title: RT_240_13_6_Lung_Benzofuran_Mouse430_2_IMFGN0023_8

description: Gene expression changes in female mouse lung tissue treated for 90 days with BFUR

treatment_protocol:
Tissue Harvest Methods: Tissue was excised from animal, minced, placed in RNA later, and stored at -80 degrees Centigrade.

in vivo Treatment: 2,3-Benzofuran, Treatment Repeat: 1, Units of Treatment Repeat: per day, Treatment Duration: 13, Units of Duration: weeks, Treatment Time: 5, Units of Treatment Time: days/wk, Vehicle for Chemical: Corn oil, Amount of Vehicle: 5, Route of Exposure: Gavage, Units of Amount of Vehicle: ml/kg, Dose or Concentration: 240, Units of Dose or Concentration: mg/kg

tag: amount to core

value: ug

tag: strain or line


title: genotype: Incrocio Manzoni - disease type: Healthy - rep2

status: Public on Sep 09 2009

type: RNA

city: Ames

first: PLEXdb Curator

middle: Sudhansu

state: IA

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

department: Virtual Reality Application Center

country: USA

institute: Iowa State University

description: Phytoplasma-free field-grown Incrocio Manzoni plant

hyb_protocol: Affy- Eukaryotic Target Hybridization

scan_protocol: Affy- Array Scanning

data_processing: The MAS5.0 Normalization is performed using the justMAS function in the simpleaffy package of Bioconductor (www.bioconductor.org). The target value is 500 for all cases. The code was developed using R2.4.1, Bioconductor 1.9, and simpleaffy 2.8.0. The CDF files were downloaded from the Bioconductor website at http://www.bioconductor.org/packages/release/AffymetrixChip.html. The normalization scripts are available from the PLEXdb team by request.

label: biotin

molecule: total RNA

organism: Vitis vinifera

source_name: leaf vein (genotype: Incrocio Manzoni - disease type: Healthy)

label_protocol: Affy-Eukaryotic Target Preparation

extract_protocol: Tris-LiCl

tag: Cultivar Incrocio Manzoni 60.13 (Riesling Renano x Pinot Bianco) (Germplasm Name); PO:0020138 leaf vein, (Organism Part); PO:0009012 plant growth and development stages (Development Stage); field soil (Growth Media).


title: WT Arabidopsis seedlings replicate 2

city: Barcelona

first: Paloma

last: Mas

address: C/ Jordi Girona 18-26

department: Genetica Molecular

country: Spain

institute: Consorcio CSIC-IRTA-UAB (CRAG)

description: Genome expression data from WT Arabidopsis seedlings

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on ATH1 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix 7G Scanner using AGCC software version 1.1

data_processing: Carmaweb software (https://carmaweb.genome.tugraz.at) was used for data processing with the gcRMA algorythm for normalization. Differentially expressed genes were identified using the empirical Bayes moderated t statistics from the LiMMA package. Genes with an FDR < 5% were selected as misregulated in TOC1-ox

organism: Arabidopsis thaliana

source_name: WT

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (Expression Analysis Technical Manual Rev. 3, 2005, Affymetrix).

growth_protocol: Seedlings were grown on MS3 medium under 12-hour light:12-hour dark (LD) cycles for 12 days.

extract_protocol: Total RNA extractions were performed with Pure Link Total RNA Purification System (Invitrogen).

treatment_protocol: Samples were collected at Zeitgeber Time 15 (ZT15).

tag: ecotype

tag: age

value: 12 days old seedlings


title: Granulocytes_fresh_control_donorA

city: Amsterdam

first: Agata

last: Drewniak

address: Plesmanlaan 125

department: Blood Cell Research

country: Netherlands

institute: Sanquin Research

description: Biological replicate 1 of 3

hyb_protocol: Agilent Technologies (Santa Clara, CA) following manufacturer’s protocol.

data_processing: The default Agilent normalization procedure, called Linear & Lowess, was applied.Exact protocol and parameter settings are described in the Agilent Feature Extraction Software User Manual 8.5 (http://chem.agilent.com/scripts/LiteraturePDF.asp?iWHID=37629).

organism: Homo sapiens

label_protocol: Dye Coupling Reaction (Amersham, England)

growth_protocol: ex vivo isolated granulocytes

extract_protocol: Total RNA extracted using Trizol according to the  manufacturer's instruction followed by additional purification using nucleospin RNA isolation kit (Machery-Nagel, Düren, Germany)

tag: granulocytes fresh

tag: control

source_name: pooled Total RNA from freshly isolated control granulocytes

tag: granulocytes

tag: percoll isolated granulocytes


title: Granulocytes_cultured18h_G-CSF/dex_donorB

description: Biological replicate 2 of 3

scan_protocol: Agilent Technologies (Santa Clara, CA) following manufacturer’s protocol.

tag: granulocytes cultured

tag: HBSS medium + G-CSF&dex 18hours


title: TOC1-ox Arabidopsis seedlings replicate 1

description: Genome expression data from TOC1-ox Arabidopsis seedlings


title: RT_2000_13_2_Lung_Naphthalenediamine_Mouse430_2_IMFGN0023_8

city: Research Triangle Park

first: Russell

middle: Scott

last: Thomas

state: NC

address: 6 Davis Drive

institute: The Hamner Institutes for Health Sciences

description: Gene expression changes in female mouse lung tissue treated for 90 days with NAPD

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: Grouped-Batch-Profile normalization

organism: Mus musculus

label_protocol: standard Affymetrix protocol

extract_protocol:
Extraction Method: Trizol
Additional Purification Method: Qiagen Rneasy

treatment_protocol:
Tissue Harvest Methods: Tissue was excised from animal, minced, placed in RNA later, and stored at -80 degrees Centigrade.

in vivo Treatment: 1,5-Naphthalenediamine, Treatment Duration: 13, Units of Duration: weeks, Treatment Time: 7, Units of Treatment Time: days/wk, Vehicle for Chemical: Rodent Chow, Route of Exposure: Diet, Dose or Concentration: 2000, Units of Dose or Concentration: ppm

tag: sample type

value: tissue

tag: tissue

value: lung

tag: array type

value: Affymetrix Mouse 430_2

tag: units of amount

tag: ratio

tag: rna integrity number

tag: bioanalyzer results

value: Good

tag: sample preservation

value: RNA later

tag: ncbi taxonomy id

tag: developmental stage

value: adult

tag: sacrifice method

value: Pentobarbital (5.2 mg/kg) and exsanguination

tag: gender

value: female

value: 18 weeks


title: RT_2000_13_14_Lung_ethylenediamine_Mouse430_2_IMFGN0023_8

description: Gene expression changes in female mouse lung tissue treated for 90 days with NEDD

treatment_protocol:
Tissue Harvest Methods: Tissue was excised from animal, minced, placed in RNA later, and stored at -80 degrees Centigrade.

in vivo Treatment: N-(1-naphthyl)ethylenediamine dihydrochloride, Treatment Duration: 13, Units of Duration: week, Treatment Time: 7, Units of Treatment Time: days/wk, Vehicle for Chemical: Rodent Chow, Route of Exposure: Diet, Dose or Concentration: 2000, Units of Dose or Concentration: ppm

tag: amount to core

value: ul

value: excellent

tag: strain or line

tag: individual

tag: age


title: RT_30_13_282_NPTH-30_Lung_07008_Mouse430_2_RSTLRI000_2

description: Gene expression changes in female mouse lung tissue treated for 90 days with NPTH

treatment_protocol:
Tissue Harvest Methods: Tissue was excised from animal, minced, placed in RNA later, and stored at -80 degrees Centigrade.

in vivo Treatment: Naphthalene, Treatment Repeat: 6, Units of Treatment Repeat: hr/day, Treatment Duration: 13, Units of Duration: weeks, Treatment Time: 5, Units of Treatment Time: days/wk, Vehicle for Chemical: Air, Route of Exposure: Inhalation, Dose or Concentration: 30, Units of Dose or Concentration: ppm

tag: dilution


title: RT_3925_13_201_TCFM_Mus_Lung_Mouse430_2_RT_HON07_MusLung

description: Gene expression changes in female mouse lung tissue treated for 90 days with TCFM

treatment_protocol:
Tissue Harvest Methods: Tissue was excised from animal, minced, placed in RNA later, and stored at -80 degrees Centigrade, Harvest Time Point: 13, Units of Harvest Time Point: weeks

in vivo Treatment: Trichlorofluoromethane, Treatment Repeat: 1, Units of Treatment Repeat: per day, Treatment Duration: 13, Units of Duration: weeks, Treatment Time: 5, Units of Treatment Time: days/wk, Vehicle for Chemical: Corn Oil, Amount of Vehicle: 5, Route of Exposure: Gavage, Units of Amount of Vehicle: ml/kg, Dose or Concentration: 3925, Units of Dose or Concentration: mg/kg

tag: sample type

value: good


title: genotype: Incrocio Manzoni - disease type: Bois Noir infected - rep2

description: Field-grown Incrocio Manzoni plant naturally infected with Bois Noir phytoplasma

source_name: leaf vein (genotype: Incrocio Manzoni - disease type: Bois Noir infected)

tag: Cultivar Incrocio Manzoni 60.13 (Riesling Renano x Pinot Bianco) (Germplasm Name); PO:0020138 leaf vein, (Organism Part); PO:0009012 plant growth and development stages (Development Stage); field soil (Growth Media).


title: RT_3000_13_207_MECL-3000_Lung_07008_Mouse430_2_RSTLRI000_2

description: Gene expression changes in female mouse lung tissue treated for 90 days with MECL

treatment_protocol:
Tissue Harvest Methods: Tissue was excised from animal, minced, placed in RNA later, and stored at -80 degrees Centigrade.

in vivo Treatment: Methylene Chloride, Treatment Repeat: 6, Units of Treatment Repeat: hr/day, Treatment Duration: 13, Units of Duration: weeks, Treatment Time: 5, Units of Treatment Time: days/wk, Vehicle for Chemical: Air, Route of Exposure: Inhalation, Dose or Concentration: 3000, Units of Dose or Concentration: ppm

tag: tissue

tag: array type


title: genotype: Incrocio Manzoni - disease type: Healthy - rep1


title: genotype: Incrocio Manzoni - disease type: Bois Noir infected - rep1


title: genotype: Chardonnay - disease type: Healthy - rep1

description: Phytoplasma-free field-grown Chardonnay plant

source_name: leaf vein (genotype: Chardonnay - disease type: Healthy)

tag: Cultivar Chardonnay (Germplasm Name); PO:0020138 leaf vein, (Organism Part); PO:0009012 plant growth and development stages (Development Stage); field soil (Growth Media).


title: RT_0_13_124_Lu_WCO1_Mouse430_2_RSTLRI601_1

description: Gene expression changes in female mouse lung tissue treated for 90 days with CTRL

treatment_protocol:
Tissue Harvest Methods: Tissue was excised from animal, minced, placed in RNA later, and stored at -80 degrees Centigrade.

in vivo Treatment: Distilled Water, Treatment Repeat: 1, Units of Treatment Repeat: per day, Treatment Duration: 13, Units of Duration: weeks, Treatment Time: 5, Units of Treatment Time: days/wk, Vehicle for Chemical: Distilled water, Amount of Vehicle: 5, Route of Exposure: Gavage, Units of Amount of Vehicle: ml/kg, Dose or Concentration: 0, Units of Dose or Concentration: mg/kg

tag: units of amount

tag: ratio

tag: rna integrity number


title: genotype: Chardonnay - disease type: Healthy - rep2


title: RT_3925_13_210_TCFM_Mus_Lung_Mouse430_2_RT_HON07_MusLung

source_name: female mouse lung tissue treated for 90 days with TCFM

tag: bioanalyzer results

tag: sample preservation

tag: ncbi taxonomy id


title: genotype: Chardonnay - disease type: Healthy - rep3


title: RT_0_13_174_CCO6_Lung_07008_Mouse430_2_RSTLRI000_2

source_name: female mouse lung tissue treated for 90 days with CTRL

treatment_protocol:
Tissue Harvest Methods: Tissue was excised from animal, minced, placed in RNA later, and stored at -80 degrees Centigrade.

in vivo Treatment: Corn Oil, Treatment Repeat: 1, Units of Treatment Repeat: per day, Treatment Duration: 13, Units of Duration: weeks, Treatment Time: 5, Units of Treatment Time: days/wk, Vehicle for Chemical: Corn Oil, Amount of Vehicle: 5, Route of Exposure: Gavage, Units of Amount of Vehicle: ml/kg, Dose or Concentration: 0, Units of Dose or Concentration: mg/kg

tag: developmental stage

tag: sacrifice method

tag: gender


title: RT_0_13_119_ACO3_Lung_07008_Mouse430_2_RSTLRI000_2

treatment_protocol:
Tissue Harvest Methods: Tissue was excised from animal, minced, placed in RNA later, and stored at -80 degrees Centigrade.

in vivo Treatment: Air, Treatment Repeat: 6, Units of Treatment Repeat: hr/day, Treatment Duration: 13, Units of Duration: weeks, Treatment Time: 5, Units of Treatment Time: days/wk, Vehicle for Chemical: Air, Route of Exposure: Inhalation, Dose or Concentration: 0, Units of Dose or Concentration: mg/m3

tag: amount to core

tag: strain or line

tag: individual


title: RT_0_13_238_ACO4_Lung_07008_Mouse430_2_RSTLRI000_2

treatment_protocol:
Tissue Harvest Methods: Tissue was excised from animal, minced, placed in RNA later, and stored at -80 degrees Centigrade.

in vivo Treatment: Air, Treatment Repeat: 6, Units of Treatment Repeat: hr/day, Treatment Duration: 13, Units of Duration: weeks, Treatment Time: 5, Units of Treatment Time: days/wk, Vehicle for Chemical: Air, Route of Exposure: Inhalation, Dose or Concentration: 0, Units of Dose or Concentration: ppm

tag: sample type

tag: dilution

tag: age


title: RT_0_13_239_ACO4_Lung_07008_Mouse430_2_RSTLRI000_2

tag: tissue

tag: array type


title: genotype: Chardonnay - disease type: Bois Noir infected - rep2

description: Field-grown Chardonnay plant naturally infected with Bois Noir phytoplasma

source_name: leaf vein (genotype: Chardonnay - disease type: Bois Noir infected)

tag: Cultivar Chardonnay (Germplasm Name); PO:0020138 leaf vein, (Organism Part); PO:0009012 plant growth and development stages (Development Stage); field soil (Growth Media).


title: RT_0_13_263_FCO1_Mus_Lung_Mouse430_2_RT_HON07_MusLung

treatment_protocol:
Tissue Harvest Methods: Tissue was excised from animal, minced, placed in RNA later, and stored at -80 degrees Centigrade, Harvest Time Point: 13, Units of Harvest Time Point: weeks

in vivo Treatment: Rodent Chow, Treatment Duration: 13, Units of Duration: weeks, Treatment Time: 7, Units of Treatment Time: days/wk, Vehicle for Chemical: Rodent Chow, Route of Exposure: Diet, Dose or Concentration: 0, Units of Dose or Concentration: ppm

tag: units of amount

tag: ratio


title: genotype: Chardonnay - disease type: Bois Noir infected - rep3


title: genotype: Chardonnay - disease type: Bois Noir infected - rep1


title: RT_0_13_95_Lu_CCO2_Mouse430_2_RSTLRI601_1

tag: rna integrity number

tag: bioanalyzer results


title: WT Arabidopsis seedlings replicate 1

tag: ecotype


title: RT_0_13_93_Lu_CCO2_Mouse430_2_RSTLRI601_1

tag: sample preservation

tag: ncbi taxonomy id

tag: developmental stage


title: RT_05_13_242_NPTH-05_Lung_07008_Mouse430_2_RSTLRI000_2

source_name: female mouse lung tissue treated for 90 days with NPTH

treatment_protocol:
Tissue Harvest Methods: Tissue was excised from animal, minced, placed in RNA later, and stored at -80 degrees Centigrade.

in vivo Treatment: Naphthalene, Treatment Repeat: 6, Units of Treatment Repeat: hr/day, Treatment Duration: 13, Units of Duration: weeks, Treatment Time: 5, Units of Treatment Time: days/wk, Vehicle for Chemical: Air, Route of Exposure: Inhalation, Dose or Concentration: 0.5, Units of Dose or Concentration: ppm

tag: amount to core

tag: sacrifice method

tag: gender


title: RT_05_13_244_NPTH-05_Lung_07008_Mouse430_2_RSTLRI000_2

tag: sample type

tag: strain or line

tag: individual


title: RT_2_13_107_VANP-2_Lung_07008_Mouse430_2_RSTLRI000_2

description: Gene expression changes in female mouse lung tissue treated for 90 days with VANP

treatment_protocol:
Tissue Harvest Methods: Tissue was excised from animal, minced, placed in RNA later, and stored at -80 degrees Centigrade.

in vivo Treatment: Vanadium Pentoxide, Treatment Repeat: 6, Units of Treatment Repeat: hr/day, Treatment Duration: 13, Units of Duration: weeks, Treatment Time: 5, Units of Treatment Time: days/wk, Vehicle for Chemical: Air, Route of Exposure: Inhalation, Dose or Concentration: 2, Units of Dose or Concentration: mg/m3

tag: tissue

tag: dilution

tag: age


title: RT_10_13_263_NPTH-10_Lung_07008_Mouse430_2_RSTLRI000_2

treatment_protocol:
Tissue Harvest Methods: Tissue was excised from animal, minced, placed in RNA later, and stored at -80 degrees Centigrade.

in vivo Treatment: Naphthalene, Treatment Repeat: 6, Units of Treatment Repeat: hr/day, Treatment Duration: 13, Units of Duration: weeks, Treatment Time: 5, Units of Treatment Time: days/wk, Vehicle for Chemical: Air, Route of Exposure: Inhalation, Dose or Concentration: 10, Units of Dose or Concentration: ppm

tag: array type

tag: units of amount


title: RT_20_13_273_NPTH-20_Lung_07008_Mouse430_2_RSTLRI000_2

treatment_protocol:
Tissue Harvest Methods: Tissue was excised from animal, minced, placed in RNA later, and stored at -80 degrees Centigrade.

in vivo Treatment: Naphthalene, Treatment Repeat: 6, Units of Treatment Repeat: hr/day, Treatment Duration: 13, Units of Duration: weeks, Treatment Time: 5, Units of Treatment Time: days/wk, Vehicle for Chemical: Air, Route of Exposure: Inhalation, Dose or Concentration: 20, Units of Dose or Concentration: ppm

tag: ratio

tag: rna integrity number


title: RT_10_13_265_NPTH-10_Lung_07008_Mouse430_2_RSTLRI000_2

tag: bioanalyzer results


title: RT_50_13_101_Lu_MACR_Mouse430_2_RSTLRI601_1

description: Gene expression changes in female mouse lung tissue treated for 90 days with MACR

treatment_protocol:
Tissue Harvest Methods: Tissue was excised from animal, minced, placed in RNA later, and stored at -80 degrees Centigrade.

in vivo Treatment: N-Methylolacrylamide, Treatment Repeat: 1, Units of Treatment Repeat: per day, Treatment Duration: 13, Units of Duration: weeks, Treatment Time: 5, Units of Treatment Time: days/wk, Vehicle for Chemical: Distilled water, Amount of Vehicle: 5, Route of Exposure: Gavage, Units of Amount of Vehicle: ml/kg, Dose or Concentration: 50, Units of Dose or Concentration: mg/kg

tag: sample preservation


title: RT_1250_13_276_TFEL_Mus_Lung_Mouse430_2_RT_HON07_MusLung

description: Gene expression changes in female mouse lung tissue treated for 90 days with TFEL

treatment_protocol:
Tissue Harvest Methods: Tissue was excised from animal, minced, placed in RNA later, and stored at -80 degrees Centigrade, Harvest Time Point: 13, Units of Harvest Time Point: weeks

in vivo Treatment: Tetrafluoroethylene, Treatment Repeat: 6, Units of Treatment Repeat: hr/day, Treatment Duration: 13, Units of Duration: weeks, Treatment Time: 5, Units of Treatment Time: days/wk, Vehicle for Chemical: Air, Route of Exposure: Inhalation, Dose or Concentration: 1250, Units of Dose or Concentration: ppm

tag: ncbi taxonomy id


title: RT_30_13_283_NPTH-30_Lung_07008_Mouse430_2_RSTLRI000_2

tag: developmental stage


title: RT_0_13_25_Lung_CornOil_Mouse430_2_IMFGN0023_8

treatment_protocol:
Tissue Harvest Methods: Tissue was excised from animal, minced, placed in RNA later, and stored at -80 degrees Centigrade.

in vivo Treatment: Corn Oil, Treatment Repeat: 1, Units of Treatment Repeat: per day, Treatment Duration: 13, Units of Duration: weeks, Treatment Time: 5, Units of Treatment Time: days/wk, Vehicle for Chemical: Corn oil, Amount of Vehicle: 5, Route of Exposure: Gavage, Units of Amount of Vehicle: ml/kg, Dose or Concentration: 0, Units of Dose or Concentration: mg/kg

tag: amount to core


title: RT_20000_13_243_ABDQ_Mus_Lung_Mouse430_2_RT_HON07_MusLung

description: Gene expression changes in female mouse lung tissue treated for 90 days with ABDQ

treatment_protocol:
Tissue Harvest Methods: Tissue was excised from animal, minced, placed in RNA later, and stored at -80 degrees Centigrade, Harvest Time Point: 13, Units of Harvest Time Point: weeks

in vivo Treatment: 1-Amino-2,4-dibromoanthraquinone, Treatment Duration: 13, Units of Duration: weeks, Treatment Time: 7, Units of Treatment Time: days/wk, Vehicle for Chemical: Rodent Chow, Route of Exposure: Diet, Dose or Concentration: 20000, Units of Dose or Concentration: ppm

tag: sacrifice method


title: RT_240_13_8_Lung_Benzofuran_Mouse430_2_IMFGN0023_8

description: Gene expression changes in female mouse lung tissue treated for 90 days with BFUR

treatment_protocol:
Tissue Harvest Methods: Tissue was excised from animal, minced, placed in RNA later, and stored at -80 degrees Centigrade.

in vivo Treatment: 2,3-Benzofuran, Treatment Repeat: 1, Units of Treatment Repeat: per day, Treatment Duration: 13, Units of Duration: weeks, Treatment Time: 5, Units of Treatment Time: days/wk, Vehicle for Chemical: Corn oil, Amount of Vehicle: 5, Route of Exposure: Gavage, Units of Amount of Vehicle: ml/kg, Dose or Concentration: 240, Units of Dose or Concentration: mg/kg

value: Excellent

tag: gender


title: RT_0_13_51_CCO5_Lung_07008_Mouse430_2_RSTLRI000_2

tag: sample type


title: RT_0_13_28_Lung_RodentChow_Mouse430_2_IMFGN0023_8

treatment_protocol:
Tissue Harvest Methods: Tissue was excised from animal, minced, placed in RNA later, and stored at -80 degrees Centigrade.

in vivo Treatment: Rodent Chow, Treatment Duration: 13, Units of Duration: weeks, Treatment Time: 7, Units of Treatment Time: days/wk, Vehicle for Chemical: Rodent Chow, Route of Exposure: Diet, Dose or Concentration: 0, Units of Dose or Concentration: ppm

tag: strain or line


title: RT_2000_13_15_Lung_ethylenediamine_Mouse430_2_IMFGN0023_8

source_name: female mouse lung tissue treated for 90 days with NEDD

treatment_protocol:
Tissue Harvest Methods: Tissue was excised from animal, minced, placed in RNA later, and stored at -80 degrees Centigrade.

in vivo Treatment: N-(1-naphthyl)ethylenediamine dihydrochloride, Treatment Duration: 13, Units of Duration: week, Treatment Time: 7, Units of Treatment Time: days/wk, Vehicle for Chemical: Rodent Chow, Route of Exposure: Diet, Dose or Concentration: 2000, Units of Dose or Concentration: ppm

tag: individual


title: RT_0_13_45_Lu_FCO2_Mouse430_2_RSTLRI601_1

tag: tissue


title: RT_0_13_258_FCO1_Mus_Lung_Mouse430_2_RT_HON07_MusLung

tag: dilution


title: RT_0_13_29_Lung_RodentChow_Mouse430_2_IMFGN0023_8

tag: age


title: RT_2000_13_199_MECL-2000_Lung_07008_Mouse430_2_RSTLRI000_2

source_name: female mouse lung tissue treated for 90 days with MECL

treatment_protocol:
Tissue Harvest Methods: Tissue was excised from animal, minced, placed in RNA later, and stored at -80 degrees Centigrade.

in vivo Treatment: Methylene Chloride, Treatment Repeat: 6, Units of Treatment Repeat: hr/day, Treatment Duration: 13, Units of Duration: weeks, Treatment Time: 5, Units of Treatment Time: days/wk, Vehicle for Chemical: Air, Route of Exposure: Inhalation, Dose or Concentration: 2000, Units of Dose or Concentration: ppm

tag: array type


title: RT_2000_13_200_MECL-2000_Lung_07008_Mouse430_2_RSTLRI000_2

tag: units of amount


title: RT_2_13_106_VANP-2_Lung_07008_Mouse430_2_RSTLRI000_2

source_name: female mouse lung tissue treated for 90 days with VANP

tag: ratio


title: RT_0_13_53r_CCO5_Lung_07008_Mouse430_2_RSTLRI000_2

tag: rna integrity number


title: RT_0_13_55r_CCO5_Lung_07008_Mouse430_2_RSTLRI000_2

tag: bioanalyzer results


title: RT_500_13_187_MECL-500_Lung_07008_Mouse430_2_RSTLRI000_2

treatment_protocol:
Tissue Harvest Methods: Tissue was excised from animal, minced, placed in RNA later, and stored at -80 degrees Centigrade.

in vivo Treatment: Methylene Chloride, Treatment Repeat: 6, Units of Treatment Repeat: hr/day, Treatment Duration: 13, Units of Duration: weeks, Treatment Time: 5, Units of Treatment Time: days/wk, Vehicle for Chemical: Air, Route of Exposure: Inhalation, Dose or Concentration: 500, Units of Dose or Concentration: ppm

tag: sample preservation


title: RT_0_13_59_Lu_CCO3_Mouse430_2_RSTLRI601_1

treatment_protocol:
Tissue Harvest Methods: Tissue was excised from animal, minced, placed in RNA later, and stored at -80 degrees Centigrade.

in vivo Treatment: Corn Oil, Treatment Repeat: 1, Units of Treatment Repeat: per day, Treatment Duration: 13, Units of Duration: weeks, Treatment Time: 5, Units of Treatment Time: days/wk, Vehicle for Chemical: Corn Oil, Amount of Vehicle: 5, Route of Exposure: Gavage, Units of Amount of Vehicle: ml/kg, Dose or Concentration: 0, Units of Dose or Concentration: mg/kg

tag: ncbi taxonomy id


title: RT_0_13_266_FCO1_Mus_Lung_Mouse430_2_RT_HON07_MusLung

tag: developmental stage


title: RT_10000_13_13_Lu_NAAC_Mouse430_2_RSTLRI601_1

description: Gene expression changes in female mouse lung tissue treated for 90 days with NAAC

treatment_protocol:
Tissue Harvest Methods: Tissue was excised from animal, minced, placed in RNA later, and stored at -80 degrees Centigrade.

in vivo Treatment: 4-Nitroanthranilic acid, Treatment Duration: 13, Units of Duration: weeks, Treatment Time: 7, Units of Treatment Time: days/wk, Vehicle for Chemical: Rodent Chow, Route of Exposure: Diet, Dose or Concentration: 10000, Units of Dose or Concentration: ppm

tag: amount to core


title: RT_100_13_177_MECL-100_Lung_07008_Mouse430_2_RSTLRI000_2

treatment_protocol:
Tissue Harvest Methods: Tissue was excised from animal, minced, placed in RNA later, and stored at -80 degrees Centigrade.

in vivo Treatment: Methylene Chloride, Treatment Repeat: 6, Units of Treatment Repeat: hr/day, Treatment Duration: 13, Units of Duration: weeks, Treatment Time: 5, Units of Treatment Time: days/wk, Vehicle for Chemical: Air, Route of Exposure: Inhalation, Dose or Concentration: 100, Units of Dose or Concentration: ppm

tag: sacrifice method


title: RT_1000_13_250_TDPP_Mus_Lung_Mouse430_2_RT_HON07_MusLung

description: Gene expression changes in female mouse lung tissue treated for 90 days with TDPP

treatment_protocol:
Tissue Harvest Methods: Tissue was excised from animal, minced, placed in RNA later, and stored at -80 degrees Centigrade, Harvest Time Point: 13, Units of Harvest Time Point: weeks

in vivo Treatment: Tris(2,3-dibromopropyl)phosphate, Treatment Duration: 13, Units of Duration: weeks, Treatment Time: 7, Units of Treatment Time: days/wk, Vehicle for Chemical: Rodent Chow, Route of Exposure: Diet, Dose or Concentration: 1000, Units of Dose or Concentration: ppm

tag: gender


title: RT_1000_13_256_TDPP_Mus_Lung_Mouse430_2_RT_HON07_MusLung

source_name: female mouse lung tissue treated for 90 days with TDPP

tag: sample type


title: RT_8187_16_PCnB_Mouse430_2_IMFGN0023_8

description: Gene expression changes in female mouse lung tissue treated for 90 days with PCNB

treatment_protocol:
Tissue Harvest Methods: Tissue was excised from animal, minced, placed in RNA later, and stored at -80 degrees Centigrade.

in vivo Treatment: Pentachloronitrobenzene, Treatment Duration: 13, Units of Duration: weeks, Treatment Time: 7, Units of Treatment Time: days/wk, Vehicle for Chemical: Rodent Chow, Route of Exposure: Diet, Dose or Concentration: 8187, Units of Dose or Concentration: ppm

tag: strain or line


title: RT_8187_13_18_Lung_PCnB_Mouse430_2_IMFGN0023_8

source_name: female mouse lung tissue treated for 90 days with PCNB

treatment_protocol:
Tissue Harvest Methods: Tissue was excised from animal, minced, placed in RNA later, and stored at -80 degrees Centigrade.

in vivo Treatment: Pentachloronitrobenzene, Treatment Duration: 13, Units of Duration: week, Treatment Time: 7, Units of Treatment Time: days/wk, Vehicle for Chemical: Rodent Chow, Route of Exposure: Diet, Dose or Concentration: 8187, Units of Dose or Concentration: ppm

tag: individual


title: RT_100_13_176_MECL-100_Lung_07008_Mouse430_2_RSTLRI000_2

tag: tissue


title: RT_10000_13_17_Lu_NAAC_Mouse430_2_RSTLRI601_1

source_name: female mouse lung tissue treated for 90 days with NAAC

tag: dilution


title: RT_50_13_102_Lu_MACR_Mouse430_2_RSTLRI601_1

source_name: female mouse lung tissue treated for 90 days with MACR

tag: age


title: RT_0_13_339_ACO1_Mus_Lung_Mouse430_2_RT_HON07_MusLung

treatment_protocol:
Tissue Harvest Methods: Tissue was excised from animal, minced, placed in RNA later, and stored at -80 degrees Centigrade, Harvest Time Point: 13, Units of Harvest Time Point: weeks

in vivo Treatment: Air, Treatment Repeat: 6, Units of Treatment Repeat: hr/day, Treatment Duration: 13, Units of Duration: weeks, Treatment Time: 5, Units of Treatment Time: days/wk, Vehicle for Chemical: Air, Route of Exposure: Inhalation, Dose or Concentration: 0, Units of Dose or Concentration: ppm

tag: array type


title: RT_100_13_178_MECL-100_Lung_07008_Mouse430_2_RSTLRI000_2

tag: units of amount


title: RT_600_13_43_DCBZ-600_Lung_07008_Mouse430_2_RSTLRI000_2

description: Gene expression changes in female mouse lung tissue treated for 90 days with DCBZ

treatment_protocol:
Tissue Harvest Methods: Tissue was excised from animal, minced, placed in RNA later, and stored at -80 degrees Centigrade.

in vivo Treatment: 1,4-Dichlorobenzene, Treatment Repeat: 1, Units of Treatment Repeat: per day, Treatment Duration: 13, Units of Duration: weeks, Treatment Time: 5, Units of Treatment Time: days/wk, Vehicle for Chemical: Corn Oil, Amount of Vehicle: 5, Route of Exposure: Gavage, Units of Amount of Vehicle: ml/kg, Dose or Concentration: 600, Units of Dose or Concentration: mg/kg

tag: ratio


title: RT_0_13_338_ACO1_Mus_Lung_Mouse430_2_RT_HON07_MusLung

tag: rna integrity number


title: RT_0_13_116_ACO3_Lung_07008_Mouse430_2_RSTLRI000_2

treatment_protocol:
Tissue Harvest Methods: Tissue was excised from animal, minced, placed in RNA later, and stored at -80 degrees Centigrade.

in vivo Treatment: Air, Treatment Repeat: 6, Units of Treatment Repeat: hr/day, Treatment Duration: 13, Units of Duration: weeks, Treatment Time: 5, Units of Treatment Time: days/wk, Vehicle for Chemical: Air, Route of Exposure: Inhalation, Dose or Concentration: 0, Units of Dose or Concentration: mg/m3

tag: bioanalyzer results


title: RT_3000_13_208_MECL-3000_Lung_07008_Mouse430_2_RSTLRI000_2

treatment_protocol:
Tissue Harvest Methods: Tissue was excised from animal, minced, placed in RNA later, and stored at -80 degrees Centigrade.

in vivo Treatment: Methylene Chloride, Treatment Repeat: 6, Units of Treatment Repeat: hr/day, Treatment Duration: 13, Units of Duration: weeks, Treatment Time: 5, Units of Treatment Time: days/wk, Vehicle for Chemical: Air, Route of Exposure: Inhalation, Dose or Concentration: 3000, Units of Dose or Concentration: ppm

tag: sample preservation


title: RT_3925_13_203_TCFM_Mus_Lung_Mouse430_2_RT_HON07_MusLung

treatment_protocol:
Tissue Harvest Methods: Tissue was excised from animal, minced, placed in RNA later, and stored at -80 degrees Centigrade, Harvest Time Point: 13, Units of Harvest Time Point: weeks

in vivo Treatment: Trichlorofluoromethane, Treatment Repeat: 1, Units of Treatment Repeat: per day, Treatment Duration: 13, Units of Duration: weeks, Treatment Time: 5, Units of Treatment Time: days/wk, Vehicle for Chemical: Corn Oil, Amount of Vehicle: 5, Route of Exposure: Gavage, Units of Amount of Vehicle: ml/kg, Dose or Concentration: 3925, Units of Dose or Concentration: mg/kg

tag: ncbi taxonomy id


title: RT_0_13_337_ACO1_Mus_Lung_Mouse430_2_RT_HON07_MusLung

tag: developmental stage


title: RT_4000_13_216_MECL-4000_Lung_07008_Mouse430_2_RSTLRI000_2

treatment_protocol:
Tissue Harvest Methods: Tissue was excised from animal, minced, placed in RNA later, and stored at -80 degrees Centigrade.

in vivo Treatment: Methylene Chloride, Treatment Repeat: 6, Units of Treatment Repeat: hr/day, Treatment Duration: 13, Units of Duration: weeks, Treatment Time: 5, Units of Treatment Time: days/wk, Vehicle for Chemical: Air, Route of Exposure: Inhalation, Dose or Concentration: 4000, Units of Dose or Concentration: ppm

tag: amount to core


title: RT_4000_13_218_MECL-4000_Lung_07008_Mouse430_2_RSTLRI000_2

tag: sacrifice method


title: RT_0_13_225_CCO4_Mus_Lung_Mouse430_2_RT_HON07_MusLung

treatment_protocol:
Tissue Harvest Methods: Tissue was excised from animal, minced, placed in RNA later, and stored at -80 degrees Centigrade, Harvest Time Point: 13, Units of Harvest Time Point: weeks

in vivo Treatment: Corn Oil, Treatment Repeat: 1, Units of Treatment Repeat: per day, Treatment Duration: 13, Units of Duration: weeks, Treatment Time: 5, Units of Treatment Time: days/wk, Vehicle for Chemical: Corn Oil, Amount of Vehicle: 5, Route of Exposure: Gavage, Units of Amount of Vehicle: ml/kg, Dose or Concentration: 0, Units of Dose or Concentration: mg/kg

tag: gender


title: RT_50000_13_292_TFEA_Mus_Lung_Mouse430_2_RT_HON07_MusLung

description: Gene expression changes in female mouse lung tissue treated for 90 days with TFEA

treatment_protocol:
Tissue Harvest Methods: Tissue was excised from animal, minced, placed in RNA later, and stored at -80 degrees Centigrade, Harvest Time Point: 13, Units of Harvest Time Point: weeks

in vivo Treatment: Tetrafluororethane, Treatment Repeat: 6, Units of Treatment Repeat: hr/day, Treatment Duration: 13, Units of Duration: weeks, Treatment Time: 5, Units of Treatment Time: days/wk, Vehicle for Chemical: Air, Route of Exposure: Inhalation, Dose or Concentration: 50000, Units of Dose or Concentration: ppm

tag: sample type


title: RT_3_13_252_NPTH-3_Lung_07008_Mouse430_2_RSTLRI000_2

description: Gene expression changes in female mouse lung tissue treated for 90 days with NPTH

treatment_protocol:
Tissue Harvest Methods: Tissue was excised from animal, minced, placed in RNA later, and stored at -80 degrees Centigrade.

in vivo Treatment: Naphthalene, Treatment Repeat: 6, Units of Treatment Repeat: hr/day, Treatment Duration: 13, Units of Duration: weeks, Treatment Time: 5, Units of Treatment Time: days/wk, Vehicle for Chemical: Air, Route of Exposure: Inhalation, Dose or Concentration: 3, Units of Dose or Concentration: ppm

tag: strain or line


title: RT_0_13_52r_CCO5_Lung_07008_Mouse430_2_RSTLRI000_2

tag: individual


title: RT_0_13_22_Lung_CornOil_Mouse430_2_IMFGN0023_8

treatment_protocol:
Tissue Harvest Methods: Tissue was excised from animal, minced, placed in RNA later, and stored at -80 degrees Centigrade.

in vivo Treatment: Corn Oil, Treatment Repeat: 1, Units of Treatment Repeat: per day, Treatment Duration: 13, Units of Duration: weeks, Treatment Time: 5, Units of Treatment Time: days/wk, Vehicle for Chemical: Corn oil, Amount of Vehicle: 5, Route of Exposure: Gavage, Units of Amount of Vehicle: ml/kg, Dose or Concentration: 0, Units of Dose or Concentration: mg/kg

tag: tissue


title: RT_0_13_121_Lu_WCO1_Mouse430_2_RSTLRI601_1

treatment_protocol:
Tissue Harvest Methods: Tissue was excised from animal, minced, placed in RNA later, and stored at -80 degrees Centigrade.

in vivo Treatment: Distilled Water, Treatment Repeat: 1, Units of Treatment Repeat: per day, Treatment Duration: 13, Units of Duration: weeks, Treatment Time: 5, Units of Treatment Time: days/wk, Vehicle for Chemical: Distilled water, Amount of Vehicle: 5, Route of Exposure: Gavage, Units of Amount of Vehicle: ml/kg, Dose or Concentration: 0, Units of Dose or Concentration: mg/kg

tag: dilution


title: RT_60_13_164_TCPN-60_Lung_07008_Mouse430_2_RSTLRI000_2

description: Gene expression changes in female mouse lung tissue treated for 90 days with TCPN

treatment_protocol:
Tissue Harvest Methods: Tissue was excised from animal, minced, placed in RNA later, and stored at -80 degrees Centigrade.

in vivo Treatment: 1,2,3-Trichloropropane, Treatment Repeat: 1, Units of Treatment Repeat: per day, Treatment Duration: 13, Units of Duration: weeks, Treatment Time: 5, Units of Treatment Time: days/wk, Vehicle for Chemical: Corn Oil, Amount of Vehicle: 5, Route of Exposure: Gavage, Units of Amount of Vehicle: ml/kg, Dose or Concentration: 60, Units of Dose or Concentration: mg/kg

tag: age


title: RT_60_13_162_TCPN-60_Lung_07008_Mouse430_2_RSTLRI000_2

source_name: female mouse lung tissue treated for 90 days with TCPN

tag: array type


title: RT_0_13_175r_CCO6_Lung_07008_Mouse430_2_RSTLRI000_2

treatment_protocol:
Tissue Harvest Methods: Tissue was excised from animal, minced, placed in RNA later, and stored at -80 degrees Centigrade.

in vivo Treatment: Corn Oil, Treatment Repeat: 1, Units of Treatment Repeat: per day, Treatment Duration: 13, Units of Duration: weeks, Treatment Time: 5, Units of Treatment Time: days/wk, Vehicle for Chemical: Corn Oil, Amount of Vehicle: 5, Route of Exposure: Gavage, Units of Amount of Vehicle: ml/kg, Dose or Concentration: 0, Units of Dose or Concentration: mg/kg

tag: units of amount


title: RT_60_13_163_TCPN-60_Lung_07008_Mouse430_2_RSTLRI000_2

tag: ratio


title: RT_50000_13_290_TFEA_Mus_Lung_Mouse430_2_RT_HON07_MusLung

source_name: female mouse lung tissue treated for 90 days with TFEA

tag: rna integrity number


title: 552 | R2Yaa, Ifnar -/-

type: protein

city: Stanford

first: Chih Long

last: Liu

state: CA

address: 269 Campus Drive

department: Medicine - Imm. & Rheum

institute: Stanford University

description: Murine antiserum was obtained from blood collected from an individual mouse of the strain R2Yaa, Ifnar -/-.  A 1:250 dilution of this antiserum was then applied onto the Utz Lab Whole Protein Autoantigen Array (V1.0), labeled with a goat anti-mouse Ig(M + G) secondary antibody conjugated to Cy3 (Jackson ImmunoResearch), and scanned with a GenePix 4000B scanner using GenePix Pro 6.1.

hyb_protocol: Murine antiserum was probed on the antigen microarray at 1:250 dilution in 5% fetal bovine serum in phosphate-buffered saline with 0.1% Tween-20, and incubated for 1.25 hours at 4 degrees Celsius.

scan_protocol: Fluorescent array images were collected for Cy3 with a GenePix 4000B fluorescent scanner at 10 micron resolution and image intensity data were extracted and analyzed with GenePix Pro 6.1 analysis software.

data_processing: After background correction and removal of flagged values, data was normalized by dividing each array value by the goat anti-mouse IgG (25 ug/ml) array feature signal intensity and then multiplying by 10,000 to obtain a normalized signal intensity value.

label: Cy3-conjugated goat anti-mouse antibody

molecule: protein

source_name: Murine antiserum, Ifnar -/-

label_protocol: Commercially available Cy3-conjugated goat anti-mouse antibody was added to the microarray at 1:4000 in 5% fetal bovine serum in phosphate-buffered saline with 0.1% Tween-20.

extract_protocol: Whole antiserum was obtained.

tag: strain

value: R2Yaa, Ifnar -/-


title: RT_0_13_27_Lung_RodentChow_Mouse430_2_IMFGN0023_8

treatment_protocol:
Tissue Harvest Methods: Tissue was excised from animal, minced, placed in RNA later, and stored at -80 degrees Centigrade.

in vivo Treatment: Rodent Chow, Treatment Duration: 13, Units of Duration: weeks, Treatment Time: 7, Units of Treatment Time: days/wk, Vehicle for Chemical: Rodent Chow, Route of Exposure: Diet, Dose or Concentration: 0, Units of Dose or Concentration: ppm

tag: bioanalyzer results

tag: sample preservation


title: RT_50000_13_293_TFEA_Mus_Lung_Mouse430_2_RT_HON07_MusLung

tag: ncbi taxonomy id

tag: developmental stage


title: RT_20_13_274_NPTH-20_Lung_07008_Mouse430_2_RSTLRI000_2

treatment_protocol:
Tissue Harvest Methods: Tissue was excised from animal, minced, placed in RNA later, and stored at -80 degrees Centigrade.

in vivo Treatment: Naphthalene, Treatment Repeat: 6, Units of Treatment Repeat: hr/day, Treatment Duration: 13, Units of Duration: weeks, Treatment Time: 5, Units of Treatment Time: days/wk, Vehicle for Chemical: Air, Route of Exposure: Inhalation, Dose or Concentration: 20, Units of Dose or Concentration: ppm

tag: amount to core

tag: sacrifice method


title: RT_2_13_109_VANP-2_Lung_07008_Mouse430_2_RSTLRI000_2

treatment_protocol:
Tissue Harvest Methods: Tissue was excised from animal, minced, placed in RNA later, and stored at -80 degrees Centigrade.

in vivo Treatment: Vanadium Pentoxide, Treatment Repeat: 6, Units of Treatment Repeat: hr/day, Treatment Duration: 13, Units of Duration: weeks, Treatment Time: 5, Units of Treatment Time: days/wk, Vehicle for Chemical: Air, Route of Exposure: Inhalation, Dose or Concentration: 2, Units of Dose or Concentration: mg/m3

tag: sample type

tag: gender


title: RT_2_13_108_VANP-2_Lung_07008_Mouse430_2_RSTLRI000_2

tag: strain or line

tag: individual


title: RT_200_13_21_Lu_DIAZ_Mouse430_2_RSTLRI601_1

description: Gene expression changes in female mouse lung tissue treated for 90 days with DIAZ

treatment_protocol:
Tissue Harvest Methods: Tissue was excised from animal, minced, placed in RNA later, and stored at -80 degrees Centigrade.

in vivo Treatment: Diazinon, Treatment Duration: 13, Units of Duration: weeks, Treatment Time: 7, Units of Treatment Time: days/wk, Vehicle for Chemical: Rodent Chow, Route of Exposure: Diet, Dose or Concentration: 200, Units of Dose or Concentration: ppm

tag: tissue

tag: dilution


title: RT_50000_13_289_TFEA_Mus_Lung_Mouse430_2_RT_HON07_MusLung

tag: array type

tag: age


title: RT_1200_13_99_PGBE-1200_Lung_07008_Mouse430_2_RSTLRI000_2

description: Gene expression changes in female mouse lung tissue treated for 90 days with PGBE

treatment_protocol:
Tissue Harvest Methods: Tissue was excised from animal, minced, placed in RNA later, and stored at -80 degrees Centigrade.

in vivo Treatment: Propylene glycol mono-t-butyl ether, Treatment Repeat: 6, Units of Treatment Repeat: hr/day, Treatment Duration: 13, Units of Duration: weeks, Treatment Time: 5, Units of Treatment Time: days/wk, Vehicle for Chemical: Air, Route of Exposure: Inhalation, Dose or Concentration: 1200, Units of Dose or Concentration: ppm

tag: units of amount

tag: ratio


title: 6723-R | R2Yaa, Ifnar -/-

tag: strain


title: 546 | R2Yaa, Ifnar -/-


title: 535 | R2Yaa, Ifnar -/-


title: 7095 | R2Yaa, Ifnar -/-


title: RT_20_13_275_NPTH-20_Lung_07008_Mouse430_2_RSTLRI000_2

tag: rna integrity number

tag: bioanalyzer results


title: 547 | R2Yaa, Ifnar -/-


title: 533 | R2Yaa, Ifnar -/-


title: RT_200_13_75_Lu_COUM_Mouse430_2_RSTLRI601_1

description: Gene expression changes in female mouse lung tissue treated for 90 days with COUM

treatment_protocol:
Tissue Harvest Methods: Tissue was excised from animal, minced, placed in RNA later, and stored at -80 degrees Centigrade.

in vivo Treatment: Coumarin, Treatment Repeat: 1, Units of Treatment Repeat: per day, Treatment Duration: 13, Units of Duration: weeks, Treatment Time: 5, Units of Treatment Time: days/wk, Vehicle for Chemical: Corn Oil, Amount of Vehicle: 5, Route of Exposure: Gavage, Units of Amount of Vehicle: ml/kg, Dose or Concentration: 200, Units of Dose or Concentration: mg/kg

tag: sample preservation

tag: ncbi taxonomy id


title: RT_1200_13_98_PGBE-1200_Lung_07008_Mouse430_2_RSTLRI000_2

source_name: female mouse lung tissue treated for 90 days with PGBE

tag: amount to core

tag: developmental stage


title: RT_1250_13_10_Lu_BBMP_Mouse430_2_RSTLRI601_1

description: Gene expression changes in female mouse lung tissue treated for 90 days with BBMP

treatment_protocol:
Tissue Harvest Methods: Tissue was excised from animal, minced, placed in RNA later, and stored at -80 degrees Centigrade.

in vivo Treatment: 2,2-Bis(bromomethyl)-1,3-propanediol, Treatment Duration: 13, Units of Duration: weeks, Treatment Time: 7, Units of Treatment Time: days/wk, Vehicle for Chemical: Rodent Chow, Route of Exposure: Diet, Dose or Concentration: 1250, Units of Dose or Concentration: ppm

tag: sample type

tag: sacrifice method


title: 5596-O | R2Yaa, Ifnar +/+

description: Murine antiserum was obtained from blood collected from an individual mouse of the strain R2Yaa, Ifnar +/+.  A 1:250 dilution of this antiserum was then applied onto the Utz Lab Whole Protein Autoantigen Array (V1.0), labeled with a goat anti-mouse Ig(M + G) secondary antibody conjugated to Cy3 (Jackson ImmunoResearch), and scanned with a GenePix 4000B scanner using GenePix Pro 6.1.

source_name: Murine antiserum, Ifnar +/+

value: R2Yaa, Ifnar +/+


title: RT_500_13_189_MECL-500_Lung_07008_Mouse430_2_RSTLRI000_2

description: Gene expression changes in female mouse lung tissue treated for 90 days with MECL

treatment_protocol:
Tissue Harvest Methods: Tissue was excised from animal, minced, placed in RNA later, and stored at -80 degrees Centigrade.

in vivo Treatment: Methylene Chloride, Treatment Repeat: 6, Units of Treatment Repeat: hr/day, Treatment Duration: 13, Units of Duration: weeks, Treatment Time: 5, Units of Treatment Time: days/wk, Vehicle for Chemical: Air, Route of Exposure: Inhalation, Dose or Concentration: 500, Units of Dose or Concentration: ppm

tag: strain or line

tag: gender


title: RT_600_13_41_DCBZ-600_Lung_07008_Mouse430_2_RSTLRI000_2

source_name: female mouse lung tissue treated for 90 days with DCBZ

treatment_protocol:
Tissue Harvest Methods: Tissue was excised from animal, minced, placed in RNA later, and stored at -80 degrees Centigrade.

in vivo Treatment: 1,4-Dichlorobenzene, Treatment Repeat: 1, Units of Treatment Repeat: per day, Treatment Duration: 13, Units of Duration: weeks, Treatment Time: 5, Units of Treatment Time: days/wk, Vehicle for Chemical: Corn Oil, Amount of Vehicle: 5, Route of Exposure: Gavage, Units of Amount of Vehicle: ml/kg, Dose or Concentration: 600, Units of Dose or Concentration: mg/kg

tag: tissue

tag: individual


title: RT_500_13_188_MECL-500_Lung_07008_Mouse430_2_RSTLRI000_2

tag: array type

tag: dilution


title: RT_3000_13_206_MECL-3000_Lung_07008_Mouse430_2_RSTLRI000_2

treatment_protocol:
Tissue Harvest Methods: Tissue was excised from animal, minced, placed in RNA later, and stored at -80 degrees Centigrade.

in vivo Treatment: Methylene Chloride, Treatment Repeat: 6, Units of Treatment Repeat: hr/day, Treatment Duration: 13, Units of Duration: weeks, Treatment Time: 5, Units of Treatment Time: days/wk, Vehicle for Chemical: Air, Route of Exposure: Inhalation, Dose or Concentration: 3000, Units of Dose or Concentration: ppm

tag: units of amount

tag: age


title: RT_2000_13_198_MECL-2000_Lung_07008_Mouse430_2_RSTLRI000_2

treatment_protocol:
Tissue Harvest Methods: Tissue was excised from animal, minced, placed in RNA later, and stored at -80 degrees Centigrade.

in vivo Treatment: Methylene Chloride, Treatment Repeat: 6, Units of Treatment Repeat: hr/day, Treatment Duration: 13, Units of Duration: weeks, Treatment Time: 5, Units of Treatment Time: days/wk, Vehicle for Chemical: Air, Route of Exposure: Inhalation, Dose or Concentration: 2000, Units of Dose or Concentration: ppm

tag: ratio


title: RT_200_13_25_Lu_DIAZ_Mouse430_2_RSTLRI601_1

source_name: female mouse lung tissue treated for 90 days with DIAZ


title: RT_250_13_119_Lu_CMPH_Mouse430_2_RSTLRI601_1

description: Gene expression changes in female mouse lung tissue treated for 90 days with CMPH

treatment_protocol:
Tissue Harvest Methods: Tissue was excised from animal, minced, placed in RNA later, and stored at -80 degrees Centigrade.

in vivo Treatment: 2-Chloromethylpyridine hydrochloride, Treatment Repeat: 1, Units of Treatment Repeat: per day, Treatment Duration: 13, Units of Duration: weeks, Treatment Time: 5, Units of Treatment Time: days/wk, Vehicle for Chemical: Distilled water, Amount of Vehicle: 5, Route of Exposure: Gavage, Units of Amount of Vehicle: ml/kg, Dose or Concentration: 250, Units of Dose or Concentration: mg/kg


title: RT_1250_13_269_TFEL_Mus_Lung_Mouse430_2_RT_HON07_MusLung

description: Gene expression changes in female mouse lung tissue treated for 90 days with TFEL

treatment_protocol:
Tissue Harvest Methods: Tissue was excised from animal, minced, placed in RNA later, and stored at -80 degrees Centigrade, Harvest Time Point: 13, Units of Harvest Time Point: weeks

in vivo Treatment: Tetrafluoroethylene, Treatment Repeat: 6, Units of Treatment Repeat: hr/day, Treatment Duration: 13, Units of Duration: weeks, Treatment Time: 5, Units of Treatment Time: days/wk, Vehicle for Chemical: Air, Route of Exposure: Inhalation, Dose or Concentration: 1250, Units of Dose or Concentration: ppm

value: ug

tag: rna integrity number


title: RT_16000_13_38_Lu_MALA_Mouse430_2_RSTLRI601_1

description: Gene expression changes in female mouse lung tissue treated for 90 days with MALA

treatment_protocol:
Tissue Harvest Methods: Tissue was excised from animal, minced, placed in RNA later, and stored at -80 degrees Centigrade.

in vivo Treatment: Malathion, Treatment Duration: 13, Units of Duration: weeks, Treatment Time: 7, Units of Treatment Time: days/wk, Vehicle for Chemical: Rodent Chow, Route of Exposure: Diet, Dose or Concentration: 14800, Units of Dose or Concentration: ppm

tag: bioanalyzer results


title: RT_1250_13_272_TFEL_Mus_Lung_Mouse430_2_RT_HON07_MusLung

source_name: female mouse lung tissue treated for 90 days with TFEL

tag: sample preservation


title: RT_200_13_24_Lu_DIAZ_Mouse430_2_RSTLRI601_1

tag: ncbi taxonomy id


title: RT_500_13_190_MECL-500_Lung_07008_Mouse430_2_RSTLRI000_2

tag: amount to core


title: RT_200_13_76_Lu_COUM_Mouse430_2_RSTLRI601_1

source_name: female mouse lung tissue treated for 90 days with COUM

tag: developmental stage


title: 7818-R | R2Yaa, Ifnar -/-

tag: strain


title: RT_20000_13_237_ABDQ_Mus_Lung_Mouse430_2_RT_HON07_MusLung

description: Gene expression changes in female mouse lung tissue treated for 90 days with ABDQ

treatment_protocol:
Tissue Harvest Methods: Tissue was excised from animal, minced, placed in RNA later, and stored at -80 degrees Centigrade, Harvest Time Point: 13, Units of Harvest Time Point: weeks

in vivo Treatment: 1-Amino-2,4-dibromoanthraquinone, Treatment Duration: 13, Units of Duration: weeks, Treatment Time: 7, Units of Treatment Time: days/wk, Vehicle for Chemical: Rodent Chow, Route of Exposure: Diet, Dose or Concentration: 20000, Units of Dose or Concentration: ppm

tag: sample type

tag: sacrifice method


title: 7818-L | R2Yaa, Ifnar -/-


title: 5597-L | R2Yaa, Ifnar +/+


title: RT_16000_13_36_Lu_MALA_Mouse430_2_RSTLRI601_1

source_name: female mouse lung tissue treated for 90 days with MALA

tag: strain or line

tag: gender


title: RT_20000_13_241_ABDQ_Mus_Lung_Mouse430_2_RT_HON07_MusLung

source_name: female mouse lung tissue treated for 90 days with ABDQ

tag: tissue

tag: individual


title: 7116-R | R2Yaa, Ifnar +/+


title: 5596-L | R2Yaa, Ifnar +/+


title: 6723-O | R2Yaa, Ifnar +/+


title: RT_0_13_171r_CCO6_Lung_07008_Mouse430_2_RSTLRI000_2

description: Gene expression changes in female mouse lung tissue treated for 90 days with CTRL

tag: array type

tag: dilution


title: RT_0_13_172_CCO6_Lung_07008_Mouse430_2_RSTLRI000_2

source_name: female mouse lung tissue treated for 90 days with CTRL

tag: units of amount

tag: age


title: RT_0_13_132_Lu_CCO3_Mouse430_2_RSTLRI601_1

tag: ratio

tag: rna integrity number


title: 7818-O | R2Yaa, Ifnar -/-


title: RT_0_13_127_Lu_WCO1_Mouse430_2_RSTLRI601_1

treatment_protocol:
Tissue Harvest Methods: Tissue was excised from animal, minced, placed in RNA later, and stored at -80 degrees Centigrade.

in vivo Treatment: Distilled Water, Treatment Repeat: 1, Units of Treatment Repeat: per day, Treatment Duration: 13, Units of Duration: weeks, Treatment Time: 5, Units of Treatment Time: days/wk, Vehicle for Chemical: Distilled water, Amount of Vehicle: 5, Route of Exposure: Gavage, Units of Amount of Vehicle: ml/kg, Dose or Concentration: 0, Units of Dose or Concentration: mg/kg

tag: bioanalyzer results

tag: sample preservation


title: 5596-R | R2Yaa, Ifnar +/+


title: 5597-R | R2Yaa, Ifnar +/+


title: RT_0_13_129_Lu_WCO1_Mouse430_2_RSTLRI601_1

tag: amount to core

tag: ncbi taxonomy id


title: RT_600_13_45_DCBZ-600_Lung_07008_Mouse430_2_RSTLRI000_2

tag: developmental stage


title: RT_0_13_235_CCO4_Mus_Lung_Mouse430_2_RT_HON07_MusLung

treatment_protocol:
Tissue Harvest Methods: Tissue was excised from animal, minced, placed in RNA later, and stored at -80 degrees Centigrade, Harvest Time Point: 13, Units of Harvest Time Point: weeks

in vivo Treatment: Corn Oil, Treatment Repeat: 1, Units of Treatment Repeat: per day, Treatment Duration: 13, Units of Duration: weeks, Treatment Time: 5, Units of Treatment Time: days/wk, Vehicle for Chemical: Corn Oil, Amount of Vehicle: 5, Route of Exposure: Gavage, Units of Amount of Vehicle: ml/kg, Dose or Concentration: 0, Units of Dose or Concentration: mg/kg

tag: sample type


title: RT_62_13_58_Lu_DBET_Mouse430_2_RSTLRI601_1

description: Gene expression changes in female mouse lung tissue treated for 90 days with DBET

treatment_protocol:
Tissue Harvest Methods: Tissue was excised from animal, minced, placed in RNA later, and stored at -80 degrees Centigrade.

in vivo Treatment: 1,2-Dibromoethane, Treatment Repeat: 1, Units of Treatment Repeat: per day, Treatment Duration: 13, Units of Duration: weeks, Treatment Time: 5, Units of Treatment Time: days/wk, Vehicle for Chemical: Corn Oil, Amount of Vehicle: 5, Route of Exposure: Gavage, Units of Amount of Vehicle: ml/kg, Dose or Concentration: 62, Units of Dose or Concentration: mg/kg

tag: sacrifice method


title: RT_62_13_56_Lu_DBET_Mouse430_2_RSTLRI601_1

source_name: female mouse lung tissue treated for 90 days with DBET

tag: strain or line


title: 7116-R&L | R2Yaa, Ifnar +/+

tag: strain


title: RT_93_13_215_IODO_Mus_Lung_Mouse430_2_RT_HON07_MusLung

description: Gene expression changes in female mouse lung tissue treated for 90 days with IODO

treatment_protocol:
Tissue Harvest Methods: Tissue was excised from animal, minced, placed in RNA later, and stored at -80 degrees Centigrade, Harvest Time Point: 13, Units of Harvest Time Point: weeks

in vivo Treatment: Iodoform, Treatment Repeat: 1, Units of Treatment Repeat: per day, Treatment Duration: 13, Units of Duration: weeks, Treatment Time: 5, Units of Treatment Time: days/wk, Vehicle for Chemical: Corn Oil, Amount of Vehicle: 5, Route of Exposure: Gavage, Units of Amount of Vehicle: ml/kg, Dose or Concentration: 93, Units of Dose or Concentration: mg/kg

tag: tissue

tag: gender


title: 7116-L | R2Yaa, Ifnar +/+


title: RT_62_13_54_Lu_DBET_Mouse430_2_RSTLRI601_1

tag: array type

tag: individual


title: RT_200_13_80_Lu_COUM_Mouse430_2_RSTLRI601_1

tag: units of amount

tag: dilution


title: RT_93_13_213_IODO_Mus_Lung_Mouse430_2_RT_HON07_MusLung

source_name: female mouse lung tissue treated for 90 days with IODO

tag: ratio

tag: age


title: RT_0_13_236_ACO4_Lung_07008_Mouse430_2_RSTLRI000_2

treatment_protocol:
Tissue Harvest Methods: Tissue was excised from animal, minced, placed in RNA later, and stored at -80 degrees Centigrade.

in vivo Treatment: Air, Treatment Repeat: 6, Units of Treatment Repeat: hr/day, Treatment Duration: 13, Units of Duration: weeks, Treatment Time: 5, Units of Treatment Time: days/wk, Vehicle for Chemical: Air, Route of Exposure: Inhalation, Dose or Concentration: 0, Units of Dose or Concentration: ppm

tag: rna integrity number

tag: bioanalyzer results


title: RT_93_13_224_IODO_Mus_Lung_Mouse430_2_RT_HON07_MusLung

tag: amount to core

tag: sample preservation


title: RT_8187_20_PCnB_Mouse430_2_IMFGN0023_8

description: Gene expression changes in female mouse lung tissue treated for 90 days with PCNB

treatment_protocol:
Tissue Harvest Methods: Tissue was excised from animal, minced, placed in RNA later, and stored at -80 degrees Centigrade.

in vivo Treatment: Pentachloronitrobenzene, Treatment Duration: 13, Units of Duration: weeks, Treatment Time: 7, Units of Treatment Time: days/wk, Vehicle for Chemical: Rodent Chow, Route of Exposure: Diet, Dose or Concentration: 8187, Units of Dose or Concentration: ppm

tag: ncbi taxonomy id

tag: developmental stage


title: RT_93_13_221_IODO_Mus_Lung_Mouse430_2_RT_HON07_MusLung

tag: sample type

tag: sacrifice method


title: RT_62_13_52_Lu_DBET_Mouse430_2_RSTLRI601_1

tag: strain or line


title: 5597-O | R2Yaa, Ifnar +/+

tag: strain


title: WT9 | C57BL/6

description: Murine antiserum was obtained from blood collected from an individual mouse of the strain C57BL/6.  A 1:250 dilution of this antiserum was then applied onto the Utz Lab Whole Protein Autoantigen Array (V1.0), labeled with a goat anti-mouse Ig(M + G) secondary antibody conjugated to Cy3 (Jackson ImmunoResearch), and scanned with a GenePix 4000B scanner using GenePix Pro 6.1.

source_name: Murine antiserum, WT


title: WT8b | C57BL/6


title: WT8a | C57BL/6


title: RT_50_13_109_Lu_MACR_Mouse430_2_RSTLRI601_1

description: Gene expression changes in female mouse lung tissue treated for 90 days with MACR

treatment_protocol:
Tissue Harvest Methods: Tissue was excised from animal, minced, placed in RNA later, and stored at -80 degrees Centigrade.

in vivo Treatment: N-Methylolacrylamide, Treatment Repeat: 1, Units of Treatment Repeat: per day, Treatment Duration: 13, Units of Duration: weeks, Treatment Time: 5, Units of Treatment Time: days/wk, Vehicle for Chemical: Distilled water, Amount of Vehicle: 5, Route of Exposure: Gavage, Units of Amount of Vehicle: ml/kg, Dose or Concentration: 50, Units of Dose or Concentration: mg/kg

tag: tissue

tag: gender


title: R. baltica_salt shift_reference_c

city: Bremen

first: Patricia

last: Wecker

address: Celsiusstr, 1

department: Molecular Ecology

country: Germany

institute: Max Planck Institut for Marine Microbiology

description: self-self hybridisation (replicate c)

hyb_protocol: Blocking, denaturing, hybridisation, washing and drying of the slides with N2 were carried out in an automated hybridisation station HS400 (Tecan, Crailsheim, Germany). The spotted arrays were blocked in prehybridisation solution containing 250 mM NaCl, 5 mM Tris/HCl at pH 8.0, 50% formamide, 0.5x SSC, 0.05% BSA, and 1% blocking reagent from Roche Diagnostics, Mannheim, Germany for 45 min at 52°C. For hybridisation at least 2 μg of Alexa 546 dye-labelled and 2 μg of Alexa 647 dye-labelled total cDNA were combined and taken up in a final volume of 100 µl DIG Easy Hyb hybridisation solution (Roche Diagnostics, Mannheim, Germany). After the blocking step the sample solution was applied to the arrays, denaturised at 95°C for 3 min and hybridised under stringent conditions at 52°C for over 12 hours. After hybridisation slides were washed at RT in ULTRArray Low Stringency Wash Buffer (Ambion, Austin, USA) and dried by N2.

scan_protocol: Slides were scanned at a resolution of 5 μm using a ScanArray Express Microarray scanner (Perkin Elmer, Wellesley, USA) with varied laser power and sensitivity level of the photomultiplier tube (PMT) for each slide. The provided image analysis software ScanArray Express Version 4.0 was used for automatic spot detection and signal quantification of both fluorophores.

data_processing:
Raw data were automatically processed using the inhouse developed microarray data analysis software tool MADA (www.megx.net/mada). First of all the spot intensities were local background corrected (spot intensity minus spot background intensity). Then signals were only assessed as positive if mean spot pixel intensity was higher than the mean local background intensity plus 2 times the standard deviation of the mean local background pixel intensity. Each gene is spotted in 3 replicates. Spot replicates with poor quality were removed from the data set according to the outlier test of MADA. For this test, first the standard deviation of all replicates is computed. Second, one replicate is omitted and the standard deviation is recalculated, if the deviation differs more than 50% from the previous deviation, the omitted replicate is regarded as outlier. This procedure is alternately repeated for all replicates
The expression is described through the ratio and intensity, where R is the fluorescence log ratio of the experiment time point relative to the control condition (e.g. R = log2 (result of channel 10min / result of channel control/reference)) and I is the log mean fluorescence intensity (e.g. I = log10 (result of channel 10min * result of channel control/reference)).
Each data point represents a regulation factor (ratio) in a logarithmic scale for one gene calculated from the positive replicates for a particular probe coming from two RNA pools (reference and sample). Normalisation was carried out by LOWESS fitting on an R-versus-I plot with a smoothing factor of 0.05. Each time point of the time-series experiment was hybridised independently three times. The expression data (ratio) of the three hybridisations were combined to one expression data point (ratio) by average and the standard deviation was calculated. Only ratios with a standard deviation less than 25% were taken as regulated.
Differentially expressed genes are determinate by a fixed threshold cut off method (i.e. a two-fold increase or decrease) based on the self-self hybridisation.

label: Alexa 546

organism: Rhodopirellula baltica

source_name: Rhodopirellula baltica salt shift reference

label_protocol: cDNA was directly labelled using the PlatinumBrightTM nucleic acid labelling kit based on KREATECH´s patented Universal Linkage System (ULS) (Biocat, Heidelberg, Germany) according to the manufacturer's protocol.

growth_protocol: For all experiments Rhodopirellula baltica SH 1T cells were grown as chemostate cultures in a mineral medium containing 10 mM glucose as sole carbon and 1 mM ammonium chloride as nitrogen source at 28°C (Rabus et al. 2002)

extract_protocol:
The culture pellets were re-suspended in 0.1 M Tris-HCL and then re-centrifuged to cell pellets that were shock-frozen in liquid nitrogen and stored at -80°C. Total RNA was isolated using the proposed protocol of the TRI Reagent® Kit by Ambion (Austin, USA).
cDNA synthesis was performed using the SuperScript direct cDNA labeling system kit by Invitrogen (Karlsruhe, DE) according to the manufacturer's instructions with random hexamers and unlabeled dCTP/dUTP.

treatment_protocol: In all cases, cells were grown to the OD600nm = 0.5 (corresponding log phase), and an aliquot of cells was collected to serve as the time-zero reference. The culture broth was collected in 500 mL tubes and swirled briefly in an ethanol-dry ice bath to rapidly cool the cultures and "freeze" the RNA profile. Subsequently, the broth was centrifuged at 6000 rpm for 20 min at 4°C (Beckman CoulterTM AvantiTM626 J-20XP, JA10 Rotor). The pellets were re-suspended in 0.1 M Tris-HCL and then re-centrifuged to cell pellets that were shock-frozen in liquid nitrogen and stored at -80°C

tag: non-treated = reference = time point zero

tag: Replicate c


title: R. baltica_salt shift_reference_b

description: self-self hybridisation (replicate b)

tag: Replicate b


title: RT_100_13_230_ETOX-100_Lung_07008_Mouse430_2_RSTLRI000_2

description: Gene expression changes in female mouse lung tissue treated for 90 days with ETOX

treatment_protocol:
Tissue Harvest Methods: Tissue was excised from animal, minced, placed in RNA later, and stored at -80 degrees Centigrade.

in vivo Treatment: Ethylene Oxide, Treatment Repeat: 6, Units of Treatment Repeat: hr/day, Treatment Duration: 13, Units of Duration: weeks, Treatment Time: 5, Units of Treatment Time: days/wk, Vehicle for Chemical: Air, Route of Exposure: Inhalation, Dose or Concentration: 100, Units of Dose or Concentration: ppm

tag: array type

tag: units of amount

tag: ratio

tag: dilution

tag: individual


title: WT7 | C57BL/6


title: WT5 | C57BL/6


title: R. baltica_salt shift_reference_a

description: self-self hybridisation (replicate a)

tag: Replicate a


title: R. baltica_salt shift_300min_a

description: salt shift 300min vs. reference

source_name: Rhodopirellula baltica, salt shift, 300min

treatment_protocol: Cells grown continuously at 28°C and in a medium with 17.5% salinity were collected by centrifugation. Aliquots were resuspend in an equal volume of medium containing 59.5% salinity and returned  for growth. Samples were collected at 10, 20, 40, 60 and 300 min

tag: Salt shifted for 300 min


title: R. baltica_salt shift_300min_c

description: salt shift 300min vs. reference


title: WT6 | C57BL/6


title: RT_100_13_86_Lu_BENZ_Mouse430_2_RSTLRI601_1

description: Gene expression changes in female mouse lung tissue treated for 90 days with BENZ

treatment_protocol:
Tissue Harvest Methods: Tissue was excised from animal, minced, placed in RNA later, and stored at -80 degrees Centigrade.

in vivo Treatment: Benzene, Treatment Repeat: 1, Units of Treatment Repeat: per day, Treatment Duration: 13, Units of Duration: weeks, Treatment Time: 5, Units of Treatment Time: days/wk, Vehicle for Chemical: Corn Oil, Amount of Vehicle: 5, Route of Exposure: Gavage, Units of Amount of Vehicle: ml/kg, Dose or Concentration: 100, Units of Dose or Concentration: mg/kg

tag: amount to core

tag: rna integrity number

tag: bioanalyzer results

tag: sample preservation

tag: ncbi taxonomy id

tag: developmental stage

tag: age


title: RT_100_13_85_Lu_BENZ_Mouse430_2_RSTLRI601_1

source_name: female mouse lung tissue treated for 90 days with BENZ

tag: sample type

tag: tissue

tag: strain or line

tag: sacrifice method

tag: gender


title: RT_600_13_44_DCBZ-600_Lung_07008_Mouse430_2_RSTLRI000_2

description: Gene expression changes in female mouse lung tissue treated for 90 days with DCBZ

treatment_protocol:
Tissue Harvest Methods: Tissue was excised from animal, minced, placed in RNA later, and stored at -80 degrees Centigrade.

in vivo Treatment: 1,4-Dichlorobenzene, Treatment Repeat: 1, Units of Treatment Repeat: per day, Treatment Duration: 13, Units of Duration: weeks, Treatment Time: 5, Units of Treatment Time: days/wk, Vehicle for Chemical: Corn Oil, Amount of Vehicle: 5, Route of Exposure: Gavage, Units of Amount of Vehicle: ml/kg, Dose or Concentration: 600, Units of Dose or Concentration: mg/kg

tag: array type

tag: units of amount

tag: ratio


title: RT_100_13_227_ETOX-100_Lung_07008_Mouse430_2_RSTLRI000_2

source_name: female mouse lung tissue treated for 90 days with ETOX

tag: dilution

tag: individual


title: R. baltica_salt shift_60min_b

description: salt shift 60min vs. reference

tag: non-treated = reference = time point zero

source_name: Rhodopirellula baltica, salt shift, 60min

tag: Salt shifted for 60min

tag: Replicate b


title: RT_100_13_82_Lu_BENZ_Mouse430_2_RSTLRI601_1

tag: amount to core

tag: rna integrity number

tag: bioanalyzer results

tag: sample preservation


title: RT_05_13_245_NPTH-05_Lung_07008_Mouse430_2_RSTLRI000_2

description: Gene expression changes in female mouse lung tissue treated for 90 days with NPTH

treatment_protocol:
Tissue Harvest Methods: Tissue was excised from animal, minced, placed in RNA later, and stored at -80 degrees Centigrade.

in vivo Treatment: Naphthalene, Treatment Repeat: 6, Units of Treatment Repeat: hr/day, Treatment Duration: 13, Units of Duration: weeks, Treatment Time: 5, Units of Treatment Time: days/wk, Vehicle for Chemical: Air, Route of Exposure: Inhalation, Dose or Concentration: 0.5, Units of Dose or Concentration: ppm

tag: sample type

tag: ncbi taxonomy id

tag: developmental stage

tag: age


title: GBM CD133- isolated cells patient 8

city: Salamanca

first: Fran

last: González

state: Salamanca

address: Plaza de España, 5-6

department: Discovery Information Systems

institute: OncoStem Pharma

description: Human glioblastoma CD133/2 negative isolated cells from patient 8

hyb_protocol: Biotinylated cRNA was purified and then fragmented (35–200 nucleotides), together with hybridization controls and hybridized to the microarrays for 16 h at 45°C. Using the GeneChip Fluidics Station 450 (Affymetrix), the biotin-labeled cRNA was revealed by successive reactions with streptavidin R-phycoerythrin conjugate, biotinylated antistreptavidine antibody and streptavidin R-phycoerythrin conjugate.

scan_protocol: The arrays were scanned in an Affymetrix  GeneChip Scanner 7G Plus.

data_processing: Preliminary data analysis was conducted using the software of the Affymetrix Expression Console from AGCC suite (Affymetrix GeneChip Command Console, version 1.1) following the statistical procedures described in the Affymetrix: Expression Console User Guide, selecting the 3’ Expression Analysis guidelines for MAS5 and PLIER algorithms in two independent steps. MAS5 calculated the present call index for each of the 54,675 probe sets on the chip (settings used were standard for the HG U133 Plus 2 array: alpha1 = 0.04, alpha2 = 0.06, Tau = 0.015, TGT = 500). PLIER algorithm was used to calculate the normalized expression values of the probe sets (using quantile normalization and PM-MM background correction methods). Statistical analysis and post-processing were performed using TIBCO Spotfire 9.1 (TIBCO Software Inc., Palo Alto CA, USA). "264TopProbeSetsNormalizedFilteredAnnotated.txt" file, attached to the Series record, contains the Spotfire processed data.

source_name: CD133- FACS sorted cells from primary glioblastomas

label_protocol: We used the GeneChip® Expression 3' Amplification Two-Cycle Target Labeling kit (Affymetrix, Santa Clara, CA, USA) to label the RNA following the manufacturer protocol. The cRNA was hybridized to Affymetrix Human U133 Plus 2 arrays according to the manufacturer protocol. Briefly, double-stranded cDNA was synthesized routinely from less than 1 ug of total RNA primed with a poly-(dT) -T7 oligonucleotide. The cDNA was used in an in vitro transcription reaction (IVT) in the presence of T7 RNA polymerase and biotin-labelled modified nucleotides during 16 hours at 37°C.

growth_protocol: We have collected fresh tumors from eight patients affected of primary GBM without previous treatment. At the moment of the surgical extraction, a vast proportion of each tumor was processed to isolate the CD133+ and CD133- cells without previous cell culture.

extract_protocol: Total RNA was extracted from CD133+ and CD133- sorted cells using Trizol (Invitrogen, Carlsbard, CA). The integrity of the RNA was confirmed with the Agilent Bioanalyzer 2100 using the RNA 6000 Pico kit (Agilent).

treatment_protocol: Cells were immunophenotyped with the human CD133/2 (293C3) phycoerythrin conjugated antibody (MACS, Miltenyibiotec). Cells, suspended in Ca2+/Mg2+ free phosphate-buffered saline (PBS) supplemented with 1% FBS and were labeled with the antibody (approximately 1 µg/106 cells) for 30 minutes on ice. Cell fluorescence was analyzed and sorted with the FACS Aria sorter (Becton Dickinson, New Jersey, USA). Before analysis, possible mature red cells were depleted by treatment with hypotonic lysis solution (0.38% ammonium chloride for 15 minutes on ice). We tested the CD133 antibody with human bone marrow (BM) cells which were treated identically to single cells from tumors. These BM cells were incubated with CD133 antibody and CD34 antibody (Pharmingen), because there are studies that show that antibodies against CD133 also identified a subset of CD34bright BM haematopoietic stem cells. Cell viability was assessed by propidium iodide (5 µg/mL; Sigma) (in flow cytometry) exclusion.

tag: organ

value: brain

tag: tissue

value: neural

tag: disease status

value: primary glioblastoma

tag: cell type (immunophenotype)

value: CD133/2 negative


title: R. baltica_salt shift_60min_c

description: salt shift 60min vs. reference

tag: Replicate c


title: GBM CD133- isolated cells patient 6

description: Human glioblastoma CD133/2 negative isolated cells from patient 6


title: RT_100_13_180_MECL-100_Lung_07008_Mouse430_2_RSTLRI000_2

description: Gene expression changes in female mouse lung tissue treated for 90 days with MECL

treatment_protocol:
Tissue Harvest Methods: Tissue was excised from animal, minced, placed in RNA later, and stored at -80 degrees Centigrade.

in vivo Treatment: Methylene Chloride, Treatment Repeat: 6, Units of Treatment Repeat: hr/day, Treatment Duration: 13, Units of Duration: weeks, Treatment Time: 5, Units of Treatment Time: days/wk, Vehicle for Chemical: Air, Route of Exposure: Inhalation, Dose or Concentration: 100, Units of Dose or Concentration: ppm

value: tissue

value: lung

tag: array type

value: Affymetrix Mouse 430_2

tag: units of amount

tag: ratio

tag: dilution

value: Good

tag: strain or line

tag: individual

tag: sacrifice method

tag: gender


title: GBM CD133- isolated cells patient 7

description: Human glioblastoma CD133/2 negative isolated cells from patient 7


title: GBM CD133- isolated cells patient 4

description: Human glioblastoma CD133/2 negative isolated cells from patient 4


title: WT4 | C57BL/6

tag: strain


title: GBM CD133- isolated cells patient 5

description: Human glioblastoma CD133/2 negative isolated cells from patient 5


title: R. baltica_salt shift_300min_b

description: salt shift 300min vs. reference

tag: non-treated = reference = time point zero

tag: Salt shifted for 300 min

tag: Replicate b


title: RT_100_13_229_ETOX-100_Lung_07008_Mouse430_2_RSTLRI000_2

tag: sample type

tag: amount to core

tag: rna integrity number

tag: bioanalyzer results

tag: sample preservation

value: RNA later

tag: ncbi taxonomy id

tag: developmental stage

value: adult

value: Pentobarbital (5.2 mg/kg) and exsanguination

value: female

tag: age


title: WT3 | C57BL/6


title: RT_10_13_261_NPTH-10_Lung_07008_Mouse430_2_RSTLRI000_2

source_name: female mouse lung tissue treated for 90 days with NPTH

treatment_protocol:
Tissue Harvest Methods: Tissue was excised from animal, minced, placed in RNA later, and stored at -80 degrees Centigrade.

in vivo Treatment: Naphthalene, Treatment Repeat: 6, Units of Treatment Repeat: hr/day, Treatment Duration: 13, Units of Duration: weeks, Treatment Time: 5, Units of Treatment Time: days/wk, Vehicle for Chemical: Air, Route of Exposure: Inhalation, Dose or Concentration: 10, Units of Dose or Concentration: ppm

tag: tissue

tag: array type

tag: units of amount

value: ul

tag: ratio

tag: dilution

value: 18 weeks


title: WT12 | C57BL/6

tag: strain


title: WT11 | C57BL/6


title: R. baltica_salt shift_60min_a

description: salt shift 60min vs. reference

tag: non-treated = reference = time point zero

tag: Salt shifted for 60min

tag: Replicate a


title: R. baltica_salt shift_20min_c

description: salt shift 20min vs. reference

source_name: Rhodopirellula baltica, salt shift, 20min

tag: Salt shifted for 20min

tag: Replicate c


title: WT10 | C57BL/6


title: WT2 | C57BL/6


title: R. baltica_salt shift_40min_a

description: salt shift 40min vs. reference

source_name: Rhodopirellula baltica, salt shift, 40min

tag: Salt shifted for 40min


title: R. baltica_salt shift_40min_b

description: salt shift 40min vs. reference

tag: Replicate b


title: RT_0_13_44_Lu_FCO2_Mouse430_2_RSTLRI601_1

treatment_protocol:
Tissue Harvest Methods: Tissue was excised from animal, minced, placed in RNA later, and stored at -80 degrees Centigrade.

in vivo Treatment: Rodent Chow, Treatment Duration: 13, Units of Duration: weeks, Treatment Time: 7, Units of Treatment Time: days/wk, Vehicle for Chemical: Rodent Chow, Route of Exposure: Diet, Dose or Concentration: 0, Units of Dose or Concentration: ppm

tag: sample type

tag: amount to core

tag: rna integrity number

tag: bioanalyzer results

tag: sample preservation

tag: strain or line

tag: individual

tag: sacrifice method

tag: gender


title: WT1 | C57BL/6

tag: strain


title: RT_0_13_340_ACO1_Mus_Lung_Mouse430_2_RT_HON07_MusLung

treatment_protocol:
Tissue Harvest Methods: Tissue was excised from animal, minced, placed in RNA later, and stored at -80 degrees Centigrade, Harvest Time Point: 13, Units of Harvest Time Point: weeks

in vivo Treatment: Air, Treatment Repeat: 6, Units of Treatment Repeat: hr/day, Treatment Duration: 13, Units of Duration: weeks, Treatment Time: 5, Units of Treatment Time: days/wk, Vehicle for Chemical: Air, Route of Exposure: Inhalation, Dose or Concentration: 0, Units of Dose or Concentration: ppm

tag: tissue

tag: array type

tag: units of amount

tag: ratio

tag: dilution

value: good

tag: ncbi taxonomy id

tag: developmental stage

tag: age


title: R. baltica_salt shift_20min_b

description: salt shift 20min vs. reference

tag: non-treated = reference = time point zero

tag: Salt shifted for 20min

tag: Replicate b


title: GBM CD133- isolated cells patient 3

description: Human glioblastoma CD133/2 negative isolated cells from patient 3

tag: organ

tag: disease status

tag: cell type (immunophenotype)


title: RT_0_13_43_Lu_FCO2_Mouse430_2_RSTLRI601_1

description: Gene expression changes in female mouse lung tissue treated for 90 days with CTRL

tag: sample type

tag: amount to core

tag: bioanalyzer results

tag: sample preservation

tag: strain or line

tag: individual

tag: sacrifice method


title: GBM CD133+ isolated cells patient 8

description: Human glioblastoma CD133/2 positive isolated cells from patient 8

source_name: CD133+ FACS sorted cells from primary glioblastomas

tag: tissue

value: CD133/2 positive


title: GBM CD133+ isolated cells patient 7

description: Human glioblastoma CD133/2 positive isolated cells from patient 7


title: GBM CD133- isolated cells patient 2

description: Human glioblastoma CD133/2 negative isolated cells from patient 2


title: 512 | R2Yaa IRF5+/-

description: Murine antiserum was obtained from blood collected from an individual mouse of the strain R2Yaa IRF5+/-.  A 1:250 dilution of this antiserum was then applied onto the Utz Lab Whole Protein Autoantigen Array (V1.0), labeled with a goat anti-mouse Ig(M + G) secondary antibody conjugated to Cy3 (Jackson ImmunoResearch), and scanned with a GenePix 4000B scanner using GenePix Pro 6.1.

source_name: Murine antiserum, IRF5+/-

tag: strain

value: R2Yaa IRF5+/-


title: R. baltica_salt shift_20min_a

description: salt shift 20min vs. reference

tag: Replicate a


title: RT_100_13_228_ETOX-100_Lung_07008_Mouse430_2_RSTLRI000_2

tag: array type

tag: units of amount

tag: ratio

tag: dilution

tag: rna integrity number

tag: ncbi taxonomy id

tag: developmental stage

tag: gender

tag: age


title: RT_0_13_42_Lu_FCO2_Mouse430_2_RSTLRI601_1

tag: sample type

tag: amount to core

tag: bioanalyzer results


title: RT_0_13_292_ACO5_Lung_07008_Mouse430_2_RSTLRI000_2

tag: sample preservation

tag: strain or line

tag: individual


title: GBM CD133+ isolated cells patient 5

description: Human glioblastoma CD133/2 positive isolated cells from patient 5

tag: organ

value: brain

tag: tissue

tag: disease status

tag: cell type (immunophenotype)


title: GBM CD133+ isolated cells patient 4

description: Human glioblastoma CD133/2 positive isolated cells from patient 4

value: neural


title: R. baltica_salt shift_40min_c

description: salt shift 40min vs. reference

tag: non-treated = reference = time point zero

tag: Salt shifted for 40min

tag: Replicate c


title: GBM CD133+ isolated cells patient 6

description: Human glioblastoma CD133/2 positive isolated cells from patient 6

value: primary glioblastoma


title: 511 | R2Yaa IRF5+/-

tag: strain


title: RT_0_13_291_ACO5_Lung_07008_Mouse430_2_RSTLRI000_2

tag: array type

tag: units of amount

tag: ratio

tag: dilution

tag: rna integrity number

tag: ncbi taxonomy id

tag: developmental stage

tag: sacrifice method


title: R. baltica_salt shift_10min_b

description: salt shift 10min vs. reference

source_name: Rhodopirellula baltica, salt shift, 10min

tag: Salt shifted for 10min

tag: Replicate b


title: GBM CD133+ isolated cells patient 3

description: Human glioblastoma CD133/2 positive isolated cells from patient 3

tag: organ

tag: tissue


title: R. baltica_salt shift_10min_a

description: salt shift 10min vs. reference

tag: Replicate a


title: R. baltica_cold shock_reference_c

description: self-self hybridisation (replicate c)

source_name: Rhodopirellula baltica cold shock reference

extract_protocol:
The culture pellets were re-suspended in 0.1 M Tris-HCL and then re-centrifuged to cell pellets that were shock-frozen in liquid nitrogen and stored at -80°C. Total RNA was isolated using the proposed protocol of the TRI Reagent® Kit by Ambion (Austin, USA).
cDNA synthesis was performed using the SuperScript direct cDNA labeling system kit by Invitrogen (Karlsruhe, DE) according to the manufacturer´s instructions with random hexamers and unlabeled dCTP/dUTP.

tag: non-treated = reference = time point zero


title: 509 | R2Yaa IRF5-/-

description: Murine antiserum was obtained from blood collected from an individual mouse of the strain R2Yaa IRF5-/-.  A 1:250 dilution of this antiserum was then applied onto the Utz Lab Whole Protein Autoantigen Array (V1.0), labeled with a goat anti-mouse Ig(M + G) secondary antibody conjugated to Cy3 (Jackson ImmunoResearch), and scanned with a GenePix 4000B scanner using GenePix Pro 6.1.

source_name: Murine antiserum, IRF5-/-

value: R2Yaa IRF5-/-


title: 510 | R2Yaa IRF5+/-


title: 508 | R2Yaa IRF5+/+

description: Murine antiserum was obtained from blood collected from an individual mouse of the strain R2Yaa IRF5+/+.  A 1:250 dilution of this antiserum was then applied onto the Utz Lab Whole Protein Autoantigen Array (V1.0), labeled with a goat anti-mouse Ig(M + G) secondary antibody conjugated to Cy3 (Jackson ImmunoResearch), and scanned with a GenePix 4000B scanner using GenePix Pro 6.1.

source_name: Murine antiserum, IRF5+/+

value: R2Yaa IRF5+/+


title: RT_0_13_232_CCO4_Mus_Lung_Mouse430_2_RT_HON07_MusLung

source_name: female mouse lung tissue treated for 90 days with CTRL

treatment_protocol:
Tissue Harvest Methods: Tissue was excised from animal, minced, placed in RNA later, and stored at -80 degrees Centigrade, Harvest Time Point: 13, Units of Harvest Time Point: weeks

in vivo Treatment: Corn Oil, Treatment Repeat: 1, Units of Treatment Repeat: per day, Treatment Duration: 13, Units of Duration: weeks, Treatment Time: 5, Units of Treatment Time: days/wk, Vehicle for Chemical: Corn Oil, Amount of Vehicle: 5, Route of Exposure: Gavage, Units of Amount of Vehicle: ml/kg, Dose or Concentration: 0, Units of Dose or Concentration: mg/kg

tag: sample type

value: tissue

value: lung

tag: amount to core

value: ug

tag: bioanalyzer results

tag: sample preservation

tag: strain or line

tag: individual

tag: gender

tag: age


title: GBM CD133+ isolated cells patient 2

description: Human glioblastoma CD133/2 positive isolated cells from patient 2

tag: disease status

tag: cell type (immunophenotype)


title: R. baltica_salt shift_10min_c

description: salt shift 10min vs. reference

tag: Replicate c


title: GBM CD133- isolated cells patient 1

description: Human glioblastoma CD133/2 negative isolated cells from patient 1

value: CD133/2 negative


title: 505 | R2Yaa IRF5+/+

tag: strain


title: 506 | R2Yaa IRF5+/-


title: RT_0_13_24_Lung_CornOil_Mouse430_2_IMFGN0023_8

treatment_protocol:
Tissue Harvest Methods: Tissue was excised from animal, minced, placed in RNA later, and stored at -80 degrees Centigrade.

in vivo Treatment: Corn Oil, Treatment Repeat: 1, Units of Treatment Repeat: per day, Treatment Duration: 13, Units of Duration: weeks, Treatment Time: 5, Units of Treatment Time: days/wk, Vehicle for Chemical: Corn oil, Amount of Vehicle: 5, Route of Exposure: Gavage, Units of Amount of Vehicle: ml/kg, Dose or Concentration: 0, Units of Dose or Concentration: mg/kg

tag: array type

value: Affymetrix Mouse 430_2

tag: units of amount

tag: ratio

tag: rna integrity number

value: Good

value: RNA later

tag: ncbi taxonomy id

tag: developmental stage

value: adult

tag: sacrifice method


title: GBM CD133+ isolated cells patient 1

description: Human glioblastoma CD133/2 positive isolated cells from patient 1

tag: organ

tag: tissue


title: 504 | R2Yaa IRF5-/-


title: RT_0_13_227_CCO4_Mus_Lung_Mouse430_2_RT_HON07_MusLung

tag: sample type

tag: amount to core

tag: dilution

tag: bioanalyzer results

value: excellent

tag: sample preservation

tag: strain or line

value: Pentobarbital (5.2 mg/kg) and exsanguination

value: female

value: 18 weeks


title: R. baltica_cold shock_reference_b

description: self-self hybridisation (replicate b)

tag: non-treated = reference = time point zero

tag: Replicate b


title: RT_50_13_106_Lu_MACR_Mouse430_2_RSTLRI601_1

description: Gene expression changes in female mouse lung tissue treated for 90 days with MACR

tag: array type

value: ul

tag: individual

tag: gender

tag: age


title: R. baltica_cold shock_reference_a

description: self-self hybridisation (replicate a)

tag: Replicate a


title: R. baltica_cold shock_300min_c

description: cold shock 300min vs. reference

source_name: Rhodopirellula baltica, cold shock, 300min

treatment_protocol: Cells grown continuously at 28°C were collected by centrifugation. Aliquots were resuspend in an equal volume of 6°C medium and returned to 6°C for growth. Samples were collected at 10, 20, 40, 60 and 300 min

tag: Cold shock treated for 300min

tag: Replicate c


title: Panc1/syk-wt cells

city: Durham

first: Jian-Liang

last: Li

address: 111 TW Alexander Dr

institute: NIEHS

description: Gene expression data from Panc1 cells transfected with syk

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hr at 45C on GeneChip U133_plus2 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix Scanner

data_processing: The data were normalized with RMA algorithm

source_name: Stable cell population derived from cell line originally obtained from ATCC

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Cells were passaged one-two times per week for 2 months, maintained at subconfluence, and harvested at ~70% confluence

extract_protocol: Total RNA was harvested according to the manufacturer's instructions for the Rneasy kit (Qiagen)

treatment_protocol: Cells were maintained under hygromycin-selection, no other special treatment

tag: cell line

value: human pancreatic adenocarcinoma cells


title: Panc1/mock cells

description: Gene expression data from Panc1 transfected with vector only


title: RT_250_13_115_Lu_CMPH_Mouse430_2_RSTLRI601_1

description: Gene expression changes in female mouse lung tissue treated for 90 days with CMPH

treatment_protocol:
Tissue Harvest Methods: Tissue was excised from animal, minced, placed in RNA later, and stored at -80 degrees Centigrade.

in vivo Treatment: 2-Chloromethylpyridine hydrochloride, Treatment Repeat: 1, Units of Treatment Repeat: per day, Treatment Duration: 13, Units of Duration: weeks, Treatment Time: 5, Units of Treatment Time: days/wk, Vehicle for Chemical: Distilled water, Amount of Vehicle: 5, Route of Exposure: Gavage, Units of Amount of Vehicle: ml/kg, Dose or Concentration: 250, Units of Dose or Concentration: mg/kg

tag: tissue

tag: units of amount

tag: ratio

tag: rna integrity number

tag: ncbi taxonomy id

tag: developmental stage

tag: sacrifice method


title: 486 | R2Yaa IRF5+/+

tag: strain


title: RT_1250_13_4_Lu_BBMP_Mouse430_2_RSTLRI601_1

description: Gene expression changes in female mouse lung tissue treated for 90 days with BBMP

treatment_protocol:
Tissue Harvest Methods: Tissue was excised from animal, minced, placed in RNA later, and stored at -80 degrees Centigrade.

in vivo Treatment: 2,2-Bis(bromomethyl)-1,3-propanediol, Treatment Duration: 13, Units of Duration: weeks, Treatment Time: 7, Units of Treatment Time: days/wk, Vehicle for Chemical: Rodent Chow, Route of Exposure: Diet, Dose or Concentration: 1250, Units of Dose or Concentration: ppm

tag: sample type

tag: amount to core

tag: dilution

tag: bioanalyzer results

tag: sample preservation

tag: strain or line


title: R. baltica_cold shock_300min_b

description: cold shock 300min vs. reference

tag: non-treated = reference = time point zero

tag: Cold shock treated for 300min

tag: Replicate b


title: 485 | R2Yaa IRF5+/+


title: 503 | R2Yaa IRF5-/-


title: RT_10000_13_19_Lu_NAAC_Mouse430_2_RSTLRI601_1

description: Gene expression changes in female mouse lung tissue treated for 90 days with NAAC

treatment_protocol:
Tissue Harvest Methods: Tissue was excised from animal, minced, placed in RNA later, and stored at -80 degrees Centigrade.

in vivo Treatment: 4-Nitroanthranilic acid, Treatment Duration: 13, Units of Duration: weeks, Treatment Time: 7, Units of Treatment Time: days/wk, Vehicle for Chemical: Rodent Chow, Route of Exposure: Diet, Dose or Concentration: 10000, Units of Dose or Concentration: ppm

tag: tissue

tag: array type

tag: individual

tag: gender

tag: age


title: 473 | R2Yaa IRF5-/-


title: 471 | R2Yaa IRF5-/-


title: RT_100_13_90_Lu_BENZ_Mouse430_2_RSTLRI601_1

description: Gene expression changes in female mouse lung tissue treated for 90 days with BENZ

tag: units of amount

tag: ratio

tag: rna integrity number

tag: ncbi taxonomy id

tag: developmental stage


title: R. baltica_cold shock_60min_b

description: cold shock 60min vs. reference

source_name: Rhodopirellula baltica, cold shock, 60min

tag: Cold shock treated for 60min


title: 472 | R2Yaa IRF5-/-

tag: strain


title: 08-032_CP_strom_CD90posi

city: Ribeirao Preto

first: Ricardo

last: Vêncio

state: SP

address: Av. Bandeirantes, 3900

department: Computing and Mathematics Department

country: Brazil

institute: Universidade de São Paulo

description: Prostate tumor-associated stromal cells.

hyb_protocol: Following fragmentation, ten micrograms of adjusted cRNA fromeach sample was hybridized for 16 hours at 45 deg C to Affymetrix GeneChip

scan_protocol: Scanning was performed using the Affymetrix GeneChip 3000 Scanner. Images were processed into CEL files with the Affymetrix GCOS software.

data_processing: Raw CEL intensity data were RMA normalized using R/Bioconductor

source_name: cancer prostate

label_protocol: Standard Affymetrix IVT labeling protocol. See Affymetrix Expression Analysis Technical Manual

extract_protocol: Prostate tissue was MACS sorted for positive cells.  Total RNA was extracted from the cell lysate using Rneasy kit (Qiagen).

value: prostate

tag: cell type

value: CD90+ MACS sorted cells

tag: gleason

tag: tumor stage

tag: tumor volume


title: R. baltica_cold shock_300min_a

description: cold shock 300min vs. reference

tag: non-treated = reference = time point zero

tag: Cold shock treated for 300min

tag: Replicate a


title: RT_250_13_118_Lu_CMPH_Mouse430_2_RSTLRI601_1

source_name: female mouse lung tissue treated for 90 days with CMPH

tag: sample type

tag: tissue

tag: array type

tag: amount to core

tag: dilution

tag: bioanalyzer results

tag: sample preservation

tag: strain or line

tag: individual

tag: sacrifice method


title: 07-008_CB_str_CD13posi

description: Bladder tumor-associated stromal cells.

source_name: cancer bladder

extract_protocol: Bladder tissue was MACS sorted for positive cells.  Total RNA was extracted from the cell lysate using Rneasy kit (Qiagen).

value: bladder

tag: cell type

value: CD13+ MACS sorted cells

tag: tumor type

value: high-grade urothelial carcinoma


title: RT_1000_13_248_TDPP_Mus_Lung_Mouse430_2_RT_HON07_MusLung

description: Gene expression changes in female mouse lung tissue treated for 90 days with TDPP

treatment_protocol:
Tissue Harvest Methods: Tissue was excised from animal, minced, placed in RNA later, and stored at -80 degrees Centigrade, Harvest Time Point: 13, Units of Harvest Time Point: weeks

in vivo Treatment: Tris(2,3-dibromopropyl)phosphate, Treatment Duration: 13, Units of Duration: weeks, Treatment Time: 7, Units of Treatment Time: days/wk, Vehicle for Chemical: Rodent Chow, Route of Exposure: Diet, Dose or Concentration: 1000, Units of Dose or Concentration: ppm

value: tissue

value: lung

tag: units of amount

value: ug

tag: ratio

tag: rna integrity number

value: good

tag: ncbi taxonomy id

tag: developmental stage

tag: gender

tag: age


title: 05-179_CD26t_2

description: Prostate cancer cells.

tag: tissue

value: CD26+ MACS sorted cells


title: 05-220_NP

description: Prostate whole tissue.

source_name: normal prostate

extract_protocol: Prostate tissue total RNA was extracted from the specimen using Rneasy kit (Qiagen).


title: RT_1250_13_6_Lu_BBMP_Mouse430_2_RSTLRI601_1

source_name: female mouse lung tissue treated for 90 days with BBMP

tag: sample type

tag: array type

value: Affymetrix Mouse 430_2

tag: amount to core

value: Good

value: RNA later

value: adult


title: R. baltica_cold shock_40min_c

description: cold shock 40min vs. reference

tag: non-treated = reference = time point zero

source_name: Rhodopirellula baltica, cold shock, 40min

tag: Cold shock treated for 40min

tag: Replicate c


title: 06-125_NB_CD13posi

description: Bladder stromal fibromuscular cells.

source_name: normal bladder


title: 06-070_NB_str_CD13posi

description: Bladder stromal fibromuscular cells.


title: R. baltica_cold shock_60min_c

description: cold shock 60min vs. reference

tag: Cold shock treated for 60min


title: CP_Str_08-028_CD90posi

tag: cell type

tag: gleason

tag: tumor stage

tag: tumor volume


title: 464 | R2Yaa IRF5+/-

description: Murine antiserum was obtained from blood collected from an individual mouse of the strain R2Yaa IRF5+/-.  A 1:250 dilution of this antiserum was then applied onto the Utz Lab Whole Protein Autoantigen Array (V1.0), labeled with a goat anti-mouse Ig(M + G) secondary antibody conjugated to Cy3 (Jackson ImmunoResearch), and scanned with a GenePix 4000B scanner using GenePix Pro 6.1.

tag: strain

value: R2Yaa IRF5+/-


title: RT_20000_13_245_ABDQ_Mus_Lung_Mouse430_2_RT_HON07_MusLung

description: Gene expression changes in female mouse lung tissue treated for 90 days with ABDQ

treatment_protocol:
Tissue Harvest Methods: Tissue was excised from animal, minced, placed in RNA later, and stored at -80 degrees Centigrade, Harvest Time Point: 13, Units of Harvest Time Point: weeks

in vivo Treatment: 1-Amino-2,4-dibromoanthraquinone, Treatment Duration: 13, Units of Duration: weeks, Treatment Time: 7, Units of Treatment Time: days/wk, Vehicle for Chemical: Rodent Chow, Route of Exposure: Diet, Dose or Concentration: 20000, Units of Dose or Concentration: ppm

tag: units of amount

tag: ratio

tag: dilution

tag: rna integrity number

tag: bioanalyzer results

tag: sample preservation

tag: strain or line

tag: ncbi taxonomy id

tag: individual

tag: sacrifice method

value: Pentobarbital (5.2 mg/kg) and exsanguination

value: female

value: 18 weeks


title: R. baltica_cold shock_40min_a

description: cold shock 40min vs. reference

tag: non-treated = reference = time point zero

tag: Cold shock treated for 40min

tag: Replicate a


title: RT_250_13_113_Lu_CMPH_Mouse430_2_RSTLRI601_1

tag: sample type

tag: tissue

tag: array type

tag: amount to core

value: ul

tag: developmental stage

tag: gender

tag: age


title: RT_240_13_10_Lung_Benzofuran_Mouse430_2_IMFGN0023_8

description: Gene expression changes in female mouse lung tissue treated for 90 days with BFUR

treatment_protocol:
Tissue Harvest Methods: Tissue was excised from animal, minced, placed in RNA later, and stored at -80 degrees Centigrade.

in vivo Treatment: 2,3-Benzofuran, Treatment Repeat: 1, Units of Treatment Repeat: per day, Treatment Duration: 13, Units of Duration: weeks, Treatment Time: 5, Units of Treatment Time: days/wk, Vehicle for Chemical: Corn oil, Amount of Vehicle: 5, Route of Exposure: Gavage, Units of Amount of Vehicle: ml/kg, Dose or Concentration: 240, Units of Dose or Concentration: mg/kg

tag: units of amount

tag: ratio

tag: rna integrity number


title: RT_60_13_165_TCPN-60_Lung_07008_Mouse430_2_RSTLRI000_2

description: Gene expression changes in female mouse lung tissue treated for 90 days with TCPN

treatment_protocol:
Tissue Harvest Methods: Tissue was excised from animal, minced, placed in RNA later, and stored at -80 degrees Centigrade.

in vivo Treatment: 1,2,3-Trichloropropane, Treatment Repeat: 1, Units of Treatment Repeat: per day, Treatment Duration: 13, Units of Duration: weeks, Treatment Time: 5, Units of Treatment Time: days/wk, Vehicle for Chemical: Corn Oil, Amount of Vehicle: 5, Route of Exposure: Gavage, Units of Amount of Vehicle: ml/kg, Dose or Concentration: 60, Units of Dose or Concentration: mg/kg

tag: dilution

tag: bioanalyzer results

tag: sample preservation

tag: strain or line


title: 05-220_CaP

description: Prostate cancer whole tissue.

value: prostate

tag: gleason

tag: tumor stage

tag: tumor volume

value: > 5 cc


title: 08-032_CP_epi_CD26posi

description: Prostate cancer cells.

tag: cell type


title: R. baltica_cold shock_40min_b

description: cold shock 40min vs. reference

tag: non-treated = reference = time point zero

tag: Cold shock treated for 40min

tag: Replicate b


title: R. baltica_cold shock_20min_c

description: cold shock 20min vs. reference

source_name: Rhodopirellula baltica, cold shock, 20min

tag: Cold shock treated for 20min

tag: Replicate c


title: 05-218_NP

description: Prostate whole tissue.

tag: tissue


title: R. baltica_cold shock_60min_a

description: cold shock 60min vs. reference

tag: Cold shock treated for 60min

tag: Replicate a


title: 463 | R2Yaa IRF5+/+

description: Murine antiserum was obtained from blood collected from an individual mouse of the strain R2Yaa IRF5+/+.  A 1:250 dilution of this antiserum was then applied onto the Utz Lab Whole Protein Autoantigen Array (V1.0), labeled with a goat anti-mouse Ig(M + G) secondary antibody conjugated to Cy3 (Jackson ImmunoResearch), and scanned with a GenePix 4000B scanner using GenePix Pro 6.1.

tag: strain

value: R2Yaa IRF5+/+


title: 461 | R2Yaa IRF5+/+


title: 456 | R2Yaa IRF5+/-

source_name: Murine antiserum, IRF5+/-


title: 453 | R2Yaa IRF5+/+


title: R. baltica_cold shock_10min_c

description: cold shock 10min vs. reference

source_name: Rhodopirellula baltica, cold shock, 10min

tag: Cold shock treated for 10min


title: 454 | R2Yaa IRF5+/-


title: 05-218_CaP

description: Prostate cancer whole tissue.

value: 3 cc


title: 452 | R2Yaa IRF5+/-


title: R. baltica_cold shock_20min_a

description: cold shock 20min vs. reference

source_name: Rhodopirellula baltica cold shock reference


title: R. baltica_cold shock_10min_a

description: cold shock 10min vs. reference


title: mus-15dpp-5ng_activin-rep1

city: Pullman

first: Lizhong

last: Yang

state: WA

address: 531 Fulmer Hall/POB 644660

department: School of Molecular Biosciences

institute: Washington State University

description: All methodolgy for this datasets was described in the manuscript of "Developmentally regulated SMAD2 and SMAD3 utilization directs activin signalling outcomes."

hyb_protocol: Standard hybridization protocol using 15ug cRNA wash/stain protocol EukGe-2v5-450

scan_protocol: Affymetrix GeneChip® Operating Software (GCOS) automates the control of GeneChip® Fluidics Stations and Scanners. In addition, GCOS acquires data, manages sample and experimental information, and performs gene expression data analysis.

data_processing: For each microarray, probe set signal values were initially normalized by scaling to a target intensity of 125.

label: Biotin

source_name: Murine 15dpp Sertoli Cell treated with 5ng activin

label_protocol: GeneChip Expression 3' - Amplification one-cycle cDNA synthesis kit (lpn-900431)

extract_protocol: Trizol

tag: Gene expression profile of Sertoli Cell treated with activin


title: 05-214_CaP

description: Prostate cancer whole tissue.


title: mus-15dpp-5ng_activin-rep2