title: Wild-type young adult biological rep 5


title: Male_control_172ppb_rep3

status: Public on Jun 24 2009

type: RNA

city: Pendleton

first: Lisa

middle: J

last: Bain

state: SC

address: P. O. Box 709

department: Biological Sciences

country: USA

institute: Clemson University

description: Control male 172_3

hyb_protocol: The array membranes were prehybridized for 4-6 hour in Express hybridization solution (Clontech, Palo Alto, CA) containing 100mg/ml denatured salmon sperm.  The denatured probe was added to each tube and incubated overnight with the array at 68oC. After the incubation, the arrays were washed four times with 2X SSC/0.5%SDS at 64oC and four times with 0.5X SSC/0.5%SDS at 64oC.

scan_protocol: After washing, the membranes were wrapped in plastic, placed on a phosphorimaging screen, and developed using a Bio-Rad Molecular Imager FX (Hercules, CA).  The intensity of each spot was quantified using the Invitrogen ResGen Pathways 4-Universal Microarray Analysis Software (Carlsbad, CA).

data_processing: The raw pixel intensity was divided by the summed pixel intensity for each array.

molecule: total RNA

organism: Fundulus heteroclitus

source_name: liver, male, control

label_protocol: Probes were generated by reverse transcription using 2ug of RNA, 0.1mM oligo dT primer, 1.2mM dNTPs lacking dATP, [33P]dATP (3000Ci/mmol, Perkin Elmer, Boston, MA) and 200U MMLV-RT at 37oC for 2 hours. Each probe was purified using Amersham’s Probe Quant-50 columns (Piscataway, NJ) and denatured by heating to 100oC before adding to the hybridization.

extract_protocol: Total RNA was extracted with TriReagent and treated with DNase I.

tag: gender

value: male

tag: tissue

value: liver

tag: treatment


title: Wild-type young adult biological rep 4

status: Public on Jun 25 2009

city: Philadelphia

first: Predrag

last: Krajacic

state: PA

address: 3700 Hamilton Walk A700 Richards

institute: University of Pennsylvania

description: Gene expression data from young adult wild type worms grown on 25ºC

hyb_protocol: Labeled cDNA was added to Affymetrix hybridization cocktails, heated at 99ºC for 5 min and hybridized for 16 h at 45ºC to GPL200 GeneChips (Affymetrix Inc., Santa Clara CA). The microarrays were then washed at low (6X SSPE) and high (100mM MES, 0.1M NaCl) stringency and stained with streptavidin-phycoerythrin. Fluorescence was amplified by adding biotinylated anti-streptavidin and an additional aliquot of streptavidin-phycoerythrin stain.

scan_protocol: Affymetrix GCS3000 laser scanner was used to collect fluorescence signal after excitation at 570 nm.

data_processing: Affymetrix Command Console and Expression Console were used to quantitate expression levels for targeted genes; default values provided by Affymetrix were applied to all analysis parameters. Probes for each targeted gene were averaged and inter-array normalization performed using the GCRMA algorithm.

label: biotin

organism: Caenorhabditis elegans

source_name: adult worm

label_protocol: 100ng of total RNA was converted to first-strand cDNA using reverse transcriptase primed by poly(T) and random oligomers that incorporated the T7 promoter sequence.  Second-strand cDNA synthesis was followed by in vitro transcription with T7 RNA polymerase for linear amplification of each transcript, and the resulting cRNA was converted to cDNA, fragmented, assessed by Bioanalyzer, and biotinylated by terminal transferase end labeling.

growth_protocol: Hypochlorite synchronized L1 stage wild type, fer-1(hc1), or fer-1(hc24) animals were grown to the young adult stage on standard NGM plates at 25°.

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

treatment_protocol: Worms were washed from the plates with M9 solution and 1000 adult worms were collected into 1.5ml tubes using gating criteria on the COPAS Biosort that excluded L4 and younger animals.  Immediately following sorting, worms were pelleted at 2,000 RPM and the supernatant was aspirated, leaving ~100µl on top of the worm pellet.  400µl of Trizol was added and the solution was vortexed for two minutes.  Worms were stored at -80° until RNA isolation.

value: whole worm

tag: strain

tag: genotype

value: wild type


title: XOC, 2 hai - rep2

city: Ames

first: PLEXdb Curator

middle: Sudhansu

state: IA

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

department: Virtual Reality Application Center

institute: Iowa State University

description:
R2XOC2H
Replication 2, Xoc-inoculated rice, tissue collected at 2HAI

hyb_protocol: Affy- Eukaryotic Target Hybridization

scan_protocol: Affy- Array Scanning

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

organism: Oryza sativa

source_name: shoot, XOC, 2 hai

label_protocol: Affy-Eukaryotic Target Preparation

extract_protocol: Hot Phenol/Guanidine Thiocyanate and RNeasy Clean up

tag: germplasm name

value: cv. nipponbare

tag: organism part

tag: development stage

value: PO:0007106 LP.03 three leaves visible

tag: age

value: 2 weeks after sowing

tag: growth media

value: LC-1 Soil Mix


title: XOC, 2 hai - rep1

description:
R1XOC2H
Replication 1, Xoc-inoculated rice, tissue collected at 2HAI


title: Male_control_172ppb_rep1

description: Control male 172_1


title: Juvenile_control_172ppb_rep4

description: Control juvenile 172_4

source_name: 7-10 pooled fish, control

value: whole juveniles

value: 6 weeks


title: Female_As exposed_172ppb_rep3

description: As female 172_3

source_name: liver, female, 172ppb arsenic

value: female

value: 172ppb sodium arsenite


title: Juvenile_control_172ppb_rep2

description: Control juvenile 172_2


title: Female_control_172ppb_rep3

description: Control female 172_3

source_name: liver, female, control


title: Female_control_172ppb_rep5

description: Control female 172_5


title: Juvenile_control_172ppb_rep1

description: Control juvenile 172_1


title: Male_As exposed_172ppb_rep5

description: As male 172_5

source_name: liver, male, 172ppb arsenic


title: Male_As exposed_172ppb_rep2

description: As male 172_2


title: Juvenile_As exposed_1720ppb_rep5

description: As juvenile 1720_5

source_name: 7-10 pooled fish, arsenic

value: parental exposure to 1,720ppb sodium arsenite


title: Wild-type young adult biological rep 3


title: Male_control_172ppb_rep4

description: Control male 172_4


title: Juvenile_control_1720ppb_rep3

description: Control juvenile 1720_3


title: Juvenile_control_1720ppb_rep5

description: Control juvenile 1720_5


title: Juvenile_As exposed_1720ppb_rep1

description: As juvenile 1720_1


title: Juvenile_control_1720ppb_rep1

description: Control juvenile 1720_1


title: Female_control_172ppb_rep4

description: Control female 172_4


title: Male_As exposed_1720ppb_rep5

description: As male 1720_5

source_name: liver, male, 1,720ppb arsenic

value: 1,720ppb sodium arsenite


title: Male_As exposed_1720ppb_rep4

description: As male 1720_4


title: Male_As exposed_1720ppb_rep2

description: As male 1720_2


title: Female_As exposed_172ppb_rep4

description: As female 172_4


title: Male_control_172ppb_rep2

description: Control male 172_2


title: Female_As exposed_172ppb_rep1

description: As female 172_1


title: Female_As exposed_172ppb_rep5

description: As female 172_5


title: Male_As exposed_1720ppb_rep3

description: As male 1720_3


title: Male_control_1720ppb_rep3

description: Control male 1720_3


title: Female_control_172ppb_rep2

description: Control female 172_2


title: Juvenile_As exposed_1720ppb_rep2

description: As juvenile 1720_2


title: Female_control_172ppb_rep1

description: Control female 172_1


title: Juvenile_As exposed_1720ppb_rep4

description: As juvenile 1720_4


title: Juvenile_As exposed_575ppb_rep5

description: As juvenile 575_5

value: parental exposure to 575ppb sodium arsenite


title: Juvenile_As exposed_575ppb_rep2

description: As juvenile 575_2


title: Juvenile_control_575ppb_rep5

description: Control juvenile 575_5


title: Juvenile_As exposed_575ppb_rep1

description: As juvenile 575_1


title: Juvenile_control_575ppb_rep3

description: Control juvenile 575_3


title: Female_As exposed_172ppb_rep2

description: As female 172_2


title: Juvenile_control_1720ppb_rep2

description: Control juvenile 1720_2


title: Juvenile_As exposed_1720ppb_rep3

description: As juvenile 1720_3


title: Male_control_1720ppb_rep5

description: Control male 1720_5


title: Male_As exposed_1720ppb_rep1

description: As male 1720_1


title: Juvenile_control_1720ppb_rep4

description: Control juvenile 1720_4


title: Male_control_1720ppb_rep4

description: Control male 1720_4


title: RNA from embryos of 3 groups of tnnt2 morpholino fish at 60 hpf_1

city: Sheffield

first: Marta

last: Milo

state: South Yorkshire

address: Western Bank

department: Biomedical Science

country: United Kingdom

institute: University of Sheffield

description: gene expression from whole zebrafish embryo

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned at 3-mm density with a GeneChip® Scanner 3000 7G 4C (Affymetrix).

data_processing: The data were analyzed using the PUMA package, Propagating Uncertainty in Microarray data (www.bioconductor.org). Fold change cut-off was set at 1 in the log2 scale. Cut-off of probability of positive ratio for the analysis of differentially expressed genes was set at 0.90.

organism: Danio rerio

source_name: Whole embryo

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

growth_protocol: Embryos were incubated in E3 medium at 28 degrees celsius according to standard protocols.

extract_protocol: RNA was isolated using the Trizol (Invitrogen) method following manufacturer’s instructions. Trizol-purified RNA was then treated with RNase-free DNase I (Roche) and purified with RNeasy spin columns (Qiagen). RNA quantity and quality was assessed with an Agilent Bioanalyzer 2100 (Agilent Technologies).

treatment_protocol: One cell zebrafish embryos were injected with morpholino antisense against control or cardiac troponin t2 (from Gene-tools). Whole embryo RNA was extracted at 32, 48, and 60h post fertilization and transcriptionally profiled. Groups contained equal numbers of embryos from each parent pair.

value: AB wildtype zebrafish

tag: genetic modification

value: morpholino antisense tnnt2 injected

tag: time


title: Male_control_1720ppb_rep2

description: Control male 1720_2

value: male


title: Male_control_1720ppb_rep1

description: Control male 1720_1

value: liver


title: Juvenile_As exposed_575ppb_rep3

description: As juvenile 575_3


title: RNA from embryos of 3 groups of Wildtype AB zebrafish at 60 hpf_2


title: Juvenile_As exposed_575ppb_rep4

description: As juvenile 575_4


title: Juvenile_control_575ppb_rep4

description: Control juvenile 575_4


title: Male_As exposed_575ppb_rep3

description: As male 575_3

source_name: liver, male, 575ppb arsenic

value: 575ppb sodium arsenite


title: Juvenile_control_575ppb_rep2

description: Control juvenile 575_2


title: Juvenile_control_575ppb_rep1

description: Control juvenile 575_1


title: Male_As exposed_575ppb_rep2

description: As male 575_2


title: Male_As exposed_575ppb_rep5

description: As male 575_5


title: Male_As exposed_575ppb_rep4

description: As male 575_4


title: RNA from embryos of 3 groups of Wildtype AB zebrafish at 60 hpf_1


title: RNA from embryos of 3 groups of tnnt2 morpholino fish at 60 hpf_3


title: Male_control_575ppb_rep5

description: Control male 575_5


title: DRG Coculture - Time point 36

city: New York City

first: prabhjot

last: dhadialla

state: NY

address: 1200 York Avenue

institute: Rockefeller University

description: raw data samples 19-21

hyb_protocol: Briefly, 500 ng of^ total RNA was used to synthesize the first strand of cDNA using ArrayScript reverse transcriptase and an oligo(dT) primer bearing a T7 promoter. The single-stranded cDNA was then converted into a double-stranded DNA (dsDNA) by DNA polymerase^ I in the presence of /E. coli/ RNase H and DNA ligase. After column purification, the dsDNA was served as a template for in vitro transcription in a reaction containing biotin-labeled UTP, unlabeled NTPs and T7 RNA Polymerase. The amplified, biotin-labeled antisense RNA (aRNA) was purified and quality was assessed using the Agilent 2100 Bioanalyzer and the RNA 6000 Nano kit. 750 ng of aRNA in 5 ul was mixed with 10 ul of hybridization reagents and heated at 65C for 10min. After cooled to room temperature, total 15 ul of the hyb solution was applied to Illumina MouseRef-8 v1.1 chip. The chip was incubated for about 18 hours at 58C. After washing and staining with streptavidin-Cy3, the chip was scanned using Illumina BeadArray Reader.

scan_protocol: The chip was incubated for about 18 hours at 58C. After washing and staining with streptavidin-Cy3, the chip was scanned using Illumina BeadArray Reader. The scanning was done using standard DirectHyb Gene Expression protocol with the following settings: Factor=1, PMT=587, Filter=100%.

data_processing: The raw data was extracted using Illumina BeadStudio software without normalization.

organism: Mus musculus

source_name: DRG co-culture

label_protocol: . ~500 ng of^ total RNA was used to prepare biotin-labeled RNA using Ambion Illumina TotalPrep RNA Amplification Kit (Cat# AMIL1791, Applied Biosystems, Foster City, CA).

growth_protocol: Wild-type mice were obtained at embryonic day 13.5 for the extraction of DRG, which contain 2 main cell populations: Schwann cells and neurons. The DRG was disassociated and maintained until a dense layer of Schwann cells existed in tight proximity to neurons ( 9 days). The onset of Schwann cell–axonal maturation was triggered by adding ascorbic acid, defining time point zero

extract_protocol: Total RNA was purified from 10 to 20 mg of wet tissue using Qiagen RNeasy Mini kit according to the manufacturer's^ recommendations (Qiagen, Valencia, CA). RNA quality was assessed using the Agilent 2100 Bioanalyzer and the RNA 6000 Nano kit (Agilent Technologies Inc., Palo Alto, CA)

treatment_protocol: Samples for microarray analysis were obtained in triplicate from separate coculture slips at 0, 0.5, 1, 6, 12, 36, and 48 h after ascorbic acid addition and were prepared for use on Illumina Mouse-8 chips (Illumina) by the Rockefeller Microarray Core Facility (New York, NY).

value: Time point 36 hour


title: RNA from embryos of 3 groups of Wildtype AB zebrafish at 60 hpf_3


title: RNA from embryos of 3 groups of tnnt2 morpholino fish at 60 hpf_2


title: DRG Coculture - Time point 6

description: raw data samples 10-12

value: Time point 6 hour


title: DRG Coculture - Time point 24

description: raw data samples 16-18

value: Time point 24 hour


title: DRG Coculture - Time point 48

description: raw data samples 22-24

value: Time point 48 hour


title: RNA from embryos of 3 groups of Wildtype AB zebrafish at 48 hpf_3


title: RNA from embryos of 3 groups of tnnt2 morpholino fish at 48 hpf_3


title: Male_As exposed_575ppb_rep1

description: As male 575_1


title: DRG Coculture - Time point 12

description: raw data samples 13-15

value: Time point 12 hour


title: RNA from embryos of 3 groups of Wildtype AB zebrafish at 48 hpf_2


title: DRG Coculture - Time point 1/2

description: raw data samples 4-6

value: Time point 1/2 hour


title: RNA from embryos of 3 groups of tnnt2 morpholino fish at 48 hpf_1


title: RNA from embryos of 3 groups of tnnt2 morpholino fish at 48 hpf_2


title: DRG Coculture - Time point 1

description: raw data samples 7-9

value: Time point 1 hour


title: Male_control_575ppb_rep4

description: Control male 575_4


title: Female_As exposed_575ppb_rep4

description: As female 575_4

source_name: liver, female, 575ppb arsenic

value: female


title: Male_control_575ppb_rep3

description: Control male 575_3


title: Male_control_575ppb_rep2

description: Control male 575_2


title: Female_As exposed_575ppb_rep3

description: As female 575_3


title: Female_As exposed_575ppb_rep5

description: As female 575_5


title: Female_As exposed_575ppb_rep2

description: As female 575_2


title: RNA from embryos of 3 groups of tnnt2 morpholino fish at 36 hpf_2


title: 1 week old heterozygous sample #2(251279910044)

city: Paris

first: Chris

last: Ottolenghi

address: rue des Saint-Peres

country: France

institute: Inserm/Univ.Paris Descartes

description: FOXL2 knock-out ovary: 1 week old heterozygous

hyb_protocol: Agilent 60-mer oligo microarray processing protocol (SSC Wash/SureHyb Chamber set-up) V4.1, April 2004.  Agilent Publication Number:  G4140-90030 V4.1 APRIL 2004.

scan_protocol: Slides were scanned with an Agilent DNA Microarray Scanner model G2505-64120 at 100% PMT in both channels, with a scan resolution of 10um.  A scan window of 61 x 21.6 mm was used, then images were cropped to size and saved in a modified two-color TIFF format.  Images were examined visually for evidence of foreign debris or major failures. Agilent Microarray Scanner User Manual (6.3) http://www.chem.agilent.com/scripts/literaturePDF.asp?iWHID=33696

data_processing: Data are extracted with Agilent Feature Extraction Software.The data were further processed as follows: After background subtraction from the Agilent analyzer raw output data,calculation of the ratio of the channels was followed by normalization of each sample values against a virtual microarray dataset by local mean regression as implemented by the lowess program on R (span 0.01). The reference virtual dataset contained the average expression values for each probe across all samples.

label_protocol: Total RNA was labeled using Agilents Fluorescent Linear Amplification kit, according to manufacturers instructions (Product Number G2554A or P/N G2556-66002, Version 3.0, June 2002).

extract_protocol: RNEasy protocol

tag: Whole organ

tag: Strain

value: NIHS-BC

tag: Gender

tag: Age

value: birth

tag: Development stage

value: 7 days postnatum

tag: Genetic modification

value: gene knock out

tag: Individual Identifier

source_name: Universal Mouse Reference RNA

extract_protocol: Total RNA was extracted from cultured cells using a Stratagene Absolutely RNA kit. DNase-treated total RNA samples from 11 cultured cell lines derived from embryo, embryo fibroblast, kidney, liver/hepatocyte, lung/alveolar macrophage, B-lymphocyte, T-lymphocyte (thymus), mammary gland, muscle myoblast, skin, and testis were pooled in equal parts

tag: Universale Mouse Reference


title: RNA from embryos of 3 groups of tnnt2 morpholino fish at 36 hpf_1

tag: strain

value: AB wildtype zebrafish


title: Female_As exposed_575ppb_rep1

description: As female 575_1

tag: gender

tag: tissue

tag: treatment


title: DRG Coculture - Time point 0

description: raw data samples 1-3

value: Time point 0


title: RNA from embryos of 3 groups of Wildtype AB zebrafish at 48 hpf_1


title: 1 week old knock-out sample #1(251279910040)

description: FOXL2 knock-out ovary: 1 week old knock-out


title: Male_control_575ppb_rep1

description: Control male 575_1

value: male


title: TCDD 3

city: Gambier

first: Wade

middle: H

last: Powell

state: OH

address: 302A College Park St.

department: Biology Dept.

institute: Kenyon College

description: TCDD 3 (biological rep)

hyb_protocol: Samples were hybridized to Xenopus laevis GeneChips (Affymetrix, Santa Clara, CA) according to manufacturer's protocol.

scan_protocol: Hybridized chips were scanned using Affymetrix GC3000 7G scanning equipment.

data_processing: Affymetrix GCOS software. Gene expression was determined using the PM/MM method in dChip (Build: Sept 10, 2007). Statistical analysis was completed via 2-way ANOVA with individual contrasts (p£0.01) using Statistical Analysis Software (SAS; Cary, NC)

organism: Xenopus laevis

source_name: 100 nM TCDD

label_protocol: Probes were labeled by the University of Wisconsin Biotechnology CenterÕs Gene Expression Microarray Facility in Madison, Wisconsin using the MessageAmp II-Biotin Enhanced kit (Ambion). Input is 1 ug RNA.

growth_protocol: Cells were grown to 90% confluence in 25 cm2 flasks

extract_protocol: RNA was extracted using QIAshedder spin columns and RNeasy kits (Qiagen, Hilden, Germany) per the procedure supplied by the manufacturer.

treatment_protocol: Cells were treated with dimethylsulfoxide (DMSO)  vehicle (0.25%) or 100 nM TCDD or 100 nM FICZ dissolved in DMSO (vehicle concentration also 0.25%)

tag: cell line

value: XLK-WG


title: RNA from embryos of 3 groups of Wildtype AB zebrafish at 36 hpf_2


title: 1 week old wild-type sample #2(251279910046)

description: FOXL2 knock-out ovary: 1 week old wild-type


title: RNA from embryos of 3 groups of tnnt2 morpholino fish at 36 hpf_3

value: morpholino antisense tnnt2 injected


title: RNA from embryos of 3 groups of Wildtype AB zebrafish at 36 hpf_3


title: 1 week old wild-type sample #1(251279910045)

source_name: FOXL2 knock-out ovary: 1 week old wild-type


title: 1 week old heterozygous sample #1(251279910043)

description: FOXL2 knock-out ovary:  1 week old heterozygous


title: 1 week old knock-out sample #2(251279910042)

description: FOXL2 knock-out ovary:  1 week old knock-out


title: newborn wild-type sample #3(251279910039)

description: FOXL2 knock-out ovary: newborn wild-type

value: newborn


title: newborn wild-type sample #2(251279910038)

source_name: FOXL2 knock-out ovary: newborn wild-type


title: Female_control_575ppb_rep4

description: Control female 575_4

value: liver


title: RNA from embryos of 3 groups of Wildtype AB zebrafish at 36 hpf_1


title: TCDD 2

description: TCDD 2 (biological rep)


title: Female_control_575ppb_rep3

description: Control female 575_3


title: Female_control_575ppb_rep5

description: Control female 575_5


title: newborn wild-type sample #1(251279910037)


title: Female_control_575ppb_rep2

description: Control female 575_2


title: TCDD 1

description: TCDD 1 (biological rep)


title: Female_control_575ppb_rep1

description: Control female 575_1


title: Juvenile_As exposed_172ppb_rep4

description: As juvenile 172_4

value: whole juveniles

tag: age

value: 6 weeks

value: parental exposure to 172ppb sodium arsenite


title: FICZ 1

description: FICZ 3 (biological rep)

source_name: 100 nM FICZ


title: Juvenile_As exposed_172ppb_rep5

description: As juvenile 172_5


title: newborn heterozygous sample #2(251279910035)

description: FOXL2 knock-out ovary: newborn heterozygous


title: newborn knock-out sample #2(251279910031)

description: FOXL2 knock-out ovary: newborn knock-out


title: FICZ 3

description: FICZ 5 (biological rep)


title: FICZ 2

description: FICZ 4 (biological rep)


title: DMSO CH 2

description: Ch 2 (biological rep)

source_name: DSMO vehicle


title: newborn knock-out sample #3(251279910033)

source_name: FOXL2 knock-out ovary: newborn knock-out


title: newborn knock-out sample #1(251279910030)


title: DMSO CH 3

description: Ch 3  (biological rep)


title: TS088-D14-rep1

status: Public on Jun 23 2009

city: Ibaragi

first: kohei

last: inoue

address: Sunayama

country: Japan

institute: Mitsubishi Chemical Medience Corporation

description: Biological replicate 1 of 4. Control samples were pooled.

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.

organism: Rattus norvegicus

source_name: rat liver, control

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.

value: Male

value: 5 weeks

value: Liver

tag: compound

value: Vehicle

tag: dose

tag: administration

value: gavage

tag: treatment time

value: 14 days

tag: vehicle

value: Corn oil

source_name: rat liver, chemically-treated


title: newborn heterozygous sample #1(251279910034)

source_name: FOXL2 knock-out ovary: newborn heterozygous

tag: Whole organ

tag: Strain

value: NIHS-BC

tag: Gender

value: female

value: birth

value: gene knock out


title: TS088-D14-rep3

description: Biological replicate 3 of 4. Control samples were pooled.


title: DMSO CH 1

description: CH 1 (biological rep)

value: XLK-WG


title: TS088-D14-rep2

description: Biological replicate 2 of 4. Control samples were pooled.


title: TS088-D14-rep4

description: Biological replicate 4 of 4. Control samples were pooled.


title: TS087-D14-rep1

value: o-Nitrotoluene


title: TS084-D14-rep4

value: Water

value: Sodium benzoate


title: TS086-D14-rep4

value: Methyleugenol


title: TS085-D14-rep2

value: Indomethacin


title: TS086-D14-rep2

value: Male


title: TS083-D14-rep4

value: 5 weeks


title: TS086-D14-rep3

value: Liver


title: TS086-D14-rep1

value: Vehicle


title: TS083-D14-rep2

value: gavage


title: TS081-D14-rep3

value: 14 days

value: Glutaraldehyde


title: TS084-D14-rep3


title: TS085-D14-rep3

value: Corn oil


title: TS081-D14-rep1


title: newborn heterozygous sample #3(251279910036)

value: NIHS-BC

value: female

tag: Age

tag: Development stage

value: newborn

tag: Genetic modification


title: TS087-D14-rep4

tag: strain


title: TS080-D14-rep4

tag: gender


title: TS087-D14-rep2

tag: tissue


title: TS082-D14-rep1

value: 4-Nitroanthranilic acid

tag: treatment


title: TS082-D14-rep2


title: TS085-D14-rep1


title: TS087-D14-rep3

value: o-Nitrotoluene


title: TS083-D14-rep3


title: TS080-D14-rep3


title: TS084-D14-rep2

value: Water


title: TS084-D14-rep1

value: Sodium benzoate


title: TS082-D14-rep4


title: TS077-D14-rep4

value: 4-Dimethylaminoazobenzene (DAB)


title: TS077-D14-rep2


title: TS080-D14-rep2


title: TS079-D14-rep4

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


title: TS082-D14-rep3

value: Male


title: TS080-D14-rep1

value: 5 weeks


title: TS077-D14-rep3

value: Liver


title: TS085-D14-rep4

value: Vehicle

value: Indomethacin


title: TS079-D14-rep2

value: gavage

value: 14 days


title: TS079-D14-rep3


title: TS078-D14-rep3

value: Chlorendic acid


title: TS078-D14-rep4


title: TS079-D14-rep1


title: TS076-D14-rep3

value: Corn oil


title: TS078-D14-rep1


title: TS076-D14-rep2


title: TS078-D14-rep2


title: TS076-D14-rep1


title: TS075-D14-rep4

value: 4-Aminoazobenzene (AAB)


title: TS076-D14-rep4


title: TS075-D14-rep3


title: TS077-D14-rep1


title: TS075-D14-rep2


title: TS081-D14-rep4

value: Glutaraldehyde


title: TS075-D14-rep1


title: TS074-D14-rep4

value: Caprolactam


title: TS072-D14-rep4


title: TS073-D14-rep4

value: Phthalamide


title: TS073-D14-rep3


title: TS074-D14-rep2

value: Water


title: TS072-D14-rep2


title: TS074-D14-rep1


title: TS072-D14-rep1


title: TS072-D14-rep3


title: TS073-D14-rep1


title: TS073-D14-rep2


title: TS074-D14-rep3


title: brain_SLDFG3

status: Public on Dec 31 2009

city: Galway

first: Michael

last: Cairns

address: University Road

department: NCBES

country: Ireland

institute: NUI Galway

description:
Atlantic salmon (Aquaculture and Catchment Management Services of the Marine Institute (Ireland) in Burrishoole, Newport, Co. Mayo)
Eight microarray hybridisations were carried out in total as part of this design. To compare brain samples total RNA from 10 individual brains (dissected of hypothalamus and pituitary) of precocious fish and 10 brains of non-precocious fish were pooled to give two pools each of five precocious (PA and PB) and non-precocious (NPA and NPB) brains. Each pool of precocious brains was compared in a dye swap experiment with each pool of non-precocious brains.

hyb_protocol: Slides were pre-hybridised in 50% formamide, 5x SSC, 0.1% SDS, 0.1 mg/ml BSA at 42 oC for 1 h, then washed twice for 5 min with 0.1x SSC and for 30 s with 18MOhm water. The slides were dried immediately by centrifugation (Eppendorf Multipuropose Centrifuge 5804) at 1500 rpm for 5 min at room temperature in a slide box lined with 3MM Whatman paper (10.8 x 7.4cm). Dust was removed from the surface of the pre-hybridised arrays using an ozone-free air duster (Kenair, UK). The purified, combined Cy5- and Cy3-labelled cDNAs (80 microlitre) were denatured at 95 C in a thermal cycler for 3 min, immediately applied to the array surface and covered with a lifter slip (Erie Scientific, USA). Each array was placed in a pre-warmed Genetix hybridisation chamber. The chamber was sealed and incubated in an oven for 16-18 h at 50 oC. Microarray wash solutions were warmed to 55 oC. All wash steps were carried out in the dark. Each array was dipped in a 50 ml Sarstedt tube filled with wash solution 1 (2X SSC, 0.1% SDS) to dislodge the coverslip. The arrays were washed twice for 5 min on a rotary table in fresh wash solution 1. The arrays were transferred to wash solution 2 (0.1X SSC) and washed twice for 1 min on a rotary table. Finally, the arrays were rinsed by immersion in RNase/DNase-free water to remove any residual salts, followed by brief immersion in 100 % isopropanol (Sigma-Aldrich) at room temperature and brief centrifugation at 1500 rpm for 2 min to dry the slides

scan_protocol: The arrays were scanned as soon as possible after washing. After hybridisation, fluorescence was measured using a confocal laser scanner (ScanArray Express HT, Perkin Elmer, USA). The high-resolution images were inspected using Genepix Pro v6.0.1.25 (Molecular Devices, USA).

data_processing: LIMMA (part of the Bioconductor R package) was applied to the design used in this experiment. The Cy5 channel signal was given the nominal label of F670 and the Cy3 channel signal was given the nominal label of F570 (and B670 and B570 for the corresponding channel backgrounds). Spots were weighted based on feature flagging in Genepix. If for any spot [% > B670+2SD2] < 50 or [% > B570+2SD2] < 50 or [Ratio of Medians (670/570)] > (10* [Rgn Ratio (670/570)]) or [Ratio of Medians (670/570)] < (0.1* [Rgn Ratio (670/570)] the spot was flagged as ‘bad’. In LIMMA this was converted to a weight of 0.1 whereas remaining good quality spots were given a weight of 1.0. Because there are two sub-arrays per slide and these are averaged, final weights can be 0.1 (both spots bad), 1.0 (both spots good) and 0.55 (one spot good and one spot bad). Median local background values were subtracted from median feature values, dye channels were swapped as appropriate and a printtiploess normalisation was applied (log2 fold ratios are given).

organism: Salmo salar

label_protocol: An indirect labelling method was used to attach Cy5 and Cy3 dyes to the cDNA. All target cDNAs were synthesised in one round. 10 Micrograms of both tester and reference total RNA was used per hybridisation. cDNA was generated by reverse transcription for 2 h at 42 oC using an anchored oligo VdT26, a random primer (V9), both at 1 micrograms/ml, and Stratascript RT enzyme (75U). Amino-allyl (aa) dUTP/dNTPs produced from a 20X stock (10 mM dCTP, dGTP, dATP and 5mM ea. of dTTP and dUTP) were incorporated into the cDNA. Contaminating enzymes and buffers were removed by purification with the Nucleospin Extract II Kit (Macherey-Nagel, Ger). Eluted cDNA was concentrated using a Vacufuge Concentrator 5301 at 42 oC (Eppendorf, Ger). The resulting cDNA pellets were resuspended in 5 microlitres of sodium bicarbonate (0.1M) (Sigma Aldrich). Cy dyes (Amersham Pharmacia Biotech, UK) were resuspended in 0.1M sodium bicarbonate and coupling to the cDNA took place in the dark for 2 h at room temperature. The labelled cDNA was again purified to remove any uncoupled Cy dye using the Nucleospin Extract II Kit.

growth_protocol: Fish were netted and transferred to an anaesthetic/sedative solution (1:1000 dilution of a stock 100 mg/ml ethyl 4-benzoate; Sigma-Aldrich). Blood samples were collected from the caudal vessels into EDTA (1.5 mg/ml blood; Sigma-Aldrich) and aprotinin (3000 KU/ml blood; Sigma-Aldrich) and fish were killed by spinal section. Fifty precocious male parr and fifty non-precocious male parr (sex determined on dissection) were sampled in January 2004. Length and weight measurements were taken. All tissues were removed to RNAlater or snap frozen in liquid nitrogen. Samples were stored at -80oC until RNA extraction.

extract_protocol: All samples were lysed and homogenized in TRIzol reagent (Invitrogen Life Technologies). Qiagen RNeasy midi columns and wash buffers were used to purify the RNA. All samples were DNase treated on-column using the Qiagen DNA-free DNase kit. The concentrations of the RNA samples were determined by UV spectrophotometry (Shimadzu UV-1601 / Eppendorf BioPhotometer) and checked for quality using the Agilent Bioanalyser-derived RNA integrity number (RIN) and by denaturing formaldehyde gel electrophoresis followed by northern blotting and subsequent analysis with a radiolabelled beta-actin probe.

tag: maturation

value: precocious

tag: developmental stage

value: Parr

value: Brain

value: non-precocious


title: TS070-D14-rep2

value: Male

tag: age

value: 5 weeks

tag: compound

value: D,L-Ethionine


title: TS071-D14-rep4

value: Liver

value: Vehicle

tag: dose

tag: administration

value: Aspirin


title: TS071-D14-rep3

value: gavage

tag: treatment time

value: 14 days

tag: vehicle


title: TS069-D14-rep2

value: Phenytoin (5,5-Diphenylhydantoin)


title: TS071-D14-rep2

value: Corn oil


title: TS071-D14-rep1


title: TS070-D14-rep3


title: TS068-D14-rep3

value: Diethylstilbestrol (DES)


title: TS069-D14-rep1


title: TS069-D14-rep3


title: TS067-D14-rep4

value: Acetamide


title: TS070-D14-rep1


title: TS069-D14-rep4

value: Water


title: TS068-D14-rep1


title: TS070-D14-rep4


title: TS068-D14-rep2


title: TS068-D14-rep4


title: TS066-D14-rep1

value: Tetrachloroethylene


title: TS066-D14-rep2


title: TS066-D14-rep4


title: TS067-D14-rep1


title: TS065-D14-rep1

value: MNNG


title: TS064-D14-rep3


title: TS064-D14-rep2


title: TS065-D14-rep2


title: TS065-D14-rep3


title: TS066-D14-rep3


title: TS063-D14-rep4

value: Benzo [a]pyrene (BP)


title: TS067-D14-rep2


title: TS063-D14-rep3


title: TS067-D14-rep3


title: TS064-D14-rep1


title: TS065-D14-rep4


title: TS064-D14-rep4


title: TS061-D14-rep3

value: 4-Acetylaminofluorene (4-AAF)


title: TS063-D14-rep1

value: Male


title: TS062-D14-rep4

value: 5 weeks

value: α-Tocopherol (Vitamin E)


title: TS061-D14-rep1

value: Liver


title: TS063-D14-rep2

value: Vehicle


title: TS061-D14-rep4


title: TS062-D14-rep2


title: TS060-D14-rep2

value: 2,5-Toluenediamine SO4


title: TS059-D14-rep1

value: gavage

value: p-Phenylenediamine 2HCl


title: TS059-D14-rep4

value: 14 days


title: TS062-D14-rep1

value: Corn oil


title: TS060-D14-rep3


title: TS062-D14-rep3


title: TS060-D14-rep4


title: TS058-D14-rep1

value: 2-Chloro-p-phenylenediamine SO4


title: TS057-D14-rep4

value: Lindane


title: TS058-D14-rep4


title: TS057-D14-rep2


title: TS059-D14-rep2

value: Water


title: TS058-D14-rep3


title: TS058-D14-rep2


title: TS057-D14-rep3


title: TS061-D14-rep2


title: TS056-D14-rep4

value: Chloroform


title: TS056-D14-rep3


title: TS056-D14-rep2


title: TS056-D14-rep1


title: TS060-D14-rep1


title: TS055-D14-rep2

value: Pentachloroethane


title: TS057-D14-rep1


title: TS055-D14-rep4


title: TS055-D14-rep3


title: TS055-D14-rep1


title: TS054-D14-rep2

value: Urethane


title: TS054-D14-rep1


title: TS054-D14-rep4


title: TS053-D14-rep4

value: Methapyrilene HCl


title: TS052-D14-rep2

value: Male

value: Tannic acid


title: TS053-D14-rep1

value: 5 weeks


title: TS051-D14-rep4

value: Liver

value: Trichloroacetic acid


title: TS053-D14-rep2

value: Vehicle


title: TS051-D14-rep3

value: gavage


title: TS052-D14-rep1


title: TS052-D14-rep3


title: TS051-D14-rep2


title: TS052-D14-rep4


title: TS054-D14-rep3


title: TS050-D14-rep4

value: Water (PH4)

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


title: TS050-D14-rep3

value: 14 days


title: TS050-D14-rep1


title: TS049-D14-rep4

value: Corn oil


title: TS051-D14-rep1


title: TS050-D14-rep2


title: TS049-D14-rep2


title: TS049-D14-rep3


title: TS049-D14-rep1


title: TS048-D14-rep3

value: 3-Methylcholanthrene (MC)


title: TS048-D14-rep2


title: TS047-D14-rep4

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


title: TS048-D14-rep4


title: TS044-D14-rep3

value: MeIQx


title: TS046-D14-rep1

value: Benz [a]anthracene (BA)


title: TS045-D14-rep2

value: PhIP


title: TS045-D14-rep1


title: TS044-D14-rep2


title: TS046-D14-rep3


title: TS047-D14-rep1


title: TS045-D14-rep3


title: TS047-D14-rep2


title: TS043-D14-rep3

value: 2-Acetylaminofluorene (2-AAF)


title: TS047-D14-rep3

value: Male


title: TS044-D14-rep4


title: TS043-D14-rep1


title: TS043-D14-rep2


title: TS045-D14-rep4


title: TS048-D14-rep1


title: TS042-D14-rep2

value: Water

value: N-Nitrosopiperidine


title: TS046-D14-rep4

value: 5 weeks

value: Liver


title: TS042-D14-rep4

value: Vehicle


title: TS043-D14-rep4

value: gavage


title: TS042-D14-rep3


title: TS042-D14-rep1


title: TS041-D14-rep2

value: N-Nitrosodimethylamine (DMN)


title: TS041-D14-rep4


title: TS040-D14-rep3

tag: time

value: Gum arabic

value: Lithocholic acid


title: TS040-D14-rep4

value: 14 days


title: TS041-D14-rep3


title: TS039-D14-rep4

value: Corn oil

value: Iodoform


title: TS039-D14-rep3


title: TS044-D14-rep1

value: MeIQx


title: TS038-D14-rep2

value: Benzoin


title: TS039-D14-rep1


title: TS040-D14-rep1


title: TS041-D14-rep1


title: TS040-D14-rep2


title: TS037-D14-rep2

value: Quercetin


title: TS038-D14-rep4


title: TS039-D14-rep2


title: TS038-D14-rep3


title: TS037-D14-rep1


title: TS036-D14-rep2


title: TS036-D14-rep4


title: TS035-D14-rep3

value: 1% CMC


title: TS036-D14-rep1

value: Male


title: TS036-D14-rep3


title: TS037-D14-rep3


title: TS035-D14-rep4


title: TS038-D14-rep1


title: TS034-D14-rep2

value: D,L-Menthol


title: TS035-D14-rep2


title: TS037-D14-rep4


title: TS034-D14-rep3


title: TS034-D14-rep1


title: TS032-D14-rep3

value: Water


title: TS033-D14-rep1

value: 5 weeks

value: 2-Chloromethylpyridine HCl


title: TS034-D14-rep4

value: Liver

value: Vehicle


title: TS033-D14-rep3

value: gavage


title: TS032-D14-rep1


title: TS033-D14-rep2


title: TS032-D14-rep4


title: TS032-D14-rep2


title: TS033-D14-rep4


title: TS031-D14-rep3

value: MC

value: Acetaminophen（Paracetamol）


title: TS031-D14-rep2

value: 14 days


title: TS035-D14-rep1


title: TS030-D14-rep1

value: Thioacetamide


title: TS029-D14-rep4

value: Methyl carbamate


title: TS030-D14-rep4


title: TS031-D14-rep4


title: TS031-D14-rep1


title: TS030-D14-rep2


title: TS028-D14-rep2

value: Corn oil

value: Furan


title: TS028-D14-rep4


title: TS029-D14-rep1


title: TS027-D14-rep4


title: TS029-D14-rep3


title: TS026-D14-rep4

value: 1,4-Dichlorobenzene (DCB)


title: TS028-D14-rep3


title: TS029-D14-rep2


title: TS028-D14-rep1


title: TS026-D14-rep3


title: TS027-D14-rep3


title: TS030-D14-rep3


title: TS026-D14-rep1


title: TS025-D14-rep4

value: Safrole


title: TS027-D14-rep1

value: Male


title: TS027-D14-rep2


title: TS025-D14-rep1


title: TS025-D14-rep3


title: TS026-D14-rep2


title: TS024-D14-rep1

value: D-Limonene


title: ZR75-30

city: Rotterdam

first: Muhammad

last: Riaz

state: Rotterdam

address: Dr. Molewaterplein 50

department: Medical Oncology

country: Netherlands

institute: Erasmuc Medical Centre

description: Gene expression data of breast cancer cell line

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing: Samples were analyzed using Genotyping console. RMA expression values were quantile normalized

label: Biotin

organism: Homo sapiens

source_name: Breast cancer cell lines

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

growth_protocol: All breast cancer cell lines are cultured under normal culturing conditions (RPMI-10%FBS) to optimal cell densities.

extract_protocol: total RNA was extracted using Trizol and purified over Qiagen Rneasy columns

tag: cell line


title: SUM52


title: TS023-D14-rep4

value: Butylated hydroxyanisole (BHA)


title: UACC893


title: TS023-D14-rep3

value: 5 weeks


title: TS024-D14-rep3


title: ZR75-1


title: TS024-D14-rep2


title: TS024-D14-rep4


title: TS023-D14-rep2


title: T47D


title: UACC812


title: TS025-D14-rep2


title: SUM225


title: SUM44


title: SUM185


title: SUM229


title: SUM149


title: SUM1315


title: SUM159


title: TS023-D14-rep1


title: Patient 130 with adenocarcinoma

city: Nagoya

first: Takashi

last: Takahashi

state: Aichi

address: 1-1 Kanokoden, Chikusa-ku

institute: Aichi Cancer Center

description: dataset II

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.

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 II

tag: Age

tag: Sex

value: M

tag: Histology

value: AD

tag: Smoking (BI)

tag: TNM (Pathological)

tag: Stage (Pathological )

value: IB

tag: Status

value: Dead

tag: Survival (days)

tag: Evidence of relapse

value: Y

tag: Site of relapse

value: Derm (skin), med LN, bone

tag: EGFR status

value: Wt

tag: K-ras Status

value: Mut

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: SK-BR-7


title: TS022-D14-rep4

tag: gender

tag: age

tag: strain

tag: tissue

value: Liver

tag: compound

value: Vehicle

tag: dose

tag: administration

value: gavage

tag: time

value: 14 days

tag: vehicle

value: Corn oil

value: Trichloroethylene

tag: treatment


title: TS022-D14-rep2

value: Male


title: Patient 127 with adenocarcinoma

description: dataset II

tag: Annotation

tag: Cohort

tag: Age

tag: Sex

tag: Histology

tag: Smoking (BI)

tag: TNM (Pathological)

tag: Stage (Pathological )

value: IA

tag: Status

value: Alive

value: N

tag: Site of relapse:


title: SUM190

tag: cell line


title: TS022-D14-rep1

tag: gender

tag: age

value: 5 weeks

tag: strain

tag: tissue

tag: compound


title: TS022-D14-rep3

tag: dose

tag: administration

tag: time

tag: vehicle

tag: treatment


title: Patient 128 with adenocarcinoma

description: dataset II

tag: Annotation

tag: Cohort

value: dataset II

tag: Age

tag: Sex

value: F

tag: Histology

value: AD

value: IB

tag: Survival (days)

tag: Evidence of relapse

tag: Site of relapse

value: PM

tag: EGFR status

tag: K-ras Status

tag: p53 Status


title: Patient 129 with adenocarcinoma

description: dataset II

value: M

tag: Smoking (BI)

tag: TNM (Pathological)

tag: Stage (Pathological )

tag: Status

value: Dead

value: Y

value: Wt


title: SK-BR-5

tag: cell line


title: Patient 125 with adenocarcinoma

description: dataset II

value: Mut


title: TS021-D14-rep4

tag: gender

tag: age

tag: strain

tag: tissue

value: Liver

tag: compound

value: Vehicle

tag: dose

tag: administration

value: gavage

tag: time

value: 14 days

tag: vehicle

value: Corn oil

value: α-Hexachlorocyclohexane(α-HCH)

tag: treatment


title: Patient 126 with adenocarcinoma

description: dataset II

tag: Annotation

tag: Cohort

tag: Age

tag: Sex

tag: Histology

value: IA

tag: Survival (days)

tag: Evidence of relapse

tag: Site of relapse

value: Brain

tag: EGFR status

tag: K-ras Status


title: Patient 124 with adenocarcinoma

description: dataset II

value: dataset II

tag: Smoking (BI)

tag: TNM (Pathological)

tag: Stage (Pathological )

tag: Status

value: Alive

value: N

tag: Site of relapse:

tag: p53 Status


title: Patient 121 with adenocarcinoma

description: dataset II

value: AD

value: IB


title: OCUB-F

tag: cell line

value: OCUB-F


title: Patient 123 with adenocarcinoma

description: dataset II

tag: Annotation

value: F


title: Patient 122 with adenocarcinoma

description: dataset II

tag: Cohort

value: Wt


title: Patient 120 with adenocarcinoma

description: dataset II

tag: Age

value: Mut


title: Patient 119 with adenocarcinoma

description: dataset II

tag: Sex


title: OCUB-M

value: OCUB-M


title: Patient 118 with adenocarcinoma

description: dataset II

tag: Histology

value: Dead


title: TS021-D14-rep2

tag: gender

value: Male

tag: age

value: 5 weeks

tag: strain

tag: tissue

value: Liver

tag: compound

value: Vehicle

tag: dose

tag: administration

value: gavage

tag: time

tag: vehicle

tag: treatment


title: TS021-D14-rep3

value: 14 days

value: Corn oil

value: α-Hexachlorocyclohexane(α-HCH)


title: Patient 117 with adenocarcinoma

description: dataset II

value: dataset II

value: M

tag: Smoking (BI)

tag: TNM (Pathological)

tag: Stage (Pathological )

value: IA

tag: Status

value: Alive

tag: Survival (days)

tag: Evidence of relapse

value: N

tag: Site of relapse:

tag: EGFR status

tag: K-ras Status

tag: p53 Status


title: MPE600

tag: cell line


title: MDA-MB-468


title: TS021-D14-rep1

tag: gender

tag: age

tag: strain

tag: tissue

tag: compound


title: MDA-MB-453


title: TS020-D14-rep4

tag: dose

tag: administration

tag: time

tag: vehicle

value: Hexachlorobenzene (HCB)

tag: treatment


title: Patient 115 with adenocarcinoma

description: dataset II

tag: Annotation

tag: Cohort

tag: Age

tag: Sex

value: F

tag: Histology

value: AD

tag: Smoking (BI)

tag: TNM (Pathological)

tag: Stage (Pathological )

tag: Status

tag: Survival (days)

value: Mut

value: Wt


title: Patient 114 with adenocarcinoma

description: dataset II

tag: Evidence of relapse

tag: Site of relapse:

tag: EGFR status

tag: K-ras Status

tag: p53 Status


title: Patient 116 with adenocarcinoma

description: dataset II

value: Dead

value: Y

tag: Site of relapse

value: PM


title: MDA-MB-436

tag: cell line


title: Patient 112 with adenocarcinoma

description: dataset II

tag: Annotation


title: Patient 111 with adenocarcinoma

description: dataset II

tag: Cohort

value: IB


title: MDA-MB-435


title: Patient 113 with adenocarcinoma

description: dataset II

tag: Age


title: TS020-D14-rep3

tag: gender

value: Male

tag: age

value: 5 weeks

tag: strain

tag: tissue

value: Liver

tag: compound

value: Vehicle

tag: dose

tag: administration

value: gavage

tag: time

value: 14 days

tag: vehicle

tag: treatment


title: TS020-D14-rep2

value: Corn oil


title: TS020-D14-rep1


title: Patient 108 with adenocarcinoma

description: dataset II

value: dataset II

tag: Sex

value: M

tag: Histology

tag: Smoking (BI)

tag: TNM (Pathological)

tag: Stage (Pathological )

value: IA

tag: Status

value: Alive

tag: Survival (days)

tag: Evidence of relapse

value: N

tag: Site of relapse:

tag: EGFR status

tag: K-ras Status


title: Patient 109 with adenocarcinoma

description: dataset II

tag: Annotation

tag: Cohort

tag: Age

value: F

value: AD

tag: Site of relapse

value: Mut

value: Wt

tag: p53 Status


title: Patient 110 with adenocarcinoma

description: dataset II

value: Dead

value: Y

value: PM


title: Patient 106 with adenocarcinoma

description: dataset II

value: Brain


title: TS019-D14-rep4

tag: gender

value: Male

tag: age

value: 5 weeks

tag: strain

tag: tissue

value: Liver

tag: compound

value: Vehicle

tag: dose

tag: administration

tag: time

tag: vehicle

value: Ethinylestradiol

tag: treatment


title: Patient 103 with adenocarcinoma

description: dataset II

value: dataset II

tag: Sex

value: M

tag: Histology

tag: Smoking (BI)

tag: TNM (Pathological)

tag: Stage (Pathological )

value: IB

tag: Status

tag: Survival (days)

tag: Evidence of relapse

tag: Site of relapse:

tag: EGFR status


title: MDA-MB-415

tag: cell line


title: MDA-MB-330


title: Patient 104 with adenocarcinoma

description: dataset II

tag: Annotation

tag: Cohort

tag: Age

value: Alive

value: N

tag: K-ras Status

tag: p53 Status


title: Patient 107 with adenocarcinoma

description: dataset II

value: AD

tag: Site of relapse

value: Bone


title: TS019-D14-rep3

tag: gender

tag: age

tag: strain

tag: tissue

tag: compound

tag: dose

tag: administration

value: gavage

tag: time

value: 14 days

tag: vehicle

value: Corn oil

tag: treatment


title: Patient 102 with adenocarcinoma

description: dataset II

tag: Sex

value: F

tag: Histology

tag: Smoking (BI)

tag: TNM (Pathological)

tag: Stage (Pathological )

value: IA

tag: Status

tag: Survival (days)

tag: Evidence of relapse

tag: Site of relapse:

tag: EGFR status

value: Mut

value: Wt


title: Patient 105 with adenocarcinoma

description: dataset II

tag: Annotation

tag: Cohort

tag: Age

tag: K-ras Status

tag: p53 Status


title: MDA-MB-361

tag: cell line


title: TS019-D14-rep2

tag: gender

value: Male

tag: age

value: 5 weeks

tag: strain

tag: tissue

value: Liver

tag: compound

tag: dose

tag: administration

tag: time

tag: vehicle

tag: treatment


title: TS019-D14-rep1

value: Vehicle

value: Ethinylestradiol


title: Patient 101 with adenocarcinoma

description: dataset II

value: dataset II

tag: Sex

value: M

tag: Histology

tag: Smoking (BI)

tag: TNM (Pathological)

tag: Stage (Pathological )

value: IB

tag: Status

tag: Survival (days)

tag: Evidence of relapse

tag: Site of relapse:

tag: EGFR status


title: MDA-MB-231

tag: cell line


title: TS018-D14-rep4

tag: gender

tag: age

tag: strain

tag: tissue

tag: compound

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


title: MDA-MB-175VIII


title: Patient 088 with adenocarcinoma

description: dataset I

tag: Annotation

tag: Cohort

value: dataset I

tag: Age

value: AD

value: IIIA

value: Dead

value: Y

tag: Site of relapse

value: LN (neck)

tag: K-ras Status

tag: p53 Status


title: MDA-MB-157


title: Patient 090 with adenocarcinoma

description: dataset I

tag: Sex

tag: Histology

tag: Smoking (BI)

tag: TNM (Pathological)

tag: Stage (Pathological )

value: IA

tag: Status

value: Local rec.


title: SK-BR-3

tag: cell line


title: Patient 089 with adenocarcinoma

description: dataset I

tag: Survival (days)

tag: Evidence of relapse

value: Brain

tag: EGFR status

value: Wt


title: Patient 086 with adenocarcinoma

description: dataset I

value: F

value: Mut


title: Patient 087 with adenocarcinoma

description: dataset I

value: IIB

value: PM, Liver


title: MDA-MB-134VI


title: MCF7


title: Patient 085 with adenocarcinoma

description: dataset I

value: M

value: Alive

value: N

tag: Site of relapse:


title: TS018-D14-rep3

tag: gender

value: Male

tag: age

value: 5 weeks

tag: strain

tag: tissue

value: Liver

tag: compound

value: Vehicle

tag: dose

tag: administration

value: gavage

tag: time

value: 14 days

tag: vehicle

value: Corn oil

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

tag: treatment


title: TS018-D14-rep2


title: TS018-D14-rep1


title: TS017-D14-rep4

value: Dieldrin


title: TS017-D14-rep3


title: TS017-D14-rep2


title: TS017-D14-rep1


title: TS016-D14-rep4

value: Dichlorodiphenyltrichloroethane (DDT)


title: Patient 080 with adenocarcinoma

description: dataset I

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: IB

tag: K-ras Status

value: Wt

tag: p53 Status


title: Patient 074 with adenocarcinoma

description: dataset I

value: M

value: IA

tag: Status

value: Alive

tag: Survival (days)

tag: Evidence of relapse

tag: Site of relapse:

tag: EGFR status

value: Mut


title: EVSA-T

tag: cell line

value: EVSA-T


title: Patient 077 with adenocarcinoma

description: dataset I

value: N


title: Patient 079 with adenocarcinoma

description: dataset I

value: IIB

value: Dead

value: Y

tag: Site of relapse

value: Bone


title: CAMA-1


title: HCC1937


title: Patient 071 with adenocarcinoma

description: dataset I

tag: Annotation


title: Hs578T


title: DU4475


title: Patient 083 with adenocarcinoma

description: dataset I

tag: Cohort

value: IIA

value: Brain


title: BT474


title: Patient 076 with adenocarcinoma

description: dataset I

value: dataset I

tag: Age

value: Local rec.,Brain


title: BT483


title: Patient 070 with adenocarcinoma

description: dataset I

tag: Sex

value: F

value: AD

value: IIIA


title: Patient 068 with adenocarcinoma

description: dataset I

value: M

tag: Histology

value: PM?bone

value: Wt


title: Patient 078 with adenocarcinoma

description: dataset I

tag: Smoking (BI)

value: IB

value: PM


title: Patient 081 with adenocarcinoma

description: dataset I

tag: TNM (Pathological)

value: Mut


title: BT549


title: Patient 072 with adenocarcinoma

description: dataset I

tag: Stage (Pathological )

value: Alive

value: N


title: Patient 084 with adenocarcinoma

description: dataset I

value: Dead

value: Y

tag: K-ras Status


title: Patient 069 with adenocarcinoma

description: dataset I

value: IA

tag: p53 Status


title: TS016-D14-rep1

tag: gender

value: Male

tag: age

value: 5 weeks

tag: strain

tag: tissue

value: Liver

tag: compound

value: Vehicle

tag: dose

tag: administration

value: gavage

tag: time

value: 14 days

tag: vehicle

value: Corn oil

value: Dichlorodiphenyltrichloroethane (DDT)

tag: treatment


title: Patient 073 with adenocarcinoma

description: dataset I

tag: Annotation

tag: Cohort

value: dataset I

tag: Age

tag: Sex

value: F

value: AD

tag: Status

tag: Survival (days)

tag: Evidence of relapse

tag: Site of relapse

value: local rec

tag: EGFR status

value: Wt


title: TS016-D14-rep2

tag: gender

tag: age

tag: strain


title: TS016-D14-rep3

tag: tissue

tag: compound

tag: dose


title: Patient 075 with adenocarcinoma

description: dataset I

value: M

tag: Histology

tag: Smoking (BI)

tag: TNM (Pathological)

tag: Stage (Pathological )

value: IB

value: Local rec.

tag: K-ras Status

tag: p53 Status

value: Mut


title: TS015-D14-rep4

value: Male

tag: administration

tag: time

tag: vehicle

value: Aldrin

tag: treatment


title: Patient 082 with adenocarcinoma

description: dataset I

tag: Annotation

tag: Cohort

tag: Age

tag: Sex

value: IA

tag: Status

value: Alive

tag: Survival (days)

tag: Evidence of relapse

value: N

tag: Site of relapse:

tag: EGFR status


title: BT20

tag: cell line


title: TS015-D14-rep3

tag: gender

tag: age

value: 5 weeks

tag: strain

tag: tissue

value: Liver

tag: compound

value: Vehicle

tag: dose

value: gavage

value: 14 days


title: TS015-D14-rep2

tag: administration

tag: time

tag: vehicle

value: Corn oil

tag: treatment


title: TS015-D14-rep1


title: TS014-D14-rep3

value: Water

value: N-Nitrosomorpholine


title: TS014-D14-rep2


title: TS014-D14-rep4


title: pTN11 at 3h, biological rep1

city: Kawasaki

first: Yoko

last: Asakura

state: Kanagawa

address: 1-1 Suzuki-cho Kawasaki-ku

department: Institule of Life Sciences

institute: Ajinomoto

description: pTN11, Genotype: r-m+

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hr at 45C on GeneChip E.coli antisense genome array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Agilent Gene Array Scanner.

data_processing: The data were analyzed with GeneChip Operation Software 1.0 (GCOS 1.0) using Affymetrix default analysis settings.

organism: Escherichia coli

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 microgram of total RNA.

growth_protocol: The cells were cultured at 30 ℃ in LB with ampicillin until the optical density at 660nm (OD) reached to 0.3. The antibiotics were then removed and the temperature was shifted up to 42 ℃ to block the plasmid replication. The culture was diluted 100-folds when its OD660 reached 0.5 (2h after the temperature shift). The cells were harvested and subjected to transcriptome analysis before (0h) and 1 h, 1 h 50 min, and 3 h after the temperature shift (OD=0.5).

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

treatment_protocol: The cells were harvested by centrifugation, and stabilized using RNA Protect Bacteria Reagent (Qiagen) in accordance with the manufacturer’s protocols (see http://www1.qiagen.com).

tag: Strain

value: MG1655 / pTN11, Genotype:r-m+


title: pHSG415 at 3h, biological rep2

description: pHSG415 (vector), Genotype: r-m-

value: MG1655 / pHSG415 (vector), Genotype:r-m-


title: pHSG415 at 3h, biological rep1

description: pHSG415 (vector), Genotype: r-m-


title: pTN9 at 3h, biological rep2

description: pTN9, Genotype: r+m+

value: MG1655 / pTN9, Genotype:r+m+


title: Patient 064 with adenocarcinoma

description: dataset I

tag: Annotation

tag: Cohort

value: dataset I

tag: Age

tag: Sex

value: M

tag: Histology

value: AD

tag: Smoking (BI)

tag: TNM (Pathological)

tag: Stage (Pathological )

tag: Status

value: Wt

tag: K-ras Status

tag: p53 Status


title: Patient 067 with adenocarcinoma

description: dataset I

value: F

value: IA

value: Alive

tag: Survival (days)

tag: Evidence of relapse

tag: Site of relapse:

tag: EGFR status


title: pTN11 at 3h, biological rep2

description: pTN11, Genotype: r-m+


title: Patient 065 with adenocarcinoma

description: dataset I

value: N

value: Mut


title: Patient 061 with adenocarcinoma

description: dataset I


title: Patient 063 with adenocarcinoma

description: dataset I

value: Dead

value: Y

tag: Site of relapse

value: PM


title: Patient 062 with adenocarcinoma

description: dataset I

value: IIA

value: Liver


title: Patient 058 with adenocarcinoma

description: dataset I

value: Brain


title: pHSG415 at 1h 50m, biological rep2

description: pHSG415 (vector), Genotype: r-m-

tag: Strain

value: MG1655 / pHSG415 (vector), Genotype:r-m-


title: Patient 066 with adenocarcinoma

description: dataset I

tag: Annotation


title: TS014-D14-rep1

tag: gender

value: Male

tag: age

value: 5 weeks

tag: strain

tag: tissue

tag: compound

value: Vehicle

tag: dose

tag: administration

value: gavage

tag: time

value: 14 days

tag: vehicle

value: Water

value: N-Nitrosomorpholine

tag: treatment


title: pTN9 at 3h, biological rep1

description: pTN9, Genotype: r+m+

value: MG1655 / pTN9, Genotype:r+m+


title: Patient 056 with adenocarcinoma

description: dataset I

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: IB

tag: Status

tag: Survival (days)

value: Wt

tag: K-ras Status

tag: p53 Status


title: Patient 059 with adenocarcinoma

description: dataset I

tag: Annotation

value: M

value: Alive

tag: Evidence of relapse

value: N

tag: Site of relapse:

tag: EGFR status


title: Patient 057 with adenocarcinoma

description: dataset I

value: Dead

value: Y

tag: Site of relapse

value: Local rec.

value: Mut


title: pHSG415 at 1h 50m, biological rep1

description: pHSG415 (vector), Genotype: r-m-

tag: Strain

value: MG1655 / pHSG415 (vector), Genotype:r-m-


title: Patient 060 with adenocarcinoma

description: dataset I

tag: Cohort

value: LN (neck)


title: TS013-D14-rep4

tag: gender

value: Male

tag: age

value: 5 weeks

tag: strain

tag: tissue

value: Liver

tag: compound

value: Vehicle

tag: dose

tag: administration

value: gavage

tag: time

value: 14 days

tag: vehicle

value: Corn oil

tag: treatment


title: TS013-D14-rep3


title: TS013-D14-rep2


title: pTN11 at 1h 50m, biological rep2

description: pTN11, Genotype: r-m+

value: MG1655 / pTN11, Genotype:r-m+


title: TS013-D14-rep1


title: TS012-D14-rep4

value: 1% CMC


title: pTN9 at 1h 50m, biological rep2

description: pTN9, Genotype: r+m+

value: MG1655 / pTN9, Genotype:r+m+


title: pTN9 at 1h 50m, biological rep1

description: pTN9, Genotype: r+m+


title: Patient 054 with adenocarcinoma

description: dataset I

tag: Annotation

value: dataset I

tag: Age

tag: Sex

value: F

tag: Histology

value: AD

tag: Smoking (BI)

tag: TNM (Pathological)

tag: Stage (Pathological )

value: IIIB

tag: Status

tag: Survival (days)

value: N

value: Wt

tag: K-ras Status

tag: p53 Status


title: TS012-D14-rep3

tag: gender

tag: age

tag: strain

tag: tissue

tag: compound


title: pTN11 at 1h 50m, biological rep1

description: pTN11, Genotype: r-m+

tag: Strain


title: TS012-D14-rep1

tag: dose

tag: administration

tag: time

tag: vehicle

tag: treatment


title: Patient 053 with adenocarcinoma

description: dataset I

tag: Annotation

tag: Cohort

tag: Age

tag: Sex

value: M

tag: Histology

tag: Smoking (BI)

tag: TNM (Pathological)

value: IIIA

value: Dead

tag: Evidence of relapse

value: Y

tag: Site of relapse

value: LN (neck)

tag: EGFR status

value: Mut


title: Patient 052 with adenocarcinoma

description: dataset I

tag: Stage (Pathological )

value: IB

tag: Status

value: Alive

tag: Survival (days)

tag: Site of relapse:

tag: K-ras Status

tag: p53 Status


title: Patient 050 with adenocarcinoma

description: dataset I

value: Unknown


title: TS012-D14-rep2

tag: gender

value: Male

tag: age

value: 5 weeks

tag: strain

tag: tissue

value: Liver

tag: compound

value: Vehicle

tag: dose

tag: administration

value: gavage

tag: time

value: 14 days

tag: vehicle

tag: treatment

value: 1% CMC


title: Patient 055 with adenocarcinoma

description: dataset I

tag: Annotation

tag: Cohort

value: dataset I

tag: Age

tag: Sex

value: F

tag: Histology

value: AD

tag: Smoking (BI)

tag: TNM (Pathological)

tag: Evidence of relapse

value: N

tag: EGFR status

value: Wt


title: Patient 051 with adenocarcinoma

description: dataset I

tag: Stage (Pathological )

tag: Status

tag: Survival (days)

tag: Site of relapse:

tag: K-ras Status

tag: p53 Status


title: TS011-D14-rep4

tag: gender

tag: age

tag: strain

tag: tissue

tag: compound

tag: dose

tag: administration

tag: time

tag: vehicle

value: Water

value: Diethylnitrosamine (DEN)


title: pTN11 at 1h, biological rep2

description: pTN11, Genotype: r-m+

tag: Strain

value: MG1655 / pTN11, Genotype:r-m+


title: pHSG415 at 1h, biological rep2

description: pHSG415 (vector), Genotype: r-m-

value: MG1655 / pHSG415 (vector), Genotype:r-m-


title: Patient 049 with adenocarcinoma

description: dataset I

tag: Annotation

tag: Cohort

tag: Age

tag: Sex

tag: Histology

tag: Smoking (BI)

tag: TNM (Pathological)

value: IIIB

value: Dead

tag: Evidence of relapse

value: Y

tag: Site of relapse

value: Brain

tag: EGFR status


title: pHSG415 at 1h, biological rep1

description: pHSG415 (vector), Genotype: r-m-


title: pTN11 at 1h, biological rep1

description: pTN11, Genotype: r-m+


title: TS011-D14-rep2

tag: gender

value: Male

tag: age

value: 5 weeks

tag: strain

tag: tissue

value: Liver

value: Vehicle

tag: treatment


title: Patient 048 with adenocarcinoma

description: dataset I

value: dataset I

tag: Stage (Pathological )

value: IA

tag: Status

value: Alive

tag: Survival (days)

tag: Site of relapse:

value: Mut

tag: K-ras Status

tag: p53 Status


title: pHSG415 at 0h, biological rep2

description: pHSG415 (vector), Genotype: r-m-

tag: Strain


title: Patient 047 with adenocarcinoma

description: dataset I

tag: Annotation

tag: Cohort

tag: Age

tag: Sex

value: M

tag: Histology

value: AD

tag: Smoking (BI)

value: IIA

value: N

value: Wt


title: TS010-D14-rep3

tag: gender

tag: age

tag: compound

tag: dose

tag: administration

value: gavage

tag: time

value: 14 days

tag: vehicle

value: Water

value: L-Ascorbic acid


title: pTN9 at 1h, biological rep1

description: pTN9, Genotype: r+m+

value: MG1655 / pTN9, Genotype:r+m+


title: TS011-D14-rep3

value: Male

value: 5 weeks

tag: strain

tag: tissue

value: Diethylnitrosamine (DEN)

tag: treatment


title: pTN11 at 0h, biological rep1

description: pTN11, Genotype: r-m+

tag: Strain

value: MG1655 / pTN11, Genotype:r-m+


title: Patient 046 with adenocarcinoma

description: dataset I

tag: Annotation

value: dataset I

value: F

tag: TNM (Pathological)

tag: Stage (Pathological )

value: IIB

tag: Status

tag: Survival (days)

tag: Evidence of relapse

value: Y

tag: Site of relapse

value: Bone

tag: EGFR status

tag: K-ras Status

tag: p53 Status


title: pTN11 at 0h, biological rep2

description: pTN11, Genotype: r-m+


title: TS010-D14-rep2

tag: gender

tag: age

value: Liver

tag: compound

value: Vehicle

tag: dose

tag: administration


title: pHSG415 at 0h, biological rep1

description: pHSG415 (vector), Genotype: r-m-

value: MG1655 / pHSG415 (vector), Genotype:r-m-


title: Patient 045 with adenocarcinoma

description: dataset I

tag: Cohort

tag: Age

tag: Sex

tag: Histology

value: AD

tag: Smoking (BI)

value: IB

value: Alive

value: Adrenal

value: Mut

value: Wt


title: TS010-D14-rep4

value: Male

value: 5 weeks

tag: strain

tag: tissue

value: gavage

tag: time

value: 14 days

tag: vehicle

value: Water

value: L-Ascorbic acid

tag: treatment


title: TS011-D14-rep1

value: Diethylnitrosamine (DEN)


title: Patient 042 with adenocarcinoma

description: dataset I

tag: Annotation

value: dataset I

value: M

tag: TNM (Pathological)

tag: Stage (Pathological )

value: IA

tag: Status

tag: Survival (days)

tag: Evidence of relapse

value: N

tag: Site of relapse:

tag: EGFR status

tag: K-ras Status


title: pTN9 at 0h, biological rep2

description: pTN9, Genotype: r+m+

tag: Strain

value: MG1655 / pTN9, Genotype:r+m+


title: pTN9 at 0h, biological rep1

description: pTN9, Genotype: r+m+


title: Patient 044 with adenocarcinoma

description: dataset I

tag: Cohort

tag: Age

tag: Sex

value: F

tag: Histology

value: AD

value: IIIA

value: Dead

value: Y

tag: Site of relapse

value: PM

tag: p53 Status


title: TS010-D14-rep1

tag: gender

value: Male

tag: age

value: 5 weeks

tag: strain

tag: tissue

value: Liver

tag: compound

value: Vehicle

tag: dose

tag: administration

tag: time

tag: vehicle

tag: treatment


title: Patient 041 with adenocarcinoma

description: dataset I

tag: Annotation

tag: Smoking (BI)

tag: TNM (Pathological)

tag: Stage (Pathological )

tag: Status

tag: Survival (days)

tag: Evidence of relapse

tag: EGFR status

value: Mut

tag: K-ras Status

value: Wt


title: TS009-D14-rep4

tag: gender

tag: age

tag: strain

value: gavage

value: 14 days

value: Water

value: D-Mannitol


title: TS009-D14-rep3

tag: tissue

tag: compound

tag: dose


title: Patient 040 with adenocarcinoma

description: dataset I

tag: Cohort

value: dataset I

tag: Age

tag: Sex

tag: Histology

tag: Site of relapse

value: Bone

tag: p53 Status


title: TS009-D14-rep2

tag: administration

tag: time

tag: vehicle

tag: treatment


title: TS009-D14-rep1


title: Patient 038 with adenocarcinoma

description: dataset I

tag: Annotation

value: F

value: AD

tag: Smoking (BI)

tag: TNM (Pathological)

tag: Stage (Pathological )

value: IB

tag: Status

tag: Survival (days)

tag: Evidence of relapse

value: Local rec.

tag: EGFR status

tag: K-ras Status


title: Patient 039 with adenocarcinoma

description: dataset I

tag: Cohort

tag: Age

tag: Sex

value: Alive

value: N

tag: Site of relapse:


title: TS008-D14-rep1

tag: gender

value: Male

tag: age

value: 5 weeks

tag: strain

tag: tissue

tag: compound

tag: dose

tag: administration

value: Phenobarbital


title: Patient 037 with adenocarcinoma

description: dataset I

tag: Annotation

tag: Histology

tag: Smoking (BI)

tag: TNM (Pathological)

tag: Stage (Pathological )

value: IA

value: Y

tag: Site of relapse

value: PM

value: Mut

tag: p53 Status


title: TS008-D14-rep4

value: Liver

value: Vehicle

value: gavage

tag: time

value: 14 days

tag: vehicle

value: Water

tag: treatment


title: TS008-D14-rep2

tag: gender


title: H37Rv sigB null mutant control vs 0.05% SDS for 60 min rep 6

city: Aurora

first: Martin

middle: I

last: Voskuil

state: CO

department: Microbiology

institute: University of Colorado Denver

description: Image: http://smd.stanford.edu/MicroArray/gifs/2009-05/83607.gif

hyb_protocol: not provided

scan_protocol: scanner model: GenePix 4000B

data_processing: VALUE is Log (base 2) of the ratio of the mean of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)

organism: Mycobacterium tuberculosis

source_name: Strain: H37Rv sigB null mutant; Treatment: Control

label_protocol: TB-Synthesis and Labeling of cDNA SKlab 01; 1. Bring 0.5-5 ug RNA (Typically 3 ug) to 11 ul and add 2 ul (~2 mg/ml) random hexamers. 2. Heat 10 min at 65C (or 2 min at 98C), snap cool on ice. 10 rxns 20 rxns 3. Add 11ul 5.0 ul 5X First-Strand buffer (51) (102) 2.5 ul 100 mM DTT (25.5) (51) 2.0 ul dNTP (5 mM A,G,C and 0.2 mM T) (20.5) (41) 1.5 ul Cy3 or Cy5 (Typically use Cy5 for sample that should change) (15.3) (30.6) Then add 1.2-1.8 ul Stratascript or 0.8-1.2 ul Superscript II RTase. 4. Incubate 10m at 25C followed by 90m at 42C in PCR machine. Can freeze or leave at 4C o/n.; Protocol Type = Labeling; Performer: Martin,,Voskuil

extract_protocol: not provided

treatment_protocol: Parameter Time = 60 min; Parameter Compound Based Treatment = "Control, no treatment "; Performer: Martin,,Voskuil

value: H37Rv sigB null mutant

value: Control

source_name: Strain: H37Rv sigB null mutant; Treatment: 0.05% SDS for 60 min

label_protocol: Parameter Amount of extract labeled = 3ug of total RNA; Parameter Type of label = Cy5; Performer: Martin,,Voskuil

growth_protocol: Parameter Starting OD = 0.2; Parameter Elapsed Time = 60 min; Parameter Culture Volume = 40 ml; Parameter Growth Temperature = 37oC; Parameter Culture Synchrony = Unsynchronized; Parameter Media = Middlebrook 7H9 supplemented with albumin-dextrose complex (ADC) and 0.01% Tween 80

extract_protocol: TB-RNA Isolation and Purification SKlab 01; 1. Centrifuge 20-30 ml of early- to mid-log culture (O.D. 0.1-0.2) 4 min at 3700 rpm, at RT-37C. Pipette off supernatant and immediately freeze on dry ice and store at ?80C. 2. Add 1 ml Trizol (Gibco-BRL) to each of 4-8 pellets, suspend first pellet by vortexing,while other pellets are still frozen. Add suspension to 0.4 ml glass beads in a 2 ml screw cap tube. 3. Shake 30s at maximum speed in bead beater. Suspend next pellet and add to glass beads. Apply next sample to bead beater. Repeat bead beating two more times with each sample.Continue to periodically invert samples for at least 5 min in Trizol. 4. Centrifuge samples 45s at max speed, remove Trizol solution to a 2 ml screw cap tube containing half of the Heavy Phase Lock Gel I, supplied by 5 Prime 3 Prime, Inc. in 1.5 ml tubes and transferred with sterile stick to 2 ml tubes, and 300 ul Chloroform:isoamyl alcohol (24:1). Invert rapidly for 15s, and continue inverting periodically for 2 min.a 5. Centrifuge 5-10m, remove aqueous layer (540 ul) and add to a 1.5 ml tube containing 270 ul isopropanol then add 270 ul high salt solution (0.8M Na Citrate, 1.2M NaCl). Invert several times and spray with Staphene and remove from the P3. Typically ppted at 4C O/N. 6. Centrifuge 10m at 4C and remove isopropanol. Add 1 ml 75% EtOHb, invert several times and centrifuge 5m. 7. Remove EtOH by aspiration. Then, dry under vacuum for 2 min [Do not over dry]. 8. Suspend RNA in 90 ml RNase free water (don?t suspend in DNaseI buffer), may need to heat 10m at 55-60C to dissolve RNA. (Optional: obtain RNA concentration) 9. Add 10 ul 10X DNaseI buffer to RNA (use no more than 80 ug RNA) and add 4 ul DNaseI (Ambion). Incubate 30m at 37C. Qiagen RNeasy purification. 1. Add 350 ul RLT buffer (add 10 ul BME to 1 ml RLT before using) and vortex. Add 260 ul 95% EtOH (or 250 ul 100% EtOH) to each sample and vortex. 2. Add to RNeasy spin column, centrifuge 15s, transfer column to a new 2 ml collection tube. Add 500 ul RPE, centrifuge 15s, discard flow-through, add 500 ul additional RPE and centrifuge 2m. If column still wet on sides, remove wash solution from tube and spin 1m to dry. 3. Transfer to a 1.5 ml collection tube, elute with 40 ul RNase free water, centrifuge 1m. 4. Determine RNA concentration with A260/A280 readings. Dilute 1 ul in 199 ul TE. [200(dilution factor)x 40 ug/A260x A260 = ug/ml]. 5. Run 1 ul RNA on 2% Agarose TAE gel. Run gel 45m at 100 volts. aIf Phase Lock Gel is not used, decrease Chloroform:isoamyl alcohol to 200ul. The yield will be less. Be careful not to remove any of the interface layer. bUsing 100% EtOH should be avoided in all steps of preparation of RNA intended for array analysis. Instead use 95% EtOH in preparation of solutions. Benzene contamination may fluoresce. cInstead of using the RNeasy purification, the DNaseI can be inactivated at 65-70C for 15m and then EtOH precipitated. The RNeasy purification may not be necessary in all applications. We find the purification gives more consistent results and is less time consuming, compared to precipitation. In addition, other purifications can be used. Note: The RNeasy column will remove much of the small tRNA and degraded RNA.; Protocol Type = Extract preparation; Performer: Martin,,Voskuil

treatment_protocol: TB-Slide Preparation SKlab 01; 1. Prepare NaOH-ethanol solution ?  dissolve NaOH in ddH2O 70 g / 280 mL 175 g / 700mL 200 g / 800 mL ?  stir until completely dissolved ?  add 95% ethanol 420 mL 1050 mL 1200mL ?  stir until completely mixed ?  if solution remains cloudy, add water until clear 2. Place slides in metal slide racks (30 slides/rack). Do not use defective slides. 3. Soak slides in the NaOH:EtOH:ddH2O solution for 2 hours with gentle rotation. 4. Rinse extensively with dH2O: ?  rinse each unit (slide/rack/container) vigorously with dH2O for 5 min ?  place slide racks in a large clean glass container, and tilt the container slightly for constant water flow. ?  wash under running water for 30 minutes. ?  do not allow the slides to dry at any time. It is critical to remove all traces of NaOH:EtOH. 5. Prepare poly-L-lysine solution in plastic container. ?  100 mL tissue culture PBS 800 mL Milli-Q water 100 mL poly-L-Lysine ?  We bring up the volume to about 1050 mL with Milli-Q water in order to submerge 3 racks of slides. ?  Mix well and split into 3 plastic containers. 6. Soak the slides in lysine solution for 45 min with shaking. Be sure to use a plastic container, because poly-L-lysine adheres to glass. Poly-L-Lysine solution may be reused. Keep the other slide filled racks in dH2O, while the first 3 are being coated. 7. After the lysine coating, rinse the slides by gently plunging up and down in 2 different changes of water. Spin dry 5' at 600 rpm. Place paper towels below rack to absorb liquid. 8. Store slides in a dessicator for 3 weeks prior to use. Slides that are older than 3 months may result in faint printing and higher background. Be sure to clean racks and containers thoroughly after each use. Built-up poly-L-Lysine on the sides of the containers may cause problems.; Protocol Type = Treatment; Performer: Martin,,Voskuil

value: 0.05% SDS for 60 min


title: H37Rv wild type control vs 0.05% SDS for 60 min rep 5

description: Image: http://smd.stanford.edu/MicroArray/gifs/2009-05/83600.gif

source_name: Strain: H37Rv wild type; Treatment: Control

value: H37Rv wild type

source_name: Strain: H37Rv wild type; Treatment: 0.05% SDS for 60 min


title: Patient 034 with adenocarcinoma

description: dataset I

tag: Cohort

value: dataset I

tag: Age

tag: Sex

value: F

value: AD

value: IIIA

tag: Status

value: Alive

tag: Survival (days)

tag: Evidence of relapse

value: LN (neck)

tag: EGFR status

value: Wt

tag: K-ras Status


title: TS007-D14-rep4

value: Male

tag: age

value: 5 weeks

tag: strain

tag: tissue

tag: compound

tag: dose

tag: administration

value: Corn oil


title: pTN9 at 1h, biological rep2

description: pTN9, Genotype: r+m+

tag: Strain

value: MG1655 / pTN9, Genotype:r+m+


title: Patient 036 with adenocarcinoma

description: dataset I

tag: Annotation

tag: Histology

tag: Smoking (BI)

tag: TNM (Pathological)

tag: Stage (Pathological )

value: IB

value: N

tag: Site of relapse:

value: Mut

tag: p53 Status


title: Patient 043 with adenocarcinoma

description: dataset I

tag: Cohort

tag: Age

tag: Sex

value: M

tag: Status

tag: Survival (days)

tag: Evidence of relapse


title: Patient 033 with adenocarcinoma

description: dataset I

value: IIIB

value: Dead

value: Y

tag: Site of relapse

value: PM

tag: EGFR status

tag: K-ras Status


title: H37Rv sigB null mutant control vs 0.05% SDS for 60 min rep 2

description: Image: http://smd.stanford.edu/MicroArray/gifs/2009-05/83603.gif

tag: strain

value: H37Rv sigB null mutant

tag: treatment

value: Control

value: 0.05% SDS for 60 min


title: H37Rv sigB null mutant control vs 5mM Diamide for 60 min rep 5

description: Image: http://smd.stanford.edu/MicroArray/gifs/2009-05/83618.gif

source_name: Strain: H37Rv sigB null mutant; Treatment: 5mM Diamide for 60 min

value: 5mM Diamide for 60 min


title: TS007-D14-rep3

tag: gender

tag: age

tag: tissue

value: Liver

tag: compound

value: Vehicle

tag: dose

tag: administration

value: gavage

tag: time

value: 14 days

tag: vehicle


title: Patient 035 with adenocarcinoma

description: dataset I

tag: Annotation

tag: Cohort

value: dataset I

tag: Age

tag: Sex

tag: Histology

value: AD

tag: Smoking (BI)

tag: TNM (Pathological)

tag: Stage (Pathological )

value: IIB

value: Alive

tag: Site of relapse:

value: Wt

tag: p53 Status


title: H37Rv sigB null mutant control vs 0.05% SDS for 60 min rep 5

description: Image: http://smd.stanford.edu/MicroArray/gifs/2009-05/83606.gif

tag: strain

tag: treatment


title: H37Rv wild type Vs H37Rv wild type rep 1

description: Image: http://smd.stanford.edu/MicroArray/gifs/2009-05/83584.gif

source_name: Strain: H37Rv wild type; Treatment: No Treatment

value: H37Rv wild type

value: No Treatment


title: Patient 032 with adenocarcinoma

description: dataset I

value: M

value: IA

tag: Status

tag: Survival (days)

tag: Evidence of relapse

value: Y

tag: Site of relapse

value: Bone

tag: EGFR status

tag: K-ras Status


title: H37Rv wild type control vs 0.05% SDS for 60 min rep 3

description: Image: http://smd.stanford.edu/MicroArray/gifs/2009-05/83598.gif

value: Control

value: 0.05% SDS for 60 min


title: TS007-D14-rep2

tag: gender

value: Male

tag: age

value: 5 weeks

tag: tissue

value: Liver

tag: compound

tag: dose

tag: administration

tag: time

tag: vehicle

value: Corn oil


title: TS007-D14-rep1

value: Vehicle

value: gavage

value: 14 days


title: H37Rv wild type Vs H37Rv wild type rep 2

description: Image: http://smd.stanford.edu/MicroArray/gifs/2009-05/83585.gif


title: Patient 031 with adenocarcinoma

description: dataset I

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: IIIB

value: Dead

value: PM

tag: p53 Status


title: TS006-D14-rep4

tag: gender

tag: strain

value: Quinoline

tag: treatment


title: H37Rv wild type vs H37Rv sigB null mutant rep 6

description: Image: http://smd.stanford.edu/MicroArray/gifs/2009-05/83595.gif

value: H37Rv wild type

value: No Treatment

source_name: Strain: H37Rv sigB null mutant; Treatment: No Treatment

value: H37Rv sigB null mutant


title: TS006-D14-rep2

value: Male

tag: age

tag: tissue

tag: compound


title: TS006-D14-rep1

value: 5 weeks

tag: dose

tag: administration

tag: time


title: TS006-D14-rep3

value: Liver

tag: vehicle


title: TS005-D14-rep3

value: Saline


title: Patient 029 with adenocarcinoma

description: dataset I

tag: Annotation

tag: Cohort

tag: Age

value: M

value: IIB

tag: Status

value: Alive

tag: Survival (days)

tag: Evidence of relapse

value: N

tag: Site of relapse:

tag: EGFR status

value: Wt

tag: K-ras Status

value: Mut


title: Patient 025 with adenocarcinoma

description: dataset I

value: dataset I

tag: Sex

tag: Histology

value: AD

tag: Smoking (BI)

tag: TNM (Pathological)

tag: Stage (Pathological )

value: IB

tag: p53 Status


title: TS005-D14-rep4

tag: gender

tag: age

tag: strain

tag: tissue

tag: compound

value: Vehicle

tag: dose

tag: administration

value: gavage

tag: time

value: 14 days

tag: treatment


title: TS005-D14-rep2

tag: vehicle


title: Patient 027 with adenocarcinoma

description: dataset I

tag: Annotation

tag: Cohort

tag: Age

tag: Status

value: Dead

tag: Survival (days)

tag: Evidence of relapse

value: Y

tag: Site of relapse

value: PM

tag: EGFR status

tag: K-ras Status


title: TS005-D14-rep1

tag: gender

value: Male

tag: age

value: 5 weeks

tag: strain

value: Liver


title: H37Rv wild type vs H37Rv sigB null mutant rep 3

description: Image: http://smd.stanford.edu/MicroArray/gifs/2009-05/83592.gif

value: H37Rv wild type

value: No Treatment

value: H37Rv sigB null mutant


title: H37Rv wild type vs H37Rv sigB null mutant rep 4

description: Image: http://smd.stanford.edu/MicroArray/gifs/2009-05/83593.gif


title: H37Rv sigB null mutant control vs 5mM Diamide for 60 min rep 4

description: Image: http://smd.stanford.edu/MicroArray/gifs/2009-05/83617.gif

value: Control

value: 5mM Diamide for 60 min


title: Patient 024 with adenocarcinoma

description: dataset I

value: dataset I

tag: Sex

value: M

tag: Histology

tag: Smoking (BI)

tag: TNM (Pathological)

tag: Stage (Pathological )

value: IIIA

value: Alive

value: N

tag: Site of relapse:

value: Wt

tag: p53 Status


title: H37Rv wild type Vs H37Rv wild type rep 5

description: Image: http://smd.stanford.edu/MicroArray/gifs/2009-05/83588.gif

tag: treatment


title: H37Rv sigB null mutant control vs 5mM Diamide for 60 min rep 2

description: Image: http://smd.stanford.edu/MicroArray/gifs/2009-05/83615.gif


title: TS004-D14-rep4

description: Biological replicate 4 of 4. Control samples were pooled.

tag: tissue

tag: compound

value: Vehicle

tag: dose

tag: administration

value: gavage

tag: time

value: 14 days

tag: vehicle

value: Saline


title: Patient 023 with adenocarcinoma

description: dataset I

tag: Annotation

tag: Cohort

tag: Age

value: AD

value: IB

tag: Status

tag: Survival (days)

tag: Evidence of relapse

tag: EGFR status

tag: K-ras Status


title: H37Rv sigB null mutant control vs 5mM Diamide for 60 min rep 6

description: Image: http://smd.stanford.edu/MicroArray/gifs/2009-05/83619.gif

tag: strain


title: Patient 021 with adenocarcinoma

description: dataset I

tag: Sex

tag: Histology

tag: Smoking (BI)

tag: TNM (Pathological)

tag: Stage (Pathological )

value: IA

tag: Site of relapse:

tag: p53 Status

value: Mut


title: Patient 026 with adenocarcinoma

description: dataset I


title: H37Rv wild type control vs 0.05% SDS for 60 min rep 2

description: Image: http://smd.stanford.edu/MicroArray/gifs/2009-05/83597.gif

value: H37Rv wild type

tag: treatment

value: 0.05% SDS for 60 min


title: H37Rv wild type control vs 5mM Diamide for 60 min rep 1

description: Image: http://smd.stanford.edu/MicroArray/gifs/2009-05/83608.gif

value: Control

source_name: Strain: H37Rv wild type; Treatment: 5mM Diamide for 60 min

value: 5mM Diamide for 60 min


title: TS004-D14-rep3

description: Biological replicate 3 of 4. Control samples were pooled.

tag: gender

value: Male

tag: age

value: 5 weeks

tag: tissue

value: Liver

tag: compound

tag: dose

tag: administration

tag: time

tag: vehicle


title: H37Rv sigB null mutant control vs 5mM Diamide for 60 min rep 3

description: Image: http://smd.stanford.edu/MicroArray/gifs/2009-05/83616.gif

tag: strain

value: H37Rv sigB null mutant


title: Patient 018 with adenocarcinoma

description: dataset I

tag: Annotation

tag: Cohort

value: dataset I

tag: Age

tag: Sex

value: M

tag: Status

value: Dead

tag: Survival (days)

tag: Evidence of relapse

value: Y

tag: Site of relapse

value: Local rec.

tag: EGFR status

value: Wt

tag: K-ras Status


title: TS004-D14-rep2

description: Biological replicate 2 of 4. Control samples were pooled.

tag: gender

tag: age

tag: tissue

value: Vehicle

value: gavage

value: 14 days

value: Saline

tag: treatment


title: TS004-D14-rep1

description: Biological replicate 1 of 4. Control samples were pooled.

tag: compound

tag: dose

tag: administration

tag: time


title: H37Rv wild type Vs H37Rv wild type rep 3

description: Image: http://smd.stanford.edu/MicroArray/gifs/2009-05/83586.gif

tag: strain

value: H37Rv wild type

value: No Treatment


title: H37Rv wild type control vs 5mM Diamide for 60 min rep 6

description: Image: http://smd.stanford.edu/MicroArray/gifs/2009-05/83613.gif

value: Control

value: 5mM Diamide for 60 min


title: Patient 016 with adenocarcinoma

description: dataset I

tag: Annotation

tag: Cohort

tag: Age

value: F

tag: Histology

value: AD

tag: Smoking (BI)

tag: TNM (Pathological)

tag: Stage (Pathological )

value: IB

value: Alive

value: N

tag: Site of relapse:

tag: p53 Status

value: Mut


title: H37Rv sigB null mutant control vs 0.05% SDS for 60 min rep 3

description: Image: http://smd.stanford.edu/MicroArray/gifs/2009-05/83604.gif

value: H37Rv sigB null mutant

value: 0.05% SDS for 60 min


title: Patient 020 with adenocarcinoma

description: dataset I

value: dataset I

tag: Sex

value: IIIA

tag: Status

tag: Survival (days)

tag: Evidence of relapse

tag: EGFR status

value: Wt

tag: K-ras Status


title: TS003-D14-rep4

tag: gender

value: Male

tag: age

value: 5 weeks

tag: tissue

value: Liver

tag: compound

value: Vehicle

tag: dose

tag: administration

value: gavage

tag: time

value: 14 days

tag: vehicle

value: Corn oil

value: Carbon tetrachloride

tag: treatment


title: TS003-D14-rep2

tag: strain


title: H37Rv wild type control vs 5mM Diamide for 60 min rep 3

description: Image: http://smd.stanford.edu/MicroArray/gifs/2009-05/83610.gif

value: H37Rv wild type

value: Control

value: 5mM Diamide for 60 min


title: TS003-D14-rep3


title: H37Rv wild type control vs 5mM Diamide for 60 min rep 2

description: Image: http://smd.stanford.edu/MicroArray/gifs/2009-05/83609.gif


title: Patient 014 with adenocarcinoma

description: dataset I

tag: Annotation

tag: Cohort

tag: Age

value: M

tag: Histology

value: AD

tag: Smoking (BI)

tag: TNM (Pathological)

tag: Stage (Pathological )

value: Dead

value: Y

tag: Site of relapse

value: LN (mediastinal)

value: Mut

tag: p53 Status


title: Patient 015 with adenocarcinoma

description: dataset I

value: dataset I

tag: Sex

value: IA

tag: Status

value: Alive

tag: Survival (days)

tag: Evidence of relapse

value: N

tag: Site of relapse:

tag: EGFR status

value: Wt

tag: K-ras Status


title: H37Rv wild type control vs 0.05% SDS for 60 min rep 6

description: Image: http://smd.stanford.edu/MicroArray/gifs/2009-05/83601.gif

tag: strain

tag: treatment

value: 0.05% SDS for 60 min


title: Patient 011 with adenocarcinoma

description: dataset I

tag: Annotation

tag: Cohort

value: F

value: IB

value: PM


title: Patient 013 with adenocarcinoma

description: dataset I

tag: Age

tag: Histology

value: IIB

value: Liver


title: H37Rv wild type Vs H37Rv wild type rep 4

description: Image: http://smd.stanford.edu/MicroArray/gifs/2009-05/83587.gif

value: H37Rv wild type

value: No Treatment


title: Patient 012 with adenocarcinoma

description: dataset I

value: M

value: AD

tag: Smoking (BI)

tag: TNM (Pathological)

value: IIIA


title: TS002-D14-rep4

tag: gender

value: Male

tag: age

value: 5 weeks

tag: tissue

tag: compound

value: Vehicle

tag: dose

tag: administration

value: gavage

tag: time

value: 14 days

tag: vehicle

value: Corn oil


title: H37Rv sigB null mutant control vs 0.05% SDS for 60 min rep 1

description: Image: http://smd.stanford.edu/MicroArray/gifs/2009-05/83602.gif

value: H37Rv sigB null mutant

value: Control

value: 0.05% SDS for 60 min


title: TS003-D14-rep1

value: Carbon tetrachloride


title: TS002-D14-rep2


title: TS002-D14-rep3


title: H37Rv wild type vs H37Rv sigB null mutant rep 2

description: Image: http://smd.stanford.edu/MicroArray/gifs/2009-05/83591.gif


title: Patient 008 with adenocarcinoma

description: dataset I

value: dataset I

tag: Sex

value: F

tag: Stage (Pathological )

value: IIIB

tag: Status

value: Alive

tag: Survival (days)

tag: Evidence of relapse

value: N

tag: Site of relapse:

tag: EGFR status

value: Wt

tag: K-ras Status

value: Mut

tag: p53 Status


title: Patient 010 with adenocarcinoma

description: dataset I

tag: Annotation

tag: Cohort

tag: Age

tag: Histology

value: AD

tag: Smoking (BI)

tag: TNM (Pathological)

value: IA


title: H37Rv wild type control vs 0.05% SDS for 60 min rep 4

description: Image: http://smd.stanford.edu/MicroArray/gifs/2009-05/83599.gif

tag: strain

value: H37Rv wild type

tag: treatment


title: TS002-D14-rep1

tag: gender

value: Male

tag: age

value: 5 weeks

tag: tissue

value: Liver

tag: compound

value: Vehicle

tag: dose

tag: administration

value: gavage

tag: time

tag: vehicle


title: TS001-D14-rep4

description: Biological replicate 4 of 4. Control samples were pooled.

value: 14 days

value: Corn oil

value: Clofibrate


title: Patient 019 with adenocarcinoma

description: dataset I

value: dataset I

tag: Sex

value: M

tag: Stage (Pathological )

value: IIIA

tag: Status

value: Dead

tag: Survival (days)

tag: Evidence of relapse

value: Y

tag: Site of relapse

value: LN (mediastinal)

tag: EGFR status

tag: K-ras Status

tag: p53 Status


title: TS001-D14-rep3

tag: gender

tag: strain

tag: treatment


title: H37Rv wild type vs H37Rv sigB null mutant rep 5

description: Image: http://smd.stanford.edu/MicroArray/gifs/2009-05/83594.gif

value: No Treatment

value: H37Rv sigB null mutant


title: H37Rv sigB null mutant control vs 5mM Diamide for 60 min rep 1

description: Image: http://smd.stanford.edu/MicroArray/gifs/2009-05/83614.gif

value: Control

value: 5mM Diamide for 60 min


title: TS001-D14-rep2

value: Male

tag: age

value: 5 weeks

tag: tissue

tag: compound


title: Patient 006 with adenocarcinoma

description: dataset I

tag: Annotation

tag: Cohort

tag: Age

tag: Histology

value: AD

tag: Smoking (BI)

tag: TNM (Pathological)

value: Brain

value: Mut

value: Wt


title: Patient 004 with adenocarcinoma

description: dataset I

tag: Sex

value: F

tag: Stage (Pathological )

value: IIA

tag: Status

value: Alive

tag: Survival (days)

tag: Evidence of relapse

value: N

tag: Site of relapse:


title: TS001-D14-rep1

tag: gender

tag: strain

value: Liver

value: Vehicle

tag: dose

tag: administration

value: gavage

tag: time

value: 14 days

tag: vehicle

value: Corn oil

value: Clofibrate


title: Patient 005 with adenocarcinoma

description: dataset I

tag: Annotation

tag: Cohort

value: dataset I

value: IIIA

value: Dead

value: Y

tag: Site of relapse

value: PM

tag: EGFR status

tag: K-ras Status

tag: p53 Status


title: H37Rv wild type control vs 5mM Diamide for 60 min rep 5

description: Image: http://smd.stanford.edu/MicroArray/gifs/2009-05/83612.gif

value: H37Rv wild type

tag: treatment

value: Control

value: 5mM Diamide for 60 min


title: Patient 030 with adenocarcinoma

description: dataset I

tag: Age

tag: Sex

value: M

tag: Histology

value: AD

tag: Smoking (BI)

tag: TNM (Pathological)

tag: Stage (Pathological )

value: IB

tag: Status

value: Wt

value: Mut


title: H37Rv wild type vs H37Rv sigB null mutant rep 1

description: Image: http://smd.stanford.edu/MicroArray/gifs/2009-05/83590.gif

tag: strain

value: No Treatment

value: H37Rv sigB null mutant


title: H37Rv wild type Vs H37Rv wild type rep 6

description: Image: http://smd.stanford.edu/MicroArray/gifs/2009-05/83589.gif


title: Patient 003 with adenocarcinoma

description: dataset I

value: F

tag: Survival (days)

tag: Evidence of relapse


title: H37Rv sigB null mutant control vs 0.05% SDS for 60 min rep 4

description: Image: http://smd.stanford.edu/MicroArray/gifs/2009-05/83605.gif

value: 0.05% SDS for 60 min


title: Patient 007 with adenocarcinoma

description: dataset I

tag: Annotation

value: dataset I

value: IA

value: Alive

value: N

tag: Site of relapse:


title: Patient 002 with adenocarcinoma

description: dataset I

tag: Cohort


title: H37Rv wild type control vs 0.05% SDS for 60 min rep 1

description: Image: http://smd.stanford.edu/MicroArray/gifs/2009-05/83596.gif


title: H37Rv wild type control vs 5mM Diamide for 60 min rep 4

description: Image: http://smd.stanford.edu/MicroArray/gifs/2009-05/83611.gif


title: TS088-D3-rep1

status: Public on Jun 22 2009

city: Osaka

first: Kayo

last: Sumida

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

department: Environmental Health Science Laboratory

institute: Sumitomo Chemical Co., Ltd.

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.

source_name: Total RNA from rat liver

tag: gender

value: Male

tag: age

tag: tissue

value: Liver

tag: compound

value: Vehicle

tag: dose

tag: administration

value: gavage

value: 3 days

tag: vehicle

value: Corn oil


title: TS087-D3-rep3

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.

tag: treatment

value: o-Nitrotoluene


title: TS088-D3-rep4


title: TS088-D3-rep3


title: TS088-D3-rep2

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.


title: TS085-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: Indomethacin


title: TS087-D3-rep2


title: Patient 001 with adenocarcinoma

description: dataset I

tag: Age

tag: Sex

value: M

tag: Histology

value: AD

tag: Smoking (BI)

tag: TNM (Pathological)

value: IB

value: Dead

value: Y

tag: Site of relapse

value: PM

tag: EGFR status

value: Mut

tag: K-ras Status

value: Wt

tag: p53 Status


title: TS085-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.

tag: gender

tag: strain


title: TS087-D3-rep4

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.

tag: age

tag: tissue


title: TS086-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: compound

tag: dose

value: Methyleugenol


title: TS087-D3-rep1

value: Male

tag: administration

tag: vehicle