title: TS086-D3-rep4

description:
Biological replicate 1 of 11. Control samples were pooled.
Please see the supplementary file 'GSE16340_73_Compounds_for_training.pdf' for the list of 47 carcinogen and 26 non-carcinogens. Please see the supplementary file 'GSE16340_15_Compounds_for_test.pdf' for the list of other test compounds.

value: Liver

tag: treatment


title: TS086-D3-rep1

status: Public on Jun 22 2009

type: RNA

city: Osaka

first: Kayo

last: Sumida

address: 1-98, Kasugadenaka 3-chome, Konohana-ku

department: Environmental Health Science Laboratory

country: Japan

institute: Sumitomo Chemical Co., Ltd.

description:
Biological replicate 3 of 8. Control samples were pooled.
Please see the supplementary file 'GSE16340_73_Compounds_for_training.pdf' for the list of 47 carcinogen and 26 non-carcinogens. Please see the supplementary file 'GSE16340_15_Compounds_for_test.pdf' for the list of other test compounds.

hyb_protocol: Fragmented cRNA was obtained by heating the solution of 1× fragmentation buffer (Invitrogen), 0.75 μg of Cy3-labeled cRNA, and 0.75 μg of Cy5-labeled cRNA at 94 deg C for 15 min. 30 μl of the fragmented mixture, 46.5 μl of water, 37.5 μl of 20× SSC, 7.5 μl of 10% SDS, and 12 μl of 5× Denhardt's solution were mixed and heated at 95 deg C for 2 min. 1.5 μl of 10 mg/ml salmon sperm DNA solution and 15 μl of formamide were added and heated at 60 deg C for 3 min. 130 μl of hybridization mixture was injected into a microarray chamber and sealed. The microarray was transferred to a hybridization chamber and incubated at 60 deg C overnight with rotation at 6 rpm. After incubation, the microarray was washed for 10 min at 30 degb C in lowstringency wash buffer (5× SSC and 0.1% SDS), washed twice for 2 min at 30 deg C in high-stringency wash buffer (0.5× SSC), and finally rinsed with 0.5× SSC and 0.01% Tween20. The microarray was dried by centrifugation at 360×g for 1 min.

scan_protocol: Scanned on an Agilent G2565AA scanner. Images were quantified using GenePix Pro Software (version 4.0).

data_processing: LOWESS normalized, background subtracted data was calculated by an R package 'sma' using processed Red signal and processed Green signal.

molecule: total RNA

organism: Rattus norvegicus

source_name: Total RNA from rat liver

label_protocol: Amino-allyl cRNA was synthesized from 5 μg of total RNA using the SuperScript Indirect RNA Amplification System (Invitrogen). Amino-allyl cRNA was amplified by in vitro transcription reaction for 3 h, purified using the RNeasy MinElute Kit (Qiagen), and used for the fluorescent dye coupling reaction with the Cy3 or Cy5 Post-Labeling Reactive Dye Pack (GE Healthcare). Amino-allyl cRNA from individual compound-treated rats and pooled time-matched control rats were labeled with Cy3 and Cy5, respectively.

growth_protocol: 4 week-old male Fischer 344 rats were purchased from Charles River Japan. They were housed in an air-conditioned room at 22±2 deg C and 55±15% humidity, with a 12 h light, 12 h dark cycle. Rats were maintained on a basal diet (CRF-1, Oriental Yeast Co.), with tap water ad libitum.

extract_protocol: Total RNA was extracted from liver using RNeasy Midi Kit (Qiagen) following manufacturer's instructions.

treatment_protocol: Each group was composed of 4 rats. At each time point for each compound, there were a group that received the test compound and a control group. Compounds were administered once daily by oral gavage at a dose of 5 ml/kg for up to 1, 3, 7, 14, or 28 days. Control animals received corresponding volumes of vehicle.

tag: gender

value: Male

tag: age

tag: strain

tag: tissue

tag: compound

value: Vehicle

tag: dose

tag: administration

value: gavage

value: 3 days

tag: vehicle

value: Methyleugenol


title: TS086-D3-rep2

description:
Biological replicate 4 of 8. Control samples were pooled.
Please see the supplementary file 'GSE16340_73_Compounds_for_training.pdf' for the list of 47 carcinogen and 26 non-carcinogens. Please see the supplementary file 'GSE16340_15_Compounds_for_test.pdf' for the list of other test compounds.


title: TS084-D3-rep4

description:
Biological replicate 2 of 8. Control samples were pooled.
Please see the supplementary file 'GSE16340_73_Compounds_for_training.pdf' for the list of 47 carcinogen and 26 non-carcinogens. Please see the supplementary file 'GSE16340_15_Compounds_for_test.pdf' for the list of other test compounds.

value: Water

value: Sodium benzoate


title: TS085-D3-rep1

value: Corn oil

value: Indomethacin


title: TS085-D3-rep2


title: TS084-D3-rep3

description:
Biological replicate 1 of 8. Control samples were pooled.
Please see the supplementary file 'GSE16340_73_Compounds_for_training.pdf' for the list of 47 carcinogen and 26 non-carcinogens. Please see the supplementary file 'GSE16340_15_Compounds_for_test.pdf' for the list of other test compounds.


title: TS084-D3-rep2


title: TS084-D3-rep1


title: Patient 009 with adenocarcinoma

status: Public on Jun 23 2009

city: Nagoya

first: Takashi

last: Takahashi

state: Aichi

address: 1-1 Kanokoden, Chikusa-ku

institute: Aichi Cancer Center

description: dataset I

hyb_protocol: standard Affymetrix protocol

scan_protocol: Whole Human Genome oligo DNA microarray with 41000 distinct probes was scanned using an Agilent DNA microarray scanner (G2505B, Agilent Technologies). Images were quantified using Agilent Feature Extraction Software (version 9.5).

data_processing: LOWESS normalized, background subtracted VALUE data obtained from ratio of processed Red signal/processed Green signal using GeneSpring software.

organism: Homo sapiens

source_name: Primary lung tumor

label_protocol: cRNA was generated and labeled with Cy3 or Cy5 (CyDye, Amersham Pharmacia Biotech, Piscataway, NJ) using the Low RNA Fluorescen

extract_protocol: Total RNA was extracted using the RNeasy kit (Qiagen, Valencia, CA), followed by treatment with DNase I. Double-stranded cDNA was synthesized from 500 ng of total RNA using MMLV-RT and poly dT primer incorporating the T7 promoter.

tag: Annotation

tag: Cohort

value: dataset I

tag: Age

tag: Sex

value: F

tag: Histology

value: AD

tag: Smoking (BI)

tag: TNM (Pathological)

tag: Stage (Pathological )

value: IIIA

tag: Status

value: Dead

tag: Survival (days)

tag: Evidence of relapse

value: Y

tag: Site of relapse

value: Liver, adrenal

tag: EGFR status

value: Mut

tag: K-ras Status

value: Wt

tag: p53 Status

source_name: Total RNA from 20 lung cell lines representing all major histological types of lung cancers, labeled with Cyanine-3 (green).


title: TS083-D3-rep3

description:
Biological replicate 1 of 10. Control samples were pooled.
Please see the supplementary file 'GSE16340_73_Compounds_for_training.pdf' for the list of 47 carcinogen and 26 non-carcinogens. Please see the supplementary file 'GSE16340_15_Compounds_for_test.pdf' for the list of other test compounds.

tag: gender

value: Male

tag: age

tag: strain

tag: tissue

value: Liver

tag: compound

value: Vehicle

tag: dose

tag: administration

tag: treatment


title: TS083-D3-rep2

description:
Biological replicate 1 of 9. Control samples were pooled.
Please see the supplementary file 'GSE16340_73_Compounds_for_training.pdf' for the list of 47 carcinogen and 26 non-carcinogens. Please see the supplementary file 'GSE16340_15_Compounds_for_test.pdf' for the list of other test compounds.

value: gavage

value: 3 days

tag: vehicle


title: TS083-D3-rep4


title: TS083-D3-rep1

description:
Biological replicate 4 of 7. Control samples were pooled.
Please see the supplementary file 'GSE16340_73_Compounds_for_training.pdf' for the list of 47 carcinogen and 26 non-carcinogens. Please see the supplementary file 'GSE16340_15_Compounds_for_test.pdf' for the list of other test compounds.


title: TS081-D3-rep3

description:
Biological replicate 2 of 7. Control samples were pooled.
Please see the supplementary file 'GSE16340_73_Compounds_for_training.pdf' for the list of 47 carcinogen and 26 non-carcinogens. Please see the supplementary file 'GSE16340_15_Compounds_for_test.pdf' for the list of other test compounds.

value: Water

value: Glutaraldehyde


title: TS081-D3-rep2

description:
Biological replicate 1 of 7. Control samples were pooled.
Please see the supplementary file 'GSE16340_73_Compounds_for_training.pdf' for the list of 47 carcinogen and 26 non-carcinogens. Please see the supplementary file 'GSE16340_15_Compounds_for_test.pdf' for the list of other test compounds.


title: TS081-D3-rep4

description:
Biological replicate 3 of 7. Control samples were pooled.
Please see the supplementary file 'GSE16340_73_Compounds_for_training.pdf' for the list of 47 carcinogen and 26 non-carcinogens. Please see the supplementary file 'GSE16340_15_Compounds_for_test.pdf' for the list of other test compounds.


title: TS079-D3-rep4

description:
Biological replicate 4 of 6. Control samples were pooled.
Please see the supplementary file 'GSE16340_73_Compounds_for_training.pdf' for the list of 47 carcinogen and 26 non-carcinogens. Please see the supplementary file 'GSE16340_15_Compounds_for_test.pdf' for the list of other test compounds.

value: 1-Chloro-2-propanol (technical)


title: TS082-D3-rep1

value: Corn oil

value: 4-Nitroanthranilic acid


title: TS080-D3-rep2


title: TS082-D3-rep4


title: TS082-D3-rep3


title: TS082-D3-rep2


title: TS080-D3-rep3


title: TS080-D3-rep4


title: TS079-D3-rep3

description:
Biological replicate 3 of 6. Control samples were pooled.
Please see the supplementary file 'GSE16340_73_Compounds_for_training.pdf' for the list of 47 carcinogen and 26 non-carcinogens. Please see the supplementary file 'GSE16340_15_Compounds_for_test.pdf' for the list of other test compounds.


title: TS081-D3-rep1


title: Sample 2_Cap1-HA_223950

type: genomic

city: Paris

first: Sadri

last: ZNAIDI

address: 25 rue du Docteur Roux

department: Mycology Department

country: France

institute: Institut Pasteur

description: Scanned images were pre-processed using the NimbleScan software (version 2.4, NimbleGen® systems, Inc). General Feature Format (GFF) reports were created for the Cy5 (tagged strain) or Cy3 (untagged control strain) intensity signals from each independent replicate, then imported into the TileScope program (http://tilescope.gersteinlab.org:8080/mosaic/pipeline.html).

hyb_protocol: Hybridization was performed as recommended by the manufacturer (NimbleGen® systems, Inc, Platform GPL4037)

scan_protocol: Scanning of the slides (n = 3) was performed using a GenePix 4000B scanner (Molecular Devices) according to the manufacturer instructions.

data_processing: Data provided in column "VALUE" were processed using the NimbleScan software. The Log2 ratio is computed and scaled to center the ratio data around zero. Scaling is performed by subtracting the bi-weight mean for the Log2-ratio values for all features on the array from each Log2-ratio value. Data in the column "VALUE" is only informative. Processing of raw data from 3 independent replicate samples was conducted using Tilescope (http://tilescope.gersteinlab.org:8080/mosaic/pipeline.html). Quantile normalization was applied to the data. The parameters used were as follows: window size of 400 bp, MaxGap of 60 bp and MinRun of 120 bp. The replicate data were combined and peak-finding (i.e. Cap1p-binding sites) was determined using the following criteria: pseudo-median signal threshold of ≥ 2-fold and p-value cut-off of ≤ 0.01.

molecule: genomic DNA

organism: Candida albicans

source_name: Cy5-labeled DNA purified upon chromatin immunoprecipitation_Anti HA antibody.

label_protocol: The IPed DNA fragments were blunted with T4 DNA polymerase and ligated to unidirectional linkers.  The DNA was then amplified by LM-PCR in the presence of aminoallyl-modified dUTP.  The labeling was carried out post-PCR using monoreactive Cy-dye NHS esters (Cy5/Cy3 Mono-Reactive Dye Packs, Amersham Biosciences) that react specifically with the aminoallyl-modified dUTP (5-(3-aminoallyl)-2’ deoxyuridine-5’-triphosphate, Sigma-Aldrich).  Both pools of labeled IPed DNA from the tagged strain (Cy5) and the untagged control strain (Cy3) were mixed and hybridized to C. albicans tiling array (platform GPL4037)

extract_protocol: Three independent cultures (50 ml each) of strains SGY243-CaEXP-CAP1-HA (tagged strain) and SGY243-CaEXP (untagged control strain) were grown overnight in SC-ura+met+cys, diluted to an OD600 of 0.005 in SC-ura-met-cys (to induce PMET3) and grown until OD600 reached 1.0. The cultures were then treated with 1.4 ml of 37% formaldehyde (final concentration 1%) to induce protein-DNA cross-links.  Cells were incubated 30 min at room temperature with agitation and the cross-linking stopped by adding 1.2 ml of 2.5 M glycine.  Cells were harvested, washed 3 times with 40 ml of ice-cold TBS buffer (20 mM Tris-HCl pH 7.5, 150 mM NaCl) and snap frozen in liquid nitrogen.  Total cell extracts were prepared by adding 0.7 ml of lysis buffer (50 mM HEPES-KOH pH 7.5, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% Na-deoxycholate, 1 mM PMSF, 1 mM benzamidine, 10 µg/mL aprotinin, 1 ug/mL leupeptin, 1 ug/mL pepstatin), 0.5 ml of acid-washed glass beads (Sigma) and bead beating 4 times for 5 min at highest settings in a mini bead-beater (Biospec Products).  Preparation of soluble chromatin fragments was performed by sonicating the extracts 4 times during 20 sec at power 2-3 (output power 8-9 RMS) using Sonic Dismembrator Model 100 sonicator (Fisher Scientific).  Immunoprecipitation was performed by incubating the sonicated extracts (from both the tagged strain and the untagged parental strain) overnight with monoclonal mouse anti-HA antibody (Santa Cruz Biotech) coupled to magnetic beads (Dynabeads Pan Mouse IgG, Dynal Biotech, Brown Deer, WI) at 4°C.  Beads were then washed twice with lysis buffer, twice with lysis buffer supplemented with 360 mM NaCl, twice with wash buffer (10 mM Tris-HCl pH 8.0, 250 mM LiCl, 0.5% NP40, 0.5% Na-deoxycholate, 1 mM EDTA) and once with TE buffer (10 mM Tris pH 8.0, 1 mM EDTA).  The cross-links were reversed by incubating the washed beads overnight in 50 µl of TE/1% SDS at 65°C.  The eluted material was then treated with proteinase K, RNase A, extracted twice with phenol:chloroform:isoamyl-alcohol (25:24:1) and the DNA precipitated with 100% ethanol and resuspended in 50 µl of TE.  40 microliters of the immunoprecipitated (IPed) DNA fragments were used for amplification and Cy5/Cy3 dye labeling prior to hybridization microarrays.

source_name: Cy3-labeled DNA purified upon chromatin immunoprecipitation_Anti HA antibody

label_protocol: See Channel 1 Label Protocol

extract_protocol: See Channel 1 Extract Protocol


title: Sample 3_Cap1-HA_223974

source_name: Cy5-labeled DNA purified upon chromatin immunoprecipitation_Anti HA antibody


title: TS080-D3-rep1


title: TS079-D3-rep1

description:
Biological replicate 1 of 6. Control samples were pooled.
Please see the supplementary file 'GSE16340_73_Compounds_for_training.pdf' for the list of 47 carcinogen and 26 non-carcinogens. Please see the supplementary file 'GSE16340_15_Compounds_for_test.pdf' for the list of other test compounds.


title: TS078-D3-rep1

value: Chlorendic acid


title: Sample 1_Cap1-HA_223947


title: TS077-D3-rep4

value: 4-Dimethylaminoazobenzene (DAB)


title: TS077-D3-rep2

description:
Biological replicate 2 of 6. Control samples were pooled.
Please see the supplementary file 'GSE16340_73_Compounds_for_training.pdf' for the list of 47 carcinogen and 26 non-carcinogens. Please see the supplementary file 'GSE16340_15_Compounds_for_test.pdf' for the list of other test compounds.


title: TS077-D3-rep1


title: TS078-D3-rep3


title: TS078-D3-rep2


title: TS075-D3-rep1

value: 4-Aminoazobenzene (AAB)


title: TS076-D3-rep3

description:
Biological replicate 2 of 10. Control samples were pooled.
Please see the supplementary file 'GSE16340_73_Compounds_for_training.pdf' for the list of 47 carcinogen and 26 non-carcinogens. Please see the supplementary file 'GSE16340_15_Compounds_for_test.pdf' for the list of other test compounds.


title: Sample 3_Cap1-CSE-HA_223937

label_protocol: The IPed DNA fragments were blunted with T4 DNA polymerase and ligated to unidirectional linkers. The DNA was then amplified by LM-PCR in the presence of aminoallyl-modified dUTP. The labeling was carried out post-PCR using monoreactive Cy-dye NHS esters (Cy5/Cy3 Mono-Reactive Dye Packs, Amersham Biosciences) that react specifically with the aminoallyl-modified dUTP (5-(3-aminoallyl)-2’ deoxyuridine-5’-triphosphate, Sigma-Aldrich). Both pools of labeled IPed DNA from the tagged strain (Cy5) and the untagged control strain (Cy3) were mixed and hybridized to C. albicans tiling array (platform GPL4037).

extract_protocol: Three independent cultures (50 ml each) of strains SGY243-CaEXP-CAP1-CSE-HA (tagged strain) and SGY243-CaEXP (untagged control strain) were grown overnight in SC-ura+met+cys, diluted to an OD600 of 0.005 in SC-ura-met-cys (to induce PMET3) and grown until OD600 reached 1.0. The cultures were then treated with 1.4 ml of 37% formaldehyde (final concentration 1%) to induce protein-DNA cross-links. Cells were incubated 30 min at room temperature with agitation and the cross-linking stopped by adding 1.2 ml of 2.5 M glycine. Cells were harvested, washed 3 times with 40 ml of ice-cold TBS buffer (20 mM Tris-HCl pH 7.5, 150 mM NaCl) and snap frozen in liquid nitrogen. Total cell extracts were prepared by adding 0.7 ml of lysis buffer (50 mM HEPES-KOH pH 7.5, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% Na-deoxycholate, 1 mM PMSF, 1 mM benzamidine, 10 µg/mL aprotinin, 1 ug/mL leupeptin, 1 ug/mL pepstatin), 0.5 ml of acid-washed glass beads (Sigma) and bead beating 4 times for 5 min at highest settings in a mini bead-beater (Biospec Products). Preparation of soluble chromatin fragments was performed by sonicating the extracts 4 times during 20 sec at power 2-3 (output power 8-9 RMS) using Sonic Dismembrator Model 100 sonicator (Fisher Scientific). Immunoprecipitation was performed by incubating the sonicated extracts (from both the tagged strain and the untagged parental strain) overnight with monoclonal mouse anti-HA antibody (Santa Cruz Biotech) coupled to magnetic beads (Dynabeads Pan Mouse IgG, Dynal Biotech, Brown Deer, WI) at 4°C. Beads were then washed twice with lysis buffer, twice with lysis buffer supplemented with 360 mM NaCl, twice with wash buffer (10 mM Tris-HCl pH 8.0, 250 mM LiCl, 0.5% NP40, 0.5% Na-deoxycholate, 1 mM EDTA) and once with TE buffer (10 mM Tris pH 8.0, 1 mM EDTA). The cross-links were reversed by incubating the washed beads overnight in 50 µl of TE/1% SDS at 65°C. The eluted material was then treated with proteinase K, RNase A, extracted twice with phenol:chloroform:isoamyl-alcohol (25:24:1) and the DNA precipitated with 100% ethanol and resuspended in 50 µl of TE. 40 microliters of the immunoprecipitated (IPed) DNA fragments were used for amplification and Cy5/Cy3 dye labeling prior to hybridization microarrays.


title: TS078-D3-rep4


title: TS076-D3-rep4

description:
Biological replicate 3 of 10. Control samples were pooled.
Please see the supplementary file 'GSE16340_73_Compounds_for_training.pdf' for the list of 47 carcinogen and 26 non-carcinogens. Please see the supplementary file 'GSE16340_15_Compounds_for_test.pdf' for the list of other test compounds.


title: TS076-D3-rep2


title: TS076-D3-rep1

description:
Biological replicate 4 of 10. Control samples were pooled.
Please see the supplementary file 'GSE16340_73_Compounds_for_training.pdf' for the list of 47 carcinogen and 26 non-carcinogens. Please see the supplementary file 'GSE16340_15_Compounds_for_test.pdf' for the list of other test compounds.


title: Sample 1_Cap1-CSE-HA_223938


title: TS074-D3-rep3

description:
Biological replicate 3 of 9. Control samples were pooled.
Please see the supplementary file 'GSE16340_73_Compounds_for_training.pdf' for the list of 47 carcinogen and 26 non-carcinogens. Please see the supplementary file 'GSE16340_15_Compounds_for_test.pdf' for the list of other test compounds.

value: Caprolactam


title: Sample 2_Cap1-CSE-HA_223940


title: TS074-D3-rep4

description:
Biological replicate 4 of 9. Control samples were pooled.
Please see the supplementary file 'GSE16340_73_Compounds_for_training.pdf' for the list of 47 carcinogen and 26 non-carcinogens. Please see the supplementary file 'GSE16340_15_Compounds_for_test.pdf' for the list of other test compounds.


title: TS075-D3-rep2

description:
Biological replicate 1 of 11. Control samples were pooled.
Please see the supplementary file 'GSE16340_73_Compounds_for_training.pdf' for the list of 47 carcinogen and 26 non-carcinogens. Please see the supplementary file 'GSE16340_15_Compounds_for_test.pdf' for the list of other test compounds.


title: TS075-D3-rep4


title: TS075-D3-rep3


title: TS074-D3-rep2

description:
Biological replicate 2 of 9. Control samples were pooled.
Please see the supplementary file 'GSE16340_73_Compounds_for_training.pdf' for the list of 47 carcinogen and 26 non-carcinogens. Please see the supplementary file 'GSE16340_15_Compounds_for_test.pdf' for the list of other test compounds.


title: TS074-D3-rep1

description:
Biological replicate 1 of 9. Control samples were pooled.
Please see the supplementary file 'GSE16340_73_Compounds_for_training.pdf' for the list of 47 carcinogen and 26 non-carcinogens. Please see the supplementary file 'GSE16340_15_Compounds_for_test.pdf' for the list of other test compounds.


title: TS073-D3-rep4

value: Phthalamide


title: TS073-D3-rep2


title: TS072-D3-rep4


title: TS072-D3-rep3


title: TS070-D3-rep2

description:
Biological replicate 3 of 8. Control samples were pooled.
Please see the supplementary file 'GSE16340_73_Compounds_for_training.pdf' for the list of 47 carcinogen and 26 non-carcinogens. Please see the supplementary file 'GSE16340_15_Compounds_for_test.pdf' for the list of other test compounds.

value: D,L-Ethionine


title: TS071-D3-rep3

description:
Biological replicate 4 of 8. Control samples were pooled.
Please see the supplementary file 'GSE16340_73_Compounds_for_training.pdf' for the list of 47 carcinogen and 26 non-carcinogens. Please see the supplementary file 'GSE16340_15_Compounds_for_test.pdf' for the list of other test compounds.

value: Aspirin


title: TS073-D3-rep1

value: Male


title: TS071-D3-rep1

description:
Biological replicate 2 of 8. Control samples were pooled.
Please see the supplementary file 'GSE16340_73_Compounds_for_training.pdf' for the list of 47 carcinogen and 26 non-carcinogens. Please see the supplementary file 'GSE16340_15_Compounds_for_test.pdf' for the list of other test compounds.

value: Liver


title: TS073-D3-rep3

value: Vehicle


title: TS070-D3-rep1

value: gavage


title: TS068-D3-rep4

value: 3 days

value: Diethylstilbestrol (DES)


title: TS071-D3-rep2


title: TS079-D3-rep2

value: Water


title: TS071-D3-rep4


title: TS072-D3-rep1

description:
Biological replicate 1 of 10. Control samples were pooled.
Please see the supplementary file 'GSE16340_73_Compounds_for_training.pdf' for the list of 47 carcinogen and 26 non-carcinogens. Please see the supplementary file 'GSE16340_15_Compounds_for_test.pdf' for the list of other test compounds.


title: TS069-D3-rep1

value: Phenytoin (5,5-Diphenylhydantoin)


title: TS069-D3-rep2


title: TS070-D3-rep4

description:
Biological replicate 1 of 8. Control samples were pooled.
Please see the supplementary file 'GSE16340_73_Compounds_for_training.pdf' for the list of 47 carcinogen and 26 non-carcinogens. Please see the supplementary file 'GSE16340_15_Compounds_for_test.pdf' for the list of other test compounds.

value: Corn oil


title: TS069-D3-rep3


title: TS070-D3-rep3


title: TS068-D3-rep1

description:
Biological replicate 3 of 7. Control samples were pooled.
Please see the supplementary file 'GSE16340_73_Compounds_for_training.pdf' for the list of 47 carcinogen and 26 non-carcinogens. Please see the supplementary file 'GSE16340_15_Compounds_for_test.pdf' for the list of other test compounds.


title: TS072-D3-rep2


title: TS069-D3-rep4


title: TS067-D3-rep4

description:
Biological replicate 2 of 7. Control samples were pooled.
Please see the supplementary file 'GSE16340_73_Compounds_for_training.pdf' for the list of 47 carcinogen and 26 non-carcinogens. Please see the supplementary file 'GSE16340_15_Compounds_for_test.pdf' for the list of other test compounds.

value: Acetamide


title: TS068-D3-rep2

description:
Biological replicate 4 of 7. Control samples were pooled.
Please see the supplementary file 'GSE16340_73_Compounds_for_training.pdf' for the list of 47 carcinogen and 26 non-carcinogens. Please see the supplementary file 'GSE16340_15_Compounds_for_test.pdf' for the list of other test compounds.


title: TS068-D3-rep3


title: TS067-D3-rep2


title: TS067-D3-rep3

description:
Biological replicate 1 of 7. Control samples were pooled.
Please see the supplementary file 'GSE16340_73_Compounds_for_training.pdf' for the list of 47 carcinogen and 26 non-carcinogens. Please see the supplementary file 'GSE16340_15_Compounds_for_test.pdf' for the list of other test compounds.


title: TS067-D3-rep1


title: TS066-D3-rep3

value: Tetrachloroethylene


title: TS065-D3-rep1

description:
Biological replicate 4 of 6. Control samples were pooled.
Please see the supplementary file 'GSE16340_73_Compounds_for_training.pdf' for the list of 47 carcinogen and 26 non-carcinogens. Please see the supplementary file 'GSE16340_15_Compounds_for_test.pdf' for the list of other test compounds.

value: MNNG


title: TS066-D3-rep2


title: TS065-D3-rep2


title: TS066-D3-rep1


title: TS062-D3-rep1

description:
Biological replicate 1 of 6. Control samples were pooled.
Please see the supplementary file 'GSE16340_73_Compounds_for_training.pdf' for the list of 47 carcinogen and 26 non-carcinogens. Please see the supplementary file 'GSE16340_15_Compounds_for_test.pdf' for the list of other test compounds.

value: α-Tocopherol (Vitamin E)


title: TS064-D3-rep4

description:
Biological replicate 3 of 6. Control samples were pooled.
Please see the supplementary file 'GSE16340_73_Compounds_for_training.pdf' for the list of 47 carcinogen and 26 non-carcinogens. Please see the supplementary file 'GSE16340_15_Compounds_for_test.pdf' for the list of other test compounds.


title: TS062-D3-rep2


title: TS064-D3-rep3

description:
Biological replicate 2 of 6. Control samples were pooled.
Please see the supplementary file 'GSE16340_73_Compounds_for_training.pdf' for the list of 47 carcinogen and 26 non-carcinogens. Please see the supplementary file 'GSE16340_15_Compounds_for_test.pdf' for the list of other test compounds.


title: TS063-D3-rep3

value: Benzo [a]pyrene (BP)


title: TS065-D3-rep3


title: TS062-D3-rep4


title: TS062-D3-rep3


title: TS064-D3-rep2


title: TS063-D3-rep1


title: TS063-D3-rep4


title: TS061-D3-rep4

description:
Biological replicate 4 of 5. Control samples were pooled.
Please see the supplementary file 'GSE16340_73_Compounds_for_training.pdf' for the list of 47 carcinogen and 26 non-carcinogens. Please see the supplementary file 'GSE16340_15_Compounds_for_test.pdf' for the list of other test compounds.

value: 4-Acetylaminofluorene (4-AAF)


title: TS063-D3-rep2


title: TS065-D3-rep4


title: TS060-D3-rep4

value: 2,5-Toluenediamine SO4


title: TS066-D3-rep4


title: TS061-D3-rep2

description:
Biological replicate 2 of 5. Control samples were pooled.
Please see the supplementary file 'GSE16340_73_Compounds_for_training.pdf' for the list of 47 carcinogen and 26 non-carcinogens. Please see the supplementary file 'GSE16340_15_Compounds_for_test.pdf' for the list of other test compounds.


title: TS061-D3-rep1

description:
Biological replicate 1 of 5. Control samples were pooled.
Please see the supplementary file 'GSE16340_73_Compounds_for_training.pdf' for the list of 47 carcinogen and 26 non-carcinogens. Please see the supplementary file 'GSE16340_15_Compounds_for_test.pdf' for the list of other test compounds.


title: TS060-D3-rep3

description:
Biological replicate 3 of 5. Control samples were pooled.
Please see the supplementary file 'GSE16340_73_Compounds_for_training.pdf' for the list of 47 carcinogen and 26 non-carcinogens. Please see the supplementary file 'GSE16340_15_Compounds_for_test.pdf' for the list of other test compounds.


title: TS061-D3-rep3


title: TS060-D3-rep2


title: TS064-D3-rep1


title: TS060-D3-rep1


title: TS059-D3-rep1

value: p-Phenylenediamine 2HCl


title: TS057-D3-rep3

description:
Biological replicate 2 of 9. Control samples were pooled.
Please see the supplementary file 'GSE16340_73_Compounds_for_training.pdf' for the list of 47 carcinogen and 26 non-carcinogens. Please see the supplementary file 'GSE16340_15_Compounds_for_test.pdf' for the list of other test compounds.

value: Male

value: Lindane


title: TS059-D3-rep2

value: Liver

value: Vehicle


title: TS059-D3-rep3

value: gavage

value: 3 days


title: TS057-D3-rep1


title: TS057-D3-rep2

description:
Biological replicate 1 of 9. Control samples were pooled.
Please see the supplementary file 'GSE16340_73_Compounds_for_training.pdf' for the list of 47 carcinogen and 26 non-carcinogens. Please see the supplementary file 'GSE16340_15_Compounds_for_test.pdf' for the list of other test compounds.


title: TS059-D3-rep4

value: Water


title: TS058-D3-rep4

description:
Biological replicate 3 of 9. Control samples were pooled.
Please see the supplementary file 'GSE16340_73_Compounds_for_training.pdf' for the list of 47 carcinogen and 26 non-carcinogens. Please see the supplementary file 'GSE16340_15_Compounds_for_test.pdf' for the list of other test compounds.

value: 2-Chloro-p-phenylenediamine SO4


title: TS055-D3-rep4

description:
Biological replicate 4 of 8. Control samples were pooled.
Please see the supplementary file 'GSE16340_73_Compounds_for_training.pdf' for the list of 47 carcinogen and 26 non-carcinogens. Please see the supplementary file 'GSE16340_15_Compounds_for_test.pdf' for the list of other test compounds.

value: Corn oil

value: Pentachloroethane


title: TS056-D3-rep4

value: Chloroform


title: TS056-D3-rep3

description:
Biological replicate 3 of 8. Control samples were pooled.
Please see the supplementary file 'GSE16340_73_Compounds_for_training.pdf' for the list of 47 carcinogen and 26 non-carcinogens. Please see the supplementary file 'GSE16340_15_Compounds_for_test.pdf' for the list of other test compounds.


title: TS056-D3-rep1

description:
Biological replicate 1 of 8. Control samples were pooled.
Please see the supplementary file 'GSE16340_73_Compounds_for_training.pdf' for the list of 47 carcinogen and 26 non-carcinogens. Please see the supplementary file 'GSE16340_15_Compounds_for_test.pdf' for the list of other test compounds.


title: TS056-D3-rep2

description:
Biological replicate 2 of 8. Control samples were pooled.
Please see the supplementary file 'GSE16340_73_Compounds_for_training.pdf' for the list of 47 carcinogen and 26 non-carcinogens. Please see the supplementary file 'GSE16340_15_Compounds_for_test.pdf' for the list of other test compounds.


title: TS057-D3-rep4


title: TS055-D3-rep2


title: TS058-D3-rep2


title: TS058-D3-rep1

description:
Biological replicate 4 of 9. Control samples were pooled.
Please see the supplementary file 'GSE16340_73_Compounds_for_training.pdf' for the list of 47 carcinogen and 26 non-carcinogens. Please see the supplementary file 'GSE16340_15_Compounds_for_test.pdf' for the list of other test compounds.


title: TS058-D3-rep3


title: TS054-D3-rep3

value: Urethane


title: TS054-D3-rep4


title: TS055-D3-rep1


title: TS055-D3-rep3


title: TS054-D3-rep1


title: TS053-D3-rep4

description:
Biological replicate 1 of 7. Control samples were pooled.
Please see the supplementary file 'GSE16340_73_Compounds_for_training.pdf' for the list of 47 carcinogen and 26 non-carcinogens. Please see the supplementary file 'GSE16340_15_Compounds_for_test.pdf' for the list of other test compounds.

value: Methapyrilene HCl


title: TS053-D3-rep3

description:
Biological replicate 4 of 7. Control samples were pooled.
Please see the supplementary file 'GSE16340_73_Compounds_for_training.pdf' for the list of 47 carcinogen and 26 non-carcinogens. Please see the supplementary file 'GSE16340_15_Compounds_for_test.pdf' for the list of other test compounds.


title: TS054-D3-rep2


title: TS052-D3-rep2

description:
Biological replicate 3 of 7. Control samples were pooled.
Please see the supplementary file 'GSE16340_73_Compounds_for_training.pdf' for the list of 47 carcinogen and 26 non-carcinogens. Please see the supplementary file 'GSE16340_15_Compounds_for_test.pdf' for the list of other test compounds.

value: Tannic acid


title: TS052-D3-rep3


title: TS052-D3-rep1

description:
Biological replicate 2 of 7. Control samples were pooled.
Please see the supplementary file 'GSE16340_73_Compounds_for_training.pdf' for the list of 47 carcinogen and 26 non-carcinogens. Please see the supplementary file 'GSE16340_15_Compounds_for_test.pdf' for the list of other test compounds.


title: TS053-D3-rep1


title: TS050-D3-rep4

value: Water (PH4)

value: N-Ethyl-N-nitrosourea (ENU)


title: TS052-D3-rep4


title: TS051-D3-rep4

value: Trichloroacetic acid


title: TS053-D3-rep2

value: Male


title: TS051-D3-rep2


title: TS051-D3-rep1


title: TS047-D3-rep1

value: 7,12-Dimethylbenz [a]anthracene (DMBA)


title: TS048-D3-rep4

description:
Biological replicate 2 of 6. Control samples were pooled.
Please see the supplementary file 'GSE16340_73_Compounds_for_training.pdf' for the list of 47 carcinogen and 26 non-carcinogens. Please see the supplementary file 'GSE16340_15_Compounds_for_test.pdf' for the list of other test compounds.

value: Liver

value: 3-Methylcholanthrene (MC)


title: TS048-D3-rep1

description:
Biological replicate 3 of 6. Control samples were pooled.
Please see the supplementary file 'GSE16340_73_Compounds_for_training.pdf' for the list of 47 carcinogen and 26 non-carcinogens. Please see the supplementary file 'GSE16340_15_Compounds_for_test.pdf' for the list of other test compounds.

value: Vehicle

value: gavage


title: TS050-D3-rep2

description:
Biological replicate 4 of 6. Control samples were pooled.
Please see the supplementary file 'GSE16340_73_Compounds_for_training.pdf' for the list of 47 carcinogen and 26 non-carcinogens. Please see the supplementary file 'GSE16340_15_Compounds_for_test.pdf' for the list of other test compounds.

value: 3 days


title: TS048-D3-rep2


title: TS047-D3-rep4


title: TS048-D3-rep3

description:
Biological replicate 1 of 6. Control samples were pooled.
Please see the supplementary file 'GSE16340_73_Compounds_for_training.pdf' for the list of 47 carcinogen and 26 non-carcinogens. Please see the supplementary file 'GSE16340_15_Compounds_for_test.pdf' for the list of other test compounds.


title: TS047-D3-rep3


title: TS050-D3-rep1


title: TS050-D3-rep3


title: TS046-D3-rep3

description:
Biological replicate 2 of 5. Control samples were pooled.
Please see the supplementary file 'GSE16340_73_Compounds_for_training.pdf' for the list of 47 carcinogen and 26 non-carcinogens. Please see the supplementary file 'GSE16340_15_Compounds_for_test.pdf' for the list of other test compounds.

value: Benz [a]anthracene (BA)


title: TS046-D3-rep4

description:
Biological replicate 3 of 5. Control samples were pooled.
Please see the supplementary file 'GSE16340_73_Compounds_for_training.pdf' for the list of 47 carcinogen and 26 non-carcinogens. Please see the supplementary file 'GSE16340_15_Compounds_for_test.pdf' for the list of other test compounds.

value: Corn oil


title: TS043-D3-rep4

description:
Biological replicate 4 of 4. Control samples were pooled.
Please see the supplementary file 'GSE16340_73_Compounds_for_training.pdf' for the list of 47 carcinogen and 26 non-carcinogens. Please see the supplementary file 'GSE16340_15_Compounds_for_test.pdf' for the list of other test compounds.

value: 2-Acetylaminofluorene (2-AAF)


title: TS044-D3-rep1

description:
Biological replicate 1 of 4. Control samples were pooled.
Please see the supplementary file 'GSE16340_73_Compounds_for_training.pdf' for the list of 47 carcinogen and 26 non-carcinogens. Please see the supplementary file 'GSE16340_15_Compounds_for_test.pdf' for the list of other test compounds.

value: MeIQx


title: TS045-D3-rep3

value: PhIP


title: TS043-D3-rep3

description:
Biological replicate 3 of 4. Control samples were pooled.
Please see the supplementary file 'GSE16340_73_Compounds_for_training.pdf' for the list of 47 carcinogen and 26 non-carcinogens. Please see the supplementary file 'GSE16340_15_Compounds_for_test.pdf' for the list of other test compounds.


title: TS043-D3-rep2

description:
Biological replicate 2 of 4. Control samples were pooled.
Please see the supplementary file 'GSE16340_73_Compounds_for_training.pdf' for the list of 47 carcinogen and 26 non-carcinogens. Please see the supplementary file 'GSE16340_15_Compounds_for_test.pdf' for the list of other test compounds.


title: TS044-D3-rep4


title: TS045-D3-rep1

description:
Biological replicate 4 of 5. Control samples were pooled.
Please see the supplementary file 'GSE16340_73_Compounds_for_training.pdf' for the list of 47 carcinogen and 26 non-carcinogens. Please see the supplementary file 'GSE16340_15_Compounds_for_test.pdf' for the list of other test compounds.


title: TS045-D3-rep2

description:
Biological replicate 1 of 5. Control samples were pooled.
Please see the supplementary file 'GSE16340_73_Compounds_for_training.pdf' for the list of 47 carcinogen and 26 non-carcinogens. Please see the supplementary file 'GSE16340_15_Compounds_for_test.pdf' for the list of other test compounds.


title: TS045-D3-rep4


title: TS046-D3-rep1


title: TS049-D3-rep3


title: TS049-D3-rep2


title: TS044-D3-rep2


title: TS044-D3-rep3


title: TS046-D3-rep2


title: TS043-D3-rep1


title: TS049-D3-rep1


title: TS042-D3-rep4

value: Water

value: N-Nitrosopiperidine


title: TS042-D3-rep3


title: TS042-D3-rep2


title: TS042-D3-rep1


title: TS040-D3-rep3

value: Gum arabic

value: Lithocholic acid


title: TS039-D3-rep2

value: Iodoform


title: TS041-D3-rep2

value: Male

value: N-Nitrosodimethylamine (DMN)


title: TS040-D3-rep2

value: Liver


title: TS039-D3-rep3


title: TS040-D3-rep1


title: TS039-D3-rep4


title: TS037-D3-rep2

value: Quercetin


title: TS038-D3-rep2

value: Vehicle

value: Benzoin


title: TS040-D3-rep4

value: gavage

value: 3 days


title: TS038-D3-rep4


title: TS041-D3-rep1


title: TS041-D3-rep4


title: TS038-D3-rep3


title: TS041-D3-rep3


title: TS037-D3-rep1


title: TS038-D3-rep1


title: TS037-D3-rep4


title: TS037-D3-rep3


title: TS039-D3-rep1

value: Corn oil


title: TS036-D3-rep3


title: TS036-D3-rep4


title: TS035-D3-rep2

value: 1% CMC


title: TS035-D3-rep1


title: TS035-D3-rep3


title: TS035-D3-rep4


title: TS036-D3-rep2


title: TS033-D3-rep4

value: 2-Chloromethylpyridine HCl


title: TS036-D3-rep1


title: TS034-D3-rep2

value: D,L-Menthol


title: TS033-D3-rep1

value: Water


title: TS034-D3-rep3


title: TS032-D3-rep2


title: TS033-D3-rep3


title: TS032-D3-rep3


title: TS034-D3-rep1


title: TS031-D3-rep4

value: MC

value: Acetaminophen（Paracetamol）


title: TS033-D3-rep2


title: TS034-D3-rep4


title: TS030-D3-rep2

value: Thioacetamide


title: TS031-D3-rep3


title: TS032-D3-rep4


title: TS029-D3-rep3

value: Methyl carbamate


title: TS029-D3-rep4

value: Male


title: TS030-D3-rep1


title: TS028-D3-rep3

value: Furan


title: TS028-D3-rep2

value: Liver


title: TS028-D3-rep1


title: TS027-D3-rep1


title: TS029-D3-rep2


title: TS030-D3-rep4


title: TS026-D3-rep4

value: 1,4-Dichlorobenzene (DCB)


title: TS027-D3-rep3

value: Vehicle


title: TS027-D3-rep4


title: TS029-D3-rep1


title: TS028-D3-rep4


title: TS027-D3-rep2


title: TS030-D3-rep3


title: TS031-D3-rep2


title: TS031-D3-rep1


title: TS026-D3-rep1


title: TS026-D3-rep3


title: TS026-D3-rep2


title: TS024-D3-rep2

value: D-Limonene


title: TS023-D3-rep3

value: gavage

value: Butylated hydroxyanisole (BHA)


title: TS025-D3-rep4

value: 3 days

value: Corn oil

value: Safrole


title: TS025-D3-rep2


title: TS025-D3-rep3


title: TS024-D3-rep3


title: TS024-D3-rep1


title: TS024-D3-rep4


title: TS023-D3-rep4


title: TS025-D3-rep1


title: TS022-D3-rep4

value: Trichloroethylene


title: TS021-D3-rep3

value: α-Hexachlorocyclohexane(α-HCH)


title: TS023-D3-rep1


title: TS022-D3-rep1


title: TS023-D3-rep2


title: TS021-D3-rep4


title: TS022-D3-rep3


title: TS022-D3-rep2


title: TS021-D3-rep1


title: TS021-D3-rep2


title: TS020-D3-rep4

value: Hexachlorobenzene (HCB)


title: TS020-D3-rep2


title: TS020-D3-rep3


title: TS020-D3-rep1


title: TS019-D3-rep2

value: Ethinylestradiol


title: TS019-D3-rep4


title: TS017-D3-rep1

value: Dieldrin


title: TS019-D3-rep1


title: TS017-D3-rep3


title: TS018-D3-rep4

value: Di(2-ethylhexyl)adipate (DEHA)


title: TS017-D3-rep2

value: Male


title: TS016-D3-rep2

value: Dichlorodiphenyltrichloroethane (DDT)


title: TS017-D3-rep4

value: Liver


title: TS018-D3-rep3


title: TS016-D3-rep3


title: TS016-D3-rep1


title: TS019-D3-rep3


title: TS016-D3-rep4


title: TS018-D3-rep1


title: TS014-D3-rep3

value: Water

value: N-Nitrosomorpholine


title: TS014-D3-rep2

value: Vehicle


title: TS018-D3-rep2

value: gavage


title: TS015-D3-rep1

value: Aldrin


title: TS015-D3-rep2

value: 3 days


title: TS015-D3-rep4

value: Corn oil


title: TS015-D3-rep3


title: TS014-D3-rep1


title: TS013-D3-rep3


title: TS013-D3-rep4


title: TS013-D3-rep1


title: TS014-D3-rep4


title: TS012-D3-rep4

value: 1% CMC


title: TS012-D3-rep1


title: TS012-D3-rep2


title: TS013-D3-rep2


title: Larynx tumor_sample T15_Replicate 1

city: São Paulo

first: Eduardo

middle: Moraes

last: Reis

state: SP

address: Av. Prof. Lineu Prestes, 748

department: Biochemistry

country: Brazil

institute: University of São Paulo

description: Experiment described in detail in the previous sections.

hyb_protocol: Labeled targets were ressuspended in 250 µl of 1x hybridization buffer [25% formamide, 12.5% of proprietary Microarray Hybridization Buffer Version 2 (Amersham Biosciences)] denatured for 2 min at 92ºC and centrifuged at 13,000 rpm for 5 min. The Cy5 (tumor or non-tumor sample) labeled cDNAs were hybridized with microarrays on an Automated Slide Processor (ASP, GE Healthcare) and incubated for 16 h at 42ºC. Following hybridization, slides were washed (1.0× SSC, 0.2% SDS 10 min at 55°C; 0.1× SSC, 0.2% SDS 10 min at 55°C; 0.1× SSC, 0.2% SDS 10 min at 55°C; 0.1× SSC 1 min at RT; 0.1× SSC 1 min at RT; dH2O 10 sec. at RT), and dried with a N2 stream.

scan_protocol: Processed slides were scanned with a 700 V PMT setting (GenIII Scanner – Amersham Biosciences).

data_processing:
Background-subtracted artifact-removed median intensities of Cy5 emissions were extracted for each spot from raw images, using the ArrayVision V.7.2 software (Imaging Research Inc., Ontario, Canada).
An array grid was first automatically aligned to locate the position of each spot in the array, and then manually adjusted to obtain the best possible alignment.
To make the experiments comparable, intensity data derived from Cy5-labeled test samples from different hybridizations were normalized by LOWESS, local weighted scatter-plot smoothing.
Intensity data from a sample with total energy comparable to the average intensity of all samples was used as a reference in the LOWESS normalization procedure.

label: NHS-ester Cy5

source_name: Larynx tumor_sample T15

label_protocol:
Labeled targets for hybridizations were generated from total mRNA in reverse transcription reactions using oligo-dT primers (CyScribe First-Strand labeling kit - Amersham Biosciences).
15 ug of total RNA from each sample were mixed with 4 uL anchored oligo (dT) C(500µg/mL), in a total volume of 11 uL, subsequently denatured at 70 for 5 min, put on ice for 30 seconds, spun down and placed at room temperature for 10 minutes.
Next, 1 uL of dNTP Mix, 1 µL of aminoallyl-dUTP, 2µL of 0.1 M DTT, 1µL of RNaseOUT (40U/µL), 4µL of 5x CyScript buffer and 1µL of CyScript reverse transcriptase (200U/µL) L with water. Afterwere added. The volume was adjusted to 20  incubation for 3 h at 42ºC, RNA was hydrolyzed by adding 2 µL of 2.5N NaOH for 15 min at 37ºC. Samples were then neutralized with 10 µL of 2 M HEPES Free Acid, and reactions were purified using 96-well Millipore Multiscreen filter plates as follows: 5 volumes of 5.3 M Guanidine-HCl: 150 mM KOAc were added to labeling reactions. The mixture was applied onto the plate and washed 4x with 80% EtOH by centrifugation at 3500 rpm for 5 min. Residual ethanol was spun out by an additional centrifugation at 3,500 rpm for 5 minutes. Labeled targets were eluted in 50 µL 10 mM Tris pH 8.5, by spinning at 3,000 rpm for 5 minutes, dried on a SpeedVac and kept at -20°C, protected from light until use. Then, cDNA was ressuspended in 40 µL of 0.1 M NaHCO3 and reacted with monoreactive NHS-ester Cy5 dye. The reaction was incubated for 2 h at room temperature and purified.

extract_protocol:
Snap-frozen tissue samples were pulverized using a mortar pestle. Next, total RNA was isolated from tissue specimens and Hep2 cell culture using TRIzol reagent (Gibco BRL Life Technologies). Total RNA was precipitated by incubating with 0.5 mL of isopropyl alcohol for 10 C. Themin, followed by centrifugation at 12,000 xg for 10 min at 4 pellet was washed with 75% ethanol, solved in RNAse-free water, passed through an RNeasy spin column (Qiagen) for purification and stored at C until further use.-80
RNA quantity and quality were evaluated using spectrophotometer, 1% agarose gel electrophoresis and also microelectrophoresis on a Bioanalyzer 2100 (Agilent Technologies). RNA from all samples was of appropriately high quality for cDNA microarray analysis.

treatment_protocol: Larynx tissue samples were obtained at the time of surgery and were immediately snap-frozen in liquid nitrogen. Prior to RNA extraction, samples were re-examined, and Giemsa-stained micro-sections obtained from each side of the frozen block were used to delimit the spatial distribution of the tumor mass or non-tumor tissue. Microdissections were performed to ensure that more than 70% of the isolated RNA was derived from cancer cells. In the case of surgical margins, only the epithelial tissue was used. Microdissected tumor samples and non-tumor samples were returned to liquid nitrogen until use.

tag: Patient :T15; Sex:M; Age (years):61; Ethnicity:caucasian; Tobacco:positive; Alcohol:positive; TNM category:T4N0M0; clinical stage:IV; NED or Recurrence (months)


title: Non-neoplastic larynx tissue_sample N6_Replicate 1

source_name: Non-neoplastic larynx tissue_sample N6

tag: Histologically normal adjacent larynx tissue samples. only the epithelial component was used for RNA isolation


title: Larynx tumor_sample T15_Replicate 2


title: Larynx tumor_sample T1_Replicate 1

source_name: Larynx tumor_sample T1

tag: Patient :T1; Sex:M; Age (years):73; Ethnicity:C; Tobacco:P; Alcohol:P; TNM category:T4N2bM0; clinical stage:IV; NED or Recurrence (months)

value: Loc/Rec (9)


title: Non-neoplastic larynx tissue_sample N6_Replicate 2


title: TS011-D3-rep4

value: Diethylnitrosamine (DEN)


title: Larynx tumor_sample T11_Replicate 1

source_name: Larynx tumor_sample T11

tag: Patient :T11; Sex:M; Age (years):44; Ethnicity:caucasian; Tobacco:positive; Alcohol:negative; TNM category:T4N2cM0; clinical stage:IV; NED or Recurrence (months):NED (42)


title: TS011-D3-rep1


title: TS010-D3-rep4

value: L-Ascorbic acid


title: TS010-D3-rep3


title: TS011-D3-rep3


title: Larynx tumor_sample T10_Replicate 1

source_name: Larynx tumor_sample T10

tag: Patient :T10; Sex:M; Age (years):72; Ethnicity:caucasian; Tobacco:positive; Alcohol:positive; TNM category:T4N2cM0; clinical stage:IV; NED or Recurrence (months)

value: locoregional (10)


title: Larynx tumor_sample T10_Replicate 2


title: Larynx tumor_sample T11_Replicate 2


title: Larynx tumor_sample T14_Replicate 2

source_name: Larynx tumor_sample T14

tag: Patient :T14; Sex:M; Age (years):67; Ethnicity:caucasian; Tobacco:positive; Alcohol:positive; TNM category:T4N1M0; clinical stage:IV; NED or Recurrence (months):locoregional (5)


title: Larynx tumor_sample T14_Replicate 1


title: TS010-D3-rep2


title: g5%t10_r5%t0

city: Wageningen

first: Heidy

last: den Besten

address: Bomenweg 2

country: Netherlands

institute: Wageningen University

description: No extra description.

hyb_protocol: The target was denatured by boiling for 1 min and immediate cooling on ice prior to hybridization. A total of 200ng of both samples was mixed and applied with the Agilent hybridization buffer to the microarray, according to Agilent manual. Hybridization was performed at 60 °C. The slide was washed according to the Agilent microarray wash protocol.

scan_protocol: Microarrays were scanned with the Agilent DNA Microarray Scanner, Model G2565BA, according to the Agilent protocol at 50% laser intensity, and 10 micron scan resolution.

data_processing: Lowess-normalization, performed in Feature Extract software, Agilent.

organism: Bacillus cereus ATCC 14579

label_protocol: cDNA was labelled as described by van Schaik et al. 2007.

extract_protocol: RNA was extracted as described by van Schaik et al. 2007, with some minor modifications.

tag: ATCC 14579 exposed to 5% NaCl for 10 min

tag: ATCC 14579 exposed to 5% NaCl for 0 min


title: Larynx tumor_sample T9_Replicate 2

source_name: Larynx tumor_sample T9

tag: Patient :T9; Sex:M; Age (years):72; Ethnicity:negroid; Tobacco:positive; Alcohol:positive; TNM category:T3N0M0; clinical stage:III; NED or Recurrence (months)


title: g5%t60_r5%t0

description: No extra description.

tag: ATCC 14579 exposed to 5% NaCl for 60 min


title: TS011-D3-rep2

tag: gender

tag: age

tag: strain


title: TS009-D3-rep3

tag: tissue

tag: compound

tag: dose

value: D-Mannitol


title: TS010-D3-rep1

tag: administration

tag: treatment

tag: vehicle


title: TS009-D3-rep2


title: TS009-D3-rep4


title: g5%t0_r5%t30

description: No extra description.

tag: ATCC 14579 exposed to 5% NaCl for 30 min


title: g5%t0_r5%t10

description: No extra description.


title: Larynx tumor_sample T9_Replicate 1


title: g5%t30_r5%t0

description: No extra description.


title: Non-neoplastic larynx tissue_sample N13_Replicate 2

source_name: Non-neoplastic larynx tissue_sample N13

tag: Histologically normal adjacent larynx tissue samples. only the epithelial component was used for RNA isolation


title: g5%t0_r5%t60

description: No extra description.


title: g2.5%t30_r2.5%t0

description: No extra description.

tag: ATCC 14579 exposed to 2.5% NaCl for 30 min

tag: ATCC 14579 exposed to 2.5% NaCl for 0 min


title: g2.5%t60_r2.5%t0

description: No extra description.

tag: ATCC 14579 exposed to 2.5% NaCl for 60 min


title: TS009-D3-rep1


title: g2.5%t0_r2.5%t30

description: No extra description.


title: Non-neoplastic larynx tissue_sample N13_Replicate 1


title: Non-neoplastic larynx tissue_sample N25_Replicate 2

source_name: Non-neoplastic larynx tissue_sample N25


title: TS008-D3-rep3

value: Phenobarbital


title: Non-neoplastic larynx tissue_sample N25_Replicate 1


title: TS008-D3-rep2

value: Male


title: TS008-D3-rep1


title: Non-neoplastic larynx tissue_sample N24_Replicate 1

source_name: Non-neoplastic larynx tissue_sample N24


title: g2.5%t10_r2.5%t0

description: No extra description.

tag: ATCC 14579 exposed to 2.5% NaCl for 10 min


title: Non-neoplastic larynx tissue_sample N10_Replicate 2

source_name: Non-neoplastic larynx tissue_sample N10


title: TS007-D3-rep4

source_name: Total RNA from rat liver


title: Non-neoplastic larynx tissue_sample N23_Replicate 2

source_name: Non-neoplastic larynx tissue_sample N23


title: TS007-D3-rep3


title: Non-neoplastic larynx tissue_sample N23_Replicate 1


title: Non-neoplastic larynx tissue_sample N10_Replicate 1


title: TS006-D3-rep4

value: Quinoline


title: TS007-D3-rep1

value: Liver


title: TS007-D3-rep2


title: g2.5%t0_r2.5%t60

description: No extra description.


title: Non-neoplastic larynx tissue_sample N22_Replicate 2

source_name: Non-neoplastic larynx tissue_sample N22


title: TS006-D3-rep3


title: g2.5%t0_r2.5%t10

description: No extra description.


title: Non-neoplastic larynx tissue_sample N24_Replicate 2


title: TS006-D3-rep2


title: Infected_hypocotyls_48h_rep3

city: London

first: Mark

last: Gijzen

state: Ontario

address: 1391 Sandford Street

country: Canada

institute: Agriculture and Agri-Food Canada

description: P. sojae was grown on V8 agar medium. Soybean seeds were sown in vermiculite and grown for 8d in darkness. Seedlings were placed in trays and each hypocotyl inoculated with a P. sojae mycelia plug, 5mm diameter, excised from V8 agar plates. Infected plant tissues were harvested at specified time point. Total RNA was extracted with Qiagen kit.

hyb_protocol: A cocktail containing 10 μg of labeled cRNA was hybridized to the Soybean GeneChips for 16 hours at 45°C as described in the Affymetrix Technical Analysis Manual (Affymetrix, Santa Clara, CA).  GeneChips were stained with Streptavidin-Phycoerythrin, followed by an anti-streptavidin antibody solution and a second Streptavidin-Phycoerythrin solution, with all liquid handling performed by a GeneChip Fluidics Station 450.

scan_protocol: GeneChips were scanned with the Affymetrix GeneChip Scanner 3000 (Affymetrix, Santa Clara, CA).

data_processing: Probe level signal intensities (.cel files) were generated using GCOS1.4 (Affymetrix Inc., Santa Clara, CA).  Gene level data (.chp files) were generated using MAS5 default values for the Statistical Expression algorithm parameters and a Target Signal of 150 for all probe sets and a Normalization Value of 1.

label: biotin

organism:
Glycine max
Phytophthora sojae

source_name: soybean hypocotyls infected with P. sojae, 48h

label_protocol: Biotinylated complimentary RNA (cRNA) was prepared from 10 μg of total RNA as per the Ambion MessageAmp II protocol (Ambion, Austin, TX).  Double-stranded cDNA was synthesized using ArrayScript and oligo(dT) primers with a T7 promoter.  Biotin-labeled cRNA was prepared by cDNA in vitro transcription using MEGAscript.  External spike-in controls (Affymetrix, Santa Clara, CA) were used.

tag: specimen

value: soybean

tag: cultivar

value: Harosoy (soybean)

value: soybean hypocotyl

tag: infection

value: P. sojae

value: P6497, race 2 (P. sojae)

tag: time


title: Infected_hypocotyls_48h_rep4

growth_protocol: P. sojae was grown on V8 agar medium. Soybean seeds were sown in vermiculite and grown for 8d in darkness.

extract_protocol: Total RNA was extracted with Qiagen kit.

tag: strain


title: Infected_hypocotyls_48h_rep1

tag: tissue


title: Infected_hypocotyls_48h_rep5


title: TS006-D3-rep1

tag: gender

tag: age

tag: compound

value: Vehicle

value: gavage

value: 3 days


title: Infected_hypocotyls_48h_rep2


title: Non-neoplastic larynx tissue_sample N21_Replicate 2

source_name: Non-neoplastic larynx tissue_sample N21


title: Infected_hypocotyls_24h_rep1

source_name: soybean hypocotyls infected with P. sojae, 24h


title: Infected_hypocotyls_24h_rep3


title: Non-neoplastic larynx tissue_sample N22_Replicate 1


title: Non-neoplastic larynx tissue_sample N21_Replicate 1


title: TS005-D3-rep4

tag: dose

tag: administration

tag: treatment

value: Saline


title: Infected_hypocotyls_24h_rep2


title: TS005-D3-rep2

tag: vehicle


title: Non-neoplastic larynx tissue_sample N4_Replicate 1

source_name: Non-neoplastic larynx tissue_sample N4

tag: Histologically normal adjacent larynx tissue samples. only the epithelial component was used for RNA isolation


title: Non-neoplastic larynx tissue_sample N20_Replicate 2

source_name: Non-neoplastic larynx tissue_sample N20


title: TS005-D3-rep3


title: Non-neoplastic larynx tissue_sample N4_Replicate 2


title: TS005-D3-rep1


title: TS004-D3-rep4


title: TS004-D3-rep3


title: Larynx tumor_sample T5_Replicate 2

source_name: Larynx tumor_sample T5

tag: Patient :T5; Sex:M; Age (years):44; Ethnicity:caucasian; Tobacco:positive; Alcohol:positive; TNM category:T4N2bM0; clinical stage:IV; NED or Recurrence (months)


title: Non-neoplastic larynx tissue_sample N20_Replicate 1


title: Infected_hypocotyls_12h_rep1

source_name: soybean hypocotyls infected with P. sojae, 12h


title: Infected_hypocotyls_6h_rep3

source_name: soybean hypocotyls infected with P. sojae, 6h


title: Infected_hypocotyls_12h_rep2


title: Larynx tumor_sample T5_Replicate 1


title: Infected_hypocotyls_6h_rep2


title: Infected_hypocotyls_12h_rep3


title: Larynx tumor_sample T2_Replicate 2

source_name: Larynx tumor_sample T2

tag: Patient :T2; Sex:M; Age (years):66; Ethnicity:caucasian; Tobacco:positive; Alcohol:positive; TNM category:T4N0M0; clinical stage:IV; NED or Recurrence (months):locoregional (10)


title: TS004-D3-rep2


title: Larynx tumor_sample T2_Replicate 1


title: Larynx tumor_sample T6_Replicate 2

source_name: Larynx tumor_sample T6

tag: Patient :T6; Sex:M; Age (years):48; Ethnicity:negroid; Tobacco:positive; Alcohol:positive; TNM category:T4N2cM0; clinical stage:IV; NED or Recurrence (months):locoregional (14)


title: Larynx tumor_sample T1_Replicate 2

source_name: Larynx tumor_sample T1

tag: Patient :T1; Sex:M; Age (years):73; Ethnicity:C; Tobacco:P; Alcohol:P; TNM category:T4N2bM0; clinical stage:IV; NED or Recurrence (months)

value: Loc/Rec (9)


title: TS003-D3-rep4

value: Corn oil

value: Carbon tetrachloride


title: TS003-D3-rep2


title: Infected_hypocotyls_6h_rep1

tag: specimen

tag: cultivar


title: TS003-D3-rep1


title: Larynx tumor_sample T6_Replicate 1


title: Larynx tumor_sample T4_Replicate 2

source_name: Larynx tumor_sample T4

tag: Patient :T4; Sex:F; Age (years):58; Ethnicity:caucasian; Tobacco:positive; Alcohol:positive; TNM category:T4N0M0; clinical stage:IV; NED or Recurrence (months):locoregional (7)


title: TS004-D3-rep1

tag: strain


title: TS003-D3-rep3

tag: tissue


title: Mycelia_V8media_rep3

description: P. sojae was grown on vegetable juice (V8) agar medium containing 2.65g calcium carbonate and 260mL of V8 juice per liter. Solid media was overlaid with sterile cellophane disks prior to culture of P. sojae, for ease of removal of mycelia at sampling. Total RNA was extracted with Trizol reagent.

organism: Phytophthora sojae

source_name: mycelia, grown on vegetable juice V8 media

growth_protocol: vegetable juice V8 media

value: mycelia

tag: growth protocol

value: vegetable juice V8 media


title: TS002-D3-rep4

tag: gender

value: Male

tag: age


title: Larynx tumor_sample T4_Replicate 1


title: Mycelia_V8media_rep2

extract_protocol: Total RNA was extracted with Trizol reagent.


title: Mycelia_H&Smedia_rep1

description: P. sojae was grown on synthetic agar medium formulated by Hoitink and Schmitthenner (1969) containing 2.4g sucrose, 0.27g asparagine, 10mg cholesterol, 10mg ascorbate, and 2mg thiamine, per liter, plus salts and minerals. Solid media was overlaid with sterile cellophane disks prior to culture of P. sojae, for ease of removal of mycelia at sampling. Total RNA was extracted with Trizol reagent.

source_name: mycelia, grown on synthetic H&S media

growth_protocol: synthetic H&S media

value: synthetic H&S media


title: Larynx tumor_sample T8_Replicate 2

source_name: Larynx tumor_sample T8

tag: Patient :T8; Sex:M; Age (years):58; Ethnicity:caucasian; Tobacco:positive; Alcohol:positive; TNM category:T4N0M0; clinical stage:IV; NED or Recurrence (months):NED (30)


title: Mycelia_H&Smedia_rep3


title: TS002-D3-rep1

source_name: Total RNA from rat liver

value: Liver

tag: compound

tag: dose

tag: administration


title: TS002-D3-rep3

tag: treatment

tag: vehicle


title: Germinating_zoospores_6h_rep3

description: P. sojae was grown on V8 agar medium for 5d and sporangia development induced by repeated flooding with water. Zoospores were encysted by agitation then collected at the specified time point by centrifugation. Total RNA was extracted using Trizol reagent.

source_name: zoospores, germinating, 6h after encystment

value: zoospore

tag: protocol

value: encystment and germination

tag: time


title: TS001-D3-rep4

value: Clofibrate


title: Mycelia_H&Smedia_rep2


title: Larynx tumor_sample T3_Replicate 2

source_name: Larynx tumor_sample T3

tag: Patient :T1; Sex:M; Age (years):73; Ethnicity:caucasian; Tobacco:positive; Alcohol:positive; TNM category:T4N2bM0; clinical stage:IV; NED or Recurrence (months)

value: locoregional (9)


title: Larynx tumor_sample T7_Replicate 2

source_name: Larynx tumor_sample T7

tag: Patient :T7; Sex:M; Age (years):53; Ethnicity:caucasian; Tobacco:positive; Alcohol:positive; TNM category:T2N2M0; clinical stage:III; NED or Recurrence (months):locoregional (5)


title: Larynx tumor_sample T8_Replicate 1


title: Larynx tumor_sample T7_Replicate 1


title: TS002-D3-rep2


title: Mycelia_V8media_rep1

tag: specimen


title: TS001-D3-rep3


title: Germinating_zoospores_2h_rep3

source_name: zoospores, germinating, 2h after encystment

growth_protocol: P. sojae was grown on V8 agar medium for 5d


title: TS001-D3-rep1


title: TS001-D3-rep2


title: Larynx tumor_sample T3_Replicate 1

label_protocol:
Labeled targets for hybridizations were generated from total mRNA in reverse transcription reactions using oligo-dT primers (CyScribe First-Strand labeling kit - Amersham Biosciences).
15 ug of total RNA from each sample were mixed with 4 uL anchored oligo (dT) (500µg/mL), in a total volume of 11 uL, subsequently denatured at 70C for 5 min, put on ice for 30 seconds, spun down and placed at room temperature for 10 minutes.
Next, 1 uL of dNTP Mix, 1 µL of aminoallyl-dUTP, 2µL of 0.1 M DTT, 1µL of RNaseOUT (40U/µL), 4µL of 5x CyScript buffer and 1µL of CyScript reverse transcriptase (200U/µL) were added. The volume was adjusted to 20 L with water. After incubation for 3 h at 42ºC, RNA was hydrolyzed by adding 2 µL of 2.5N NaOH for 15 min at 37ºC. Samples were then neutralized with 10 µL of 2 M HEPES Free Acid, and reactions were purified using 96-well Millipore Multiscreen filter plates as follows: 5 volumes of 5.3 M Guanidine-HCl: 150 mM KOAc were added to labeling reactions. The mixture was applied onto the plate and washed 4x with 80% EtOH by centrifugation at 3500 rpm for 5 min. Residual ethanol was spun out by an additional centrifugation at 3,500 rpm for 5 minutes. Labeled targets were eluted in 50 µL 10 mM Tris pH 8.5, by spinning at 3,000 rpm for 5 minutes, dried on a SpeedVac and kept at -20°C, protected from light until use. Then, cDNA was ressuspended in 40 µL of 0.1 M NaHCO3 and reacted with monoreactive NHS-ester Cy5 dye. The reaction was incubated for 2 h at room temperature and purified.

extract_protocol:
Snap-frozen tissue samples were pulverized using a mortar pestle. Next, total RNA was isolated from tissue specimens and Hep2 cell culture using TRIzol reagent (Gibco BRL Life Technologies). Total RNA was precipitated by incubating with 0.5 mL of isopropyl alcohol for 10 min, followed by centrifugation at 12,000 xg for 10 min at 4C. The pellet was washed with 75% ethanol, solved in RNAse-free water, passed through an RNeasy spin column (Qiagen) for purification and stored at -80C until further use.
RNA quantity and quality were evaluated using spectrophotometer, 1% agarose gel electrophoresis and also microelectrophoresis on a Bioanalyzer 2100 (Agilent Technologies). RNA from all samples was of appropriately high quality for cDNA microarray analysis.

value: Locoregional (9)


title: Germinating_zoospores_6h_rep1


title: Germinating_zoospores_2h_rep1


title: Germinating_zoospores_6h_rep2


title: Germinating_zoospores_2h_rep2


title: Germinating_zoospores_0h_rep2

source_name: zoospores, germinating, 0h after encystment


title: Germinating_zoospores_0h_rep1


title: TS087-D28-rep4

status: Public on Jun 21 2009

city: Kitakatsushika-gun

first: Hiroshi

last: Matsumoto

state: Saitama

address: 1600 Shimotakano, Sugito-machi

institute: Chemicals Evaluation and Research Institute, Japan

description:
Biological replicate 4 of 4. Control samples were pooled.
Please see the supplementary file 'GSE16394_73_Compounds_for_training.pdf' for the list of 47 carcinogen and 26 non-carcinogens. Please see the supplementary file 'GSE16394_15_Compounds_for_test.pdf' for the list of other test compounds.

treatment_protocol: Each group was composed of 4 rats. At each time point for each compound, there was a group that received the test compound and a control group. Compounds were administered once daily by oral gavage at a dose of 5 ml/kg for up to 1, 3, 7, 14, or 28 days. Control animals received corresponding volumes of vehicle.

value: Vehicle

value: 28 days

value: o-Nitrotoluene


title: TS088-D28-rep1

description:
Biological replicate 1 of 4. Control samples were pooled.
Please see the supplementary file 'GSE16394_73_Compounds_for_training.pdf' for the list of 47 carcinogen and 26 non-carcinogens. Please see the supplementary file 'GSE16394_15_Compounds_for_test.pdf' for the list of other test compounds.

value: gavage


title: TS088-D28-rep4


title: TS088-D28-rep2

description:
Biological replicate 2 of 4. Control samples were pooled.
Please see the supplementary file 'GSE16394_73_Compounds_for_training.pdf' for the list of 47 carcinogen and 26 non-carcinogens. Please see the supplementary file 'GSE16394_15_Compounds_for_test.pdf' for the list of other test compounds.


title: TS088-D28-rep3

description:
Biological replicate 3 of 4. Control samples were pooled.
Please see the supplementary file 'GSE16394_73_Compounds_for_training.pdf' for the list of 47 carcinogen and 26 non-carcinogens. Please see the supplementary file 'GSE16394_15_Compounds_for_test.pdf' for the list of other test compounds.


title: TS086-D28-rep3

value: Methyleugenol


title: TS087-D28-rep3

value: Corn oil


title: TS086-D28-rep4


title: TS087-D28-rep1


title: TS087-D28-rep2


title: TS085-D28-rep3

value: Indomethacin


title: TS085-D28-rep2


title: TS085-D28-rep4


title: TS084-D28-rep4

value: Water

value: Sodium benzoate


title: TS085-D28-rep1

value: Male


title: TS086-D28-rep1


title: TS086-D28-rep2


title: TS084-D28-rep3


title: TS083-D28-rep4


title: TS083-D28-rep3


title: TS083-D28-rep1


title: TS084-D28-rep1


title: TS084-D28-rep2


title: TS082-D28-rep3

value: 4-Nitroanthranilic acid


title: TS082-D28-rep4

value: Liver


title: TS083-D28-rep2


title: TS081-D28-rep4

value: Glutaraldehyde


title: TS081-D28-rep3


title: TS080-D28-rep1


title: TS082-D28-rep2


title: TS080-D28-rep3


title: TS080-D28-rep2


title: TS079-D28-rep4

value: 1-Chloro-2-propanol (technical)


title: TS078-D28-rep3

value: Chlorendic acid


title: TS080-D28-rep4


title: TS079-D28-rep3


title: TS081-D28-rep1


title: TS081-D28-rep2


title: TS079-D28-rep2


title: TS078-D28-rep4


title: TS078-D28-rep2


title: TS078-D28-rep1


title: TS082-D28-rep1


title: TS077-D28-rep3

value: 4-Dimethylaminoazobenzene (DAB)


title: TS077-D28-rep2


title: TS079-D28-rep1


title: TS077-D28-rep1


title: TS076-D28-rep1


title: TS075-D28-rep3

value: 4-Aminoazobenzene (AAB)


title: TS076-D28-rep2

value: Vehicle


title: TS076-D28-rep3

value: 28 days


title: TS074-D28-rep4

value: Caprolactam


title: TS074-D28-rep3

value: gavage


title: TS075-D28-rep2


title: TS075-D28-rep1


title: TS076-D28-rep4


title: TS073-D28-rep3

value: Phthalamide


title: TS072-D28-rep4

value: Corn oil


title: TS071-D28-rep4

value: Aspirin


title: TS075-D28-rep4


title: TS073-D28-rep2


title: TS077-D28-rep4


title: TS074-D28-rep2

value: Water


title: TS072-D28-rep1


title: TS074-D28-rep1


title: TS072-D28-rep3


title: TS073-D28-rep4


title: TS072-D28-rep2


title: TS071-D28-rep2


title: TS071-D28-rep1


title: TS070-D28-rep2

value: D,L-Ethionine


title: TS073-D28-rep1

value: Male


title: TS071-D28-rep3


title: TS070-D28-rep4


title: TS069-D28-rep4

value: Phenytoin (5,5-Diphenylhydantoin)


title: TS069-D28-rep3

value: Liver


title: TS070-D28-rep1


title: TS069-D28-rep2


title: TS068-D28-rep2

value: Diethylstilbestrol (DES)


title: TS069-D28-rep1


title: TS068-D28-rep4


title: TS068-D28-rep3


title: TS070-D28-rep3


title: TS068-D28-rep1


title: TS067-D28-rep4

value: Acetamide


title: TS067-D28-rep1


title: TS067-D28-rep3


title: TS066-D28-rep4

value: Tetrachloroethylene


title: TS066-D28-rep3


title: TS066-D28-rep1


title: TS066-D28-rep2


title: TS065-D28-rep3

value: MNNG


title: TS065-D28-rep2


title: TS065-D28-rep1


title: TS067-D28-rep2


title: TS065-D28-rep4


title: TS064-D28-rep2


title: TS064-D28-rep3


title: TS064-D28-rep1


title: TS063-D28-rep1

value: Benzo [a]pyrene (BP)


title: TS061-D28-rep4

value: Vehicle

value: 4-Acetylaminofluorene (4-AAF)


title: TS062-D28-rep1

value: 28 days

value: α-Tocopherol (Vitamin E)


title: TS062-D28-rep3

value: gavage


title: TS061-D28-rep1

value: Corn oil


title: TS064-D28-rep4


title: TS063-D28-rep4


title: TS063-D28-rep2


title: TS063-D28-rep3


title: TS061-D28-rep3


title: TS060-D28-rep4

value: 2,5-Toluenediamine SO4


title: TS061-D28-rep2


title: TS062-D28-rep2


title: TS060-D28-rep2

value: Water


title: TS060-D28-rep3


title: TS062-D28-rep4


title: TS059-D28-rep4

value: p-Phenylenediamine 2HCl


title: TS059-D28-rep2

value: Male


title: TS060-D28-rep1


title: TS059-D28-rep3


title: TS059-D28-rep1


title: TS058-D28-rep4

value: 2-Chloro-p-phenylenediamine SO4


title: TS058-D28-rep3

value: Liver


title: TS057-D28-rep3

value: Lindane


title: TS058-D28-rep1


title: TS058-D28-rep2


title: TS057-D28-rep2


title: TS056-D28-rep4

value: Chloroform


title: TS055-D28-rep3

value: Pentachloroethane


title: TS057-D28-rep1


title: TS054-D28-rep2

value: Urethane


title: TS054-D28-rep3


title: TS054-D28-rep1


title: TS054-D28-rep4


title: TS055-D28-rep2


title: TS055-D28-rep1


title: TS057-D28-rep4


title: TS056-D28-rep3


title: TS056-D28-rep1


title: TS053-D28-rep4

value: Methapyrilene HCl


title: TS056-D28-rep2

value: Vehicle


title: TS053-D28-rep3


title: TS052-D28-rep3

value: Tannic acid


title: TS053-D28-rep1

value: 28 days


title: TS052-D28-rep4


title: TS053-D28-rep2


title: TS051-D28-rep4

value: Trichloroacetic acid


title: TS052-D28-rep2

value: gavage


title: TS051-D28-rep3


title: TS051-D28-rep2


title: TS050-D28-rep1

value: Water (PH4)

value: N-Ethyl-N-nitrosourea (ENU)


title: TS050-D28-rep3


title: TS050-D28-rep2


title: TS052-D28-rep1

value: Water


title: TS051-D28-rep1


title: TS050-D28-rep4


title: TS049-D28-rep1

value: Corn oil


title: TS049-D28-rep4

value: Male


title: TS049-D28-rep2


title: TS049-D28-rep3


title: TS048-D28-rep1

value: 3-Methylcholanthrene (MC)


title: TS048-D28-rep3

value: Liver


title: TS048-D28-rep2


title: TS048-D28-rep4


title: TS047-D28-rep4

value: 7,12-Dimethylbenz [a]anthracene (DMBA)


title: TS047-D28-rep3


title: TS047-D28-rep2


title: TS046-D28-rep2

value: Benz [a]anthracene (BA)


title: TS045-D28-rep4

value: PhIP


title: TS045-D28-rep3


title: TS046-D28-rep1


title: TS047-D28-rep1


title: TS046-D28-rep4


title: TS045-D28-rep1


title: TS045-D28-rep2


title: TS046-D28-rep3


title: TS041-D28-rep4

value: N-Nitrosodimethylamine (DMN)


title: TS044-D28-rep3

value: MeIQx


title: TS044-D28-rep4

value: Vehicle


title: TS044-D28-rep1


title: TS042-D28-rep1

value: N-Nitrosopiperidine


title: TS044-D28-rep2

value: 28 days


title: TS043-D28-rep3

value: 2-Acetylaminofluorene (2-AAF)


title: TS043-D28-rep4

value: gavage


title: TS042-D28-rep2


title: TS042-D28-rep3


title: TS042-D28-rep4


title: TS043-D28-rep2


title: TS040-D28-rep2

value: Gum arabic

value: Lithocholic acid


title: TS043-D28-rep1


title: TS040-D28-rep4


title: TS041-D28-rep1

value: Water


title: TS041-D28-rep2


title: TS041-D28-rep3


title: TS039-D28-rep3

value: Corn oil

value: Iodoform


title: TS040-D28-rep3

value: Male


title: TS038-D28-rep2

value: Liver

value: Benzoin


title: TS039-D28-rep4


title: TS038-D28-rep3


title: TS037-D28-rep4

value: Quercetin


title: TS039-D28-rep2


title: TS038-D28-rep1


title: TS038-D28-rep4


title: TS039-D28-rep1


title: TS036-D28-rep1


title: TS036-D28-rep2


title: TS037-D28-rep3


title: TS036-D28-rep3


title: TS036-D28-rep4


title: TS037-D28-rep2


title: TS035-D28-rep3

value: 1% CMC


title: TS035-D28-rep4


title: TS035-D28-rep1


title: TS034-D28-rep2

value: D,L-Menthol


title: TS034-D28-rep1


title: TS034-D28-rep4


title: TS034-D28-rep3


title: TS033-D28-rep4

value: 2-Chloromethylpyridine HCl


title: TS037-D28-rep1

value: Vehicle


title: TS035-D28-rep2


title: TS033-D28-rep3


title: TS033-D28-rep2


title: TS032-D28-rep2


title: TS032-D28-rep4


title: TS032-D28-rep3


title: TS032-D28-rep1


title: TS030-D28-rep4

value: Thioacetamide


title: TS030-D28-rep2

value: 28 days


title: TS030-D28-rep3


title: TS030-D28-rep1


title: TS029-D28-rep2

value: Methyl carbamate


title: TS031-D28-rep1

value: gavage

value: MC

value: Acetaminophen（Paracetamol）


title: TS031-D28-rep2


title: TS029-D28-rep3

value: Water


title: TS033-D28-rep1


title: TS031-D28-rep3


title: TS029-D28-rep1


title: TS029-D28-rep4


title: TS028-D28-rep4

value: Corn oil

value: Furan


title: TS027-D28-rep4

value: Male


title: TS028-D28-rep3

value: Liver


title: TS028-D28-rep1


title: TS028-D28-rep2


title: TS027-D28-rep3


title: TS031-D28-rep4


title: TS025-D28-rep1

value: Safrole


title: TS025-D28-rep2


title: TS027-D28-rep1


title: TS025-D28-rep3


title: TS025-D28-rep4


title: TS022-D28-rep2

value: Trichloroethylene


title: TS026-D28-rep1

value: 1,4-Dichlorobenzene (DCB)


title: TS026-D28-rep2


title: TS026-D28-rep3


title: TS024-D28-rep2

value: D-Limonene


title: TS024-D28-rep3


title: TS024-D28-rep1


title: TS022-D28-rep4


title: TS023-D28-rep1

value: Butylated hydroxyanisole (BHA)


title: TS022-D28-rep1

value: Vehicle


title: TS022-D28-rep3


title: TS021-D28-rep4

value: α-Hexachlorocyclohexane(α-HCH)


title: TS027-D28-rep2

value: 28 days


title: TS023-D28-rep4


title: TS021-D28-rep3


title: TS021-D28-rep2


title: TS023-D28-rep3


title: TS024-D28-rep4


title: TS026-D28-rep4


title: TS018-D28-rep4

value: Di(2-ethylhexyl)adipate (DEHA)


title: TS021-D28-rep1

value: gavage


title: TS019-D28-rep4

value: Ethinylestradiol


title: TS019-D28-rep3


title: TS019-D28-rep2


title: TS018-D28-rep3


title: TS020-D28-rep1

value: Hexachlorobenzene (HCB)


title: TS017-D28-rep3

value: Dieldrin


title: TS017-D28-rep2

value: Corn oil


title: TS019-D28-rep1


title: TS016-D28-rep3

value: Dichlorodiphenyltrichloroethane (DDT)


title: TS016-D28-rep4

value: Male


title: TS016-D28-rep2

value: Liver


title: TS016-D28-rep1


title: TS020-D28-rep4


title: TS015-D28-rep4

value: Aldrin


title: TS020-D28-rep3


title: TS020-D28-rep2


title: TS015-D28-rep2


title: TS018-D28-rep2


title: TS014-D28-rep3

value: Water

value: N-Nitrosomorpholine


title: TS014-D28-rep4


title: TS014-D28-rep1


title: TS014-D28-rep2


title: TS018-D28-rep1


title: TS013-D28-rep2


title: TS013-D28-rep4


title: TS012-D28-rep2

value: 1% CMC


title: TS012-D28-rep4


title: TS012-D28-rep3


title: TS017-D28-rep4


title: TS012-D28-rep1


title: TS017-D28-rep1


title: TS023-D28-rep2

value: Butylated hydroxyanisole (BHA)


title: TS015-D28-rep1

value: Vehicle


title: TS015-D28-rep3


title: TS011-D28-rep2

value: Diethylnitrosamine (DEN)


title: TS013-D28-rep1

value: 28 days


title: TS013-D28-rep3


title: TS007-D28-rep4


title: TS011-D28-rep4


title: TS007-D28-rep1


title: TS008-D28-rep3

value: Phenobarbital


title: TS011-D28-rep3

value: gavage


title: TS006-D28-rep3

value: Quinoline


title: TS006-D28-rep2


title: TS010-D28-rep4

value: L-Ascorbic acid


title: TS006-D28-rep1


title: TS010-D28-rep1


title: TS010-D28-rep3


title: TS010-D28-rep2


title: TS008-D28-rep4


title: TS009-D28-rep4

value: D-Mannitol


title: TS008-D28-rep2


title: TS008-D28-rep1


title: TS006-D28-rep4

value: Corn oil


title: TS005-D28-rep3

value: Saline


title: TS005-D28-rep2

value: Male


title: TS007-D28-rep2

value: Liver


title: TS007-D28-rep3


title: TS011-D28-rep1


title: TS005-D28-rep1


title: TS009-D28-rep1


title: TS009-D28-rep3


title: TS004-D28-rep3


title: TS003-D28-rep3

value: Carbon tetrachloride


title: TS002-D28-rep3


title: TS004-D28-rep2


title: TS002-D28-rep4


title: TS004-D28-rep1


title: TS004-D28-rep4


title: TS002-D28-rep2


title: TS005-D28-rep4


title: TS001-D28-rep4

value: Clofibrate


title: TS002-D28-rep1


title: TS003-D28-rep2


title: TS003-D28-rep1


title: TS001-D28-rep1


title: TS001-D28-rep2


title: Ltr051-Cy5 / L929-Cy3 (2)

city: Tsukuba

first: Taro

last: Takemura

state: Ibaraki

address: 1-2-1 Sengen

department: Nanotechnology Innovation Station

institute: National Institute for Materials Science

description: This is one of three microarrays comparing Ltr051 with L929.

hyb_protocol: 825 ng of Cy5 labeled sample is mixed with 825 ng of Cy3 labeled sample. The mix is hybridized to microarrays in Agilent Hyb Chambers at 65 oC for 17 hours.

scan_protocol: Each microarray slide was scaned individually using GenePix 4000B scanner and GenPix Pro software was used for image qantitation.

data_processing: The data was normalized using LOWESS method.

molecule: polyA RNA

organism: Mus musculus

label_protocol: 5 ug of the aRNA was labelled using Cy5 fluorescent dyes.

extract_protocol:
Total RNA was extracted with RNeasy Mini Kit (Qiagen).
Amino-allyl RNA was synthesized from 1 ug of total RNA sample using Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion).

tag: cell line

tag: ev71 infection

value: sensitive

label_protocol: 5 ug of the aRNA was labelled using Cy3 fluorescent dyes.

value: insensitive


title: Ltr051-Cy5 / L929-Cy3


title: TS003-D28-rep4

tag: strain

tag: tissue


title: gacA mutant vs. wild-type (Biological replicate 2)

status: Public on Jun 20 2009

city: Irapuato

first: Jose Luis

last: Hernandez-Flores

state: Guanajuato

address: Km 9.6 Libramiento Norte Carretera Irapuato-León

department: Ingeniería Genética

country: Mexico

institute: Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional

description:
The GacS/GacA two component signal transduction system controls important pathogenicity and virulence mechanisms in several Gram-negative bacteria. In the present study we hybridized a genomic microarray of P. syringae pv. phaseolicola NPS3121 to compare transcriptional profiles from wild type strain and a gacA- null mutant obtained in our laboratory with a Tox- phenotype when grown at 18°C in minimal medium.

Overall design Transcriptional profiles of a P. syringae pv. phaseolicola NPS3121 null gacA mutant were compared to those of the wild-type strain. Cultures were grown in minimal medium at 18°C (which is the temperature at which phaseolotoxin is produced and the bacteria achieves full virulence) and harvested during the late log phase of the exponential growth. RNA from three biological replicates and each with two technical replicates were hybridize to control variation that might affect data interpretation.

hyb_protocol: Labelled probes were dried and resuspended in 40 µl of hybridization solution (25% hybridization buffer supplied in the CyScribe kit, 25% nuclease-free water and 50% formamide). The probe was immediately applied onto the array and covered with a cover slip (Hybri-slips, Sigma-Aldrich Co.), and hybridized 16 hours at 45°C in a humid hybridization chamber (Corning Incorporated). After hybridization, the slides were washed once in solutions 1–4 (wash solution 1: 2% SSC, 0.1% SDS at 45 ºC; wash solution 2: 0.1% SSC, 0.1% SDS; wash solution 3: 0.1% SSC; wash solution 4: 0.01% SSC) for 5 min with gentle stirring/agitation. Washed slides were dried by centrifugation for 1 min at 1600 r.p.m.

scan_protocol: Slides were scanned with an Axon GenePix® 4000 B scanner at a resolution of 10 µm adjusting the laser and gain parameters to obtain similar levels of fluorescence intensity in both channels.

data_processing: Spot intensities were quantified using Axon GenePix Pro 6.0 image analysis software. The mean of the signals and the median of backgrounds were used for further analysis. Raw data was imported into the R 2.2.1 software (http://www.R-project.org). Background correction was done using the method Robust Multichip Analysis "RMA" (Irizarry et al., 2003) whereas normalization of the signal intensities within slides was carried out using the "printtiploess" method (Yang et al., 2002) using the LIMMA package (Smyth and Speed, 2003) (www.bioconductor.org). Normalized data were log2 transformed and then fitted into mixed model ANOVAs (Benjamini and Hochberg, 1995; Wolfinger et al., 2001; Gibson, 2004) using the Mixed procedure. The p-values of the gacA effects were adjusted by the False Discovery Rate method “FDR” (Benjamini and Hochberg, 1995). Estimates of the expression differences were calculated using the mixed model. Based on these statistical analyses, the spots with tests with an FDR value less or equal to 5% and with changes in signal intensity between gacA and wild type strain of 1.5 fold or higher difference were considered as differentially expressed.

organism: Pseudomonas savastanoi pv. phaseolicola

source_name: P. syringae pv. phaseolicola NPS3121 gacA mutant

label_protocol: Purified total RNA (30 ug) was mixed with 3 uL of random nonamer primers and was incubated at 70ºC for 5 min. Reactions were held at room temperature for 10 min to allow the primers and the RNA template to anneal. To each reaction, the following were added: 1 uL of Cy5/Cy3-dCTP (1 mM) (Amersham Biosciences, Piscataway, NJ, U.S.A.), 2 uL of 0.1 M dithiothreitol, 4 uL of 5X Cyscript buffer, 1 uL of dNTP mixture (15 mM dATP, dTTP, and dGTP; 5 mM dCTP), 1uL of Cy3/Cy5 labeled dUTP and 200 U of CyScript reverse transcriptase. Reactions were incubated at 42ºC for 2 h. CyDye labelled single strand cDNA using the CyScribe GFX Purification Kit (Amersham Biosciences, Piscataway, NJ, U.S.A.) and according to the protocol recommended by the supplier. The purified labeled cDNA was then quantified to have with a Nanodrop equipment to final amount of 150 pg of each labeled cDNA.

growth_protocol: Overnight culture of gacA- mutant strain P. syringae pv. phaseolicola NPS3121 was used to inoculate KB medium, and it was allowed to grow at 18 °C to the mid exponential growth phase (A600 = 0.6).

treatment_protocol: For microarray experiments, wild type strain and gacA- mutant strain of P. syringae pv. phaseolicola were grown in 5 mL of  KB medium with selection antibiotics. Cells were washed with deionized water and resuspended to inoculate 100 mL of minimal medium to an optical density of 0.1 (600 nm); the cultures were grown with constant shaking at 18°C until they reached an optical density of 0.9 (600 nm). The culture was then harvested to obtain a cell pellet used for RNA

tag: gentoype

value: gacA null  mutant

tag: genetic background

source_name: P. syringae pv. phaseolicola NPS3121 wild type

growth_protocol: Overnight culture of strain NPS3121 was used to inoculate the KB medium, and it was allowed to grow at 18 °C to the mid exponential growth phase (A600 = 0.6).

extract_protocol: Total RNA was isolated using Trizol reagent as recommended by the manufacturer (Invitrogen). A second step of purification was performed using RNeasy MinElute spin columns (Qiagen) to remove contaminating DNA. RNAs were eluted in 50 µl of diethylpyrocarbonate (DEPC)-treated water and the concentration was determined using the NanoDrop equipment. RNA integrity was checked by analytical agarose gel electrophoresis.

treatment_protocol: P. syringae pv. phaseolicola NPS3121 was inoculated and grown on KB medium at 18o C to an optical density of 0.6 (OD 600nm). This culture are considered as control the of experiment.

tag: genotype

value: wild type


title: gacA mutant vs. wild-type (Technical replicate 3)

treatment_protocol: For microarray experiments, wild type strain and gacA- mutant strain of P. syringae pv. phaseolicola were grown in 5 mL of  KB medium with selection antibiotics. Cells were washed with deionized water and resuspended to inoculate 100 mL of minimal medium to an optical density of 0.1 (600 nm); the cultures were grown with constant shaking at 18°C until they reached an optical density of 0.9 (600 nm). The culture was then harvested to obtain a cell pellet used for RNA extraction.


title: L929-Cy5 / Ltr246-Cy3


title: gacA mutant vs. wild-type (Biological replicate 3)

source_name: P. syringae pv. phaseolicola gacA mutant


title: L929-Cy5 / Ltr051-Cy3


title: biofilm, cra mutant, rep 2

city: Mumbai

first: Shamlan

last: Reshamwala

address: Powai

country: India

institute: Indian Institute of Technology Bombay

description: cra  deletion mutant vs. wild type

hyb_protocol: Hybridization was done using Agilent’s in-situ hybridization kit (5184-3568).

scan_protocol: Agilent Microarray Scanner was used.

data_processing: Data from the images was extracted using Feature Extraction software of Agilent. Data was normalized using intensity-dependent (Lowess) normalization.

organism: Escherichia coli str. K-12 substr. MG1655

source_name: E. coli MG1655 wild type

label_protocol: Samples were labelled using the Agilent Low Input RNA amplification kit (Agilent, Cat# 5184-3523), and purified using RNeasy mini kit (Qiagen).

growth_protocol: E. coli MG1655 wild type and cra mutant cells were cultured for 48 hours at 26 degC on colony-forming antigen (CFA) agar plates.

extract_protocol: Total RNA was extracted using RNeasy Minikit (Qiagen) according to the manufacturer’s instructions.

treatment_protocol: The cells were scraped off the plate after incubation was complete. 500 μl RNAlater (Ambion) was added to stabilize RNA, and stored at 4°C till further processing.

tag: substrain

tag: mutation

source_name: E. coli MG1655 cra mutant

value: cra deletion


title: gacA mutant vs. wild-type (Technical replicate 2)


title: Ltr246-Cy5 / L929-Cy3 (2)


title: gacA mutant vs. wild-type (Technical replicate 1)

treatment_protocol: P. syringae pv. phaseolicola NPS3121 was inoculated and grown on KB medium at 18o C to an optical density of 0.6 (OD 600nm).


title: tumor 30

status: Public on Jun 19 2009

city: New York

first: Jiun

last: Kang

state: NY

address: 1130 St. Nicholas Avenue

department: Pathology

country: USA

institute: Columbia University

hyb_protocol: The pellet was resuspended in 40 mL of a hybridization solution containing 50% formamide, 10% dextran sulfate, 2X saline sodium citrate, 4% sodium dodecyl sulfate, and 200 mg yeast tRNA. The hybridization solution was denatured for 10 minutes at 72C and incubated for 1 hour at 37C to allow blocking of repetitive sequences. Hybridizations were performed in slide chambers for 48 hours at 37C.

scan_protocol: After post-hybridization washes, arrays were rinsed, spun dry, scanned into two 16-bit TIFF image files using a GenePix4200A two-color fluorescent scanner, and signal was quantified using GenePix software (Axon Instruments).

data_processing: Log2-transformed fluorescence ratios were calculated from background-subtracted median intensity values, and these ratios were used for normalization using intensity normalization methods. To adjust for effects due to variation between the red and green dyes, LOWESS normalization was applied. Then, the ratio of the red/ green channel of each clone was calculated and log2 transformed. Spot quality criteria were set as foreground to background greater than 3.0 and standard deviation of triplicates less than 0.2. The breakpoint detection and status assignment of genomic regions was performed using GLAD software.

source_name: genomic DNA

label_protocol: Genomic DNA was labeled with the Bioprime DNA Labeling System (Invitrogen, Carlsbad, CA) as described by the manufacturer.

extract_protocol: The genomic DNA was extracted using a genomic DNA purification kit (Promega, Madison, WI).

tag: gender

value: female

tag: age

tag: stage

value: ia

tag: sample

value: patient tumor DNA

value: male

value: human normal DNA (Promega)


title: tumor 25

value: iiia


title: tumor 33


title: tumor 18


title: tumor 26


title: gacA mutant vs. wild-type (Biological replicate 1)


title: XM3L

city: Vicksburg

first: Natalia

last: Vinas

state: MS

address: 3909 Halls Ferry Rd

institute: Mississippi State University

description: Microarray image processing and data pre-processing were performed using Agilent's Feature Extraction software v 9.5.

hyb_protocol: Standard Agilent two-color protocol (Agilent 60-mer oligo microarray processing protocol) was used.

scan_protocol: The microarrays were washed and scanned with a laser-based detection system (Agilent, Palo Alto, CA).

data_processing: The intensity of each spot was summarized by the median pixel intensity. A log transformed signal ratio between the experimental (Cy5) channel and the reference (Cy3) channel was calculated for each spot, followed by within-array lowess transformation and between array scale normalization on median intensities (Zahurak et al., 2007). Probes that did not hybridize were removed from consideration.

organism: Pimephales promelas

source_name: Liver from male fathead minnow exposed to a field site

label_protocol: cDNA synthesis, cRNA labeling, amplification and hybridization were performed following the manufacturer's kits and protocols (Agilent Low RNA Input Fluorescent Linear Amplification Kit).

growth_protocol: To conduct the field exposures at each field site, FHM were transported from the laboratory to the field site in aerated, insulated tanks.  At each site, 25 males and 25 females were placed in separate wire mesh minnow traps with the entrance funnel plugged.  The traps were anchored to the bottom in the stream current with the top of the traps submerged. Fish were removed from the traps 48 h later and transported back to the laboratory in aerated, insulated tanks containing the stream water.  Immediately upon arrival at the laboratory, four males and four females were sacrificed as described for the laboratory exposures. Liver and gonads were removed and stored in liquid nitrogen until processed for arrays. All procedures involving live fish were reviewed and approved by the University of Minnesota Institutional Animal Care and Use Committee (IACUC).

extract_protocol: Total RNA was isolated using the RNA Stat-60 reagent (Tel-test, Friendswood, TX).

treatment_protocol: Fathead minnow liver exposed in vivo for 48h to field site 21

value: liver

tag: exposure

value: field site 21

source_name: Reference

value: liver, brain, and gonad from control fathead minnow females and males


title: tumor 24


title: tumor 29

value: ib


title: Ltr246-Cy5 / L929-Cy3


title: XM4L


title: biofilm, cra mutant, rep 1

description: cra  deletion mutant vs. wild type


title: XM1L


title: 13M6L

treatment_protocol: Fathead minnow liver exposed in vivo for 48h to field site 13

value: field site 13


title: tumor 4


title: tumor 2


title: tumor 34

value: iib


title: tumor 3


title: tumor 8


title: 13M5L


title: 11M2L

treatment_protocol: Fathead minnow liver exposed in vivo for 48h to field site 11

value: field site 11


title: 12M3L

treatment_protocol: Fathead minnow liver exposed in vivo for 48h to field site 12

value: field site 12


title: tumor 15


title: tumor 9


title: tumor 10


title: tumor 16


title: 11M3L


title: 7M2L

treatment_protocol: Fathead minnow liver exposed in vivo for 48h to field site 7

value: field site 7


title: 11M5L


title: 12M2L


title: XM2L


title: 11M1L


title: 13M3L


title: 12M4L


title: tumor 17


title: tumor 12


title: 12M5L


title: 7M3L


title: 13M2L


title: 7M1L


title: tumor 1

value: iia


title: 7M4L


title: tumor 6


title: tumor 19


title: tumor 27


title: XM4G

source_name: Testis from fathead minnow exposed to a field site

treatment_protocol: Fathead minnow testis exposed in vivo for 48h to field site 21

value: testis


title: XM2G


title: XM3G


title: tumor 32


title: tumor 35

value: female


title: 12M7G

treatment_protocol: Fathead minnow testis exposed in vivo for 48h to field site 12


title: XM1G


title: 13M4G

treatment_protocol: Fathead minnow testis exposed in vivo for 48h to field site 13


title: tumor 13


title: 13M5G


title: 12M5G


title: tumor 14

value: ia


title: 13M2G


title: 12M4G


title: tumor 5

value: patient tumor DNA


title: 11M6G

treatment_protocol: Fathead minnow testis exposed in vivo for 48h to field site 11


title: PG301 array

status: Public on Jun 18 2009

city: Durham

first: Anne

last: Casper

state: NC

address: 381 CARL Building, Research Drive, Box 3054

department: Department of Molecular Genetics and Microbiology

institute: Duke University

description: PG301 is an illegitimate diploid from a mating between a rad52 mutant version of the GAL-POL1 strain described in Lemoine, F. et al. Cell, Vol. 120, 587-598 (2005)  and a rad52 mutant version of the test mater 1225alpha (also described in Lemoine et al.).  Genomic DNA from PG301 was competitively hybridized with genomic DNA from the isogenic reference strain MS71.  This experiment allows the determination of chromosomal rearrangements in PG301.

hyb_protocol: Described in Lemoine, F. et al. Cell, Vol. 120, 587-598 (2005).

scan_protocol: Array scanned in Genepix 4000b scanner.

data_processing: The log2 R/G ratios for all probes in the array were collapsed to a single value in the case of repeated probes and normalized according to the median value for the entire array.

organism: Saccharomyces cerevisiae

source_name: PG301 chromosomal DNA labeled with Cy5

label_protocol: Direct incorporation with klenow polymerase and random priming

extract_protocol: Genomic DNA was harvested by standard protocol:  Cells were treated with zymolyase to obtain spheroblasts.  SDS was used to disrupt the cell membrane.  Potassium acetate was used to precipitate protein and lipids.  DNA was precipitated with isopropanol.  RNAse A was used to degrade RNA.

tag: ploidy

value: diploid

tag: recombination

value: illegitimate

source_name: MS71 chromosomal DNA labeled with Cy3

tag: isogenicity

value: isogenic to the strain in Channel 1


title: 13M3G


title: tumor 23

value: male

value: human normal DNA (Promega)


title: 11M5G

value: liver, brain, and gonad from control fathead minnow females and males


title: 11M4G


title: tumor 22

value: ib


title: PG298 array

description: PG298 is an illegitimate diploid from a mating between a rad52 mutant version of the GAL-POL1 strain described in Lemoine, F. et al. Cell, Vol. 120, 587-598 (2005)  and a rad52 mutant version of the test mater 1225alpha (also described in Lemoine et al.).  Genomic DNA from PG298 was competitively hybridized with genomic DNA from the isogenic reference strain MS71.  This experiment allows the determination of chromosomal rearrangements in PG298.

source_name: PG298 chromosomal DNA labeled with Cy5


title: 12M1G


title: 7M5G

treatment_protocol: Fathead minnow testis exposed in vivo for 48h to field site 7


title: 11M2G


title: PG300 array

description: PG300 is an illegitimate diploid from a mating between a rad52 mutant version of the GAL-POL1 strain described in Lemoine, F. et al. Cell, Vol. 120, 587-598 (2005)  and a rad52 mutant version of the test mater 1225alpha (also described in Lemoine et al.).  Genomic DNA from PG300 was competitively hybridized with genomic DNA from the isogenic reference strain MS71.  This experiment allows the determination of chromosomal rearrangements in PG300.

source_name: PG300 chromosomal DNA labeled with Cy5


title: 7M2G


title: PG284 array

description: PG284 is an illegitimate diploid from a mating between an rad52 mutant version of the GAL-POL1 strain described in Lemoine, F. et al. Cell, Vol. 120, 587-598 (2005)  and a rad52 mutant version of the test mater 1225alpha (also described in Lemoine et al.).  Genomic DNA from PG284 was competitively hybridized with genomic DNA from the isogenic reference strain MS71.  This experiment allows the determination of chromosomal rearrangements in PG284.

source_name: PG284 chromosomal DNA labeled with Cy5


title: PG273 array

description: PG273 is an illegitimate diploid from a mating between an rad52 mutant version of the GAL-POL1 strain described in Lemoine, F. et al. Cell, Vol. 120, 587-598 (2005)  and a rad52 mutant version of the test mater 1225alpha (also described in Lemoine et al.).  Genomic DNA from PG273 was competitively hybridized with genomic DNA from the isogenic reference strain MS71.  This experiment allows the determination of chromosomal rearrangements in PG273.

source_name: PG273 chromosomal DNA labeled with Cy5


title: 7M3G


title: PG297 array

description: PG297 is an illegitimate diploid from a mating between a rad52 mutant version of the GAL-POL1 strain described in Lemoine, F. et al. Cell, Vol. 120, 587-598 (2005)  and a rad52 mutant version of the test mater 1225alpha (also described in Lemoine et al.).  Genomic DNA from PG297 was competitively hybridized with genomic DNA from the isogenic reference strain MS71.  This experiment allows the determination of chromosomal rearrangements in PG297.

source_name: PG297 chromosomal DNA labeled with Cy5


title: PG286 array

description: PG286 is an illegitimate diploid from a mating between a rad52 mutant version of the GAL-POL1 strain described in Lemoine, F. et al. Cell, Vol. 120, 587-598 (2005)  and a rad52 mutant version of the test mater 1225alpha (also described in Lemoine et al.).  Genomic DNA from PG286 was competitively hybridized with genomic DNA from the isogenic reference strain MS71.  This experiment allows the determination of chromosomal rearrangements in PG286.

source_name: PG286 chromosomal DNA labeled with Cy5


title: 7M4G


title: PG282 array

description: PG282 is an illegitimate diploid from a mating between an rad52 mutant version of the GAL-POL1 strain described in Lemoine, F. et al. Cell, Vol. 120, 587-598 (2005)  and a rad52 mutant version of the test mater 1225alpha (also described in Lemoine et al.).  Genomic DNA from PG282 was competitively hybridized with genomic DNA from the isogenic reference strain MS71.  This experiment allows the determination of chromosomal rearrangements in PG282.

source_name: PG282 chromosomal DNA labeled with Cy5


title: PG272 array

description: PG272 is an illegitimate diploid from a mating between an rad52 mutant version of the GAL-POL1 strain described in Lemoine, F. et al. Cell, Vol. 120, 587-598 (2005)  and a rad52 mutant version of the test mater 1225alpha (also described in Lemoine et al.).  Genomic DNA from PG272 was competitively hybridized with genomic DNA from the isogenic reference strain MS71.  This experiment allows the determination of chromosomal rearrangements in PG272.

source_name: PG272 chromosomal DNA labeled with Cy5