title: Cont-preT-AGA, rep10

description:
SAMPLE_14541
Placenta sample purchased from the Research Centre for Women’s and Infants’ Health (RCWIH) BioBank (Toronto, Canada), which utilizes a systematic sampling procedure in which four tissue biopsies (one sample/quadrant) are collected and pooled per placenta. At the time of sample collection and purchase, PE was defined as the onset of systolic pressure ≥ 140 mmHg and/or diastolic pressure ≥ 90 mmHg after the 20th week of gestation, accompanied by proteinuria (greater than 300 mg protein/day, or greater ≥ 2+ by dipstick). CH: chronic maternal hypertension; systolic pressure ≥ 140 mmHg and/or sustained diastolic ≥ 90 mmHg before the 20th week of gestation. Preterm: delivery prior to 34 weeks gestation. SGA: small-for-gestational-age infant; neonatal birth weight < 10th percentile for gestational age and sex. AGA: average-for-gestational age infant.

tag: diagnosis

value: non-PE

tag: tissue

value: Placenta

tag: maternal age

tag: maternal bmi

tag: maternal ethnicity

value: East Indian

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

value: C-Section

value: F


title: CY507 1

status: Public on May 10 2016

type: RNA

city: Stanford

first: Fiona

last: Strouts

state: CA

address: Campus Drive

country: USA

institute: Stanford

description: CY507 1

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

scan_protocol: Scan Power : 100 PMT Volts : 526 Pixel Size : 10 Laser on time : 193493 Laser Power : 3.11 Scan Date : 2012-11-06 Scan Temperature : 32.58 Scan Time : 14:55:59 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

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

molecule: total RNA

organism: Homo sapiens

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

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

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

tag: reference sample name

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

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

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

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

tag: test sample name

tag: time point (days)


title: CY507 -11

description: CY507 -11

scan_protocol: Scan Power : 100 PMT Volts : 559 Pixel Size : 10 Laser on time : 193456 Laser Power : 3.09 Scan Date : 2012-11-06 Scan Temperature : 32.22 Scan Time : 14:19:10 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

value: Human Universal Reference RNA (Stratagene)

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


title: Genomic DNA from diffuse astrocytoma DA2

type: genomic

city: London

first: Denise

last: Sheer

address: Blizard Institute, 4 Newark Street

department: Neuroscience & Trauma

country: United Kingdom

institute: Barts & The London School of Medicine & Dentistry

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

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

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

label: Cy5 and Cy3

molecule: genomic DNA

source_name: Paediatric diffuse astrocytoma

label_protocol: standard Illumina protocol

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

treatment_protocol: Fresh frozen tissue

tag: pathology

value: Diffuse astrocytoma

tag: age (yrs)

tag: gender

value: female

tag: tumour location

value: Cerebral cortex


title: CY507 -2

description: CY507 -2

scan_protocol: Scan Power : 100 PMT Volts : 562 Pixel Size : 10 Laser on time : 193480 Laser Power : 3.11 Scan Date : 2012-11-06 Scan Temperature : 32.49 Scan Time : 14:42:02 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

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


title: PHH_5D_MD_exp2

city: Maastricht

first: Linda

last: Rieswijk

address: Universiteitssingel 50

department: Toxicogenomics

country: Netherlands

institute: Maastricht University

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

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

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

label: Biotin

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

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

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

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

tag: cell type

value: primary human hepatocytes

tag: study type

value: Single Dose Toxicity

tag: assay type

value: ex vivo

tag: strain

tag: compound

value: aflatoxin B1

tag: dose

tag: dose unit

value: uM

tag: dose duration

tag: duration unit

value: days

tag: dose frequency

value: daily

tag: vehicle

value: DMSO

tag: route

value: medium


title: PHH_5D_MD_control_exp2

description: raw data file: C2_Herhaling_(HG-U133_Plus_2).CEL


title: PHH_5D_MD_exp3


title: PHH_LD_5D_control_exp2


title: PHH_LD_5D_control_exp1

description: raw data file: C1-Afb1_(HG-U133_Plus_2).CEL


title: CY506 5

description: CY506 5

scan_protocol: Scan Power : 100 PMT Volts : 521 Pixel Size : 10 Laser on time : 193405 Laser Power : 3.07 Scan Date : 2012-11-06 Scan Temperature : 31.45 Scan Time : 13:28:02 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

tag: reference sample name

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

tag: test sample name

tag: time point (days)


title: CY506 7

description: CY506 7

scan_protocol: Scan Power : 100 PMT Volts : 534 Pixel Size : 10 Laser on time : 193441 Laser Power : 3.07 Scan Date : 2012-11-06 Scan Temperature : 32.00 Scan Time : 14:03:41 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

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


title: PHH_5D_MD_exp1


title: Cont-preT-AGA, rep7

city: Toronto

first: Brian

last: Cox

state: Ontario

address: 1 King's College Circle

department: Physiology

country: Canada

institute: University of Toronto

description:
SAMPLE_13784
Placenta sample purchased from the Research Centre for Women’s and Infants’ Health (RCWIH) BioBank (Toronto, Canada), which utilizes a systematic sampling procedure in which four tissue biopsies (one sample/quadrant) are collected and pooled per placenta. At the time of sample collection and purchase, PE was defined as the onset of systolic pressure ≥ 140 mmHg and/or diastolic pressure ≥ 90 mmHg after the 20th week of gestation, accompanied by proteinuria (greater than 300 mg protein/day, or greater ≥ 2+ by dipstick). CH: chronic maternal hypertension; systolic pressure ≥ 140 mmHg and/or sustained diastolic ≥ 90 mmHg before the 20th week of gestation. Preterm: delivery prior to 34 weeks gestation. SGA: small-for-gestational-age infant; neonatal birth weight < 10th percentile for gestational age and sex. AGA: average-for-gestational age infant.

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

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

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

label: biotin

source_name: Human placenta from Cont-preT-AGA pregnancy

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

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

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

tag: diagnosis

value: non-PE

tag: tissue

value: Placenta

tag: maternal age

tag: maternal bmi

tag: maternal ethnicity

value: Asian

tag: maternal blood type

tag: previous nulliparity

value: Yes

tag: previous miscarriage

value: No

tag: previous hypertensive pregnancy

tag: mean uterine pi

tag: mean umbilical pi

tag: maximum systolic bp

tag: maximum diastolic bp

tag: mode proteinuria

tag: hellp diagnosis

tag: iugr diagnosis

tag: attempted vaginal delivery

tag: mode of delivery

value: Vaginal

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: CY506 3

description: CY506 3

scan_protocol: Scan Power : 100 PMT Volts : 520 Pixel Size : 10 Laser on time : 193387 Laser Power : 3.09 Scan Date : 2012-11-06 Scan Temperature : 31.12 Scan Time : 13:10:01 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

tag: reference sample name

value: Human Universal Reference RNA (Stratagene)

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

tag: test sample name

tag: time point (days)


title: CY506 1

description: CY506 1

scan_protocol: Scan Power : 100 PMT Volts : 501 Pixel Size : 10 Laser on time : 193374 Laser Power : 3.09 Scan Date : 2012-11-06 Scan Temperature : 30.84 Scan Time : 12:56:01 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0


title: PHH_5D_MD_control_exp1

tag: cell type

tag: study type

tag: assay type

tag: strain

tag: compound

tag: dose

tag: dose unit

tag: dose duration

tag: duration unit

tag: dose frequency

tag: vehicle

tag: route


title: CY507 7

description: CY507 7

scan_protocol: Scan Power : 100 PMT Volts : 560 Pixel Size : 10 Laser on time : 193548 Laser Power : 3.10 Scan Date : 2012-11-06 Scan Temperature : 32.77 Scan Time : 15:50:49 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

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


title: CY506 -11

description: CY506 -11

scan_protocol: Scan Power : 100 PMT Volts : 510 Pixel Size : 10 Laser on time : 193341 Laser Power : 3.06 Scan Date : 2012-11-06 Scan Temperature : 30.14 Scan Time : 12:23:56 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

data_processing:
Extraction Software : GenePix Pro
Extraction Software Version : 5.0.0.51
Datafile type : GenePix Results 3
Image Origin : 640, 4120


title: CY506 -2

description: CY506 -2

scan_protocol: Scan Power : 100 PMT Volts : 504 Pixel Size : 10 Laser on time : 193358 Laser Power : 3.07 Scan Date : 2012-11-06 Scan Temperature : 30.51 Scan Time : 12:40:23 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0


title: PE-Term-AGA, rep6

description:
SAMPLE_13700
Placenta sample purchased from the Research Centre for Women’s and Infants’ Health (RCWIH) BioBank (Toronto, Canada), which utilizes a systematic sampling procedure in which four tissue biopsies (one sample/quadrant) are collected and pooled per placenta. At the time of sample collection and purchase, PE was defined as the onset of systolic pressure ≥ 140 mmHg and/or diastolic pressure ≥ 90 mmHg after the 20th week of gestation, accompanied by proteinuria (greater than 300 mg protein/day, or greater ≥ 2+ by dipstick). CH: chronic maternal hypertension; systolic pressure ≥ 140 mmHg and/or sustained diastolic ≥ 90 mmHg before the 20th week of gestation. Preterm: delivery prior to 34 weeks gestation. SGA: small-for-gestational-age infant; neonatal birth weight < 10th percentile for gestational age and sex. AGA: average-for-gestational age infant.

source_name: Human placenta from PE-Term-AGA pregnancy

tag: diagnosis

value: PE

tag: tissue

tag: maternal age

tag: maternal bmi

tag: maternal ethnicity

value: Caucasian

tag: maternal blood type

value: O

tag: previous nulliparity

tag: previous miscarriage

tag: previous hypertensive pregnancy

tag: mean uterine pi

tag: mean umbilical pi

tag: maximum systolic bp

tag: maximum diastolic bp

tag: mode proteinuria

tag: hellp diagnosis

tag: iugr diagnosis

tag: attempted vaginal delivery

tag: mode of delivery

value: 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


title: PE-Term-AGA, rep5

description:
SAMPLE_13514
Placenta sample purchased from the Research Centre for Women’s and Infants’ Health (RCWIH) BioBank (Toronto, Canada), which utilizes a systematic sampling procedure in which four tissue biopsies (one sample/quadrant) are collected and pooled per placenta. At the time of sample collection and purchase, PE was defined as the onset of systolic pressure ≥ 140 mmHg and/or diastolic pressure ≥ 90 mmHg after the 20th week of gestation, accompanied by proteinuria (greater than 300 mg protein/day, or greater ≥ 2+ by dipstick). CH: chronic maternal hypertension; systolic pressure ≥ 140 mmHg and/or sustained diastolic ≥ 90 mmHg before the 20th week of gestation. Preterm: delivery prior to 34 weeks gestation. SGA: small-for-gestational-age infant; neonatal birth weight < 10th percentile for gestational age and sex. AGA: average-for-gestational age infant.

tag: diagnosis

tag: tissue

tag: maternal age

tag: maternal bmi

tag: maternal ethnicity

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: chorioamnionitis diagnosis


title: CY505 D5

description: CY505 D5

scan_protocol: Scan Power : 100 PMT Volts : 498 Pixel Size : 10 Laser on time : 188454 Laser Power : 3.11 Scan Date : 2012-09-19 Scan Temperature : 33.59 Scan Time : 16:18:32 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

data_processing:
Extraction Software : GenePix Pro
Extraction Software Version : 5.0.0.51
Datafile type : GenePix Results 3
Image Origin : 640, 4800

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

tag: reference sample name

tag: test sample name

tag: time point (days)


title: CY505 D-2

description: CY505 D-2

scan_protocol: Scan Power : 100 PMT Volts : 496 Pixel Size : 10 Laser on time : 188393 Laser Power : 3.12 Scan Date : 2012-09-19 Scan Temperature : 33.29 Scan Time : 15:18:04 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0


title: CY505 D3

description: CY505 D3

scan_protocol: Scan Power : 100 PMT Volts : 498 Pixel Size : 10 Laser on time : 188437 Laser Power : 3.11 Scan Date : 2012-09-19 Scan Temperature : 33.50 Scan Time : 16:01:24 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0


title: CY505 D7

description: CY505 D7

scan_protocol: Scan Power : 100 PMT Volts : 499 Pixel Size : 10 Laser on time : 188471 Laser Power : 3.09 Scan Date : 2012-09-19 Scan Temperature : 33.65 Scan Time : 16:35:36 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0


title: Cont-Term-CH, rep4

description:
SAMPLE_13746
Placenta sample purchased from the Research Centre for Women’s and Infants’ Health (RCWIH) BioBank (Toronto, Canada), which utilizes a systematic sampling procedure in which four tissue biopsies (one sample/quadrant) are collected and pooled per placenta. At the time of sample collection and purchase, PE was defined as the onset of systolic pressure ≥ 140 mmHg and/or diastolic pressure ≥ 90 mmHg after the 20th week of gestation, accompanied by proteinuria (greater than 300 mg protein/day, or greater ≥ 2+ by dipstick). CH: chronic maternal hypertension; systolic pressure ≥ 140 mmHg and/or sustained diastolic ≥ 90 mmHg before the 20th week of gestation. Preterm: delivery prior to 34 weeks gestation. SGA: small-for-gestational-age infant; neonatal birth weight < 10th percentile for gestational age and sex. AGA: average-for-gestational age infant.

source_name: Human placenta from Cont-Term-CH pregnancy

value: AB

tag: maximum systolic bp

tag: maximum diastolic bp

tag: mode proteinuria

tag: hellp diagnosis

tag: iugr diagnosis

tag: attempted vaginal delivery

tag: mode of delivery

tag: ga (week)

tag: ga (day)

tag: infant gender

value: F

tag: newborn weight z-score

tag: apgar score (1 min)

tag: apgar score (5 min)

tag: nicu transfer

tag: placental weight z-score


title: CY505 D1

description: CY505 D1

scan_protocol: Scan Power : 100 PMT Volts : 496 Pixel Size : 10 Laser on time : 188418 Laser Power : 3.11 Scan Date : 2012-09-19 Scan Temperature : 33.41 Scan Time : 15:42:08 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

tag: reference sample name

tag: test sample name


title: CY505 D-11

description: CY505 D-11

scan_protocol: Scan Power : 100 PMT Volts : 506 Pixel Size : 10 Laser on time : 188366 Laser Power : 3.11 Scan Date : 2012-09-19 Scan Temperature : 33.13 Scan Time : 14:50:22 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

tag: time point (days)


title: PE-PreT-AGA, rep5

description:
SAMPLE_13025
Placenta sample purchased from the Research Centre for Women’s and Infants’ Health (RCWIH) BioBank (Toronto, Canada), which utilizes a systematic sampling procedure in which four tissue biopsies (one sample/quadrant) are collected and pooled per placenta. At the time of sample collection and purchase, PE was defined as the onset of systolic pressure ≥ 140 mmHg and/or diastolic pressure ≥ 90 mmHg after the 20th week of gestation, accompanied by proteinuria (greater than 300 mg protein/day, or greater ≥ 2+ by dipstick). CH: chronic maternal hypertension; systolic pressure ≥ 140 mmHg and/or sustained diastolic ≥ 90 mmHg before the 20th week of gestation. Preterm: delivery prior to 34 weeks gestation. SGA: small-for-gestational-age infant; neonatal birth weight < 10th percentile for gestational age and sex. AGA: average-for-gestational age infant.

source_name: Human placenta from PE-PreT-AGA pregnancy

tag: diagnosis

tag: tissue

tag: maternal age

tag: maternal bmi

tag: maternal ethnicity

value: Black

tag: maternal blood type

tag: previous nulliparity

tag: previous miscarriage

tag: previous hypertensive pregnancy

tag: mean uterine pi

tag: mean umbilical pi

tag: maximum systolic bp

tag: maximum diastolic bp

tag: umbilical cord diameter

tag: chorioamnionitis diagnosis


title: Cont-preT-AGA, rep4

description:
SAMPLE_12218
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: mode proteinuria

tag: hellp diagnosis

tag: iugr diagnosis

tag: attempted vaginal delivery

tag: mode of delivery

tag: ga (week)

tag: ga (day)

tag: infant gender

tag: newborn weight z-score

tag: apgar score (1 min)

tag: apgar score (5 min)

tag: nicu transfer

tag: placental weight z-score


title: Cont-preT-AGA, rep5

description:
SAMPLE_12621
Placenta sample purchased from the Research Centre for Women’s and Infants’ Health (RCWIH) BioBank (Toronto, Canada), which utilizes a systematic sampling procedure in which four tissue biopsies (one sample/quadrant) are collected and pooled per placenta. At the time of sample collection and purchase, PE was defined as the onset of systolic pressure ≥ 140 mmHg and/or diastolic pressure ≥ 90 mmHg after the 20th week of gestation, accompanied by proteinuria (greater than 300 mg protein/day, or greater ≥ 2+ by dipstick). CH: chronic maternal hypertension; systolic pressure ≥ 140 mmHg and/or sustained diastolic ≥ 90 mmHg before the 20th week of gestation. Preterm: delivery prior to 34 weeks gestation. SGA: small-for-gestational-age infant; neonatal birth weight < 10th percentile for gestational age and sex. AGA: average-for-gestational age infant.

tag: diagnosis

tag: tissue

tag: maternal age

tag: maternal bmi

tag: maternal ethnicity

tag: maternal blood type

tag: previous nulliparity

tag: previous miscarriage

tag: previous hypertensive pregnancy

tag: mean uterine pi

tag: mean umbilical pi

tag: maximum systolic bp


title: CY504 D7

description: CY504 D7

scan_protocol: Scan Power : 100 PMT Volts : 503 Pixel Size : 10 Laser on time : 188349 Laser Power : 3.11 Scan Date : 2012-09-19 Scan Temperature : 33.10 Scan Time : 14:33:15 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

tag: reference sample name

tag: test sample name

tag: time point (days)


title: PE-PreT-AGA, rep4

description:
SAMPLE_12172
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: maximum diastolic bp

tag: mode proteinuria

tag: hellp diagnosis

tag: iugr diagnosis

tag: attempted vaginal delivery

tag: mode of delivery

tag: ga (week)

tag: ga (day)

tag: infant gender

tag: newborn weight z-score

tag: apgar score (1 min)

tag: apgar score (5 min)

tag: nicu transfer

tag: umbilical cord diameter

tag: chorioamnionitis diagnosis


title: Cont-preT-AGA, rep3

description:
SAMPLE_11893
Placenta sample purchased from the Research Centre for Women’s and Infants’ Health (RCWIH) BioBank (Toronto, Canada), which utilizes a systematic sampling procedure in which four tissue biopsies (one sample/quadrant) are collected and pooled per placenta. At the time of sample collection and purchase, PE was defined as the onset of systolic pressure ≥ 140 mmHg and/or diastolic pressure ≥ 90 mmHg after the 20th week of gestation, accompanied by proteinuria (greater than 300 mg protein/day, or greater ≥ 2+ by dipstick). CH: chronic maternal hypertension; systolic pressure ≥ 140 mmHg and/or sustained diastolic ≥ 90 mmHg before the 20th week of gestation. Preterm: delivery prior to 34 weeks gestation. SGA: small-for-gestational-age infant; neonatal birth weight < 10th percentile for gestational age and sex. AGA: average-for-gestational age infant.

tag: diagnosis

tag: tissue

tag: maternal age

tag: maternal bmi

tag: maternal ethnicity

tag: maternal blood type

value: B

tag: previous nulliparity

tag: previous miscarriage

tag: previous hypertensive pregnancy

tag: mean uterine pi

tag: mean umbilical pi

tag: maximum systolic bp

tag: placental weight z-score


title: CY504 D3

description: CY504 D3

scan_protocol: Scan Power : 100 PMT Volts : 487 Pixel Size : 10 Laser on time : 188303 Laser Power : 3.10 Scan Date : 2012-09-19 Scan Temperature : 33.01 Scan Time : 13:46:42 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

tag: reference sample name

tag: test sample name

tag: time point (days)


title: CY504 D1

description: CY504 D1

scan_protocol: Scan Power : 100 PMT Volts : 485 Pixel Size : 10 Laser on time : 188274 Laser Power : 3.10 Scan Date : 2012-09-19 Scan Temperature : 32.77 Scan Time : 13:18:20 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0


title: CY504 D5

description: CY504 D5

scan_protocol: Scan Power : 100 PMT Volts : 499 Pixel Size : 10 Laser on time : 188323 Laser Power : 3.11 Scan Date : 2012-09-19 Scan Temperature : 33.01 Scan Time : 14:07:53 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0


title: Cont-preT-AGA, rep2

description:
SAMPLE_11836
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

value: Other

tag: maximum diastolic bp

tag: mode proteinuria

tag: hellp diagnosis

tag: iugr diagnosis

tag: attempted vaginal delivery

tag: mode of delivery

tag: ga (week)

tag: ga (day)

tag: infant gender

tag: newborn weight z-score

tag: apgar score (1 min)

tag: apgar score (5 min)

tag: nicu transfer

tag: umbilical cord diameter

tag: chorioamnionitis diagnosis


title: PHH_WO_LD_exp3 [miRNA]

hyb_protocol: The hybridization was performed following standard protocols, after which the microarray slides were washed and scanned using a DNA microarray scanner (Agilent Technologies).

scan_protocol: Samples were labeled according to the manufacturers protocol.

data_processing: The scanned images were converted into TXT files using the Feature Extraction Software v10.7.3.1 from Agilent Technologies, which were imported in R 2.15.3 (http://www.r-project.org) for quality control with an in-house developed pipeline. Filtering and normalization was performed using AgiMicroRna (32). Total gene signals were log2-transformed and quantile-normalized. The selection criteria for determining differentially expressed microRNAs (DE-miRs) were identical to those for DEGs.

label_protocol: MicroRNA expression profiling was performed using Agilent Sureprint G3 Unrestricted Human miRNA V19 8 × 60 K microarrays.

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

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

tag: cell type

value: primary human hepatocytes

tag: main source

value: liver

tag: study type

value: Wash out effect

tag: assay type

value: ex vivo

tag: strain

tag: agent

value: aflatoxin B1

tag: dose

tag: dose unit

value: uM

tag: dose duration

tag: duration unit

value: days

tag: dose frequency

value: daily

tag: vehicle

value: DMSO

tag: route

value: medium


title: PHH_WO_LD_exp2 [miRNA]

description: Agilent Sureprint G3 Unrestricted Human miRNA V19 8 × 60 K microarrays


title: PHH_WO_LD_control_exp2 [miRNA]


title: PHH_WO_LD_exp1 [miRNA]


title: PHH_WO_LD_control_exp1 [miRNA]


title: PHH_5D_MD_exp2

hyb_protocol: MicroRNA expression profiling was performed using Agilent Sureprint G3 Unrestricted Human miRNA V19 8 × 60 K microarrays. The hybridization was performed following standard protocols, after which the microarray slides were washed and scanned using a DNA microarray scanner (Agilent Technologies).

scan_protocol: DNA microarray scanner

label_protocol: standard Agilent labeling kit

value: Single Dose Toxicity

tag: compound


title: PHH_5D_MD_exp3


title: PHH_5D_MD_exp1


title: PHH_WO_LD_control_exp3 [miRNA]


title: PHH_5D_MD_control_exp3

description: US10063773_254606410402_S01_miRNA_107_Sep09_2_1.txt


title: PE-Term-AGA, rep4

description:
SAMPLE_11653
Placenta sample purchased from the Research Centre for Women’s and Infants’ Health (RCWIH) BioBank (Toronto, Canada), which utilizes a systematic sampling procedure in which four tissue biopsies (one sample/quadrant) are collected and pooled per placenta. At the time of sample collection and purchase, PE was defined as the onset of systolic pressure ≥ 140 mmHg and/or diastolic pressure ≥ 90 mmHg after the 20th week of gestation, accompanied by proteinuria (greater than 300 mg protein/day, or greater ≥ 2+ by dipstick). CH: chronic maternal hypertension; systolic pressure ≥ 140 mmHg and/or sustained diastolic ≥ 90 mmHg before the 20th week of gestation. Preterm: delivery prior to 34 weeks gestation. SGA: small-for-gestational-age infant; neonatal birth weight < 10th percentile for gestational age and sex. AGA: average-for-gestational age infant.

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

tag: diagnosis

value: PE

tag: tissue

value: Placenta

tag: maternal age

tag: maternal bmi

tag: maternal ethnicity

tag: maternal blood type

value: A

tag: previous nulliparity

value: No

tag: previous miscarriage

tag: previous hypertensive pregnancy

value: Yes

tag: mean uterine pi

tag: mean umbilical pi

tag: maximum systolic bp

tag: maximum diastolic bp

tag: mode proteinuria

tag: hellp diagnosis

tag: iugr diagnosis

tag: attempted vaginal delivery

tag: mode of delivery

value: Vaginal

tag: ga (week)

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


title: PHH_5D_MD_control_exp2

description: US10063773_254606410401_S01_miRNA_107_Sep09_2_3.txt

tag: cell type

value: primary human hepatocytes

tag: study type

tag: assay type

tag: strain

tag: compound

tag: dose

tag: dose unit

tag: dose duration

tag: duration unit

tag: dose frequency

tag: vehicle

tag: route


title: PHH_5D_MD_control_exp1

description: US10063773_254606410401_S01_miRNA_107_Sep09_1_1.txt


title: CY504 D-2

description: CY504 D-2

scan_protocol: Scan Power : 100 PMT Volts : 487 Pixel Size : 10 Laser on time : 188259 Laser Power : 3.10 Scan Date : 2012-09-19 Scan Temperature : 32.64 Scan Time : 13:03:06 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

tag: reference sample name

value: Human Universal Reference RNA (Stratagene)

tag: test sample name

tag: time point (days)


title: CY503 D5

description: CY503 D5

scan_protocol: Scan Power : 100 PMT Volts : 500 Pixel Size : 10 Laser on time : 188180 Laser Power : 3.07 Scan Date : 2012-09-19 Scan Temperature : 32.00 Scan Time : 11:40:52 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0


title: PHH_5D_LD_exp2


title: PE-PreT-AGA, rep2

description:
SAMPLE_11221
Placenta sample purchased from the Research Centre for Women’s and Infants’ Health (RCWIH) BioBank (Toronto, Canada), which utilizes a systematic sampling procedure in which four tissue biopsies (one sample/quadrant) are collected and pooled per placenta. At the time of sample collection and purchase, PE was defined as the onset of systolic pressure ≥ 140 mmHg and/or diastolic pressure ≥ 90 mmHg after the 20th week of gestation, accompanied by proteinuria (greater than 300 mg protein/day, or greater ≥ 2+ by dipstick). CH: chronic maternal hypertension; systolic pressure ≥ 140 mmHg and/or sustained diastolic ≥ 90 mmHg before the 20th week of gestation. Preterm: delivery prior to 34 weeks gestation. SGA: small-for-gestational-age infant; neonatal birth weight < 10th percentile for gestational age and sex. AGA: average-for-gestational age infant.

tag: diagnosis

tag: tissue

tag: maternal age

tag: maternal bmi

tag: maternal ethnicity

value: Caucasian

tag: maternal blood type

value: O

tag: 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: C-Section

tag: ga (week)

tag: ga (day)

tag: infant gender

value: F

tag: newborn weight z-score

tag: apgar score (1 min)

tag: apgar score (5 min)

tag: nicu transfer

tag: umbilical cord diameter

tag: chorioamnionitis diagnosis


title: PHH_5D_LD_exp1

tag: cell type

tag: study type

tag: assay type

value: ex vivo

tag: strain

tag: compound

value: aflatoxin B1

tag: dose

tag: dose unit

value: uM

tag: dose duration

tag: duration unit

value: days

tag: dose frequency

tag: vehicle

tag: route


title: PHH_5D_LD_control_exp3

value: Single Dose Toxicity

value: DMSO

value: daily

value: medium


title: CY503 D7

description: CY503 D7

scan_protocol: Scan Power : 100 PMT Volts : 507 Pixel Size : 10 Laser on time : 188224 Laser Power : 3.10 Scan Date : 2012-09-19 Scan Temperature : 32.40 Scan Time : 12:24:13 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

tag: reference sample name

tag: test sample name

tag: time point (days)


title: CY504 D-11

description: CY504 D-11

scan_protocol: Scan Power : 100 PMT Volts : 490 Pixel Size : 10 Laser on time : 188245 Laser Power : 3.11 Scan Date : 2012-09-19 Scan Temperature : 32.49 Scan Time : 12:47:46 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0


title: PHH_5D_LD_exp3


title: CY503 D1

description: CY503 D1

scan_protocol: Scan Power : 100 PMT Volts : 492 Pixel Size : 10 Laser on time : 188148 Laser Power : 3.07 Scan Date : 2012-09-19 Scan Temperature : 31.39 Scan Time : 11:08:54 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0


title: CY503 D-11

description: CY503 D-11

scan_protocol: Scan Power : 100 PMT Volts : 489 Pixel Size : 10 Laser on time : 188110 Laser Power : 3.06 Scan Date : 2012-09-19 Scan Temperature : 30.63 Scan Time : 10:30:05 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0


title: CY503 D3

description: CY503 D3

scan_protocol: Scan Power : 100 PMT Volts : 501 Pixel Size : 10 Laser on time : 188165 Laser Power : 3.06 Scan Date : 2012-09-19 Scan Temperature : 31.73 Scan Time : 11:24:51 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0


title: PHH_5D_LD_control_exp2


title: CY503 D-2

description: CY503 D-2

scan_protocol: Scan Power : 100 PMT Volts : 499 Pixel Size : 10 Laser on time : 188132 Laser Power : 3.09 Scan Date : 2012-09-19 Scan Temperature : 31.06 Scan Time : 10:52:18 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0


title: PHH_5D_LD_exp1

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


title: PHH_5D_LD_control_exp1


title: B. breve UCC2003-atsR2 v. B. breve UCC2003

city: Cork

first: Muireann

last: Egan

address: Western Road

country: Ireland

institute: University College Cork

description: Gene expression array

hyb_protocol: Labelled cDNA was hybridized using the Agilent Gene Expression hybridization kit (part number 5188-5242) as described in the Agilent Two-Color Microarray-Based Gene Expression Analysis v4.0 manual (G4140-90050).

scan_protocol: Following hybridization, all microarrays were washed in accordance with Agilent’s standard procedures and scanned using an Agilent DNA microarray scanner (model G2565A).

data_processing: Generated scans were converted to data files with Agilent's Feature Extraction software (Version 9.5).

organism: Bifidobacterium breve UCC2003

source_name: B. breve UCC2003-atsR2 grown in mMRS supplemented with 0.05 % cysteine and 0.5 % ribose

label_protocol: Labelling was performed as described previously (van Hijum, S. A. F. T., J. A. De, R. J. Baerends, H. A. Karsens, N. E. Kramer, R. Larsen, C. D. den Hengst, C. J. Albers, J. Kok & O. P. Kuipers, (2005) A generally applicable validation scheme for the assessment of factors involved in reproducibility and quality of DNA-microarray data. BMC.Genomics 6: 77).

growth_protocol: Bifidobacterium breve UCC2003 or Bifidobacterium breve UCC2003-atsR2 was grown in modified de Man, Rogosa and Sharpe (MRS) medium (De Man, J. C., A. Rogosa & M. E. Sharpe, (1960) A medium for the cultivation of lactobacilli. J. Appl. Bacteriol. 23: 130-135), ,supplemented with 0.05% (w/v) L-cysteine-HCl (Sigma-Aldrich, Steinhein, Germany) and containing 0.5% ribose or 0.5 % N-acetylglucosamine-6-sulfate. The strains were grown under anaerobic conditions in a Modular Atmosphere Controlled System (Davidson & Hardy Ltd., Dublin, Ireland) to an optical density OD600 of 0.5

extract_protocol: Method for cell disruption was performed as described previously (van Hijum, S. A. F. T., J. A. De, R. J. Baerends, H. A. Karsens, N. E. Kramer, R. Larsen, C. D. den Hengst, C. J. Albers, J. Kok & O. P. Kuipers, (2005) A generally applicable validation scheme for the assessment of factors involved in reproducibility and quality of DNA-microarray data. BMC.Genomics 6: 77).RNA isolation, RNA quality control and complementary DNA synthesis was performed as described previously (van Hijum, S. A. F. T., J. A. De, R. J. Baerends, H. A. Karsens, N. E. Kramer, R. Larsen, C. D. den Hengst, C. J. Albers, J. Kok & O. P. Kuipers, (2005) A generally applicable validation scheme for the assessment of factors involved in reproducibility and quality of DNA-microarray data. BMC.Genomics 6: 77).

tag: genotype

value: atsR2 mutant

source_name: B. breve UCC2003 grown in mMRS supplemented with 0.05 % cysteine and 0.5 % ribose

value: wild type


title: B. breve UCC2003 grown on N-acetylglucosamine-6-sulfate v. B. breve UCC2003 grown on ribose

description: Gene expression array

source_name: B. breve UCC2003 grown in mMRS supplemented with 0.05% cysteine and 0.5% N-acetylglucosamine-6-sulfate

source_name: B. breve UCC2003 grown in mMRS supplemented with 0.05% cysteine and 0.5% ribose


title: Control S. coelicolor WT 42h replicate3

city: Beijing

first: Xiao

last: Li

address: NO.1 Beichen West Road, Chaoyang District

country: China

institute: Institute of Microbiology, Chinese Academy of Sciences

description:
WT 42h-3
Raw data file: US10313827_256469310001_S01_GE2_1105_Oct12_2_2.txt
Biological replicate 3 of 3 of WT at 42h

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

scan_protocol: Scanned on an Agilent G2565AA scanner. Images were quantified using Agilent Feature Extraction Software (version A.7.5).

data_processing: Agilent Feature Extraction Software (version A.7.5) was used for background subtraction and LOWESS normalization.

organism: Streptomyces coelicolor

source_name: S. coelicolor M145, 42h

label_protocol: Labelled with Cy3 and Cy5 during cDNA synthesis from total RNA using Superscript II Kit (Invitrogen) as manufacturers instructions. Samples purified using QIAGEN PCR purification kit before hybridization.

growth_protocol: Strepotmyces coelicolor strains, including WT, scbRDM and ScbR2DM, were cultured in liquid SMM medium at 28°C 250rpm for 30h and 42h

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

treatment_protocol: Cells were collected by filtration and frozen in liquid nitrogen for storage

tag: genotype/variation

value: WT

tag: time

tag: growth phase

value: transitional phase


title: scbRDM mutant 30h replicate1

description:
scbRDM-1
Raw data file: US10313827_256469310001_S01_GE2_1105_Oct12_1_1.txt
Biological replicate 1 of 3 of scbRDM at 30h

source_name: scbRDM, 30h

value: scbRDM mutant

value: exponential phase


title: Control S. coelicolor WT 42h replicate1

description:
WT 42h-1
Raw data file: US10313827_256469310001_S01_GE2_1105_Oct12_1_4.txt
Biological replicate 1 of 3 of WT at 42h


title: Control S. coelicolor WT 42h replicate2

description:
WT 42h-2
Raw data file: US10313827_256469310001_S01_GE2_1105_Oct12_2_1.txt
Biological replicate 2 of 3 of WT at 42h


title: scbR2DM mutant 42h replicate2

description:
ScbR2DM-2
Raw data file: US10313827_256469310001_S01_GE2_1105_Oct12_2_1.txt
Biological replicate 2 of 3 of scbR2DM at 42h

source_name: scbR2DM, 42h

value: scbR2DM mutant


title: AH375, biological rep2

city: Montréal

first: Xavier

last: Deschênes-Simard

state: Québec

address: 3655 Sir William Osler

department: Medicine

institute: McGill University

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C with rotation (60 rpm) on GeneChip® Mouse Gene 2.0 ST Array. The DNA chips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: The DNA chips were scanned using the GeneChip® Scanner 3000 7G/4 Color Early Access.

data_processing: The data were analyzed with FlexArray 1.6.3 using Affymetrix default analysis settings. Raw data were normalized with a Robust Multi-array Average (RMA) algorithm.

organism: Mus musculus

source_name: AH375 cell line, pancreatic ductal cells from PDAC, 52-week-old Pdx1-Cre;LSL-KRasG12D mouse

label_protocol: Biotinylated cRNA were prepared according to the protocol from the Ambion® WT Expression kit for Affymettrix® GeneChip®Whole Transcrpit (WT) Expression Arrays.

growth_protocol: Cells were propagated on surfaces coated with laminin (#354239, BD Biosciences) in pancreatic medium.

extract_protocol: TRIzol extraction of total RNA was performed according to the manufacturer's instructions. The mRNA solution was further purified using the RNeasy MinElute Cleanup Kit (#74204, Qiagen).

tag: age (weeks)

tag: tissue

value: Pancreas

tag: lesion

value: PDAC

tag: cell line


title: Control S. coelicolor WT 30h replicate3

description:
WT 30h-3
Raw data file: US10313827_256469310001_S01_GE2_1105_Oct12_1_3.txt
Biological replicate 3 of 3 of WT at 30h

source_name: S. coelicolor M145, 30h

tag: strain


title: Cont-Term-CH, rep2

description:
SAMPLE_10119
Placenta sample purchased from the Research Centre for Women’s and Infants’ Health (RCWIH) BioBank (Toronto, Canada), which utilizes a systematic sampling procedure in which four tissue biopsies (one sample/quadrant) are collected and pooled per placenta. At the time of sample collection and purchase, PE was defined as the onset of systolic pressure ≥ 140 mmHg and/or diastolic pressure ≥ 90 mmHg after the 20th week of gestation, accompanied by proteinuria (greater than 300 mg protein/day, or greater ≥ 2+ by dipstick). CH: chronic maternal hypertension; systolic pressure ≥ 140 mmHg and/or sustained diastolic ≥ 90 mmHg before the 20th week of gestation. Preterm: delivery prior to 34 weeks gestation. SGA: small-for-gestational-age infant; neonatal birth weight < 10th percentile for gestational age and sex. AGA: average-for-gestational age infant.

tag: diagnosis

value: non-PE

value: Placenta

tag: maternal age

tag: maternal bmi

tag: maternal ethnicity

value: Asian

tag: maternal blood type

value: O

tag: previous nulliparity

value: Yes

tag: previous miscarriage

tag: previous hypertensive pregnancy

tag: mean uterine pi

tag: mean umbilical pi

tag: maximum systolic bp

tag: maximum diastolic bp

tag: mode proteinuria

tag: hellp diagnosis

value: No

tag: iugr diagnosis

tag: attempted vaginal delivery

tag: mode of delivery

value: C-Section

tag: ga (week)

tag: ga (day)

tag: infant gender

value: F

tag: newborn weight z-score

tag: apgar score (1 min)

tag: apgar score (5 min)

tag: nicu transfer

tag: placental weight z-score

tag: umbilical cord diameter

tag: chorioamnionitis diagnosis


title: B. breve UCC2003 v. B. breve UCC2003-atsR2

description: Gene expression array

tag: genotype

value: atsR2 mutant


title: Control S. coelicolor WT 30h replicate1

description:
WT 30h-1
Raw data file: US10313827_256469310001_S01_GE2_1105_Oct12_1_1.txt
Biological replicate 1 of 3 of WT at 30h

tag: strain

tag: genotype/variation

tag: time

tag: growth phase


title: scbR2DM mutant 42h replicate3

description:
ScbR2DM-3
Raw data file: US10313827_256469310001_S01_GE2_1105_Oct12_2_2.txt
Biological replicate 3 of 3 of scbR2DM at 42h


title: Test, red light-exposed sample, rep b

status: Public on May 09 2016

city: Paris

first: Angela

last: Falciatore

address: 15 rue de l'ecole de Medicine

department: UMR 7238, LCQB

country: France

institute: CNRS

description: B - Biological replicate 2 of 2, dye swap of A

hyb_protocol: For each hybridization, 300 ng of D0 cRNA was mixed with 300 ng of cRNA from the corresponding light-treated sample (red, far-red lights or dark). Two biologically independent experiments were performed for each condition, using dye switch. The cRNA mixture was fragmented and hybridized on 8x60K P. tricornutum whole-genome 60-mer oligonucleotide microarrays (Agilent Technologies) in an Agilent Hybridization rotary oven (G2545A, 10 rpm, 65°C, 17.5 h). Hybridization was performed according to manufacturer indications, with the Gene Expression Hybridization Kit (Agilent, 5188-5242). The slides were washed with buffer 1 and pre-warmed buffer 2 from Gene Expression Wash Buffer kit (Agilent, 5188-5327), according to the Agilent protocol.

scan_protocol: The microarray sides were scanned twice at 2 µm resolution on an Agilent laser scanner (G2505 CA). The resulting images were processed using Agilent Feature Extraction software v11.5.

data_processing: Microarray normalization was performed by global lowess using Goulphar (Lemoine et al, 2006). For each gene, the Cy5/Cy3 ratios corresponding to the different probes were averaged.

organism: Phaeodactylum tricornutum

source_name: cell culture, control dark, 12 h

label_protocol: 200 ng of total RNA was reverse transcribed, amplified and labelled with Cy3-CTP or Cy5-CTP using the Low Input Quick Amp Labelling Kit, Two-Color (Agilent, 5190-2306).

growth_protocol: The wild type CCMP2561 strain of Phaeodactylum tricornutum Bohlin was routinely grown in f/2 medium (Guillard, 1975) at 18°C under white fluorescent lights (Philips TL-D De Luxe Pro 950) in 12h light, 12h dark cycles (12L/12D) under 60 µE (µmol m-2 s-1) of photons. Cultures were kept in exponential growth phase diluting them every three days with fresh medium and their axenicity assessed through contamination tests. Duplicate cultures of each treatment were grown in 1000 ml Erlenmeyers, shaked at 90 rpm to prevent settling of cells.

extract_protocol: 100 ml of culture (108 total cells) were filtered (grade 589/2, Whatman, 28414108), washed with PBS and flash frozen in liquid nitrogen. Total RNA was extracted by adding TriPure isolation Reagent (Roche, 11667165001) to the frozen filters and following the manufacturer’s instructions, with a further purification by ammonium acetate precipitation as described in Huysman et al., 2013. The recovered RNA was processed with the RNA cleanup protocol of the RNeasy Mini Kit (Qiagen, 74106) performing the in-column DNAse treatment. The eluted RNA was then quantified using a spectrophotometer and its integrity checked on 2% agar gel.

treatment_protocol: Experiment started at a cellular concentration of 1*106 cells/ml. After 12 hours of dark, the reference dark 0 point (D0) was taken. Then, cells were exposed for 30 minutes to 5 µE (µmol photons m-2 s-1) of red (660 nm) or far-red (750 nm) lights, or kept in dark for the same time, and sampled at the end of the treatments. The different light wavelengths were provided from LED sources (Heliospectra and M2M engineering, for red and far-red respectively).

source_name: cell culture, red (660 nm), 0.5 h


title: B. breve UCC2003 grown on ribose v. B.breve UCC2003 grown on N-acetylglucosamine-6-sulfate

description: Gene expression array

value: wild type


title: Control S. coelicolor WT 30h replicate2

description:
WT 30h-2
Raw data file: US10313827_256469310001_S01_GE2_1105_Oct12_1_2.txt
Biological replicate 2 of 3 of WT at 30h

value: WT


title: Test, far-red light-exposed sample, rep a

description: A - Biological replicate 1 of 2

source_name: cell culture, far red (765 nm), 0.5 h


title: AH375, biological rep3

tag: age (weeks)

tag: tissue

tag: lesion

tag: cell line


title: 1499, biological rep3

source_name: 1499 cell line, pancreatic ductal cells from ADM/PanIN1, 9-week-old Pdx1-Cre;LSL-KRasG12D mouse


title: scbR2DM mutant 42h replicate1

description:
ScbR2DM-1
Raw data file: US10313827_256469310001_S01_GE2_1105_Oct12_1_4.txt
Biological replicate 1 of 3 of scbR2DM at 42h

value: transitional phase


title: 1499, biological rep2


title: Test, far-red light-exposed sample, rep b


title: Control, dark-treated sample, rep b

source_name: cell culture, dark,0.5 h


title: Control, dark-treated sample, rep a

description: A - Biological replicate 1 of 2


title: scbRDM mutant 30h replicate3

description:
scbRDM-3
Raw data file: US10313827_256469310001_S01_GE2_1105_Oct12_1_3.txt
Biological replicate 3 of 3 of scbRDM at 30h

value: scbRDM mutant


title: AH375, biological rep1


title: 1499, biological rep1


title: Control-32°C TCH4 vs. Heat-conditioned-32°C CCH4

city: Nouzilly

first: Anne

last: Collin

address: UR83 Recherches Avicoles

institute: INRA

hyb_protocol: Transcriptome profiling was performed using a Custom Gene Expression 8x60K Gallus gallus array (Agilent Technologies). A total of 64 samples were analyzed, corresponding to 8 slides. 300 ng of Cy3-labeled cRNA (specific activity >9) and 300 ng of Cy5-labeled cRNA (specific activity >9) were combined for each single array, and the washing steps were then performed according to the manufacturer’s recommendations.

scan_protocol: The slides were scanned using a G2565CA Scanner System (Agilent Technologies), using a scan protocol with a resolution of 3 µm and a dynamic range of 20 bit. The resulting .tiff images were analyzed with Feature Extraction Software (Agilent Technologies) using the GE2_107_Sep09 protocol to obtain background subtracted and spatially detrended Processed Signal intensities.

data_processing: The data were filtered on the basis of information on the quality of the spots for the normalization step considering that the signal must be more than 1.5 times the background noise. Normalization was performed by global loess function of the package Limma (Smyth, 2004).

organism: Gallus gallus

source_name: Pectoralis major muscle

label_protocol: Cyanine-3 (Cy3) and Cyanine-5 (Cy5) labeled cRNAs were prepared from 100 ng of total RNA using the Two-Color Low Input Quick Amp Labeling Kit (Agilent Technologies). Synthetic RNAs (Two-Color RNA Spike-In Kit, Agilent Technologies) were added as an internal quality control. The obtained cRNAs were purified using RNeasy Mini Spin columns (Qiagen) and subsequently run onto a Bioanalyzer 2100 using RNA 6000 Nano chips (Agilent Technologies) to assess their profiles.

growth_protocol: Cobb500 eggs were incubated at INRA UE1295 PEAT before chickens were reared in standard conditions until 34d of age

extract_protocol: Total RNA was extracted from Pectoralis major muscle using the Qiagen RNeasy Midi Kit (Qiagen) according to the manufacturer’s instructions.

treatment_protocol: Eggs were either incubated in standard conditions (Controls T, 37.8°C and 56% relative humidity RH during all embryogenesis) or submitted to heat during  incubation (heat-conditioned C, 39.5°C and 65% RH during 12h/d from day 7 to 16 of embryogenesis). At 34 days posthatch they were submitted to a heat challenge (32°C during 5h, respectively TCH and CCH) or not (21°C, respectively T and C). Chickens were characterized by low body temperatures in C and CCH treatments and high body temperatures in T and TCH treatments.

value: Cobb 500

tag: gender

value: male

tag: age

value: 34 days posthatch

tag: incubation treatment

value: Control

tag: ambient temperature at 34 days (°c)

value: Heat-conditioned

tag: ambient temperature at 34 days


title: scbRDM mutant 30h replicate2

description:
scbRDM-2
Raw data file: US10313827_256469310001_S01_GE2_1105_Oct12_1_2.txt
Biological replicate 2 of 3 of scbRDM at 30h

value: exponential phase


title: Test, red light-exposed sample, rep a

description: A - Biological replicate 1 of 2


title: Control-21°C T3 vs. Heat-conditioned-21°C C3


title: Control-32°C TCH4 vs. Control-21°C T4


title: Heat-conditioned-21°C C3 vs. Control-21°C T3


title: Heat-conditioned-32°C CCH4 vs. Control-32°C TCH4


title: Heat-conditioned-32°C CCH2 vs. Heat-conditioned-21°C C2


title: Heat-conditioned-32°C CCH7 vs. Heat-conditioned-21°C C7


title: Control-32°C TCH3 vs. Heat-conditioned-32°C CCH3


title: Control-21°C T1 vs. Heat-conditioned-21°C C1


title: Control-21°C T8 vs. Control-32°C TCH8


title: Heat-conditioned-21°C C2 vs. Heat-conditioned-32°C CCH2


title: Heat-conditioned-21°C C6 vs. Heat-conditioned-32°C CCH6


title: Heat-conditioned-21°C C1 vs. Control-21°C T1


title: Control-32°C TCH8 vs. Control-21°C T8


title: Control-32°C TCH3 vs. Control-21°C T3


title: Heat-conditioned-32°C CCH3 vs. Control-32°C TCH3


title: Control-21°C T8 vs. Heat-conditioned-21°C C8


title: Control-21°C T3 vs. Control-32°C TCH3


title: Control-32°C TCH2 vs. Heat-conditioned-32°C CCH2


title: Heat-conditioned-32°C CCH2 vs. Control-32°C TCH2


title: Control-32°C TCH1 vs. Control-21°C T1


title: Heat-conditioned-21°C C7 vs. Control-21°C T7


title: Heat-conditioned-32°C CCH6 vs. Heat-conditioned-21°C C6


title: Control-21°C T1 vs. Control-32°C TCH1


title: Heat-conditioned-21°C C8 vs. Heat-conditioned-32°C CCH8


title: Heat-conditioned-21°C C8 vs. Control-21°C T8


title: Heat-conditioned-32°C CCH7 vs. Control-32°C TCH7


title: Control-21°C T7 vs. Heat-conditioned-21°C C7


title: Heat-conditioned-21°C C7 vs. Heat-conditioned-32°C CCH7


title: Heat-conditioned-32°C CCH8 vs. Heat-conditioned-21°C C8


title: Heat-conditioned-32°C CCH5 vs. Heat-conditioned-21°C C5


title: Control-32°C TCH2 vs. Control-21°C T2


title: Control-21°C T5 vs. Control-32°C TCH5


title: Control-21°C T4 vs. Control-32°C TCH4


title: Heat-conditioned-32°C CCH1 vs. Heat-conditioned-21°C C1


title: Heat-conditioned-21°C C5 vs. Heat-conditioned-32°C CCH5


title: Heat-conditioned-32°C CCH6 vs. Control-32°C TCH6


title: Control-21°C T5 vs. Heat-conditioned-21°C C5


title: Control-32°C TCH7 vs. Heat-conditioned-32°C CCH7


title: Heat-conditioned-32°C CCH8 vs. Control-32°C TCH8


title: Heat-conditioned-21°C C1 vs. Heat-conditioned-32°C CCH1


title: Heat-conditioned-21°C C2 vs. Control-21°C T2


title: Heat-conditioned-21°C C5 vs. Control-21°C T5


title: Control-32°C TCH8 vs. Heat-conditioned-32°C CCH8


title: Control-32°C TCH6 vs. Heat-conditioned-32°C CCH6


title: Heat-conditioned-21°C C6 vs. Control-21°C T6


title: Control-21°C T6 vs. Control-32°C TCH6


title: Control-32°C TCH1 vs. Heat-conditioned-32°C CCH1


title: Heat-conditioned-21°C C4 vs. Control-21°C T4


title: Control-21°C T4 vs. Heat-conditioned-21°C C4


title: Control-32°C TCH5 vs. Control-21°C T5


title: Control-21°C T2 vs. Control-32°C TCH2


title: Control-21°C T7 vs. Control-32°C TCH7


title: Control-32°C TCH5 vs. Heat-conditioned-32°C CCH5


title: Control-21°C T2 vs. Heat-conditioned-21°C C2


title: Heat-conditioned-21°C C4 vs. Heat-conditioned-32°C CCH4


title: Control-32°C TCH7 vs. Control-21°C T7


title: Heat-conditioned-32°C CCH4 vs. Heat-conditioned-21°C C4


title: Heat-conditioned-32°C CCH1 vs. Control-32°C TCH1


title: Control-32°C TCH6 vs. Control-21°C T6


title: Heat-conditioned-32°C CCH3 vs. Heat-conditioned-21°C C3


title: Heat-conditioned-32°C CCH5 vs. Control-32°C TCH5


title: Heat-conditioned-21°C C3 vs. Heat-conditioned-32°C CCH3


title: Mouse WT-3

city: Navi Mumbai

first: SANJEEV

middle: K

last: WAGHMARE

state: MAHARASHTRA

address: Sector 22, Kharghar

department: STEM CELL BIOLOGY GROUP

country: India

institute: ACTREC, TATA MEMORIAL CENTRE

description: Gene expression data from mouse hair follicle stem cells at postnatal day 49

hyb_protocol: Streptavidin-Phycoerythrin (Molecular Probes) was used as the fluorescent conjugate to detect hybridized target sequences (GeneChip(R) Mouse Gene 2.0 ST arrays (Affymetrix, USA).

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

data_processing: The data was analyzed with Affymetrix Expression Console(version 1.4.1) and Transcriptome Analysis Console (TAC version 3.0) using Affymetrix default analysis settings and global scaling as normalization method.

source_name: Mouse hair follicle stem cells

label_protocol: Terminal deoxynucleotidyl transferase (TdT) by using the Affymetrix proprietary DNA Labeling Reagent that is covalently linked to biotin

growth_protocol: Mouse hair follicle stem cells at postnatal day 49

extract_protocol: RNA extraction was done by using the Absolutely RNA Miniprep Kit - Agilent Technologies as per manufacturers instruction

treatment_protocol: Hair follicle stem cells were isolated by flow cytometry by using CD34 and alpha-6-integrin (hair follicle stem cells markers)

value: Mouse skin

value: Wild type mouse

value: postnatal day 49


title: Control-21°C T6 vs. Heat-conditioned-21°C C6


title: Mouse TG-3

value: K14-sPLA2-IIA (Transgenic mouse)


title: Mouse WT-2


title: OHT_2ac_cl6

city: Copenhagen N

first: Marianne

middle: Terndrup

last: Pedersen

address: Ole Maaloes Vej 5

department: University of Copenhagen

country: Denmark

institute: BRIC

hyb_protocol: Samples were hybridized to Agilent SurePrint G3 Mouse GE 8x60K arrays (Agilent G4852A) using Gene Expression Hybridization kit (Agilent #5188-5242) according to manufacturer’s instructions.

scan_protocol: Arrays were scanned according to manufacturers instructions.

data_processing:
Using the R Bioconductor 'limma' package the raw data was background corrected ('backgroundCorrect' with 'normexp' method and offset=75) and normalized ('normalizeBetweenArrays' with 'cyclicloess' method).
log2 transformed loess normalized values

source_name: Embryonic stem cells (ESCs)

label_protocol: Samples were labeled according to manufacturer’s instructions using LowInput QuickAmp Labeling Kit One Color (Agilent #5190-2305) and One-Color RNA Spike-In kit (Agilent #5188-5282).

growth_protocol: Embryonic stem cell (ESC) lines of the specified genotypes were derived from C57Bl/6 mice and cultured on gelatin-coated plates in the presence of leukemia inhibitory factor (LIF) in serum-free N2B27 supplemented with MEK inhibitor PD0325901 and GSK3 inhibitor.

extract_protocol: Total RNA was purified using RNeasy (Qiagen).

treatment_protocol: ESCs were grown in the absence or presence of 500 nM OHT for 12 days to ensure full recombination and cultured for another 6 days before harvesting.

tag: esc genotype

tag: treatment

value: OHT


title: OHT_2ac_cl4

description: RNA extracted from the 2ac ESC clone #4 (control and OHT treated) was hybridised to arrays twice due to suboptimal hybridisation of the Ctrl-treated sample in the first experiment.


title: OHT_2abc_cl324.13


title: OHT_2ac_cl5


title: OHT_2abc_cl280.4


title: Mouse TG-1


title: Mouse TG-2


title: Mouse WT-1


title: OHT_2ac_cl4_B


title: OHT_2abc_cl324.9


title: Ctrl_2abc_cl324.13


title: Ctrl_2abc_cl280.4


title: Ctrl_2ac_cl5


title: Ctrl_2ac_cl6


title: Ctrl_2ac_cl4_B


title: genotype: M - drought: Drought - rep1

city: Ames

first: PLEXdb Curator

middle: Sudhansu

state: IA

address: 1023  Crop Genomes Informatics Lab (Iowa State University)

department: Virtual Reality Application Center

institute: Iowa State University

description:
Mutant: Borgia pale-green mutant (MD-597).
Drought: irrigation was drastically reduced from the booting stage (stage 45 of the Zadoks scale, Zadoks et al., 1974) until maturity by watering the pots with the amount of water necessary to maintain the pots at 1/3 of field capacity (May still include original submitter created erros/discrepancies)

hyb_protocol: Affymetrix Basic Protocol

scan_protocol: Affy- Array Scanning

data_processing: The MAS5.0 Normalization was performed using the justMAS function in the simpleaffy package of Bioconductor (www.bioconductor.org, Version: 2.12.1). The target value is 500 for all cases. The code was developed using R2.4.1 to 2.13.0, Bioconductor 1.9 to 2.12.1, and simpleaffy 2.8.0. to 2.28.0 The CDF files were downloaded from the Bioconductor website at http://www.bioconductor.org/packages/release/AffymetrixChip.html.

organism: Triticum turgidum

source_name: flag leaf (genotype: M - drought: Drought)

label_protocol: Affymetrix one-cycle target labeling

extract_protocol: QIAGEN RNeasy Plant Mini Kit

tag: germplasm name

value: Borgia

tag: organism part

tag: development stage

tag: growth media

value: not specified


title: genotype: M - drought: CTRL - rep3

description:
Mutant: Borgia pale-green mutant (MD-597).
CTRL: the soil was maintained at its maximum water holding capacity during the whole experiment. (May still include original submitter created erros/discrepancies)

source_name: flag leaf (genotype: M - drought: CTRL)


title: genotype: M - drought: CTRL - rep1


title: genotype: M - drought: Drought - rep3


title: genotype: WT - drought: Drought - rep2

description:
WT: Borgia.
Drought: irrigation was drastically reduced from the booting stage (stage 45 of the Zadoks scale, Zadoks et al., 1974) until maturity by watering the pots with the amount of water necessary to maintain the pots at 1/3 of field capacity (May still include original submitter created erros/discrepancies)

source_name: flag leaf (genotype: WT - drought: Drought)


title: genotype: M - drought: Drought - rep2


title: genotype: M - drought: CTRL - rep2


title: genotype: WT - drought: Drought - rep3


title: Ctrl_2abc_cl324.9


title: genotype: WT - drought: CTRL - rep3

description:
WT: Borgia.
CTRL: the soil was maintained at its maximum water holding capacity during the whole experiment. (May still include original submitter created erros/discrepancies)

source_name: flag leaf (genotype: WT - drought: CTRL)


title: genotype: WT - drought: CTRL - rep2


title: genotype: WT - drought: Drought - rep1


title: genotype: WT - drought: CTRL - rep1


title: 25 C grown wild-type versus reference RNA, bio rep 1, tech rep 1

city: Chapel Hill

first: Loni

last: Townsley

state: NC

address: 250 Bell Tower Dr Genome Sciences Building #4144

department: Biology

institute: University of North Carolina

description: Reference RNA was harvested from wild-type strain. Each sample contains two technical replicates within the same .gpr file, becasue each oligonucleotide was printed twice on the same slide.

hyb_protocol: Dye-coupled test samples were mixed with the corresponding reference sample and dried. Amine silane slides containing 70-mer oligonucleotides, representing most of the open reading frames present in the V. cholerae N16961 genome, were UV cross-linked at 250 mJ and prehybridized in a solution containing 5x SSC (1x SSC is 0.15 M NaCl plus 0.015 M sodium citrate), 0.1% sodium dodecyl sulfate, and 1% bovine serum albumin for at least 45 min at 42°C. The hybridization mix was prepared by resuspending dried samples in a solution containing 15 µg salmon sperm DNA, 15 µg tRNA, 3x SSC, and 0.1% sodium dodecyl sulfate. Concentrated hybridization mix was applied to the slides and incubated at 65°C for 12 to 20 h.

scan_protocol: Slides were washed, dried, and scanned using an Axon scanner to determine the fluorescence in each open reading frame-specific spot. The raw data were obtained by using the software package GenePix 4.1 (Axon).

data_processing: Normalized signal ratios were obtained with LOWESS print-tip normalization using the Bioconductor packages (http://www.bioconductor.org) in R environment. Differentially regulated genes were determined (with three biological and two technical replicates for each data point) with the significance analysis of microarrays (SAM) package using twofold differences in gene expression and a 3% false discovery rate as a cutoff value.

organism: Vibrio cholerae

source_name: Reference RNA

label_protocol: RNA samples from test and reference samples were used in a reverse transcription reaction as follows: 3 µg of RNA and 5 µg of random hexamers were denatured at 80°C for 8 min and then chilled on ice for 5 min. The reaction mixture, containing first-strand buffer, 0.01 M dithiothreitol, aminoallyl deoxynucleoside triphosphate labeling mix with amino acid-dUTP in a 3 (dTTP):2 (amino acid-dUTP) ratio, and 400 U SuperScript III (Invitrogen), was added to cooled samples and incubated at 42°C for 3 to 4 h. The cDNA-RNA mixture, samples were incubated at 65°C for 10 min in the presence of 100 mM NaOH and 10 mM EDTA. Reactions were neutralized by the addition of 1 M HEPES, pH 7.0, at a final concentration of 0.5 M HEPES. cDNA was purified from the reactions using a PCR purification kit (Qiagen) with phosphate wash and phosphate elution buffers and dried. Cleaned and dried samples were resuspended in freshly prepared 50 mM Na-bicarbonate buffer, pH 9.0. One vial of Cy3/Cy5 fluor was mixed with each sample and incubated for 1 h in the dark at room temperature. Unincorporated dye molecules were removed using PCR purification kit (Qiagen). Dye incorporation and cDNA concentrations were determined by measuring optical densities at 260, 550, and 650 nm.

growth_protocol: V. cholerae was grown aerobically overnight at 37 C in LB broth, then diluted 1:200 in fresh medium, and harvested either at mid-exponential phase at an OD600 of 0.4 or 1 h after shift to 15 C or 25 C.

extract_protocol: Two ml aliquots of cultures were collected by centrifugation for 2 min at room temperature. Cell pellets were immediately resuspended in 1 ml Trizol reagent (Invitrogen) and stored at –80˚C. Total RNA was isolated from the cell pellets according to the manufacturer’s instructions (Invitrogen). Contaminating DNA was removed by incubating RNA with RNase-free DNase I (Ambion), and an RNeasy Mini kit (QIAGEN) was used to clean up RNA after DNase digestion.

tag: strain

value: A1552, wild-type

source_name: RNA from cells grown at 25 C

tag: growth protocol

value: grown at 25 C


title: 15 C grown wild-type versus reference RNA, bio rep 3, tech rep 2

source_name: RNA from cells grown at 15 C

value: grown at 15 C


title: 25 C grown wild-type versus reference RNA, bio rep 3, tech rep 2


title: 15 C grown wild-type versus reference RNA, bio rep 3, tech rep 1


title: 15 C grown wild-type versus reference RNA, bio rep 1, tech rep 2


title: 15 C grown wild-type versus reference RNA, bio rep 2, tech rep 1


title: 15 C grown wild-type versus reference RNA, bio rep 2, tech rep 2


title: 25 C grown wild-type versus reference RNA, bio rep 3, tech rep 1


title: uninfected  293 vs inf Chikungunya  293

city: Berlin

first: Hans-Joachim

last: Mollenkopf

address: Charitéplatz 1

country: Germany

institute: Max-Planck-Institute for Infection Biology

description: 60 min post infection

hyb_protocol: Whole genome 4x44K microarrays were done according to the supplier’s protocol (Agilent Technologies) using the SSC wash protocol.

scan_protocol: Scanning of microarrays was performed with 5 µm resolution using a G2565CA high-resolution microarray laser scanner (Agilent Technologies)

data_processing:
Raw microarray image data were analyzed with the Image Analysis / Feature Extraction software G2567AA (Version A.10.5.1, Agilent).
Array dye normalization was performed with the Feature Extraction software (Agilent Technologies) as outlined in the protocol GE2_1100_Jul11 using multiplicative detrending for background subtraction and rank consistent probes together with the normalization method linear and lowess.
The extracted MAGE-ML files were analyzed with the Rosetta Resolver Biosoftware (Rosetta Biosoftware).

source_name: HEK 293 cell culture

label_protocol: RNA labeling was performed with thequick Amp Labeling Kit (Agilent Technologies) according supplier's instructions.

growth_protocol: HEK 293 cells were cultured in complete DMEM medium.

extract_protocol: Cells were lysed 18 h post infection using Trizol (Invitrogen)  followed by total RNA isolation according the manufacturer´s protocol using Glycogen as carrier.

treatment_protocol: Transfection was done by adding 4x10e5 293 cells (in complete DMEM medium) to a mixture of serum-free RPMI medium, HiperFect (Qiagen) and Allstars siRNAs (Qiagen, final siRNA concentration: 20 nM). Infection with CHIKV-GFP was performed 72 h p.t. at an MOI of ~3.

value: human embryonic kidneys (HEK)

tag: protocol

value: CHIKV uninfected

tag: cell type

value: CHIKV infected


title: 25 C grown wild-type versus reference RNA, bio rep 2, tech rep 2


title: allstars inf Chikungunya  293 vs allstars uninfected  293

description: 60 min post infection

tag: tissue

value: allstar transfected, CHIKV uninfected

value: allstar transfected, CHIKV infected


title: 25 C grown wild-type versus reference RNA, bio rep 2, tech rep 1


title: inf Chikungunya  293 vs uninfected  293

description: 60 min post infection


title: 37 C grown wild-type versus reference RNA, bio rep 3, tech rep 2

source_name: RNA from cells grown at 37 C

value: grown at 37 C


title: allstars uninfected  293 vs allstars inf Chikungunya  293

description: 60 min post infection


title: 15 C grown wild-type versus reference RNA, bio rep 1, tech rep 1


title: 37 C grown wild-type versus reference RNA, bio rep 2, tech rep 2


title: 37 C grown wild-type versus reference RNA, bio rep 2, tech rep 1


title: 37 C grown wild-type versus reference RNA, bio rep 3, tech rep 1


title: 37 C grown wild-type versus reference RNA, bio rep 1, tech rep 2


title: 37 C grown wild-type versus reference RNA, bio rep 1, tech rep 1


title: Monocyte_Differentiation_Maturation(MSC)_donorC

city: Montreal

first: Panojot

last: Bifsha

state: QC

address: 3175 Chemin de la Côte Ste-Catherine

department: Pediatrics

institute: CHU Sainte-Justine

hyb_protocol: According to Agilent recommendations.

scan_protocol: Scanned on an Agilent Technologies Scanner G2505B US45103062. According to agilent recommendations using Agilent Feature Extraction Software.

data_processing: Simple Loess normalization was performed without background correction of the raw data after which differential expression and statistical significance were assessed using the “limma” algorithm. More stringent correction of the resulting p-values was done by calculating the false discovery rate (FDR) according to the Benjamini-Hochberg method.

label_protocol: According to Agilent recommendations.

growth_protocol: Monocytes were isolated by CD14 positive selection (Stemcell Technology) (purity above 95%) from peripheral blood of adult donors.

extract_protocol: Total RNA was extracted from cell samples using QIAzol Lysis Reagent (Qiagen) and purified using mRNA Easy Kit (Qiagen, Valencia, CA).

treatment_protocol: iDC were obtained by culturing monocytes for 5 days in the presence of human recombinant GM-CSF (50 ng/ml) and IL-4 (10 ng/ml). LPS treatment (1 ug/ml) for 2 days was used to induce DC maturation. Umbilical cord blood MSC (ratio MSC:monocytes=1:5) were plated during the phase of DC differentiation or/and maturation.

tag: donor id

value: donorC

value: Adult

value: Blood

value: Monocytes

tag: cell subtype

source_name: Universal Reference total RNA

tag: sample type

value: Pool of 10 cell lines


title: Monocyte_Differentiation_Maturation(MSC)_donorA

value: donorA

tag: age


title: Monocyte_Differentiation(MSC)_Maturation(MSC)_donorB

value: donorB


title: Monocyte_Differentiation(MSC)_Maturation(MSC)_donorC


title: Monocyte_Differentiation(MSC)_Maturation(MSC)_donorA


title: 25 C grown wild-type versus reference RNA, bio rep 1, tech rep 2


title: Monocyte_Differentiation(MSC)_Maturation_donorC


title: Monocyte_Differentiation_Maturation(MSC)_donorB


title: Monocyte_Differentiation(MSC)_Maturation_donorB


title: Monocyte_Differentiation_Maturation_donorC

value: mDC (mature DCs)


title: Monocyte_Differentiation(MSC)_Maturation_donorA


title: Monocyte_Differentiation_Maturation_donorA


title: Monocyte_Differentiation_Maturation_donorB


title: prostate_cancer_primary_134

city: San Diego

first: Elai

last: Davicioni

address: 10355 Science Center Dr

institute: GenomeDx Biosciences

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials and protocols

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing: Data was normalized uisng SCAN (SCAN.UPC package from Bioconductor)

source_name: FFPE prostate cancer

label_protocol: RNA was amplified, fragmented and biotinylated using the WT-Ovation FFPE system (NuGen, San Carlos, CA) according to the manufacturer’s recommendations with minor modifications

extract_protocol: After histopathologic review of formalin-fixed, paraffin-embedded (FFPE) tumor blocks from each case by 2 expert genitourinary pathologists, the tumor block with the index lesion was selected for specimen processing. The index lesion was identified as the prostatectomy FFPE block with the highest pathologic Gleason grade, regardless of its volume. Two [x] 0.6-mm diameter tissue biopsy punch tool cores were sampled to enrich for tumor cells from the highest Gleason grade in the index lesion and placed in a microfuge tube for RNA extraction.

tag: pathologic gleason score

tag: pathologic stage

tag: preoperative psa


title: prostate_cancer_primary_138


title: prostate_cancer_primary_131


title: prostate_cancer_primary_139


title: prostate_cancer_primary_133


title: prostate_cancer_primary_125


title: prostate_cancer_primary_120


title: prostate_cancer_primary_129


title: prostate_cancer_primary_135


title: prostate_cancer_primary_127


title: prostate_cancer_primary_128


title: prostate_cancer_primary_121


title: prostate_cancer_primary_118


title: prostate_cancer_primary_124


title: Monocyte_Differentiation(MSC)_donorA

value: iDC-MSC


title: Monocyte_Differentiation(MSC)_donorB


title: prostate_cancer_primary_132


title: prostate_cancer_primary_122


title: Monocyte_Differentiation_donorC

value: iDC (immature DCs)


title: Monocyte_Differentiation(MSC)_donorC


title: Monocyte_Differentiation_donorB


title: prostate_cancer_primary_114


title: Huh7.5.1, miR-146a-5p over-expressing biological rep1

city: Strasbourg

first: Mirjam

middle: B.

last: Zeisel

address: 3, rue Koeberlé

institute: Inserm

description: Gene expression data from miR-146a-5p over-expressing cells

hyb_protocol: Following fragmentation and end-labelling, 2.07 μg of cDNAs were hybridized for 16 hours at 45° C on GeneChip® Human Gene 1.0 ST arrays (Affymetrix) interrogating 28.869 genes represented by approximately 27 probes spread across the full length of the gene. The chips were washed and stained in the GeneChip® Fluidics Station 450 (Affymetrix).

scan_protocol: GeneChips were scanned using the GeneChip® Scanner 3000 7G (Affymetrix) at a resolution of 0.7 µm.

data_processing: Raw data (CEL Intensity files) from genome-wide mRNA profiling were extracted from the scanned images using the Affymetrix GeneChip® Command Console (AGCC) version 4.0. CEL files were further processed with Affymetrix Expression Console software version 1.3.1 (P/N 702387 Rev. 3) to calculate probe set signal intensities using Robust Multi-array Average (RMA) algorithms with default settings. Differentially expressed genes were selected using the FCROS method (Dembele and Kastner, BMC Bioinformatics, 2014) setting selection error at 0.03.

source_name: Huh7.5.1 cells

label_protocol: Biotinylated single strand cDNA targets were prepared, starting from 150 ng of total RNA, using the Ambion WT Expression Kit (Cat # 4411974) and the Affymetrix GeneChip® WT Terminal Labeling Kit (Cat # 900671) according to Affymetrix recommendations (P/N 702808 Rev. 1).

extract_protocol: For total RNA purification, Huh7.5.1 cells were lysed using TRI-reagent (MRC) according to manufacturer's intructions.

tag: cell line

tag: transfection


title: prostate_cancer_primary_115


title: Huh7.5.1, control biological rep 2

description: Gene expression data from control cells

value: Non-targeting control


title: prostate_cancer_primary_137


title: Huh7.5.1, control biological rep 1

description: Gene expression data from control cells


title: prostate_cancer_primary_117


title: prostate_cancer_primary_123


title: Monocyte_Differentiation_donorA


title: prostate_cancer_primary_113


title: Huh7.5.1, miR-146a-5p over-expressing biological rep3


title: prostate_cancer_primary_130


title: prostate_cancer_primary_136


title: prostate_cancer_primary_116


title: prostate_cancer_primary_126


title: Huh7.5.1, control biological rep 3

description: Gene expression data from control cells


title: Huh7.5.1, miR-146a-5p over-expressing biological rep2


title: prostate_cancer_primary_107


title: prostate_cancer_primary_111


title: prostate_cancer_primary_108


title: prostate_cancer_primary_109


title: prostate_cancer_primary_110


title: prostate_cancer_primary_106


title: prostate_cancer_primary_102


title: prostate_cancer_primary_112


title: prostate_cancer_primary_101


title: prostate_cancer_primary_119


title: prostate_cancer_primary_104


title: prostate_cancer_primary_98


title: prostate_cancer_primary_100


title: prostate_cancer_primary_95


title: prostate_cancer_primary_99


title: prostate_cancer_primary_94


title: prostate_cancer_primary_93


title: prostate_cancer_primary_105


title: prostate_cancer_primary_97


title: prostate_cancer_primary_91


title: prostate_cancer_primary_92


title: prostate_cancer_primary_89


title: prostate_cancer_primary_90


title: prostate_cancer_primary_85


title: prostate_cancer_primary_88


title: prostate_cancer_primary_96


title: prostate_cancer_primary_83


title: prostate_cancer_primary_80


title: prostate_cancer_primary_77


title: prostate_cancer_primary_84


title: prostate_cancer_primary_81


title: prostate_cancer_primary_82


title: prostate_cancer_primary_103


title: prostate_cancer_primary_71


title: prostate_cancer_primary_72


title: prostate_cancer_primary_78


title: prostate_cancer_primary_86


title: prostate_cancer_primary_73


title: prostate_cancer_primary_76


title: prostate_cancer_primary_67


title: prostate_cancer_primary_64


title: prostate_cancer_primary_74


title: prostate_cancer_primary_75


title: prostate_cancer_primary_69


title: prostate_cancer_primary_65


title: prostate_cancer_primary_60


title: prostate_cancer_primary_61


title: prostate_cancer_primary_63


title: prostate_cancer_primary_58


title: prostate_cancer_primary_55


title: prostate_cancer_primary_53


title: prostate_cancer_primary_51


title: prostate_cancer_primary_56


title: prostate_cancer_primary_59


title: prostate_cancer_primary_54


title: prostate_cancer_primary_87


title: prostate_cancer_primary_62


title: prostate_cancer_primary_44


title: prostate_cancer_primary_47


title: prostate_cancer_primary_48


title: prostate_cancer_primary_41


title: prostate_cancer_primary_42


title: prostate_cancer_primary_79


title: prostate_cancer_primary_43


title: prostate_cancer_primary_49


title: prostate_cancer_primary_50


title: prostate_cancer_primary_39


title: prostate_cancer_primary_46


title: prostate_cancer_primary_45


title: prostate_cancer_primary_68


title: prostate_cancer_primary_70


title: Pancreas with Kras activation and Prox1 heterozygosity rep3

city: Memphis

first: Geoffrey

last: Neale

state: TN

address: 262 Danny Thomas Place

department: Hartwell Center

institute: St Jude Childrens Research Hospital

hyb_protocol: Six (6) micrograms of cDNA were fragmented and then hybridized for 16 hr at 45C on an Affymetrix HT MG-430 PM GeneChip array. Following hybridization, arrays were washed and stained using theAffymetrix Gene Titan system.

scan_protocol: GeneChips were scanned using the Affymetrix Gene Titan system.

data_processing: Probe signals were quantile normalized and summarized by the RMA algorithm using Partek Genomics Suite software v6.5.

source_name: Postnatal day 7 whole pancreas

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix 3’IVT Express protocol starting with 100 ng of total RNA (GeneChip 3’ IVT Express Kit 702646 Rev. 8, 2008-2010, Affymetrix)

growth_protocol: Mice were housed and maintained in a controlled environment and all procedures were performed in accordance with St Jude IACUC guidelines.

extract_protocol: Total RNA was extracted using Trizol and the PureLink RNA Mini kit (Lifesciences).

value: Whole pancreas

tag: genotype

value: Postnatal day 7

tag: gender

value: Male


title: prostate_cancer_primary_37


title: prostate_cancer_primary_66


title: Pancreas with Kras activation and Prox1 heterozygosity rep2


title: prostate_cancer_primary_35


title: prostate_cancer_primary_30


title: Pancreas with Kras activation and Prox1 heterozygosity rep1


title: prostate_cancer_primary_31


title: prostate_cancer_primary_40


title: prostate_cancer_primary_29


title: prostate_cancer_primary_36


title: prostate_cancer_primary_32


title: prostate_cancer_primary_28


title: prostate_cancer_primary_52


title: prostate_cancer_primary_57


title: prostate_cancer_primary_27


title: prostate_cancer_primary_34


title: Pancreas with Kras activation rep3

value: Female


title: prostate_cancer_primary_33


title: Pancreas with Kras activation rep2


title: prostate_cancer_primary_24


title: CC0996T

city: Bethesda

first: Maxwell

last: Lee

state: MD

address: Building 37, Room 5120

department: CCR

institute: National Cancer Institute, NIH

description: Hybridized to SNP5.0

hyb_protocol: fragmentation is confirmed by the presence of a smear between 50 to 200bp, the sample was end labeled with biotin and hybridized onto the array.  The chip was incubated at 49oC for 18 hours in the Affymetrix Genechip system hybridization oven

scan_protocol: The arrays were then washed using Affymetrix fluidics stations, and scanned using the Affymetrix GeneChip Scanner 3000.

data_processing:
Raw GenomeWideSNP_5 CEL files were pre-processed using PennCNV [Wang K, 2007]. This protocol extracts allele-specific signal intensities from genotyping arrays, and then integrates information on SNP spacing and SNP allele frequencies to generate CNV calls by a hidden Markov model (HMM) algorithm.
PennCNV-Affy is a data-preprocessing protocol for Affymetrix genome-wide 5.0. The protocol converts raw CEL files into a signal intensity file that contains Log R Ratio (LRR) and B Allele Frequency (BAF) values.
CNV data can be calculated from LRR (2*2^LRR).

source_name: tumor

label_protocol: As per manufacturer protocol (Affymetrix)

extract_protocol: blood DNA was extracted and purified using standard phenol/chloroform method and tumor DNA was extracted using Purification Tissue Kit (Centra System.)

value: tumor

tag: disease state

value: cardia cancer


title: prostate_cancer_primary_25


title: prostate_cancer_primary_21


title: prostate_cancer_primary_26


title: CC0996B

description: Hybridized to SNP5.0

source_name: blood

value: blood

value: control


title: WT pancreas rep1

value: Wild type

tag: strain


title: Pancreas with Kras activation rep1


title: prostate_cancer_primary_20


title: resting NK cells_normoxia_biological rep5

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

institute: University Heidelberg

hyb_protocol: Hybridization (16h x 45°C) was processed according to the standard Affymetrix protocol.

scan_protocol: Affymetrix GeneArray Scanner3000

data_processing: The data were analyzed with a commercial software called JMP Genomics, version 6, from SAS. Gene expression profiling was performed using arrays of HuGene-2_0-st-type from Affymetrix. A Custom CDF Version 17 with Entrez based gene definitions was used to annotate the arrays. The Raw fluorescence intensity values were normalized applying quantile normalization, RMA background correction and Medianpolish Probeset Summary

source_name: resting NK cells_normoxia

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

growth_protocol: Freshly isolated NK cells were plated at one million cells per mL RPMI 1640 supplemented with 10% fetal bovine serum and 2 mM L-glutamine in a 3ºC humidified atmosphere of 5% carbon dioxide (normoxia). One percent oxygen (hypoxia) was established in an oxygen controlled carbon dioxide incubator with a nitrogen gas line.

extract_protocol: Total RNA was prepared from NK cells stored in RNAlater using a spin column protocol followed by DNAse treatment according to the manufacturer's instructions.

treatment_protocol: Parallel NK cell cultures were grown under normoxia or hypoxia for 22 hours with or without 45 ng/mL IL-15 present during the final 6 hours.

tag: subject status

value: healthy donor

value: peripheral blood

value: Natural killer (NK) cells

tag: cultured under

value: Normoxia for 22hrs

tag: treated with

value: none (control)


title: WT pancreas rep2

tag: tissue


title: prostate_cancer_primary_38


title: WT pancreas rep3


title: prostate_cancer_primary_22


title: primed NK cells_normoxia_biological rep5

source_name: primed NK cells_normoxia

tag: cell type

value: 45 ng/mL IL-15 during the final 6h


title: resting NK cells_hypoxia_biological rep5

source_name: resting NK cells_hypoxia

value: Hypoxia for 22hrs


title: prostate_cancer_primary_23


title: CC1220B

description: Hybridized to SNP5.0


title: primed NK cells_hypoxia_biological rep5

source_name: primed NK cells_hypoxia


title: prostate_cancer_primary_19


title: resting NK cells_normoxia_biological rep4


title: prostate_cancer_primary_18


title: primed NK cells_normoxia_biological rep4


title: E0410B

description: Hybridized to SNP5.0


title: E1860T

description: Hybridized to SNP5.0

value: esophageal cancer


title: resting NK cells_hypoxia_biological rep4


title: CC1220T

description: Hybridized to SNP5.0


title: E1860B

description: Hybridized to SNP5.0


title: E1910T

description: Hybridized to SNP5.0


title: prostate_cancer_primary_16


title: prostate_cancer_primary_17


title: E1905T

description: Hybridized to SNP5.0


title: primed NK cells_hypoxia_biological rep4


title: resting NK cells_normoxia_biological rep3


title: E1910B

description: Hybridized to SNP5.0


title: prostate_cancer_primary_11


title: E1885T

description: Hybridized to SNP5.0


title: primed NK cells_normoxia_biological rep3


title: E1905B

description: Hybridized to SNP5.0


title: resting NK cells_hypoxia_biological rep3


title: primed NK cells_hypoxia_biological rep3


title: prostate_cancer_primary_14


title: prostate_cancer_primary_10


title: resting NK cells_normoxia_biological rep2


title: GBM.17

city: Barretos

first: Lucas

middle: Tadeu

last: Bidinotto

state: SP

address: Antenor Duarte Vilela, 1331

country: Brazil

institute: Barretos Cancer Hospital

hyb_protocol: Equal quantity of Cy3- and Cy5-labelled DNA was hybridized into Agilent Human Genome CGH 8 x 60K microarray slide overnight, and washed according to supplier’s default protocol.

scan_protocol: The slides were scanned and decoded by the software Feature Extraction v. 10.7 (Agilent Technologies), using the protocol CGH_107_Sep09.

data_processing: The signal intensities were log2 transformed, and the spots were mapped in the most recent version of the human genome (hg19). The data was Lowess normalized and smoothing corrected. The data was CBS segmented.

source_name: Central Nervous System tumor

label_protocol: Four hundred nanograms of both tumor and blood DNA was digested by AluI and RsaI restriction enzymes, and incubated with random primers. Blood DNA was labeled with cyanine-3 (Cy3), whereas tumor DNA was labeled with cyanine-5 (Cy5)

extract_protocol: The DNA from patients blood was isolated using QIAmp DNA blood Mini Kit (Qiagen), and DNA from tumor frozen tissue was isolated using DNeasy Blood & Tissue Kit (Qiagen) according to the protocols provided by the supplier.

tag: tumor

value: Glioblastoma

source_name: Matched-patient leucocyte

tag: reference

value: Matched-patient leucocyte


title: E1882B

description: Hybridized to SNP5.0


title: prostate_cancer_primary_13

tag: age