title: Lung-Rt Caudal Lobe_Lung_LP_0,1_7w_504_AC,PS_Lung_THI07041_Rat230_2_THI 07041

description: LP_0,1_7w_504_AC,PS_Lung_THI07041_Rat230_2_THI 07041: A total of 102 rats will be separated into six exposure groups: each group consisting of 17 male CD Sprague-Dawley rats, 10 to 15 weeks old.  The six exposure groups were each exposed via two routes: 1. nose-only inhalation exposures --- air or cigarette smoke; 2. whole-body inhalation exposures -- air or manufactured silica sand or Iraqi sand.  The nose only exposures were conducted 3 hours per day, 5 days per week for 6 weeks.  During the last two weeks of the nose - only exposures, whole-body exposure were also conducted 18-19 hours per day, 7 days per week.

treatment_protocol:
in vivo Treatment: Air Control, Treatment Repeat: 5, Units of Treatment Repeat: days/wk, Treatment Duration: 5, Units of Duration: weeks, Treatment Time: 3, Units of Treatment Time: hr/day, Route of Exposure: nose-only inhalation, Dose or Concentration: 0, Units of Dose or Concentration: mg/L
Treatment_2: in vivo Treatment: Silica, in vivo Treatment: Silica, in vivo Treatment: Silica, in vivo Treatment: Silica, Treatment Repeat: 7, Treatment Repeat: 7, Treatment Repeat: 7, Treatment Repeat: 7, Units of Treatment Repeat: days/wk, Units of Treatment Repeat: days/wk, Units of Treatment Repeat: days/wk, Units of Treatment Repeat: days/wk, Treatment Duration: 2, Treatment Duration: 2, Treatment Duration: 2, Treatment Duration: 2, Units of Duration: weeks, Units of Duration: weeks, Units of Duration: weeks, Units of Duration: weeks, Treatment Time: 18, Treatment Time: 18, Treatment Time: 18, Treatment Time: 18, Units of Treatment Time: hr/day, Units of Treatment Time: hr/day, Units of Treatment Time: hr/day, Units of Treatment Time: hr/day, Route of Exposure: whole body inhalation, Route of Exposure: whole body inhalation, Route of Exposure: whole body inhalation, Route of Exposure: whole body inhalation, Dose or Concentration: 1, Dose or Concentration: 1, Dose or Concentration: 1, Dose or Concentration: 1, Units of Dose or Concentration: mg/m3, Units of Dose or Concentration: mg/m3, Units of Dose or Concentration: mg/m3, Units of Dose or Concentration: mg/m3

tag: array type

tag: amount to core

tag: units of amount

tag: ratio

tag: dilution

tag: rna integrity number

tag: bioanalyzer results

tag: sample preservation

tag: strain

tag: individual

tag: developmental state

tag: sacrifice method

tag: units of age

value: weeks

tag: tissue

value: Lung

value: Silica


title: TIFY3/YHE711 - repeat 2 - mAdbID:108932

status: Public on Jan 01 2012

type: RNA

city: Bethesda

first: Huei-Fung

last: Tsai

state: MD

address: 10 Center Dr. Bldg. 10 Rm. 11N228

department: LCID

country: USA

institute: NIH/NIAID

description: mAdb experiment ID: 108932

hyb_protocol: Agilent Hybridization Other: According to the manufacture's recommended protocol (Two-Color Microarray-Based Gene Expression Analysis, Agilent).

scan_protocol: Scan_MicronsPerPixelX: 5 Scan_MicronsPerPixelY: 5 Scan_ScannerName: Agilent Technologies Scanner G2505C US45103101 Agilent Scanning Protocol Other: Arrays were scanned at 5um resolution and 100/10% PMT XDR on an Agilent DNA Microarray Scanner G2505B.

data_processing:
Agilent Data Processing Protocol
Calculation Method: Images were auto gridded, analyzed and data extracted using Agilent Feature Extraction Software. Spot values were normalized using the default linear-lowess normalization.
FeatureExtractor_Version: 10.7.3.1
Protocol_Name: GE2_107_Sep09 (Read Only)

molecule: total RNA

organism: Saccharomyces cerevisiae

source_name: mt TIFY3 - Cy5

label_protocol:
Cy5 Labeling Protocol
Other: Ten micrograms of total RNA were used for each labeling. The RNA was reversed transcribed to cDNA to incorporate the fluorescent Cy5-dUTP (GE Health Care).

extract_protocol:
Trizol Extraction Protocol
Other: Total RNA was isolated from log-phase culture of S. cerevisiae grown in YPD using Trizole (Invitrogen) and RNeasy MiniElute cleanup kit (Qiagen).

tag: genotype/variation

value: ure2 mutant

tag: developmental stage

value: log-phase culture

source_name: WT YHE711 Control - Cy3

label_protocol:
Cy3 Labeling Protocol
Other: Ten micrograms of total RNA were used for each labeling. The RNA was reversed transcribed to cDNA to incorporate the fluorescent Cy3-dUTP (GE Health Care).

value: wild-type


title: Lung-Rt Caudal Lobe_Lung_LP_048,0_7w_201_CS,AC_Lung_THI07041_Rat230_2_THI 07041

city: Raleigh

first: David

last: Dorman

address: 4700 Hillsborough Street

institute: North Carolina State Universisy

description: LP_048,0_7w_201_CS,AC_Lung_THI07041_Rat230_2_THI 07041: A total of 102 rats will be separated into six exposure groups: each group consisting of 17 male CD Sprague-Dawley rats, 10 to 15 weeks old.  The six exposure groups were each exposed via two routes: 1. nose-only inhalation exposures --- air or cigarette smoke; 2. whole-body inhalation exposures -- air or manufactured silica sand or Iraqi sand.  The nose only exposures were conducted 3 hours per day, 5 days per week for 6 weeks.  During the last two weeks of the nose - only exposures, whole-body exposure were also conducted 18-19 hours per day, 7 days per week.

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: RMA normalization using Bioconductor Package in R

label: biotin

organism: Rattus norvegicus

source_name: Lung-Rt Caudal Lobe

label_protocol: standard Affymetrix protocol

extract_protocol:
Extraction Method: Trizol
Additional Purification Method: Qiagen RNAeasy Mini kit

treatment_protocol:
in vivo Treatment: Cigarette smoke, Treatment Repeat: 5, Units of Treatment Repeat: days/wk, Treatment Duration: 5, Units of Duration: weeks, Treatment Time: 3, Units of Treatment Time: hr/day, Route of Exposure: nose-only inhalation, Dose or Concentration: 0.48, Units of Dose or Concentration: mg WTPM/L
Treatment_2: in vivo Treatment: Air Control, in vivo Treatment: Air Control, in vivo Treatment: Air Control, in vivo Treatment: Air Control, Treatment Repeat: 7, Treatment Repeat: 7, Treatment Repeat: 7, Treatment Repeat: 7, Units of Treatment Repeat: days/wk, Units of Treatment Repeat: days/wk, Units of Treatment Repeat: days/wk, Units of Treatment Repeat: days/wk, Treatment Duration: 2, Treatment Duration: 2, Treatment Duration: 2, Treatment Duration: 2, Units of Duration: weeks, Units of Duration: weeks, Units of Duration: weeks, Units of Duration: weeks, Treatment Time: 18, Treatment Time: 18, Treatment Time: 18, Treatment Time: 18, Units of Treatment Time: hr/day, Units of Treatment Time: hr/day, Units of Treatment Time: hr/day, Units of Treatment Time: hr/day, Route of Exposure: whole body inhalation, Route of Exposure: whole body inhalation, Route of Exposure: whole body inhalation, Route of Exposure: whole body inhalation, Dose or Concentration: 0, Dose or Concentration: 0, Dose or Concentration: 0, Dose or Concentration: 0, Units of Dose or Concentration: mg/m3, Units of Dose or Concentration: mg/m3, Units of Dose or Concentration: mg/m3, Units of Dose or Concentration: mg/m3

value: ul

value: excellent

value: RNA later

value: Sprague-Dawley

value: adult

value: anesthetized with sodium pentobarbital and exsanguinated by transection of the abdominal aorta

tag: Sex

value: Male

tag: age

tag: in vivo treatment

value: Cigarette smoke

tag: treatment2_in vivo treatment

value: Air control


title: YHE711/TIFY3 - repeat 4 - rev. label - mAdbID:108934

description: mAdb experiment ID: 108934

source_name: mt TIFY3 - Cy3

source_name: WT YHE711 Control - Cy5


title: TIFY3/YHE711 - repeat 3 - mAdbID:108933

description: mAdb experiment ID: 108933


title: Lung-Rt Caudal Lobe_Lung_LP_0,1_7w_501_AC,PS_Lung_THI07041_Rat230_2_THI 07041

description: LP_0,1_7w_501_AC,PS_Lung_THI07041_Rat230_2_THI 07041: A total of 102 rats will be separated into six exposure groups: each group consisting of 17 male CD Sprague-Dawley rats, 10 to 15 weeks old.  The six exposure groups were each exposed via two routes: 1. nose-only inhalation exposures --- air or cigarette smoke; 2. whole-body inhalation exposures -- air or manufactured silica sand or Iraqi sand.  The nose only exposures were conducted 3 hours per day, 5 days per week for 6 weeks.  During the last two weeks of the nose - only exposures, whole-body exposure were also conducted 18-19 hours per day, 7 days per week.

tag: array type

tag: amount to core

tag: units of amount

tag: ratio


title: Lung-Rt Caudal Lobe_Lung_LP_0,1_7w_502_AC,PS_Lung_THI07041_Rat230_2_THI 07041

description: LP_0,1_7w_502_AC,PS_Lung_THI07041_Rat230_2_THI 07041: A total of 102 rats will be separated into six exposure groups: each group consisting of 17 male CD Sprague-Dawley rats, 10 to 15 weeks old.  The six exposure groups were each exposed via two routes: 1. nose-only inhalation exposures --- air or cigarette smoke; 2. whole-body inhalation exposures -- air or manufactured silica sand or Iraqi sand.  The nose only exposures were conducted 3 hours per day, 5 days per week for 6 weeks.  During the last two weeks of the nose - only exposures, whole-body exposure were also conducted 18-19 hours per day, 7 days per week.

tag: dilution

tag: rna integrity number

tag: bioanalyzer results

tag: sample preservation


title: CAI4strain_rep2

city: Memphis

first: Katherine

middle: S

last: Barker

state: TN

address: 881 Madison Avenue, Room 305

department: Clinical Pharmacy

institute: University of Tennessee Health Science Center

description: Gene expression data from NRM1/NRM1 log-phase cells

hyb_protocol: The cRNA pellet was suspended in 10 µl of RNase-free water, and 10 µg was fragmented at 95°C for 35 min in 200 mM Tris-acetate (pH 8.1), 500 mM potassium acetate, and 150 mM magnesium acetate. The fragmented cRNA was hybridized for 16 h at 45°C to an Affymetrix custom expression array (CAN07a520619F; manufactured by Affymetrix) for C. albicans. Arrays were washed at 25°C with 6x SSPE (1x SSPE is 0.18 M NaCl, 10 mM NaH2PO4, and 1 mM EDTA [pH 7.7]) and 0.01% Tween 20 followed by a stringent wash at 50°C with 100 mM MES (morpholineethanesulfonic acid), 0.1 M NaCl, and 0.01% Tween 20. Affymetrix Fluidics Station 450 was used for hybridizations and washes according to standard EukGE-WS2v5 protocol. The arrays were then stained with phycoerythrin-conjugated streptavidin (Molecular Probes).

scan_protocol: The fluorescence intensities were determined using a GCS 3000 high-resolution confocal laser scanner (Affymetrix). The scanned images were analyzed using software resident in the GeneChip operating system, version 2.0 (Affymetrix). Sample loading and variations in staining were standardized by scaling the average of the fluorescent intensities of all genes on an array to a constant target intensity of 250. The signal intensity for each gene was calculated as the average intensity difference, represented by (PM –MM)/number of probe pairs, where PM and MM denote perfectly matched and mismatched probes, respectively.

data_processing: Algorithm: ExpressionStat 5.0. Probe sets were deleted from subsequent analysis if they were called absent by the Affymetrix criterion and displayed an absolute value below 20 in all experiments. The expression value of each gene was normalized to the median expression of all genes in each chip as well as to the median expression for that gene across all chips in the study. A pairwise comparison of gene expression was performed for each matched experiment.

organism: Candida albicans

source_name: strain CAI4 (wildtype)

label_protocol: First- and second-strand cDNA was synthesized from 15 µg total RNA, using a SuperScript double-stranded cDNA synthesis kit (Invitrogen) and an oligo-dT24-T7 primer (Proligo) according to the manufacturers' instructions. cRNA was synthesized and labeled with biotinylated UTP and CTP by in vitro transcription, using T7 promoter-coupled double-stranded cDNA as a template and a BioArray HighYield RNA transcript labeling kit (Enzo Diagnostics). Double-stranded cDNA synthesized from the previous steps was washed twice with 70% ethanol and suspended in 22 µl of RNase-free water. The cDNA was incubated as recommended with reaction buffer, biotin-labeled ribonucleotides,dithiothreitol, RNase inhibitor mix, and T7 RNA polymerase for 5 h at 37°C. The labeled cRNA was separated from unincorporatedribonucleotides with a Chroma Spin-100 column (Clontech) and was ethanol precipitated at –20°C overnight.

growth_protocol: Cells were grown overnight at 30deg Celsius in YPD (1% yeast extract, 2% peptone, and 1% dextrose) with agitation, and these saturated cultures were used to seed 20ml YPD cultures (OD600= 0.2) which were grown with agitation for 3hrs at 30deg Celsius.

extract_protocol: RNA was isolated from frozen cell pellets using the hot-phenol method (Schmitt, M. E., T. A. Brown, and B. L. Trumpower. 1990. Nucleic Acids Res. 18:3091-3092.). Briefly, cells were resuspended in 12 ml AE buffer (50 mM sodium acetate [pH 5.2] and 10 mM EDTA) at room temperature, after which 800 µl 25% sodium dodecyl sulfate and 12 ml acid phenol (Fisher Scientific, Houston, TX) were added. The cell lysate was then incubated for 10 min at 65°C with vigorous shaking each minute, cooled on ice for 5 min, and subjected to centrifugation for 15 min at 11,952 x g. The supernatants were transferred to new tubes containing 15 ml chloroform, mixed, and subjected to centrifugation at 200 x g for 10 min. RNA was precipitated from the resultingaqueous layer by mixing that portion in new tubes with 1 volume of isopropanol and 0.1 volume of 2 M sodium acetate [pH 5.0] and subjecting the mixture to centrifugation at 17,211 x g for 35 min at 4°C. The supernatants were removed, the pellet was resuspended in 10 ml 70% ethanol, and the RNA was collected by centrifugation at 17,211 x g for 20 min at 4°C. The supernatants were again removed, and the RNA was resuspended in 50 to 200 µl diethyl pyrocarbonate-treated water. The RNA was stored at –80°C until needed.

tag: genotype


title: Subject 8

city: Atlanta

first: Gregory

last: Doho

state: GA

address: 1365B Clifton Rd NE

institute: Emory University

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: BeadChips were scanned using Illumina BeadArray Scanner

data_processing: The data were normalized using quantile-normalization with GenomeStudio V2010.2

organism: Homo sapiens

source_name: PBMC

label_protocol: PCR product was prepared with standard Illumina protocol for arrays

extract_protocol: Total RNA was isolated using RNeasy kits (QIAGEN, Valencia, CA) according to manufacturer instructions.

treatment_protocol: All subjects who underwent IFN-alpha treatment received either pegylated IFN-alfa-2b (Pegintron, Schering Plough, Kenilworth, NJ; 1.5µg/kg)(n=5) or pegylated IFN-alfa-2a (Pegasys, Roche-Genentech, San Francisco, CA; 180mg)(n=6) administered subcutaneously and ribavirin (800–1400 mg/day). Participation in the treatment versus control group was determined by patients and their physician based on scheduling constraints and personal preferences and was not based on standardized criteria or controlled by study protocol.

tag: treatment

value: Control

tag: week 12 madrs score

tag: week 12 mfi score

value: f

tag: race

value: af am

tag: education

value: college degree

tag: past md

value: no

tag: past subsabuse

value: yes

tag: bl madrs

tag: bl mfi

tag: bmi


title: KC392strain_rep1

description: Gene expression data from nrm1-/nrm1- log-phase cells

source_name: strain KC392 (nrm1-/nrm1-)

value: CAI4 Canrm1D::hisG / Canrm1D::hisG


title: Subject 5

tag: age

tag: Sex

value: m

value: cau

value: some college


title: Lung-Rt Caudal Lobe_Lung_LP_0,1_7w_305_AC,IS_Lung_THI07041_Rat230_2_THI 07041

description: LP_0,1_7w_305_AC,IS_Lung_THI07041_Rat230_2_THI 07041: A total of 102 rats will be separated into six exposure groups: each group consisting of 17 male CD Sprague-Dawley rats, 10 to 15 weeks old.  The six exposure groups were each exposed via two routes: 1. nose-only inhalation exposures --- air or cigarette smoke; 2. whole-body inhalation exposures -- air or manufactured silica sand or Iraqi sand.  The nose only exposures were conducted 3 hours per day, 5 days per week for 6 weeks.  During the last two weeks of the nose - only exposures, whole-body exposure were also conducted 18-19 hours per day, 7 days per week.

treatment_protocol:
in vivo Treatment: Air Control, Treatment Repeat: 5, Units of Treatment Repeat: days/wk, Treatment Duration: 5, Units of Duration: weeks, Treatment Time: 3, Units of Treatment Time: hr/day, Route of Exposure: nose-only inhalation, Dose or Concentration: 0, Units of Dose or Concentration: mg/L
Treatment_2: in vivo Treatment: Iraqi Sand, in vivo Treatment: Iraqi Sand, in vivo Treatment: Iraqi Sand, in vivo Treatment: Iraqi Sand, Treatment Repeat: 7, Treatment Repeat: 7, Treatment Repeat: 7, Treatment Repeat: 7, Units of Treatment Repeat: days/wk, Units of Treatment Repeat: days/wk, Units of Treatment Repeat: days/wk, Units of Treatment Repeat: days/wk, Treatment Duration: 2, Treatment Duration: 2, Treatment Duration: 2, Treatment Duration: 2, Units of Duration: weeks, Units of Duration: weeks, Units of Duration: weeks, Units of Duration: weeks, Treatment Time: 18, Treatment Time: 18, Treatment Time: 18, Treatment Time: 18, Units of Treatment Time: hr/day, Units of Treatment Time: hr/day, Units of Treatment Time: hr/day, Units of Treatment Time: hr/day, Route of Exposure: whole body inhalation, Route of Exposure: whole body inhalation, Route of Exposure: whole body inhalation, Route of Exposure: whole body inhalation, Dose or Concentration: 1, Dose or Concentration: 1, Dose or Concentration: 1, Dose or Concentration: 1, Units of Dose or Concentration: mg/m3, Units of Dose or Concentration: mg/m3, Units of Dose or Concentration: mg/m3, Units of Dose or Concentration: mg/m3

tag: array type

tag: amount to core

tag: units of amount

value: ul

tag: ratio

tag: dilution

value: excellent

value: RNA later

tag: strain

tag: individual

tag: developmental state

tag: sacrifice method

tag: units of age

value: weeks

tag: tissue

value: Lung

tag: in vivo treatment

tag: treatment2_in vivo treatment

value: Iraqi Sand


title: Subject 7

tag: treatment

tag: week 12 madrs score

tag: week 12 mfi score

tag: race

tag: education

value: some highschool

tag: past md

tag: past subsabuse

tag: bl madrs

tag: bl mfi


title: HCG7/BG14 - repeat 1 - mAdbID:106666

description: mAdb experiment ID: 106666

scan_protocol: Agilent Scanning Protocol Other: Arrays were scanned at 5um resolution and 100/10% PMT XDR on an Agilent DNA Microarray Scanner G2505B.

data_processing:
Agilent Data Processing Protocol
Calculation Method: Images were auto gridded, analyzed and data extracted using Agilent Feature Extraction Software. Spot values were normalized using the default linear-lowess normalization.

organism: Nakaseomyces glabratus

source_name: WT BG14 Control - Cy3

extract_protocol:
Trizol Extraction Protocol
Other: Total RNA was isolated from log-phase culture of C. glabrata grown in YPD using Trizole (Invitrogen) and RNeasy MiniElute cleanup kit (Qiagen).

tag: strain

tag: developmental stage

value: log-phase culture

tag: genotype/variation

value: Wild Type

source_name: mt HCG7 - Cy5

value: ure2 mutant


title: Subject 6

value: Control

tag: age

tag: Sex

value: f

value: af am

value: college degree

tag: bmi


title: Subject 4

value: m

value: no


title: Subject 2

value: cau

value: some college

value: yes


title: CAI4strain_rep1

tag: genotype


title: KC392strain_rep2

value: CAI4 Canrm1D::hisG / Canrm1D::hisG


title: Lung-Rt Caudal Lobe_Lung_LP_0,1_7w_304_AC,IS_Lung_THI07041_Rat230_2_THI 07041

description: LP_0,1_7w_304_AC,IS_Lung_THI07041_Rat230_2_THI 07041: A total of 102 rats will be separated into six exposure groups: each group consisting of 17 male CD Sprague-Dawley rats, 10 to 15 weeks old.  The six exposure groups were each exposed via two routes: 1. nose-only inhalation exposures --- air or cigarette smoke; 2. whole-body inhalation exposures -- air or manufactured silica sand or Iraqi sand.  The nose only exposures were conducted 3 hours per day, 5 days per week for 6 weeks.  During the last two weeks of the nose - only exposures, whole-body exposure were also conducted 18-19 hours per day, 7 days per week.

tag: array type

tag: amount to core

tag: units of amount

value: ul

tag: ratio

tag: dilution

tag: rna integrity number

tag: bioanalyzer results

value: excellent

tag: sample preservation

value: RNA later

value: Sprague-Dawley

tag: individual

tag: developmental state

value: adult

tag: sacrifice method

value: anesthetized with sodium pentobarbital and exsanguinated by transection of the abdominal aorta

value: Male

tag: units of age

value: weeks

tag: tissue

tag: in vivo treatment

value: Air control

tag: treatment2_in vivo treatment


title: sml1_BrdU_HU_60_min

type: genomic

city: Montpellier

first: Philippe

last: Pasero

address: 141 rue de la Cardonille

country: France

institute: Institute of Human Genetics - CNRS

hyb_protocol: DNA was hybridized to Affymetrix Genechip S. cerevisiae Tiling 1.0R Array (5 bpresolution, Affymetrix PN 900645) using the GeneChip Hybridization, Wash, and Stain Kit (Affymetrix, PN 900720).

scan_protocol: Tiling arrays were scanned with the GeneChip scanner 3000 7G

data_processing: results file descriptions: signal bar files generated for each strains contains log2 (IP/Input) for signal intensity.

molecule: genomic DNA

source_name: BrdU-IP from sml1 deletion mutant cells in HU, 60 min

label_protocol: 7 µg of amplified DNA was fragmented and labelled using the GeneChip WT Double-Stranded DNA Terminal Labelling kit (Affymetrix, PN 900812) following manufacturer's recommendations.  7 µg of amplified DNA was fragmented and labelled using the GeneChip WT Double-Stranded DNA Terminal Labelling kit (Affymetrix, PN 900812) following manufacturer recommendations.

growth_protocol: G1-synchronised cells were released into S phase in the presence of Hydroxyurea (200mM) and BrdU (400µg/ml) for the indicated time.

extract_protocol: For immunoprecipitation of BrdU-labelled DNA, 1.5x109 cells were lysed for 5 x 2 minutes in NIB buffer (17 % glycerol, 50 mM MOPS buffer, 150mM potassium acetate, 2 mM magnesium chloride, 500 µM spermidine and 150 µM spermine, pH7.2) with Zirconium beads on a Vibrax (VXR basic, Ika) at 4C. DNA was isolated using Qiagen Genomic DNA extraction kit and sonicated to reach an average DNA size of 300-600 bp. For each immunoprecipitation, 10 µl of mouse anti-BrdU IgG1 (BDBioscience 555627) was prebound to Dynabeads M-280 Sheep anti-mouse IgG (Invitrogen 112.02) and added to the denatured purified DNA.  For immunoprecipitation of BrdU-labelled DNA, 1.5x109 cells were lysed for 5 x 2 minutes in NIB buffer (17 % glycerol, 50 mM MOPS buffer, 150mM potassium acetate, 2 mM magnesium chloride, 500 µM spermidine and 150 µM spermine, pH7.2) with Zirconium beads on a Vibrax (VXR basic, Ika) at 4C. DNA was isolated using Qiagen Genomic DNA extraction kit and sonicated to reach an average DNA size of 300-600 bp. For each immunoprecipitation, 10 µl of mouse anti-BrdU IgG1 (BDBioscience 555627) was prebound to Dynabeads M-280 Sheep anti-mouse IgG (Invitrogen 112.02) and added to the denatured purified DNA.  For immunoprecipitation of BrdU-labelled DNA, 1.5x109 cells were lysed for 5 x 2 minutes in NIB buffer (17 % glycerol, 50 mM MOPS buffer, 150mM potassium acetate, 2 mM magnesium chloride, 500 µM spermidine and 150 µM spermine, pH7.2) with Zirconium beads on a Vibrax (VXR basic, Ika) at 4C. DNA was isolated using Qiagen Genomic DNA extraction kit and sonicated to reach an average DNA size of 300-600 bp. For each immunoprecipitation, 10 µl of mouse anti-BrdU IgG1 (BDBioscience 555627) was prebound to Dynabeads M-280 Sheep anti-mouse IgG (Invitrogen 112.02) and added to the denatured purified DNA.  For immunoprecipitation of BrdU-labelled DNA, 1.5.109 cells were lysed for 5 x 2 min in NIB buffer (17% glycerol, 50 mM MOPS buffer, 150 mM potassium acetate, 2 mM magnesium chloride, 500 µM  spermidine and 150 µM  spermine, pH 7.2) with zirconium beads on a vibrax (VXR basic, IKA) at 4°C. DNA was isolated using Qiagen Genomic DNA extraction kit and sonicated to reach an average DNA size of 300-600 bp. For each immunoprecipitation, 10µl of mouse anti-BrdU IgG1 (BD Biosciences) was prebound to Dynabeads M-280 Sheep anti-mouse IgG (Invitrogen) and added to the denaturated purified DNA.

tag: strain

tag: antibody

value: BrdU

tag: vendor/catalog

value: BDBioscience 555627

tag: genotype/variation

value: sml1 deletion mutant cells

tag: time point

value: 60 min

source_name: Genomic DNA from Saccharomyces cerevisiae

tag: fraction

value: input


title: TIFY3/YHE711 - repeat 1 - mAdbID:108931

description: mAdb experiment ID: 108931

value: ure2 mutant

tag: developmental stage

value: log-phase culture

value: wild-type


title: sgs1_BrdU_HU_60_min

source_name: BrdU-IP from sgs1 deletion mutant cells in HU, 60 min

value: sgs1 deletion mutant cells


title: fhm_ovary_con_F

city: Duluth

first: Daniel

middle: L.

last: Villeneuve

state: MN

address: 6201 Congdon Blvd

department: Mid-Continent Ecology Division

institute: US EPA

hyb_protocol: The Agilent one-color microarray hybridization protocol (One-Color Microarray-Based Gene Expression Analysis, version 5.7, Agilent Technologies, Palo Alto, CA) was used for microarray hybridizations following the manufacturer’s protocol and recommendations.

scan_protocol: An Axon GenePix® 4000B Microarray Scanner (Molecular Devices Inc.) was used to scan microarray images at 5 μm resolution

data_processing: Microarray image processing and data pre-processing were performed Agilent's Feature Extraction software v 9.5 following the manufacturer’s protocol and recommendations.  Fastlo normalization was implemented in R 2.10.1

organism: Pimephales promelas

source_name: ovary from fish exposed to control water for 96 h

label_protocol: cDNA synthesis, cRNA labeling, amplification and hybridization were performed following the manufacturer's kits and protocols (Quick Amp Labeling Kit; Agilent, Palo Alto, CA)

growth_protocol: Sexually mature adult fathead minnows (5-6 month old) and zebrafish (ab wild-type strain; 6-7 month old) were obtained from an on-site aquatic culture facility at the US EPA Mid-Continent Ecology Division, Duluth, MN, USA. Both species were held under a 16:8 light:dark photoperiod and fed brine shrimp to satiation twice daily. However, fathead minnows were fed frozen adult brine shrimp (San Francisco Bay Brand, Newark, CA, USA) while zebrafish were fed newly hatched (< 24 h old) brine shrimp nauplii (BioMarine Brand artemia cysts; Hawthorne, CA, USA). Fish survival, water temperature (mean ± SD; 25.0±0.3; both species), and dissolved oxygen (mean ± SD; zebrafish 6.7±0.3 mg/L; fathead 7.0±0.2) were monitored daily over the duration of the exposure and did not vary significantly between treatment groups or species.

extract_protocol: Total RNA was isolated from ovary tissue of both fathead minnow and zebrafish using RNeasy kits (Qiagen, Valencia, CA, USA). RNA quality was evaluated using an Agilent 2100 Bioanalyzer (Agilent, Wilmington, DE, USA) and RNA was quantified spectrophotometrically (Nanodrop). Total RNA samples were stored at -80oC until used for microarray analyses.

treatment_protocol: Fish were exposed to 0, 0.01, 0.1, 1.0, 10, or 100 µg BPA/L delivered in a continuous flow (45 ml/min) of sand filtered, UV treated, Lake Superior Water, without the use of carrier solvents. Following approximately 36 h of chemical (or control water) delivery to condition the tanks (20 L aquaria filled with 10 L of exposure water) and exposure apparatus, exposures were initiated by loading fish into the conditioned tanks. The design employed six replicate tanks per treatment. Three of the replicates were loaded with three male and three female zebrafish per tank, while the remaining three replicates were loaded with three male and three female fathead minnows. Addition of fish to the exposure tanks was staggered by replicate such that all sampling could be completed within 60 min of the desired 96 h exposure duration. Zebrafish were loaded and sampled one day prior to loading and sampling the fathead minnows so that three of the four exposure days for each species directly overlapped. After 96 h of exposure, fish were anesthetized in a buffered solution of tricaine methanesulfonate (MS-222; Finquel; Argent, Redmond, WA, USA) and weighed. Blood was collected from the caudal vasculature using microhematocrit tubes, centrifuged to separate the plasma, and plasma was stored at -80oC until analyzed. Liver, gonad, and brain tissues (including pituitary gland) were snap frozen in liquid nitrogen and stored at -80oC until extracted.

tag: ct-id

tag: agent

value: CONTROL

value: ovary

tag: rep(tank)

value: FHM 1

tag: take down date

tag: gender

value: F

tag: FISH wet wt (g)

tag: gonad wt (g)

tag: ex vivo t production (ng/ml/12h)

tag: ex vivo e2 (ng/ml/12h)

tag: plasma vtg (mg/ml)

tag: array rep

tag: slide

tag: array


title: Lung-Rt Caudal Lobe_Lung_LP_0,1_7w_302_AC,IS_Lung_THI07041_Rat230_2_THI 07041

description: LP_0,1_7w_302_AC,IS_Lung_THI07041_Rat230_2_THI 07041: A total of 102 rats will be separated into six exposure groups: each group consisting of 17 male CD Sprague-Dawley rats, 10 to 15 weeks old.  The six exposure groups were each exposed via two routes: 1. nose-only inhalation exposures --- air or cigarette smoke; 2. whole-body inhalation exposures -- air or manufactured silica sand or Iraqi sand.  The nose only exposures were conducted 3 hours per day, 5 days per week for 6 weeks.  During the last two weeks of the nose - only exposures, whole-body exposure were also conducted 18-19 hours per day, 7 days per week.

tag: array type

tag: amount to core

tag: units of amount

value: ul

tag: ratio

tag: dilution

tag: rna integrity number

tag: bioanalyzer results

value: good

tag: sample preservation

value: RNA later

tag: strain

value: Sprague-Dawley

tag: individual

tag: developmental state

value: adult

tag: sacrifice method

value: anesthetized with sodium pentobarbital and exsanguinated by transection of the abdominal aorta

tag: Sex

tag: age

tag: units of age

tag: tissue

value: Lung

tag: in vivo treatment

tag: treatment2_in vivo treatment

value: Iraqi Sand


title: rtt101_BrdU_HU_60_min

source_name: BrdU-IP from rtt101 deletion mutant cells in HU, 60 min

tag: antibody

value: BrdU

tag: vendor/catalog

value: BDBioscience 555627

tag: genotype/variation

value: rtt101 deletion mutant cells

tag: time point

value: 60 min

tag: fraction

value: input


title: fhm_ovary_con_E

tag: ct-id

tag: agent

value: CONTROL

tag: rep(tank)

value: FHM 3

tag: take down date

tag: gender

tag: FISH wet wt (g)

tag: gonad wt (g)

tag: ex vivo t production (ng/ml/12h)

tag: ex vivo e2 (ng/ml/12h)

tag: plasma vtg (mg/ml)

tag: array rep

value: E

tag: slide

tag: array


title: fhm_ovary_con_D

tag: tissue

value: ovary

value: F

value: D


title: Lung-Rt Caudal Lobe_Lung_LP_0,1_7w_301_AC,IS_Lung_THI07041_Rat230_2_THI 07041

description: LP_0,1_7w_301_AC,IS_Lung_THI07041_Rat230_2_THI 07041: A total of 102 rats will be separated into six exposure groups: each group consisting of 17 male CD Sprague-Dawley rats, 10 to 15 weeks old.  The six exposure groups were each exposed via two routes: 1. nose-only inhalation exposures --- air or cigarette smoke; 2. whole-body inhalation exposures -- air or manufactured silica sand or Iraqi sand.  The nose only exposures were conducted 3 hours per day, 5 days per week for 6 weeks.  During the last two weeks of the nose - only exposures, whole-body exposure were also conducted 18-19 hours per day, 7 days per week.

tag: array type

tag: amount to core

tag: units of amount

value: ul

tag: dilution

tag: rna integrity number

tag: bioanalyzer results

value: good

tag: sample preservation

value: RNA later

tag: strain

tag: individual

tag: developmental state

tag: sacrifice method

tag: Sex

value: Male

tag: age

tag: units of age

value: weeks

tag: in vivo treatment

value: Air control

tag: treatment2_in vivo treatment


title: rrm3_BrdU_HU_60_min

source_name: BrdU-IP from rrm3 deletion mutant cells in HU, 60 min

tag: antibody

value: BrdU

tag: vendor/catalog

tag: genotype/variation

value: rrm3 deletion mutant cells

tag: time point

tag: fraction


title: fhm_ovary_con_C

tag: ct-id

tag: agent

tag: tissue

tag: rep(tank)

value: FHM 2

tag: take down date

tag: gender

tag: FISH wet wt (g)

tag: gonad wt (g)

tag: ex vivo t production (ng/ml/12h)

tag: ex vivo e2 (ng/ml/12h)

tag: plasma vtg (mg/ml)

tag: array rep

value: C

tag: slide

tag: array


title: Lung-Rt Caudal Lobe_Lung_LP_0,1_7w_503_AC,PS_Lung_THI07041_Rat230_2_THI 07041

description: LP_0,1_7w_503_AC,PS_Lung_THI07041_Rat230_2_THI 07041: A total of 102 rats will be separated into six exposure groups: each group consisting of 17 male CD Sprague-Dawley rats, 10 to 15 weeks old.  The six exposure groups were each exposed via two routes: 1. nose-only inhalation exposures --- air or cigarette smoke; 2. whole-body inhalation exposures -- air or manufactured silica sand or Iraqi sand.  The nose only exposures were conducted 3 hours per day, 5 days per week for 6 weeks.  During the last two weeks of the nose - only exposures, whole-body exposure were also conducted 18-19 hours per day, 7 days per week.

tag: array type

tag: amount to core

tag: units of amount

tag: ratio

tag: dilution

tag: bioanalyzer results

value: excellent

tag: sample preservation

tag: strain

value: Sprague-Dawley

tag: individual

tag: developmental state

value: adult

tag: sacrifice method

value: anesthetized with sodium pentobarbital and exsanguinated by transection of the abdominal aorta

tag: Sex

tag: age

tag: units of age

value: Lung

tag: in vivo treatment

tag: treatment2_in vivo treatment

value: Silica


title: Subject 1

tag: treatment

value: Control

tag: week 12 madrs score

tag: week 12 mfi score

value: m

tag: race

value: am ind

tag: education

value: college degree

tag: past md

value: no

tag: past subsabuse

tag: bl madrs

tag: bl mfi

tag: bmi


title: Lung-Rt Caudal Lobe_Lung_LP_0,0_7w_104_AC,AC_Lung_THI07041_Rat230_2_THI 07041

description: LP_0,0_7w_104_AC,AC_Lung_THI07041_Rat230_2_THI 07041: A total of 102 rats will be separated into six exposure groups: each group consisting of 17 male CD Sprague-Dawley rats, 10 to 15 weeks old.  The six exposure groups were each exposed via two routes: 1. nose-only inhalation exposures --- air or cigarette smoke; 2. whole-body inhalation exposures -- air or manufactured silica sand or Iraqi sand.  The nose only exposures were conducted 3 hours per day, 5 days per week for 6 weeks.  During the last two weeks of the nose - only exposures, whole-body exposure were also conducted 18-19 hours per day, 7 days per week.

treatment_protocol:
in vivo Treatment: Air control, Treatment Repeat: 5, Units of Treatment Repeat: days/wk, Treatment Duration: 5, Units of Duration: weeks, Treatment Time: 3, Units of Treatment Time: hr/day, Route of Exposure: nose-only inhalation, Dose or Concentration: 0, Units of Dose or Concentration: mg/L
Treatment_2: in vivo Treatment: Air control, in vivo Treatment: Air control, in vivo Treatment: Air control, in vivo Treatment: Air control, Treatment Repeat: 7, Treatment Repeat: 7, Treatment Repeat: 7, Treatment Repeat: 7, Units of Treatment Repeat: days/wk, Units of Treatment Repeat: days/wk, Units of Treatment Repeat: days/wk, Units of Treatment Repeat: days/wk, Treatment Duration: 2, Treatment Duration: 2, Treatment Duration: 2, Treatment Duration: 2, Units of Duration: weeks, Units of Duration: weeks, Units of Duration: weeks, Units of Duration: weeks, Treatment Time: 18, Treatment Time: 18, Treatment Time: 18, Treatment Time: 18, Units of Treatment Time: hr/day, Units of Treatment Time: hr/day, Units of Treatment Time: hr/day, Units of Treatment Time: hr/day, Route of Exposure: whole body inhalation, Route of Exposure: whole body inhalation, Route of Exposure: whole body inhalation, Route of Exposure: whole body inhalation, Dose or Concentration: 0, Dose or Concentration: 0, Dose or Concentration: 0, Dose or Concentration: 0, Units of Dose or Concentration: mg/m3, Units of Dose or Concentration: mg/m3, Units of Dose or Concentration: mg/m3, Units of Dose or Concentration: mg/m3

tag: array type

tag: amount to core

tag: units of amount

value: ul

tag: ratio

tag: dilution

tag: bioanalyzer results

tag: sample preservation

value: RNA later

tag: strain

tag: individual

tag: developmental state

value: Male

value: weeks

tag: tissue


title: Subject 3

tag: treatment

tag: week 12 madrs score

tag: week 12 mfi score

tag: age

tag: Sex

tag: race

value: af am

tag: education

value: high school degree

value: yes


title: wt_30degres_BrdU_HU_60_min

source_name: BrdU-IP from sml1 wild-type cells in HU at 30°C, 60 min

tag: antibody

value: BrdU

tag: vendor/catalog

value: BDBioscience 555627

tag: genotype/variation

value: sml1 wild-type cells

tag: time point

value: 60 min

tag: fraction

value: input


title: rad53_sml1_BrdU_HU_60_min

source_name: BrdU-IP from rad53sml1 double deletion mutant in HU, 60 min

value: rad53sml1 double deletion mutant


title: ZFX over expressing embryonic stem cells Clone 5 Rep1

city: New York

first: Stuart

middle: M

last: Chambers

state: NY

address: 1270 York Ave

institute: Sloan-Kettering Institute

hyb_protocol: 750ng of each sample was hybridized to Illumina human6 oligonucleotide array, at 58 degree for 18h

scan_protocol: Chips were scanned with Illumina BeadArray Reader v.3.5.49.29917

data_processing: Data was exported from Illumina BeadStudio BSGX 3.3.7. Quantile normalization and model-based expression measurements were performed using the Illumina analysis package (LUMI) available through open-source Bioconductor project (www.bioconductor.org) within the statistical programming language R (http://cran.r-project.org/).

source_name: ZFX over expression - Bacterial Artificial Chromosome containing ZFX

label_protocol: Illumina TotalPrep RNA Amplification kit (Ambion, cat number:IL1719), following the manufacturer's protocol of a single in vitro transcription amplification. Input amount: 500 ng of total RNA. Incubation of labeling reaction: 16h

growth_protocol: All lines were grown in standard human embryonic stem cell conditions

extract_protocol: Standard Trizol (Invitrogen) extraction protocol

treatment_protocol: A bacterial artificial chromosome containing the ZFX locus was delivered to embryonic stem cells and clones were selected using drug resistance.  Overexpression was confirmed using qRT-PCR.

tag: parental cell line

tag: cell type

value: embryonic stem cells


title: Control embryonic stem cell Clone 3 Rep2

source_name: Clonally derived stem cells


title: rad52_BrdU_HU_60_min

source_name: BrdU-IP from rad52 deletion mutant in HU, 60 min

tag: strain

value: rad52 deletion mutant


title: ZFX over expressing embryonic stem cells Clone 5 Rep2


title: Lung-Rt Caudal Lobe_Lung_LP_0,0_7w_105_AC,AC_Lung_THI07041_Rat230_2_THI 07041

description: LP_0,0_7w_105_AC,AC_Lung_THI07041_Rat230_2_THI 07041: A total of 102 rats will be separated into six exposure groups: each group consisting of 17 male CD Sprague-Dawley rats, 10 to 15 weeks old.  The six exposure groups were each exposed via two routes: 1. nose-only inhalation exposures --- air or cigarette smoke; 2. whole-body inhalation exposures -- air or manufactured silica sand or Iraqi sand.  The nose only exposures were conducted 3 hours per day, 5 days per week for 6 weeks.  During the last two weeks of the nose - only exposures, whole-body exposure were also conducted 18-19 hours per day, 7 days per week.

source_name: Lung-Rt Caudal Lobe

tag: array type

tag: amount to core

tag: units of amount

tag: ratio

tag: dilution

tag: rna integrity number

tag: bioanalyzer results

value: excellent

tag: sample preservation

value: Sprague-Dawley

tag: individual

tag: developmental state

value: adult

tag: sacrifice method

value: anesthetized with sodium pentobarbital and exsanguinated by transection of the abdominal aorta

tag: units of age

value: Lung

tag: in vivo treatment

value: Air control

tag: treatment2_in vivo treatment


title: Control embryonic stem cell Clone 3 Rep1

tag: parental cell line


title: Lung-Rt Caudal Lobe_Lung_LP_0,0_7w_103_AC,AC_Lung_THI07041_Rat230_2_THI 07041

description: LP_0,0_7w_103_AC,AC_Lung_THI07041_Rat230_2_THI 07041: A total of 102 rats will be separated into six exposure groups: each group consisting of 17 male CD Sprague-Dawley rats, 10 to 15 weeks old.  The six exposure groups were each exposed via two routes: 1. nose-only inhalation exposures --- air or cigarette smoke; 2. whole-body inhalation exposures -- air or manufactured silica sand or Iraqi sand.  The nose only exposures were conducted 3 hours per day, 5 days per week for 6 weeks.  During the last two weeks of the nose - only exposures, whole-body exposure were also conducted 18-19 hours per day, 7 days per week.

value: ul

value: RNA later

tag: Sex

value: Male

tag: age

value: weeks

tag: tissue


title: fhm_ovary_con_A

tag: ct-id

tag: agent

value: CONTROL

value: ovary

tag: rep(tank)

value: FHM 1

tag: take down date

tag: gender

value: F

tag: FISH wet wt (g)

tag: gonad wt (g)

tag: ex vivo t production (ng/ml/12h)

tag: ex vivo e2 (ng/ml/12h)

tag: plasma vtg (mg/ml)

tag: array rep

value: A

tag: slide

tag: array


title: Lung-Rt Caudal Lobe_Lung_LP_0,0_7w_102_AC,AC_Lung_THI07041_Rat230_2_THI 07041

description: LP_0,0_7w_102_AC,AC_Lung_THI07041_Rat230_2_THI 07041: A total of 102 rats will be separated into six exposure groups: each group consisting of 17 male CD Sprague-Dawley rats, 10 to 15 weeks old.  The six exposure groups were each exposed via two routes: 1. nose-only inhalation exposures --- air or cigarette smoke; 2. whole-body inhalation exposures -- air or manufactured silica sand or Iraqi sand.  The nose only exposures were conducted 3 hours per day, 5 days per week for 6 weeks.  During the last two weeks of the nose - only exposures, whole-body exposure were also conducted 18-19 hours per day, 7 days per week.

tag: array type

tag: amount to core

tag: units of amount

tag: ratio

tag: dilution

tag: rna integrity number

tag: bioanalyzer results

tag: sample preservation

tag: strain

tag: individual

tag: developmental state

tag: sacrifice method

tag: units of age

tag: in vivo treatment

tag: treatment2_in vivo treatment


title: mec1_tel1_sml1_BrdU_HU_60_min

source_name: BrdU-IP from mec1tel1sml1 triple deletion mutant in HU, 60 min

tag: antibody

value: BrdU

tag: vendor/catalog

value: BDBioscience 555627

tag: genotype/variation

value: mec1tel1sml1 triple deletion mutant

tag: time point

value: 60 min

tag: fraction

value: input


title: ZFX over expressing embryonic stem cells Clone 2 Rep2

tag: parental cell line

tag: cell type

value: embryonic stem cells


title: MDAMB231-Q0 rep3

city: durham

first: Hsiu-Ni

last: Kung

state: NC

address: CIEMAS 2141, 101 Science Drive

institute: Duke

hyb_protocol: Affymetrix standard protocol

scan_protocol: Affymetrix standard protocol

data_processing: RMA express

source_name: human breast cancer cell line

label_protocol: Affymetrix standard protocol

growth_protocol: DMEM with 10%FBS

extract_protocol: RNAs were extracted with Ambion mirVana kit

treatment_protocol: DMEM with 10%FBS with 4mM glutamine (Q4) or no glutamine (Q0) for 24 hours

tag: treatment

value: no glutamine

tag: cell line


title: fhm_ovary_bpa100_E

source_name: ovary from fish exposed to bpa for 96 h

tag: ct-id

tag: agent

value: BPA

tag: dose

value: 100 µg BPA/L

tag: tissue

tag: rep(tank)

value: FHM 3

tag: take down date

tag: gender

tag: FISH wet wt (g)

tag: gonad wt (g)

tag: ex vivo t production (ng/ml/12h)

tag: ex vivo e2 (ng/ml/12h)

tag: plasma vtg (mg/ml)

tag: array rep

value: E

tag: slide

tag: array


title: fhm_ovary_bpa100_D

value: FHM 2

value: D


title: MDAMB231-Q0 rep2

tag: treatment


title: fhm_ovary_bpa100_C

value: ovary

value: C


title: ZFX over expressing embryonic stem cells Clone 2 Rep1

tag: parental cell line

tag: cell type


title: ctf4_rad9_BrdU_HU_60_min

source_name: BrdU-IP from ctf4rad9 deletion double mutant in HU, 60 min

tag: strain

tag: antibody

tag: vendor/catalog

tag: genotype/variation

value: ctf4rad9 deletion double mutant

tag: time point

tag: fraction


title: ctf18_dun1_BrdU_HU_60_min

source_name: BrdU-IP from ctf18dun1 deletion double mutant in HU, 60 min

value: ctf18dun1 deletion double mutant


title: Embryonic stem cells Rep2

source_name: Original stem cells


title: fhm_ovary_bpa100_B

tag: ct-id

tag: agent

tag: dose

tag: tissue

tag: rep(tank)

value: FHM 1

tag: take down date

tag: gender

value: F

tag: FISH wet wt (g)

value: B


title: dun1_BrdU_HU_60_min

source_name: BrdU-IP from dun1 deletion mutant in HU, 60 min

value: BrdU

value: BDBioscience 555627

value: dun1 deletion mutant

value: 60 min

source_name: Genomic DNA from Saccharomyces cerevisiae


title: fhm_ovary_bpa100_A

value: BPA

tag: gonad wt (g)

tag: ex vivo t production (ng/ml/12h)

tag: ex vivo e2 (ng/ml/12h)

tag: plasma vtg (mg/ml)

tag: array rep

value: A

tag: slide

tag: array


title: ctf4_dun1_BrdU_HU_60_min

source_name: BrdU-IP from ctf4dun1 deletion double mutant in HU, 60 min

tag: strain

tag: antibody

tag: vendor/catalog

tag: genotype/variation

value: ctf4dun1 deletion double mutant

tag: time point

value: input


title: Embryonic stem cells Rep1

tag: parental cell line

tag: cell type

value: embryonic stem cells


title: zf_ovary_bpa1_F

organism: Danio rerio

tag: ct-id

tag: agent

tag: dose

value: 1.0 µg BPA/L

tag: tissue

tag: rep(tank)

value: ZF 3

tag: take down date


title: MDAMB231-Q0 rep1

tag: treatment

value: no glutamine

tag: cell line


title: fhm_ovary_bpa10_E

value: 10 µg BPA/L

value: ovary

value: FHM 3

tag: gender

tag: FISH wet wt (g)

tag: gonad wt (g)

tag: ex vivo t production (ng/ml/12h)

tag: ex vivo e2 (ng/ml/12h)

tag: plasma vtg (mg/ml)

tag: array rep

value: E

tag: slide


title: asf1_BrdU_HU_60_min

source_name: BrdU-IP from asf1 deletion mutant in HU, 60 min

tag: strain

tag: antibody

tag: vendor/catalog

tag: genotype/variation

value: asf1 deletion mutant

tag: time point

tag: fraction


title: MDAMB231-Q4 rep3

value: 4mM glutamine


title: MDAMB231-Q4 rep2


title: MCF7-Q0 rep3


title: MDAMB231-Q4 rep1


title: fhm_ovary_bpa10_C

tag: ct-id

tag: agent

tag: dose

tag: tissue

tag: rep(tank)

value: FHM 2

tag: take down date

value: F

value: C

tag: array


title: fhm_ovary_bpa10_D

value: BPA

tag: gender

tag: FISH wet wt (g)

tag: gonad wt (g)

tag: ex vivo t production (ng/ml/12h)

tag: ex vivo e2 (ng/ml/12h)

value: D


title: HAM_Train_9

city: London

first: Charles

middle: R. M.

last: Bangham

address: Norfolk Place

department: Immunology

country: United Kingdom

institute: Imperial College London

description: globin-reduced total RNA

hyb_protocol: Following the manufacturer’s protocol, cRNA was hybridized overnight to HumanHT-12 V3 expression BeadChip arrays (Illumina, San Diego, CA, USA).

scan_protocol: Standard Illumina scanning protocol (Illumina BeadStation 500).

data_processing: Microarray signal intensity values were acquired with BeadStudio version 2.0 software (Illumina). Raw gene expression values were normalised and analysed with GeneSpring GX7.3.1 software (Agilent Technologies). Normalization followed a standard 2-step procedure for one-colour arrays: first, BeadStudio raw gene expression values were transformed by setting signal values <10 to 10, then per-gene normalisation was applied by dividing each probe’s intensity by the median intensity value for all samples.

source_name: Whole blood

label_protocol: The globin-depleted mRNA was amplified and labeled using the Illumina TotalPrep RNA Amplification kit (Ambion).

extract_protocol: RNA was extracted using the Tempus Spin Isolation kit (Applied Biosystems) and RNA quality was assessed on an Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA, USA); all samples scored integrity values ≥9 (scale: 0-10). Globin mRNA was depleted using the GLOBIN-clearTM-Human kit (Ambion, Austin, TX, USA).

tag: ethnicity

value: African Caribbean

tag: age

tag: proviral load

tag: disease status

value: HAM

tag: barcode


title: HAM_Train_8

description: globin-reduced total RNA


title: MCF7-Q0 rep1

tag: treatment

tag: cell line


title: HAM_Train_10

description: globin-reduced total RNA


title: fhm_ovary_bpa10_B

tag: ct-id

tag: agent

tag: dose

tag: plasma vtg (mg/ml)

tag: array rep

value: B

tag: slide


title: Drinking source water_3

city: Nanjing

first: Yan

last: Zhang

address: Xianlin Avenue

country: China

institute: Nanjing University

description: Gene expression data from mice liver after 90 days

hyb_protocol: Wash and stain the arrays with GeneChip® fluidics station 450.

scan_protocol: Scan the arrays with the GeneArray scanner 3000 by the GeneChip® Operating Software (GCOS) or Command Console® (AGCC) Software.

data_processing: Image analysis and quantification of probe values were performed using the GeneChip® Operating Software (Affymetrix). RMA data was generated with Partek GS 6.5.

organism: Mus musculus

source_name: Drinking source water

label_protocol: Fragmentation of the labeled aRNA prepares the target for hybridization to GeneChip® 3’ expression arrays with GeneChip® hybridization oven 640.

growth_protocol: The mice were maintained in a 12-h light/12-h dark cycle at 25°C and 50% humidity, with free access to food and water.

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

treatment_protocol: The mice were randomly divided into two groups: the control group (n=10, treated with distilled water) and the DSW group (n=10, treated with DSW)

tag: strain

tag: gender

value: male

tag: tissue

value: liver

tag: exposure duration


title: MCF7-Q4 rep3


title: HAM_Train_6

description: globin-reduced total RNA

tag: ethnicity

value: African


title: HAM_Train_7

description: globin-reduced total RNA

tag: age


title: MCF7-Q4 rep2


title: HAM_Train_5

description: globin-reduced total RNA

value: M

value: Caucasian

tag: proviral load


title: MCF7-Q0 rep2

value: no glutamine


title: Drinking source water_2


title: fhm_ovary_bpa1_E

value: 1.0 µg BPA/L

value: ovary

tag: rep(tank)

value: FHM 3

tag: take down date

tag: FISH wet wt (g)

tag: gonad wt (g)

tag: ex vivo t production (ng/ml/12h)

tag: ex vivo e2 (ng/ml/12h)

value: E

tag: array


title: Control_3

source_name: Control


title: HAM_Train_3

description: globin-reduced total RNA

value: F

tag: disease status

tag: barcode


title: Drinking source water_1


title: fhm_ovary_bpa1_C

tag: ct-id

tag: agent

tag: dose

value: FHM 2

tag: plasma vtg (mg/ml)

tag: array rep

value: C

tag: slide


title: HAM_Train_4

description: globin-reduced total RNA

tag: gender

tag: ethnicity

tag: age


title: fhm_ovary_bpa1_D

value: BPA

tag: tissue

tag: rep(tank)

tag: take down date

value: D


title: HAM_Train_2

description: globin-reduced total RNA

value: African Caribbean

tag: proviral load

value: HAM


title: fhm_ovary_bpa1_F

tag: FISH wet wt (g)

tag: gonad wt (g)

tag: ex vivo t production (ng/ml/12h)

tag: ex vivo e2 (ng/ml/12h)


title: HAM_Train_1

description: globin-reduced total RNA

tag: disease status

tag: barcode


title: fhm_ovary_bpa10_A

tag: ct-id

tag: agent

tag: dose

value: 10 µg BPA/L

value: FHM 1

value: A

tag: array


title: Control_1

tag: strain

tag: gender

value: male

value: liver

tag: exposure duration


title: G1, S & G2/M of the first cell cycle G48_repl1

first: Eric

last: Blanc

address: New Hunt's House

department: MRC Centre for Developmental Neurobiology

institute: King's College London

description: Gene expression data for cells 48 hours after activation (G1, S & G2/M of the first cell cycle)

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix Gene Chip scanner 7G.

data_processing: The data were normalised using the VSN algorithm, followed by median polish summarisation implemented in R/Bioconductor

source_name: T cells (from peripheral blood)

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Normal, non-activated, quiescent human T cells were isolated by negative selection (Dynal, InVitrogen) from single-donor buffy coats of four different donors (National Blood Service)

treatment_protocol: The T cells were stimulated with anti-CD3/CD28 magnetic beads (Dynal, InVitrogen) or PMA/ionomycin (Sigma)

tag: time [h]

tag: cell cycle phase

value: G1, S & G2/M of the first cell cycle

tag: cell type

value: T cells from peripheral blood


title: MCF7-Q4 rep1

tag: treatment

value: 4mM glutamine

tag: cell line


title: MicrodissectedHZ_14dayWtGP(Cog)_Replicate3

city: Parkville

first: Trevor

middle: L

last: Cameron

address: Royal Children's Hospital, Flemington Road

country: Australia

institute: Murdoch Childrens Research Institute

hyb_protocol: All aRNA samples were hybridized to 44K mouse whole genome microarrays (Agilent Technologies), in strict accordance with the manufacturer’s specifications.

scan_protocol: All microarrays were scanned at 5um resolution on a G2565BA DNA Microarray Scanner (Agilent Technologies),

data_processing: The scanned images were analyzed with Feature Extraction 9.5.3 software (Agilent Technologies) using default parameters. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Microdissected Wt Hypertrophic Zone (Cog Background), 2 Weeks

label_protocol: Amplified RNA samples (2ug) were labelled with Cy3 using the ULS Fluorescent Labeling Kit for Agilent Arrays (Kreatech Diagnostics), according to the manufacturer’s specifications. Fluorophore incorporation and yield were determined by spectrophotometry using a Nanodrop ND-1000 spectrophotometer (Thermo Fisher Scientific).

growth_protocol: Col10a1 p.Asn617Lys mice (Schmid), ColXTgcog mice (Cog), as well as wildtype littermates were sacrificed in accordance with Institutional Animal Ethics guidelines at two weeks post-partum.

extract_protocol: Microdissected tissues were collected in TRIzol reagent (Invitrogen) for RNA extraction and purification, which was performed following the manufacturer’s specifications. All total RNA samples were subjected to two rounds of linear amplification using the MessageAmp II aRNA Amplification Kit (Ambion), following the manufacturer’s protocol. 100-150ng of first-round amplified aRNA was used as template for each second round amplification. Following total RNA extraction and amplification, the yield, purity, and integrity of all RNA samples were validated by capillary electrophoresis with a Bioanalyzer 2100 (Agilent Technologies), using a Series II RNA 6000 Pico Kit (Agilent Technologies), according to the manufacturer’s specifications.

treatment_protocol: Tibiae were dissected and embedded in Tissue-Tek OCT (Sakura Fine Technical), snap-frozen in isopentane, and stored at -80° C. 10mm tibial sections were prepared using a cryostat (Leica CM1850), mounted on RNAse-free SuperFrost Plus slides (Biolab Scientific), and stored at -80° C. Immediately prior to microdissection, sections were fixed in 70% ethanol, rinsed in RNAse-free water, and dehydrated in 70%, 95%, and 100% ethanol for 30 seconds each, and air-dried. Schmid, Cog, and wildtype hypertrophic zones were microdissected from slides immobilized on the stage of an inverted light microscope (Leica DM IL) using an ophthalmic scalpel (Feather) fixed to the scanning xy-object guide. Light microscopy was performed using an Eclipse 80i light microscope (Nikon).

value: Cog background

tag: genotype/variation

value: wild type

tag: tissue

value: Tibial Growth Plate

tag: age

value: 14 Days


title: early G1 G02_repl1

description: Gene expression data for cells 2 hours after activation (early G1)

value: early G1


title: fhm_ovary_bpa1_A

value: BPA

value: 1.0 µg BPA/L

value: ovary

tag: rep(tank)

tag: take down date

value: F

tag: FISH wet wt (g)

tag: gonad wt (g)

tag: ex vivo t production (ng/ml/12h)

tag: ex vivo e2 (ng/ml/12h)

tag: plasma vtg (mg/ml)

tag: array rep

tag: slide


title: AC-High_Train_8

description: globin-reduced total RNA

tag: gender

tag: ethnicity

value: African Caribbean

tag: proviral load

tag: disease status

value: AC-High

tag: barcode


title: fhm_ovary_bpa1_B

tag: ct-id

tag: agent

tag: dose

value: FHM 1

value: B

tag: array


title: Control_2

tag: strain

value: male

tag: tissue

value: liver

tag: exposure duration


title: early G1 G03_repl1

description: Gene expression data for cells 3 hours after activation (early G1)

tag: time [h]

tag: cell cycle phase

tag: cell type

value: T cells from peripheral blood


title: early G1 G01_repl1

description: Gene expression data for cells 1 hour after activation (early G1)


title: MicrodissectedHZ_14dayWtGP(Cog)_Replicate1

tag: genotype/variation

tag: age


title: fhm_ovary_bpae-1_D

value: 0.1 µg BPA/L

tag: rep(tank)

value: FHM 3

tag: take down date

tag: gender

tag: FISH wet wt (g)

tag: gonad wt (g)

tag: ex vivo t production (ng/ml/12h)

tag: ex vivo e2 (ng/ml/12h)

tag: plasma vtg (mg/ml)

tag: array rep

value: D

tag: slide


title: MicrodissectedHZ_14dayWtGP(Cog)_Replicate2

tag: strain

value: Cog background

value: wild type

tag: tissue

value: Tibial Growth Plate


title: late G1 G24_repl1

description: Gene expression data for cells 24 hours after activation (late G1)

tag: time [h]

value: late G1


title: AC-High_Train_7

description: globin-reduced total RNA

tag: ethnicity

tag: proviral load

tag: disease status

tag: barcode


title: AC-High_Train_9

description: globin-reduced total RNA

value: Caucasian

tag: age


title: MicrodissectedHZ_14dayCogGP_Replicate3

source_name: Microdissected Cog Hypertrophic Zone, 2 Weeks

tag: genotype/variation

value: ColXTgcog

value: 14 Days


title: AC-High_Train_5

description: globin-reduced total RNA

tag: gender

value: F


title: AC-High_Train_6

description: globin-reduced total RNA

value: African Caribbean

value: AC-High


title: fhm_ovary_bpae-1_C

tag: ct-id

tag: agent

value: BPA

tag: dose

value: ovary

tag: rep(tank)

value: FHM 2

tag: take down date

tag: FISH wet wt (g)

value: C

tag: array


title: early G1 G08_repl3

description: Gene expression data for cells 8 hours after activation (early G1)

tag: cell cycle phase

value: early G1

tag: cell type

value: T cells from peripheral blood


title: fhm_ovary_bpae-1_E

value: 0.1 µg BPA/L

tag: tissue

value: FHM 3

tag: gonad wt (g)

tag: ex vivo t production (ng/ml/12h)

tag: ex vivo e2 (ng/ml/12h)

tag: plasma vtg (mg/ml)

tag: array rep

value: E

tag: slide


title: MicrodissectedHZ_14dayCogGP_Replicate1

tag: strain

value: Cog background

tag: genotype/variation

value: Tibial Growth Plate

tag: age


title: AC-High_Train_4

description: globin-reduced total RNA

tag: gender

tag: ethnicity

tag: proviral load

tag: disease status

tag: barcode


title: MicrodissectedHZ_14dayCogGP_Replicate2


title: fhm_ovary_bpae-1_B

tag: ct-id

tag: agent

tag: dose

tag: rep(tank)

value: FHM 1

tag: take down date

tag: FISH wet wt (g)

value: B

tag: array


title: fhm_ovary_bpae-1_A

tag: tissue

tag: gonad wt (g)

tag: ex vivo t production (ng/ml/12h)

tag: ex vivo e2 (ng/ml/12h)

tag: plasma vtg (mg/ml)

tag: array rep

value: A


title: late G1 G24_repl2

tag: time [h]

tag: cell cycle phase

value: late G1

tag: cell type


title: fhm_ovary_bpae-2_E

value: 0.01 µg BPA/L

tag: gender

value: F

tag: slide


title: MicrodissectedHZ_14dayWtGP(Sch)_Replicate3

source_name: Microdissected Wt Hypertrophic Zone (Schmid Background), 2 Weeks

tag: strain

value: Schmid background

tag: genotype/variation

value: wild type

tag: age

value: 14 Days


title: early G1 G08_repl2


title: early G1 G08_repl1


title: AC-High_Train_1

description: globin-reduced total RNA

tag: ethnicity

value: African Caribbean

tag: proviral load

tag: disease status

value: AC-High

tag: barcode


title: fhm_ovary_bpae-2_C

tag: ct-id

tag: agent

value: BPA

tag: dose

tag: tissue

value: ovary

tag: rep(tank)

value: FHM 2

tag: take down date

tag: FISH wet wt (g)

tag: gonad wt (g)

value: C

tag: array


title: AC-High_Train_2

description: globin-reduced total RNA

tag: gender

value: African


title: early G1 G04_repl2

description: Gene expression data for cells 4 hours after activation (early G1)

tag: time [h]

tag: cell cycle phase

value: early G1

tag: cell type

value: T cells from peripheral blood


title: MicrodissectedHZ_14daySchmidGP_Replicate3

source_name: Microdissected Schmid Hypertrophic Zone, 2 Weeks

tag: strain

tag: genotype/variation

value: Col10a1 p.Asn617Lys

value: Tibial Growth Plate

tag: age


title: fhm_ovary_con_B

source_name: ovary from fish exposed to control water for 96 h

value: CONTROL

tag: ex vivo t production (ng/ml/12h)

tag: ex vivo e2 (ng/ml/12h)

tag: plasma vtg (mg/ml)

tag: array rep

value: B

tag: slide


title: AC-Low_Train_9

description: globin-reduced total RNA

value: F

tag: ethnicity

tag: proviral load

tag: disease status

value: AC-Low

tag: barcode


title: early G1 G04_repl1


title: AC-High_Train_3

description: globin-reduced total RNA

value: M


title: MicrodissectedHZ_14dayWtGP(Sch)_Replicate2

value: Schmid background

value: wild type

tag: tissue

value: 14 Days


title: G0 G00_repl4

description: Gene expression data for quiescent cells


title: fhm_ovary_bpae-2_D

source_name: ovary from fish exposed to bpa for 96 h

tag: ct-id

tag: agent

value: BPA

tag: dose

value: 0.01 µg BPA/L

tag: rep(tank)

value: FHM 3

tag: take down date

tag: gender

tag: FISH wet wt (g)

tag: gonad wt (g)

value: D

tag: array


title: MicrodissectedHZ_14dayWtGP(Sch)_Replicate1

tag: strain

tag: genotype/variation

tag: age


title: fhm_ovary_bpae-2_B

value: ovary

value: FHM 2

tag: ex vivo t production (ng/ml/12h)

tag: ex vivo e2 (ng/ml/12h)

tag: plasma vtg (mg/ml)

tag: array rep

tag: slide


title: G0 G00_repl3

tag: time [h]

tag: cell cycle phase

tag: cell type

value: T cells from peripheral blood


title: MicrodissectedHZ_14daySchmidGP_Replicate2

value: Col10a1 p.Asn617Lys

tag: tissue


title: AC-Low_Train_11

description: globin-reduced total RNA

tag: ethnicity

value: African Caribbean

tag: proviral load

tag: disease status

tag: barcode


title: MicrodissectedHZ_14daySchmidGP_Replicate1

value: Tibial Growth Plate


title: AC-Low_Train_7

description: globin-reduced total RNA

tag: gender

value: Caucasian


title: G0 G00_repl2


title: fhm_ovary_bpae-2_A

tag: ct-id

tag: agent

tag: dose

tag: rep(tank)

value: FHM 1

tag: take down date

value: F

tag: FISH wet wt (g)

tag: gonad wt (g)

value: A

tag: array


title: G0 G00_repl1

tag: time [h]


title: AC-Low_Train_8

description: globin-reduced total RNA

value: M

tag: age

value: AC-Low


title: AC-Low_Train_5

description: globin-reduced total RNA


title: AC-Low_Train_6

description: globin-reduced total RNA


title: AC-Low_Train_4

description: globin-reduced total RNA


title: AC-Low_Train_1

description: globin-reduced total RNA


title: CTR_Train_9

description: globin-reduced total RNA

value: CTR


title: AC-Low_Train_2

description: globin-reduced total RNA


title: AC-Low_Train_3

description: globin-reduced total RNA


title: metestrus stage rep3

city: Taipei

first: Chung-Hao

last: Lu

state: Taipei

address: 92, Sec. 2, Zhongshan N. Rd

department: Department of Medical Research

country: Taiwan

institute: Mackay Memorial Hospital

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

source_name: mouse oviduct

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

extract_protocol: RNA was extracted, clean-up and DNase I treatment with QIAGEN RNeasy kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

tag: strain

value: ICR

value: 6 weeks

value: oviduct

tag: developmental stage

value: metestrus stage


title: CTR_Train_8

description: globin-reduced total RNA

tag: ethnicity


title: CTR_Train_6

description: globin-reduced total RNA

tag: proviral load


title: estrus stage rep3

tag: tissue

value: estrus stage


title: CTR_Train_2

description: globin-reduced total RNA

tag: disease status

tag: barcode


title: CTR_Train_4

description: globin-reduced total RNA

tag: gender


title: CTR_Train_1

description: globin-reduced total RNA


title: late G1 G16_repl1

description: Gene expression data for cells 16 hours after activation (late G1)

tag: cell cycle phase

value: late G1

tag: cell type


title: Mouse liver

city: Taichung

first: Chien-Yun

last: Hsiang

address: 91 Hsueh-Shih Road

institute: China Medical University

hyb_protocol: Fluorescent targets were hybridized to the Mouse Whole Genome OneArrayTM (Phalanx Biotech Group, Hsinchu, Taiwan).

scan_protocol: Mouse Whole Genome OneArrayTM was scanned by an Axon 4000 scanner (Molecular Devices, Sunnyvale, CA, USA).

data_processing: The Cy5 fluorescent intensity of each spot was analyzed by genepix 4.1 software (Molecular Devices). The signal intensity of each spot was corrected by subtracting background signals in the surrounding. We filtered out spots that signal-to-noise ratio was less than 1 or control probes. Spots that passed these criteria were normalized by the limma package of the R program.

source_name: Liver

label_protocol: Fluorescence-labeled RNA targets were prepared from 5 μg of total RNA using MessageAmpTM aRNA kit (Ambion, Austin, TX, USA) and cyanine (Cy5) dye (Amersham Pharmacia, Piscataway, NJ, USA).

extract_protocol: Total RNAs were extracted from organs using RNeasy Mini kit (Qiagen, Valencia, CA, USA).

value: FVB (NF-κB transgenic mice)

value: Male

value: Liver

tag: treatment

value: No


title: proestrus stage rep3

value: proestrus stage


title: proestrus stage rep2


title: estrus stage rep2


title: metestrus stage rep2


title: estrus stage rep1


title: proestrus stage rep1


title: metestrus stage rep1


title: CTR_Train_5

description: globin-reduced total RNA

value: Caucasian


title: diestrus stage rep3

value: diestrus stage


title: CTR_Train_7

description: globin-reduced total RNA

value: F


title: CTR_Train_3

description: globin-reduced total RNA

value: African Caribbean


title: Mouse liver-Radiation-3 h

value: Radiation (8.5 Gy total-body irradiation)


title: diestrus stage rep1


title: diestrus stage rep2


title: LPS & HBD3 rep 3

city: Edinburgh

first: Graeme

middle: Richard

last: Grimes

address: Western General Hospital, Crewe Road

department: Human Genetics Unit

institute: University of Edinburgh, The Institute of Genetics and Cancer

description: LPS & HBD3 rep 3

data_processing: The data were normalised using quantile normalisation with LIMMA in R

source_name: Bone marrow derived macrophages

label_protocol: Amplified, biotinylated cRNA was synthesized using Illumina® TotalPrep Amplification Kit (Ambion, Austin, Texas)

growth_protocol: Bone marrow was flushed from femurs of Balb/c mice and incubated for 7-10 days in the presence of macrophage colony stimulating factor (M-CSF, 20ng/ml)

extract_protocol: RNA was extracted using RNA bee (AMS Biotechnology)

treatment_protocol: Macrophages at a concentration 5 x 10E5 cells per well (6 well plate) were incubated overnight in the absence of M-CSF. Cells were treated as described above, then incubated for 1 hour at 37 degrees.

value: Balb/c

value: Bone marrow derived macrophages

value: LPS & hBD3

tag: time

value: 1 hour


title: Mouse brain

source_name: Brain

value: Brain


title: LPS rep 3

description: LPS rep 3

value: LPS 50ng/ml


title: Mouse intestine-Radiation-3 h

source_name: Intestine

value: Intestine


title: SigA2stat_29851002

city: Jouy en Josas

first: Nathalie

last: Pigeonneau

address: domaine de Vilvert

department: Micalis

institute: INRA

description: Stationary phase, replicate 2.

hyb_protocol: Standard NimbleGen protocol.

scan_protocol: Standard NimbleGen protocol.

data_processing:
Identification of peaks corresponding to SigA binding sites on the Bacillus subtilis chromosome was done as described previously (Reppas et al., 2006, Mol Cell 24: 747-757 [PMID 17157257]).
Signal intensities were converted as log2 ratio (ChIP-DNA/Control-DNA) and corrected for dye bias using Loess regression on the MA plot.
The signal was smoothed by two rounds of sliding window averaging. The sliding window contained 29 probes (the middle probe and 14 probes on each side) corresponding to approximately 320 bp.

organism: Bacillus subtilis

source_name: ChIP_DNA from BSB1 strain expressing SigA-SPA protein, stationary phase

label_protocol: Standard NimbleGen protocol. ChIP DNA is labelled with Cy5 and control DNA is labelled with Cy3.

growth_protocol: BSB1 cells expressing the SigA-SPA protein were grown in 2 liters of LB medium (Erythromycin 0.6 mg/L, IPTG 0.5mM) supplemented with 0.3% glucose with vigorous shaking at 37°C. At stationary growth phase (OD600nm ≈ 1.5), 400mL was treated with formaldehyde.

extract_protocol: Cells were treated with formaldehyde 0.6 % final concentration, and cross-linking was carried out for 20 minutes at room temperature before quenching with 125 mM glycine (final concentration). Cells were harvested, washed twice with buffer A (10 mM Tris-HCl pH 7.5, 150 mM NaCl) and treated with lysozyme (1 mg/mL) in buffer B (10 mM Tris-HCl pH 7.5, 150 mM NaCl, 0.2 mM EDTA, 0.1% (v/v) TritonX-100) supplemented with 0.1 mg/mL of RNase A. DNA was then sheared by sonication in order to obtain 0.2 to 1 Kbp fragments. Cell debris were removed by centrifugation at 20’000g for 30 minutes. 400 μL of Anti-FLAG M2 agarose beads (Sigma) washed with buffer B were added to the supernatant and incubation was continued for 2 h with rotation at 4 °C. Beads were then harvested, washed 3 times with large volumes of buffer B and resuspended in 500 μL of buffer C (100 mM Tris-HCl pH 8, 100 g/L SDS, 10 mM EDTA). Cross-links were dissociated by incubation at 65 °C for 18 hours. DNA fragments co-purified with SigA-SPA were extracted using the QIAquick PCR Purification kit (Qiagen). Contaminating RNA was treated with RNase A and a second purification of the DNA fragments was done. These fragments (ChIP-DNA) and DNA isolated from the whole cell extract fraction before the immunopurification (control DNA) were sent to NimbleGen.

tag: growth phase

value: stationary

tag: chip antibody

value: mouse anti-FLAG M2

tag: antibody vendor

value: Sigma

tag: antibody catalog number

tag: antibody lot number

source_name: Control_DNA from BSB1 strain expressing SigA-SPA protein, stationary phase


title: Mouse intestine

tag: strain

value: FVB (NF-κB transgenic mice)

value: Male

value: No


title: Mouse brain-radiation-3h


title: HBD3 rep 3

description: HBD3 rep 3

value: hBD3 5mg/ml


title: Untreated rep 3

description: Untreated rep 3


title: DMN3Days-2Out-rep2

city: Erie

first: Michael

middle: A

last: Campbell

state: PA

address: 4205 College Drive

department: School of Science

institute: Penn State Erie

hyb_protocol: Agilent’s Gene Expression Hybridization Kit (Cat# 5188-5242), 1.65 μg  of cyanine 3-labeled linearly amplified cRNA was added to a hybridization cocktail and  then fragmented. The hybridization cocktail was then dispensed into the wells of gasket  slides (4 samples/slide: Cat# G2534-60012) on top of which a Potato 4x44K Gene  Expression Microarray, (Cat# G2514F, AMADID 015425) was placed. This microarray  “sandwich” was then sealed in a hybridization chamber. The microarrays were  hybridized at 65°C rotating at 10 RPMs for 17 hours. Slides were washed in Agilent’s  Gene Expression Wash Buffers according to manufacturer specifications.

scan_protocol: The arrarys were scanned using an Agilent Microarrya Scanner using a single channel   microarrays were scanned on the Agilent Microarray Scanner. Scanner data extraction  and analysis was performed using Feature Extraction software version 10.7.3.1.  microarrays were scanned on the Agilent Microarray Scanner. Scanner data extraction  and analysis was performed using Feature Extraction software version 10.7.3.1.  microarrays were scanned on the Agilent Microarray Scanner. Scanner data extraction  and analysis was performed using Feature Extraction software version 10.7.3.1.

data_processing:
The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters.
Samples weree analyzed usingusing R and the limma package. The data was analyzed using single emission channel, corrected for backgroun and normalized between arrays using a loess method.  Comparisons between treatments was established using an empirical Bayes method.

organism: Solanum tuberosum

source_name: potato tubers

label_protocol: Agilent’s 1-Color Quick Amp Labeling Kit (Cat# 5190-0442)

growth_protocol: Field grown potato tubers stored at 4 C until termination of dormancy

extract_protocol: Tissue was frozen in liquid N2, total RNA was isolated using a RiboPure RNA isolation kit (www.ambion.com).

value: tuber meristems

value: DMN for three days and then vented to the air for two days


title: AC-Low_Train_10

description: globin-reduced total RNA

source_name: Whole blood

value: F

value: African Caribbean

tag: age

value: AC-Low


title: LPS & HBD3 rep 2

description: LPS & HBD3 rep 2

value: Balb/c

value: Bone marrow derived macrophages

value: LPS & hBD3


title: LPS rep 2

description: LPS rep 2

value: LPS 50ng/ml

value: 1 hour


title: Untreated rep2

description: Untreated rep2


title: HBD3 rep 1

description: BMDM HBD3 rep 1


title: DMN3Days-rep3

value: DMN for three days


title: DMN3Days-rep2


title: LPS rep 1

description: LPS rep 1


title: Untreated rep1

description: BMDM Untreated rep1


title: DMN3Days-2Out-rep3


title: LPS & HBD3 rep 1

description: LPS & HBD3 rep 1


title: HBD3 rep 2

description: HBD3 rep 2


title: DMN3Days-2Out-rep1


title: Control3Days-rep3

value: water for three days


title: DMN3Days-rep1


title: SigA2expo_29857002

description: Exponential phase, replicate 2.

source_name: ChIP_DNA from BSB1 strain expressing SigA-SPA protein, exponential phase

growth_protocol: BSB1 cells expressing the SigA-SPA protein were grown in 2 liters of LB medium (Erythromycin 0.6 mg/L, IPTG 0.5mM) supplemented with 0.3% glucose with vigorous shaking at 37°C. At mid-log growth phase (OD600nm ≈ 0.4), 1 liter was treated with formaldehyde.

value: exponential

value: mouse anti-FLAG M2

value: Sigma

source_name: Control_DNA from BSB1 strain expressing SigA-SPA protein, exponential phase


title: CD11b+Gr1+ cells from the lung of control wild type mice rep2

first: Dingcheng

last: Gao

address: 1300 York Ave

department: CT Surgery

institute: Weill Cornell Medical College

hyb_protocol: Labeled samples were hybridized 16 hours at 45° at 60rpm, followed by washing and staining with streptavidin-phycoerythrin in the Affymetrix Fluidics Station 450

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Probe level analysis was performed using robust multi array average (RMA) normalization, and data analysis was performed using ArrayAssist software package (Stratagene)
probe group file: MoEx-1_0-st-v1.r2.pgf
meta-probeset file: MoEx-1_0-st-v1.r2.dt1.mm8.mps

source_name: Lung of control wild type mice

label_protocol: RNA quality was measured using Agilent’s RNA 6000 Pico LabChip. Complementary DNA was synthesized and amplified with WT-Ovation™ Pico RNA Amplification System (NuGene Technologies Inc), followed by sense transcript cDNA generation, fragmentation and labeling with WT-Ovation™ Exon Module and FL-Ovation™ cDNA Biotin Module V2 (NuGene Technologies Inc).

growth_protocol: Mice were challenged with LLC-RFP cells (5×10^6 cells, subcutaneous injection) for 9 days. Single cell suspensions were prepared from lungs of both tumor challenged and control wild type mice and stained with antibodies against CD11b and Gr1. Approximately 1×10^5 CD11b+GR1+ myeloid progenitor cells were sorted by FACS (Aria II, BD Bioscience).

extract_protocol: Total RNA was extracted from sorted CD11b+Gr1+ cells by using Picopure RNA Isolation kit (Arcturus)

tag: days

value: Lung

tag: genotype

value: wild-type


title: CD11b+Gr1+ cells from the lung of control wild type mice rep1

tag: tissue


title: SigA1stat_29856702

description: Stationary phase, replicate 1.

value: stationary


title: Control3Days-rep2

value: tuber meristems


title: SA461 hESC endothelial differentiation Day 10 sample rep3

first: Nicole

middle: Margaret

last: Kane

address: 30 Guilford Street

institute: University College London

hyb_protocol: Hybridization was performed overnight on a µParaflo microfluidic chip using a micro-circulation pump (Atactic Technologies). On the microfluidic chip, each detection probe consisted of a chemically modified nucleotide coding segment complementary to target microRNA (from miRBase, http://microrna.sanger.ac.uk/sequences/) or other RNA (control or customer defined sequences) and a spacer segment of polyethylene glycol to extend the coding segment away from the substrate. The detection probes were made by in situ synthesis using PGR (photogenerated reagent) chemistry. The hybridization melting temperatures were balanced by chemical modifications of the detection probes. Hybridization used 100 uL 6xSSPE buffer (0.90 M NaCl, 60 mM Na2HPO4, 6 mM EDTA, pH 6.8) containing 25% formamide at 34 °C.

scan_protocol: Fluorescence images were collected using a laser scanner (GenePix 4000B, Molecular Device) and digitized using Array-Pro image analysis software (Media Cybernetics).

data_processing: Background is determined using a regression-based background mapping method. The regression is performed on 5% to 25% of the lowest intensity data points excluding blank spots. Raw data matrix is then subtracted by the background matrix.  Normalization is carried out using a LOWESS (Locally-weighted Regression) method on the background-subtracted data. The normalization is to remove system related variations, such as sample amount variations, different labeling dyes, and signal gain differences of scanners so that biological variations can be faithfully revealed [B. M. Bolstad, R. A. Irizarry, M. Astrandand T. P. Speed, (2003) A comparison of normalization methods for high density oligonucleotide array data based on variance and bias, Bioinformatics, 19 (2), 185-193].  A transcript to be listed as detectable must meets at least two conditions: signal intensity higher than 3×(background standard deviation) and spot CV < 0.5. CV is calculated by (standard deviation)/(signal intensity). When repeating probes are present on an array, a transcript is listed as detectable only if the signals from at least 50% of the repeating probes are above detection level.  t-Tests are performed between different sample groups. T-values are calculated for each miRNA, and p-values are computed from the theoretical t-distribution. miRNAs with p-values below a critical p-value (typically 0.01) are selected for cluster analysis. The clustering is done using hierarchical method and is performed with average linkage and Euclidean distance metric.  All data processes, except clustering plot, are carried out using in-house developed computer programs. The clustering plot is generated using TIGR MeV (Multiple Experimental Viewer) software from The Institute for Genomic Research.

source_name: SA461 hESC cell line

label_protocol: Microarray assay was performed using a service provider (LC Sciences). The assay started from 4 to 8 µg total RNA sample, which was size fractionated using a YM-100 Microcon centrifugal filter (Millipore) and the small RNAs (< 300 nt) isolated were 3’-extended with a poly(A) tail using poly(A) polymerase. An oligonucleotide tag was then ligated to the poly(A) tail for later fluorescent Cy3/Cy5 dye staining.

growth_protocol: hESC-ECs were derived from human embryonic stem cell line SA461 via a published directed differentiation protocol (Kane et al, ATVB, 2010). SA461 hESC cells were maintained under feeder-free pluripotent conditions.

extract_protocol: miRNeasy

tag: cell line

tag: developmental state

value: differentiation Day 10

value: Day 10


title: SA461 hESC endothelial differentiation Day 10 sample rep2


title: SA461 hESC endothelial differentiation Day 10 sample rep4


title: Control3Days-rep1


title: SigA2trans_29856602

description: Transition phase, replicate 2.

source_name: ChIP_DNA from BSB1 strain expressing SigA-SPA protein, transitive phase

growth_protocol: BSB1 cells expressing the SigA-SPA protein were grown in 2 liters of LB medium (Erythromycin 0.6 mg/L, IPTG 0.5mM) supplemented with 0.3% glucose with vigorous shaking at 37°C. At the transition growth phase (OD600nm ≈ 1.2), 400 mL was treated with formaldehyde.

value: transition

source_name: Control_DNA from BSB1 strain expressing SigA-SPA protein, transitive phase


title: SA461 hESC endothelial differentiation Day 10 sample rep1


title: CD11b+Gr1+ cells from the lung of control wild type mice rep3


title: CD11b+Gr1+ cells from the lung of tumor challenged mice rep1

source_name: Lung of tumor challenged mice

value: 9 days


title: SA461 hESC endothelial differentiation Day 4 sample rep3

value: differentiation Day 4

value: Day 4


title: SA461 hESC endothelial differentiation Day 4 sample rep4


title: Control-rep 1

value: control


title: SigA1trans_2985680

description: Transition phase, replicate 1.


title: CD11b+Gr1+ cells from the lung of  tumor challenged mice rep2


title: SA461 hESC endothelial differentiation Day 4 sample rep2


title: Control-rep 3


title: SA461 hESC endothelial differentiation Day 4 sample rep1


title: MCF7 24h rep2

first: Yi-Yu

last: Su

department: Graduate Institute of Physiology

institute: National Taiwan university

description: replicate 2

data_processing: The data were normalised using quantile normalisation in Partek

source_name: MCF7 24h

growth_protocol: a humidified incubator with 5% CO2 and 95% room air at 37℃

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: Cells were incubated in a hypoxia chamber (InVivO2-200, Ruskinn Technology, Leeds, UK) for 24 h with a hypoxia gas mixture containing 5% CO2, 95% N2 at 37 ℃.  The oxygen concentration in the hypoxic chamber was maintained at 0.5%.  After 24 h of hypoxic growth, cells were incubated in a well humidified incubator with 5% CO2 and 95% room air at 37 ℃.  Samples were collected respectively at 0, 1, 4, 8, 12 and 24 hours after reoxygenation.

value: 0.5% of hypoxia for 24h followed by 24h of reoxygenation in normoxia


title: MCF7 24h rep3

description: replicate 3


title: MCF7 24h rep1

description: replicate 1


title: SA461 hESC endothelial differentiation Day 2 sample rep4

value: differentiation Day 2

value: Day 2


title: MCF7 12h rep2

description: replicate 2

source_name: MCF7 12h

value: 0.5% of hypoxia for 24h followed by 12h of reoxygenation in normoxia


title: SA461 hESC endothelial differentiation Day 2 sample rep3


title: Control-rep 2


title: SA461 hESC endothelial differentiation Day 2 sample rep2


title: MCF7 12h rep3

description: replicate 3


title: SA461 hESC endothelial differentiation Day 2 sample rep1


title: A673 siSTEAP1_3

city: Heidelberg

first: Thomas

middle: Georg Philipp

last: Grunewald

address: Im Neuenheimer Feld 280

department: Division of Translational Pediatric Sarcoma Research

country: Germany

institute: German Cancer Research Center (DKFZ)

description:
STEAP1 knock-down
A673 cells treated with STEAP1 siRNA

hyb_protocol: The amplified and fragmented biotinylated cRNA was hybridized to Affymetrix Human Gene 1.0 ST arrays using standard procedures

scan_protocol: Genechip Scanner 3000 7G

data_processing: Normalization incorporated (separately for each RNA type data set) background correction, quantile normalization, and probe-level summation by RMA using Expression Console 1.1 (Affymetrix).

source_name: Ewing tumor cell line A673

label_protocol: Total RNA (200 ng) was amplified and labeled using the Affymetrix GeneChip Whole Transcript (WT) Sense Target Labeling Kit according to the Affymetric protocol.

growth_protocol: Cells were grown at 37°C, 95% CO2 in RPMI1640 medium, 10% fetal calf serum, 1% glutamine

extract_protocol: At 80% confluency of the cells, RNA was isolated with Trizol following the Affymetrix protocol.

treatment_protocol: A673 and SK-N-MC cells were resuspened in medium containing 5 nM siRNA reagent and incubated for 48h.

value: Ewing tumor

tag: sirna treatment group


title: SA461 time matched pluripotent hESC Day 10 sample rep4

value: pluripotent hESC Day 10


title: A673 siSTEAP1_2


title: SA461 time matched pluripotent hESC Day 10 sample rep3


title: SA461 time matched pluripotent hESC Day 10 sample rep2


title: MCF7 12h rep1

description: replicate 1


title: SK-N-MC siSTEAP1_3

description:
STEAP1 knock-down
SK-N-MC cells treated with STEAP1 siRNA

source_name: Ewing tumor cell line SK-N-MC

value: SK-N-MC


title: SigA1expo_29853902

description: Exponential phase, replicate 1.

value: exponential

value: mouse anti-FLAG M2

value: Sigma


title: SK-N-MC siSTEAP1_2


title: MCF7 4h rep2

description: replicate 2

source_name: MCF7 4h

value: 0.5% of hypoxia for 24h followed by 4h of reoxygenation in normoxia


title: MCF7 4h rep1

description: replicate 1


title: MCF7 4h rep3

description: replicate 3


title: MCF7 8h rep1

description: replicate 1

source_name: MCF7 8h

value: 0.5% of hypoxia for 24h followed by 8h of reoxygenation in normoxia


title: A673 control_2

description:
STEAP1 knock-down
A673 cells treated with control siRNA


title: SA461 time matched pluripotent hESC Day 10 sample rep1

value: Day 10


title: MCF7 1h rep3

description: replicate 3

source_name: MCF7 1h

value: 0.5% of hypoxia for 24h followed by 1h of reoxygenation in normoxia


title: MCF7 8h rep2

description: replicate 2


title: MCF7 8h rep3

description: replicate 3


title: MCF7 1h rep2

description: replicate 2


title: SK-N-MC control

description:
STEAP1 knock-down
SK-N-MC cells treated with control siRNA


title: SA461 time matched pluripotent hESC Day 4 sample rep4

value: pluripotent hESC Day 4


title: SA461 time matched pluripotent hESC Day 4 sample rep2

value: Day 4


title: SA461 time matched pluripotent hESC Day 4 sample rep3


title: MCF7 1h rep1

description: replicate 1


title: SA461 time matched pluripotent hESC Day 4 sample rep1


title: Wild type control vs. OsbZIP39deltaC-OX line 28

city: Tsukuba

first: Hideyuki

last: Takahashi

address: Kannondai 2-1-2

country: Japan

institute: National Institute of Agrobiological Sciences

description: One (line28) of two independent OsbZIP39deltaC overexpression lines.

hyb_protocol: We followed the manufacturer's instructions for the Agilent two-color experiment.

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

data_processing: Agilent Feature Extraction Software was used for background subtraction and LOWESS normalization.

organism: Oryza sativa

source_name: Wild type control

growth_protocol: 7-day-old rice seedling, growing on the MS medum

extract_protocol: Total RNA extracted using the RNeasy Plant Mini Kit following manufacturer's instructions

tag: cultivar

value: Kita-ake

value: shoot

value: wild type

source_name: OsbZIP39deltaC-OX line28

value: OsbZIP39deltaC-OX line28


title: SA461 time matched pluripotent hESC Day 2 sample rep4

value: pluripotent hESC Day 2

value: Day 2


title: Wild type control vs. OsbZIP39deltaC-OX line 12

description: One (line12) of two independent OsbZIP39deltaC overexpression lines.

label_protocol: We followed the manufacturer's instructions for the Agilent two-color experiment.

source_name: OsbZIP39deltaC-OX line12

value: OsbZIP39deltaC-OX line12


title: SA461 time matched pluripotent hESC Day 2 sample rep3


title: MCF7 0h rep1

description: replicate 1

source_name: MCF7 0h

value: 0.5% of hypoxia for 24h followed by 0h of reoxygenation in normoxia


title: SA461 time matched pluripotent hESC Day 2 sample rep2


title: MCF7 0h rep3

description: replicate 3


title: Oma1_KO

city: Oviedo

first: Jose

last: Freije

state: Asturias

address: C/ Fernando Bongera s/n

department: Bioquimica y Biologia Molecular

country: Spain

institute: Universidad de Oviedo

description: Gene expression data from white adipose tissue derived from mouse maintaing 20 weeks with high-fat diet.

hyb_protocol: Following fragmentation, cRNA were hybridized on Affymetrix Mouse Gene 1.0 ST Array according to the protocols recommended by the manufacturer (Affymetrix, Santa Clara, CA, USA).

scan_protocol: Washing and scanning were performed using Fluidics Station 400 and GeneChip Scanner (Affymetrix Inc.).

data_processing: After scanning, rawdata (Affymetrix Cel files) were processed with RMAExpress (http://RMAExpress.bmbolstad.com), using default settings

source_name: White adipose tissue derived from Oma1 KO mouse

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2001, Affymetrix).

value: white adipose tissue

value: Oma1-deficient mouse

value: 24 weeks old


title: Oma1_WT

source_name: White adipose tissue derived from Oma1 WT mouse

value: Control mouse


title: MCF7 0h rep2

description: replicate 2

hyb_protocol: Standard Illumina hybridization protocol


title: WT mice

city: Hong Kong

first: Chor Fung

last: NG

address: Shatin, New Territories

department: School of Biomedical Sciences

country: Hong Kong

institute: The Chinese University of Hong Kong

description: total RNA

hyb_protocol: Samples were hybridized to Affymetrix mouse Gene 1.0 using Affymetrix hybridization kit materials. Heat the Hybridization Cocktail at 99°C for 5 minutes. Cool to 45°C for 5 min, and centrifuge at max. speed for 1 minute. Place array in 45°C hybridization oven, at 60 rpm, and incubate for 16 h. Arrays washed using GeneChip fluidics station 450 (Affymetrix).

scan_protocol: Arrays were scanned using GeneArray Scanner 3000 (Affymetrix).

data_processing: Data was extracted from scanned images and checked for quality control with Affymetrix Expression Console software v1.0. The intensity data was normalized using RMA and expression data analysis was further performed using Partek Genomics Suite v.6.4.

source_name: wild-type liver

label_protocol: Samples were enzymatically fragmented and biotinylated using GeneChip WT Terminal Labeling Kit (Affymetrix).

growth_protocol: Livers were dissected from each animal. Left Lobe was used for RNA extraction.

extract_protocol: The livers were rinsed in cold DEPC-treated PBS to remove blood, and immediately snap-frozen in liquid nitrogen. RNA was extracted using Trizol and RNeasy Mini Kit (Qiagen) according to manufacturers' instructions. 300 ng of total RNA was reversed transcribed. cDNA synthesis and amplification was performed using GeneChip WT cDNA synthesis and amplification kit

tag: sample type

value: pooled liver RNA samples of 3 mice

tag: genetic background

value: Hybrid Black Swiss/129-SV/J

value: 10-11 weeks

value: left lobe liver

value: wild-type


title: HAM_Test_9

description: globin-reduced total RNA

hyb_protocol: Following the manufacturer’s protocol, cRNA was hybridized overnight to HumanWG6 v3 expression BeadChip arrays (Illumina, San Diego, CA, USA).

source_name: Whole blood

tag: gender

value: M

tag: ethnicity

value: Caucasian

tag: proviral load

tag: disease status

value: HAM

tag: barcode


title: FHL2 KO mice

description: total RNA

source_name: FHL2-deficient liver


title: HAM_Test_10

description: globin-reduced total RNA

value: F

value: African Caribbean


title: SA461 time matched pluripotent hESC Day 2 sample rep1

source_name: SA461 hESC cell line

value: pluripotent hESC Day 2

tag: time

value: Day 2


title: SA461 Parental pluripotent hESC control sample rep4

value: Parental pluripotent hESC control

value: control


title: DKO + FliC 2

city: Atlanta

first: Gregory

last: Doho

address: 1365B Clifton Rd NE

institute: Emory University

scan_protocol: BeadChips were scanned using Illumina BeadArray Scanner

data_processing: The data were normalized using quantile-normalization with GenomeStudio V2010.2

source_name: DKO + FliC

label_protocol: PCR product was prepared with standard Illumina protocol for arrays

growth_protocol: Generation of WT, T5KO, N4KO and T5/N4-DKO was previously described 7. Mice were bred and maintained at Emory University and used between 6 and 8 weeks of age.

extract_protocol: Total RNA was isolated using RNeasy kits (QIAGEN, Valencia, CA) according to manufacturer instructions.

treatment_protocol: Flagellin (FliC) from WT Salmonella enterica serovar Typhimurium (SL3201, fljB–) was purified through sequential cation and anion-exchange chromatography and purity was verified as previously described.

tag: mouse ko type

value: DKO

tag: tissue type

value: Colon

tag: treatment

value: Flagelin


title: DKO + PBS 3

source_name: DKO + PBS

value: PBS


title: DKO + FliC 3


title: SA461 Parental pluripotent hESC control sample rep3


title: SA461 Parental pluripotent hESC control sample rep2


title: HAM_Test_7

first: Charles

last: Bangham

institute: Imperial College London

description: globin-reduced total RNA

data_processing: Microarray signal intensity values were acquired with BeadStudio version 2.0 software (Illumina). Raw gene expression values were normalised and analysed with GeneSpring GX7.3.1 software (Agilent Technologies). Normalization followed a standard 2-step procedure for one-colour arrays: first, BeadStudio raw gene expression values were transformed by setting signal values <10 to 10, then per-gene normalisation was applied by dividing each probe’s intensity by the median intensity value for all samples.

tag: age


title: DKO + FliC 1


title: HAM_Test_8

description: globin-reduced total RNA


title: HAM_Test_6

description: globin-reduced total RNA


title: HAM_Test_4

description: globin-reduced total RNA


title: HAM_Test_5

description: globin-reduced total RNA


title: HAM_Test_3

description: globin-reduced total RNA


title: IPAFKO + FliC 3

source_name: IPAFKO + FliC

value: IPAFKO


title: DKO + PBS 2


title: DKO + PBS 1


title: HAM_Test_2

description: globin-reduced total RNA


title: ES

city: Suita

first: hideshi

last: ishii

state: Osaka

address: Yamadaoka 2-2

department: Department of Gastroenterological Surgery

institute: Osaka University Graduate School of Medicine

description: TaqMan Array Mouse Stem Cell Pluripotency Card

hyb_protocol: not applicable

scan_protocol: using HT7900

data_processing: Reverse transcription of mRNA was performed using SuperScriptIII (Invitrogen). To confirm the PCR amplification of cDNA, 25–35 cycles of PCR were performed using a PCR kit (Takara, Kyoto, Japan) on the Geneamp PCR system 9600 (Applied Biosystems). For quantitative assessments, gene expression was evaluated by real-time RT-PCR analysis using the TaqMankit (Applied Biosystems).

source_name: ES

label_protocol: not applicable

growth_protocol: Cultured in DMEM or ES certified medium with 10% FBS

extract_protocol: Using a RNA extraction kit (Qiagen)

tag: cell type

value: ES


title: IPAFKO + FliC 1


title: IPAFKO + FliC 2


title: HAM_Test_1

address: Norfolk Place

description: globin-reduced total RNA

label_protocol: The globin-depleted mRNA was amplified and labeled using the Illumina TotalPrep RNA Amplification kit (Ambion).


title: mi-iPS

source_name: mi-iPS

treatment_protocol: Reverse transcription of mRNA was performed using SuperScriptIII (Invitrogen).

value: mi-iPS


title: Chinese Spring PEG LYC-DIG

city: Zhengzhou

first: Yongchun

last: Li

state: Henan

address: Nongye Road No. 62

department: National Engineering Research Center for Wheat

institute: Henan Agricultural University

description: Chinese Spring

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip wheat Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneArrayTM scanner 3000.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

organism: Triticum aestivum

source_name: roots PEG

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

growth_protocol: Seeds were surface-sterilized in 70% alcohol for 5 min, 0.1% HgCl for 15min and washed 6 times (2 min each) in distilled water, then germinated and cultured in Petri dishes with water in a temperature-controlled cultivation chamber at 25 °C with a 14 hour photoperiod.

extract_protocol: RNA was extracted using Trizol (Invitrogen) and purified by RNeasy Mini Kit (Qiagen). Purified RNAs were labeled and prepared for hybridization according to the protocols (Section 2: Eukaryotic Sample and Array Processing) outlined in the GeneChip® Expression Analysis Technical Manual (http://www.affymetrix. com/support/technical/manual/ expression_manual.affx).

treatment_protocol: Seedlings at the two leaf stage were stressed by polyethyleneglycol (PEG) 6000 solutions and the osmotic potential is -0.49 MPa.

tag: tissue

value: roots

value: Chinese Spring

value: PEG


title: IPAFKO + PBS 3

source_name: IPAFKO + PBS


title: IPAFKO + PBS 2


title: Luohan PEG DIG-4-2

description: Luohan 2 cultivar

value: Luohan No. 2


title: IPAFKO + PBS 1


title: AC_Test_17

description: globin-reduced total RNA

scan_protocol: Standard Illumina scanning protocol (Illumina BeadStation 500).

extract_protocol: RNA was extracted using the Tempus Spin Isolation kit (Applied Biosystems) and RNA quality was assessed on an Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA, USA); all samples scored integrity values ≥9 (scale: 0-10). Globin mRNA was depleted using the GLOBIN-clearTM-Human kit (Ambion, Austin, TX, USA).

value: F

value: AC


title: mASC_parent

value: mASC