date

tag: treatment

value: responder

tag: reference

value: Stratagene Universal Human Reference RNA