title: ELF36CL_contralateral_site

data_processing: Bioconductor [Gentleman et al. Genome Biology 2004] and R language [Ihaka and Gentleman. Journal of Computational and Graphical Statistics 136366] were used for pre-processing of the 30 hybridizations. The microarray data was normalized by the gcRMA method [Wu et al. Journal of the American Statistical Association 2004].

treatment_protocol: endobronchial epithelial lining fluid collected by bronchoscopic microsampling [Kahn&Kuner et al. 20036]


title: SH14-T1 prostate tumour

status: Public on Dec 31 2011

type: genomic

city: London

first: Xueying

last: Mao

address: Charterhouse Square

country: United Kingdom

institute: Queen Mary

description: SNP genotype data from prostate cancer patient at diagnosis

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000 7G.

data_processing: CEL files and CHP files generated by Affymetrix Genechip Operating Software. Very weakly hybridized SNPs were filtered by the same software. The signal intensity data from SNP array were analyzed by in-house software- GOLF and commerical software-Partek.

label: Biotin

molecule: genomic DNA

organism: Homo sapiens

label_protocol: standard Affymetrix protocol

extract_protocol: Fresh frozen samples were digested by Proteinase K and RNaseA. DNA was extracted from these samples using phenol/chroloform.

tag: tissue

tag: individual


title: ELF37IPN

type: RNA

city: Heidelberg

first: Ruprecht

last: Kuner

address: Im Neuenheimer Feld 460

department: Molecular Genetics

country: Germany

institute: German Cancer Research Center and National Center of Tumor Diseases

description: qRT-PCR gene expression data of human endobronchial epithelial lining fluid ELF37IPN

data_processing: The accuracy of measurements for all samples was optimized by using technical duplicates. Statistical analysis was performed calculating the mean Ct value (number of PCR cycles up to a constant fluorescent signal threshold) across the duplicates of each sample within the logarithmic PCR cycle phase. Measurements above the maximum of 40 cycles were defined as Ct 40. Next, relative quantification method based on the delta delta Ct-method was used [Pfaffl MW, Nucleic Acids Res, 2001] for statistical analyses. For each sample, the gene expression value (Ct) of the experimental gene (Gx) were normalized (delta Ct = CtGx-CtGh) using the mean of two housekeeping genes (Gh). We used ESD (Esterase D) and POLR2A (DNA directed RNA polymerase II polypeptide A) as internal control genes [Kuner et al, Lung Cancer, 2009]. All delta Ct values were compared to a reference value (median of all delta Ct values from samples of the contralateral site or the matched normal sample) obtaining the normalized, relative value (delta delta Ct) or expression level (2^-delta delta Ct).

label: FAM dye

molecule: total RNA

source_name: human endobronchial lining fluid, nodule site, benign

extract_protocol:
Total RNA extraction of ELF samples was performed using RNeasy Micro Kit (Qiagen, Hilden, Germany) according to the manufacturersÆ instructions.
Total RNA was reversely transcribed including oligo d(T) and random primers (50 pmol each) with the RevertAidÖ First Strand cDNA Synthesis Kit (Fermentas, Burlington, ON, Canada). Expression analysis of 16 genes was done for each sample in technical duplicates by using the quantitative real-time PCR system (ABI Prism 7900HT Sequence Detection System; Applied Biosystems, Weiterstadt, Germany) and gene specific primers and probes (Taqman assays, ABI). PCR conditions were used for all Taqman assays according to the manufacturers instructions.

treatment_protocol: The bronchoscopic microsampling device (BMS) was inserted through a guided sheath into the bronchi, positioned fluoroscopically, and deployed for ten seconds at the nearest possible point next to the lesion. The collection probe containing the absorbed ELF was sectioned and immediately shock-frozen in liquid nitrogen. In each patient, BMS procedures were repeated twice at the site of the lesion (IPN) and at the corresponding subsegmental bronchus of the contralateral lung (CL) as internal control [Kahn et al, JTCS 2009]

tag: site

value: nodule site

tag: disease state

value: benign


title: ELF26IPN

description: qRT-PCR gene expression data of human endobronchial epithelial lining fluid ELF26IPN


title: ELF36IPN_nodule_site

description: Gene expression data from human endobronchial epithelial lining fluid

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip« U133 Plus 2.0 in the Affymetrix GeneChip« Hybridization Oven 640. GeneChips were washed and stained in the Affymetrix GeneChip« Fluidics Station 450.

scan_protocol: Hybridized microarrays were scanned with the Affymetrix GeneChip« Scanner 3000.

label: biotin

label_protocol: Total RNA (150 ng) was amplified using GeneChip« 3Æ IVT Express Kit (Affymetrix). Labeling, hybridization and scanning was processed according to the manufacturersÆ instructions (Affymetrix)

extract_protocol: total RNA was extracted using the RNeasy Micro Kit (Qiagen, Hilden, Germany) according to the manufacturersÆ instructions.

tag: cell type

value: endobronchial epithelial lining fluid

tag: patient

value: tumor patient

value: squamous cell carcinoma


title: ELF34CL_contralateral_site

data_processing: Bioconductor [Gentleman et al. Genome Biology 2004] and R language [Ihaka and Gentleman. Journal of Computational and Graphical Statistics 134346] were used for pre-processing of the 30 hybridizations. The microarray data was normalized by the gcRMA method [Wu et al. Journal of the American Statistical Association 2004].

source_name: human endobronchial epithelial lining fluid

treatment_protocol: endobronchial epithelial lining fluid collected by bronchoscopic microsampling [Kahn&Kuner et al. 20034]

value: contralateral site


title: ELF13IPN

description: qRT-PCR gene expression data of human endobronchial epithelial lining fluid ELF13IPN


title: ELF14IPN

description: qRT-PCR gene expression data of human endobronchial epithelial lining fluid ELF14IPN


title: ELF34IPN_nodule_site


title: P107-TL1 prostate tumour


title: ELF39CL_contralateral_site

data_processing: Bioconductor [Gentleman et al. Genome Biology 2004] and R language [Ihaka and Gentleman. Journal of Computational and Graphical Statistics 139396] were used for pre-processing of the 30 hybridizations. The microarray data was normalized by the gcRMA method [Wu et al. Journal of the American Statistical Association 2004].

treatment_protocol: endobronchial epithelial lining fluid collected by bronchoscopic microsampling [Kahn&Kuner et al. 20039]

value: adenocarcinoma


title: ELF11IPN

description: qRT-PCR gene expression data of human endobronchial epithelial lining fluid ELF11IPN


title: ELF2IPN

description: qRT-PCR gene expression data of human endobronchial epithelial lining fluid ELF2IPN


title: ELF39IPN_nodule_site


title: SH17-N normal prostate

value: normal prostate


title: WX92-TL1 prostate tumour


title: ELF43IPN

description: qRT-PCR gene expression data of human endobronchial epithelial lining fluid ELF43IPN

source_name: human endobronchial lining fluid, nodule site, large cell lung carcinoma

value: large cell lung carcinoma


title: ELF72IPN

description: qRT-PCR gene expression data of human endobronchial epithelial lining fluid ELF72IPN

source_name: human endobronchial lining fluid, nodule site, NSCLC

value: NSCLC


title: ELF32CL_contralateral_site

data_processing: Bioconductor [Gentleman et al. Genome Biology 2004] and R language [Ihaka and Gentleman. Journal of Computational and Graphical Statistics 132326] were used for pre-processing of the 30 hybridizations. The microarray data was normalized by the gcRMA method [Wu et al. Journal of the American Statistical Association 2004].

treatment_protocol: endobronchial epithelial lining fluid collected by bronchoscopic microsampling [Kahn&Kuner et al. 20032]


title: WX73-TL2 prostate tumour


title: ELF32IPN_nodule_site


title: ELF22CL_contralateral_site

data_processing: Bioconductor [Gentleman et al. Genome Biology 2004] and R language [Ihaka and Gentleman. Journal of Computational and Graphical Statistics 122226] were used for pre-processing of the 30 hybridizations. The microarray data was normalized by the gcRMA method [Wu et al. Journal of the American Statistical Association 2004].

treatment_protocol: endobronchial epithelial lining fluid collected by bronchoscopic microsampling [Kahn&Kuner et al. 20022]


title: WX73-TL1 prostate tumour


title: WX76-TL2 prostate tumour


title: ELF20IPN

description: qRT-PCR gene expression data of human endobronchial epithelial lining fluid ELF20IPN


title: WX73-N normal prostate


title: ELF18CL_contralateral_site

data_processing: Bioconductor [Gentleman et al. Genome Biology 2004] and R language [Ihaka and Gentleman. Journal of Computational and Graphical Statistics 118186] were used for pre-processing of the 30 hybridizations. The microarray data was normalized by the gcRMA method [Wu et al. Journal of the American Statistical Association 2004].

treatment_protocol: endobronchial epithelial lining fluid collected by bronchoscopic microsampling [Kahn&Kuner et al. 20018]


title: ELF3IPN

description: qRT-PCR gene expression data of human endobronchial epithelial lining fluid ELF3IPN


title: ELF18IPN_nodule_site


title: WX76-TL1 prostate tumour


title: WX92-TL2 prostate tumour


title: WX47-N normal prostate


title: ELF9CL_contralateral_site

data_processing: Bioconductor [Gentleman et al. Genome Biology 2004] and R language [Ihaka and Gentleman. Journal of Computational and Graphical Statistics 1996] were used for pre-processing of the 30 hybridizations. The microarray data was normalized by the gcRMA method [Wu et al. Journal of the American Statistical Association 2004].

treatment_protocol: endobronchial epithelial lining fluid collected by bronchoscopic microsampling [Kahn&Kuner et al. 2009]


title: WX39-N normal prostate


title: ELF71IPN

description: qRT-PCR gene expression data of human endobronchial epithelial lining fluid ELF71IPN

source_name: human endobronchial lining fluid, nodule site, squamous cell carcinoma


title: WX47-TL1 prostate tumour


title: ELF42IPN

description: qRT-PCR gene expression data of human endobronchial epithelial lining fluid ELF42IPN


title: ELF9IPN_nodule_site


title: ELF48IPN

description: qRT-PCR gene expression data of human endobronchial epithelial lining fluid ELF48IPN


title: WX39-TR1 prostate tumour

value: prostate tumor


title: ELF29IPN

description: qRT-PCR gene expression data of human endobronchial epithelial lining fluid ELF29IPN


title: WX33-N normal prostate


title: ELF22IPN_nodule_site


title: ELF17IPN

description: qRT-PCR gene expression data of human endobronchial epithelial lining fluid ELF17IPN

source_name: human endobronchial lining fluid, nodule site, carcinoid

value: carcinoid


title: ELF24IPN

description: qRT-PCR gene expression data of human endobronchial epithelial lining fluid ELF24IPN


title: ELF10IPN

description: qRT-PCR gene expression data of human endobronchial epithelial lining fluid ELF10IPN


title: WX33-TL1 prostate tumour

description: SNP genotype data from prostate cancer patient at diagnosis


title: WX92-N normal prostate


title: ELF5IPN

description: qRT-PCR gene expression data of human endobronchial epithelial lining fluid ELF5IPN


title: WX33-TR1 prostate tumour


title: ELF4IPN

description: qRT-PCR gene expression data of human endobronchial epithelial lining fluid ELF4IPN


title: ELF30IPN

description: qRT-PCR gene expression data of human endobronchial epithelial lining fluid ELF30IPN


title: WX33-TL2 prostate tumour


title: WX21-TR1 prostate tumour


title: ELF77IPN

description: qRT-PCR gene expression data of human endobronchial epithelial lining fluid ELF77IPN

source_name: human endobronchial lining fluid, nodule site, adenocarcinoma


title: WX21-N normal prostate


title: early_black_upper_extremity_10.8_mpi_54_yr_s3

city: Ames

first: Oliver

last: Couture

state: IA

address: 2255 Kildee

country: USA

institute: Iowa State University

hyb_protocol: Labeled targets were hybridized to the Affymetrix Human GeneChip® Human Genome U133 plus 2.0 for 16–18 hours at 45 °C and 60 rounds per minute (Hybridization Oven 640, Affymetrix, Santa Clara, CA, USA). Spike controls were added to complementary RNA before hybridization. Washing and staining with streptavidine-phycoerythrine was performed in an automatic fluidics station (GeneChip® Fluidics Station 400, Affymetrix, Santa Clara, CA, USA).

scan_protocol: Scanning was performed with GeneChip® Scanner 3000 (Affymetrix, Santa Clara, CA, USA). The quality of the hybridization and overall chip performance was evaluated by visual inspection of the raw scanned data and the quality control measures in the Affymetrix *.RPT report file; except that we did not monitor the Affymetrix 3'5' ratios since there are no recommended values for amplified porcine tissues.

data_processing: Supplied in CHP files, Algorithm: ExpressionStat 5.0

source_name: early, black, upper extremity, 10.8 mpi, 54 yr

label_protocol: Transcription and labeling of complementary RNA was performed with biotinylated UTP and CTP (Affymetrix IVT labeling Kit). The target complementary RNA was fragmented, washed, and stained according to the manufacturer instructions. The quality and quantity of labeled complementary RNA was evaluated spectrophotometrically and with the Agilent 2100 Bioanalyzer (Agilent Technologies, Inc., Santa Clara, CA).

extract_protocol: Following laser capture microdissection, the cap was incubated in 50 μl PicoPureTM RNA extraction buffer (Molecular Devices Corporation, Sunnyvale, CA) at 42°C for 30 minutes. After DNase (Qiagen, Valencia, CA) treatment, total RNA was eluted in 12 μl of Elution Buffer. RNA quality was monitored with Agilent 2100 Bioanalyzer (Agilent Technologies, Inc., Santa Clara, CA), the Agilent RNA 6000 Pico chip, and Eukaryote Total RNA Pico by evaluating the features of the electropherogram and the RNA integrity numbers. 28S and 18S rRNA bands were expected and the intensity of the 28S bands was expected to be higher than the intensity of the 18S. The RNA Integrity Numbers (RIN) were expected to be greater than 6.0. Samples that failed these criteria were repeated.  The LCM RNA and 500 pg control RNA were amplified using the RiboAmpTM HS kit (Molecular Devices Corporation, Sunnyvale, CA). RNA was reverse transcribed and double-stranded cDNAs synthesized and purified.  The first-round cDNA was transcribed using T7 RNA polymerase. The resulting RNA was purified and used in the second round of amplification. The quality and quantity of amplified RNA was evaluated spectrophotometrically and with the Agilent 2100 Bioanalyzer (Agilent Technologies, Inc., Santa Clara, CA). The required A260/280 ratio was in the range 1.8-2.1. Samples that failed these criteria were repeated.

treatment_protocol: After harvest, the sample was placed immediately in liquid nitrogen. The full-thickness human and porcine wound samples were snap-frozen in chilled Tissue-Tek® Optimal Cutting Temperature embedding medium (Sakura Finetechnical U.S.A., Torrance, CA). The biopsies were sectioned at 7μm, fixed in 75% ethanol, dehydrated and air dried. The slides were loaded into the Arcturus® AutoPix Laser Capture Microdissection system (Molecular Devices Corporation, Sunnyvale, CA). A laser spot size of 25 μm diameter was used with 85-95mW power and 8,500-10,000 ms duration. The offset and overlap was 25%. The efficiency of the microdissection was evaluated by examining the cap after capture and by examining the tissue before and after lift off from the cap. 10-20 sites were captured per sample or 500-1000 cells.

tag: scaring

value: early

tag: color

value: black

tag: location

value: upper extremity

tag: time

tag: age

value: 54 yr


title: WX21-TL1 prostate tumour


title: ELF76IPN

description: qRT-PCR gene expression data of human endobronchial epithelial lining fluid ELF76IPN


title: ELF75IPN

description: qRT-PCR gene expression data of human endobronchial epithelial lining fluid ELF75IPN


title: early_black_upper_extremity_10.8_mpi_54_yr_s1


title: ELF73IPN

description: qRT-PCR gene expression data of human endobronchial epithelial lining fluid ELF73IPN


title: EC activated by PymT

city: New York

first: Bisen

last: Ding

state: NY

address: 1300 York Avenue

institute: Cornell Medical College

hyb_protocol: Fragmented cRNA was hybridized to the gene chips, washed, and stained with streptavidinphycoerythrin.

scan_protocol: The probe arrays were scanned with the Genechip System confocal scanner.

data_processing: Affymetrix Microarray suite 5.0 as used to analyze the data (Algorithm: ExpressionStat 5.0).

source_name: Human umbilical endothelial cells

label_protocol: The Superscript choice kit (Invitrogen, Carlsbad, CA) was used to make cDNA with a T7-(dT)24 primer incorporating a T7 RNA polymerase promoter. The biotin labeled cRNA was made by in vitro transcription (Enzo Diagnostics).

extract_protocol: The protocol used to extract RNA was according to Manufacturers specifications QIAGEN Rneasy kit.

value: mature

tag: treatment

value: PymT


title: ELF1IPN

description: qRT-PCR gene expression data of human endobronchial epithelial lining fluid ELF1IPN

value: nodule site


title: EC activated by MAPK

value: MAPK


title: WX12-N normal prostate


title: WX39-TM1 prostate tumour


title: ELF70IPN

description: qRT-PCR gene expression data of human endobronchial epithelial lining fluid ELF70IPN


title: EC activated by Akt

value: Akt


title: ELF69IPN

description: qRT-PCR gene expression data of human endobronchial epithelial lining fluid ELF69IPN


title: early_white_neck_6.7_mpi_19_yr_s2

source_name: early, white, neck, 6.7 mpi, 19 yr

value: white

value: neck

value: 6.7 mpi

value: 19 yr


title: WX12-TL1 prostate tumour


title: WX9-N normal prostate

value: normal prostate


title: EC infected with GFP

value: GFP


title: WX11-TL2 prostate tumour


title: WX12-TL2 prostate tumour


title: ELF65IPN

description: qRT-PCR gene expression data of human endobronchial epithelial lining fluid ELF65IPN

value: adenocarcinoma


title: siNFE2_2 of K562 cells

city: Bei Jing

first: Jia

last: Yu

address: Dong Dan San Tiao #5

department: Biochemistry

country: China

institute: Peking Union Medical College

hyb_protocol: SAM

scan_protocol: The BeadArray Reader

data_processing: The raw intensity of Illumina MicroRNA expression array was scanned and extracted using BeadArray Reader(illumina,San Diego,CA), with the data corrected by background subtraction and normalized in GenomeStudio V2010.2 module(illumina,San Diego,CA). We normalized the intenstiydata with average normalization algorithm. Individual MicroRNAs were examined using the detection p-value metric provided by Illumina inwhich the signal generated from each MicroRNA is compared to negative controls. A threshold of p<0.05 was used as a cutoff.MicroRNA that did not reach this threshold were eliminated from the analysis.

source_name: K562 cells siNFE2

extract_protocol: Trizol

tag: k562 cells


title: siNFe2_1 of K562 cells


title: ELF64IPN

description: qRT-PCR gene expression data of human endobronchial epithelial lining fluid ELF64IPN


title: siGATA1_2 of K562 cells

source_name: K562 cells siGATA1


title: WX11-TL1 prostate tumour


title: ELF61IPN

description: qRT-PCR gene expression data of human endobronchial epithelial lining fluid ELF61IPN


title: CL1-0 cells expressing HA-G9a

city: Taipei

first: Min-Liang

last: Kuo

address: No. 1,Section 1, Jen-Ai Road

country: Taiwan

institute: National Taiwan University

description:
Gene expression data from CL1-0 cells expressing HA-G9a vector
CL1-0/HA-G9a

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

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

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 100.

source_name: Lung  adenocarcinoma

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

growth_protocol: Cells were cultured in 5% CO2 incubator at 37℃.

extract_protocol: Qiagene RNeasy mini kit extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Cell were selected with puromycin for two weeks.  Stably transduced cells were use for this experiment.

tag: cell line

value: lung adenocarcinoma cell line CL1-0

tag: cellular basis of adc

value: Type II alveolar cell

tag: protocol

value: G9a overexpression


title: CL1-5 cells expressing G9a shRNA2

description:
Gene expression data from CL1-5 cells expressing G9a shRNA
CL1-5/G9a KD

value: lung adenocarcinoma cell line CL1-5

value: G9a knockdown


title: ELF60IPN

description: qRT-PCR gene expression data of human endobronchial epithelial lining fluid ELF60IPN


title: siGATA1_1 of K562 cells


title: CL1-5 cells expressing control shRNA

description:
Gene expression data from CL1-5 cells expressing control shRNA
CL1-5

value: control shRNA expression


title: ELF54IPN

description: qRT-PCR gene expression data of human endobronchial epithelial lining fluid ELF54IPN


title: CL1-0 cells expressing control vector

description:
Gene expression data from CL1-0 cells expressing control vector
CL1-0

value: control vector expression


title: ELF52IPN

description: qRT-PCR gene expression data of human endobronchial epithelial lining fluid ELF52IPN

value: nodule site


title: siEKLF_2 of K562 cells

source_name: K562 cells siEKLF

value: siEKLF


title: Overexpression of pcDNA3.1_2 in K562 cells

source_name: K562 cells overexpression of pcDNA3.1

value: overexpression of pcDNA3.1


title: siEKLF_1 of K562 cells

tag: k562 cell


title: WX1-N normal prostate

description: SNP genotype data from prostate cancer patient at diagnosis

tag: tissue


title: WX8-N normal prostate

tag: individual


title: WX9-TL1 prostate tumour


title: WX9-TR1 prostate tumour

value: prostate tumor


title: ELF39IPN

description: qRT-PCR gene expression data of human endobronchial epithelial lining fluid ELF39IPN

tag: site


title: ELF35IPN

description: qRT-PCR gene expression data of human endobronchial epithelial lining fluid ELF35IPN

tag: disease state


title: WX1-TR2 prostate tumour


title: WX8-TR1 prostate tumour


title: Overexpression of pcDNA3.1 in K562 cells


title: ELF31IPN

description: qRT-PCR gene expression data of human endobronchial epithelial lining fluid ELF31IPN


title: Overexpression of NFE2_2 in K562 cells

source_name: K562 cells overexpression of NFE2

value: overexpression of NFE2


title: siCON_2 of K562 cells

source_name: K562 cells siCON

value: siCON


title: ELF28IPN

description: qRT-PCR gene expression data of human endobronchial epithelial lining fluid ELF28IPN


title: WX11-N normal prostate


title: WX1-TR1 prostate tumour


title: Overexpression of NFE2_1 in K562 cells


title: Blood genomic DNA in patient with gastric cancer HRGC-102

city: daejeon

first: Tae-Wook

last: Kang

address: 111 Gwahangno, Yuseong-gu

country: South Korea

institute: KRIBB

hyb_protocol: Standard Affymetrix protocol (The labeled DNA was hybridized to a Genomic-Wide Human SNP Array 6.0 for 16-18 hours in a rotating oven at 50℃ and 60 rpm.)

scan_protocol: Standard Affymetrix protocol (The SNP Array 6.0 was scanned with the Affymetirx GeneChip Scanner 3000 using Affymetrix GeneChip Operating Software (GCOS; version 1.4))

data_processing:
Standard Affymetrix protocol (Signal intensity data was analyzed by the Dynamic Model (DM) algorithm. A contrast QC of greater than or equal to 0.4 should be used to determine whether a sample should be repeated or used for downstream ananlysis.)
Standard Affymetrix protocol (Genotypes were called by the Affymetrix Genotyping Console Software (GTC; version 3.0.1) based on the Birdseed version 2 algorithm.

source_name: Blood DNA in patient with gastric cancer

label_protocol: Standard Affymetrix protocol (The fragmented DNA was labeled using DNA Labeling Reagent and TdT enzyme for 4.25 hours at 37℃.)

extract_protocol: Genomic DNA was extracted from blood samples using the Qiagen DNeasy Kit according to standard instructions.

value: gastric cancer

tag: gender

value: male

value: blood

tag: tsi, raw drug sensitivity

tag: tsi.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: fu, raw drug sensitivity

tag: fu.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: oxa, raw drug sensitivity

tag: oxa.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: dtax, raw drug sensitivity

tag: dtax.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: cdp, raw drug sensitivity

tag: cdp.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: tax, raw drug sensitivity

tag: saha, raw drug sensitivity

tag: saha.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: pxd, raw drug sensitivity

tag: pxd.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: cg2, raw drug sensitivity

tag: cg2.30, binary data (i.e. >= 30 or < 30) at 30% cutoff


title: Blood genomic DNA in patient with gastric cancer HRGC-105

tag: disease state

tag: gender

value: female

tag: tissue

tag: tsi, raw drug sensitivity

tag: tax.30, binary data (i.e. >= 30 or < 30) at 30% cutoff


title: Overexpression of GATA1_2 in K562 cells

source_name: K562 cells overexpression of GATA1

tag: k562 cell

value: overexpression of GATA1


title: ELF25IPN

description: qRT-PCR gene expression data of human endobronchial epithelial lining fluid ELF25IPN

tag: site

value: adenocarcinoma


title: ELF19IPN

description: qRT-PCR gene expression data of human endobronchial epithelial lining fluid ELF19IPN


title: Blood genomic DNA in patient with gastric cancer HRGC-100

tag: tsi.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: fu, raw drug sensitivity

tag: fu.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: oxa, raw drug sensitivity

tag: oxa.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: dtax, raw drug sensitivity

tag: dtax.30, binary data (i.e. >= 30 or < 30) at 30% cutoff


title: Overexpression of EKLF_2 in K562 cells

source_name: K562 cells overexpression of EKLF

value: overexpression of EKLF


title: ELF21IPN

description: qRT-PCR gene expression data of human endobronchial epithelial lining fluid ELF21IPN


title: Blood genomic DNA in patient with gastric cancer HRGC-103

tag: cdp, raw drug sensitivity

tag: cdp.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: tax, raw drug sensitivity

tag: saha, raw drug sensitivity

tag: saha.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: pxd, raw drug sensitivity

tag: pxd.30, binary data (i.e. >= 30 or < 30) at 30% cutoff


title: siCON_1 of K562 cells


title: ELF27IPN

description: qRT-PCR gene expression data of human endobronchial epithelial lining fluid ELF27IPN

tag: disease state


title: ELF16IPN

description: qRT-PCR gene expression data of human endobronchial epithelial lining fluid ELF16IPN


title: Blood genomic DNA in patient with gastric cancer HRGC-98

tag: gender

tag: tissue

tag: tsi, raw drug sensitivity

tag: tax.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: cg2, raw drug sensitivity

tag: cg2.30, binary data (i.e. >= 30 or < 30) at 30% cutoff


title: Blood genomic DNA in patient with gastric cancer HRGC-99

tag: tsi.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: fu, raw drug sensitivity

tag: fu.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: oxa, raw drug sensitivity

tag: oxa.30, binary data (i.e. >= 30 or < 30) at 30% cutoff


title: 72h K562_2 induced by hemin into erythroid differentiation

source_name: K562 cells 72h induction

tag: k562 cell

value: hemin 72h


title: Overexpression of GATA1_1 in K562 cells


title: WX76-N normal prostate

value: normal prostate

tag: individual


title: Blood genomic DNA in patient with gastric cancer HRGC-97

tag: dtax, raw drug sensitivity

tag: dtax.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: cdp, raw drug sensitivity

tag: cdp.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: tax, raw drug sensitivity

tag: saha, raw drug sensitivity

tag: saha.30, binary data (i.e. >= 30 or < 30) at 30% cutoff


title: 72h K562_1 induced by hemin into erythroid differentiation


title: Blood genomic DNA in patient with gastric cancer HRGC-106

tag: disease state

tag: gender

tag: tissue

tag: tsi, raw drug sensitivity

tag: tax.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: pxd, raw drug sensitivity

tag: pxd.30, binary data (i.e. >= 30 or < 30) at 30% cutoff


title: ELF15IPN

description: qRT-PCR gene expression data of human endobronchial epithelial lining fluid ELF15IPN

tag: site


title: ELF12IPN

description: qRT-PCR gene expression data of human endobronchial epithelial lining fluid ELF12IPN


title: Blood genomic DNA in patient with gastric cancer HRGC-101

tag: tsi.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: fu, raw drug sensitivity

tag: fu.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: oxa, raw drug sensitivity

tag: oxa.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: cg2, raw drug sensitivity

tag: cg2.30, binary data (i.e. >= 30 or < 30) at 30% cutoff


title: ELF8IPN

description: qRT-PCR gene expression data of human endobronchial epithelial lining fluid ELF8IPN


title: 48h K562_2 induced by hemin into erythroid differentiation

source_name: K562 cells 48h induction

value: hemin 48h


title: Overexpression of EKLF in K562 cells

tag: k562 cell


title: Blood genomic DNA in patient with gastric cancer HRGC-95

tag: dtax, raw drug sensitivity

tag: dtax.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: cdp, raw drug sensitivity

tag: cdp.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: tax, raw drug sensitivity

tag: saha, raw drug sensitivity

tag: saha.30, binary data (i.e. >= 30 or < 30) at 30% cutoff


title: Blood genomic DNA in patient with gastric cancer HRGC-96

tag: disease state

tag: gender

tag: tissue

tag: tsi, raw drug sensitivity

tag: tax.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: pxd, raw drug sensitivity

tag: pxd.30, binary data (i.e. >= 30 or < 30) at 30% cutoff


title: ELF7IPN

description: qRT-PCR gene expression data of human endobronchial epithelial lining fluid ELF7IPN

tag: site


title: ELF6IPN

description: qRT-PCR gene expression data of human endobronchial epithelial lining fluid ELF6IPN


title: 48h K562_1 induced by hemin into erythroid differentiation

value: hemin, 48h


title: 0h K562_2 induced by hemin into erythroid differentiation

source_name: K562 cells 0h induction

tag: k562 cells

value: 0h hemin


title: Genotyping of Isolate CB94

city: Marseille

first: LEROY

last: Quentin

address: 27 Boulevard Jean Moulin

country: France

institute: URMITE

description:
CGH-CB94
Genotyping of Isolate CB94 compare to NMI

hyb_protocol: Hybridizations were carried out using two samples of labeled amplified gDNA (150 pmol of each) that were labeled with Cy3 or Cy5 d-CTP. The pooled samples were hybridized using the GE hybridization kit (Agilent Technologies) as recommended by the manufacturer. The mixture was applied to a Surhyb 1 array (Agilent Technologies) and hybridized on the Coxiella burnetii array using an Agilent hybridization chamber (Agilent Technologies). Microarrays were hybridized for 17 h at 62°C in a rotating oven. Microarrays were washed using GE washing buffers (Agilent Technologies), with 5 min of Wash-buffer 1 at room temperature, followed by 1 min of Wash-buffer 2 at 37°C. Microarrays were dried using an acetonitrile bath (VWR, Fontenay sous Bois, France)

scan_protocol: Microarrays werescanned using a microarray scanner C (Agilent Technologies) with XDR at a 5-µm resolution

data_processing: The signal intensity and local background were measured for each spot using the array pictures with Feature Extractor software (Agilent Technologies). Data filtering normalizations were obtained using processing signal from obtained data raw extraction using Feature Extractor. Data with low intensity were not included in the analyses.

organism: Coxiella burnetii

label_protocol: 10 ng of gDNA were amplified with the processive polymerase phi29 using the GenomiPhi illustrator V2 kit (GE HealthCare, Lifescience, Orsay, France). The amplified gDNA was labeled with the Bioprime CGH Labeling kit (Invitrogen) using d-CTP Cy3/5 fluorochromes (GE HealthCare Lifescience) as recommended by the manufacturer. Labeled amplified gDNA was purified using Pure Link PCR purification columns (Invitrogen).

growth_protocol: C. burnetii were grown at 35°C on L929 cells using MEM (GIBCO, Invitrogen, Cergy-Pontoise, France) supplemented with 4% SVF (GIBCO) and 1% L-glutamine (GIBCO). Monolayers of cells and the supernatants from three 175 cm² flasks were harvested and incubated with 1% trypsin (GIBCO) for 1 hour at 37°C. Released bacteria were purified from L929 cell debris by differential centrifugation. Purified bacteria were resuspended in 400 µl of PBS and stored at -80°C

extract_protocol: 200 µl of purified bacteria were incubated for 30 min at 70°C with 200 µl of AL lysis buffer (Qiagen, Courtaboeuf, France) and 20 µl of proteinase K (Qiagen). gDNA was extracted and purified using a QiaAmp DNA mini kit as recommended by the manufacturer (Qiagen)

tag: strain

source_name: NMI

value: NMI


title: Genotyping of Isolate CB125

description:
CGH-CB125
Genotyping of Isolate CB125 compare to NMI


title: ILpanicle, biological rep3

city: Hyderabad

first: Sarla

last: Neelamraju

state: Andhra Pradesh

address: Rajendranagar

department: Crop Improvement Section

country: India

institute: Directorate of Rice Research

description: gene expression data from young fully emerged panicle of IL50-7

hyb_protocol: 10 ug of fragmented cRNA were hybridized on Rice Affymetrix GeneChip (51K oligoarray),washed and stained with streptavidin-phycoerythrin in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000

data_processing: The array data were analyzed using GeneChip Operating Software version GCOS 1.2 and GeneSpring software version GX 9.0.6.

organism: Oryza sativa

source_name: ILpanicle

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 8 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Plants were grown in DRR field according to standard procedures

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

tag: line

tag: organ

value: fully emerged young panicle


title: Genotyping of Isolate CB113

description:
CGH-CB113
Genotyping of Isolate CB113 compare to NMI


title: ILpanicle, biological rep2


title: ILpanicle, biological rep1


title: 0h K562_1 induced by hemin into erythroid differentiation

value: hemin 0h


title: Genotyping of Isolate CB109

description:
CGH-CB109
Genotyping of Isolate CB109 compare to NMI


title: WX8-TL1 prostate tumour

description: SNP genotype data from prostate cancer patient at diagnosis

tag: individual


title: Blood genomic DNA in patient with gastric cancer HRGC-92

tag: tsi.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: fu, raw drug sensitivity

tag: fu.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: oxa, raw drug sensitivity

tag: oxa.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: dtax, raw drug sensitivity

tag: dtax.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: cdp, raw drug sensitivity

tag: cdp.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: cg2, raw drug sensitivity

tag: cg2.30, binary data (i.e. >= 30 or < 30) at 30% cutoff


title: Ctrl

city: Sinjuku-ku

first: Masami

last: Tanaka

state: Tokyo

address: Sinjuku 6-1-1

country: Japan

institute: Tokyo Medical University

hyb_protocol: 100 ng of total RNA was labeled and hybridized using Human microRNA Microarray Kit (Agilent Technologies) according to manufacture's protocol (Protocol for use with Agilent microRNA microarrays Version 1.5)

scan_protocol: Images was scanned with Agilent scanner G2505C at 5µm resolution.

data_processing: The scanned images was analyzed automatically in Agilent feature extraction 10.7.0 (Agilent) using default protocol (miRNA_107_Sep09). No interarray normalization method was employed.

source_name: plasma, Ctrl

extract_protocol: Total RNA was extracted by using ISOGEN-LS  (Nippon gene) according to manufacturer’s instruction.

tag: tissue

value: plasma

tag: disease status

value: healthy control


title: Blood genomic DNA in patient with gastric cancer HRGC-93

tag: disease state

value: gastric cancer

tag: gender

tag: tsi, raw drug sensitivity

tag: tax, raw drug sensitivity

tag: tax.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: saha, raw drug sensitivity

tag: saha.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: pxd, raw drug sensitivity

tag: pxd.30, binary data (i.e. >= 30 or < 30) at 30% cutoff


title: FL

source_name: plasma, FL

label_protocol: 100 ng of total RNA was labeled and hybridized using Human microRNA Microarray Kit (Agilent Technologies) according to manufacture's protocol (Protocol for use with Agilent microRNA microarrays Version 1.5)

value: follicular lymphoma (FL)


title: Genotyping of Isolate CB102

description:
CGH-CB102
Genotyping of Isolate CB102 compare to NMI

tag: strain


title: ILleaf, biological rep2

description: gene expression data from flag leaf of  IL50-7

source_name: ILleaf

tag: line

tag: organ

value: flag leaf


title: ILleaf, biological rep1


title: ILleaf, biological rep3


title: Blood genomic DNA in patient with gastric cancer HRGC-91

value: male

value: blood

tag: tsi.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: fu, raw drug sensitivity

tag: fu.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: oxa, raw drug sensitivity

tag: oxa.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: dtax, raw drug sensitivity

tag: dtax.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: cdp, raw drug sensitivity

tag: cdp.30, binary data (i.e. >= 30 or < 30) at 30% cutoff


title: KMR3panicle, biological rep3

description: gene expression data from young fully emerged panicle of KMR3


title: DLBCL

source_name: plasma, DLBCL

tag: tissue

tag: disease status

value: diffuse large B-cell lymphoma (DLBCL)


title: KMR3panicle, biological rep2


title: Blood genomic DNA in patient with gastric cancer HRGC-88

tag: disease state

tag: gender

value: female

tag: tsi, raw drug sensitivity

tag: tax, raw drug sensitivity

tag: tax.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: saha, raw drug sensitivity

tag: saha.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: cg2, raw drug sensitivity

tag: cg2.30, binary data (i.e. >= 30 or < 30) at 30% cutoff


title: 17dpiP1_17dpiC4

city: Acton

first: Sebastian

last: Kurscheid

state: ACT

address: 57 Garran Road

department: JCSMR

country: Australia

institute: Australian National University

description: Biological replicate 4 of 4; 10 mosquitoes per infected (visually confirmed by fluorescent microscopy) and uninfected sample used for extraction of total RNA

hyb_protocol: Equal amounts of linearily amplified, Cy3/Cy5-labeled were fragmented by incubating the samples in fragmentation buffer for exactly 30 minutes in a water bath at 60C; fragmented cRNA were combined in 2x GEx hybridization buffer; hybridization solution was immediately loaded onto arrays and hybridized in a oven set to 65C rotating at 10rpm for 17h. Prior to scanning arrays were washed according go manufacturer's instructions (Agilent Low Input Quick Amp Labeling protocol Version 6.5 May 2010)

scan_protocol: Scanned with Agilent G2505C Microarray Scanner The information about each probe on the array was extracted from the image data using Agilent Feature Extraction 10.9 (FE)

data_processing: Intensities were not background corrected. The median red (Cy5) and green (Cy3) intensities are used to calculate the ratio of expression for each element on the array, in terms of M (log2(Red/Green)) and A ((log2(Red) + log2(Green))/2)). The M values are then global loess normalized within each array using the LIMMA microarray processing package in “R” (Smyth, 2004).

organism: Anopheles gambiae

source_name: A. gambiae P. breghei infected vs uninfected control 17 days post infection

label_protocol: 50ng of isolated total RNA per sample (QCed for A260/280 using NanoDrop and integrity using Bio Analyzer) were reverse transcribed using T7 RNA polymerase and labeled with either Cy3 or Cy5 (dependig on channel - see sample descriptions for details) using the Agilent Low Input Quick Amp labeling procedure, following the manufacturer's instructions (Version 6.5, May 2010).

growth_protocol: Mosquitoes were infected with Plasmodium berghei NK65 redstar by feeding on infeced mice. Control mosquitoes were fed on clean mice. Fed mosquitoes were kept at 21 degree since blood meal, and unfed ones were discarded. 10 and 17 days post blood feeding, mosquitoes were harvested and total RNA were isolated.

extract_protocol: Total RNA was extracted using the Rneasy Mini Kit (Qiagen) following the manufacturer's instructions

value: A. gambiae mosquitoes

tag: treatment

value: infected with P. berghei

tag: time

value: 17 days post infection

source_name: A. gambiae mosquitoes

value: uninfected controls


title: Blood genomic DNA in patient with gastric cancer HRGC-89

tag: tsi.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: fu, raw drug sensitivity

tag: fu.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: oxa, raw drug sensitivity

tag: oxa.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: dtax, raw drug sensitivity

tag: pxd, raw drug sensitivity

tag: pxd.30, binary data (i.e. >= 30 or < 30) at 30% cutoff


title: 17dpiP1_17dpiC3

description: Biological replicate 3 of 4; 10 mosquitoes per infected (visually confirmed by fluorescent microscopy) and uninfected sample used for extraction of total RNA

tag: tissue


title: KMR3panicle, biological rep1

tag: line

tag: organ


title: Blood genomic DNA in patient with gastric cancer HRGC-94

tag: disease state

tag: gender

tag: tsi, raw drug sensitivity

tag: dtax.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: cdp, raw drug sensitivity

tag: cdp.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: tax, raw drug sensitivity

tag: saha, raw drug sensitivity


title: KMR3leaf, biological rep2

description: gene expression data from flag leaf of KMR3


title: Blood genomic DNA in patient with gastric cancer HRGC-85

tag: tsi.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: fu, raw drug sensitivity

tag: fu.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: tax.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: saha.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: cg2, raw drug sensitivity

tag: cg2.30, binary data (i.e. >= 30 or < 30) at 30% cutoff


title: Blood genomic DNA in patient with gastric cancer HRGC-90

tag: tissue

tag: oxa, raw drug sensitivity

tag: oxa.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: dtax, raw drug sensitivity

tag: pxd, raw drug sensitivity

tag: pxd.30, binary data (i.e. >= 30 or < 30) at 30% cutoff


title: 17dpiP1_17dpiC2

description: Biological replicate 2 of 4; 10 mosquitoes per infected (visually confirmed by fluorescent microscopy) and uninfected sample used for extraction of total RNA

tag: treatment

tag: time


title: Blood genomic DNA in patient with gastric cancer HRGC-86

tag: disease state

tag: gender

tag: tsi, raw drug sensitivity

tag: dtax.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: cdp, raw drug sensitivity

tag: cdp.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: tax, raw drug sensitivity


title: KMR3leaf, biological rep3

tag: line

tag: organ


title: Blood genomic DNA in patient with gastric cancer HRGC-82

tag: tissue

tag: tsi.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: fu, raw drug sensitivity

tag: fu.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: tax.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: saha, raw drug sensitivity

tag: saha.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: cg2, raw drug sensitivity

tag: cg2.30, binary data (i.e. >= 30 or < 30) at 30% cutoff


title: 10dpiP1_10dpiC3

source_name: A. gambiae P. breghei infected vs uninfected control 10 days post infection

tag: treatment

tag: time

value: 10 days post infection


title: Blood genomic DNA in patient with gastric cancer HRGC-80

tag: disease state

tag: gender

tag: tsi, raw drug sensitivity

tag: oxa, raw drug sensitivity

tag: oxa.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: dtax, raw drug sensitivity

tag: dtax.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: pxd, raw drug sensitivity

tag: pxd.30, binary data (i.e. >= 30 or < 30) at 30% cutoff


title: KMR3leaf, biological rep1

tag: line

tag: organ


title: 17dpiP1_17dpiC1

description: Biological replicate 1 of 4; 10 mosquitoes per infected (visually confirmed by fluorescent microscopy) and uninfected sample used for extraction of total RNA

tag: tissue


title: Blood genomic DNA in patient with gastric cancer HRGC-81

tag: tsi.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: fu, raw drug sensitivity

tag: fu.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: cdp, raw drug sensitivity

tag: cdp.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: tax, raw drug sensitivity

tag: tax.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: saha, raw drug sensitivity

tag: saha.30, binary data (i.e. >= 30 or < 30) at 30% cutoff


title: Blood genomic DNA in patient with gastric cancer HRGC-84

tag: disease state

tag: gender

tag: tsi, raw drug sensitivity

tag: oxa, raw drug sensitivity

tag: oxa.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: cg2, raw drug sensitivity

tag: cg2.30, binary data (i.e. >= 30 or < 30) at 30% cutoff


title: 10dpiP1_10dpiC4

tag: tissue

tag: treatment

tag: time


title: Blood genomic DNA in patient with gastric cancer HRGC-76

tag: tsi.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: fu, raw drug sensitivity

tag: fu.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: dtax, raw drug sensitivity

tag: dtax.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: pxd, raw drug sensitivity

tag: pxd.30, binary data (i.e. >= 30 or < 30) at 30% cutoff


title: Blood genomic DNA in patient with gastric cancer HRGC-77

tag: disease state

tag: cdp, raw drug sensitivity

tag: cdp.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: tax, raw drug sensitivity

tag: tax.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: saha, raw drug sensitivity

tag: saha.30, binary data (i.e. >= 30 or < 30) at 30% cutoff


title: TN1 stem at T24, biological rep2

city: shanghai

first: Yubing

last: Wang

address: 300 fenglin road

institute: Institute of Plant Physiology and Ecology

description: Expression data from rice after brown planthopper attack

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

scan_protocol: GeneChips were scanned using the GeneChip® Scanner 3000: Affymetrix.

source_name: rice stem of tillering stage seedlings TN1 variety

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (3 ivt express kit manual,Ver4.0, Affymetrix).

growth_protocol: BPH susceptible and resistant rice varieties of TN1（Taichung Native 1） and Rathu Heenati （RHT）were used in this study. The pre-germinated seeds were sown in a plastic tray ( 60 × 45 × 45 cm) and were grown at 28℃/23℃（14h-day and 10h-night cycles）

treatment_protocol: The 2nd to 3rd instar nymphs of BPH were transferred to tillering stage seedings (10 BPH nymphs per plant) in a box covered with nylon-mesh.

tag: tissue

value: stem

tag: strain

value: Taichung Native 1

tag: phenotype

value: sensitive variety to brown planthopper

tag: developmental stage

value: tillering stage

tag: infestation

value: brown planthopper


title: Blood genomic DNA in patient with gastric cancer HRGC-74

value: gastric cancer

tag: gender

tag: tsi, raw drug sensitivity

tag: tsi.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: fu, raw drug sensitivity

tag: fu.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: oxa, raw drug sensitivity

tag: oxa.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: cg2, raw drug sensitivity

tag: cg2.30, binary data (i.e. >= 30 or < 30) at 30% cutoff


title: Blood genomic DNA in patient with gastric cancer HRGC-78

tag: disease state

tag: dtax, raw drug sensitivity

tag: dtax.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: cdp, raw drug sensitivity

tag: cdp.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: tax, raw drug sensitivity

tag: pxd, raw drug sensitivity

tag: pxd.30, binary data (i.e. >= 30 or < 30) at 30% cutoff


title: Blood genomic DNA in patient with gastric cancer HRGC-83

tag: gender

tag: tissue

tag: tax.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: saha, raw drug sensitivity

tag: saha.30, binary data (i.e. >= 30 or < 30) at 30% cutoff


title: Blood genomic DNA in patient with gastric cancer HRGC-75

tag: tsi, raw drug sensitivity

tag: tsi.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: fu, raw drug sensitivity

tag: fu.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: oxa, raw drug sensitivity


title: 10dpiP1_10dpiC2

tag: treatment

tag: time


title: Sigma70 LP-3

city: College Station

first: James

last: Winkler

state: TX

address: 3122 TAMU

institute: Texas A&M University

description: RNA, heat shocked for 1 hour

hyb_protocol: Hybridization occurred as described by the Agilent two-color prokaryotic microarray protocol (18 hours total time).

scan_protocol: Arrays were washed according to the Agilent gene expression microarray protocol and then subsequently scanned using an Axon Genepix 4200A microarray scanner.

data_processing: Data were normalized using LOWESS (MIDAS) and analyzed for statistical significance using the Rank Product method in the MultiExperimentViewer

organism: Escherichia coli

source_name: Sigma70 LP

label_protocol: The Fairplay III Kit (Stratagene) and Cy3/Cy5 dyes (Amersham) were used to generate labeled cDNA for microarray hybridization

growth_protocol: All strains were grown in M9 minimal media supplemented with 25 ug/ml streptomycin and 0.52 mM arginine. Samples were grown to OD = 0.5 @ 30 C; experimental samples were then transferred to a shaking water bath @ 42 C.

extract_protocol: The Zymo Fungal/Bacterial RNA extraction kit was used to extract RNA from all samples. In-column DNaseI treatment was used to eliminate genomic DNA carryover as described by the manufacturer.

treatment_protocol: Control samples (285c/empty vector) were harvested via filtration and resuspended in RNALater once they had reached OD = 0.5. Experimental samples were harvested after 1 hour of heat shock at 42 C in an analogous procedure.

tag: transformation

tag: genotype

value: 285c rpoD mutation

source_name: 285c/control vector at 30 C 3

value: empty vector


title: TN1 stem at T24, biological rep1

tag: strain

tag: phenotype

tag: developmental stage

tag: infestation


title: 10dpiP1_10dpiC1

tag: tissue


title: Sigma70 LP-2

description: RNA, heat shocked for 1 hour

source_name: 285c/control vector at 30 C 2


title: Blood genomic DNA in patient with gastric cancer HRGC-72

source_name: Blood DNA in patient with gastric cancer

tag: disease state

tag: gender

tag: oxa.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: dtax, raw drug sensitivity

tag: dtax.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: cdp, raw drug sensitivity

tag: cdp.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: tax, raw drug sensitivity

tag: pxd, raw drug sensitivity

tag: pxd.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: cg2, raw drug sensitivity

tag: cg2.30, binary data (i.e. >= 30 or < 30) at 30% cutoff


title: Blood genomic DNA in patient with gastric cancer HRGC-79

value: male

tag: tsi, raw drug sensitivity

tag: tsi.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: fu, raw drug sensitivity

tag: fu.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: oxa, raw drug sensitivity

tag: tax.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: saha, raw drug sensitivity

tag: saha.30, binary data (i.e. >= 30 or < 30) at 30% cutoff


title: TN1 stem at T8, biological rep3

tag: tissue

tag: strain

tag: phenotype

tag: developmental stage

tag: infestation

tag: time


title: Blood genomic DNA in patient with gastric cancer HRGC-73

tag: disease state

tag: gender

value: blood

tag: oxa.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: dtax, raw drug sensitivity

tag: dtax.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: cdp, raw drug sensitivity

tag: cdp.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: tax, raw drug sensitivity

tag: pxd, raw drug sensitivity

tag: pxd.30, binary data (i.e. >= 30 or < 30) at 30% cutoff


title: TN1 stem at T8, biological rep2


title: Sigma70 LP-1

description: RNA, heat shocked for 1 hour

tag: transformation

tag: treatment

tag: genotype

source_name: 285c/control vector at 30 C 1


title: Blood genomic DNA in patient with gastric cancer HRGC-71

tag: tissue

tag: tsi, raw drug sensitivity

tag: tsi.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: fu, raw drug sensitivity

tag: fu.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: oxa, raw drug sensitivity

tag: tax.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: saha, raw drug sensitivity

tag: saha.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: cg2, raw drug sensitivity

tag: cg2.30, binary data (i.e. >= 30 or < 30) at 30% cutoff


title: TN1 stem at T24, biological rep3

tag: strain

tag: phenotype

tag: developmental stage

tag: infestation

tag: time


title: TN1 stem at T8, biological rep1


title: Sigma70 LB-3

description: RNA, heat shocked for 1 hour

source_name: Sigma70 LB

tag: transformation

tag: treatment

tag: genotype


title: TN1 stem at T0, biological rep3

tag: tissue


title: Sigma70 LB-1

description: RNA, heat shocked for 1 hour


title: Sigma70 LB-2

description: RNA, heat shocked for 1 hour


title: TN1 stem at T0, biological rep2


title: TN1 stem at T0, biological rep1


title: RHT stem at T24, biological rep3

source_name: rice stem of tillering stage seedlings RHT variety

value: Rathu Heenati

value: resistant variety to brown planthopper


title: Blood genomic DNA in patient with gastric cancer HRGC-67

tag: disease state

tag: gender

tag: tsi, raw drug sensitivity

tag: tsi.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: fu, raw drug sensitivity

tag: oxa.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: dtax, raw drug sensitivity

tag: dtax.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: cdp, raw drug sensitivity

tag: cdp.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: tax, raw drug sensitivity

tag: pxd, raw drug sensitivity

tag: pxd.30, binary data (i.e. >= 30 or < 30) at 30% cutoff


title: Blood genomic DNA in patient with gastric cancer HRGC-69

tag: fu.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: oxa, raw drug sensitivity

tag: tax.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: saha, raw drug sensitivity

tag: saha.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: cg2, raw drug sensitivity

tag: cg2.30, binary data (i.e. >= 30 or < 30) at 30% cutoff


title: RHT stem at T24, biological rep1

tag: tissue

tag: strain

tag: phenotype

tag: developmental stage

tag: infestation

tag: time


title: RM4810-REP2

type: mixed

city: Albany

first: Craig

middle: T

last: Parker

state: CA

address: 800 Buchanan St

department: PSM

institute: USDA ARS

hyb_protocol: Labeled reference genomic DNA and test cDNAs were combined in 45 µl Pronto! cDNA hybridization solution (Corning, Corning, NY) and heated to 95°C for 5 min. Then, 15 µl of the hybridization mixture was put onto a microarray slide and sealed with a cover slip. The microarray slide was placed in a hybridization chamber (Corning) and incubated at 42°C for 18 h. Following hybridization, the slides were washed twice in 2× SSC, 0.1% sodium dodecyl sulfate at 42°C for 10 min, followed by twice in 1× SSC at room temperature for 10 min, and finally twice in 0.2× SSC at room temperature for 5 min. The microarray slides were dried by centrifugation at 300 × g for 10 min before scanning.

scan_protocol: Scanned on an Axon GenePix4000B scanner at 10nm resolution using GenePix software. Images were quantified using GenePix software (version 6.0).

data_processing: Fluorescence ratios were calculated after local background was subtracted from spot signals. To compensate for any effect of the amount of template and uneven Cy-dye incorporation, data normalization (centering) was performed by bringing the median natural logarithm of the ratios for each group of spots printed by the same pin to zero using the following equation: ln(Ti ) = ln(Ri /Gi ) - c, where T is the centered ratio, i is the gene index, R and G are the red and green intensities, respectively, and c is the 50th percentile of all red/green ratios.

organism: Aliarcobacter butzleri RM4018

label_protocol: 2 µg of genomic DNA were Cy3-dUTP labeled during random primed synthesis with Klenow fragment (NEB) at 37°C for 16 h. 20 µg of total RNA were labeled during reverse transcription with random primed hexamers to cDNA with Cy5-dUTP using Stratascript (Stratagene, Palo Alto, CA) at 42°C for 16 h.

growth_protocol: Liquid cultures of A. butzleri were obtained by BHI and incubated at 30°C on a shaking platform set at 150 rpm. RNA was isolated from 5 ml of mid-logarithmic phase cultures.

extract_protocol: A. butzleri genomic DNA was prepared with the Qiagen Dneasy Blood and Tissue kit. Total A. butzleri RNA was extracted from cultures with RNA-BeeTM RNA Isolation Kit according to the manufacturer’s specifications.

tag: genotype/variation

value: wild type

source_name: Genomic DNA Arcobacter butzleri str. RM4018

tag: reference


title: RHT stem at T24, biological rep2


title: RM4810-REP3

value: Genomic DNA Arcobacter butzleri str. RM4018


title: S034_Scz_F_70

city: Stevenage

first: Julie

last: Huxley-Jones

state: Hertfordshire

address: Gunnels Wood Road

department: Computational Biology

institute: GlaxoSmithKline Pharmaceuticals

hyb_protocol: For each batch, 10ug total RNA was processed to Biotin-labeled cRNA and hybridized to HG-U133_Plus_2.0 GeneChips in accordance with the Affymetrix protocol (Affymetrix, Santa Clara, CA, USA,).

scan_protocol: Arrays were scanned on a GeneChip Scanner 3000 and fluorescence intensity for each feature of the array was obtained by using GeneChip Operating Software (Affymetrix).

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 150.

source_name: Brain BA22 post-mortem schizophrenic

extract_protocol: Total RNA was extracted from frozen BA22 using a Polytron type homogenizer (YellowLine DI 25 Basic) and TriZol reagent (Invitrogen, Paisley, UK) in a ratio of 1 ml of TriZol to 20 mg of tissue. RNA was further purified using RNeasy mini-columns (Qiagen, Valencia, CA, USA) including on-column DNAse-1 step and elution in water. Although pH was analysed in brain lysates using a pH meter, this was not considered to be rigorous enough to exclude or include samples and instead the RNA integrity number (RIN) was used to assess the quality of the RNA as the primary inclusion criterion. The quantity of extracted RNA was determined by spectrophotometry and quality was assessed using an Agilent 2100 Bioanalyzer (South Plainfield, NJ, USA) to determine the RIN. Based on the RIN, samples were classified into three quality groups—pass (RIN >7.0); borderline (RIN 6.0–7.0); fail (RIN<6.0). Following classification, there were 41 pass (RIN range of samples 7.0–9.0: average=7.7), 16 borderline (RIN range of samples 6.0–6.9; average=6.4) and 5 fail samples. Samples in the fail category were excluded from the study, and the remaining samples were randomized into four batches, containing an equal number of schizophrenic/control and male/female samples, for target generation and hybridization.

tag: gender

value: Female

tag: age

tag: post-mortem delay

tag: ph

tag: disease state

value: schizophrenic

value: superior temporal cortex (Brodmann Area 22, BA22)


title: Blood genomic DNA in patient with gastric cancer HRGC-68

value: female

tag: tsi, raw drug sensitivity

tag: tsi.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: fu, raw drug sensitivity

tag: fu.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: oxa, raw drug sensitivity

tag: oxa.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: dtax, raw drug sensitivity

tag: dtax.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: cdp, raw drug sensitivity

tag: cdp.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: tax, raw drug sensitivity

tag: saha, raw drug sensitivity

tag: pxd, raw drug sensitivity

tag: pxd.30, binary data (i.e. >= 30 or < 30) at 30% cutoff


title: S031_Scz_M_79

label_protocol: For each batch, 10ug total RNA was processed to Biotin-labeled cRNA and hybridized to HG-U133_Plus_2.0 GeneChips in accordance with the Affymetrix protocol (Affymetrix, Santa Clara, CA, USA,).

tag: gender

value: Male

tag: age

tag: post-mortem delay

tag: tissue


title: Blood genomic DNA in patient with gastric cancer HRGC-66

tag: disease state

tag: tsi, raw drug sensitivity

tag: tsi.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: tax.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: saha.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: cg2, raw drug sensitivity

tag: cg2.30, binary data (i.e. >= 30 or < 30) at 30% cutoff


title: RHT stem at T8, biological rep2

value: stem

tag: strain

tag: phenotype

tag: developmental stage

tag: infestation

tag: time


title: RHT stem at T8, biological rep1

value: tillering stage


title: S029_Scz_F_53

tag: ph


title: S035_Scz_F_87

tag: gender


title: RHT stem at T8, biological rep3

value: brown planthopper


title: RM4810-sigma7-REP3

tag: genotype/variation

tag: reference


title: RM4810-REP1


title: Blood genomic DNA in patient with gastric cancer HRGC-70

value: gastric cancer

tag: tissue

tag: fu, raw drug sensitivity

tag: fu.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: oxa, raw drug sensitivity

tag: oxa.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: dtax, raw drug sensitivity

tag: dtax.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: cdp, raw drug sensitivity

tag: cdp.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: tax, raw drug sensitivity

tag: saha, raw drug sensitivity

tag: pxd, raw drug sensitivity

tag: pxd.30, binary data (i.e. >= 30 or < 30) at 30% cutoff


title: RHT stem at T0, biological rep3

tag: strain

tag: phenotype

tag: developmental stage

tag: infestation

tag: time


title: RM4810-sigma7-REP2

tag: genotype/variation

tag: reference


title: RM4810-sigma7-REP1


title: S027_Scz_M_77

tag: gender

tag: age

tag: post-mortem delay

tag: ph

tag: disease state

tag: tissue


title: S028_Scz_F_28


title: S025_Scz_M_41


title: RHT stem at T0, biological rep1


title: RM4810-antisigma7-REP3


title: Blood genomic DNA in patient with gastric cancer HRGC-64

tag: tsi, raw drug sensitivity

tag: tsi.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: fu, raw drug sensitivity

tag: fu.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: oxa, raw drug sensitivity

tag: oxa.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: dtax, raw drug sensitivity

tag: dtax.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: cdp, raw drug sensitivity

tag: cdp.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: tax, raw drug sensitivity

tag: saha.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: cg2, raw drug sensitivity

tag: cg2.30, binary data (i.e. >= 30 or < 30) at 30% cutoff


title: Blood genomic DNA in patient with gastric cancer HRGC-61

tag: gender

tag: tax.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: saha, raw drug sensitivity

tag: pxd, raw drug sensitivity

tag: pxd.30, binary data (i.e. >= 30 or < 30) at 30% cutoff


title: S024_Scz_M_75

tag: age

tag: post-mortem delay

tag: ph

tag: disease state

tag: tissue


title: RM4810-antisigma7-REP2

tag: genotype/variation

tag: reference


title: Blood genomic DNA in patient with gastric cancer HRGC-62

tag: tsi, raw drug sensitivity

tag: tsi.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: fu, raw drug sensitivity

tag: fu.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: oxa, raw drug sensitivity

tag: oxa.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: dtax, raw drug sensitivity

tag: dtax.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: cdp, raw drug sensitivity

tag: cdp.30, binary data (i.e. >= 30 or < 30) at 30% cutoff


title: Salt-tolerant-stressed-A

city: New Delhi

first: Vandna

last: Rai

state: Delhi

address: Pusa campus

department: Genomics

institute: NRCPB

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

scan_protocol: According to standard Affymetrix protocol.

data_processing: GCOS version 1.0 signal intensity.

source_name: Salt-tolerant-stressed-A

growth_protocol: Samples were grown in hydroponic conditions till two weeks

extract_protocol: Trizol.

treatment_protocol: Two weeks young seedlings were applied to stress. For salt 50mM NaCl and for drought seedlings were kept outside of media for 24hrs.

value: leaf

tag: strain

value: salt-tolerant

tag: stress

value: salt


title: Blood genomic DNA in patient with gastric cancer HRGC-60

tag: gender

value: blood

tag: tax, raw drug sensitivity

tag: tax.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: saha, raw drug sensitivity

tag: saha.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: pxd, raw drug sensitivity

tag: pxd.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: cg2, raw drug sensitivity

tag: cg2.30, binary data (i.e. >= 30 or < 30) at 30% cutoff


title: RM4810-antisigma7-REP1

tag: genotype/variation

tag: reference


title: Salt-tolerant -stressed-B

source_name: Salt-tolerant -stressed-B

label_protocol: According to standard Affymetrix protocol

tag: tissue


title: S023_Scz_F_97

tag: age

tag: post-mortem delay

tag: ph

tag: disease state


title: S022_Scz_M_44


title: Blood genomic DNA in patient with gastric cancer HRGC-58

tag: tsi, raw drug sensitivity

tag: tsi.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: fu, raw drug sensitivity

tag: fu.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: oxa, raw drug sensitivity

tag: oxa.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: dtax, raw drug sensitivity

tag: dtax.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: cdp, raw drug sensitivity

tag: cdp.30, binary data (i.e. >= 30 or < 30) at 30% cutoff


title: Salt-tolerant-control-A

source_name: Salt-tolerant-control-A

tag: strain

tag: stress

value: control


title: RHT stem at T0, biological rep2

tag: tissue

value: Rathu Heenati

tag: phenotype

value: resistant variety to brown planthopper

tag: developmental stage

tag: infestation

tag: time


title: RM4810-sigma5-REP2

tag: genotype/variation

tag: reference

value: Genomic DNA Arcobacter butzleri str. RM4018


title: Salt-tolerant-control-B

source_name: Salt-tolerant-control-B


title: S019_Scz_M_79

tag: gender

tag: age

tag: post-mortem delay

tag: ph

tag: disease state


title: Salt-sensitive-stressed-A

source_name: Salt-sensitive-stressed-A

value: salt-sensitive


title: RM4810-sigma5-REP3


title: RM4810-sigma5-REP1


title: Salt-sensitive-stressed-B

source_name: Salt-sensitive-stressed-B


title: S021_Scz_M_71

value: schizophrenic


title: S012_Scz_M_63

value: superior temporal cortex (Brodmann Area 22, BA22)


title: Salt-sensitive-control-B

source_name: Salt-sensitive-control-B


title: RM4810-antisigma5-REP3


title: Blood genomic DNA in patient with gastric cancer HRGC-57

value: male

tag: tsi, raw drug sensitivity

tag: tsi.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: fu, raw drug sensitivity

tag: fu.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: oxa, raw drug sensitivity

tag: oxa.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: dtax, raw drug sensitivity

tag: dtax.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: tax, raw drug sensitivity

tag: saha, raw drug sensitivity

tag: saha.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: pxd, raw drug sensitivity

tag: pxd.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: cg2, raw drug sensitivity

tag: cg2.30, binary data (i.e. >= 30 or < 30) at 30% cutoff


title: Blood genomic DNA in patient with gastric cancer HRGC-56

tag: gender

tag: tissue

tag: cdp, raw drug sensitivity

tag: cdp.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: tax.30, binary data (i.e. >= 30 or < 30) at 30% cutoff


title: Blood genomic DNA in patient with gastric cancer HRGC-54

tag: disease state

tag: tsi, raw drug sensitivity

tag: tsi.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: fu, raw drug sensitivity

tag: fu.30, binary data (i.e. >= 30 or < 30) at 30% cutoff


title: Blood genomic DNA in patient with gastric cancer HRGC-59

tag: oxa, raw drug sensitivity

tag: oxa.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: dtax, raw drug sensitivity

tag: dtax.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: tax, raw drug sensitivity


title: S011_Scz_M_82

value: Male

tag: age

tag: post-mortem delay

tag: ph


title: RM4810-antisigma5-REP2

tag: genotype/variation

tag: reference


title: S013_Scz_F_65

tag: gender

value: Female

tag: tissue


title: Salt-sensitive-control-A

source_name: Salt-sensitive-control-A

tag: strain

tag: stress


title: Blood genomic DNA in patient with gastric cancer HRGC-52

tag: disease state

tag: tsi, raw drug sensitivity

tag: tsi.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: cdp, raw drug sensitivity

tag: cdp.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: tax.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: saha, raw drug sensitivity

tag: saha.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: pxd, raw drug sensitivity

tag: pxd.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: cg2, raw drug sensitivity

tag: cg2.30, binary data (i.e. >= 30 or < 30) at 30% cutoff


title: RM4810-antisigma5-REP1

tag: genotype/variation

tag: reference


title: S009_Scz_M_87

tag: gender

tag: age

tag: post-mortem delay

tag: ph

tag: tissue


title: RM4810-sigma4-REP3


title: S007_Scz_F_67

tag: disease state


title: Tolerant-drought str-B

source_name: Tolerant-drought str-B

tag: strain

value: drought-tolerant

tag: stress

value: drought


title: Blood genomic DNA in patient with gastric cancer HRGC-53

value: gastric cancer

tag: tsi, raw drug sensitivity

tag: tsi.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: fu, raw drug sensitivity

tag: fu.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: oxa, raw drug sensitivity

tag: oxa.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: dtax, raw drug sensitivity

tag: dtax.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: cdp, raw drug sensitivity

tag: cdp.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: tax, raw drug sensitivity


title: Blood genomic DNA in patient with gastric cancer HRGC-49

tag: gender

tag: tax.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: saha, raw drug sensitivity

tag: saha.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: pxd, raw drug sensitivity

tag: pxd.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: cg2, raw drug sensitivity

tag: cg2.30, binary data (i.e. >= 30 or < 30) at 30% cutoff


title: Blood genomic DNA in patient with gastric cancer HRGC-50

tag: disease state

tag: tissue

tag: tsi, raw drug sensitivity

tag: tsi.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: fu, raw drug sensitivity


title: Blood genomic DNA in patient with gastric cancer HRGC-47

tag: fu.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: oxa, raw drug sensitivity

tag: oxa.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: dtax, raw drug sensitivity

tag: dtax.30, binary data (i.e. >= 30 or < 30) at 30% cutoff


title: Tolerant-drought strA

source_name: Tolerant-drought strA

value: leaf

tag: strain

tag: stress


title: S006_Scz_M_79

tag: gender

tag: age

tag: post-mortem delay

tag: ph


title: RM4810-sigma4-REP2

tag: genotype/variation

tag: reference


title: RM4810-sigma4-REP1


title: S005_Scz_M_82

tag: disease state

tag: tissue


title: Blood genomic DNA in patient with gastric cancer HRGC-55

tag: tsi, raw drug sensitivity

tag: tsi.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: cdp, raw drug sensitivity

tag: cdp.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: tax, raw drug sensitivity

tag: tax.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: saha, raw drug sensitivity

tag: saha.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: pxd, raw drug sensitivity

tag: pxd.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: cg2, raw drug sensitivity

tag: cg2.30, binary data (i.e. >= 30 or < 30) at 30% cutoff


title: RM4810-antisigma4-REP3


title: S004_Scz_F_88

tag: gender

tag: age

tag: post-mortem delay

tag: ph


title: RM4810-antisigma4-REP2

tag: genotype/variation

tag: reference


title: Blood genomic DNA in patient with gastric cancer HRGC-45

tag: disease state

tag: tissue

tag: tsi, raw drug sensitivity

tag: tsi.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: fu, raw drug sensitivity

tag: fu.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: oxa, raw drug sensitivity

tag: oxa.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: dtax, raw drug sensitivity

tag: dtax.30, binary data (i.e. >= 30 or < 30) at 30% cutoff


title: Sens-drought str-B

source_name: Sens-drought str-B

tag: strain

value: drought-sensitive

tag: stress


title: Sens-drought str-A

source_name: Sens-drought str-A


title: S003_Scz_F_89

tag: gender

tag: age


title: Sens-drought-control-B

source_name: Sens-drought-control-B


title: S002_Scz_M_82

tag: post-mortem delay

tag: ph


title: Tolerant-drought-control-A

source_name: Tolerant-drought-control-A


title: Blood genomic DNA in patient with gastric cancer HRGC-46

source_name: Blood DNA in patient with gastric cancer

tag: cdp, raw drug sensitivity

tag: cdp.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: tax, raw drug sensitivity

tag: tax.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: saha, raw drug sensitivity

tag: saha.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: pxd, raw drug sensitivity

tag: pxd.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: cg2, raw drug sensitivity

tag: cg2.30, binary data (i.e. >= 30 or < 30) at 30% cutoff


title: Blood genomic DNA in patient with gastric cancer HRGC-51

tag: disease state

value: female

tag: tissue

tag: tsi, raw drug sensitivity

tag: tsi.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: fu, raw drug sensitivity

tag: fu.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: oxa, raw drug sensitivity

tag: oxa.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: dtax, raw drug sensitivity

tag: dtax.30, binary data (i.e. >= 30 or < 30) at 30% cutoff


title: Tolerant-drought-control-B

source_name: Tolerant-drought-control-B

tag: strain

tag: stress


title: RM4810-antisigma4-REP1

tag: genotype/variation

source_name: Genomic DNA Arcobacter butzleri str. RM4018

tag: reference


title: Blood genomic DNA in patient with gastric cancer HRGC-44

tag: gender

value: blood

tag: cdp, raw drug sensitivity

tag: cdp.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: tax, raw drug sensitivity

tag: tax.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: saha, raw drug sensitivity

tag: saha.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: pxd, raw drug sensitivity

tag: pxd.30, binary data (i.e. >= 30 or < 30) at 30% cutoff


title: RM4810-sigma2-REP3


title: Blood genomic DNA in patient with gastric cancer HRGC-43

tag: disease state

tag: tissue

tag: tsi, raw drug sensitivity

tag: tsi.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: fu, raw drug sensitivity

tag: fu.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: oxa, raw drug sensitivity

tag: cg2, raw drug sensitivity

tag: cg2.30, binary data (i.e. >= 30 or < 30) at 30% cutoff


title: S001_Scz_F_75

source_name: Brain BA22 post-mortem schizophrenic

tag: gender

tag: age

tag: post-mortem delay

tag: ph


title: Blood genomic DNA in patient with gastric cancer HRGC-48

tag: oxa.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: dtax, raw drug sensitivity

tag: dtax.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: cdp, raw drug sensitivity

tag: cdp.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: tax, raw drug sensitivity

tag: saha, raw drug sensitivity


title: RM4810-sigma2-REP2

tag: genotype/variation

tag: reference


title: RM4810-sigma2-REP1


title: Tuberculoid Patient 6

city: Los Angeles

first: Philip

middle: T.

last: Liu

address: 615 Charles E Young Drive South, 410 OHRC

department: Department of Orthopaedic Surgery

institute: University of California at Los Angeles

hyb_protocol: Samples were processed by Ausragen through the Discovarray miRNA profiling service.  Hybridization, washing, staining, imaging, and signal extraction were performed according to Affymetrix-recommended procedures, except that the 20X GeneChip Eukaryotic Hybridization Control cocktail was omitted from the hybridization.

scan_protocol: Samples were processed by Ausragen through the Discovarray miRNA profiling service.  The signal processing implemented for the Ambion miRCHIP is a multi-step process involving probe specific signal detection calls, background estimate and correction, constant variance stabilization and either array scaling or global normalization. For each probe, an estimated background value is subtracted that is derived from the median signal of a set of G-C-matched anti-genomic controls. Arrays within a specific analysis experiment were normalized together according to the variance stabilization method described by Huber et al. (Huber et al., 2002). Detection calls were based on a Wilcoxon rank-sum test of the miRNA probe signal compared to the distribution of signals from GC-content matched anti-genomic probes.

data_processing: Samples were analyzed by Ausragen through the Discovarray miRNA profiling service, and normalized using Variation Stabilization Normalization (VSN).

source_name: leprosy skin lesion biopsy

label_protocol: Samples were processed by Ausragen through the Discovarray miRNA profiling service.  Total RNA is dephosphorylated with calf intestinal phosphatase and the pCp-Biotin labeling molecule is ligated to the 3’ ends of the RNA molecules. Labeled RNA is purified using BioSpin6 (Bio-Rad, Hercules CA).

growth_protocol: N/A, samples were skin biopsy specimens from leprosy patients.

extract_protocol: RNA was extracted from the OCT embedded and sections biopsies using guanidinium-isothiocyanate (CTC) buffer as previously described (Bleharski et al., 2003).

tag: leprosy type

value: tuberculoid


title: Tuberculoid Patient 5


title: C032_Control_M_76

source_name: Brain BA22 post-mortem control

tag: disease state

value: control

tag: tissue


title: RM4810-antisigma2-REP3


title: Tuberculoid Patient 3


title: Tuberculoid Patient 4


title: Blood genomic DNA in patient with gastric cancer HRGC-42

tag: tsi, raw drug sensitivity

tag: tsi.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: fu, raw drug sensitivity

tag: fu.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: oxa, raw drug sensitivity

tag: tax.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: saha.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: pxd, raw drug sensitivity

tag: pxd.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: cg2, raw drug sensitivity

tag: cg2.30, binary data (i.e. >= 30 or < 30) at 30% cutoff


title: RM4810-antisigma2-REP2


title: C024_Control_F_78

tag: gender

tag: age

tag: post-mortem delay

tag: ph


title: Sens-drought-control-A

source_name: Sens-drought-control-A

tag: strain

tag: stress


title: C028_Control_F_54

tag: disease state

tag: tissue


title: Blood genomic DNA in patient with gastric cancer HRGC-40

tag: tsi, raw drug sensitivity

tag: tsi.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: fu, raw drug sensitivity

tag: oxa.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: dtax, raw drug sensitivity

tag: dtax.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: cdp, raw drug sensitivity

tag: cdp.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: tax, raw drug sensitivity

tag: saha, raw drug sensitivity


title: Tuberculoid Patient 2

tag: leprosy type


title: RM4810-antisigma2-REP1

tag: genotype/variation

tag: reference


title: Blood genomic DNA in patient with gastric cancer HRGC-41

tag: gender

tag: fu.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: oxa, raw drug sensitivity

tag: tax.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: saha.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: pxd, raw drug sensitivity

tag: pxd.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: cg2, raw drug sensitivity

tag: cg2.30, binary data (i.e. >= 30 or < 30) at 30% cutoff


title: Blood genomic DNA in patient with gastric cancer HRGC-39

tag: disease state

tag: tissue

tag: tsi, raw drug sensitivity

tag: tsi.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: fu, raw drug sensitivity

tag: oxa.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: dtax, raw drug sensitivity

tag: dtax.30, binary data (i.e. >= 30 or < 30) at 30% cutoff


title: C023_Control_M_38

tag: gender

tag: age

tag: post-mortem delay

tag: ph


title: RM4810-sigma1-REP3

tag: genotype/variation

tag: reference


title: C022_Control_F_68


title: C033_Control_M_81


title: Lepromatous Patient 6

tag: leprosy type

value: lepromatous


title: RM4810-sigma1-REP2

value: Genomic DNA Arcobacter butzleri str. RM4018


title: Blood genomic DNA in patient with gastric cancer HRGC-38

tag: fu.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: oxa, raw drug sensitivity

tag: cdp, raw drug sensitivity

tag: cdp.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: tax, raw drug sensitivity

tag: tax.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: saha, raw drug sensitivity

tag: saha.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: pxd, raw drug sensitivity

tag: pxd.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: cg2, raw drug sensitivity


title: RM4810-sigma1-REP1


title: Lepromatous Patient 5


title: Blood genomic DNA in patient with gastric cancer HRGC-36

tag: disease state

tag: gender

tag: tissue

tag: tsi, raw drug sensitivity

tag: tsi.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: fu, raw drug sensitivity

tag: oxa.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: dtax, raw drug sensitivity

tag: dtax.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: cg2.30, binary data (i.e. >= 30 or < 30) at 30% cutoff


title: RM4810-antisigma1-REP3

tag: genotype/variation

tag: reference


title: Tuberculoid Patient 1

tag: leprosy type


title: C020_Control_M_25

tag: age

tag: post-mortem delay

tag: ph


title: Lepromatous Patient 4


title: RM4810-antisigma1-REP2


title: C018_Control_F_67


title: C019_Control_F_46


title: Lepromatous Patient 2


title: Lepromatous Patient 1


title: RM4810-antisigma1-REP1


title: E.globulus_Clone B_Ramet 2_Xylem

city: Porto Alegre

first: Giancarlo

last: Pasquali

state: RS

address: Av. Bento Gonçalves, 9500 - Pr. 43.431 - Lab. 212

department: Centro de Biotecnologia

country: Brazil

institute: Universidade Federal do Rio Grande do Sul

description: G10 - Total RNA extracted from the vascular tissues of the trunk of 4-years-old, field-grown Eucalyptus globuluss tree, genotype B, ramet 2, planted at Hortoflorestal Barbanegra, Eldorado do Sul, RS, Brazil.

hyb_protocol: Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

data_processing: The raw data (.ftr file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).

organism: Eucalyptus globulus

source_name: trunk vascular tissue (xylem), 4-years-old, field-grown tree

label_protocol: Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

growth_protocol: Differentiating xylem tissues and mature leaves were collected from 4-year-old, field-grown E. grandis and E. globulus trees located at Aracruz Celulose S.A. (Hortoflorestal Barbanegra, Eldorado do Sul, RS, Brazil).

extract_protocol: Total RNA was extracted using the PureLink Reagent (Invitrogen) according to manufacturer´s miniprep protocol.

treatment_protocol: Xylem was collected by scraping the exposed vascular tissue after the removal of the 0.5-1 cm-tick stem bark. Two lines of genetically unrelated matrixes were chosen for both species and each line was represented by two clones (biological duplicates), therefore completing 4 xylem samples for E. grandis, and 4 xylem samples for E. globulus. From both clones of one of the E. grandis  lines, mature leaves were also collected. To minimize the proportion of primary xylem mainly located in the main veins of leaves, only leaf blades without the central vein of mature leaves were used for this study. Tissue samples were immediately frozen in liquid nitrogen and stored at -80 °C.

tag: genotype

value: E. globulus clone B

tag: clonal individual

value: Ramet 2


title: C017_Control_M_72

tag: gender

tag: disease state

value: superior temporal cortex (Brodmann Area 22, BA22)


title: Blood genomic DNA in patient with gastric cancer HRGC-32

value: male

tag: tissue

tag: tsi, raw drug sensitivity

tag: fu.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: oxa, raw drug sensitivity

tag: cdp, raw drug sensitivity

tag: cdp.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: tax, raw drug sensitivity

tag: tax.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: saha, raw drug sensitivity

tag: saha.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: pxd, raw drug sensitivity

tag: pxd.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: cg2, raw drug sensitivity


title: Blood genomic DNA in patient with gastric cancer HRGC-29

tag: tsi.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: fu, raw drug sensitivity

tag: oxa.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: dtax, raw drug sensitivity

tag: dtax.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: cg2.30, binary data (i.e. >= 30 or < 30) at 30% cutoff


title: Blood genomic DNA in patient with gastric cancer HRGC-27

tag: disease state

tag: gender

tag: tissue

tag: tsi, raw drug sensitivity

tag: fu.30, binary data (i.e. >= 30 or < 30) at 30% cutoff


title: Blood genomic DNA in patient with gastric cancer HRGC-28

tag: oxa, raw drug sensitivity

tag: cdp, raw drug sensitivity

tag: cdp.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: tax, raw drug sensitivity

tag: tax.30, binary data (i.e. >= 30 or < 30) at 30% cutoff


title: C016_Control_M_60

value: Male

tag: age

tag: post-mortem delay

tag: ph


title: Colony 6

city: Kansas City

first: Chris

middle: W

last: Seidel

state: MO

institute: Stowers Institute

hyb_protocol: Slides were hybridized with a mixture of Alexa Fluor 555- and 647-labeled DNA probes. Hybridizations were performed at 63C overnight under standard conditions (3X SSC, 0.2 mg/ml salmon sperm DNA, 25 mM HEPES, 0.25% SDS), and slides were washed at room temperature successively with 0.6X SSC/0.03% SDS and then 0.06X SSC prior to scanning.

scan_protocol: Microarray images were acquired with a GenePix 4000B scanner (Axon Instruments, Foster City, CA). For image analysis, GenePix Pro 6.0 software was used (Axon Instruments).

data_processing: GPR files were processed in the R environment using the Limma library. The Alexa 647 and Alexa 555 signals were background subtracted and normalized using print tip loess. Replicate spots were averaged. The data was further normalized per chromosome using the median chromosomal value of all probes grouped by chromosome.

label: Alexa 555

organism: Saccharomyces cerevisiae

source_name: Colony 6

label_protocol: BioPrime Plus Array CGH Kit (Invitrogen).

growth_protocol: Cells were grown in YPD to saturation at 30C.

extract_protocol: Genomic DNA was extracted using the YeaStar™ Genomic DNA Kit (ZymoResearch).

tag: background strain

tag: genotype

value: MATalpha ura3-52 lys2-801 ade2-101 trp1D1 his3D200 leu2D1 +Chr XI

label: Alexa 647

source_name: WT


title: E.globulus_Clone B_Ramet 1_Xylem

description: G09 - Total RNA extracted from the vascular tissues of the trunk of 4-years-old, field-grown Eucalyptus globuluss tree, genotype B, ramet 1, planted at Hortoflorestal Barbanegra, Eldorado do Sul, RS, Brazil.

tag: clonal individual

value: Ramet 1


title: C021_Control_M_25


title: Colony 10

source_name: Colony 10

value: MATalpha ura3-52 lys2-801 ade2-101 trp1D1 his3D200 leu2D1 +Chr X


title: WT self-hybridization

value: MATalpha ura3-52 lys2-801 ade2-101 trp1D1 his3D200 leu2D1


title: E.globulus_Clone A_Ramet 2_Xylem

description: G08 - Total RNA extracted from the vascular tissues of the trunk of 4-years-old, field-grown Eucalyptus globuluss tree, genotype A, ramet 2, planted at Hortoflorestal Barbanegra, Eldorado do Sul, RS, Brazil.

value: E. globulus clone A


title: C014_Control_M91


title: C011_Control_F_89

value: Female


title: Blood genomic DNA in patient with gastric cancer HRGC-25

value: gastric cancer

tag: tsi.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: fu, raw drug sensitivity

tag: oxa.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: dtax, raw drug sensitivity

tag: dtax.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: saha, raw drug sensitivity

tag: saha.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: pxd, raw drug sensitivity

tag: pxd.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: cg2, raw drug sensitivity

tag: cg2.30, binary data (i.e. >= 30 or < 30) at 30% cutoff


title: Blood genomic DNA in patient with gastric cancer HRGC-37

tag: disease state

tag: gender

value: unknown, gastric,

tag: tissue

value: blood

tag: tsi, raw drug sensitivity

tag: fu.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: oxa, raw drug sensitivity

tag: cdp, raw drug sensitivity

tag: cdp.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: tax, raw drug sensitivity

tag: tax.30, binary data (i.e. >= 30 or < 30) at 30% cutoff


title: E.globulus_Clone A_Ramet 1_Xylem

description: G07 - Total RNA extracted from the vascular tissues of the trunk of 4-years-old, field-grown Eucalyptus globuluss tree, genotype A, ramet 1, planted at Hortoflorestal Barbanegra, Eldorado do Sul, RS, Brazil.

tag: genotype

tag: clonal individual


title: Blood genomic DNA in patient with gastric cancer HRGC-21

tag: tsi.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: fu, raw drug sensitivity

tag: oxa.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: dtax, raw drug sensitivity

tag: dtax.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: saha, raw drug sensitivity

tag: saha.30, binary data (i.e. >= 30 or < 30) at 30% cutoff


title: C010_Control_F_90

tag: gender

tag: age

tag: post-mortem delay

tag: ph

tag: disease state

value: control

tag: tissue


title: Rad-r3

label_protocol: BioPrime Labeling kit (Invitrogen).

growth_protocol: Briefly, a diploid strain was first grown on a plate containing a high concentration of radicicol (100μg/ml) or vehicle control; three of the largest radicicol-resistant colonies along with a colony from the vehicle plate were cultured overnight in drug-free media and then retested for radicicol resistance.

extract_protocol: YeaStar Genomic kit (ZymoResearch).

tag: background strain

tag: phenotype

value: radicicol resistant

value: radicicol sensitive


title: Blood genomic DNA in patient with gastric cancer HRGC-26

value: female

tag: tsi, raw drug sensitivity

tag: fu.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: oxa, raw drug sensitivity

tag: cdp, raw drug sensitivity

tag: cdp.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: tax, raw drug sensitivity

tag: tax.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: pxd, raw drug sensitivity

tag: pxd.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: cg2, raw drug sensitivity

tag: cg2.30, binary data (i.e. >= 30 or < 30) at 30% cutoff


title: C005_Control_M_91

tag: gender

tag: age

tag: post-mortem delay


title: E.grandis_Clone B_Ramet 2_Xylem

description: G06 - Total RNA extracted from the vascular tissues of the trunk of 4-years-old, field-grown Eucalyptus grandis tree, genotype B, ramet 2, planted at Hortoflorestal Barbanegra, Eldorado do Sul, RS, Brazil.

organism: Eucalyptus grandis

tag: genotype

value: E. grandis clone B

tag: clonal individual

value: Ramet 2


title: Rad-r2

tag: background strain

tag: phenotype


title: Rad-r1


title: C007_Control_M_54

tag: ph

tag: disease state

tag: tissue

value: superior temporal cortex (Brodmann Area 22, BA22)


title: Blood genomic DNA in patient with gastric cancer HRGC-30

tag: tsi, raw drug sensitivity

tag: tsi.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: fu, raw drug sensitivity

tag: fu.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: oxa, raw drug sensitivity

tag: oxa.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: dtax, raw drug sensitivity

tag: dtax.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: cdp, raw drug sensitivity

tag: cdp.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: saha, raw drug sensitivity

tag: saha.30, binary data (i.e. >= 30 or < 30) at 30% cutoff


title: Blood genomic DNA in patient with gastric cancer HRGC-23

tag: gender

value: male

tag: tax, raw drug sensitivity

tag: tax.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: pxd, raw drug sensitivity

tag: pxd.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: cg2, raw drug sensitivity

tag: cg2.30, binary data (i.e. >= 30 or < 30) at 30% cutoff


title: Blood genomic DNA in patient with gastric cancer HRGC-24

tag: disease state

tag: tissue

tag: tsi, raw drug sensitivity

tag: tsi.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: fu, raw drug sensitivity


title: E.grandis_Clone A_Ramet 2_Xylem

description: G04 - Total RNA extracted from the vascular tissues of the trunk of 4-years-old, field-grown Eucalyptus grandis tree, genotype A, ramet 2, planted at Hortoflorestal Barbanegra, Eldorado do Sul, RS, Brazil.

tag: genotype

value: E. grandis clone A

tag: clonal individual


title: C008_Control_F_94

tag: age

tag: post-mortem delay

tag: ph


title: E.grandis_Clone B_Ramet 1_Xylem

description: G05 - Total RNA extracted from the vascular tissues of the trunk of 4-years-old, field-grown Eucalyptus grandis tree, genotype B, ramet 1, planted at Hortoflorestal Barbanegra, Eldorado do Sul, RS, Brazil.

value: Ramet 1


title: Blood genomic DNA in patient with gastric cancer HRGC-22

tag: gender

tag: fu.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: oxa, raw drug sensitivity

tag: oxa.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: dtax, raw drug sensitivity

tag: dtax.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: cdp, raw drug sensitivity

tag: cdp.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: saha, raw drug sensitivity

tag: saha.30, binary data (i.e. >= 30 or < 30) at 30% cutoff