title: Gastroc m. Drug Treatment 7 Days DexTs 2

description: dexamethasone + testosterone

scan_protocol: Standard Affymetrix protocol for the rat 230-2 array.


title: Gastroc m. Drug Treatment 7 Days DexTs 3

status: Public on Jul 01 2009

type: RNA

city: Bronx

first: christopher

middle: p

last: cardozo

state: NY

address: 130 West Kingsbridge Road

department: CMSCI

country: USA

institute: Bronx VA Medical Center

description: dexamethasone + testosterone

hyb_protocol: Standard Affymetrix protocol for the rat 230-2 array.

data_processing:
Normalization, initial filtering, and determination of significant changes in expression were performed using BRB Array tools v 3.6
Data for each array were normalized using the median for the entire array; expression values were set to 10 if below this value, and excluded from further analysis if more than 20% of the values were at least 1.5-fold greater or smaller than the median for that probe set.

label: biotin

molecule: total RNA

organism: Rattus norvegicus

source_name: gastrocnemius muscle

extract_protocol: Muscle (20 mg) was homogenized in guanidine isothiocyanate buffer using a polytron.  Total RNA was extracted using phenol chloroform then cleaned up using RNA easy columgs.

treatment_protocol: Male Wistar rats (250 g) were administered vehicle (propylene glycol), dexamethasone (0.7 mg/kg/day), or dexamethasone plus testosterone (28 mg/kg/day) for 7 days using Alzet pumps.

tag: male Wistar-Hannover rat approx 250 g


title: Ectodermal explant after treatment with beta globin (control), 3rd biological replicate

city: Bozeman

first: Kate

last: McInnerney

state: MT

address: 109 Lewis Hall

department: Microbiology

institute: Montana State University

description: gene expression of ectodermal explant expression of zic1 or beta globin control.

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

scan_protocol: GeneChips were scanned using the Affymetrix GCOS Scanner 3000.

data_processing: Data was analyzed with Agilent Genespring GX v. 7.3.1 using Affymetrix GCOS generated flag data from scaled CHP files, and RMA-normalized CEL files.

organism: Xenopus laevis

source_name: Neuralized ectodermal explants from zic1 and beta globin (control) injected embryos

label_protocol: Biotinylated cRNA were prepared according to the standard one-cycle Affymetrix protocol from 2 micrograms total RNA (Expression Analysis Technical Manual, 2004, Affymetrix).

extract_protocol: RNA extracted with phenol/chloroform and purified by alcohol and sodium acetate precipitation

treatment_protocol: Ectodermal explants were harvested from stage 9 embryos injected at the 2 cell stage with hormone-inducible zic1 or beta globin as control, each plus noggin to neuralize the explants. After incubation to the equivalent of stage 12 they were incubated with cycloheximide for 30 min to prevent further protein synthesis, followed by addition of dexamethasone to activate injected hormone-inducible zic1. Three hours later ectodermal explants were harvested and treated with proteinase K.

tag: Neuralized ectodermal explants free from mesoderm


title: Gastroc m. Drug Treatment 7 Days DexTs 1

description: dexamethasone + testosterone

label_protocol: Standard Affymetrix protocol for the rat 230-2 array.


title: Gastroc m. Drug Treatment 7 days Control 2

description: vehicle


title: stageII colorectal cancer patient5 with no recurrence in discovery phase

status: Public on Jul 02 2009

city: Suita

first: masakazu

last: miyake

state: Osaka

address: Yamadaoka 2-2

department: Gastroenterological Surgery

country: Japan

institute: Graduate School of Medicine, Osaka University

description: no additional information

hyb_protocol: Hybridized for 16 h at 42 °C. Hybridization buffer and washing protocol was followed by the protocol supplied by Hitachi Software Engineering Co., Ltd. (DNA Chip Research Inc. / AceGene website)

scan_protocol: ScanArray HT (PerkinElmer Japan Co., Ltd.) was used for scanning. Array images were analyzed with DNASIS Array V2.6(Hitachi Software Engineering Co., Ltd.).

data_processing: In each sample, the Cy5/Cy3 ratio values were log-transformed and global equalization to remove a deviation of the signal intensity between whole Cy3- and Cy5-fluorescence was performed by subtracting a median of all log (Cy5/Cy3) values from each log (Cy5/Cy3) value. Genes with missing values in more than 10% of samples were excluded from further analysis.

organism: Homo sapiens

source_name: 40 Total RNA mixture from normal colorectal mucosa labeled with Cyanine-3 (green).

label_protocol: Amino Allyl aRNA was synthesized by Amino Allyl MessageAmp aRNA Amplification Kit (Ambion).CyeDye coupling and fragmentation were performed using the protocol supplied by Hitachi Software Engineering Co., Ltd. (DNA Chip Research Inc. / AceGene website)

treatment_protocol: no treatment

tag: Tissue

value: mixture of normal colorectal mucosa

source_name: Total RNA from primary colorectal cancer of stageII patient with no recurrence labeled with Cyanine-5 (red).

extract_protocol:
Tumor samples were collected within 30 minutes from the time of resection, cut in 5-mm cubes, and immediately stored with RNAase inhibitor and stored at -85°C until RNA extraction.
Total RNA was purified from the clinical samples utilizing TRIzol reagent (Invitrogen, San Diego, CA) using the protocol supplied by the manufacturer.

value: stageII colorectal cancer with no recurrence


title: Ectodermal explant after zic1 misexpression, 1st biological replicate


title: Ectodermal explant after treatment with beta globin (control), 2nd biological replicate


title: Gastroc m. Drug Treatment 7 Days Control 3

description: vehicle


title: Ectodermal explant after zic1 misexpression, 2nd biological replicate


title: Ectodermal explant after treatment with beta globin (control), 1st biological replicate


title: Gastroc m. Drug Treatment 7 Days Dex 3

description: dexamethasone


title: Gastroc m. Drug Treatment 7 Days Dex 1

description: dexamethasone


title: Gastroc m. Drug Treatment 7 Days Control 1

description: vehicle


title: stageII colorectal cancer patient1 with no recurrence in discovery phase

description: no additional information

extract_protocol: Total RNA was purified from the clinical samples utilizing TRIzol reagent (Invitrogen, San Diego, CA) using the protocol supplied by the manufacturer.


title: Congenic NP (NP.P)-rep2

city: Indianapolis

first: Charles

middle: H

last: Turner

state: IN

address: 723 W. Michigan St. SL 220C

department: Biomedical Engineering

institute: Indiana University Purdue University Indiapanolis

description: Gene expression data from proximal femur

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 17 hr at 45C on Rat Genome 230 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station.

scan_protocol: GeneChips were scanned using the standard Affymetrix protocol.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 1000.

source_name: Congenic NP (NP.P)

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

extract_protocol: Whole femora were harvested from 4-week-old NP, P, NP.P and P.NP animals.  RNA was isolated from proximal femora using Trizol (Invtirogen, CA) and Rneasy Mini Kit (Qiagen Inc., CA) according to the manufacturer’s directions.

tag: Bone, Femur


title: Congenic P (P.NP)-rep4

source_name: Congenic P (P.NP)


title: Congenic NP (NP.P)-rep5


title: Congenic P (P.NP)-rep2


title: Congenic P (P.NP)-rep5


title: Alcohol-preferring-rep2

source_name: Alcohol-preferring


title: Alcohol-preferring-rep4


title: Congenic NP (NP.P)-rep3


title: Alcohol-non-preferring-rep4

source_name: Alcohol-non-preferring


title: Congenic NP (NP.P)-rep4


title: Alcohol-preferring-rep5


title: Alcohol-non-preferring-rep3


title: Alcohol-preferring-rep1


title: Alcohol-non-preferring-rep5


title: Alcohol-preferring-rep3


title: Alcohol-non-preferring-rep1


title: Congenic NP (NP.P)-rep1


title: Congenic P (P.NP)-rep3


title: Congenic P (P.NP)-rep1


title: Alcohol-non-preferring-rep2


title: DEN03 Male Fischer-344 24 hours afterd iethylnitrosamine administration, replicate 3,

status: Public on Jun 30 2009

city: Mexico

first: Adriana

last: Marquez-Quiñones

state: DF

address: AV. Instituto Politecnico Nacional No. 2508

department: Cell Biology

country: Mexico

institute: CINVESTAV

description: DEN is a carcinogen used as initiator in the modified resistant hepatocyte model.

hyb_protocol: 8h at 42ºC in the automatic hybridization machine discovery from Ventana. After hybridization, slides were washed twice in Ribowash buffer for 5 minutes with agitation and then once with 0.1xSSC buffer.

scan_protocol: Scanning with Genepix 400A microarray scanner (Axon instruments). Image analysis was made by Genepix Pro V6 software, each spot was evaluated and selectioned to be analysed by Bioplot software.

data_processing: Background substraction with lowess allowed value 10, log transformation and LOWESS normatilization.

source_name: Total RNA from Diethylnitrosamine-treated Male Fischer344 rat liver labeled with Cyanine-5.

label_protocol: Reverse transcription of 5µg total RNA with ChipShotTM reverse transcriptase from Promega. Using Cy5-dCTP from Amersham Biosciences. The reverse transcription was made following the ChipShotTM labeling System instructions (Promega). cDNA purification was made by Promega ChipShotTM labeling Clean-up System, dye incorporation was verified by measuring the absorbance at 260, 550nm.

growth_protocol: Animals had free access to food (PMI Feeds Inc., Laboratories Diet) and water at all times; each rat consumed approximately 12-15 g of food and 10-15 ml of water per day. After treatment, the animals were transferred to the holding room and kept under controlled conditions of 12 h light/12 h dark, 50% relative humidity, and 21 ºC. Animal care followed institutional guidelines for the use of laboratory animals.

extract_protocol: Sacrifice by exsanguination under ether anesthesia. Liver was excised, washed in physiological saline solution, immersed in RNalater and stored at -80ºC. Isolation of total RNA from liver samples following the instructions for Quagen Rneasy mini kit. Quality and quantity were determined by capilary electrophoresis (RNA 6000 nano assay, Agilent)

treatment_protocol: Single sdministration of 200 mg/kg of Diethylnitrosamine i.p. and sacrificed 24 h later.

tag: Strain

tag: Gender

value: Male

tag: Weight

tag: Treatment

value: Diethylnitrosamine 200mg/kg and sacrificed 24 h later.

value: liver

tag: Other

value: Necrosis in liver

source_name: Total RNA from normal Male Fischer344 rat liver labeled with Cyanine-3.

label_protocol: Reverse transcription of 5µg total RNA with ChipShotTM reverse transcriptase from Promega. Using Cy3-dCTP from Amersham Biosciences. The reverse transcription was made following the ChipShotTM labeling System instructions (Promega). cDNA purification was made by Promega ChipShotTM labeling Clean-up System, dye incorporation was verified by measuring the absorbance at 260, 650nm.

growth_protocol: Animals had free access to food (PMI Feeds Inc., Laboratories Diet) and water at all times; each rat consumed approximately 12-15 g of food and 10-15 ml of water per day. After treatment, the animals were transferred to the holding room and kept under controlled conditions of 12 h light/12 h dark, 50% relative humidity, and 21 o C. Animal care followed institutional guidelines for the use of laboratory animals.

value: normal liver


title: DEN04 Male Fischer-344 24 hours afterd iethylnitrosamine administration, replicate 4,

source_name: Total RNA from Diethylnitrosamine-treated Male Fischer344 rat liver labeled with Cyanine-3.

label_protocol: Reverse transcription of 5µg total RNA with ChipShotTM reverse transcriptase from Promega. Using Cy3-dCTP from Amersham Biosciences. The reverse transcription was made following the ChipShotTM labeling System instructions (Promega). cDNA purification was made by Promega ChipShotTM labeling Clean-up System, dye incorporation was verified by measuring the absorbance at 260, 550nm.

source_name: Total RNA from normal Male Fischer344 rat liver labeled with Cyanine-5.

label_protocol: Reverse transcription of 5µg total RNA with ChipShotTM reverse transcriptase from Promega. Using Cy5-dCTP from Amersham Biosciences. The reverse transcription was made following the ChipShotTM labeling System instructions (Promega). cDNA purification was made by Promega ChipShotTM labeling Clean-up System, dye incorporation was verified by measuring the absorbance at 260, 650nm.


title: CAPE+DEN02, Male Fischer 344 CAPE pre-treatment 12 h before diethylnitrosamine administration replicate 2

description: CAPE is an anticarcinogenic compound and diethylnitrosamine is a carcinogen used as initiator in the modified resistant hepatocyte model.

source_name: Total RNA from Male Fischer 344 rat liver, treated liver, labeled with Cyanine-3.

treatment_protocol: Administration of 20 mg/kg of CAPE 12 h before diethylnitrosamine, and 200 mg/kg of Diethylnitrosamine and sacrificed 24 h later.

value: Were pre-treated with CAPE 12 h before Diethylnitrosamine administration and sacrificed 24 h after diethylnitrosamine.

source_name: Total RNA from normal liver labeled with Cyanine-5.


title: CAPE+DEN04, Male Fischer 344 CAPE pre-treatment 12 h before diethylnitrosamine administration replicate 2


title: CAPE+DEN01, Male Fischer 344 CAPE pre-treatment 12 h before diethylnitrosamine administration replicate 1

source_name: Total RNA from Male Fischer 344 rat liver, treated liver, labeled with Cyanine-5.

source_name: Total RNA from normal liver labeled with Cyanine-3.


title: CAPE+DEN03, Male Fischer 344 CAPE pre-treatment 12 h before diethylnitrosamine administration replicate 3


title: DEN01 Male Fischer-344 24 hours afterd iethylnitrosamine administration, replicate 1,


title: CAPE03 Male Fischer 344 12 hours after CAPE administration, replicate 3

description: CAPE is anticarcinogenic compound from propolis bee hives.

source_name: Total RNA from CAPE-treated Male Fischer 344 rat liver labeled with Cyanine-5.

treatment_protocol: 20 mg/kg of CAPE and sacrificed 12 h later.

value: CAPE administration and sacrificed 12 h later.

value: normal liver histology


title: CAPE01 Male Fischer 344 12 hours after CAPE administration, replicate 1


title: DEN02 Male Fischer-344 24 hours afterd iethylnitrosamine administration, replicate 2,


title: CAPE02 Male Fischer 344 12 hours after CAPE administration, replicate 2

source_name: Total RNA from CAPE-treated Male Fischer 344 rat liver labeled with Cyanine-3.


title: p53 -/- Whole Mouse Embryo Heat Shock C

status: Public on May 01 2009

city: College Station

first: Jennifer

last: Goldsby

state: TX

address: 112 Cater-Mattil

department: Nutrition and Food Sciences

institute: Texas A&M University

description: IACUC approval was obtained for all aspects of the animal care and treatment.

hyb_protocol: CodeLink Gene Expression System: Single-Assay Bioarray Hybridization and Detection according to manufacturer's instructions http://www.appliedmicroarrays.com/pdf/codelink_bioarray_processing_protocol.pdf

scan_protocol: CodeLink Gene Expression System: Single-Assay Bioarray Hybridization and Detection according to manufacturer's instructions http://www.appliedmicroarrays.com/application_notes/63005079.pdf

data_processing: Median normalized values derived from CodeLink Expression Analysis Version 4.1.0.29054

label: biotin, Alexa-647 Streptavidin

organism: Mus musculus

source_name: p53 -/- Whole Mouse Embryo Heat Shock

label_protocol: CodeLink Gene Expression System: Manual Labelled cRNA Target Preparation according to manufacturer's instructions http://www.appliedmicroarrays.com/pdf/iexpress2006_web.pdf

extract_protocol: 3-7 whole embryos were placed and pooled in RNAlater (Ambion), and the total RNA was extracted using mirVana™ miRNA Isolation Kit (Ambion) according to the manufacturer's instructions.  The concentration and quality of the total RNA were assessed using a Nanodrop (Nanodrop) and Agilent 2100 Bioanalyzer (Agilent Technologies) respectively.

tag: C57BL/6, p53 -/- males and females, GD8.5-9 whole embryos collected 5h after heat shock treatment.


title: CAPE04 Male Fischer 344 12 hours after CAPE administration, replicate 4


title: p53 -/- Whole Mouse Embryo Heat Shock A


title: p53 -/- Whole Mouse Embryo Heat Shock B


title: Mixture of normal tissue from 5 different patients, mixture no.5

status: Public on Apr 01 2009

city: Nagoya

first: Takashi

last: Takahashi

state: Aichi

address: 1-1 Kanokoden, Chikusa-ku

institute: Aichi Cancer Center

hyb_protocol: Cy5-sample cRNA and Cy3-common reference cRNA were hybridized to a custom Agilent oligonucleotide microarray, containing a total of 21,619 spots corresponding to 18,175 unique genes, followed by confocal laser scanning (Agilent Technologies).

scan_protocol: Scanned on an Agilent G2565AA scanner. Images were quantified using Agilent Feature Extraction Software (version A.7.5).

data_processing: LOWESS normalized, background subtracted VALUE data obtained from log10 of processed Red signal/processed Green signal. Agilent software was used.

source_name: Normal lung tissue

label_protocol: cRNA was generated and labeled with Cy3 or Cy5 (CyDye, Amersham Pharmacia Biotech, Piscataway, NJ) using the Low RNA Fluorescent Linear Amplification kit (Agilent Technologies, Palo Alto, CA).

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 250 ng of total RNA using MMLV-RT and poly dT primer incorporating the T7 promoter.

tag: Annotation

tag: Position in Figure 1 (L to R)

tag: Age

tag: Sex

tag: Histology

value: Normal lung tissue

tag: Smoking (BI)

tag: pTNM

tag: pStage

tag: Status

tag: Survival (days)

tag: Evidence of relapse

tag: Site of relapse

tag: EGFR status

tag: K-ras Status

tag: p53 Status

tag: Gefitinib treatment

tag: Position in Figure 2 (L to R)

tag: Expression profile-based classification

tag: Invasion

tag: Necrosis

tag: Grade

tag: BAC features

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


title: Mixture of normal tissue from 5 different patients, mixture no.4

tag: Annotation

tag: Position in Figure 1 (L to R)

tag: Age

tag: Sex

tag: Histology

tag: Smoking (BI)


title: p53 -/- Whole Mouse Embryo Control D

source_name: p53 -/- Whole Mouse Embryo Control

tag: C57BL/6, p53 -/- males and females, GD8.5-9 whole embryos collected 5h after control treatment.


title: p53 +/- Whole Mouse Embryo Heat Shock D

source_name: p53 +/- Whole Mouse Embryo Heat Shock

tag: C57BL/6, p53 +/- males and females, GD8.5-9 whole embryos collected 5h after heat shock treatment.


title: p53 +/- Whole Mouse Embryo Control B

source_name: p53 +/- Whole Mouse Embryo Control

tag: C57BL/6, p53 +/- males and females, GD8.5-9 whole embryos collected 5h after control treatment.


title: p53 -/- Whole Mouse Embryo Control B


title: p53 +/+ Whole Mouse Embryo Heat Shock B

source_name: p53 +/+ Whole Mouse Embryo Heat Shock

tag: C57BL/6, p53 +/+ males and females, GD8.5-9 whole embryos collected 5h after heat shock treatment.


title: p53 +/- Whole Mouse Embryo Control A


title: p53 +/+ Whole Mouse Embryo Control D

source_name: p53 +/+ Whole Mouse Embryo Control

tag: C57BL/6, p53 +/+ males and females, GD8.5-9 whole embryos collected 5h after control treatment.


title: Mixture of normal tissue from 5 different patients, mixture no.2

tag: pTNM

tag: pStage

tag: Status

tag: Survival (days)

tag: Evidence of relapse

tag: Site of relapse

tag: EGFR status

tag: K-ras Status

tag: p53 Status

tag: Gefitinib treatment

tag: Position in Figure 2 (L to R)


title: p53 +/- Whole Mouse Embryo Heat Shock A


title: p53 +/- Whole Mouse Embryo Heat Shock C


title: p53 +/- Whole Mouse Embryo Control D


title: p53 +/+ Whole Mouse Embryo Control C


title: p53 -/- Whole Mouse Embryo Control C


title: p53 +/- Whole Mouse Embryo Heat Shock B


title: p53 +/+ Whole Mouse Embryo Control B


title: p53 +/+ Whole Mouse Embryo Heat Shock C


title: Patient 08 with small cell lung cancer

source_name: Primary lung tumor

tag: Annotation

tag: Position in Figure 1 (L to R)

tag: Age

tag: Sex

tag: Histology

value: SCLC

tag: Smoking (BI)

tag: Expression profile-based classification

tag: Invasion

tag: Necrosis

tag: Grade

tag: BAC features


title: Mixture of normal tissue from 5 different patients, mixture no.3

tag: pTNM

tag: pStage

tag: Status

tag: Survival (days)

tag: Evidence of relapse

tag: Site of relapse


title: p53 +/- Whole Mouse Embryo Control C

tag: C57BL/6, p53 +/- males and females, GD8.5-9 whole embryos collected 5h after control treatment.


title: Patient 09 with small cell lung cancer

tag: Annotation

tag: Position in Figure 1 (L to R)

tag: EGFR status

tag: K-ras Status

tag: p53 Status

tag: Gefitinib treatment

tag: Position in Figure 2 (L to R)


title: Mixture of normal tissue from 5 different patients, mixture no.1

tag: Age

tag: Sex

tag: Histology

tag: Smoking (BI)

tag: Expression profile-based classification

tag: Invasion

tag: Necrosis


title: p53 +/+ Whole Mouse Embryo Heat Shock D

tag: C57BL/6, p53 +/+ males and females, GD8.5-9 whole embryos collected 5h after heat shock treatment.


title: Patient 04 with small cell lung cancer

tag: pTNM

tag: pStage

tag: Status

tag: Survival (days)

tag: Evidence of relapse

tag: Site of relapse

tag: Grade

tag: BAC features


title: Patient 02 with small cell lung cancer

tag: Annotation

tag: Position in Figure 1 (L to R)

tag: EGFR status

tag: K-ras Status

tag: p53 Status

tag: Gefitinib treatment

tag: Position in Figure 2 (L to R)


title: Patient 024 with squamous cell carcinoma

tag: Age

tag: Sex

value: M

tag: Histology

value: SQ

tag: Smoking (BI)

value: IIIA

value: Dead

value: Y

value: Brain, local rec.

value: Wt

tag: Gefitinib treatment:

tag: Position in Figure 2 (L to R):

tag: Invasion:

tag: Necrosis:

tag: Grade:

tag: BAC features:


title: Patient 023 with squamous cell carcinoma

tag: Annotation

tag: pTNM

tag: pStage

value: IIB

tag: Status

tag: Survival (days)

tag: Evidence of relapse

tag: Site of relapse

value: Local rec


title: p53 -/- Whole Mouse Embryo Control A

tag: C57BL/6, p53 -/- males and females, GD8.5-9 whole embryos collected 5h after control treatment.


title: p53 +/+ Whole Mouse Embryo Control A

tag: C57BL/6, p53 +/+ males and females, GD8.5-9 whole embryos collected 5h after control treatment.


title: Patient 031 with squamous cell carcinoma

tag: Position in Figure 1 (L to R)

tag: Age

tag: Sex

tag: Histology

value: IA

value: Unknown

tag: Site of relapse:

tag: EGFR status

tag: K-ras Status

tag: p53 Status

value: Mut


title: Patient 032 with squamous cell carcinoma

tag: Annotation

tag: Smoking (BI)

tag: Gefitinib treatment

tag: Position in Figure 2 (L to R):

tag: Invasion:

tag: Necrosis:

tag: Grade:

tag: BAC features:


title: Patient 03 with small cell lung cancer

tag: pTNM

tag: pStage

tag: Status

tag: Survival (days)

tag: Evidence of relapse

tag: Site of relapse

tag: Position in Figure 2 (L to R)

tag: Expression profile-based classification

tag: Invasion

tag: Necrosis

tag: Grade

tag: BAC features


title: Patient 030 with squamous cell carcinoma

tag: Annotation

tag: Position in Figure 1 (L to R)

tag: Age

tag: Sex

tag: Histology

tag: Smoking (BI)

value: IB

value: Alive

value: N

tag: Site of relapse:

tag: EGFR status

tag: K-ras Status

tag: p53 Status

tag: Gefitinib treatment:

tag: Position in Figure 2 (L to R):


title: Patient 035 with squamous cell carcinoma

tag: pTNM

tag: pStage

tag: Status

tag: Survival (days)

tag: Evidence of relapse

tag: Site of relapse

value: LN (mediastinal)

tag: Invasion:

tag: Necrosis:

tag: Grade:

tag: BAC features:


title: Patient 022 with squamous cell carcinoma

tag: Annotation

tag: Position in Figure 1 (L to R)

tag: Age

tag: Sex

tag: Histology

tag: Smoking (BI)

value: PM


title: Patient 034 with squamous cell carcinoma

value: M

value: Kidney

tag: EGFR status

tag: K-ras Status

tag: p53 Status

tag: Gefitinib treatment:

tag: Position in Figure 2 (L to R):


title: Patient 026 with squamous cell carcinoma

value: SQ

tag: pTNM

tag: pStage

value: IIIB

tag: Status

tag: Survival (days)

tag: Evidence of relapse


title: Patient 07 with small cell lung cancer

value: SCLC

tag: Site of relapse

tag: Gefitinib treatment

tag: Position in Figure 2 (L to R)

tag: Expression profile-based classification

tag: Invasion

tag: Necrosis

tag: Grade

tag: BAC features


title: p53 +/+ Whole Mouse Embryo Heat Shock A

tag: C57BL/6, p53 +/+ males and females, GD8.5-9 whole embryos collected 5h after heat shock treatment.


title: Patient 028 with squamous cell carcinoma

tag: Annotation

tag: Position in Figure 1 (L to R)

tag: Age

tag: Sex

tag: Histology

tag: Smoking (BI)

value: IIIA

value: Dead

tag: Site of relapse:

tag: EGFR status

tag: K-ras Status

tag: p53 Status

tag: Invasion:

tag: Necrosis:

tag: Grade:

tag: BAC features:


title: Patient 027 with squamous cell carcinoma

tag: pTNM

tag: pStage

tag: Status

tag: Survival (days)

tag: Evidence of relapse

value: Wt

tag: Gefitinib treatment:

tag: Position in Figure 2 (L to R):


title: Patient 020 with squamous cell carcinoma

tag: Annotation

tag: Position in Figure 1 (L to R)

tag: Age

tag: Sex

value: F

tag: Histology

value: Y

tag: Site of relapse


title: Patient 019 with squamous cell carcinoma

tag: Smoking (BI)

value: IA

tag: Site of relapse:

tag: EGFR status

tag: K-ras Status

tag: p53 Status

tag: Invasion:


title: Patient 01 with small cell lung cancer

tag: pTNM

tag: pStage

tag: Status

tag: Gefitinib treatment

tag: Position in Figure 2 (L to R)

tag: Expression profile-based classification

tag: Invasion

tag: Necrosis

tag: Grade

tag: BAC features


title: Patient 05 with small cell lung cancer

tag: Annotation

tag: Position in Figure 1 (L to R)

tag: Age

tag: Sex

tag: Histology

tag: Survival (days)

tag: Evidence of relapse

tag: Site of relapse


title: Patient 029 with squamous cell carcinoma

tag: Smoking (BI)

tag: pTNM

tag: pStage

tag: Site of relapse:

tag: EGFR status

tag: K-ras Status

tag: p53 Status

tag: Gefitinib treatment:

tag: Position in Figure 2 (L to R):

tag: Invasion:

tag: Necrosis:

tag: Grade:

tag: BAC features:


title: Patient 021 with squamous cell carcinoma

tag: Annotation

tag: Position in Figure 1 (L to R)

tag: Age

tag: Sex

tag: Histology

tag: Status


title: Patient 015 with squamous cell carcinoma

tag: Smoking (BI)

tag: pTNM

tag: pStage

tag: Survival (days)

tag: Evidence of relapse

tag: Site of relapse

value: Mut


title: Patient 013 with squamous cell carcinoma

value: IIB

tag: Site of relapse:

tag: EGFR status

tag: K-ras Status

tag: p53 Status

tag: Gefitinib treatment:

tag: Position in Figure 2 (L to R):


title: Patient 018 with squamous cell carcinoma

tag: Annotation

tag: Position in Figure 1 (L to R)

value: IB

value: Alive

tag: Invasion:

tag: Necrosis:

tag: Grade:

tag: BAC features:


title: Patient 011 with squamous cell carcinoma

tag: Age

tag: Sex

tag: Histology

tag: Smoking (BI)

tag: pTNM

tag: Status

value: LN (mediastinal)


title: Patient 010 with squamous cell carcinoma

tag: pStage

tag: Survival (days)

tag: Evidence of relapse

tag: Site of relapse

value: PM

tag: EGFR status


title: Patient 008 with squamous cell carcinoma

tag: Annotation

value: M

tag: K-ras Status

tag: p53 Status

tag: Gefitinib treatment:

tag: Position in Figure 2 (L to R):


title: Patient 012 with squamous cell carcinoma

tag: Position in Figure 1 (L to R)

value: Bone

tag: Invasion:

tag: Necrosis:

tag: Grade:

tag: BAC features:


title: Patient 004 with squamous cell carcinoma

tag: Age

tag: Sex

tag: Histology

value: SQ

tag: Smoking (BI)

tag: pTNM

value: PM, brain


title: Patient 001 with squamous cell carcinoma

tag: pStage

tag: Status

tag: Survival (days)

tag: Evidence of relapse

value: N

tag: Site of relapse:


title: Patient 017 with squamous cell carcinoma

tag: Annotation

value: IIIA

tag: EGFR status

tag: K-ras Status

tag: p53 Status

tag: Gefitinib treatment:


title: Patient 009 with squamous cell carcinoma

tag: Position in Figure 1 (L to R)

value: Dead

tag: Site of relapse

value: Liver

tag: Position in Figure 2 (L to R):

tag: Invasion:

tag: Necrosis:

tag: Grade:


title: Patient 002 with large cell neuroendocrine carcinoma

tag: Age

tag: Sex

tag: Histology

value: LCNEC

tag: Smoking (BI)

tag: pTNM

value: Wt

tag: BAC features:


title: Patient 014 with squamous cell carcinoma

tag: Annotation

tag: pStage

tag: Status

tag: Survival (days)

tag: Evidence of relapse

value: Y

value: Local rec


title: Patient 016 with large-cell carcinoma

tag: Position in Figure 1 (L to R)

value: LA

tag: EGFR status

tag: K-ras Status

value: Mut

tag: p53 Status

tag: Gefitinib treatment:


title: Patient 025 with squamous cell carcinoma

value: IB

value: Alive

tag: Site of relapse:

tag: Position in Figure 2 (L to R):

tag: Invasion:

tag: Necrosis:

tag: Grade:


title: Patient 018 with large-cell carcinoma

tag: Age

tag: Sex

tag: Histology

tag: Smoking (BI)

tag: pTNM


title: Patient 006 with squamous cell carcinoma

tag: Annotation

tag: pStage

value: IA

tag: Status

tag: Survival (days)

tag: BAC features:


title: Patient 005 with squamous cell carcinoma

tag: Position in Figure 1 (L to R)

value: M

tag: Evidence of relapse

tag: EGFR status

tag: K-ras Status

tag: p53 Status


title: Patient 06 with small cell lung cancer

value: SCLC

tag: Site of relapse

tag: Gefitinib treatment

tag: Position in Figure 2 (L to R)

tag: Expression profile-based classification

tag: Invasion

tag: Necrosis

tag: Grade

tag: BAC features


title: Patient 033 with squamous cell carcinoma

tag: Annotation

tag: Age

tag: Sex

tag: Histology

value: SQ

tag: Smoking (BI)

tag: pTNM

tag: pStage

value: LN (mediastinal)

tag: Gefitinib treatment:

tag: Position in Figure 2 (L to R):

tag: Invasion:

tag: Necrosis:

tag: Grade:


title: Patient 001 with large cell neuroendocrine carcinoma

tag: Position in Figure 1 (L to R)

value: IIIB

tag: Status

tag: Survival (days)

tag: Evidence of relapse

tag: Site of relapse

value: Brain

tag: EGFR status

tag: K-ras Status

tag: p53 Status

tag: BAC features:


title: Patient 002 with squamous cell carcinoma

tag: Annotation

tag: Age

tag: Sex

tag: Histology

tag: Smoking (BI)

value: IIB

value: N

tag: Site of relapse:


title: Patient 015 with large-cell carcinoma

tag: pTNM

tag: pStage

tag: Gefitinib treatment:

tag: Position in Figure 2 (L to R):

tag: Invasion:

tag: Necrosis:


title: Patient 007 with squamous cell carcinoma

tag: Position in Figure 1 (L to R)

tag: Status

tag: Survival (days)

tag: Evidence of relapse

tag: Grade:


title: Patient 003 with squamous cell carcinoma

tag: Annotation

value: IIIA

value: Dead

tag: Site of relapse

value: PM

tag: EGFR status

tag: K-ras Status

tag: p53 Status

tag: BAC features:


title: Patient 011 with large-cell carcinoma

tag: Age

tag: Sex

tag: Histology

tag: Smoking (BI)

tag: pTNM

tag: Site of relapse:

value: Wt


title: Patient 014 with large-cell carcinoma

tag: Position in Figure 1 (L to R)

value: F

value: LA

tag: pStage

value: Y

tag: Gefitinib treatment:

tag: Position in Figure 2 (L to R):

tag: Invasion:

tag: Necrosis:


title: Patient 012 with large-cell carcinoma

tag: Annotation

tag: Status

tag: Survival (days)

tag: Evidence of relapse

tag: Site of relapse

value: PM, Local rec.

value: Mut

tag: Grade:


title: Patient 017 with large-cell carcinoma

tag: Age

tag: Sex

value: M

value: IB

value: Alive

tag: EGFR status

tag: K-ras Status

tag: p53 Status

tag: BAC features:


title: Patient 010 with large-cell carcinoma

tag: Position in Figure 1 (L to R)

tag: Histology

tag: Smoking (BI)

tag: pTNM

tag: pStage

tag: Site of relapse:


title: Patient 009 with large-cell carcinoma

tag: Annotation

tag: Status

tag: Gefitinib treatment:

tag: Position in Figure 2 (L to R):

tag: Invasion:

tag: Necrosis:


title: Patient 013 with large-cell carcinoma

tag: Age

tag: Sex

tag: Survival (days)

tag: Evidence of relapse

tag: Grade:


title: Patient 007 with large-cell carcinoma

tag: Position in Figure 1 (L to R)

value: IA

tag: EGFR status

tag: K-ras Status

tag: p53 Status

tag: BAC features:


title: Patient 008 with large-cell carcinoma

tag: Histology

tag: Smoking (BI)

tag: pTNM

tag: pStage

tag: Site of relapse


title: Patient 002 with large-cell carcinoma

tag: Annotation

value: IIA

tag: Status

tag: Site of relapse:

tag: Gefitinib treatment:

tag: Position in Figure 2 (L to R):

tag: Invasion:


title: Patient 005 with large-cell carcinoma

tag: Age

tag: Sex

value: IIIB

tag: Survival (days)

tag: Evidence of relapse

value: LN (mediastinal)

tag: Necrosis:

tag: Grade:


title: Patient 090 with adenocarcinoma

tag: Position in Figure 1 (L to R)

tag: Histology

value: AD

value: Local rec.

tag: EGFR status

tag: K-ras Status

tag: p53 Status

tag: Position in Figure 2 (L to R)

tag: Expression profile-based classification

value: Non-TRU

tag: Invasion

value: Definite

tag: Necrosis

value: Negative

tag: Grade

value: Poorly

tag: BAC features


title: Patient 004 with large-cell carcinoma

tag: Annotation

tag: Age

value: LA

tag: Smoking (BI)

tag: pTNM

tag: pStage

value: IIB

tag: Status

value: Dead

tag: Site of relapse

value: PM

value: Wt

tag: Gefitinib treatment:

tag: Position in Figure 2 (L to R):

tag: Invasion:

tag: BAC features:


title: Patient 002 with adenocarcinoma AS002

tag: Position in Figure 1 (L to R)

tag: Sex

value: M

tag: Histology

value: AS

value: IIIA

tag: Survival (days)

tag: Evidence of relapse

value: Y

value: Skin

tag: EGFR status

tag: K-ras Status

tag: p53 Status

value: Mut

tag: Necrosis:

tag: Grade:


title: Patient 006 with large-cell carcinoma

tag: Annotation

tag: Age

tag: Smoking (BI)

tag: pTNM

tag: pStage

value: IIIB

value: LN (mediastinal)


title: Patient 003 with adenocarcinoma AS003

value: IA

tag: Status

tag: Site of relapse

value: Brain

tag: Gefitinib treatment

tag: Position in Figure 2 (L to R):

tag: Invasion:


title: Patient 086 with adenocarcinoma

tag: Position in Figure 1 (L to R)

tag: Sex

value: F

tag: Histology

value: AD

tag: Survival (days)

tag: Gefitinib treatment:

tag: Position in Figure 2 (L to R)

tag: Expression profile-based classification

value: TRU-a

tag: Invasion

value: Definite

tag: Necrosis

value: Negative

tag: Grade

value: Moderately

tag: BAC features


title: Patient 004 with adenocarcinoma AS004

tag: Annotation

tag: Age

tag: Smoking (BI)

tag: pTNM

tag: pStage

value: Alive

tag: Evidence of relapse

value: N

tag: Site of relapse:

tag: EGFR status

value: Wt

tag: K-ras Status

tag: p53 Status

tag: Necrosis:

tag: Grade:

tag: BAC features:


title: Patient 003 with large-cell carcinoma

tag: Position in Figure 1 (L to R)

tag: Sex

value: M

tag: Histology

value: LA

value: IIB

tag: Status

value: Dead

tag: Survival (days)

tag: Gefitinib treatment:

tag: Position in Figure 2 (L to R):

tag: Invasion:


title: Patient 089 with adenocarcinoma

tag: Annotation

tag: Age

tag: Smoking (BI)

tag: pTNM

tag: pStage

value: Y

tag: Site of relapse

tag: Position in Figure 2 (L to R)

tag: Expression profile-based classification

value: Non-TRU

tag: Invasion

tag: Necrosis

tag: Grade

value: Poorly

tag: BAC features


title: Patient 085 with adenocarcinoma

tag: Position in Figure 1 (L to R)

tag: Sex

tag: Histology

tag: Status

tag: Evidence of relapse

tag: Site of relapse:

tag: EGFR status

tag: K-ras Status

tag: p53 Status

value: Positive


title: Patient 087 with adenocarcinoma

tag: Annotation

tag: Age

value: F

tag: Smoking (BI)

tag: pTNM

tag: pStage

tag: Survival (days)

value: PM, Liver

value: Mut

tag: Gefitinib treatment:


title: Patient 083 with adenocarcinoma

value: AD

value: IIA

tag: Site of relapse

value: Brain

tag: Position in Figure 2 (L to R)

tag: Expression profile-based classification

value: TRU-b

tag: Invasion

value: Definite but focal

tag: Necrosis

value: Focal

tag: Grade

tag: BAC features


title: Patient 001 with large-cell carcinoma

tag: Position in Figure 1 (L to R)

tag: Sex

value: M

tag: Histology

value: IB

tag: Status

value: Alive

tag: Evidence of relapse

value: N

tag: Site of relapse:

tag: EGFR status

value: Wt

tag: Position in Figure 2 (L to R):

tag: Invasion:

tag: Necrosis:

tag: Grade:

tag: BAC features:


title: Patient 088 with adenocarcinoma

tag: Annotation

tag: Age

tag: Smoking (BI)

tag: pTNM

tag: pStage

value: IIIA

value: Dead

tag: Survival (days)

value: Y

tag: Site of relapse

value: LN (neck)

tag: K-ras Status

tag: p53 Status

tag: Gefitinib treatment:

tag: Position in Figure 2 (L to R)

tag: Expression profile-based classification

value: Non-TRU

value: Definite


title: Patient 001 with adenocarcinoma AS001

tag: Position in Figure 1 (L to R)

tag: Sex

tag: Histology

value: AS

tag: Status

tag: Evidence of relapse

value: Bone

tag: EGFR status

tag: Position in Figure 2 (L to R):


title: Patient 084 with adenocarcinoma

tag: Annotation

tag: Age

value: AD

tag: Smoking (BI)

value: PM

value: Mut

tag: Invasion

tag: Necrosis

value: Positive

tag: Grade

value: Poorly

tag: BAC features


title: Patient 078 with adenocarcinoma

value: M

tag: pTNM

tag: pStage

value: IB

tag: Survival (days)

tag: Site of relapse

tag: K-ras Status

tag: p53 Status

tag: Gefitinib treatment:


title: Patient 077 with adenocarcinoma

tag: Position in Figure 1 (L to R)

tag: Sex

value: F

tag: Histology

value: IA

tag: Status

value: Alive

tag: Evidence of relapse

value: N

tag: Site of relapse:

tag: Position in Figure 2 (L to R)

tag: Expression profile-based classification

value: TRU-a

value: Definite but focal

value: Negative

value: Well


title: Patient 073 with adenocarcinoma

tag: Annotation

tag: Age

tag: Smoking (BI)

value: Dead

value: Y

value: local rec

tag: EGFR status

value: Wt

tag: Invasion

value: Definite

tag: Necrosis

value: Focal

tag: Grade


title: Patient 080 with adenocarcinoma

value: AD

tag: pTNM

tag: pStage

tag: Survival (days)

value: Mut

tag: K-ras Status

tag: p53 Status

value: Moderately

tag: BAC features


title: Patient 072 with adenocarcinoma

tag: Position in Figure 1 (L to R)

tag: Sex

value: M

tag: Histology

value: IIIA

tag: Status

tag: Evidence of relapse

tag: Gefitinib treatment:

value: Poorly


title: Patient 081 with adenocarcinoma

tag: Annotation

tag: Age

value: F

tag: Smoking (BI)

tag: Site of relapse

value: PM

tag: Position in Figure 2 (L to R)

tag: Expression profile-based classification

value: Non-TRU

value: Positive


title: Patient 067 with adenocarcinoma

tag: pTNM

tag: pStage

value: IA

value: Alive

value: N

tag: Site of relapse:

tag: EGFR status

value: TRU-b

tag: Invasion

value: Not obvious

tag: Necrosis

value: Negative

tag: Grade

value: Well


title: Patient 074 with adenocarcinoma

tag: Position in Figure 1 (L to R)

tag: Sex

tag: Histology

value: AD

tag: Survival (days)

value: Wt

tag: K-ras Status

tag: p53 Status

value: Definite

tag: BAC features


title: Patient 075 with adenocarcinoma

tag: Annotation

tag: Age

value: M

tag: Smoking (BI)

value: IB

tag: Status

value: Dead

tag: Evidence of relapse

value: Y

tag: Site of relapse

value: Local rec.

value: Mut

tag: Gefitinib treatment:


title: Patient 079 with adenocarcinoma

tag: pTNM

tag: pStage

value: IIB

value: Bone

tag: EGFR status

tag: Position in Figure 2 (L to R)

tag: Expression profile-based classification

value: Non-TRU

tag: Invasion

value: Positive

value: Poorly


title: Patient 071 with adenocarcinoma

tag: Position in Figure 1 (L to R)

tag: Sex

tag: Histology

value: IA

value: Alive

tag: Survival (days)

value: N

tag: Site of relapse:

value: TRU-b

tag: Necrosis

tag: Grade


title: Patient 064 with adenocarcinoma

tag: Annotation

tag: Age

value: AD

tag: Smoking (BI)

tag: Status

value: Wt

tag: K-ras Status

tag: p53 Status

value: Negative

tag: BAC features


title: Patient 068 with adenocarcinoma

value: M

tag: pTNM

tag: pStage

tag: Evidence of relapse

tag: Site of relapse

value: PM?bone

tag: EGFR status

tag: Gefitinib treatment

tag: Position in Figure 2 (L to R)

value: Definite

value: Moderately


title: Patient 065 with adenocarcinoma

tag: Position in Figure 1 (L to R)

tag: Sex

value: F

tag: Histology

tag: Survival (days)

tag: Site of relapse:

value: Mut

tag: Gefitinib treatment:

tag: Expression profile-based classification

tag: Invasion

value: Focal


title: Patient 062 with adenocarcinoma

tag: Annotation

tag: Age

tag: Smoking (BI)

value: IIA

tag: Status

value: Dead

value: Y

value: Liver

tag: K-ras Status

tag: p53 Status

value: Non-TRU

tag: Necrosis

tag: Grade


title: Patient 059 with adenocarcinoma

tag: pTNM

tag: pStage

value: IB

value: Alive

tag: Evidence of relapse

value: N

tag: EGFR status

tag: Position in Figure 2 (L to R)

value: Poorly

tag: BAC features


title: Patient 063 with adenocarcinoma

tag: Position in Figure 1 (L to R)

tag: Sex

tag: Histology

value: AD

value: IA

tag: Survival (days)

tag: Site of relapse

value: PM

value: Wt

tag: Gefitinib treatment:

value: Negative


title: Patient 070 with adenocarcinoma

tag: Annotation

tag: Age

value: F

tag: Smoking (BI)

value: IIIA

tag: Status

value: Bone

tag: Expression profile-based classification

value: TRU-b

tag: Invasion

value: Definite

value: Well


title: Patient 016 with squamous cell carcinoma

value: M

value: SQ

tag: pTNM

tag: pStage

value: IIIB

value: Dead

value: Y

value: Bone, liver

tag: K-ras Status

tag: p53 Status

tag: Position in Figure 2 (L to R):

tag: Invasion:

tag: Necrosis:

tag: Grade:

tag: BAC features:


title: Patient 056 with adenocarcinoma

tag: Position in Figure 1 (L to R)

tag: Sex

tag: Histology

value: AD

value: IB

tag: Survival (days)

tag: Evidence of relapse

tag: Site of relapse

tag: EGFR status

tag: Gefitinib treatment

tag: Position in Figure 2 (L to R)

value: Not obvious

tag: Necrosis

tag: Grade

tag: BAC features


title: Patient 061 with adenocarcinoma

tag: Annotation

tag: Age

tag: Smoking (BI)

tag: pTNM

tag: pStage

value: IA

tag: Status

value: Alive

value: N

tag: Site of relapse:

value: Wt

tag: K-ras Status

tag: p53 Status

tag: Gefitinib treatment:

tag: Expression profile-based classification

value: Non-TRU

tag: Invasion

value: Moderately


title: Patient 060 with adenocarcinoma

tag: Position in Figure 1 (L to R)

tag: Sex

tag: Histology

tag: Survival (days)

tag: Evidence of relapse

tag: Site of relapse

value: LN (neck)

tag: EGFR status

value: Mut

value: Definite

value: Positive

value: Poorly


title: Patient 066 with adenocarcinoma

tag: Annotation

tag: Age

value: M

tag: Smoking (BI)

tag: Position in Figure 2 (L to R)

value: TRU-b

value: Definite but focal

tag: Necrosis

value: Negative

tag: Grade

value: Well

tag: BAC features


title: Patient 053 with adenocarcinoma

value: AD

tag: pTNM

tag: pStage

value: IIIA

tag: Status

value: Dead

value: Y

tag: K-ras Status

tag: p53 Status

tag: Gefitinib treatment:


title: Patient 069 with adenocarcinoma

tag: Position in Figure 1 (L to R)

tag: Sex

value: F

tag: Histology

value: IA

value: Alive

tag: Survival (days)

value: PM

value: Wt

tag: Gefitinib treatment

tag: Expression profile-based classification

tag: Invasion

value: Focal


title: Patient 058 with adenocarcinoma

tag: Annotation

tag: Age

tag: Smoking (BI)

tag: Evidence of relapse

tag: Site of relapse

value: Brain

tag: EGFR status

value: Mut

tag: Position in Figure 2 (L to R)

value: Non-TRU

value: Definite

value: Moderately


title: Patient 054 with adenocarcinoma

tag: pTNM

tag: pStage

value: IIIB

tag: Status

value: N

tag: Site of relapse:

tag: K-ras Status

tag: Necrosis

value: Negative

tag: Grade

value: Poorly

tag: BAC features


title: Patient 057 with adenocarcinoma

tag: Position in Figure 1 (L to R)

tag: Sex

tag: Histology

value: AD

value: IB

value: Dead

tag: Survival (days)

value: Local rec.

tag: p53 Status

tag: Gefitinib treatment

tag: Expression profile-based classification

value: Not obvious

value: Well


title: Patient 055 with adenocarcinoma

tag: Annotation

tag: Age

value: F

tag: Smoking (BI)

value: IIIA

value: Alive

tag: Evidence of relapse

tag: EGFR status

value: Wt

tag: Gefitinib treatment:

tag: Invasion


title: Patient 052 with adenocarcinoma

tag: pTNM

tag: pStage

tag: Status

tag: Site of relapse:

tag: K-ras Status

tag: Position in Figure 2 (L to R)

value: Non-TRU

tag: Necrosis

value: Positive


title: Patient 050 with adenocarcinoma

tag: Position in Figure 1 (L to R)

tag: Sex

value: M

tag: Histology

tag: Survival (days)

value: Unknown

value: Mut

tag: p53 Status

value: Definite but focal

tag: Grade

tag: BAC features


title: Patient 048 with adenocarcinoma

tag: Annotation

tag: Age

tag: Smoking (BI)

value: IA

tag: Evidence of relapse

value: N

tag: EGFR status

tag: Expression profile-based classification

value: TRU-b

value: Negative

value: Moderately


title: Patient 049 with adenocarcinoma

value: AD

tag: pTNM

tag: pStage

value: IIIB

tag: Status

value: Dead

value: Y

tag: Site of relapse

value: Brain

tag: Gefitinib treatment:

tag: Invasion

value: Definite

value: Poorly


title: Patient 047 with adenocarcinoma

tag: Position in Figure 1 (L to R)

tag: Sex

tag: Histology

value: IIA

value: Alive

tag: Site of relapse:

tag: K-ras Status

value: Wt

tag: Position in Figure 2 (L to R)

value: Not obvious

tag: Necrosis

value: Well


title: Patient 046 with adenocarcinoma

tag: Annotation

tag: Age

value: F

tag: Smoking (BI)

value: IIB

tag: Survival (days)

value: Bone

value: Mut

tag: p53 Status

tag: Grade

tag: BAC features


title: Patient 051 with adenocarcinoma

tag: pTNM

tag: pStage

value: IB

tag: Status

tag: Evidence of relapse

value: N

tag: EGFR status

tag: Expression profile-based classification

value: TRU-a

value: Positive


title: Patient 045 with adenocarcinoma

tag: Position in Figure 1 (L to R)

tag: Sex

tag: Histology

value: AD

value: Y

tag: Site of relapse

value: Adrenal

tag: Gefitinib treatment:

value: Non-TRU

tag: Invasion

value: Negative


title: Patient 040 with adenocarcinoma

tag: Annotation

tag: Age

tag: Smoking (BI)

value: IIIA

value: Dead

tag: K-ras Status

tag: Position in Figure 2 (L to R)

value: Definite

tag: Necrosis

value: Poorly


title: Patient 038 with adenocarcinoma

value: F

tag: pTNM

tag: pStage

tag: Survival (days)

value: Local rec.

value: Wt

tag: p53 Status

tag: Grade

value: Moderately

tag: BAC features


title: Patient 042 with adenocarcinoma

tag: Position in Figure 1 (L to R)

tag: Sex

value: M

value: IA

tag: Status

value: Alive

tag: Evidence of relapse

tag: Site of relapse:

tag: EGFR status

tag: Expression profile-based classification

value: Definite but focal

value: Well


title: Patient 039 with adenocarcinoma

tag: Annotation

tag: Age

tag: Histology

value: AD

tag: Smoking (BI)

value: IB

value: N

value: Mut

tag: Gefitinib treatment:

value: TRU-a

tag: Invasion


title: Patient 041 with adenocarcinoma

tag: pTNM

tag: pStage

value: IIIA

value: Dead

tag: Survival (days)

value: Y

tag: Site of relapse

value: PM

tag: K-ras Status

tag: Position in Figure 2 (L to R)

tag: Necrosis

value: Negative


title: Patient 082 with adenocarcinoma

tag: Position in Figure 1 (L to R)

tag: Sex

tag: Status

tag: Evidence of relapse

value: Wt

tag: p53 Status

value: Non-TRU

value: Definite

tag: Grade

tag: BAC features


title: Patient 043 with adenocarcinoma

tag: Annotation

tag: Age

value: M

tag: Histology

tag: Smoking (BI)

tag: Site of relapse:

tag: EGFR status

tag: Expression profile-based classification

value: Positive

value: Poorly


title: Patient 044 with adenocarcinoma

value: F

tag: pTNM

tag: pStage

tag: Survival (days)

tag: Site of relapse

tag: K-ras Status

tag: Gefitinib treatment

value: TRU-b

tag: Invasion


title: Patient 034 with adenocarcinoma

tag: Position in Figure 1 (L to R)

tag: Sex

value: AD

tag: Status

value: Alive

tag: Evidence of relapse

value: LN (neck)

tag: p53 Status

tag: Gefitinib treatment:

tag: Position in Figure 2 (L to R)

tag: Necrosis


title: Patient 035 with adenocarcinoma

tag: Annotation

tag: Age

tag: Histology

tag: Smoking (BI)

value: IIB

value: N

tag: Site of relapse:

tag: EGFR status

value: TRU-a

tag: Grade

value: Well

tag: BAC features


title: Patient 027 with adenocarcinoma

tag: pTNM

tag: pStage

value: Dead

tag: Survival (days)

value: Y

tag: Site of relapse

value: PM

value: Mut

tag: K-ras Status

tag: Expression profile-based classification

tag: Invasion


title: Patient 028 with adenocarcinoma

tag: Position in Figure 1 (L to R)

tag: Sex

value: IA

tag: Status

tag: Evidence of relapse

value: Wt

tag: p53 Status

tag: Gefitinib treatment:

tag: Position in Figure 2 (L to R)

value: Not obvious

value: Negative


title: Patient 036 with adenocarcinoma

tag: Annotation

tag: Age

value: F

tag: Histology

tag: Smoking (BI)

value: IB

tag: Site of relapse:

tag: EGFR status

tag: Necrosis


title: Patient 029 with adenocarcinoma

value: M

value: AD

tag: pTNM

tag: pStage

tag: Survival (days)

tag: K-ras Status

value: Non-TRU

value: Definite

tag: Grade

value: Poorly

tag: BAC features


title: Patient 037 with adenocarcinoma

tag: Position in Figure 1 (L to R)

tag: Sex

tag: Status

value: Alive

tag: Evidence of relapse

tag: Site of relapse

tag: Gefitinib treatment

tag: Expression profile-based classification

value: TRU-a

tag: Invasion

value: Definite but focal


title: Patient 033 with adenocarcinoma

tag: Annotation

tag: Age

tag: Histology

tag: Smoking (BI)

value: IIIB

value: Dead

value: Y

tag: p53 Status

tag: Gefitinib treatment:

tag: Position in Figure 2 (L to R)

value: Well


title: Patient 025 with adenocarcinoma

tag: pTNM

tag: pStage

tag: Survival (days)

value: N

tag: Site of relapse:

tag: EGFR status

value: Wt

tag: K-ras Status

value: Mut

tag: Necrosis

value: Positive

tag: Grade

value: Moderately


title: Patient 030 with adenocarcinoma

tag: Position in Figure 1 (L to R)

tag: Sex

value: M

value: IB

tag: Status

tag: Evidence of relapse

tag: Expression profile-based classification

tag: BAC features


title: Patient 031 with adenocarcinoma

tag: Annotation

tag: Age

value: F

tag: Histology

value: AD

tag: Smoking (BI)

tag: Site of relapse

value: PM

tag: p53 Status

tag: Gefitinib treatment

value: TRU-b

tag: Invasion

value: Not obvious

value: Negative


title: Patient 026 with adenocarcinoma

tag: pTNM

tag: pStage

value: IA

value: Alive

tag: Survival (days)

tag: Site of relapse:

tag: EGFR status

tag: K-ras Status

tag: Gefitinib treatment:

tag: Position in Figure 2 (L to R)


title: Patient 021 with adenocarcinoma

tag: Position in Figure 1 (L to R)

tag: Sex

tag: Status

tag: Evidence of relapse

tag: Expression profile-based classification

value: TRU-a

value: Definite

tag: Necrosis

tag: Grade

tag: BAC features


title: Patient 023 with adenocarcinoma

tag: Annotation

tag: Age

tag: Histology

tag: Smoking (BI)

value: N

tag: p53 Status

tag: Invasion


title: Patient 032 with adenocarcinoma

tag: pTNM

tag: pStage

tag: Survival (days)

value: Y

tag: Site of relapse

value: Bone

tag: EGFR status

value: Wt

tag: K-ras Status

value: Non-TRU

value: Poorly


title: Patient 022 with adenocarcinoma

tag: Position in Figure 1 (L to R)

tag: Sex

tag: Status

tag: Evidence of relapse

tag: Site of relapse:

tag: Gefitinib treatment:

tag: Position in Figure 2 (L to R)

value: Definite but focal

value: Well


title: Patient 019 with adenocarcinoma

tag: Annotation

tag: Age

value: M

tag: Histology

value: AD

value: IIIA

value: Dead

value: LN (mediastinal)

tag: Expression profile-based classification

tag: Necrosis

value: Focal

tag: Grade

tag: BAC features


title: Patient 020 with adenocarcinoma

value: F

tag: Smoking (BI)

tag: pTNM

tag: pStage

value: Alive

tag: Survival (days)

tag: p53 Status

value: TRU-b

tag: Invasion

value: Negative

value: Moderately


title: Patient 017 with adenocarcinoma

tag: Position in Figure 1 (L to R)

tag: Sex

value: IA

tag: Status

tag: Evidence of relapse

value: N

tag: EGFR status

tag: K-ras Status

value: Mut

value: TRU-a

value: Definite


title: Patient 018 with adenocarcinoma

tag: Annotation

tag: Age

tag: Histology

value: IB

value: Y

tag: Site of relapse

value: Local rec.

value: Wt

tag: Gefitinib treatment:

tag: Position in Figure 2 (L to R)

value: Definite but focal

value: Well


title: Patient 014 with adenocarcinoma

value: M

value: AD

tag: Smoking (BI)

tag: pTNM

value: IIIA

value: Dead

value: LN (mediastinal)

tag: Expression profile-based classification

value: Non-TRU

tag: Necrosis

tag: Grade

tag: BAC features


title: Patient 016 with adenocarcinoma

tag: Position in Figure 1 (L to R)

tag: Sex

value: F

tag: pStage

value: Alive

tag: Survival (days)

tag: Site of relapse:

tag: p53 Status

tag: Invasion

value: Positive

value: Moderately


title: Patient 013 with adenocarcinoma

tag: Annotation

tag: Age

tag: Histology

value: IIB

tag: Status

tag: Evidence of relapse

value: Liver

tag: EGFR status

value: Mut

tag: K-ras Status

value: TRU-b

value: Definite


title: Patient 009 with adenocarcinoma

tag: Smoking (BI)

tag: pTNM

value: Y

tag: Site of relapse

value: Liver, adrenal

value: Wt

tag: Gefitinib treatment:

tag: Position in Figure 2 (L to R)

tag: Expression profile-based classification

value: TRU-a

tag: Necrosis

value: Poorly


title: Patient 006 with adenocarcinoma

tag: Position in Figure 1 (L to R)

tag: Sex

value: M

value: AD

tag: pStage

value: IIIA

value: Dead

tag: Survival (days)

value: Brain

tag: Grade

tag: BAC features


title: Patient 007 with adenocarcinoma

tag: Annotation

tag: Age

value: F

tag: Histology

value: IA

tag: Status

value: Alive

value: N

tag: Site of relapse:

tag: p53 Status

tag: Invasion

value: Definite but focal

value: Negative


title: Patient 008 with adenocarcinoma

tag: Smoking (BI)

tag: pTNM

value: IIIB

tag: Evidence of relapse

tag: EGFR status

tag: K-ras Status

value: Mut

tag: Gefitinib treatment:

value: Well


title: Patient 015 with adenocarcinoma

tag: Position in Figure 1 (L to R)

tag: Sex

tag: pStage

value: Wt

tag: Position in Figure 2 (L to R)

tag: Expression profile-based classification

value: Definite

tag: Necrosis


title: Patient 011 with adenocarcinoma

tag: Annotation

tag: Age

tag: Histology

value: IB

tag: Survival (days)

value: Y

tag: Site of relapse

value: PM

value: TRU-b

tag: Grade

value: Moderately

tag: BAC features


title: 1dpa control 2

status: Public on Jan 31 2009

city: Corvallis

first: Robert

middle: L

last: Tanguay

state: OR

department: EMT

institute: Oregon State University

description: The caudal fin of zebrafish larvae at 2day post fertilization was amputated. Regenerating fin tissue was collected at 2dpf, 1,  2 and 3 days post amputation for mRNA abundance analysis.

hyb_protocol: Hybridization was conducted as stipulated by Affymetrix GeneChip Expression Analysis Technical Manual (701021 Rev. 5).

scan_protocol: Affymetrix fluidics station 400 was used to wash the arrays. Arrays were scanned with an Affymetrix scanner 3000.

data_processing: Data was GC-RMA preprocessed and each gene was normalized to the median using Gene Spring 7.1 software.

label: Labeling and probe processing was conducted under manufactures recommendations.

organism: Danio rerio

source_name: 1 day post amputation larval regenerating fin; replicate 2

label_protocol: A total of 100ng of RNA from the larval fin tissue  at 2dpf, and 1, 2 and 3 dpa were used to generate biotinylated complementary RNA (cRNA) using the Two-Cycle Target Labeling kit (Affymetrix, Santa Clara, CA).

extract_protocol: Caudal fins from two day old embryos (AB strain, Eugene, OR) were amputated. The caudal fin at 2dpf were used as the unamputaed control and the larvae were reared until 1, 2 and 3 days post amputation (dpa) when their regenerating fin tissue was amputated and collected for RNA analysis. RNA was extracted from the fin tissue using the RNAqueous Micro kit (Ambion, Austin, TX). Three groups at each time point, each comprised of 150 larval fins, were pooled to make an individual replicate. The quality and quantity of RNA was analyzed by UV absorbance. The abundance of ribosomal RNA and degree of degradation was determined in electropherogram patterns using the 2100 Bioanalyzer and RNA 6000 Nano chips (Agilent Technologies, Palo Alto, CA).

tag: AB strain larval zebrafish - regenerating caudal fin.


title: 1dpa Beclo 2

description: The caudal fin of zebrafish larvae at 2day post fertilization were amputated, follwed by exposure with Beclomethsone or vehicle. Regenerating fin tissue was collected at 1days post amputation for mRNA abundance analysis.

source_name: 1 day post amputation fin; Beclo Exposed; replicate 2

label_protocol: A total of 100ng of RNA from the larval fin tissue (+/-Beclomethsone) at 1dpa were used to generate biotinylated complementary RNA (cRNA) using the Two-Cycle Target Labeling kit (Affymetrix, Santa Clara, CA).

extract_protocol: Caudal fins from two day old embryos (AB strain, Eugene, OR) were amputated and the animals were exposed to either DMSO (vehicle control) or 1uM Beclomethasone (Sigma) in the water for 1dpa. After several rinses in fish water, the regenerating fin tissue was amputated and collected for RNA analysis. RNA was extracted from the fin tissue using the RNAqueous Micro kit (Ambion, Austin, TX). Three groups at each time point and treatment, each comprised of 150 larval fins, were pooled to make an individual replicate. The quality and quantity of RNA was analyzed by UV absorbance. The abundance of ribosomal RNA and degree of degradation was determined in electropherogram patterns using the 2100 Bioanalyzer and RNA 6000 Nano chips (Agilent Technologies, Palo Alto, CA).

tag: AB strain larval zebrafish - regenerating caudal fin


title: Patient 002 with adenocarcinoma

value: AD

tag: Smoking (BI)

tag: pTNM

tag: Status

tag: Evidence of relapse

tag: Site of relapse:

tag: EGFR status

tag: K-ras Status

tag: p53 Status

value: TRU-a

tag: Invasion


title: 1dpa Beclo 3

source_name: 1 day post amputation fin; Beclo Exposed; replicate 3


title: Patient 003 with adenocarcinoma

tag: Annotation

tag: Position in Figure 1 (L to R)

tag: Age

tag: Sex

value: F

tag: pStage

value: IIIA

value: Dead

tag: Gefitinib treatment:

tag: Position in Figure 2 (L to R)

tag: Expression profile-based classification

tag: Necrosis


title: Patient 010 with adenocarcinoma

tag: Histology

tag: Smoking (BI)

tag: pTNM

value: IA

value: Alive

tag: Survival (days)

value: N

value: Not obvious

tag: Grade

tag: BAC features


title: Patient 001 with adenocarcinoma

value: M

tag: Status

tag: Evidence of relapse

tag: Site of relapse

tag: EGFR status

value: Mut

tag: K-ras Status

tag: p53 Status

value: Negative

value: Poorly


title: 14 day 60 uM # 22

status: Public on Jan 27 2009

city: morelia

first: alfonso

last: méndez-bravo

state: michoacan

address: ciudad universitaria

department: instituto de investigaciones químico-biológicas

institute: universidad michoacana de san nicolas de hidalgo

hyb_protocol: Probes were mixed, concentrated by precipitation and resuspended in the hybridization solution (50% formamide, 5X SSC, 0.1% SDS, 0.4 μg/ l tRNA and 0.2 μg/ l Salmon Sperm DNA) for 14h. Slides were washed 5 min in each of the following solutions: a) 2x SSC, 0.1% SDS/42°C, b) 0.1x SSC/RT and two final washes with 0.05x SSC/RT carried out.

scan_protocol: Slides were scanned with an Axon GenePix 4000 B scanner at a resolution of 10 µm adjusting the laser and gain parameters to obtain similar levels of fluorescence intensity in both channels. Spot intensities were quantified using Axon GenePix Pro 6.0 image analysis software. The mean of the signals and the median of backgrounds were used for further analysis.

data_processing: Raw data were imported into the R 2.2.1 software (http://www.R-project.org). Background correction was done using the method "substract" whereas normalization of the signal intensities within slides was carried out using the "printtiploess" method (Yang et al., 2002) using the LIMMA package (Smyth et al., 2003, www.bioconductor.org).

organism: Arabidopsis thaliana

source_name: total RNA mix 1:1 shoot/root (w/w)

label_protocol: For each treatment by time combination, four biological replicates were used for probe synthesis. For each sample, 1.5 μg total RNA were amplified in the presence of aminoallyl-dUTP (Ambion) using the Aminoallyl Message Amp II kit (Ambion). Resulting amplified RNA probes were further labeled with fluorescent Cy3 and Cy5 dyes (Amersham). The fluorescent dye-labeled probes were then purified using RNeasy columns (Qiagen).

growth_protocol: Arabidopsis thaliana ecotype Col-0 seeds were surface sterilized with 95% (v/v) ethanol for 5 min and 20% (v/v) bleach for 7 min. After five washes in distilled water, seeds were germinated and grown on agar plates containing 0.2x Murashige and Skoog (0.2x MS) medium. Plates were placed vertically at an angle of 65˚ to allow root growth along the agar surface and to allow unimpeded growth of the hypocotyl into the air. For plant growth, we used a plant growth cabinet (Percival Scientific AR95L, Perry, IA), with a photoperiod of 16 h of light, 8 h of darkness, light intensity of 300 µmol/m-2/s-1 and temperature of 22 oC.

extract_protocol: Total RNA was isolated from shoots or roots using the Trizol reagent (Invitrogen) and purified with the RNeasy kit (Qiagen) following the manufacturer’s instructions.

treatment_protocol: 6 days after germination, plants were transferred to control or N-isobutyl decanamide 60 µM containing solid MS medium for different times prior to RNA extraction.

tag: Age

value: 14 days

tag: Treatment

value: 60 µM decanamide

tag: modified aRNA from total RNA was labeled

tag: Biological replicate 3


title: 1dpa control 1

source_name: 1 day post amputation larval regenerating fin; replicate 1

tag: AB strain larval zebrafish - regenerating caudal fin.


title: 1dpa Beclo 1

source_name: 1 day post amputation fin; Beclo Exposed; replicate 1

tag: AB strain larval zebrafish - regenerating caudal fin


title: Patient 004 with adenocarcinoma

tag: Annotation

tag: Position in Figure 1 (L to R)

tag: Sex

tag: Histology

tag: Smoking (BI)

tag: pStage

value: IIA

tag: Site of relapse:

value: Wt

tag: Gefitinib treatment:

tag: Position in Figure 2 (L to R)

tag: Expression profile-based classification

value: TRU-b

tag: Invasion

value: Definite

tag: Necrosis


title: Patient 024 with adenocarcinoma

tag: Age

value: AD

tag: pTNM

tag: Status

tag: Survival (days)

tag: Evidence of relapse

tag: EGFR status

tag: K-ras Status

tag: p53 Status

value: TRU-a

tag: Grade

tag: BAC features


title: 14 day 60 uM # 23

tag: Treatment

tag: modified aRNA from total RNA was labeled

tag: Biological replicate 4


title: 14 day 0 uM # 21

value: 0 µM decanamide

tag: Biological replicate 1


title: 14 day 0 uM # 24

tag: Biological replicate 2


title: 7 day 0 uM # 20

value: 7 days


title: 1dpa control 3

source_name: 1 day post amputation larval regenerating fin; replicate 3

tag: AB strain larval zebrafish - regenerating caudal fin.


title: 7 day 60 uM # 18

tag: Biological replicate 3


title: 7 day 60 uM # 19

tag: Age


title: 7 day 0 uM # 17


title: Patient 012 with adenocarcinoma

tag: Annotation

tag: Position in Figure 1 (L to R)

tag: Sex

tag: Histology

tag: Smoking (BI)

tag: pTNM

tag: pStage

value: IIIA

value: Alive

tag: Site of relapse:

tag: Gefitinib treatment:

tag: Position in Figure 2 (L to R)

tag: Expression profile-based classification

value: Non-TRU

tag: Invasion

tag: Necrosis

value: Focal

value: Moderately


title: 3 day 0 uM # 13

value: 3 days

tag: Treatment

tag: modified aRNA from total RNA was labeled

tag: Biological replicate 1


title: 3 day 60 uM # 15

tag: Age

tag: Biological replicate 4


title: 1 day 0 uM # 12

value: 1 days

tag: Biological replicate 2


title: 3 day 60 uM # 14

tag: Biological replicate 3


title: 14 day 60 uM # 5

value: 14 days


title: 14 day 60 uM # 8

value: 60 µM decanamide


title: 7 day 60 uM # 6


title: 1 day 60 uM # 7


title: 3 day 0 uM # 16


title: 7 day 60 uM # 3


title: 3 day 60 uM # 4


title: 1 day 0 uM # 9


title: 1 day 60 uM # 11


title: 1 day 0 uM # 32


title: 7 day 0 uM # 29


title: 7 day 0 uM # 28


title: 14 day 0 uM # 30


title: 3 day 0 uM # 27


title: 3 day 60 uM # 1


title: 1 day 0 uM # 25


title: 1 day 60 uM # 2


title: 14 day 0 uM # 31


title: 3 day 0 uM # 26


title: Patient 005 with adenocarcinoma

tag: Annotation

tag: Position in Figure 1 (L to R)

tag: Sex

value: F

tag: Histology

tag: Status

value: Dead

tag: Survival (days)

tag: Evidence of relapse

value: Y

tag: Site of relapse

value: PM

tag: EGFR status

value: Mut

tag: K-ras Status

tag: p53 Status

value: Negative

tag: Grade

value: Well

tag: BAC features


title: WT80d(15) vs TG80d(21)

status: Public on Jan 01 2009

city: Miami

first: Roberta

last: Brambilla

state: FL

address: 1095 NW 14th Terrace

institute: Miller School of Medicine University of Miami

description:
1.  Brambilla, R., V. Bracchi-Ricard, W.H. Hu, B. Frydel, A. Bramwell, S. Karmally, E.J. Green, and J.R. Bethea. 2005. Inhibition of astroglial nuclear factor kappaB reduces inflammation and improves functional recovery after spinal cord injury. J Exp Med 202:145-156.
2.  Szalai, A.J., S. Nataf, X.Z. Hu, and S.R. Barnum. 2002. Experimental allergic encephalomyelitis is inhibited in transgenic mice expressing human C-reactive protein. J Immunol 168:5792-5797.

hyb_protocol: Equal amounts of labeled aRNA were hybridized to Agilent Whole Mouse Genome Oligo microarrays for 17 hours at 65°C according to manufacturer's instructions.

scan_protocol: The microarrays were scanned at 5 micron resolution using a GenePix 4100A scanner (Axon Instruments at Molecular Devices) and the resulting images were analyzed with the software package GenePix Pro 5.1 (Axon Instruments at Molecular Devices).

data_processing: Data extracted from the images were transferred to the software package Acuity 4.0 (Axon Instruments) for normalization and statistical analysis. Each array was normalized for signal intensities across the whole array and locally, using Lowess normalization. Features for further analysis were selected according to the following quality criteria: (1) at least 90% of the pixels in the spot had intensity higher than background plus two standard deviations; (2), there were less than 2% saturated pixels in the spot; (3) signal to noise ratio (defined as ratio of the background subtracted mean pixel intensity to standard deviation of background) was 3 or above for each channel; (4) the spot diameter was between 45 and 75 micron; (5) the regression coefficient of ratios of pixel intensity was 0.6 or above.

source_name: Spinal cords WT, induced with EAE at 80 days post-induction

label_protocol: 1ug of total RNA was amplified and labeled using Amino Allyl MessageAmp aRNA Amplification Kit (Ambion, Cat#1753) and Cy3- and Cy5-NHS ethers (Amersham, Cat # PA23001 and PA25001, respectively).

growth_protocol: Experiments were performed according to protocols approved by the Institutional Animal Care and Use Committee of the University of Miami. All mice used were obtained by breeding heterozygous GFAP-IkappaBalpha-dn males with WT females. WT littermates were used as controls. Animals were housed in a 12 hr light/dark cycle in a virus/antigen free facility with controlled temperature and humidity and provided with water and food ad libitum.

extract_protocol: To isolate total RNA from the samples, 1 mL of TRI Reagent (Molecular Research Center Cat #TRI-118) was added per 5 X 106 cells. The sample was then macerated using a Kinematica AG Polytron PT-2100 for 1 min. After a 5 min incubation at room temperature 0.2 volumes of chloroform was added and mixed, following by a 3 min incubation at room temperature and 10 min centrifugation at 12,000 g 4°C. The top aqueous layer was transferred to a new tube containing 0.5 volume of isopropanol and 2 to 10 ul of polyacryl carrier (Molecular Recearch Center, Cat #PC152). After mixing, the precipitate containing the total RNA was collected by 15 min of centrifugation at 12,000 g 4°C. The pellet was then washed two times with 70% ethanol. Total RNA was additionally purified with RNeasy Mini Kit (Qiagen, Cat # 74106). Total RNA yield was determined spectrophotometrically.

treatment_protocol: Mice were immunized with MOG(35-55) peptide to induce EAE, as previously described (2). MOG peptide was synthesized by standard 9-fluorenyl-methoxycarbonyl chemistry and was >95% pure as determined by reversed-phase-HPLC (Biosynthesis International, Lewisville, TX). Mice were injected subcutaneously on days 0 and 7 with 150 ug of MOG peptide emulsified in complete Freund’s adjuvant (DIFCO Laboratories, Detroit, MI). In addition, on days 0 and 2 post immunization (p.i.), mice were given pertussis toxin (500 ng/mouse, Sigma-Aldrich, St. Louis, MO) by intra-peritoneal injection. Mice were sacrificed 10, 17 or 80 days after induction of EAE.

tag: Strain

value: C57BL/6, WT

tag: Gender

value: female

tag: Age

value: 60 day

tag: Tissue

value: spinal cord

source_name: Spinal cords GFAP-IkappaBalpha-dn transgenic mice, induced with EAE at 80 days post-induction


title: WT17d(4) vs TG17d(7)

source_name: Spinal cords WT, induced with EAE at 17 days post-induction

source_name: Spinal cords GFAP-IkappaBalpha-dn transgenic mice, induced with EAE at 17 days post-induction


title: DF 4 h (Cy3) vs. 0 h (Cy5)

city: Charlestown

first: Jin Mo

last: Park

state: MA

address: 149 Thirteenth Street

department: Cutaneous Biology Research Center

institute: Massachusetts General Hospital

description: Replicate 2 of 2

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequentially with GE Wash Buffer 1 at room temperature and GE Wash Buffer 2 at 31°C.

data_processing: LOWESS normalized, background-subtracted data obtained from log2 of processed test signal/processed reference signal. Agilent software was used.

source_name: Dermal fibroblasts, IL-1-treated (4 h)

label_protocol: Fluorescent cRNA was generated from 5 µg of total RNA using Agilent Two-Color Quick Amp Labeling Kit. The reaction and purification conditions were based on the manufacturer's protocol.

growth_protocol: Mouse dermal fibroblasts were cultured in DMEM medium containing antibiotics and 10% FBS.

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

treatment_protocol: Cells were incubated with 20 ng/ml IL-1 for 0, 1, 2, or 4 h.

source_name: Dermal fibroblasts, untreated (0 h)


title: WTn(4) vs WT80d(14)

source_name: Spinal cords WT mice, naive


title: WT17d(1) vs WT80d(13)


title: DF 1 h (Cy3) vs. 0 h (Cy5)

description: Replicate 2 of 2

source_name: Dermal fibroblasts, IL-1-treated (1 h)


title: DF 2 h (Cy3) vs. 0 h (Cy5)

description: Replicate 2 of 2

source_name: Dermal fibroblasts, IL-1-treated (2 h)


title: DF 2 h (Cy5) vs. 0 h (Cy3)

description: Replicate 1 of 2


title: TG17d(1) vs TGn(5)

source_name: Spinal cords GFAP-IkappaBalpha-dn transgenic mice, naive


title: TGn(8) vs WTn(4)


title: WT80d(13) vs TG80d(26)


title: TG80d(21) vs TG17d(1)


title: DF 1 h (Cy5) vs. 0 h (Cy3)

description: Replicate 1 of 2

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequentially with GE Wash Buffer 1 at room temperature and GE Wash Buffer 2 at 31°C.ly with GE Wash Buffer 1 at room temperature and GE Wash Buffer 2 at 31°C.


title: TG80d(27) vs TGn(8)


title: TG10d(1-5) vs WT10d(4-3)

source_name: Spinal cords GFAP-IkappaBalpha-dn transgenic mice induced with EAE at 10 days post-induction

value: C57BL/6 GFAP-IkappaBalpha-dn transgenic

source_name: Spinal cords WT mice induced with EAE at 10 days post-induction


title: TGn(5) vs WTn(2)


title: WT10d(1-4) vs TG10d(1-5)

source_name: Spinal cords WT induced with EAE at 10 days post-induction

value: C57BL/6, GFAP-IkappaBalpha-dn transgenic (1)


title: TG10d(1-2) vs WT10d(1-4)


title: WTn(2) vs WT17d(1)


title: WTn(3) vs TGn(7)


title: TG17d(7) vs WT17d(1)

source_name: Spinal cords GFAP-IkappaBalpha-dn transgenic mice induced with EAE at 17 days post-induction

source_name: Spinal cords WTmice, induced with EAE at 17 days post-induction


title: Lymph Node H6

status: Public on Dec 31 2008

city: Lincoln

first: Rodger

last: Johnson

state: NE

address: University of Nebraska East Campus Loop Animal Science Bldg. A218i

department: Animal Science

institute: University of Nebraska

hyb_protocol: The samples were hybridized overnight using Ambion slide hyb buffer at 42ºC for 16 hours. Slides were washed per manufacturers’ suggestions and scanned with an Axon 4000B scanner.

scan_protocol: Images were quantified using an Axon 4000B scanner.

data_processing: Global Median Normalization was performed.  Data points (F635 Median - B635 and F532 Median - B532) falling in the range of -150 to 150 in intensity value and those with ratios less than -15 and greater than 15 were removed.

organism: Sus scrofa

source_name: Lymph Node H6

label_protocol: Two µg of total RNA was reverse-transcribed using oligo-DT primer and reagents from the Ambion Amino Allyl MessageAmp aRNA Amplification Kit (Ambion, Austin, TX). Following cRNA generation, 5 µg of cRNA was coupled to CY5.

extract_protocol: RNAs were extracted using Trizol-chlorofrom method.

value: Lymph Node; Line:HD; Viremia Class:High; Infection Status:Uninfected

source_name: Lymph Node Reference Sample

label_protocol: Two µg of total RNA was reverse-transcribed using oligo-DT primer and reagents from the Ambion Amino Allyl MessageAmp aRNA Amplification Kit (Ambion, Austin, TX). Following cRNA generation, 5 µg of cRNA was coupled to CY3.

tag: The reference sample was developed from four uninfected control full sibling littermates of infected pigs that had a Principle Component value of 0 and that were not included in the sample of 28 infected pigs used in the microarray experiment. The reference sample consisted of two pigs from Line Index and two pigs from Line HD. Tissue

value: Lymph Node


title: Lymph Node H5

source_name: Lymph Node H5


title: Lymph Node H2

source_name: Lymph Node H2


title: Lymph Node H1

source_name: Lymph Node H1


title: Lymph Node G4

source_name: Lymph Node G4

value: Lymph Node; Line:HD; Viremia Class:Low; Infection Status:Uninfected


title: Lymph Node G3

source_name: Lymph Node G3


title: Lymph Node G5

source_name: Lymph Node G5


title: Lymph Node G6

source_name: Lymph Node G6


title: Lymph Node G1

source_name: Lymph Node G1


title: Lymph Node G7

source_name: Lymph Node G7


title: Lymph Node F3

source_name: Lymph Node F3

value: Lymph Node; Line:Index; Viremia Class:High; Infection Status:Uninfected


title: Lymph Node H4

source_name: Lymph Node H4


title: Lymph Node F7

source_name: Lymph Node F7


title: Lymph Node G2

source_name: Lymph Node G2


title: Lymph Node H3

source_name: Lymph Node H3


title: Lymph Node F4

source_name: Lymph Node F4


title: Lymph Node F6

source_name: Lymph Node F6


title: TG80d(26) vs WT80d(15)

source_name: Spinal cords GFAP-IkappaBalpha-dn transgenic mice, induced with EAE at 80 days post-induction

source_name: Spinal cords WT, induced with EAE at 80 days post-induction


title: Lymph Node F5

source_name: Lymph Node F5

source_name: Lymph Node Reference Sample


title: Lymph Node H7

source_name: Lymph Node H7


title: Lymph Node F2

source_name: Lymph Node F2


title: WT80d(14) vs TG80d(27)


title: Lymph Node F1

source_name: Lymph Node F1


title: WT10d(10-4) vs TG10d(1-3)

source_name: Spinal cords WT mice induced with EAE at 10 days post-induction

source_name: Spinal cords GFAP-IkappaBalpha-dn transgenic mice induced with EAE at 10 days post-induction


title: Lymph Node E7

source_name: Lymph Node E7

value: Lymph Node; Line:Index; Viremia Class:Low; Infection Status:Uninfected


title: 1 day 60 uM # 10

source_name: total RNA mix 1:1 shoot/root (w/w)

value: 1 days

tag: Treatment

value: 60 µM decanamide

tag: modified aRNA from total RNA was labeled

tag: Biological replicate 3


title: DF 4 h (Cy5) vs. 0 h (Cy3)

description: Replicate 1 of 2

source_name: Dermal fibroblasts, IL-1-treated (4 h)

source_name: Dermal fibroblasts, untreated (0 h)


title: TG17d(3) vs WT17d(4)

source_name: Spinal cords GFAP-IkappaBalpha-dn transgenic mice, induced with EAE at 17 days post-induction

source_name: Spinal cords WT, induced with EAE at 17 days post-induction


title: Lymph Node E4

source_name: Lymph Node E4


title: Lymph Node E5

source_name: Lymph Node E5


title: Lymph Node E6

source_name: Lymph Node E6


title: Lymph Node E3

source_name: Lymph Node E3


title: Lymph Node D2

source_name: Lymph Node D2

value: Lymph Node; Line:HD; Viremia Class:High; Infection Status:Infected with PRRSV strain 97-7985


title: Lymph Node D5

source_name: Lymph Node D5

source_name: Lymph Node Reference Sample


title: Lymph Node D1

source_name: Lymph Node D1


title: Lymph Node C7

source_name: Lymph Node C7

value: Lymph Node; Line:HD; Viremia Class:Low; Infection Status:Infected with PRRSV strain 97-7985


title: Lymph Node D6

source_name: Lymph Node D6


title: Lymph Node E1

source_name: Lymph Node E1


title: Lymph Node D7

source_name: Lymph Node D7


title: Lymph Node C3

source_name: Lymph Node C3


title: Lymph Node C4

source_name: Lymph Node C4


title: Lymph Node C2

source_name: Lymph Node C2


title: Lymph Node D3

source_name: Lymph Node D3


title: Lymph Node E2

source_name: Lymph Node E2


title: Lymph Node C5

source_name: Lymph Node C5


title: Lymph Node B7

source_name: Lymph Node B7

value: Lymph Node; Line:Index; Viremia Class:High; Infection Status:Infected with PRRSV strain 97-7985


title: Lymph Node D4

source_name: Lymph Node D4


title: Lymph Node B6

source_name: Lymph Node B6


title: Lymph Node C6

source_name: Lymph Node C6


title: Lymph Node B5

source_name: Lymph Node B5


title: Lymph Node C1

source_name: Lymph Node C1

source_name: Lymph Node Reference Sample


title: Lymph Node B4

source_name: Lymph Node B4


title: Lymph Node B3

source_name: Lymph Node B3


title: Lymph Node B1

source_name: Lymph Node B1


title: Lymph Node A3

source_name: Lymph Node A3

value: Lymph Node; Line:Index; Viremia Class:Low; Infection Status:Infected with PRRSV strain 97-7985


title: Lymph Node A4

source_name: Lymph Node A4


title: Lymph Node A5

source_name: Lymph Node A5


title: Lymph Node A7

source_name: Lymph Node A7


title: Lymph Node A6

source_name: Lymph Node A6


title: Lymph A1

source_name: Lymph A1


title: Lung H5

source_name: Lung H5

value: Lung; Line:HD; Viremia Class:High; Infection Status:Uninfected

source_name: Lung Reference Sample

value: Lung


title: Lung G6

source_name: Lung G6

value: Lung; Line:HD; Viremia Class:Low; Infection Status:Uninfected


title: Lung G7

source_name: Lung G7


title: Lymph Node A2

source_name: Lymph Node A2


title: Lung E6

source_name: Lung E6

value: Lung; Line:Index; Viremia Class:Low; Infection Status:Uninfected


title: Lung H3

source_name: Lung H3


title: Lung F3

source_name: Lung F3

value: Lung; Line:Index; Viremia Class:High; Infection Status:Uninfected


title: Lung H4

source_name: Lung H4


title: Lung G4

source_name: Lung G4


title: Lung H1

source_name: Lung H1


title: Lung G1

source_name: Lung G1


title: Lung H6

source_name: Lung H6


title: Lung F4

source_name: Lung F4


title: Lung G2

source_name: Lung G2


title: Lung H7

source_name: Lung H7


title: Lung F2

source_name: Lung F2


title: Lung F6

source_name: Lung F6


title: Lung F1

source_name: Lung F1

source_name: Lung Reference Sample


title: Lung G3

source_name: Lung G3


title: Lung F5

source_name: Lung F5


title: Lung E5

source_name: Lung E5


title: Lung F7

source_name: Lung F7


title: Lung H2

source_name: Lung H2


title: Lung E7

source_name: Lung E7


title: Lung G5

source_name: Lung G5


title: Lung E4

source_name: Lung E4


title: Lung D3

source_name: Lung D3

value: Lung; Line:HD; Viremia Class:High; Infection Status:Infected with PRRSV strain 97-7985


title: Lung D6

source_name: Lung D6


title: Lung E3

source_name: Lung E3


title: Lung D1

source_name: Lung D1

value: Lung; Line:HD; Viremia Class:High; Infection Status:Infected PRRSV strain 97-7985


title: Human-LMD dissected breast cancer 9B

city: Sendai

first: Shuji

last: Nagasaki

state: Miyagi-ken

address: 2-1 Seiryo-machi, Aoba-ku

institute: Tohoku University Graduate School of Medicine

description:
Breast carcinoma were embedded in Tissue-Tek optimal cutting temperature compound(Sakura Finetechnical Co.Ltd., Tokyo, Japan) and frozen sectioned at a thickness of 8 micro mm. Approximately 5000 cells were laser transferred from the carcinoma tissue and applied to microarray analysis. Each population of the cells was estimated to be >98% homogeneous as determined by microscopic visualization of the captured cells.
Tissue estradiol concentrations were measured by liquid chromatography/electrospray tandem mass spectrometry (LC-MS/MS) analysis.

hyb_protocol: The standard protocol described in Affymetrix GeneChip expression analysis manual.

data_processing: Data processing was performed according to Affymetrix GeneChip expression analysis manual. Expression signals were extracted and normalized using MAS5.0.

source_name: human-LMD dissected breast cancer estradiol conc.:266pg/g

extract_protocol: Total RNA was extracted using RNeasy Mini Kit(Qiagen) according to the instruction manual

tag: Tissue:human-LMD dissected breast cancer

tag: Type:Invasive ductal carcinoma

tag: Tissue estradiol conc.:266pg/g


title: Lung D7

source_name: Lung D7


title: Lung D2

source_name: Lung D2


title: Lung D5

source_name: Lung D5

value: Lung; Line:HD; Viremia Level:High; Infection Status:Infected PRRSV strain 97-7985


title: Human-LMD dissected breast cancer 11B

scan_protocol: The standard protocol described in Affymetrix GeneChip expression analysis manual.

source_name: human-LMD dissected breast cancer estradiol conc.:325.42pg/g

tag: Tissue estradiol conc.:325.42pg/g


title: Human-LMD dissected breast cancer 15B

source_name: human-LMD dissected breast cancer estradiol conc.:550pg/g

label_protocol: The standard protocol described in Affymetrix GeneChip expression analysis manual.

tag: Tissue estradiol conc.:550pg/g


title: Lung C6

source_name: Lung C6

value: Lung; Line:HD; Viremia Class:Low; Infection Status:Infected with PRRSV strain 97-7985

source_name: Lung Reference Sample


title: Human-LMD dissected breast cancer 16B

source_name: human-LMD dissected breast cancer estradiol conc.:600pg/g

tag: Tissue estradiol conc.:600pg/g


title: Human-LMD dissected breast cancer 12B

source_name: human-LMD dissected breast cancer estradiol conc.:358.9pg/g

tag: Tissue estradiol conc.:358.9pg/g


title: Lung C7

source_name: Lung C7


title: Human-LMD dissected breast cancer 10B

source_name: human-LMD dissected breast cancer estradiol conc.:300pg/g

tag: Tissue estradiol conc.:300pg/g


title: Human-LMD dissected breast cancer 14B

source_name: human-LMD dissected breast cancer estradiol conc.:383.18pg/g

tag: Tissue estradiol conc.:383.18pg/g


title: Lung C4

source_name: Lung C4

value: Lung; Line:HD; Viremia Level:Low; Infection Status:Infected with PRRSV strain 97-7985


title: Lung E2

source_name: Lung E2


title: Lung D4

source_name: Lung D4


title: Lung C5

source_name: Lung C5


title: Human-LMD dissected breast cancer 13B

source_name: human-LMD dissected breast cancer estradiol conc.:381.5pg/g

tag: Tissue estradiol conc.:381.5pg/g


title: Human-LMD dissected breast cancer 7B

source_name: human-LMD dissected breast cancer estradiol conc.:40pg/g

tag: Tissue estradiol conc.:40pg/g


title: Lymph Node B2

source_name: Lymph Node B2

source_name: Lymph Node Reference Sample

value: Lymph Node


title: Human-LMD dissected breast cancer 8B

source_name: human-LMD dissected breast cancer estradiol conc.:241.18pg/g

tag: Tissue estradiol conc.:241.18pg/g


title: Human-LMD dissected breast cancer 6B

source_name: human-LMD dissected breast cancer estradiol conc.:18.21pg/g

tag: Tissue estradiol conc.:18.21pg/g


title: Lung C3

source_name: Lung C3

tag: Tissue

tag: The reference sample was developed from four uninfected control full sibling littermates of infected pigs that had a Principle Component value of 0 and that were not included in the sample of 28 infected pigs used in the microarray experiment. The reference sample consisted of two pigs from Line Index and two pigs from Line HD. Tissue


title: Lung C2

source_name: Lung C2

source_name: Lung Reference Sample


title: Human-LMD dissected breast cancer 4B

source_name: human-LMD dissected breast cancer estradiol conc.:9pg/g

tag: Tissue estradiol conc.:9pg/g


title: Human-LMD dissected breast cancer 1B

source_name: human-LMD dissected breast cancer estradiol conc.:under detection limit

tag: Tissue estradiol conc.:under detection limit


title: Lung B7

source_name: Lung B7 Source

value: Lung; Line:Index; Viremia Class:High; Infection Status:Infected with PRRSV strain 97-7985


title: Lung A5

source_name: Lung A5 Source

value: Lung; Line:Index; Viremia Class:Low; Infection Status:Infected with PRRSV strain 97-7985

tag: The reference sample was developed from four uninfected control full sibling littermates of infected pigs that had a PC value of 0 and that were not included in the sample of 28 infected pigs used in the microarray experiment. The reference sample consisted of two pigs from Line Index and two pigs from Line HD. Tissue


title: Lung C1

source_name: Lung C1 Source


title: Lung B2

source_name: Lung B2 Source


title: Lung B1

source_name: Lung B1 Source

value: Lung; Line:Index; Viremia Level:High; Infection Status:Infected with PRRSV strain 97-7985.


title: Human-LMD dissected breast cancer 2B

tag: Tissue:human-LMD dissected breast cancer

tag: Type:Invasive ductal carcinoma


title: Human-LMD dissected breast cancer 3B

source_name: human-LMD dissected breast cancer estradiol conc.:8pg/g

tag: Tissue estradiol conc.:8pg/g


title: Lung B3

source_name: Lung B3 Source

value: Lung; Line:Index; Viremia Class:High; Infection Status:Infected with PRRSV strain 97-7985.


title: Lung B5

source_name: Lung B5 Source


title: Lung B6

source_name: Lung B6 Source


title: Human-LMD dissected breast cancer 5B

source_name: human-LMD dissected breast cancer estradiol conc.:10.5pg/g

tag: Tissue estradiol conc.:10.5pg/g


title: Lung A6

source_name: Lung A6 Source

value: Lung; Line:Index; Viremia Class:Low; Infection Status:Infected with PRRSV strain 97-7985.


title: Lung B4

source_name: Lung B4 Source


title: CL1-5_CM WITH T1_10

city: Taichung

first: Chen-Yu

last: Lee

address: 250, Kuo Kuang Rd.

department: Institute of Biomedical Sciences

country: Taiwan

institute: National Chung Hsing University

description: The images captured by a scanner were converted from true color to a gray scale, and digitized by analysis software GenePix 5.0 (Axon, Union City, CA). All experiments were performed three times.

hyb_protocol: Microarray hybridization and Colorimetric detection: The membrane carrying the double-stranded cDNA targets was pre-hybridized in 3 ml of hybridization buffer (5× SSC, 0.1% N-lauroylsarcosine, 0.1% SDS, 1% blocking reagent made by Roche Molecular Biochemicals, and 50 ug/ml salmon sperm DNA) at 68 C for 1 hour before hybridization was carried out. cDNA probes were resuspended in 15 ul hybridization buffer containing 200 ug/ml d(A)10 and  400 ug/ml human COT-1 DNA (GIBCO-BRL; Gaithersburg, MD) to prevent non-specific binding, and were hybridized to the cDNA fragments on the membrane by a Southern hybridization procedure. The 15 ul reaction mixture was sealed with the microarray membrane in a hybridization assembly (SureSeal, Hybaid, Middlesex, UK) at 68 C for 12 hours. The membrane was then washed with 2× SSC containing 0.1% SDS for 5 min at room temperature followed by three washes with 0.1× SSC containing 0.1% SDS at 65 C for 15 min each. After hybridization, the membrane was blocked by 1 ml of 1% blocking reagent (Roche Molecular Biochemicals; Mannheim, Germany) containing 2% dextran sulphate at room temperature for 1 hour, and then was rinsed with 1 X TBS buffer solution (10 mM Tris-HCl, pH 7.4, 150 mM NaCl, 0.3% BSA). To detect the spots on the membrane in a single-color mode, AP-conjugated anti-Dig (GIBCO-BRL; Gaithersburg, MD) was employed. The membrane was incubated with a 3-ml mixture containing 1000 X diluted AP-conjugated anti-Dig, 4% polyethylene glycol 8000 (Sigma, St. Louis, MO), and 0.3% BSA in 1 X TBS buffer for 2 hours. The membrane was then washed with 1 X TBS buffer three times, for 10 min each. The chromogen was generated by treating the membrane with AP substrate in 1 X substrate buffer (pH=9.5) for 1 hour at 37 C. The color development reactions were stopped by AP stop solution.

scan_protocol: To measure the expression levels of the genes, the microarray was scanned using a flatbed scanner (PowerLook 3000, UMAX, Taipei, Taiwan).

data_processing:
The averaged intensity for each gene (there were three copies on a chip for each gene) was used for the subsequent analyses. To reduce the variation arising from experimental results derived from different microarrays, the intensity values of the spots from each microarray were rescaled using a quantile normalization method and a housekeeping gene, GAPDH. To reduce background noise, any background intensity lower than 2,330 was assigned the value of 2,330.
Genes were clustered into groups on the basis of expression profiles by the self-organizing maps (SOMs) algorithm using the Acuity 3.0 program (Axon Instruments, Union City, CA). After cluster analysis by the SOM method, genes whose expression profiles correlated with the concentration of tanshinone I were identified.

label: 30 ug of total RNAs was labeled with digoxigenin during reverse transcription.

source_name: CL1-5 with condition medium and Tanshinone I 10 ug/ml

label_protocol: The labeling reactions were performed during reverse transcription in the presence of 6 uM random primers; 0.5 mM each dATP, dCTP, and dGTP; 40 uM dTTP; 40 uM Dig-16-dUTP (Roche Molecular Biochemicals; Mannheim, Germany); 1X reaction buffer; 10 mM DTT; 0.5 unit/ul Ribonuclease inhibitor (GIBCO-BRL; Gaithersburg, MD); and 200 units of MMLV reverse transcriptase (GIBCO-BRL; Gaithersburg, MD) in a 50-ul solution. The reaction mixture was incubated at room temperature for 10 minutes, then transferred to 42 C for 90 minutes, and was stopped by heating the reaction mixture to 99 C for 5 minutes. The RNA was degraded by adding of 5.5 ul of 3 M NaOH followed by a 30-min incubation at 50 C. The labeled samples were neutralized by the addition of 5.5 ul of 3 M acetic acid, and then precipitated by adding 50 ul of 7.5 M ammonium acetate, 20 ug of linear polyacrylamide as a carrier, 375 ul of absolute alcohol, and water, to make a total of 525 ul. The solution was mixed evenly and stood at –80 C for 30 min, and then was centrifuged at 14,000 rpm for 20 min to precipitate a single stranded DNA probe. The pellet was washed with 1 ml of 70% of ethanol and dried by speed vacuum, then dissolved in 5 ul of de-ionized water.

extract_protocol: Total RNA of the specimens was extracted using RNAzol B (Tel-Test, Friendswood, TX).

tag: CELL LINE

value: highly invasive human lung adenocarcinoma cell line, CL1-5

tag: TREATMENT:macrophage-conditioned medium (CM)-stimulated CL1-5 cells and Tanshinone I (10 ug/ml)


title: Lung A7

source_name: Lung A7 Source


title: CL1-5_CM WITH T1_1

source_name: CL1-5 with condition medium and Tanshinone I 1 ug/ml

tag: TREATMENT:macrophage-conditioned medium (CM)-stimulated CL1-5 cells and Tanshinone I (1 ug/ml)


title: CL1-5_CM WITH T1_0.1

source_name: CL1-5 with condition medium and Tanshinone I 0.1 ug/ml

tag: TREATMENT:macrophage-conditioned medium (CM)-stimulated CL1-5 cells and Tanshinone I (0.1 ug/ml)


title: MDA-MB 231 CLONE 15 dnSNAI1 CY3

city: Bron

first: Hector

last: Hernandez-Vargas

state: Rhone

address: 36 bis Rue de la Batterie

country: France

institute: Genomics Consulting

hyb_protocol: Hybridization was performed into the “CNIO Oncochip” cDNA microarray v 1.1c . The microarray platform contains 9,726 clones corresponding to 6,386 different genes, which includes 2,489 clones that have been printed in duplicate to assess reproducibility

scan_protocol: Slides were washed, dried, and then scanned in a Scanarray 5000 XL scanner (GSI Lumonics, Kanata, Ontario, Canada) to obtain 10-m resolution images, which were then quantified using the GenePix Pro 5.0 program (Axon Instruments, Inc., Union City, CA).

data_processing: Data from the fluorescence intensity measurements of each array experiment were processed using GenePix Pro 5.0 and MS Excel programs

source_name: MDA-MB 231 CLONE 15 dnSNAI1 CY3

label_protocol: 3 ug of total RNA were used to synthesize the double-stranded cDNA using T7-(dThd) 24 oligo primers by the Superscript Choice System (Life Technologies, Inc.). In vitro transcription was conducted with Megascript T7 (Ambion, Austin, TX). Amplified RNA was obtained and purified using TRIZOL reagent, and 3 g of amplified RNA was used to generate fluorescence antisense RNAs by transcriptional synthesis using SuperScript enzyme protocol (Life Technologies, Inc.). All of the samples were labeled with either Cy5-dUTP or Cy3-dUTP fluorochromes (Amersham, Uppsala, Sweden).

extract_protocol: Total RNA from the different cell lines was extracted using TRIZOL reagent (Life Technologies, Inc., Gaithersburg, MD) as indicated by the manufacturer.

tag: MDA-MB 231 CLONE 15 dnSNAI1 CY3

source_name: MDA-MB-231 CONTROL

tag: MDA-MB-231 CONTROL


title: CL1-5_CM WITH T1_0.01

source_name: CL1-5 with condition medium and Tanshinone I 0.01 ug/ml

tag: TREATMENT:macrophage-conditioned medium (CM)-stimulated CL1-5 cells and Tanshinone I (0.01 ug/ml)


title: Lung A3

source_name: Lung A3 source

value: Lung;

tag: Line

value: Index;

tag: Viremia Class

value: Low;

tag: Infection Status

value: Infected with PRRSV strain 97-7985.

source_name: Lung Reference Sample


title: Lung A4

source_name: Lung A4 source

tag: Tissue

value: Lung; Line:Index; Viremia Class:Low; Infection Status:Infected wtih PRRSV strain 97-7985

value: Lung


title: MDA-MB 231 CLONE 14 dnSNAI1 CY5

hyb_protocol: Hybridization was performed into the “CNIO Oncochip” cDNA microarray v 1.1c . The microarray platform contains 9,726 clones corresponding to 6,386 different genes, which includes 2,489 clones that have been printed in duplicate to assess reproducibility.

source_name: MDA-MB 231 CLONE 14 dnSNAI1 CY5

tag: MDA-MB 231 CLONE 14 dnSNAI1 CY5

label_protocol: . 3 g of total RNA were used to synthesize the double-stranded cDNA using T7-(dThd) 24 oligo primers by the Superscript Choice System (Life Technologies, Inc.). In vitro transcription was conducted with Megascript T7 (Ambion, Austin, TX). Amplified RNA was obtained and purified using TRIZOL reagent, and 3 g of amplified RNA was used to generate fluorescence antisense RNAs by transcriptional synthesis using SuperScript enzyme protocol (Life Technologies, Inc.). All of the samples were labeled with either Cy5-dUTP or Cy3-dUTP fluorochromes (Amersham, Uppsala, Sweden).


title: Lung A2

source_name: Lung A2 Source

value: Index

value: Low

value: Infected with PRRSV strain 97-7985

tag: The reference sample was developed from four uninfected control full sibling littermates of infected pigs that had a PC value of 0 and that were not included in the sample of 28 infected pigs used in the microarray experiment. The reference sample consisted of two pigs from Line Index and two pigs from Line HD. Tissue


title: Lung A1

source_name: Lung A1 source

tag: The reference sample was developed from four uninfected control full sibling littermates of infected pigs that had a PC value of 0 and that were not included in the sample of 28 infected pigs used in the microarray experiment.  The reference sample consisted of two pigs from Line Index and two pigs from Line HD.


title: MDA-MB-231 CLONE 14 dnSNAI1 CY3

description: The microarray platform contains 9,726 clones corresponding to 6,386 different genes, which includes 2,489 clones that have been printed in duplicate to assess reproducibility

source_name: MDA-MB-231 CLONE 14 dnSNAI1 CY3

tag: MDA-MB-231 CLONE 14 dnSNAI1 CY3

source_name: MDA-MB 231 CONTROL

tag: MDA-MB 231 CONTROL


title: MDA-MB 231 CLONE 15 dnSNAI1 CY5

source_name: MDA-MB 231 CLONE 15 dnSNAI1 CY5

tag: MDA-MB 231 CLONE 15 dnSNAI1 CY5


title: Lung E1

source_name: Lung E1

value: Lung; Line:Index; Viremia Class:Low; Infection Status:Uninfected

tag: The reference sample was developed from four uninfected control full sibling littermates of infected pigs that had a Principle Component value of 0 and that were not included in the sample of 28 infected pigs used in the microarray experiment. The reference sample consisted of two pigs from Line Index and two pigs from Line HD. Tissue


title: CL1-5_CM

source_name: CL1-5 with condition medium treatment

tag: CELL LINE

tag: TREATMENT:macrophage-conditioned medium (CM)-stimulated CL1-5 cells


title: CL1-5_WITHOUT CM

source_name: CL1-5 without condition medium treatment

tag: TREATMENT

value: without macrophage-conditioned medium (CM) and Tanshinone I