title: WP9C177NO

description: female neonate

source_name: pooled control for WP9C177NO


title: TAX577089

status: Public on Jun 27 2012

type: RNA

city: Lund

first: Johan

last: Staaf

address: Medicon Village

country: Sweden

institute: SCIBLU - Swegene Centre for Integrative Biology at Lund University

hyb_protocol: Microarrays were hybridized as described (PMID: 17334996)

scan_protocol: Arrays were washed as described (PMID: 17334996) and fluorescence was recorded using an Agilent G2565AA microarray scanner (Agilent Technologies).

data_processing: TIFF images were analyzed using the Gene Pix Pro software (Axon Instruments, Foster City, CA), and the quantified data matrix was loaded into a local installation of BioArray Software Environment (BASE) (http://base.thep.lu.se). Quantified intensities for tumor sample were stored as channel 1 (ch1) whereas quantified intensities for reference sample were stored as channel 2 (ch2). Median spot pixel values were used to calculate background corrected intensities (Int1 and Int2). Spots were removed and regarded as missing values if either: (1) flagged during image-analysis, (2) background corrected intensity value >64999 signal units, (3) background corrected intensity value <1 signal units. For spots, log ratio (M) was calculated as log2(Int1/Int2) and average intensity (A) was calculated as log10(Int1*Int2)/2. Prior to normalization only oligonucleotide probes without cross-hybridization to other genomic regions or transcripts were selected. Normalization was performed using block (print tip) based lowess. After normalization, a probe presence filter was applied to select only probes with suffcient presence, followed by imputation of missing values using weighted nearest-neighbor imputation (WENNI). Probes were subsequently merged on probe identifier and row-centered across the entire data set.

molecule: total RNA

organism: Homo sapiens

source_name: Breast tumor

label_protocol: Fluorescently labeled DNA targets for hybridization were prepared according to manufacturers' instructions from 5ug of total RNA using the Corning Pronto Plus System 6 kit as described (PMID:17334996)

extract_protocol: Total RNA from fresh frozen breast tumor tissue was extracted using Trizol reagent (Invitrogen) followed by the RNeasy Midi Purification kit (Qiagen). RNA concentrations were measured using a Nanodrop (NanoDrop Technologies). RNA integrity was determined by an Agilent Bioanalyzer.

tag: tissue

value: Breast tumor

tag: hu subtype

value: LumA

tag: familial status

value: familial

tag: er

tag: osbin

tag: os

tag: pgr

tag: primary

tag: grade

tag: brca status

value: brcax

tag: pam50 classification

tag: pam50 correlation

tag: brca1 methylation status

source_name: Stratagene Universal reference RNA

tag: reference

value: Stratagene Universal reference RNA


title: WP9C167NO

city: Maastricht

first: Kevin

last: Hochstenbach

address: Universiteitssingel 50

department: Health Risk Analysis and Toxicology

country: Netherlands

institute: Maastricht University

description: male neonate

hyb_protocol: Hybridization according to Agilent instructions.

scan_protocol: Slides were scanned on a GenePix® 4000B Microarray Scanner (Molecular Devices, Sunnyvale, USA). Cy3 and Cy5 were excited at wavelengths of 532 and 635 nm, respectively. Laser power was set to 100%. The photo multiplier tube gain was set to a saturation tolerance of 0.02% to minimize background and saturated spots. Photomultiplier gain was set to 587 (Cy3) and 705 (Cy5) for replicates 1 and 2, and 628 (Cy3) and 560 (Cy5) for replicates 3 and 4, based on automatic establishment of ideal scan settings. The images obtained (resolution 5 micron, 16 bit tiff image) were processed with Imagene 8.0.1 software (Biodiscovery, El Segundo, USA) to measure mean signal intensities for spots and local backgrounds followed by a quality control in Microsoft Excel.

data_processing: Data preparations were performed in GeneSight software (BioDiscovery) and included in chronological order: background subtraction, omission of bad spots (controls and irregularly shaped spots), LOWESS normalization, log (base=2) transformations, calculation of difference of test compound versus respective vehicle control.

source_name: pooled control for WP9C167NO

label_protocol: The Two-Color Microarray-Based Gene Expression Analysis kit from Agilent Technologies (Amstelveen, The Netherlands) was used to generate Cyanine (Cy) labelled cRNA according to the manufacturer’s protocol.

extract_protocol: Total RNA was isolated from the RNAlater-preserved whole blood samples using the RiboPure-Blood system (Ambion) according to the manufacturer’s instructions. RNA yield and purity was measured by means of Nanodrop equipment (Wilmington, DE, USA) and integrity was verified by automated gel electrophoresis (2100 BioAnalyzer, Agilent Technologies, Amstelveen, the Netherlands).

value: Human cord blood

tag: gender

value: male

tag: age

value: neonate


title: WP9C184NO

description: female neonate

source_name: pooled control for WP9C184NO

value: female


title: WP9C164NO

description: female neonate

source_name: pooled control for WP9C164NO


title: WP9C166NO

description: male neonate

source_name: pooled control for WP9C166NO


title: WP9C171NO

description: female neonate

source_name: pooled control for WP9C171NO


title: WP9C162NO

description: male neonate

source_name: pooled control for WP9C162NO


title: WP9C160NO

description: male neonate

source_name: pooled control for WP9C160NO


title: TAX577095

value: sporadic

value: Unclassified


title: WP9C165NO

description: female neonate

source_name: pooled control for WP9C165NO


title: WP9C159NO

description: female neonate

source_name: pooled control for WP9C159NO


title: TAX577086

value: Normal

value: other


title: TAX577085


title: TAX577082


title: WP9C157NO

description: female neonate

source_name: pooled control for WP9C157NO


title: TAX577084


title: TAX577083


title: TAX577080


title: TAX577079


title: WP9C151NO

description: female neonate

source_name: pooled control for WP9C151NO


title: TAX577075

value: nonClassified

value: LumB


title: TAX577077


title: TAX577078

value: negative


title: WP9C152NO

description: male neonate

source_name: pooled control for WP9C152NO


title: WP9C155NO

description: female neonate

source_name: pooled control for WP9C155NO


title: WP9C149NO

description: female neonate

source_name: pooled control for WP9C149NO


title: WP9C156NO

description: female neonate

source_name: pooled control for WP9C156NO


title: WP9C150NO

description: female neonate

source_name: pooled control for WP9C150NO


title: WP9C147NO

description: female neonate

source_name: pooled control for WP9C147NO


title: WP9C148NO

description: female neonate

source_name: pooled control for WP9C148NO


title: TAX577074

source_name: Breast tumor

source_name: Stratagene Universal reference RNA


title: TAX577071


title: WP9C142NO

description: female neonate

source_name: pooled control for WP9C142NO


title: WP9C146NO

description: female neonate

source_name: pooled control for WP9C146NO


title: WP9C145NO

description: male neonate

source_name: pooled control for WP9C145NO


title: TAX577081


title: WP9C134NO

description: female neonate

source_name: pooled control for WP9C134NO


title: WP9C136NO

description: male neonate

source_name: pooled control for WP9C136NO


title: TAX577063


title: WP9C141NO

description: male neonate

source_name: pooled control for WP9C141NO


title: TAX577065


title: TAX577058


title: WP9C116NO

description: female neonate

source_name: pooled control for WP9C116NO


title: WP9C126NO

description: female neonate

source_name: pooled control for WP9C126NO


title: colonic tumor tissue, SSH, replicate 10

city: Cordoba

first: German

middle: Alexis

last: Gonzalez

state: Cordoba

address: Av. Armada Argentina 3555

department: School of Engineering

country: Argentina

institute: Catholic University of Cordoba

description:
6362 T2 SSH
Indirect strategy.

hyb_protocol: A pre-hybridization step was carried out. Then, hybridization buffer 2X was added to all samples, followed by an incubation at 42°C for 16 h in a hybridization chamber (InSlide Out, Boekel Scientific, Pennsylvania, PA, USA).

scan_protocol: Scanned on a VersArray ChipReader scanner (Bio-Rad Laboratories, Hercules, CA). Images were quantified using the software SpotReader (version 1.3.1.0, Niles Scientific, USA).

data_processing: R-2.14 was used for background correction (norm exp with offset=50) and printip LOESS normalization. These functions are implemented in the limma package. Flagged genes were considered missing values. Finally, linear mixed models were applied per gene.

label: Alexa 647

source_name: Human colonic tissue, tumor

label_protocol: 1 µg of total RNA were primed with T7-oligo (dT) primer and reversed transcribed at 46°C for 2 h in the presence of 400 U SuperScript III RTase (Invitrogen), and dNTP mix 10 mM.  In vitro transcription was carried out with 1.5 µL ATP (100 mM), 1.5 µL CTP (100 mM), 1.5 µL GTP (100 mM), 0.75 µL UTP (100 mM), 2 µL aa-UTP (50 mM), 4 µL T7 Reaction Buffer 10X and 7 µL T7 Enzyme Mix at 37ºC for 14 h.

growth_protocol: Not applicable.

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

value: M

tag: state

value: advanced

tag: diagnosis

value: colon cancer

tag: histological subtype

value: tubular adenocarcinoma

tag: infiltration

value: pericolonic adipose tissue

tag: differentiation

value: moderate

tag: linfonodes

tag: tissue type

value: tumor

tag: patient identifier

tag: strategy

value: SSH followed by conventional microarray

label: Alexa 555

source_name: Human Universal Reference RNA (Clontech)

tag: sample type

value: reference

value: many normal human tissues


title: WP9C114NO

description: male neonate

source_name: pooled control for WP9C114NO

tag: tissue

value: Human cord blood

value: male

value: neonate


title: TAX577056

value: Breast tumor

tag: hu subtype

tag: familial status

value: familial

tag: er

tag: osbin

tag: os

tag: pgr

tag: primary

tag: grade

tag: brca status

value: brcax

tag: pam50 classification

value: Stratagene Universal reference RNA


title: colonic non-tumoral tissue, SSH, replicate 7

description:
809 A2 SSH
Indirect strategy.

source_name: Human colonic tissue, non-tumor

tag: gender

value: F

tag: age

tag: state

tag: diagnosis

value: large intestine cancer

tag: histological subtype

value: papillary tubular adenocarcinoma

tag: infiltration

value: serose

tag: differentiation

value: adjacent non-tumor


title: colonic non-tumoral tissue, SSH, replicate 9

description:
4885 A2 SSH
Indirect strategy.

value: M

value: advanced

value: cecum cancer

value: tubular adenocarcinoma

value: peri-intestinal adipose tissue

value: moderate

tag: linfonodes

tag: tissue type

tag: patient identifier

tag: strategy

tag: sample type

tag: tissue


title: colonic tumor tissue, SSH, replicate 7

description:
809 T2 SSH
Indirect strategy.

value: tumor

value: SSH followed by conventional microarray

value: reference

value: many normal human tissues


title: WP9C108NO

description: female neonate

source_name: pooled control for WP9C108NO

value: Human cord blood

value: female

value: neonate


title: colonic tumor tissue, SSH, replicate 9

description:
4885 T2 SSH
Indirect strategy.


title: colonic non-tumoral tissue, SSH, replicate 6

description:
740 A2 SSH
Indirect strategy.

value: F

value: colon cancer

value: peri-intestinal adipose tissue and vesical wall


title: TAX577054

value: Breast tumor

tag: hu subtype

tag: familial status

value: sporadic

tag: er

tag: osbin

tag: os

tag: pgr

tag: primary

tag: pam50 correlation

tag: brca1 methylation status

value: negative

tag: reference

value: Stratagene Universal reference RNA


title: TAX577050

tag: grade

tag: brca status

tag: pam50 classification


title: TAX577046


title: colonic non-tumoral tissue, SSH, replicate 10

description:
6362 A2 SSH
Indirect strategy.

tag: gender

value: M

tag: age

tag: state

value: advanced

tag: diagnosis

tag: histological subtype

value: tubular adenocarcinoma

tag: infiltration

value: pericolonic adipose tissue

tag: differentiation

tag: linfonodes

tag: tissue type

value: adjacent non-tumor

tag: patient identifier


title: colonic tumor tissue, SSH, replicate 8

description:
4096 T2 SSH
Indirect strategy.

value: cecum cancer

value: papillary tubular adenocarcinoma

value: subserose

value: moderate

value: tumor

tag: strategy

value: SSH followed by conventional microarray

tag: sample type

value: reference

tag: tissue


title: colonic tumor tissue, SSH, replicate 6

description:
740 T2 SSH
Indirect strategy.

value: F

value: colon cancer

value: peri-intestinal adipose tissue and vesical wall

value: many normal human tissues


title: colonic non-tumoral tissue, SSH, replicate 8

description:
4096 A2 SSH
Indirect strategy.


title: TAX577051

value: Breast tumor

tag: hu subtype

tag: familial status

value: sporadic

tag: er

tag: osbin

tag: os

tag: pgr

tag: primary

tag: pam50 correlation

tag: brca1 methylation status

value: negative

tag: reference

value: Stratagene Universal reference RNA


title: WP9C109NO

description: female neonate

source_name: pooled control for WP9C109NO

value: Human cord blood

tag: gender

value: female

tag: age

value: neonate


title: colonic non-tumoral tissue, SSH, replicate 4

description:
393 A SSH
Indirect strategy.

tag: state

value: advanced

tag: diagnosis

tag: histological subtype

value: tubular adenocarcinoma

tag: infiltration

value: pericolonic adipose tissue

tag: differentiation

tag: linfonodes

tag: tissue type

value: adjacent non-tumor


title: WP9C105NO

description: female neonate

source_name: pooled control for WP9C105NO

tag: tissue


title: TAX577041

source_name: Breast tumor

tag: hu subtype

tag: familial status

value: familial

tag: er

tag: osbin

tag: grade

tag: brca status

value: brcax

tag: pam50 classification


title: colonic non-tumoral tissue, SSH, replicate 5

description:
620 A SSH
Indirect strategy.

tag: gender

value: M

value: large intestine cancer

value: adventitial adipose tissue

value: moderate

tag: patient identifier

tag: strategy

value: SSH followed by conventional microarray

tag: sample type

value: reference


title: TAX577037

value: Breast tumor

tag: os

tag: pgr

tag: primary

value: LumB

tag: pam50 correlation

tag: brca1 methylation status

source_name: Stratagene Universal reference RNA

tag: reference


title: WP9C104NO

description: female neonate

source_name: pooled control for WP9C104NO

tag: tissue

value: Human cord blood

tag: age


title: colonic tumor tissue, SSH, replicate 3

description:
339 T SSH
Indirect strategy.

value: F

tag: state

tag: diagnosis

value: cecum cancer

tag: histological subtype

tag: infiltration

value: subserose

tag: differentiation

value: poor

tag: linfonodes

tag: tissue type

value: tumor

value: many normal human tissues


title: colonic tumor tissue, SSH, replicate 4

description:
393 T SSH
Indirect strategy.

tag: gender

value: advanced

value: colon cancer

value: tubular adenocarcinoma

value: pericolonic adipose tissue

tag: patient identifier

tag: strategy


title: WP9C099NO

description: female neonate

source_name: pooled control for WP9C099NO

value: female

value: neonate


title: TAX577035

tag: hu subtype

tag: familial status

value: familial

tag: er

tag: osbin

tag: os

tag: pgr

tag: grade

tag: brca status

value: brcax

tag: pam50 classification

value: Stratagene Universal reference RNA


title: colonic non-tumoral tissue, SSH, replicate 2

description:
309 A SSH
Indirect strategy.

value: M

tag: age

tag: state

tag: diagnosis

tag: histological subtype

value: papillary tubular adenocarcinoma

value: moderate

value: adjacent non-tumor

value: SSH followed by conventional microarray

tag: sample type

value: reference

tag: tissue


title: WP9C091NO

description: female neonate

source_name: pooled control for WP9C091NO

value: Human cord blood

tag: gender


title: TAX577030

value: Breast tumor

value: Normal

value: sporadic

tag: primary

tag: pam50 correlation

tag: brca1 methylation status

tag: reference


title: colonic non-tumoral tissue, conventional, replicate 10

description:
6362 A directa
Direct strategy.

value: advanced

value: colon cancer

value: tubular adenocarcinoma

tag: infiltration

tag: differentiation

tag: linfonodes

tag: tissue type

tag: patient identifier

tag: strategy

value: conventional microarray

value: many normal human tissues


title: TAX577029

tag: hu subtype

tag: familial status

tag: er

tag: osbin

tag: os

tag: pgr

tag: grade

tag: brca status

tag: pam50 classification


title: colonic tumor tissue, SSH, replicate 5

description:
620 T SSH
Indirect strategy.

tag: gender

tag: age

tag: state

tag: diagnosis

value: large intestine cancer

tag: histological subtype

value: adventitial adipose tissue

value: tumor

tag: sample type

tag: tissue


title: colonic tumor tissue, SSH, replicate 1

description:
147 T SSH
Indirect strategy.

value: F

tag: infiltration

value: pericolonic adipose tissue

tag: differentiation

tag: linfonodes

tag: tissue type

tag: patient identifier

tag: strategy


title: colonic non-tumoral tissue, SSH, replicate 3

description:
339 A SSH
Indirect strategy.

value: cecum cancer

value: subserose

value: poor

value: adjacent non-tumor


title: WP9C085NO

description: male neonate

source_name: pooled control for WP9C085NO

value: Human cord blood

value: male

value: neonate


title: TAX577028

value: Breast tumor

tag: hu subtype

tag: familial status

value: familial

tag: er

tag: osbin

tag: os

tag: pgr

tag: primary

value: other

tag: pam50 correlation

tag: brca1 methylation status

tag: reference

value: Stratagene Universal reference RNA


title: colonic tumor tissue, conventional, replicate 10

description:
6362 T directa
Direct strategy.

tag: gender

value: M

tag: age

tag: state

value: advanced

tag: diagnosis

value: colon cancer

tag: histological subtype

value: tubular adenocarcinoma

value: moderate

value: conventional microarray

tag: sample type

value: reference

tag: tissue

value: many normal human tissues


title: colonic non-tumoral tissue, SSH, replicate 1

description:
147 A SSH
Indirect strategy.

value: F

tag: infiltration

value: pericolonic adipose tissue

tag: differentiation

tag: linfonodes

tag: tissue type

tag: patient identifier

tag: strategy

value: SSH followed by conventional microarray


title: WP9C077NO

description: female neonate

source_name: pooled control for WP9C077NO

value: Human cord blood

value: female


title: colonic tumor tissue, conventional, replicate 9

description:
4885 T directa
Direct strategy.

value: cecum cancer

value: peri-intestinal adipose tissue

value: tumor


title: colonic non-tumoral tissue, conventional, replicate 8

description:
4096 A directa
Direct strategy.

value: papillary tubular adenocarcinoma

value: subserose

value: adjacent non-tumor


title: WP9C079NO

description: female neonate

source_name: pooled control for WP9C079NO

value: neonate


title: colonic tumor tissue, SSH, replicate 2

description:
309 T SSH
Indirect strategy.

value: M

value: advanced

value: colon cancer


title: colonic non-tumoral tissue, conventional, replicate 9

description:
4885 A directa
Direct strategy.

value: tubular adenocarcinoma

value: moderate

value: conventional microarray

value: reference


title: TAX577027

value: Breast tumor

tag: hu subtype

tag: familial status

value: familial

tag: er

tag: osbin

tag: os

tag: pgr

tag: primary

tag: grade

tag: brca status

value: brcax

tag: pam50 classification

value: Stratagene Universal reference RNA


title: TAX577026

tag: tissue

value: sporadic

tag: pam50 correlation

tag: brca1 methylation status

tag: reference


title: TAX577025

value: Basal

value: negative


title: WP9C076NO

description: female neonate

source_name: pooled control for WP9C076NO

value: Human cord blood

tag: gender

value: female

tag: age


title: colonic tumor tissue, conventional, replicate 8

description:
4096 T directa
Direct strategy.

tag: state

tag: diagnosis

value: cecum cancer

tag: histological subtype

value: papillary tubular adenocarcinoma

tag: infiltration

value: subserose

tag: differentiation

tag: linfonodes

tag: tissue type

value: tumor

tag: patient identifier

tag: strategy

tag: sample type

value: many normal human tissues


title: colonic non-tumoral tissue, conventional, replicate 7

description:
809 A directa
Direct strategy.

value: F

value: advanced

value: large intestine cancer

value: serose

value: moderate

value: adjacent non-tumor


title: colonic tumor tissue, conventional, replicate 7

description:
809 T directa
Direct strategy.

value: conventional microarray

value: reference


title: WP9C073NO

description: female neonate

source_name: pooled control for WP9C073NO

value: neonate


title: WP9C072NO

description: male neonate

source_name: pooled control for WP9C072NO

value: male


title: TAX577020

value: Breast tumor

tag: hu subtype

tag: familial status

value: sporadic

tag: er

tag: osbin

tag: os

tag: pgr

tag: primary

tag: grade

tag: brca status

value: other

tag: pam50 classification

value: Stratagene Universal reference RNA


title: TAX577023

tag: tissue

value: non malignant

value: Normal

tag: pam50 correlation

tag: brca1 methylation status

tag: reference


title: colonic non-tumoral tissue, conventional, replicate 6

description:
740 A directa
Direct strategy.

tag: gender

tag: age

tag: state

tag: diagnosis

value: colon cancer

tag: histological subtype

value: tubular adenocarcinoma

tag: infiltration

value: peri-intestinal adipose tissue and vesical wall

tag: differentiation

tag: linfonodes

tag: tissue type

tag: patient identifier

source_name: Human Universal Reference RNA (Clontech)

value: many normal human tissues


title: colonic tumor tissue, conventional, replicate 5

description:
620 T directa
Direct strategy.

source_name: Human colonic tissue, tumor

value: M

value: advanced

value: large intestine cancer

value: adventitial adipose tissue

value: tumor

tag: strategy

tag: sample type


title: TAX577021

tag: hu subtype

value: nonClassified

tag: familial status

tag: er

tag: osbin

tag: os

tag: pgr

tag: primary

tag: grade

tag: brca status

tag: pam50 classification


title: WP9C067NO

description: female neonate

source_name: pooled control for WP9C067NO

tag: tissue

value: Human cord blood

tag: gender

value: female

tag: age

value: neonate


title: WP9C068NO

description: female neonate

source_name: pooled control for WP9C068NO


title: colonic tumor tissue, conventional, replicate 6

description:
740 T directa
Direct strategy.

value: F

tag: state

tag: diagnosis

tag: histological subtype

tag: infiltration

tag: differentiation

value: moderate

tag: linfonodes

tag: tissue type

value: conventional microarray

value: reference


title: colonic non-tumoral tissue, conventional, replicate 3

description:
339 A directa
Direct strategy.

source_name: Human colonic tissue, non-tumor

value: cecum cancer

value: subserose

value: poor

value: adjacent non-tumor

tag: patient identifier

tag: strategy

tag: sample type


title: WP9C064NO

description: male neonate

source_name: pooled control for WP9C064NO

value: male


title: colonic non-tumoral tissue, conventional, replicate 2

description:
309 A directa
Direct strategy.

value: M

value: advanced

value: colon cancer

value: papillary tubular adenocarcinoma

value: many normal human tissues


title: colonic non-tumoral tissue, conventional, replicate 5

description:
620 A directa
Direct strategy.

value: large intestine cancer

value: tubular adenocarcinoma

value: adventitial adipose tissue


title: colonic tumor tissue, conventional, replicate 3

description:
339 T directa
Direct strategy.

value: F

value: tumor


title: colonic tumor tissue, conventional, replicate 4

description:
393 T directa
Direct strategy.

value: pericolonic adipose tissue

value: moderate

value: conventional microarray


title: colonic non-tumoral tissue, conventional, replicate 4

description:
393 A directa
Direct strategy.

value: reference


title: colonic tumor tissue, conventional, replicate 2

description:
309 T directa
Direct strategy.

value: subserose


title: TAX577017

source_name: Breast tumor

value: Breast tumor

tag: hu subtype

value: Basal

tag: familial status

value: sporadic

tag: er

tag: osbin

tag: os

tag: pgr

tag: primary

tag: pam50 correlation

tag: brca1 methylation status

value: negative

tag: reference

value: Stratagene Universal reference RNA


title: colonic non-tumoral tissue, conventional, replicate 1

description:
147 A directa
Direct strategy.

tag: gender

tag: age

tag: state

value: advanced

tag: diagnosis

value: colon cancer

tag: histological subtype

tag: infiltration

value: adjacent non-tumor

tag: tissue


title: WP9C062NO

description: male neonate

source_name: pooled control for WP9C062NO

value: Human cord blood

value: male

value: neonate


title: WP9C061NO

description: male neonate

source_name: pooled control for WP9C061NO


title: TAX577019

tag: hu subtype

value: familial

tag: grade

tag: brca status

value: brcax

tag: pam50 classification

source_name: Stratagene Universal reference RNA


title: colonic tumor tissue, conventional, replicate 1

description:
147 T directa
Direct strategy.

value: F

value: tubular adenocarcinoma

value: pericolonic adipose tissue

tag: differentiation

value: moderate

tag: linfonodes

tag: tissue type

value: tumor

tag: patient identifier

tag: strategy

tag: sample type

value: many normal human tissues


title: WP9C060NO

description: female neonate

source_name: pooled control for WP9C060NO

tag: gender

value: female


title: TAX577007

value: Breast tumor

value: Normal

tag: familial status

value: sporadic

tag: er

tag: osbin

tag: os

tag: pgr

tag: primary

tag: pam50 correlation

tag: brca1 methylation status

tag: reference


title: WP9C059NO

description: female neonate

source_name: pooled control for WP9C059NO

tag: tissue

tag: age


title: TAX577006

tag: hu subtype

value: nonClassified

tag: grade

tag: brca status

tag: pam50 classification

value: Stratagene Universal reference RNA


title: TAX577004

value: negative


title: gastric tumor tissue, SSH, replicate 12

description:
92T SSH
Indirect strategy.

source_name: Human gastric tissue, tumor

value: M

tag: state

value: advanced

tag: lauren type

value: intestinal

tag: histological subtype

tag: infiltration

value: muscularis propria

tag: differentiation

value: poor

tag: linfonodes

tag: tissue type

tag: patient identifier

tag: strategy

value: SSH followed by conventional microarray

tag: sample type

value: reference


title: gastric non-tumoral tissue, SSH, replicate 11

description:
91A SSH
Indirect strategy.

source_name: Human gastric tissue, non-tumor

tag: gender

value: tubular adenocarcinoma

value: subserose

value: moderate

value: adjacent non-tumor


title: gastric non-tumoral tissue, SSH, replicate 12

description:
92A SSH
Indirect strategy.

tag: tissue

value: many normal human tissues


title: gastric tumor tissue, SSH, replicate 11

description:
91T SSH
Indirect strategy.

tag: age

value: tumor


title: WP9C058NO

description: male neonate

source_name: pooled control for WP9C058NO

value: Human cord blood

value: male

value: neonate


title: gastric non-tumoral tissue, SSH, replicate 8

description:
84A SSH
Indirect strategy.

value: serose


title: gastric tumor tissue, SSH, replicate 9

description:
89T SSH
Indirect strategy.

value: M

value: difuse

value: signet-ring cell


title: gastric non-tumoral tissue, SSH, replicate 7

description:
81A SSH
Indirect strategy.

value: advanced


title: WP9C056NO

description: male neonate

source_name: pooled control for WP9C056NO


title: TAX577568

value: Breast tumor

tag: hu subtype

value: LumB

tag: familial status

value: familial

tag: er

tag: osbin

tag: os

tag: pgr

tag: primary

value: brcax

tag: pam50 correlation

tag: brca1 methylation status

tag: reference

value: Stratagene Universal reference RNA


title: TAX577003

value: sporadic

tag: grade

tag: brca status

tag: pam50 classification

value: Normal

value: negative


title: TAX577561

value: other


title: TAX577562


title: WP9C055NO

description: male neonate

source_name: pooled control for WP9C055NO

value: Human cord blood


title: gastric non-tumoral tissue, SSH, replicate 9

description:
89A SSH
Indirect strategy.

tag: state

tag: lauren type

tag: histological subtype

tag: infiltration

tag: differentiation

value: poor

tag: linfonodes

tag: tissue type

value: adjacent non-tumor

tag: patient identifier

tag: strategy

value: SSH followed by conventional microarray

source_name: Human Universal Reference RNA (Clontech)

tag: sample type

value: reference

value: many normal human tissues


title: gastric tumor tissue, SSH, replicate 10

description:
90T SSH
Indirect strategy.

tag: gender

value: F

tag: age

value: intestinal

value: tubular adenocarcinoma

value: serose

value: moderate

value: tumor

tag: tissue


title: gastric non-tumoral tissue, SSH, replicate 10

description:
90A SSH
Indirect strategy.

value: advanced


title: gastric non-tumoral tissue, SSH, replicate 6

description:
75A SSH
Indirect strategy.

value: M


title: WP9C057NO

description: female neonate

source_name: pooled control for WP9C057NO

value: female

value: neonate


title: gastric tumor tissue, SSH, replicate 8

description:
84T SSH
Indirect strategy.


title: gastric tumor tissue, SSH, replicate 7

description:
81T SSH
Indirect strategy.

value: difuse

value: signet-ring cell


title: gastric tumor tissue, SSH, replicate 6

description:
75T SSH
Indirect strategy.

value: poor


title: gastric non-tumoral tissue, SSH, replicate 4

description:
41A SSH
Indirect strategy.

value: adjacent non-tumor


title: TAX577559

value: non malignant

tag: hu subtype

value: Normal

tag: familial status

tag: er

tag: osbin

tag: os

tag: pgr

tag: primary

value: other

tag: pam50 correlation

tag: brca1 methylation status

tag: reference

value: Stratagene Universal reference RNA


title: gastric non-tumoral tissue, SSH, replicate 5

description:
54A SSH
Indirect strategy.

value: F

tag: state

tag: lauren type

value: intestinal

tag: histological subtype

tag: infiltration

tag: differentiation

tag: linfonodes

tag: tissue type

value: SSH followed by conventional microarray

value: reference

value: many normal human tissues


title: WP9C053NO

description: male neonate

source_name: pooled control for WP9C053NO

tag: tissue

value: Human cord blood

tag: gender

value: male

tag: age


title: WP9C054NO

description: female neonate

source_name: pooled control for WP9C054NO

value: female


title: TAX577558

value: Breast tumor

tag: hu subtype

value: LumA

tag: familial status

value: sporadic

tag: er

tag: osbin

tag: grade

tag: brca status

tag: pam50 classification


title: WP9C051NO

description: male neonate

source_name: pooled control for WP9C051NO

value: neonate


title: gastric tumor tissue, SSH, replicate 4

description:
41T SSH
Indirect strategy.

tag: state

value: advanced

value: difuse

value: signet-ring cell

value: serose

value: poor

value: tumor

tag: patient identifier

tag: strategy

tag: sample type


title: TAX577551

tag: os

tag: pgr

tag: primary

value: Normal

tag: pam50 correlation

tag: brca1 methylation status

tag: reference

value: Stratagene Universal reference RNA


title: WP9C050NO

description: male neonate

source_name: pooled control for WP9C050NO

tag: tissue

tag: gender

tag: age


title: gastric tumor tissue, SSH, replicate 5

description:
54T SSH
Indirect strategy.

value: F

tag: lauren type

value: intestinal

tag: histological subtype

value: tubular adenocarcinoma

tag: infiltration

tag: differentiation

value: moderate

tag: linfonodes

tag: tissue type

value: SSH followed by conventional microarray

value: reference


title: gastric tumor tissue, SSH, replicate 2

description:
38T SSH
Indirect strategy.

value: M

tag: state

value: subserose

tag: patient identifier

tag: strategy

value: many normal human tissues


title: gastric tumor tissue, SSH, replicate 3

description:
40T SSH
Indirect strategy.

value: advanced

value: muscularis propria

tag: sample type


title: TAX577537

source_name: Breast tumor

value: Breast tumor

tag: hu subtype

value: nonClassified

tag: familial status

value: sporadic

tag: er

tag: osbin

tag: os

tag: pgr

tag: primary

tag: grade

tag: brca status

tag: pam50 classification

value: Unclassified


title: TAX577534

tag: tissue

value: other

value: LumB

tag: pam50 correlation

tag: brca1 methylation status

tag: reference


title: TAX577540

value: Stratagene Universal reference RNA


title: TAX577533


title: gastric non-tumoral tissue, SSH, replicate 1

description:
17A SSH
Indirect strategy.

tag: gender

tag: age

tag: state

tag: lauren type

value: intestinal

tag: histological subtype

tag: infiltration

value: serose

tag: differentiation

tag: linfonodes

tag: tissue type

value: adjacent non-tumor

tag: patient identifier


title: TAX577532

tag: hu subtype

value: LumA

tag: familial status

tag: er

tag: osbin

tag: os

tag: pgr

tag: primary

tag: grade

value: Normal


title: WP9C049NO

description: male neonate

source_name: pooled control for WP9C049NO

tag: tissue

value: Human cord blood

tag: gender

value: male

tag: age

value: neonate


title: WP9C046NO

description: female neonate

source_name: pooled control for WP9C046NO

value: female


title: gastric non-tumoral tissue, conventional, replicate 11

description:
91A directa
Direct strategy.

value: M

tag: state

value: advanced

tag: lauren type

tag: histological subtype

value: tubular adenocarcinoma

value: subserose

value: moderate

tag: strategy

value: conventional microarray

tag: sample type

value: reference

value: many normal human tissues


title: gastric tumor tissue, conventional, replicate 12

description:
92T directa
Direct strategy.

value: intestinal

tag: infiltration

value: muscularis propria

tag: differentiation

value: poor

tag: linfonodes

tag: tissue type

value: tumor

tag: patient identifier


title: gastric non-tumoral tissue, conventional, replicate 12

description:
92A directa
Direct strategy.

value: adjacent non-tumor


title: WP9C045NO

description: female neonate

source_name: pooled control for WP9C045NO

value: Human cord blood


title: WP9C047NO

description: male neonate

source_name: pooled control for WP9C047NO

value: male


title: gastric tumor tissue, SSH, replicate 1

description:
17T SSH
Indirect strategy.

value: serose

value: SSH followed by conventional microarray


title: TAX577528

value: Breast tumor

tag: hu subtype

value: LumA

tag: familial status

value: sporadic

tag: er

tag: osbin

tag: os

tag: brca status

tag: pam50 classification

value: Unclassified

tag: pam50 correlation

tag: brca1 methylation status

source_name: Stratagene Universal reference RNA

tag: reference

value: Stratagene Universal reference RNA


title: gastric tumor tissue, conventional, replicate 10

description:
90T directa
Direct strategy.

source_name: Human gastric tissue, tumor

tag: gender

value: F

tag: age

tag: state

value: advanced

tag: lauren type

tag: histological subtype

value: tubular adenocarcinoma

value: moderate

tag: strategy

value: conventional microarray

tag: tissue


title: WP9C044NO

description: male neonate

source_name: pooled control for WP9C044NO

value: neonate


title: COPD [261361_mRNA]

city: Seattle

first: Ji-Hoon

last: Cho

state: WA

address: 401 Terry Avenue North

country: USA

institute: Institute for Systems Biology

description: COPD

hyb_protocol: Labeling was performed as described in Agilent protocol

scan_protocol: Hybridized slides were washed and scanned with ScanArray Express (Perkin Elmer)

data_processing: Gene expression data was normalized by quantile method, and transformed in log2-scale

source_name: Lung tissue from smoker with COPD

label_protocol: Samples were prepared for mRNA microarray analysis using Agilent Quick Amp Labeling technologies (Santa Clara, California,USA).

extract_protocol: Total RNA was isolated from frozen tissue samples using a freeze fracture protocol, followed by Trizol extraction and precipitation at  -20ºC overnight to increase the yield of small RNAs. RNA integrity was determined by capillary electrophoresis on an Agilent 2100 Bioanalyzer. Only RNA with an integrity number $7 was used in the profiling studies.

tag: diagnosis

value: COPD

tag: fvc-group

tag: gold stage

tag: gender (1=male, 2=female)

tag: pkyrs


title: TAX577523

tag: hu subtype

value: nonClassified

tag: familial status

tag: er

tag: osbin

tag: os

tag: pgr

tag: primary

tag: grade

tag: brca status


title: gastric non-tumoral tissue, conventional, replicate 10

description:
90A directa
Direct strategy.

source_name: Human gastric tissue, non-tumor

tag: gender

tag: age

tag: state

tag: lauren type

value: intestinal

tag: histological subtype

tag: infiltration

tag: differentiation

tag: linfonodes

tag: tissue type

value: adjacent non-tumor

tag: patient identifier

tag: sample type

value: reference

value: many normal human tissues


title: gastric tumor tissue, conventional, replicate 11

description:
91T directa
Direct strategy.

value: M

value: subserose

value: tumor

tag: strategy

tag: tissue


title: gastric non-tumoral tissue, conventional, replicate 9

description:
89A directa
Direct strategy.

value: difuse

value: signet-ring cell

value: serose

value: poor


title: WP9C041NO

description: female neonate

source_name: pooled control for WP9C041NO

value: Human cord blood

value: female


title: COPD [148362_mRNA]

description: COPD

tag: diagnosis

tag: fvc-group

tag: gold stage

tag: gender (1=male, 2=female)

tag: pkyrs


title: gastric tumor tissue, conventional, replicate 9

description:
89T directa
Direct strategy.

tag: gender

tag: age

value: advanced

value: conventional microarray

source_name: Human Universal Reference RNA (Clontech)


title: COPD [271100_mRNA]

description: COPD

value: COPD


title: WP9C040NO

description: male neonate

source_name: pooled control for WP9C040NO

value: male

value: neonate


title: TAX577520

value: Breast tumor

tag: hu subtype

tag: familial status

value: sporadic

tag: er

tag: osbin

tag: os

tag: pgr

tag: primary

tag: grade

tag: brca status

tag: pam50 classification

tag: pam50 correlation

tag: brca1 methylation status

value: negative

tag: reference

value: Stratagene Universal reference RNA


title: TAX577521

tag: tissue

value: Normal


title: TAX577517

value: nonClassified

value: Unclassified


title: gastric non-tumoral tissue, conventional, replicate 7

description:
81A directa
Direct strategy.

value: M

tag: state

tag: lauren type

value: difuse

tag: histological subtype

value: signet-ring cell

tag: infiltration

tag: differentiation

tag: linfonodes

tag: tissue type

value: adjacent non-tumor

tag: patient identifier

tag: strategy

tag: sample type

value: reference

value: many normal human tissues


title: COPD [20278_mRNA]

description: COPD

tag: diagnosis

tag: fvc-group

tag: gold stage

tag: age

tag: gender (1=male, 2=female)

tag: pkyrs


title: COPD [192758_mRNA]

description: COPD


title: WP9C037NO

description: male neonate

source_name: pooled control for WP9C037NO

tag: tissue

value: Human cord blood

tag: gender


title: TAX577516

tag: hu subtype

tag: familial status

tag: er

tag: osbin

tag: os

tag: pgr

tag: primary

tag: grade

tag: brca status

tag: pam50 classification

tag: pam50 correlation

tag: brca1 methylation status

tag: reference


title: TAX577514

value: LumB

value: familial

value: brcax


title: gastric tumor tissue, conventional, replicate 8

description:
84T directa
Direct strategy.

tag: age

tag: state

value: advanced

tag: lauren type

value: intestinal

tag: histological subtype

value: tubular adenocarcinoma

tag: infiltration

value: serose

tag: differentiation

value: moderate

tag: linfonodes

tag: tissue type

value: tumor

tag: patient identifier

tag: strategy

value: conventional microarray

tag: sample type


title: gastric non-tumoral tissue, conventional, replicate 8

description:
84A directa
Direct strategy.

tag: gender

value: M

tag: tissue


title: WP9C038NO

description: female neonate

source_name: pooled control for WP9C038NO

value: female

value: neonate


title: TAX577513

value: Breast tumor

tag: hu subtype

value: nonClassified

tag: familial status

tag: er

tag: osbin

tag: os

tag: pgr

tag: primary

tag: grade

tag: brca status

tag: pam50 classification

value: Basal

value: negative

value: Stratagene Universal reference RNA


title: gastric tumor tissue, conventional, replicate 7

description:
81T directa
Direct strategy.

tag: age

tag: state

tag: lauren type

value: difuse

tag: histological subtype

value: signet-ring cell

tag: infiltration

tag: differentiation

value: poor

tag: linfonodes

value: reference

value: many normal human tissues


title: TAX577512

tag: tissue

tag: hu subtype

value: LumA

value: familial

value: brcax

value: Normal

tag: pam50 correlation

tag: brca1 methylation status

tag: reference


title: WP9C035NO

description: female neonate

source_name: pooled control for WP9C035NO

value: Human cord blood

tag: gender


title: COPD [234573_mRNA]

description: COPD

tag: diagnosis

value: COPD

tag: fvc-group

tag: gold stage

tag: gender (1=male, 2=female)

tag: pkyrs


title: WP9C033NO

description: male neonate

source_name: pooled control for WP9C033NO

value: male

tag: age

value: neonate


title: COPD [119716_mRNA]

description: COPD


title: WP9C039NO

description: female neonate

source_name: pooled control for WP9C039NO

value: female


title: gastric tumor tissue, conventional, replicate 6

description:
75T directa
Direct strategy.

value: M

tag: state

value: advanced

tag: lauren type

value: intestinal

value: tubular adenocarcinoma

value: serose

tag: tissue type

value: tumor

tag: patient identifier

tag: strategy

value: conventional microarray

tag: sample type


title: COPD [158231_mRNA]

description: COPD


title: gastric non-tumoral tissue, conventional, replicate 5

description:
54A directa
Direct strategy.

value: F

tag: histological subtype

tag: infiltration

tag: differentiation

value: moderate

tag: linfonodes

value: adjacent non-tumor

value: reference

tag: tissue

value: many normal human tissues


title: COPD [220968_mRNA]

description: COPD

tag: diagnosis


title: WP9C034NO

description: male neonate

source_name: pooled control for WP9C034NO

value: Human cord blood

tag: gender


title: gastric non-tumoral tissue, conventional, replicate 6

description:
75A directa
Direct strategy.

value: poor


title: WP9C036NO

description: female neonate

source_name: pooled control for WP9C036NO


title: COPD [271851_mRNA]

description: COPD

value: COPD

tag: fvc-group

tag: gold stage


title: WP9C030NO

description: male neonate

source_name: pooled control for WP9C030NO

value: male

value: neonate


title: gastric tumor tissue, conventional, replicate 5

description:
54T directa
Direct strategy.


title: TAX577509

source_name: Breast tumor

value: Breast tumor

tag: hu subtype

value: nonClassified

tag: familial status

value: familial

tag: er

tag: osbin

tag: os

tag: pgr

tag: primary

tag: grade

tag: brca status

value: brcax

tag: pam50 classification

tag: pam50 correlation

tag: brca1 methylation status

tag: reference

value: Stratagene Universal reference RNA


title: gastric non-tumoral tissue, conventional, replicate 4

description:
41A directa
Direct strategy.

tag: age

tag: state

value: advanced

tag: lauren type

value: difuse

tag: histological subtype

value: signet-ring cell

tag: infiltration

value: serose

tag: differentiation

tag: linfonodes

tag: tissue type

tag: patient identifier

tag: strategy

tag: sample type

tag: tissue


title: TAX577506

tag: hu subtype

value: LumA

tag: familial status

value: sporadic

tag: er

tag: osbin

tag: os

tag: pgr

tag: primary

tag: grade

tag: brca status

source_name: Stratagene Universal reference RNA


title: COPD [270854_mRNA]

description: COPD

tag: diagnosis

tag: fvc-group

tag: gold stage

tag: age

tag: gender (1=male, 2=female)

tag: pkyrs


title: gastric non-tumoral tissue, SSH, replicate 3

description:
40A SSH
Indirect strategy.

tag: gender

value: F

tag: state

tag: lauren type

value: intestinal

tag: histological subtype

value: tubular adenocarcinoma

tag: infiltration

value: muscularis propria

tag: differentiation

value: moderate

tag: linfonodes

tag: tissue type

value: adjacent non-tumor

tag: patient identifier

tag: strategy

value: SSH followed by conventional microarray

tag: sample type

value: reference

value: many normal human tissues


title: COPD [30753_mRNA]

description: COPD

tag: diagnosis

value: COPD


title: WP9C027NO

description: female neonate

source_name: pooled control for WP9C027NO

tag: tissue

value: Human cord blood

value: female

value: neonate


title: TAX577504

value: Breast tumor

tag: hu subtype

tag: familial status

value: familial

tag: er

tag: osbin

tag: os

tag: pgr

tag: primary

tag: grade

tag: brca status

value: brcax

tag: pam50 classification

tag: pam50 correlation

tag: brca1 methylation status

tag: reference

value: Stratagene Universal reference RNA


title: TAX577502

value: LumB

value: sporadic


title: TAX577501

value: other


title: TAX577498


title: WP9C026NO

description: female neonate

source_name: pooled control for WP9C026NO

tag: gender

tag: age


title: WP9C029NO

description: female neonate

source_name: pooled control for WP9C029NO


title: gastric tumor tissue, conventional, replicate 4

description:
41T directa
Direct strategy.

source_name: Human gastric tissue, tumor

value: F

tag: state

value: advanced

tag: lauren type

value: difuse

tag: histological subtype

value: signet-ring cell

tag: infiltration

value: serose

tag: differentiation

value: poor

tag: linfonodes

tag: tissue type

value: tumor

tag: patient identifier

tag: strategy

value: conventional microarray

tag: sample type


title: gastric tumor tissue, conventional, replicate 3

description:
40T directa
Direct strategy.

value: intestinal

value: tubular adenocarcinoma

value: muscularis propria

value: moderate

value: reference

tag: tissue

value: many normal human tissues


title: gastric non-tumoral tissue, conventional, replicate 3

description:
40A directa
Direct strategy.

source_name: Human gastric tissue, non-tumor

value: adjacent non-tumor


title: TAX577507

value: Breast tumor

tag: hu subtype

value: LumA

tag: familial status

value: sporadic

tag: er

tag: osbin

tag: os

tag: pgr

tag: primary

tag: grade

tag: brca status

tag: pam50 classification

value: Stratagene Universal reference RNA


title: COPD [192361_mRNA]

description: COPD

source_name: Lung tissue from smoker with COPD

tag: diagnosis

value: COPD

tag: fvc-group

tag: gold stage

tag: age

tag: gender (1=male, 2=female)

tag: pkyrs


title: COPD [294945_mRNA]

description: COPD


title: WP9C023NO

description: male neonate

source_name: pooled control for WP9C023NO

tag: tissue

value: Human cord blood

tag: gender

value: male

value: neonate


title: COPD [219183_mRNA]

description: COPD


title: WP9C022NO

description: female neonate

source_name: pooled control for WP9C022NO

value: female


title: gastric tumor tissue, conventional, replicate 2

description:
38T directa
Direct strategy.

value: M

tag: state

value: advanced

tag: lauren type

tag: histological subtype

tag: infiltration

value: subserose

tag: differentiation

value: poor

tag: linfonodes

tag: tissue type

value: tumor

tag: patient identifier

tag: strategy

value: conventional microarray

source_name: Human Universal Reference RNA (Clontech)

tag: sample type


title: WP9C024NO

description: female neonate

source_name: pooled control for WP9C024NO


title: COPD [275177_mRNA]

description: COPD

tag: diagnosis

tag: fvc-group


title: gastric non-tumoral tissue, conventional, replicate 2

description:
38A directa
Direct strategy.

tag: age

value: intestinal

value: tubular adenocarcinoma

value: reference

value: many normal human tissues


title: gastric non-tumoral tissue, conventional, replicate 1

description:
17A directa
Direct strategy.

value: serose

value: moderate

value: adjacent non-tumor


title: COPD [126571_mRNA]

description: COPD

value: COPD

tag: gold stage

tag: gender (1=male, 2=female)


title: WP9C020NO

description: female neonate

source_name: pooled control for WP9C020NO

tag: tissue

value: Human cord blood


title: COPD [132625_mRNA]

description: COPD

tag: pkyrs


title: TAX577494

value: Breast tumor

tag: hu subtype

value: Basal

tag: familial status

value: familial

tag: er

tag: osbin

tag: os

tag: pgr

tag: primary

tag: grade

tag: brca status

value: brcax

tag: pam50 classification

tag: pam50 correlation

tag: brca1 methylation status

value: negative

tag: reference

value: Stratagene Universal reference RNA


title: TAX577493

value: sporadic


title: TAX577491

value: nonClassified


title: gastric tumor tissue, conventional, replicate 1

description:
17T directa
Direct strategy.

tag: gender

value: M

tag: age

tag: state

value: advanced

tag: lauren type

value: intestinal

tag: histological subtype

tag: infiltration

tag: differentiation

tag: linfonodes

tag: tissue type

value: tumor

tag: patient identifier

tag: strategy

value: conventional microarray

tag: sample type


title: COPD [295167_mRNA]

description: COPD

tag: diagnosis

tag: fvc-group

tag: gold stage

tag: gender (1=male, 2=female)

tag: pkyrs


title: TAX577489

tag: tissue

tag: hu subtype

tag: familial status

tag: er

tag: osbin

tag: os

tag: pgr

tag: primary

tag: grade

tag: brca status

tag: pam50 classification

value: Unclassified

tag: pam50 correlation

tag: brca1 methylation status

tag: reference


title: COPD [122541_mRNA]

description: COPD

tag: diagnosis

tag: fvc-group

tag: gold stage

tag: age


title: COPD [59320_mRNA]

description: COPD

tag: gender (1=male, 2=female)

tag: pkyrs


title: WP9C018NO

description: female neonate

source_name: pooled control for WP9C018NO

tag: tissue

tag: gender

value: female

value: neonate


title: Lung fibrous lesion-VI

city: Matsumoto

first: Masayuki

last: Hanaoka

state: Nagano

address: Asahi 3-1-1

department: First Department of Medicine

country: Japan

institute: Shinshu University School of Medicine

description:
VI-2
When extracting the differentially expressed genes in the fibrous lesions, the profiling dataset from the emphysematous lesions was used as background

hyb_protocol: 2 μg of total RNA was processed, biotinylated, fragmented, and hybridized to the GeneChip Human Genome U133 Plus 2.0 Array (Affymetrix, Santa Clara, CA, USA). Immediately following hybridization, the probe array underwent an automated washing and staining protocol on the Affymetrix Fluidics Station 450.

scan_protocol: The prepared GeneChips were then scanned using the Affymetrix GeneChip Scanner 3000.

data_processing: The scanned images were analysed with GeneChip Operating Software version 1.4 (Affymetrix 690036) and Microarray Suite version 5.0 (Affymetrix). The profiling dataset from the emphysematous lesions was used as background when extracting the differentially expressed genes in the fibrous lesions, and the data from the fibrous lesions were used as background when extracting the differentially expressed genes in the emphysematous lesions. The trimmed mean target intensity of each array was set to 500. Differentially expressed genes were extracted using DNA Microarray Viewer (Kurabo, Osaka, Japan).

label: biotin

source_name: Fibrous lesion_CPFE patient

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA (Expression Analysis Technical Manual Rev. 5, Affymetrix).

growth_protocol: We profiled six specimens from lung tissues  (three specimens from emphysematous lesions and three specimens from fibrous lesions) obtained from three patients with CPFE. The patients were all male ex-smokers (smoking from 38 to 72 pack years) with primary lung cancer. Pulmonary fibrosis complicated with emphysema was confirmed by high-resolution CT before operation; the fibrotic and emphysematous lesions were located within the resected lobes.

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

treatment_protocol:
Immediately after the lobectomy, the lung tissues with fibrosis and emphysema were separated from the resected lobes, and the lung tissue adjacent to each specimen was cut for histological confirmation of the absence of cancer cells. The pathological types of fibrosis and emphysema were confirmed after hematoxylin and eosin staining by a pathologist who was blinded to the purpose of the study
Lung tissue specimens were immediately frozen in dry ice and stored at -80 °C.

tag: patient id no.

value: VI

tag: nationality

value: Japanese

value: male

tag: disease

value: combined pulmonary fibrosis and emphysema (CPFE)

value: lung


title: Lung emphysematous lesion-VI

description:
VI-1
When extracting the differentially expressed genes in the emphysematous lesions, the data from the fibrous lesions were used as background.

source_name: Emphysematous lesion_CPFE patient


title: TAX577481

value: Breast tumor

tag: hu subtype

value: LumB

tag: familial status

tag: er

tag: osbin

tag: os

tag: pgr

tag: primary

tag: grade


title: Lung emphysematous lesion-V

description:
V-1
When extracting the differentially expressed genes in the emphysematous lesions, the data from the fibrous lesions were used as background.

value: V


title: TAX577482

value: nonClassified

value: sporadic

tag: brca status

tag: pam50 classification

value: Normal

tag: pam50 correlation

tag: brca1 methylation status

value: positive

tag: reference

value: Stratagene Universal reference RNA


title: COPD [12861_mRNA]

description: COPD

tag: diagnosis

value: COPD

tag: fvc-group

tag: gold stage

tag: age

tag: gender (1=male, 2=female)

tag: pkyrs


title: COPD [157421_mRNA]

description: COPD


title: TAX577487

tag: tissue

value: non malignant

tag: hu subtype

tag: familial status

tag: er

value: other


title: Lung fibrous lesion-V

description:
V-2
When extracting the differentially expressed genes in the fibrous lesions, the profiling dataset from the emphysematous lesions was used as background

tag: patient id no.

tag: nationality

tag: gender

tag: disease


title: WP9C013NO

description: female neonate

source_name: pooled control for WP9C013NO

value: Human cord blood

value: female

value: neonate


title: Normal/Smoker [218081_mRNA]

description: Normal

source_name: Lung tissue from smoker with no evidence of obstructive lung disease


title: WP9C019NO

description: female neonate

source_name: pooled control for WP9C019NO


title: Normal/Smoker [290677_mRNA]

description: Normal


title: WP9C016NO

description: female neonate

source_name: pooled control for WP9C016NO


title: TAX577480

source_name: Breast tumor

value: familial

tag: osbin

tag: os

tag: pgr

tag: primary

tag: grade

tag: brca status

value: brcax

tag: pam50 classification

value: Basal

tag: pam50 correlation

source_name: Stratagene Universal reference RNA


title: Lung fibrous lesion-IV

description:
IV-2
When extracting the differentially expressed genes in the fibrous lesions, the profiling dataset from the emphysematous lesions was used as background

value: IV

value: Japanese

value: male

tag: age

value: combined pulmonary fibrosis and emphysema (CPFE)

value: lung


title: WP9C015NO

description: female neonate

source_name: pooled control for WP9C015NO

tag: tissue


title: gastric non-tumoral tissue, SSH, replicate 2

description:
38A SSH
Indirect strategy.

source_name: Human gastric tissue, non-tumor

value: M

tag: state

value: advanced

tag: lauren type

value: intestinal

tag: histological subtype

value: tubular adenocarcinoma

tag: infiltration

value: subserose

tag: differentiation

value: poor

tag: linfonodes

tag: tissue type

value: adjacent non-tumor

tag: patient identifier

tag: strategy

value: SSH followed by conventional microarray

tag: sample type

value: reference

value: many normal human tissues


title: WP9C017NO

description: male neonate

source_name: pooled control for WP9C017NO

value: Human cord blood

tag: gender

value: neonate


title: Normal/Smoker [188486_mRNA]

description: Normal

tag: diagnosis

value: Normal


title: WP9C012NO

description: female neonate

source_name: pooled control for WP9C012NO

value: female


title: TAX577468

value: Breast tumor

tag: hu subtype

value: nonClassified

tag: familial status

value: sporadic

tag: er

tag: osbin

tag: os

tag: pgr

tag: primary

tag: grade

tag: brca status

value: other

tag: brca1 methylation status

tag: reference

value: Stratagene Universal reference RNA


title: TAX577474

tag: tissue

value: LumB

tag: pam50 classification

tag: pam50 correlation


title: TAX577467

value: LumA

value: Unclassified


title: WP9C010NO

description: female neonate

source_name: pooled control for WP9C010NO

tag: age


title: TAX577464


title: Normal/Smoker [290165_mRNA]

description: Normal


title: Normal/Smoker [162039_mRNA]

description: Normal


title: TAX577463

value: negative


title: Lung emphysematous lesion-IV

description:
IV-1
When extracting the differentially expressed genes in the emphysematous lesions, the data from the fibrous lesions were used as background.

tag: patient id no.

value: IV

tag: nationality

value: Japanese

tag: gender

value: male

tag: disease

value: combined pulmonary fibrosis and emphysema (CPFE)

value: lung


title: WP9C006NO

description: female neonate

source_name: pooled control for WP9C006NO

value: Human cord blood

value: neonate


title: TAX577460

tag: hu subtype

tag: familial status

tag: er


title: TAX577459

value: Basal

tag: osbin

tag: os

tag: pgr


title: WP9C009NO

description: male neonate

source_name: pooled control for WP9C009NO


title: Normal/Smoker [24201_mRNA]

description: Normal

tag: diagnosis

value: Normal


title: Normal/Smoker [224671_mRNA]

description: Normal


title: WP9C005NO

description: female neonate

source_name: pooled control for WP9C005NO

value: female


title: WP9C003NO

description: male neonate

source_name: pooled control for WP9C003NO


title: Day: 56. Dose : 80ug. Replicate 8

status: Public on Jun 26 2012

city: Huntington

first: James

last: Denvir

state: WV

address: One John Marshall Drive

department: Biochemistry and Microbiology

institute: Marshall University School of Medicine

hyb_protocol: Hybridized in the presence of 2X Hi-RPM hybrideizationbuffer (Agilent) at 65 C for a7 hours

scan_protocol: Scanned on Agilent scanner model G2505C

data_processing: Agilent Feature Extraction v10 was used for background subtraction and lowess normalization.

organism: Mus musculus

source_name: lung, aspirated with 80µg MWCNT, sacrificed after 56 days

label_protocol: 200 ng of total RNA labeled with QuickAmp labeling kit (Agilent) in the presence of cyadine-3 dCTP or cyadine-5 dCTP (Perkin Elmer)

growth_protocol: Male C57BL/6J mice (7 weeks old) were obtained from Jackson Laboratories, housed one per cage and and carred  for according to AAALAC-accredited, specific pathogen-free environmentally controlled facility. The animals were allowed to aclimate for 5 days before experimental use.

extract_protocol: Mice were euthanized with pentobarbital (100 mg/kg body weight, i.p.) and exsanguinaized by transection of abdominal aorta.  Lungs were removed and immediately placed in tubes containing RNAlater and stored at -80°C until RNA extraction.  Total RNA was extracted using RNeasy Midi kit according to manufacturer's protocol (Qaigen, CA).  RNA quality was determined using OD 260/280 ratio, and RNA with a ratio of >1.9 was used for further analysis.  Also, RNA integrity was analyzed using Agilent 2100 Bioanalyzer according to manufacturer's protocol (Agilent Technologies, CA)

treatment_protocol: MWCNT were obtained form Mitsui & Company, and prepared as previously described (Porter et al. 2010).  Mice were treated with vehicle (control) or MWCNT 10, 20, 40, 80 µg by pharyngeal aspiration.

tag: strain

tag: dose (ug)

tag: time (days)

source_name: Universal Mouse Reference RNA

tag: vendor

value: Statagene

tag: catalog#

value: reference


title: Day: 56. Dose : 80ug. Replicate 4


title: WP9C002NO

description: female neonate

source_name: pooled control for WP9C002NO

tag: tissue

tag: age


title: Day: 56. Dose : 80ug. Replicate 7


title: WP9C004NO

description: female neonate

source_name: pooled control for WP9C004NO


title: Normal/Smoker [80343_mRNA]

description: Normal

source_name: Lung tissue from smoker with no evidence of obstructive lung disease


title: Day: 56. Dose : 80ug. Replicate 1


title: WP9C001NO

description: male neonate

source_name: pooled control for WP9C001NO


title: Day: 56. Dose : 40ug. Replicate 5

source_name: lung, aspirated with 40µg MWCNT, sacrificed after 56 days


title: Day: 56. Dose : 40ug. Replicate 7


title: Day: 56. Dose : 40ug. Replicate 8


title: Day: 56. Dose : 80ug. Replicate 3


title: Day: 56. Dose : 20ug. Replicate 8

source_name: lung, aspirated with 20µg MWCNT, sacrificed after 56 days


title: Day: 56. Dose : 40ug. Replicate 1


title: Day: 56. Dose : 20ug. Replicate 3


title: Day: 56. Dose : 20ug. Replicate 7


title: Day: 56. Dose : 80ug. Replicate 6


title: Day: 56. Dose : 80ug. Replicate 5


title: Normal/Smoker [231005_mRNA]

description: Normal


title: Day: 56. Dose : 20ug. Replicate 5


title: Day: 56. Dose : 40ug. Replicate 4


title: Day: 56. Dose : 20ug. Replicate 4


title: Day: 56. Dose : 40ug. Replicate 3


title: Day: 56. Dose : 80ug. Replicate 2


title: Day: 56. Dose : 40ug. Replicate 6


title: Day: 56. Dose : 40ug. Replicate 2


title: Day: 56. Dose : 20ug. Replicate 6


title: Day: 56. Dose : 20ug. Replicate 2


title: Day: 56. Dose : 20ug. Replicate 1


title: Day: 56. Dose : 10ug. Replicate 8

source_name: lung, aspirated with 10µg MWCNT, sacrificed after 56 days


title: Day: 56. Dose : 10ug. Replicate 7


title: Day: 56. Dose : 10ug. Replicate 6


title: Day: 56. Dose : 10ug. Replicate 1


title: Day: 56. Dose : 10ug. Replicate 2


title: Day: 56. Dose : 10ug. Replicate 4


title: Day: 56. Dose : 10ug. Replicate 3


title: Tongue dorsum scraping_224-01

type: genomic

city: Boston

first: Bruce

middle: J

last: Paster

state: MA

address: 140 Fenway

institute: The Forsyth Institute

description: 16S rRNA genes are PCR amplified from DNA extracts using 16S rRNA universal forward and reverse primers and labeled via incorporation of Cy3-dCTP in a second nested PCR.

hyb_protocol: Prior to hybridization, slides were blocked with sodium borohydride (NaBH4, 1X PBS, 99% ethanol) in order to reduce unreactive aldehyde groups, thus minimizing the fluorescent background.  Fourteen microliter of each labeled and purified PCR sample were mixed with 6 µl of hybridization buffer containing 2X SSC, 0.2 µg/µl yeast tRNA, 0.1% SDS, and heated for 5 minutes at 100oC. After that, 10 µl of each solution were loaded slowly at one corner and under the cover slip, allowing capillary action to pull the solution over the array. Slides were then placed on incubation racks in a humidified chamber, and hybridization was then performed at 55oC for 16 h in a microarray incubator. Slides were removed from the hybridization chamber and sunk into a water bath containing a washing solution (2X SSC, 10%SDS, at 55oC) to remove the cover slips. The slides were washed using an automated microarray robotic instrument. A washing program was set up as follow: one washing in buffer (2X SSC, 10%SDS) at 55oC for 2 minutes, a second washing in 2X SSC buffer at room temperature for 2 minutes, and a final washing in 0.1X SSC buffer at room temperature for 2 minutes. Once the slides are finished spinning in the centrifuge, they were removed and placed in a light-proof container until scanning.

scan_protocol: The microarray slides are scanned using an Axon 4000B scanner and crude data is extracted using GenePix Pro software. Data are normalized by comparing individual signal intensities to the average of signals from universal probes.

data_processing: Individual probe spot net intensity was calculated by subtracting the foreground intensity (F532) with background intensity (B532); intensity was set to 1 if net intensity is <1 or signal to noise ratio (F532/B532) < 2; between-the-array signal normalization was done based on mean universal 16S sequence probe intensities; signals were also scaled to be within the same minimal and maximal intensities range across arrays; normalized and scaled intensities of the same probe sequence were then averaged. The averaged unique probe intensities were then raised to the power of 0.3 and then converted to ordinal numbers on a 0-5 scale, with 0=not detected and 1 to 5 reflect increasing signal strength. For detail analysis procedure see: http://bioinformatics.forsyth.org/homim

molecule: genomic DNA

source_name: Tongue dorsum scraping

label_protocol: Two separate PCR reactions were set up with, respectively, forward primer 5´-CCA GAG TTT GAT YMT GGC-3´ with reverse primer  5´-GAA GGA GGT GWT CCA RCC GCA -3´, and forward primer 5´-GAC TAG AGT TTG ATY MTG GC-3´ with reverse primer 5´-GYT ACC TTG TTA CGA CTT-3´.  Two µl of genomic DNA template were added to the reaction mixture (final volume 25 µl) containing 20 pmol of each primer, 40 nmol  of deoxytriphosphates, 1.5 mM Mg2+ and 1 U of Platinum  High Fidelity Taq polymerase (Invitrogen, San Diego, CA). The samples were preheated at 94°C for 2 min, followed by 32 cycles of amplification under the following conditions: 94°C for 30 s, 55°C for 30 s, and 68°C for 1.5 min, with an additional 1 s for each cycle. A final 10 min elongation step at 68°C was added. The results of the PCR amplification were examined by electrophoresis in a 1% agarose gel. The two parallel PCR reactions were combined and the products purified with QIAquick PCR Purification Kit (Qiagen).Purified PCR products were labeled via the incorporation of Cy3-dCTP during a second reaction. Briefly, 7 μL of each product were added into a 25 μL reaction mixture containing 15 pmol of the forward primer 9F (5`-GAGTTTGATYMTGGCTCAG-3`) , 5 pmol of the 1492R primer , 2.5 μL 10X high fidelity PCR buffer, 2 mM MgSO4, 2.5 μL of deoxynucleotide triphosphate mixture without deoxycytidine triphosphate (10 mM, 0.2 mM final concentration of each deoxynucleotide), 2.5 μL of deoxycytidine triphosphate mixture (1 μL of 1 mM Cy3-dCTP + 4 μL of 2 mM dCTP, 0.2 mM final concentration), 0.25 μL 10% Triton X, and 1.25 U Taq polymerase. The PCR program included an initial denaturation step at 94C for 2 minutes, followed by 40 cycles of denaturation at 94C for 30s, annealing at 55C for 30s, elongation at 68C for 1.5 minute with an additional 1 s for each cycle, and a final elongation step at 68C for 10 minutes.

extract_protocol: DNA was extracted directly from clinical samples. MasterAmp Buccal Swabs© (Epicentre Biotechnologies, Inc) were used to collect epithelial cells and resident microbes, and DNA was extracted utilizing the protocols and reagents provided in the Epicentre MasterAmp© kit.

tag: disease status

value: HIV+ ART-

tag: sample group

value: untreated HIV infected patients


title: Tongue dorsum scraping_226-01

value: HIV- control

value: healthy HIV negative control


title: Tongue dorsum scraping_225-01


title: Day: 56. Dose : 0ug. Replicate 7

source_name: lung, control treated, sacrificed after 56 days

tag: gender


title: Day: 56. Dose : 0ug. Replicate 6


title: Tongue dorsum scraping_223-01


title: Day: 56. Dose : 0ug. Replicate 8


title: Day: 56. Dose : 0ug. Replicate 2


title: Tongue dorsum scraping_221-01


title: Day: 56. Dose : 10ug. Replicate 5


title: Day: 56. Dose : 0ug. Replicate 4


title: Tongue dorsum scraping_217-01


title: Tongue dorsum scraping_218-01


title: Tongue dorsum scraping_219-01

value: HIV+ ART+

value: HIV infected patients receiving antiretroviral therapy


title: Day: 56. Dose : 0ug. Replicate 3


title: Day: 56. Dose : 0ug. Replicate 1


title: Day: 56. Dose : 0ug. Replicate 5


title: Day: 28. Dose : 80ug. Replicate 4

source_name: lung, aspirated with 80µg MWCNT, sacrificed after 28 days


title: Day: 28. Dose : 80ug. Replicate 8


title: Tongue dorsum scraping_228-01


title: Day: 28. Dose : 80ug. Replicate 5


title: Tongue dorsum scraping_215-01


title: Tongue dorsum scraping_222-01


title: Day: 28. Dose : 80ug. Replicate 7


title: Tongue dorsum scraping_214-01


title: Day: 28. Dose : 80ug. Replicate 6


title: Tongue dorsum scraping_213-01


title: Day: 28. Dose : 80ug. Replicate 3


title: Day: 28. Dose : 40ug. Replicate 8

source_name: lung, aspirated with 40µg MWCNT, sacrificed after 28 days


title: Day: 28. Dose : 80ug. Replicate 2


title: Tongue dorsum scraping_212-01


title: Day: 28. Dose : 80ug. Replicate 1


title: Day: 28. Dose : 40ug. Replicate 6


title: Day: 28. Dose : 40ug. Replicate 7


title: Day: 28. Dose : 40ug. Replicate 5


title: Arsenite-transformed human prostate epithelial cells, CAsE-PE_33wk, miRNA

city: Tucson

first: Paul

last: Severson

state: AZ

address: 1515 N Campbell Ave

department: Pharmacology and Toxicology

institute: University of Arizona

hyb_protocol: Combined Cy3- and Cy5-labeled samples were vacuum concentrated to volume of 91.5 µl. 12.5 µl of human Cot-1 DNA (1µg/µl, Invitrogen Cat. No. 15279-011), 26 µl of Agilent blocking agent (10x) and 130 µl of Agilent hybridization buffer (2x) were added. Samples were heated for 3 min at 95 oC, transferred to 37 oC, incubated for 30 min, and then used for microarray hybridization for 28h at 65 oC. After hybridization, slides were washed in Agilent Oligo aCGH/ChIP-on-Chip Wash Buffer 1 for 5 min at room temperature, then in Agilent Oligo aCGH/ChIP-on-Chip Wash Buffer 2 for 5 min at 37 oC, washed in acetronitrile for 10 s at room temperature and finally in stabilization and drying solution for 30 s at room temperature.

scan_protocol: Slides were scanned using an Axon GenePix 4000B microarray scanner (Axon Instruments, Inc., Foster City, CA, USA) and GenePix 6.0 software at 5 µm resolution and PMT settings 750 (635nm) and 600 (532nm).

data_processing: Output from GenePix (*.gpr files) were imported to R using the limma package. Individual channels were first spatially normalized within arrays using ma2D function from the package marray and then loess normalized between arrays using the function normalize.loess from package affy. The RG object was transformed to an MA object and M values were again loess normalized between arrays.

source_name: Arsenite-transformed human prostate epithelial cells, immunoprecipitated DNA

label_protocol: DNA amplification was based on random prime synthesis using the BioPrime DNA Labeling System (Invitrogen, Carlsbad, CA). The DNA sample or equivalent amount of input in a total volume of 21 ul was mixed with 20 ul of 2.5x Random Primers Solution, denatured by heating for 5 min at 95 C in a thermal cycler, and cooled on ice for 5 min. 5 ul of 10x dUTP Nucleotide Mix, 3 ul of 1 mM dTTP and 1 ul of Exo-Klenow Fragment, were added and incubated at 37 C for 20 h. Amplified DNA was purified using a QIAquick PCR purification kit (Qiagen, Valencia, CA) and quantified on a ND-1000 spectrophotometer (Nanodrop Technologies, Wilmington, DE). The typical yield was 4-5 ug of amplified DNA per 50 ul reaction. Equal amounts (2 ug) of amplified immunoprecipitated and input DNA were labeled using the BioPrime DNA Labeling System (Invitrogen) with Cy3 or Cy5 dyes, respectively. DNA in a volume of 42 ul was mixed with 40 ul 2.5x Random Primers Solution, denatured by heating for 5 min at 95 C in a thermal cycler, and cooled on ice for 5 min. 10 ul of 10x dUTP Nucleotide Mix, 4 ul of 1 mM dTTP, 2 ul of Cy3- or Cy5-dUTP (1mM) (GE Healthcare, Piscataway, NJ, USA) and 2 ul of Exo-Klenow Fragment were added and the mixture was incubated for 20 h at 37 C. Labeled targets were purified using the QIAquick PCR purification kit (Qiagen). The efficiency of labeling was determined using ND-1000 spectrophotometer (Nanodrop Technologies).

growth_protocol: PrEC cells were cultured in PrEBM with added BulletKit. RWPE-1 and its arsenite-transformed descendent cell lines were cultured in K-SFM with 50 µg/mL BPE, 5 ng/mL EGF, and 1% vol/vol antibiotic-antimycotic solution.

extract_protocol:
Extraction: Genomic DNA was extracted using the DNeasy Blood and Tissue Kit (Qiagen). 5 μg of RNase-treated DNA was dried under vacuum and resuspended with 50 μl SDS lysis buffer (1% SDS, 10mM EDTA, 50mM Tris-HCl, pH 8.1) and 450 μl of ChIP dilution buffer (0.01% SDS, 1.1% Triton X-100, 1.2mM EDTA, 16.7mM Tris-HCl, pH 8.1, 167mM NaCl). Vortex for ~20 minutes to fully resuspend the DNA. Sonicate the samples 5x for 10 seconds (5 times total) at 8 watts. Make sure that most of the DNA is between 300-600 bp long. Set aside 50 μl of sample in a new microfuge tube - Input DNA.
Immunoprecipitation: Denature both the sample and input DNA in a heatblock set at 100 °C for 10 minutes. Cool down on ice. When cold, add 2 μl of anti-methylcytosine (5MeC) antibody to sample DNA. Rotate tubes overnight at 4°C. Next day add 90 ul of Pro-A sepharose slurry (Pharmacia) to each tube. Rotate at 4 C for 1hr. Transfer samples and beads to a Handee spin cup column with paper filter (Pierce). Spin samples for ~10 seconds in a picofuge to remove the buffer. Wash beads for 5 min at 4 C with 400 ul each of the following buffers: low salt buffer (0.1% SDS, 1% Triton X100, 2mM EDTA, 20mM Tris-HCl, pH 8.1, 150mM NaCl), high salt buffer (0.1% SDS, 1% Triton X100, 2mM EDTA, 20mM Tris-HCl, pH 8.1, 500mM NaCl), LiCl buffer (0.25M LiCl, 1% NP40, 1% deoxycholate, 1mM EDTA, 10mM Tris-HCl, pH 8.1), wash twice with TE (10mM Tris-HCl, 1mM EDTA, pH 8.0). After each wash, spin columns in picofuge for 10 s. After the final TE wash, elute the DNA from the beads by adding 250 ul of pre-warmed (60°C) QG buffer (Qiagen Quick Spin Kit). Incubate the spin column with the QG buffer in a heat block set at 100oC for 5 min. Gently vortex the samples for 5 min at RT. Spin the sample for ~10 seconds in a picofuge and transfer the eluate to a clean 1.5 ml microfuge tube. Repeat the elution step. Add 450 μl of prewarmed QG buffer to the input DNA, incubate for 5 minutes at 100 °C, shake for 5 min. at RT, and spin in a picofuge. Add 150 μl of isopropanol to 500 μl of eluate or diluted input. Put the samples in a QIAquick column and spin for 1 minute at maximum speed. Wash with 750 ul PE buffer. Elute twice with 30 ul of PCR H2O. Vacuum concentrate.

tag: cell line

tag: cell type

value: prostate

tag: treatment

value: 33 weeks 5µM sodium arsenite

tag: phenotype

value: malignant

tag: medip antibody

value: anti-methylcytosine

tag: antibody vendor

value: Diagenode

tag: antibody catalog #

tag: antibody lot#

source_name: Arsenite-transformed human prostate epithelial cells, input DNA


title: Day: 28. Dose : 40ug. Replicate 1

tag: strain

value: male

tag: dose (ug)


title: Day: 28. Dose : 40ug. Replicate 3

tag: time (days)

tag: vendor


title: Day: 28. Dose : 20ug. Replicate 8

source_name: lung, aspirated with 20µg MWCNT, sacrificed after 28 days

tag: catalog#


title: MKN28 Cells: Vector vs ZIC1 Transfected

city: Hangzhou

first: Jing

last: Zhong

address: Second Affiliated Hospital, School of Medicine Zhejiang University

country: China

hyb_protocol: 875ng of each Cy3-cRNA and Cy5-cRNA, 11µl of 10×Blocking Agent, 2.2 µl of 25×Fragmentation Buffer with 55µl of 2×GEx Hybridization Buffer.cRNA from Fragmentation Mix and 2x GE Hybridization Buffer HI-RPM were added and samples were applied to microarrays enclosed in hybridization chamber (Agilent G2534A) at 65°C for 17 hours. After hybridization, slides were washed sequentially.

scan_protocol: Scanned on an Agilent G2565BA scanner.

data_processing: The scanned images were analyzed with Agilent Feature Extraction. LOWESS was used for normalization.

source_name: MKN28 Cells: ZIC1 Transfected

label_protocol: 4 µg of purified RNA were primed with 10 µl DMSO, 3.4µl of 0.3M NaHCO3, then mixed with Cy3 or Cy5 at 25°C for 1 h, and 9µl 4M Hydroxylamine at 25°C for 15 min.

growth_protocol: MKN28 gastric cancer cell lines were cultured in RPMI 1640 medium (Invitrogen, CA, USA) supplemented with 10% fetal bovine serum (FBS) and incubated at 5％ CO2, 37℃ and 95% humidity.

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

tag: tissue

value: stomach

value: gastric cancer

tag: tumor stage

value: high degree differentiation

source_name: MKN28 Cells: Vector Transfected


title: Tongue dorsum scraping_207-01

tag: disease status

tag: sample group


title: Day: 28. Dose : 40ug. Replicate 4

tag: gender

source_name: Universal Mouse Reference RNA

value: Statagene


title: Tongue dorsum scraping_208-01


title: Arsenite-transformed human prostate epithelial cells, CAsE-PE_30wk, miRNA

tag: cell line

tag: cell type

value: 30 weeks 5µM sodium arsenite


title: Immortalized human prostate epithelial cells, RWPE-1_p29, miRNA

source_name: Immortalized human prostate epithelial cells, immunoprecipitated DNA

tag: treatment

tag: phenotype

value: immortal

source_name: Immortalized human prostate epithelial cells, input DNA


title: Tongue dorsum scraping_204-01


title: Tongue dorsum scraping_206-01


title: Tongue dorsum scraping_205-01


title: Tongue dorsum scraping_166-03


title: Normal human prostate epithelial cells, PrEC_p3, miRNA

source_name: Human prostate epithelial cells, immunoprecipitated DNA

value: PrEC

value: normal

tag: medip antibody

tag: antibody vendor

source_name: Human prostate epithelial cells, input DNA


title: Normal human prostate epithelial cells, PrEC_p4, miRNA

tag: antibody catalog #

tag: antibody lot#


title: Immortalized human prostate epithelial cells, RWPE-1_p17, miRNA


title: Day: 28. Dose : 20ug. Replicate 6

tag: strain

tag: dose (ug)

value: reference


title: Day: 28. Dose : 40ug. Replicate 2

tag: time (days)

tag: vendor


title: Day: 28. Dose : 20ug. Replicate 2

tag: catalog#


title: Day: 28. Dose : 20ug. Replicate 7


title: Day: 28. Dose : 20ug. Replicate 5


title: Day: 28. Dose : 20ug. Replicate 1


title: Day: 28. Dose : 20ug. Replicate 3


title: Day: 28. Dose : 10ug. Replicate 7

source_name: lung, aspirated with 10µg MWCNT, sacrificed after 28 days


title: Tongue dorsum scraping_158-03

value: HIV+ ART+


title: Day: 28. Dose : 10ug. Replicate 8


title: Day: 28. Dose : 20ug. Replicate 4


title: Day: 28. Dose : 10ug. Replicate 4


title: Day: 28. Dose : 10ug. Replicate 6


title: Day: 28. Dose : 0ug. Replicate 6

source_name: lung, control treated, sacrificed after 28 days


title: Day: 28. Dose : 10ug. Replicate 3


title: Day: 28. Dose : 10ug. Replicate 5


title: Day: 28. Dose : 0ug. Replicate 2


title: Day: 28. Dose : 0ug. Replicate 7


title: Day: 28. Dose : 10ug. Replicate 1


title: Day: 28. Dose : 0ug. Replicate 3


title: Day: 28. Dose : 10ug. Replicate 2


title: Leaf_4w_50 mM NaCl+2.5 mM HCO3-_rep2

city: Melbourne

first: Muhammad

last: Javid

state: Victoria

address: Building 142, cnr Tin Alley, Parkville

department: Agriculture and Food Systems

country: Australia

institute: The University of Melbourne

description:
US22520_006
Gene expression after 4weeks in 50 mM NaCl and 2.5 mMHCO3- combined treatment-Brassica juncea leaf

hyb_protocol: The fragmented Cy3 labelled cRNA was then prepared for hybridisation to the Agilent 4x44k custom eArrays using the GX hybridisation kit (Agilent – 5188-5242) where each hybridisation reaction had a final volume of 70ul.  The Agilent hybridisation chambers were prepared according to manufacturer’s instructions.  Each sample was loaded on to the Agilent hybridisation gaskets slide which is placed into a hybridisation chamber.  The 4x44k eArray slide was carefully lowered onto the gasket to create a sealed array for each sample.  The hybridisation chambers were then placed in a rotating hybridisation oven at 65C for 17 hours.

scan_protocol: After hybridization, the chip was washed using the appropriate protocols as outlined in the Agilent manual using the GX washing buffers (Agilent – 5188-5327).  Upon completion of the washing, the chips are then scanned in the Agilent DNA Microarray Scanner (High Resolution).  The scanner operating software, Agilent Scan Control, converts the signal on the array into a TIFF file for subsequent analysis.

data_processing: The data was then extracted using Agilent Feature Extraction 10.5.1.1. and the protocol GE1-v5_10_Apr08

organism: Brassica juncea

source_name: Leaf_4wks_50mM NaCl+2.5mM HCO3- combined treatment

label_protocol: A total of 1ug was labelled using the Ambion Total Prep RNA amplification kit (Applied Biosystems - AMIL1791).  The quantity of amplified product was ascertained using the Agilent Bioanalyser 2100 using the NanoChip protocol.  For the Agilent 4x44k chip format, 1600ng of amplified cRNA was used for the Cy3 coupling process using an ULS labelling kit (Kreatech EA-006).  After coupling the dye, the reaction was cleaned using the KREApure columns in the kit.  The Cy3 labelled cRNA samples were then fragmented using the Ambion fragmentation kit (Applied Biosystems – AM8740).

growth_protocol: Brassica juncea genotype NDR8501 was hydroponically grown on modified Hoagland solution. The experiment was conducted in an evaporatively cooled glasshouse with a photosynthetic photon flux density of 500-700 μmol-m-2 s-1 at 22/16oC under a 16/8 h light/dark cycle during March-April, 2010.

extract_protocol: Total RNA was extracted using the RNAeasy plant kit (Qiagen, USA) following the manufacturer’s instructions.

treatment_protocol: Following the method of Javid et al. (submitted) with some modifications, one-week-old seedlings of NDR 8501 were grown in a slightly acidic control solution (pH 6.0). Then Salinity treatment (50 mM NaCl) was applied in two split doses to avoid osmotic shock. For the alkaline salinity treatment, the nutrient solution was buffered with 2.5 mM bicarbonate (HCO3-) followed by two split doses of 50 mM NaCl on two consecutive days. Solutions were aerated constantly and changed on every third day to avoid nutrient deficiency and pH fluctuation till four weeks of treatment. The middle fully expanded leaves from single stressed and non-stressed plants observed for physiological responses were collected, immediately snap frozen in liquid N2 and stored at -80C until RNA extraction. The entire experiment was conducted in three biological replications.

tag: genotype/variation

tag: tissues

value: Leaf

tag: age

value: 5 weeks

tag: treated with

value: 50mM NaCl + 2.5mM HCO3- for 4 wks


title: Day: 28. Dose : 0ug. Replicate 5

tag: gender


title: Day: 28. Dose : 0ug. Replicate 4


title: Day: 28. Dose : 0ug. Replicate 8


title: Leaf_4w_0_Control_rep3

description:
US22520_009
Gene expression after 4weeks in control (0) treatment-Brassica juncea leaf

source_name: Leaf_4wks_no treatment


title: PBS Mouse 2

city: Bilthoven

first: Mirjam

middle: M

last: Schaap

address: Antonie van Leeuwenhoeklaan 9

institute: RIVM

description: quality control: approved

hyb_protocol: According to the protocol provided with the Affymetrix 3'IVT Express Labeling Kit  According to the protocol provided with the Affymetrix 3'IVT Express Labeling Kit (#901229)

scan_protocol: According to Affymetrix protocols, using a GeneChip HT Array Plate Scanner (Affymetrix)

data_processing: The raw data were subjected to a set of quality control checks. After passing array quality control, the arrays were annotated according to de Leeuw et al. (2008) and expression values were calculated using the robust multi-array average (RMA) algorithm (Affy package, version 1.22.0; Irizarry et al. 2003) available from the Bioconductor project (http://www.bioconductor.org) for the R statistical language (http://cran.r-project.org)). The normalized data was statistically analyzed for differential gene expression using a mixed linear model with coefficients for block (random) and each experimental group (fixed) (Smyth 2004; Wolfinger et al. 2001). A contrast analysis was applied to compare each exposure with the corresponding vehicle control. For hypothesis testing, a permutation-based Fs test was used (Cui et al. 2005). False discovery rate (FDR) correction was performed globally across all contrasts according to Storey and Tibshirani (2003). Only the annotated genes were used for further analysis.

source_name: Primary mouse hepatocytes Mouse #2

label_protocol: Biotins labeled cRNA samples were prepared as described in the Affymetrix GeneChip HT 3” IVT Express Technical Manual (Affymetrix) using 200 ng of purified total RNA as template for the reaction.

growth_protocol: Primary mouse hepatocytes were isolated from 8-10 weeks old male C57BL/6 mice by a modified two-step collagenase perfusion technique. Cells were cultured in a sandwich configuration in 6-wells  at 1.3 x 106 cells per well.

extract_protocol: RNA was extracted using QIAzol and purified using the miRNeasy mini kit and the QIAcube (Qiagen), according to the manufacturer’s protocol.

treatment_protocol: Hepatocytes were exposed for 24 hours to the 16 non-genotoxic carcinogens. Control cells were vehicle-treated (DMSO or PBS, 0.5%). After 24 hours of exposure, cells were collected in 1 ml RNAprotect (QIAgen) and stored at -80˚C for RNA isolation.

value: Male

value: 8-9 weeks

tag: exposure


title: Day: 28. Dose : 0ug. Replicate 1


title: Leaf_4w_50mM NaCl_rep1

description:
US22520_003
Gene expression after 4weeks in 50 mM NaCl treatment-Brassica juncea leaf

source_name: Leaf_4wks_50mM NaCl treatment

value: 50mM NaCl for 4 wks


title: Day: 7. Dose : 80ug. Replicate 5

source_name: lung, aspirated with 80µg MWCNT, sacrificed after 7 days

value: male


title: Day: 7. Dose : 80ug. Replicate 6


title: 30 μM HCE Mouse 2

description: quality control: approved

value: 30 μM HCE


title: Day: 7. Dose : 80ug. Replicate 8


title: Day: 7. Dose : 80ug. Replicate 7


title: Day: 7. Dose : 80ug. Replicate 2


title: 1 μM CSA Mouse 2

description: quality control: approved

value: 1 μM CSA


title: Day: 7. Dose : 80ug. Replicate 4


title: 100 μM WY Mouse 2

description: quality control: approved

value: 100 μM WY


title: Leaf_4w_50mM NaCl_rep3

description:
US22520_007
Gene expression after 4weeks in 50 mM NaCl treatment-Brassica juncea leaf


title: Leaf_4w_50 mM NaCl+2.5 mM HCO3-_rep3

description:
US22520_008
Gene expression after 4weeks in 50 mM NaCl and 2.5 mMHCO3- combined treatment-Brassica juncea leaf


title: Day: 7. Dose : 80ug. Replicate 1

value: Statagene


title: Leaf_4w_0_Control_rep1

description:
US22520_001
Gene expression after 4weeks in control (0) treatment-Brassica juncea leaf


title: Day: 7. Dose : 40ug. Replicate 6

source_name: lung, aspirated with 40µg MWCNT, sacrificed after 7 days


title: 10 nM TCDD Mouse 2

description: quality control: approved

value: 10 nM TCDD


title: Day: 7. Dose : 40ug. Replicate 8


title: Leaf_4w_50mM NaCl_rep2

description:
US22520_004
Gene expression after 4weeks in 50 mM NaCl treatment-Brassica juncea leaf


title: Day: 7. Dose : 40ug. Replicate 7


title: Day: 7. Dose : 80ug. Replicate 3


title: Day: 7. Dose : 40ug. Replicate 5


title: 30 μM ARO Mouse 2

description: quality control: approved

value: 30 μM ARO


title: Day: 7. Dose : 40ug. Replicate 4


title: Leaf_4w_0_Control_rep2

description:
US22520_005
Gene expression after 4weeks in control (0) treatment-Brassica juncea leaf


title: Leaf_4w_50 mM NaCl+2.5 mM HCO3-_rep1

description:
US22520_002
Gene expression after 4weeks in 50 mM NaCl and 2.5 mMHCO3- combined treatment-Brassica juncea leaf


title: Day: 7. Dose : 20ug. Replicate 8

source_name: lung, aspirated with 20µg MWCNT, sacrificed after 7 days


title: Day: 7. Dose : 40ug. Replicate 1


title: Day: 7. Dose : 20ug. Replicate 5


title: Day: 7. Dose : 20ug. Replicate 6


title: Day: 7. Dose : 40ug. Replicate 2


title: 1 nM OA Mouse 2

description: quality control: approved

value: 1 nM OA


title: Day: 7. Dose : 20ug. Replicate 2


title: Day: 7. Dose : 20ug. Replicate 1


title: 10 μM LAC Mouse 2

description: quality control: approved

value: 10 μM LAC


title: DMSO Mouse 2

description: quality control: approved

value: 0.5 % DMSO


title: Day: 7. Dose : 20ug. Replicate 4

value: reference


title: 1 mM PB Mouse 2

description: quality control: approved

value: 1 mM PB


title: 30 μM FK506 Mouse 2

description: quality control: approved


title: 1 mM CF Mouse 2

description: quality control: approved

value: 1 mM CF


title: Day: 7. Dose : 40ug. Replicate 3


title: Day: 7. Dose : 20ug. Replicate 7


title: 300 μM CT Mouse 2

description: quality control: approved

value: 300 μM CT


title: Day: 7. Dose : 20ug. Replicate 3


title: Day: 7. Dose : 10ug. Replicate 7

source_name: lung, aspirated with 10µg MWCNT, sacrificed after 7 days


title: Day: 7. Dose : 10ug. Replicate 5


title: Day: 7. Dose : 10ug. Replicate 8


title: 10 μM TCPOBOP Mouse 2

description: quality control: approved

value: Male

value: 10 μM TCPOBOP


title: MNU-transformed human prostate epithelial cells, WPE1-NB26, slide 1

hyb_protocol: Labeled MeDIPs (n=2) and labeled inputs (n=2) were all combined. This pool of the 4 labeling reactions was divided into two equal parts and each was vacuum concentrated to volume of 187.5 µl. 12.5 µl of human Cot-1 DNA (1µg/µl, Invitrogen Cat. No. 15279-011), 50 µl of Agilent blocking agent (10x) and 250 µl of Agilent hybridization buffer (2x) were added to each half. Samples were heated for 3 min at 95 oC, transferred to 37 oC, incubated for 30 min, and then one of the halves was used for microarray hybridization (1 slide of a 2 slide array) for 28h at 65 oC. After hybridization, slides were washed in Agilent Oligo aCGH/ChIP-on-Chip Wash Buffer 1 for 5 min at room temperature, then in Agilent Oligo aCGH/ChIP-on-Chip Wash Buffer 2 for 5 min at 37 oC, washed in acetronitrile for 10 s at room temperature and finally in stabilization and drying solution for 30 s at room temperature.

source_name: Toxicant-transformed human prostate epithelial cells, immunoprecipitated DNA

label_protocol: DNA amplification was based on random prime synthesis using the BioPrime DNA Labeling System (Invitrogen, Carlsbad, CA). The DNA sample or equivalent amount of input in a total volume of 21 ul was mixed with 20 ul of 2.5x Random Primers Solution, denatured by heating for 5 min at 95 C in a thermal cycler, and cooled on ice for 5 min. 5 ul of 10x dUTP Nucleotide Mix, 3 ul of 1 mM dTTP and 1 ul of Exo-Klenow Fragment, were added and incubated at 37 C for 20 h. Amplified DNA was purified using a QIAquick PCR purification kit (Qiagen, Valencia, CA) and quantified on a ND-1000 spectrophotometer (Nanodrop Technologies, Wilmington, DE). The typical yield was 4-5 ug of amplified DNA per 50 ul reaction. Equal amounts (2 ug) of amplified immunoprecipitated and input DNA were labeled in duplicate using the BioPrime DNA Labeling System (Invitrogen) with Cy3 or Cy5 dyes, respectively. For each reaction, DNA in a volume of 42 ul was mixed with 40 ul 2.5x Random Primers Solution, denatured by heating for 5 min at 95 C in a thermal cycler, and cooled on ice for 5 min. 10 ul of 10x dUTP Nucleotide Mix, 4 ul of 1 mM dTTP, 2 ul of Cy3- or Cy5-dUTP (1mM) (GE Healthcare, Piscataway, NJ, USA) and 2 ul of Exo-Klenow Fragment were added and the mixture was incubated for 20 h at 37 C. Labeled targets were purified using the QIAquick PCR purification kit (Qiagen). The efficiency of labeling was determined using ND-1000 spectrophotometer (Nanodrop Technologies).

growth_protocol: HUC cells were cultured in Urothelial Cell Medium. UROtsa cells and each of their toxicant-transformed descendants were cultured in DMEM supplemented with 5% FBS, 100 units/ml penicillin and 50 μg/ml streptomycin. BFTC cell lines were cultured in DMEM supplemented with 10% FBS, 100 units/ml penicillin and 50 μg/ml streptomycin. Nucleic acids from bladder tumor specimens were purchased from Origene Technologies. PrEC cells were cultured in PrEBM with added BulletKit. RWPE-1 and its toxicant-transformed descendent cell lines were cultured in K-SFM with 50 µg/mL BPE, 5 ng/mL EGF, and 1% vol/vol antibiotic-antimycotic solution. The prostate cancer cell lines PC3, LNCaP and DU145 were cultured in IMDM, RMPI-1640 and IMDM, respectively, with 10% FBS and 1% vol/vol antibiotic-antimycotic solution.

treatment_protocol: Toxicant exposures are described in the characteristics section. The monomethylarsonous acid, sodium arsenite and cadmium chloride exposures were continuous. The MNU exposure was for 1 hour at a time, after which cells were given fresh media and grown to confluence. This exposure, wash and growth cycle was repeated three more times.

tag: cell line

tag: cell type

value: prostate

tag: treatment

value: 4 cycles of 1 hour 100µg/mL N-methyl-N-nitrosourea

value: malignant

value: anti-methylcytosine

value: Diagenode

source_name: Toxicant-transformed human prostate epithelial cells, input DNA


title: 1 nM CA Mouse 2

description: quality control: approved

value: 8-9 weeks

value: 1 nM CA


title: Day: 7. Dose : 10ug. Replicate 6

value: male

source_name: Universal Mouse Reference RNA

value: Statagene


title: Arsenite-transformed human prostate epithelial cells, CAsE-PE_33wk, slide 1

value: 33 weeks 5µM sodium arsenite

tag: phenotype

tag: medip antibody

tag: antibody vendor


title: Cadmium-transformed human prostate epithelial cells, CTPE, slide 1

description: CTPE

value: 10 weeks 10µM cadmium chloride

tag: antibody catalog #

tag: antibody lot#


title: Prostate carcinoma cell line, DU145, slide 1

source_name: Prostate carcinoma cell line, immunoprecipitated DNA

source_name: Prostate carcinoma cell line, input DNA


title: Day: 7. Dose : 10ug. Replicate 2

tag: strain

tag: dose (ug)

tag: time (days)

value: reference


title: Day: 7. Dose : 10ug. Replicate 4

tag: vendor

tag: catalog#


title: 3 μM SAR Mouse 2

description: quality control: approved

tag: age

value: 3 μM SAR


title: Prostate adenocarcinoma cell line, PC3, slide 1

source_name: Prostate adenocarcinoma cell line, immunoprecipitated DNA

source_name: Prostate adenocarcinoma cell line, input DNA


title: 1 mM TCE Mouse 2

description: quality control: approved

value: 1 mM TCE


title: Arsenite-transformed human prostate epithelial cells, CAsE-PE_30wk, slide 1

value: 30 weeks 5µM sodium arsenite


title: Day: 7. Dose : 10ug. Replicate 3


title: Immortalized human prostate epithelial cells, RWPE-1_p29, slide 1

source_name: Immortalized human prostate epithelial cells, immunoprecipitated DNA

value: immortal

source_name: Immortalized human prostate epithelial cells, input DNA


title: 100 μM HCH Mouse 2

description: quality control: approved

value: Male

value: 100 μM HCH


title: Day: 7. Dose : 0ug. Replicate 7

source_name: lung, control treated, sacrificed after 7 days


title: Day: 7. Dose : 10ug. Replicate 1


title: Day: 7. Dose : 0ug. Replicate 8


title: Day: 7. Dose : 0ug. Replicate 6


title: Day: 7. Dose : 0ug. Replicate 5


title: Normal human prostate epithelial cells, PrEC_p4, slide 1

source_name: Human prostate epithelial cells, immunoprecipitated DNA

value: PrEC

value: prostate

value: normal

source_name: Human prostate epithelial cells, input DNA


title: 30 μM FK506 Mouse 1

description: quality control: approved

source_name: Primary mouse hepatocytes Mouse #1


title: 1 mM CF Mouse 1

description: quality control: approved

value: 1 mM CF


title: Day: 7. Dose : 0ug. Replicate 4


title: Day: 7. Dose : 0ug. Replicate 3


title: Bladder tumor specimen CD564409, slide 1

source_name: Bladder tumor specimen, immunoprecipitated DNA

tag: tissue

value: bladder tumor

value: urinary bladder

value: malignant

value: anti-methylcytosine

value: Diagenode

source_name: Bladder tumor specimen, input DNA


title: 1 nM OA Mouse 1

description: quality control: approved

tag: gender

value: 8-9 weeks

value: 1 nM OA


title: 100 μM HCH Mouse 1

description: quality control: approved

tag: exposure


title: Day: 7. Dose : 0ug. Replicate 1

value: male

value: Statagene

value: reference


title: Normal human prostate epithelial cells, PrEC_p3, slide 1

tag: cell line


title: Day: 1. Dose : 80ug. Replicate 6

source_name: lung, aspirated with 80µg MWCNT, sacrificed after 1 day


title: 30 μM HCE Mouse 1

description: quality control: approved

value: 30 μM HCE


title: Day: 1. Dose : 80ug. Replicate 7


title: Day: 1. Dose : 80ug. Replicate 8


title: Immortalized human prostate epithelial cells, RWPE-1_p17, slide 1

tag: cell type

value: immortal


title: Bladder tumor specimen CD564293, slide 1

tag: treatment


title: Day: 1. Dose : 80ug. Replicate 5


title: Day: 1. Dose : 80ug. Replicate 4


title: Bladder tumor specimen CD564450, slide 1

tag: phenotype


title: PBS Mouse 1

description: quality control: approved

value: Male


title: Bladder tumor specimen CD565095, slide 1

tag: medip antibody


title: Prostate carcinoma cell line, LNCaP, slide 1

description: LNCaP

value: LNCaP

tag: antibody vendor


title: Day: 1. Dose : 80ug. Replicate 3


title: 1 mM TCE Mouse 1

description: quality control: approved

value: 1 mM TCE


title: Day: 1. Dose : 80ug. Replicate 1


title: Day: 1. Dose : 80ug. Replicate 2


title: Blackfoot urothelial carcinoma cell line 909, slide 1

source_name: Urothelial carcinoma cell line, immunoprecipitated DNA

tag: antibody catalog #

source_name: Urothelial carcinoma cell line, input DNA


title: Day: 1. Dose : 40ug. Replicate 8

source_name: lung, aspirated with 40µg MWCNT, sacrificed after 1 day


title: Blackfoot urothelial carcinoma cell line 905, slide 1

tag: antibody lot#


title: Cadmium-transformed human urothelial cells, URO-CDSC, slide 1

description: URO-CDSC

source_name: Toxicant-transformed human urothelial cells, immunoprecipitated DNA

value: UROtsa

value: ureter

value: 52 weeks 1µM cadmium chloride

source_name: Toxicant-transformed human urothelial cells, input DNA


title: 30 μM ARO Mouse 1

description: quality control: approved

tag: strain

value: 30 μM ARO


title: Day: 1. Dose : 40ug. Replicate 5

tag: dose (ug)

source_name: Universal Mouse Reference RNA


title: Day: 1. Dose : 40ug. Replicate 4

tag: time (days)


title: Bladder tumor specimen CD563428, slide 1

value: bladder tumor

value: urinary bladder

value: malignant


title: Bladder tumor specimen CD565196, slide 1

value: anti-methylcytosine

value: Diagenode


title: 10 nM TCDD Mouse 1

description: quality control: approved

value: 8-9 weeks

value: 10 nM TCDD