title: 20090919_IND_13_2500_02

city: Campbelltown

first: Rebekah

last: Cook

state: NSW

address: Narellan Road

department: CompleMED

country: Australia

institute: University of Western Sydney

hyb_protocol: The Affymetrix Processing Service by the Ramaciotti Centre for Gene Function Analysis (RCGFA) was used for this purpose. The Affymetrix GeneChip® Hybridization, Wash and Stain kit was used for this purpose

scan_protocol: The Affymetrix Processing Service by the Ramaciotti Centre for Gene Function Analysis (RCGFA) was used for this purpose. The GeneChip® Scanner 3000 linked to the Affymetrix® Microarray Suite was most likely used here. Each probe array scanned twice. The software calculates an average of the two images, defines the probe cells and computes an intensity for each cell. Each complete probe array image is stored in a separate

data_processing: The R program for statistical computing was used together with the bioconductor libraries; limma, affy, gplots, altcdfenvs, yeast2cdf, affyPLM, yeast2db and annaffy to analyse our microarray data sets. Quality control measures were taken to assess the quality of our data. The data was then normalised and summarised by the Robust Multiarray Averaging (RMA) method and a linear modelling approach was applied for differential gene expression analysis. Multiple statistical methods were applied to our data including Bonferroni, FDR and Fold change cut off parameters to determine statistical significance.

source_name: Yeast at OD of ~0.6, treated with INDIA13, 20 min.

label_protocol: The Affymetrix Processing Service by the Ramaciotti Centre for Gene Function Analysis (RCGFA) was used for this purpose. The GeneChip® 3' IVT Express Kit was used for cDNA synthesis and biotin labelling

growth_protocol: BY4743 was maintained in a glycerol stock at -80 °C, aliquiots were taken and stored on YEPD plates at 4 °C. In biological duplicate, 25 ml minimal medium was inoculated overnight with one colony to an OD of between 0.5 and 1.0.

extract_protocol: TRIzol method for RNA isolation was used following manufacturer's protocol

treatment_protocol: Cells were grown overnight in replicate to the required OD, treated (2.5 mg/ml dried extract) or untreated for 20 min, cells were then harvested by centrifugation and either snap frozen or stored in TRIzol at 4 °C for immediate isolation of RNA

tag: equisetum arvense sample


title: WT1(Cy5) vs. WT_Blap 1 (Cy3)

status: Public on Dec 31 2011

type: RNA

city: Valencia

first: Jose

last: Gadea

address: Ingeniero Fausto Elio

department: Stress

country: Spain

institute: IBMCP

description: no further description

hyb_protocol: Slides were hybridised using manual chambers according to manufacturer. Briefly, slides were prehybridized in 5 x SSC,0.1% SDS, and 0.1 mg/mL BSA for 45m, and rinse in 0.1 x SSC two times before drying. Both samples were resuspended in 50% formamide, 5 x SSC, 0.1% SDS, and 0.1 mg/mL of  sonicated salmon sperm DNA, denatured for 5 m and injected between slide and coverslip (Lifterslips). Hyb was performed overnight at 42ºC. Washes a) Arrays were inmersed in 2 x SSC, 0.1% SDS at 42°C until the coverslip moves freely away from the slide. b) Transferred to 2 x SSC, 0.1% SDS at 42°C for 5 minutes. c) Transferred  to 0.1 x SSC, 0.1% SDS at room temperature for 5 minutes. Repeat step d) Transferred  to 0.1 x SSC at room temperature for 1 minute. Repeated 4 times e) Rinsed  in 0.01 x SSC for 10 seconds. 9. Dried by centrifugation at 1,600 x g for 2 minutes.

scan_protocol: Slides were scanning at 10um resolution using a 4200B Molecular Devices scanner, adjusting PMT values so that ratio Cy5/Cy3 total intensity is close to 1. Image analysis was performed using GenePix 6.0 software.

data_processing: ocal background was used for background sustraction. Background-substrated signals were used for ratio calculations. Data were normalized by global-median and print-tip loess. Features whose background-substrated intensity do not reach two times background intensity were flagged as bad and rejected for further analysis (Value=null). Equal for features affected by hyb and washing artefacts, if any. Original value data are log ratios of lowess-normalized Cy5/Cy3 signals.

molecule: total RNA

organism: Saccharomyces cerevisiae

source_name: Wt BY4741 strain in log phase culture

label_protocol: Indirect labelling

extract_protocol: standard protocol (acid-phenol extraction).

treatment_protocol: Cells were grown at 28ºC in YPD rich medium until Ab660=0.6. 50 ml of yeast culture was treated with  vehicle (1% DMSO)  for 1 hour. Cells were then harvested by centrifugation and washed with cold water. Dried cell pellet was kept at-80 until RNA purification

tag: strain

tag: genotype

value: :MATa, his3Δ1, leu2Δ0, LYS2, met15Δ0, ura3Δ0

source_name: Wt BY4741 strain in log phase culture treated with b-lapachone

treatment_protocol: Cells were grown at 28ºC in YPD rich medium until Ab660=0.6. 50 ml of yeast culture was treated with 10 ug/ml b-lapachone in DMSO for 1 hour. Cells were then harvested by centrifugation and washed with cold water. Dried cell pellet was kept at-80 until RNA purification


title: 20090919_IND_13_2500_01

label: biotin


title: liver_highfat_rep1

city: Hohhot

first: Heping

last: Zhang

address: No.306 Zhaowuda road

country: China

institute: Inner Mongolia Agricultural University

description: Gene expression data of liver of hypercholesterolemic rat

hyb_protocol: Purified cRNA was broken down to 35 to 200 base fragments and incubated at 94℃ for 35 min. The fragmented and labelled cRNA was applied to the Rat Genome 230 2.0 Array. Hybridization was carried out in a mixture containing probe array controls, BSA (Invitrogen, Carlsbad, CA, USA) and herring sperm DNA (Promega, Madison, WI, USA) for 16 h at 45℃.

scan_protocol: GeneChips were scanned using GeneArrayTM scanner 3000

data_processing: Gene expression values were calculated from the fluorescence signal by Affymetrix GeneChip Operating Software, as described by Affymetrix GeneChip standard procedures.

organism: Rattus norvegicus

source_name: Hypercholesterolemic rat as control

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: Rats in high fat and probiotic treated group were fed with fat-rich diet to form hypercholesterol models in the first 30 d. In the next 30 d, in addition to fat-rich diet, rats in high fat group were daily supplied with 1 ml of normal saline and rats in probiotic treated group were daily supplied with L. casei Zhang (2 × 108cfu) dissolved in 1 ml of normal saline by intragastric administration.

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

tag: tissue

value: liver

tag: treatment

value: high fat control


title: genomic DNA from colon cancer tissue_CRC2004T

type: genomic

city: Daejeon

first: Han-Chul

last: Lee

address: 111 Gwahangno, Yuseong-gu

department: Medical Genome Research Center

country: South Korea

institute: KRIBB

description: tumor colon sample

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation27 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: BeadStudio software v3.2

molecule: genomic DNA

organism: Homo sapiens

source_name: Colon

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from LBC samples using Qiagen DNeasy Kit according to standard instructions

tag: gender

value: Female

value: Colon cancer tissue

tag: disease state

value: tumor


title: liver_probiotic_rep3

description: Gene expression data of liver of hypercholesterolemic rat treated with probiotic Lactobacillus casei Zhang

source_name: Hypercholesterolemic rat treated with probiotic Lactobacillus casei Zhang

value: Lactobacillus casei Zhang


title: liver_probiotic_rep2


title: genomic DNA from colon cancer tissue_CRC2003T

description: tumor colon sample

value: Male


title: genomic DNA from colon cancer adjacent normal tissue_CRC2004N

description: normal colon sample

value: normal


title: 20090919_EUR_11_2500_02

source_name: Yeast at OD of ~0.6, treated with EUROPE11, 20 min.


title: genomic DNA from colon cancer adjacent normal tissue_CRC2003N

description: normal colon sample


title: 20090919_EUR_11_2500_01


title: 20090919_CHN_08_2500_02

source_name: Yeast at OD of ~0.6, treated with CHINA8, 20 min.


title: genomic DNA from colon cancer tissue_CRC2005T

description: tumor colon sample


title: liver_probiotic_rep1


title: P123-TL1 prostate tumour

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

label_protocol: As per manufacturer (Affymetrix)

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

tag: individual

value: Prostate tissue


title: dengue Patient_Timepoint3  31

city: Singapore

first: Ahmad Nazri

last: Mohamed Naim

address: 60 Biopolis Street, Genome, #02-01

department: Infectious disease

country: Singapore

institute: Genome institute of Singapore

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were analysed in Genespring GX7.3 software. Measurements less than 0.01 was set to 0.0 1. Data was then normalised at the 50th percentile.

source_name: Human whole blood

label_protocol: Biotinylated cRNA were pared with the Illumina TotalP RNA Amplification Kit for Illumina arrays

extract_protocol: Total RNA was extracted from whole blood drawn in pax-gene vacutainer tubes by PAX-gene RNA kit (Qiagen). Quality control was performed with NanoDrop 1000 instrument

tag: sample type

value: Patient

tag: collection time

value: 2 to 5 weeks after symptoms


title: dengue Patient_Timepoint3  30


title: genomic DNA from colon cancer adjacent normal tissue_CRC2002N

description: normal colon sample


title: genomic DNA from colon cancer tissue_CRC2002T

description: tumor colon sample


title: WX92-PL1 High grade PIN


title: dengue Patient_Timepoint3  29


title: genomic DNA from colon cancer tissue_CRC2001T

description: tumor colon sample


title: 20090701_CHN_08_2500_02


title: P123-N normal prostate


title: 20090701_CHN_08_2500_01


title: WX73-PL1 High grade PIN


title: 20090919_CHN_08_2500_01


title: genomic DNA from colon cancer adjacent normal tissue_CRC2001N

description: normal colon sample


title: dengue Patient_Timepoint3  27


title: dengue Patient_Timepoint3  26


title: P123-PL1 High grade PIN


title: P107-PL1 High grade PIN


title: dengue Patient_Timepoint3  28


title: 20090919_USA_06_2500_02

source_name: Yeast at OD of ~0.6, treated with USA6, 20 min.


title: 20090919_USA_06_2500_01


title: WX47-PL1 High grade PIN


title: dengue Patient_Timepoint3  25


title: WX68-PL1 High grade PIN


title: dengue Patient_Timepoint3  24


title: 20090919_USA_02_2500_02

source_name: Yeast at OD of ~0.6, treated with USA2, 20 min.


title: dengue Patient_Timepoint3  23


title: dengue Patient_Timepoint3  22


title: 20090919_USA_02_2500_01


title: dengue Patient_Timepoint3  21


title: 20090919_USA_07_2500_01

source_name: Yeast at OD of ~0.6, treated with USA7, 20 min.


title: 20090919_CTL_00_0000_02

source_name: Yeast at OD of ~0.6, non treated, 20 min.


title: 20090919_USA_07_2500_02


title: WX21-PL1 High grade PIN


title: dengue Patient_Timepoint3  20


title: 20090919_CTL_00_0000_01


title: WX68-N normal prostate


title: dengue Patient_Timepoint3  19


title: WX33-PR1 High grade PIN


title: 20090701_CTL_00_0000_02


title: dengue Patient_Timepoint3  18


title: 20090701_CTL_00_0000_01


title: WX12-PM1 High grade PIN


title: Hip DCX C

city: Zurich

first: Oliver

last: Bracko

address: Schafmattstrasse 18

country: Switzerland

institute: ETH Zurich

hyb_protocol: Cy3 labeled cDNAs were hybridized overnight for 17 hours at 65 degrees Celsius to Agilent whole mouse genome Oligo Microarrays 4 x 44K using Agilent's recommended hybridization chamber and oven

scan_protocol: Scanning done by Agilent Microarray scanning system

data_processing: Raw Cy3 data were normalized to the median and all values that were smaller than 1 were set to zero. All genes that had zero values in at least 11 of 12 arrays were deleted from the list, leaving 29,148 genes for analysis. Data were analyzed using the CARMA software suite (www.carmaweb.genome.tugraz.at/carma). The values were log2 transformed and quantile normalized. Expression differences were calculated over 3 replicates between 2 groups of experiments with the LIMMA package employing a modified t-statistic. Benjamini and Hochberg False discovery rate was used to calculate p-values. Final gene lists contain all genes with a p-value <=0.05. Expression values of genes that were represented twice or more on the array were averaged.

organism: Mus musculus

source_name: DCX-DsRed Hippocampus

label_protocol: Cy3 labelling according to Miltenzi Biotec undisclosed protocol.

extract_protocol: RNA from 1,000 cells from each cell population was isolated with TRIzol reagent (Invitrogen), amplified and reverse transcribed using the SuperAmp protocol (Miltenyi).

treatment_protocol: Two previously described transgenic mouse lines were used for FACS sorting of SOX+ and DCX+ cells: one line expressed GFP under the Sox2 promoter and the other line expressed DsRed under the Dcx promoter6,23. For each experiment, 10 hippocampi and SVZs (from coronal sections) were dissected and pooled from 6- to 8-week-old mice. Dissected tissue was chopped into ~1 mm3 pieces using sterile razor blades and dissociated by incubation for 30 minutes in a solution containing 0.01% papain (25 u/mg, Worthington Biochemicals), 0.1% neutral protease (0.5 u/mg, Roche), and 0.01% DNaseI (2788 u/mg, Worthington Biochemicals). The cell suspension was mixed with an equal volume of DMEM:F12 media (containing 1 mM L-glutamine and 10% fetal bovine serum) and filtered through a 70-µm nylon mesh, mixed with an equal amount of Percoll solution and pelleted (20,000 g for 30 minutes). Cellular debris was removed, and cells were spun down and dissolved in 2 ml DMEM:F12 plus N2. For FACS, GFP was excited with a 488-nm water-cooled argon laser; DsRed was excited with a 561-nm solid-state laser. The filters used were 530/30 nm for GFP and 630/22 nm for DsRed using a BD FACSvantage Diva system (BD Biosciences).

tag: age

value: 6-8 weeks

value: Hippocampus

tag: genotype/variation

value: DCX-DsRed


title: Digestive Gland-Chlorpyrifos-Rep4 [MytArray 1.0]

city: Alessandria

first: Francesco

last: Dondero

address: Via Michel 11

department: Department of Environmental and Life Sciences

country: Italy

institute: University of Piemonte Orientale "Amedeo Avogadro"

hyb_protocol: 43°C, 16/20 h, hybridization buffer Northern Max (Ambion). Pre-hybridization for 1h in same conditions.

scan_protocol: The BioRad Chip Reader was used to generate TIFF files at 5 micron resolution. Then the digital images were processed using the Axon GenePix software to obtain gpr files. Gpr files were saved as gpr 3.0.

data_processing: Kooperberg background subtracted, loess normalized. Data obtained from log2 of processed Ch1 signal/processed Ch2 signal. LIMMA software was used

organism: Mytilus galloprovincialis

source_name: digestive gland tissue, animals exposed to 4.5 mg/L chlorpyrifos for 4 days in aquaria

label_protocol: 15 µg of total RNA were primed with 0.5 µg oligodT(19)VN primer at 70°C for 10 min, then reversed transcribed at 42°C for 2 h in the presence of 400 U ReverseAid MuLV H minus  RTase (Fermentas), and 100 µM each dATP, dTTP, dGTP, with 25 µM dCTP, 25 µM Cy3-labeled dCTP or Cy5-label dCTP

extract_protocol: Total RNA extracted from pools made of 6 different digestive gland pieces using Trizol following manufacturer's instructions

treatment_protocol: animals exposed in aquaria

value: female

value: digestive gland tissue

tag: agent

value: chlorpyrifos

tag: dose

tag: time

value: 4 days

source_name: digestive gland tissue,vehicle treated (0.02% DMSO) for four days

value: vehicle (0.02% DMSO)


title: Digestive Gland-Nickel-Rep4 [MytArray 1.0]

source_name: digestive gland tissue, animals exposed to 0.77 mg/L Nickel for 4 days in aquaria

value: Nickel


title: dengue Patient_Timepoint3  16


title: dengue Patient_Timepoint3  17


title: SVZ Sox2 C

source_name: Sox2-GFP SVZ

value: SVZ


title: WX12-PL3 High grade PIN


title: WX68-TL1 prostate tumour


title: WX8-PR1 High grade PIN


title: Chinese_sample_155

city: Shanghai

first: Haiyi

last: Lou

address: 320 Yueyang Road

institute: CAS-MPG PICB

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

data_processing: Data genotyped by Birdsuite provided as Series supplementary file; CHP data in tables was processed by Affymetrix Power Tools 1.10.2

source_name: blood

extract_protocol: Genomic DNA was extracted from mononuclear cell preparations of leukemic blasts obtained from peripheral blood using the Qiagen DNA Blood Mini Kit. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer and agarose gel electrophoresis.

value: blood

tag: population

value: Chinese


title: dengue Patient_Timepoint3  15


title: SVZ Sox2 B


title: WX9-PR1 High grade PIN


title: Hip Sox2 C

source_name: Sox2-GFP Hippocampus


title: dengue Patient_Timepoint3  14


title: dengue Patient_Timepoint3  13


title: Digestive Gland-Chlorpyrifos-Rep3 [MytArray 1.0]


title: Digestive Gland-Chlorpyrifos-Rep2 [MytArray 1.0]


title: Chinese_sample_150


title: Hip Sox2 B


title: WX8-PL1 High grade PIN


title: Chinese_sample_152


title: Chinese_sample_148

value: male


title: Hip Sox2 A


title: Digestive Gland-Nickel-Rep3 [MytArray 1.0]


title: Chinese_sample_146


title: dengue Patient_Timepoint3  12


title: Chinese_sample_154


title: dengue Patient_Timepoint3  11


title: Chinese_sample_153


title: Digestive Gland-Chlorpyrifos-Rep1 [MytArray 1.0]


title: SVZ Sox2 A


title: Digestive Gland-Nickel-Rep1 [MytArray 1.0]


title: Digestive Gland-Nickel-Rep2 [MytArray 1.0]


title: Chinese_sample_149


title: dengue Patient_Timepoint3  10


title: Chinese_sample_151


title: Hip DCX B


title: Hip DCX A


title: Digestive Gland-Chlorpyrifos-Rep4

scan_protocol: Scanned on Chip Reader (Bio-rad Laboratories) at 5 µm resolution

source_name: animals exposed to 4.5 mg/L chlorpyrifos for 4 days in aquaria

tag: annual period

value: October

value: digestive gland

source_name: vehicle treated (0.02% DMSO) for four days, injected after three days with 50 μl of a solution of Artificial Sea Water containing 0.05 % ethanol


title: Digestive Gland-Chlorpyrifos-Estradiol-Rep4

source_name: animals exposed to 4.5 mg/L chlorpyrifos for 3 days in aquaria and further injected into the posterior adductor muscle with 25 pmoles 17β-estradiol


title: dengue Patient_Timepoint3  8

value: Patient


title: Cy3-VC_Cy5-TTF1

city: Nagoya

first: Takashi

last: Takahashi

state: Aichi

address: 1-1 Kanokoden, Chikusa-ku

country: Japan

institute: Aichi Cancer Center

hyb_protocol: According to Agilent protocol

scan_protocol: Whole Human Genome oligo DNA microarray with 41000 distinct probes was scanned using an Agilent DNA microarray scanner (G2505B, Agilent Technologies). Images were quantified using Agilent Feature Extraction Software (version A.7.5.1).

data_processing: LOWESS normalized, background subtracted VALUE data obtained from ratio of processed Red signal/processed Green signal using Agilent Feature Extraction Software (version A.7.5.1).

source_name: vector control in HPL1D

label_protocol: Cy5-sample cRNA and Cy3-sample cRNA were generated and hybridized to a Whole Human Genome oligo DNA microarray kit (Agilent Technologies) with 41000 distinct probes.

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

tag: cell line

source_name: stable TTF-1 transfectant of HPL1D


title: dengue Patient_Timepoint3  9

source_name: Human whole blood

value: 2 to 5 weeks after symptoms


title: Chinese_sample_144


title: Cy3-TTF1_Cy5-VC


title: blood_healthy1_family311_rep1

city: Tampere

first: Henna

last: Mattila

address: Biokatu 8

department: Institute of Medical Technology

country: Finland

institute: University of Tampere

description: Gene expression after NMD inhibition, healthy control

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed. A total of 12 arrays were hybridized, one for every individual. Samples were hybridized to

scan_protocol: Microarray slides were scanned (Agilent microarray scanner G2565BA ) after hybridization, and data was extracted using Feature Extraction software, version A.7.5.1.

data_processing:
Feature Extraction software, version A.7.5.1.
For data analysis, the raw microarray expression values of the rMeanSignal and gMeanSignal variables were first background-adjusted and a natural logarithm of a ratio of the variables rMeanSignal and gMeanSignal was taken. The log-ratio values were normalized between arrays by using the quantile normalization method. A linear mixed model was then used as a method for identifying the set of differentially expressed genes in a considered experimental set-up. The normalized expression values of each gene at Xq27-28 were separately modeled by the linear mixed model that included the treatment effect (i.e., the affected person versus healthy) as a fixed effect and the family effect as a random effect. In the model analysis, a considered gene was declared differentially expressed if the calculated estimate for the parameter associated with the fixed treatment effect was greater than zero, and if, at the same time, the p-value in the t-test for the null hypothesis concerning the fixed effect parameter being zero was smaller than the cut-off value of 0.025.

label_protocol: Twenty micrograms of total RNA were used to generate fluorescent Cy-3-labeled cRNA (control cells) and Cy-5-labeled cRNA (treated cells) using an Agilent Fluorescent Direct Label Kit. Labeled RNAs were pooled and hybridized to the Agilent 44K Whole Human Genome Oligonucleotide Microarrays (Agilent Technologies).

growth_protocol: The cell lines were derived by Epstein-Barr virus transformation of peripheral mononuclear leukocytes from patients and their healthy brothers. Lymphoblastoid cell lines were grown in RPMI-1640 medium (Lonza, Walkersville, MD, USA) supplemented with 10% fetal bovine serum (Sigma-Aldrich, St. Louis, MO, USA) and antibiotics.

extract_protocol: Total RNA was extracted from treated and untreated cells with Trizol according to the manufacturer’s instructions (Invitrogen, Carlsbad, CA, USA). RNA yields were quantified using an ND-1000 spectrophotometer (Nanodrop Technologies, Wilmington, DE, USA).

treatment_protocol: The emetine treatment protocol was described previously by Ionov et al. (Oncogene 2004;23:639-645). Briefly, for each cell line, we treated half of the subconfluent cells with 100 μg/ml of emetine dihydrochloride hydrate (Fluka, Buchs, Switzerland) and the rest were used as untreated controls. Both the treated and untreated cells were incubated for 10 h at 37°C. After this, actinomycin D (Sigma-Aldrich) was added to the treated and untreated cells, and they were incubated for 4 h at 37°C. Cells were collected and pellets were snap-frozen.

tag: cancer status

value: Healthy

value: NMD inhibited with Emetine and treated with Actinomycin D

tag: cell type

value: lymphoblastoid cell line

value: control treated with Actinomycin D


title: dengue Patient_Timepoint3  6


title: dengue Patient_Timepoint3  7


title: Digestive Gland-Chlorpyrifos-Rep3

value: female

tag: tissue


title: dengue Patient_Timepoint3  5


title: blood_cancer1_family311_rep1

description: Gene expression after NMD inhibition, prostate cancer patient

value: Prostate cancer patient

tag: gleason score

tag: treatment


title: Chinese_sample_141

tag: gender


title: Chinese_sample_145


title: Chinese_sample_142


title: Digestive Gland-Estradiol-Rep4

source_name: animals injected into the posterior adductor muscle with 25 pmoles 17β-estradiol


title: Chinese_sample_143


title: Digestive Gland-Chlorpyrifos-Estradiol-Rep3


title: blood_healthy1_family248_rep1

tag: individual


title: blood_cancer1_family248_rep1


title: Digestive Gland-Estradiol-Rep3


title: dengue Patient_Timepoint3  3

tag: sample type


title: dengue Patient_Timepoint3  2

tag: collection time


title: blood_healthy2_family232_rep1


title: dengue Patient_Timepoint3  1


title: Digestive Gland-Chlorpyrifos-Estradiol-Rep2


title: dengue Patient_Timepoint3  4


title: blood_healthy1_family232_rep1


title: Digestive Gland-Chlorpyrifos-Estradiol-Rep1


title: blood_cancer2_family232_rep1


title: Chinese_sample_139


title: Digestive Gland-Estradiol-Rep1


title: dengue Patient_Timepoint2  30

value: 3 to 7 dys after symptoms


title: Chinese_sample_147


title: blood_healthy1_family43_rep1


title: dengue Patient_Timepoint2  29


title: dengue Patient_Timepoint2  31


title: Chinese_sample_138


title: blood_cancer1_family232_rep1


title: blood_cancer1_family43_rep1


title: Chinese_sample_140


title: Digestive Gland-Chlorpyrifos-Rep1


title: dengue Patient_Timepoint2  28


title: blood_cancer1_family15_rep1


title: blood_healthy1_family15_rep1


title: dengue Patient_Timepoint2  27


title: Chinese_sample_134


title: Digestive Gland-Chlorpyrifos-Rep2


title: Digestive Gland-Mixture-Rep5 [MytArray 1.1]

source_name: digestive gland tissue, animals exposed to 0.610 mg/L Chlorpyrifos and 0.135 mg/L Nickel for 4 days in aquaria

value: digestive gland tissue

value: mixture (Chlorpyrifos and Nickel)

value: 4 days

value: vehicle (0.02% DMSO)


title: Chinese_sample_131

value: blood

value: Chinese


title: Chinese_sample_135


title: IGP92

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: Large-scale gene expression profiles were investigated in 48 normal and 47 prostate tumor tissue samples using Affymetrix GeneChip Exon 1.0 ST microarrays. Gene expression profiles were compared among TMPRSS2-ERG fusion-positive and negative prostate tumors as well as benign samples.

hyb_protocol: Affymetrix WT Sense Target Labeling Assay, hybridization done following manufacturer's instructions

scan_protocol: Arrays were scanned using the Affymetrix Gene Chip scanner 3000 7G system.

data_processing: Gene expression profiles were obtained by applying the Robust Multichip Average (RMA) implementation included in the Affymetrix Power Tools (APT). APT creates expression values for 17881 transcript clusters as defined in the meta-probe set files provided by Affymetrix.

source_name: Human prostate epithelium

label_protocol: Affymetrix WT Sense Target Labeling Assay, follwed by manufacturer's instructions (using 1ug of total RNA)

extract_protocol: AllPrep DNA/RNA Mini kit (Qiagen) according to the manufacturerÆs instructions. Briefly, tissue sections were homogenized in 1 ml RLT Plus buffer using TissueLyser (Qiagen). After DNA separation, 1.5 volumes of 100% ethanol were added to the total RNA and the mixture was purified. The quantity and quality of the total RNA was checked using the Nanodrop and Bioanalyzer.

treatment_protocol: During radical prostatectomy, tissue samples from the peripheral zone of the prostate were taken with a 6 mm punch biopsy instrument immediately after surgical removal of the prostate from tumerous and non-tumerous areas . The punches were immersed in RNAlater (Qiagen) for 24h at room temperature and subsequently stored at -80C. To confirm the presence of tumor, all punches were sectioned, and tumor cell content was determined in every 10th section. Only sections containing at least 70% tumor cells were included in the study. Normal prostate tissue samples were obtained from  patients who underwent radical prostatectomy for prostate cancer. Also these punches were sectioned and inspected for presence of normal prostatic epithelial cells in every 10th section. Only sections containing between 20-40% normal prostatic epithelial cells were included in the study.

tag: tissuer type

value: Benign

tag: tumor type


title: Chinese_sample_137


title: dengue Patient_Timepoint2  26


title: Digestive Gland-Estradiol-Rep2

value: October

value: digestive gland


title: Chinese_sample_132

value: male


title: Chinese_sample_136


title: Digestive Gland-Mixture-Rep4 [MytArray 1.1]

tag: agent

value: 0.610 mg/L Chlorpyrifos and 0.135 mg/L Nickel


title: dengue Patient_Timepoint2  25

value: Patient


title: IGP90


title: Digestive Gland-Nickel-Rep1 [MytArray 1.1]

value: Nickel

tag: dose


title: Digestive Gland-Mixture-Rep3 [MytArray 1.1]

tag: time


title: dengue Patient_Timepoint2  24


title: Chinese_sample_130

tag: population


title: Digestive Gland-Chlorpyrifos-Rep3 [MytArray 1.1]

value: chlorpyrifos


title: dengue Patient_Timepoint2  23


title: Chinese_sample_127


title: Chinese_sample_129


title: IGP88


title: Digestive Gland-Mixture-Rep1 [MytArray 1.1]

value: female


title: IGP89


title: Digestive Gland-Mixture-Rep2 [MytArray 1.1]


title: IGP87


title: dengue Patient_Timepoint2  21


title: Chinese_sample_133


title: IGP91


title: dengue Patient_Timepoint2  22


title: dengue Patient_Timepoint2  20


title: IGP86


title: Digestive Gland-Chlorpyrifos-Rep2 [MytArray 1.1]


title: Chinese_sample_128


title: Chinese_sample_124


title: Digestive Gland-Chlorpyrifos-Rep1 [MytArray 1.1]


title: IGP85


title: dengue Patient_Timepoint2  18


title: Chinese_sample_126


title: IGP83

value: Tumor

value: TMPRSS2-ERG Fusion-negative


title: dengue Patient_Timepoint2  19

value: 3 to 7 dys after symptoms


title: IGP82

value: unclear


title: dengue Patient_Timepoint2  17


title: B16F10_mousemelanomatumor_invivoTNF9_swap

city: São Paulo

first: Renato

middle: David

last: Puga

state: São Paulo

address: Dr Ovidio Pires de Campos,785

department: Instituto de Psiquiatria

country: Brazil

institute: Universidade de São Paulo

description: Dye swap

hyb_protocol: Hibridization - Solution: FormamidE 25%; Denhardts 5x; SSC 5x; PolyA 4ug; Cot12ug; Esperma de salmao 10ug / Temperature:42C / Time:12-16h / Touch Down: Washing - Round 1 - Solution: SSC2x/SDS 0,1% / Temperature:42C / Time:5 min. / Washing Number: 1x Washing - Round 2 - Solution: SSC 0,1x/SDS 0,1% / Temperature:TA / Time:5 min. / Washing Number: 2x Washing - Round 3 - Solution: SSC 0,1x / Temperature:TA / Time:1 min. / Washing Number: 5x

scan_protocol: Hardware: Perkinelmer / Software: ScanArray

data_processing: Lowesss

label: Alexa 555

source_name: Reference sample, pool of RNA of four different melanoma cell lines

label_protocol: Cy3 or Cy5 labeled aRNA

extract_protocol: Trizol

tag: cell lines

tag: condition

value: Grown in DMEM till 70-80% confluency

label: Alexa 647

source_name: B16F10 mouse melanoma tumor in vivo TNF group animal 9

extract_protocol: kit Pico Pure RNA Isolation Kit

tag: strain

value: Male

tag: age

value: 6-8 weeks

value: TNF

tag: treatment duration

value: 3 hours


title: dengue Patient_Timepoint2  16


title: B16F10_mousemelanomatumor_invivoTNF9_main

description: All samples were submitted to two rounds of RNA amplification. AminoalylUTP was incorported during the second round of amplification to allow fluorophore labelling.

tag: cell line


title: IGP84

value: Benign


title: IGP81


title: dengue Patient_Timepoint2  15


title: B16F10_mousemelanomatumor_invivoTNF18_swap

description: Dye swap

source_name: B16F10 mouse melanoma tumor in vivo TNF group animal 18

tag: treatment


title: dengue Patient_Timepoint2  14


title: Chinese_sample_123

tag: tissue

value: blood

value: Chinese

tag: gender


title: Chinese_sample_121


title: B16F10_mousemelanomatumor_invivoTNF18_main


title: IGP80

value: TMPRSS2-ERG Fusion-positive


title: Chinese_sample_125


title: Chinese_sample_122


title: dengue Patient_Timepoint2  13

tag: sample type

value: Patient


title: B16F10_mousemelanomatumor_invivoTNF13_swap

description: Dye swap

source_name: B16F10 mouse melanoma tumor in vivo TNF group animal 13


title: B16F10_mousemelanomatumor_invivoTNF13_main


title: IGP79


title: IGP78


title: IGP75


title: IGP76


title: B16F10_mousemelanomatumor_invivoTNF10_main

source_name: B16F10 mouse melanoma tumor in vivo TNF group animal 10


title: dengue Patient_Timepoint2  11

tag: collection time


title: dengue Patient_Timepoint2  12


title: B16F10_mousemelanomatumor_invivoTNF10_swap

description: Dye swap


title: Chinese_sample_120


title: Chinese_sample_118

value: male


title: B16F10_mousemelanomatumor_invivomelphalan+TNF15_swap

description: Dye swap

source_name: B16F10 mouse melanoma tumor in vivo melphalan+TNF group animal 15


title: IGP64

tag: tissuer type


title: dengue Patient_Timepoint2  10


title: dengue Patient_Timepoint2  9


title: IGP62

tag: tumor type


title: dengue Patient_Timepoint2  8


title: IGP61


title: B16F10_mousemelanomatumor_invivomelphalan+TNF14_swap

description: Dye swap

source_name: B16F10 mouse melanoma tumor in vivo melphalan+TNF group animal 14


title: Chinese_sample_119

source_name: blood


title: Chinese_sample_117


title: dengue Patient_Timepoint2  6


title: IGP60


title: Chinese_sample_114


title: Chinese_sample_115


title: IGP59


title: dengue Patient_Timepoint2  5


title: B16F10_mousemelanomatumor_invivomelphalan+TNF12_swap

description: Dye swap

source_name: B16F10 mouse melanoma tumor in vivo melphalan+TNF group animal 12


title: B16F10_mousemelanomatumor_invivomelphalan+TNF15_main


title: Chinese_sample_112


title: Chinese_sample_116


title: B16F10_mousemelanomatumor_invivomelphalan+TNF14_main


title: Chinese_sample_113


title: dengue Patient_Timepoint2  7


title: dengue Patient_Timepoint2  4


title: Chinese_sample_109


title: Chinese_sample_111


title: IGP57


title: B16F10_mousemelanomatumor_invivomelphalan+TNF11_swap

description: Dye swap

source_name: B16F10 mouse melanoma tumor in vivo melphalan+TNF group animal 11


title: Chinese_sample_110


title: dengue Patient_Timepoint2  2


title: IGP52


title: Chinese_sample_108


title: Chinese_sample_107


title: IGP51


title: IGP54


title: B16F10_mousemelanomatumor_invivomelphalan+TNF1_swap

description: Dye swap

source_name: B16F10 mouse melanoma tumor in vivo melphalan+TNF group animal 1


title: Chinese_sample_103


title: Chinese_sample_106


title: B16F10_mousemelanomatumor_invivoMelphalan9_swap

description: Dye swap

source_name: B16F10 mouse melanoma tumor in vivo melphalan group animal 9


title: B16F10_mousemelanomatumor_invivomelphalan+TNF1_main


title: IGP55


title: dengue Patient_Timepoint1  30

value: Less than 72 hour after symptoms


title: dengue Patient_Timepoint1  31


title: B16F10_mousemelanomatumor_invivomelphalan+TNF11_main


title: dengue Patient_Timepoint2  1


title: Chinese_sample_105


title: Chinese_sample_104


title: IGP49


title: IGP48


title: B16F10_mousemelanomatumor_invivomelphalan+TNF12_main


title: dengue Patient_Timepoint1  29


title: dengue Patient_Timepoint2  3


title: B16F10_mousemelanomatumor_invivomelphalan5_swap

description: Dye swap

source_name: B16F10 mouse melanoma tumor in vivo melphalan group animal 5


title: IGP47


title: IGP45


title: dengue Patient_Timepoint1  28

source_name: Human whole blood


title: B16F10_mousemelanomatumor_invivomelphalan5_main


title: Chinese_sample_101


title: B16F10_mousemelanomatumor_invivomelphalan3_swap

description: Dye swap

source_name: B16F10 mouse melanoma tumor in vivo melphalan group animal 3


title: dengue Patient_Timepoint1  27


title: dengue Patient_Timepoint1  26


title: IGP44


title: dengue Patient_Timepoint1  25


title: B16F10_mousemelanomatumor_invivomelphalan3_main


title: B16F10_mousemelanomatumor_invivomelphalan13_swap

description: Dye swap

source_name: B16F10 mouse melanoma tumor in vivo melphalan group animal 13


title: IGP43

source_name: Human prostate epithelium


title: Chinese_sample_99

value: female


title: IGP42

value: Tumor


title: dengue Patient_Timepoint1  24


title: Chinese_sample_102


title: B16F10_mousemelanomatumor_invivoMelphalan9_main

source_name: Reference sample, pool of RNA of four different melanoma cell lines


title: IGP41


title: B16F10_mousemelanomatumor_invivomelphalan13_main


title: dengue Patient_Timepoint1  23


title: dengue Patient_Timepoint1  22


title: Chinese_sample_97


title: B16F10_mousemelanomatumor_invivocontrol8_swap

description: Dye swap

source_name: B16F10 mouse melanoma tumor in vivo control group animal 8


title: IGP38

value: TMPRSS2-ERG Fusion-negative


title: IGP39


title: IGP37


title: dengue Patient_Timepoint1  21


title: B16F10_mousemelanomatumor_invivocontrol5_swap

description: Dye swap

source_name: B16F10 mouse melanoma tumor in vivo control group animal 5


title: dengue Patient_Timepoint1  20


title: B16F10_mousemelanomatumor_invivocontrol8_main


title: Chinese_sample_100


title: IGP40


title: IGP36


title: B16F10_mousemelanomatumor_invivocontrol5_main


title: B16F10_mousemelanomatumor_invivocontrol4_swap

description: Dye swap

value: Saline Time of

source_name: B16F10 mouse melanoma tumor in vivo control group animal 4


title: Chinese_sample_95


title: Chinese_sample_98


title: dengue Patient_Timepoint1  18


title: B16F10_mousemelanomatumor_invivocontrol4_main


title: dengue Patient_Timepoint1  19


title: IGP35


title: dengue Patient_Timepoint1  17


title: IGP33


title: dengue Patient_Timepoint1  16


title: B16F10_mousemelanomatumor_invivocontrol3_swap

description: Dye swap

source_name: B16F10 mouse melanoma tumor in vivo control group animal 3


title: Chinese_sample_94


title: IGP32


title: dengue Patient_Timepoint1  15


title: Chinese_sample_92


title: B16F10_mousemelanomatumor_invivocontrol3_main


title: IGP31


title: B16F10_mousemelanomatumorcells_invivocontrol10_swap

description: Dye swap

source_name: B16F10 mouse melanoma tumor in vivo control group animal 10


title: Chinese_sample_96


title: IGP30

value: unclear


title: dengue Patient_Timepoint1  14


title: Genotyping of Isolate HzS

city: Marseille

first: LEROY

last: Quentin

address: 27 Boulevard Jean Moulin

country: France

institute: URMITE

description:
CGH-HzS
Genotyping of Isolate HzS  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

source_name: HzS

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)

value: HzS

source_name: NMI

value: NMI


title: Chinese_sample_93

source_name: blood


title: B16F10_mousemelanomatumor_invivocontrol10_main

value: Male

value: 6-8 weeks

value: Grown in DMEM till 70-80% confluency


title: IGP29


title: Chinese_sample_91


title: dengue Patient_Timepoint1  12


title: dengue Patient_Timepoint1  11


title: Chinese_sample_90


title: Genotyping of Isolate Pq

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

source_name: Pq

value: Pq


title: IGP28


title: Genotyping of Isolate CB93

description:
CGH-CB93
Genotyping of Isolate CB93 compare to NMI


title: Genotyping of Isolate HzR

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

source_name: HzR

value: HzR


title: Chinese_sample_86

value: blood

value: Chinese


title: IGP26


title: Chinese_sample_89


title: Chinese_sample_87


title: dengue Patient_Timepoint1  13

value: Patient


title: dengue Patient_Timepoint1  10


title: Chinese_sample_88

value: male


title: IGP25

value: TMPRSS2-ERG Fusion-positive


title: dengue Patient_Timepoint1  9

value: Less than 72 hour after symptoms


title: IGP23

value: Tumor


title: Chinese_sample_81


title: Genotyping of Isolate CB97

description:
CGH-CB97
Genotyping of Isolate CB97 compare to NMI


title: Genotyping of Isolate CB132

description:
CGH-CB132
Genotyping of Isolate CB132 compare to NMI


title: Chinese_sample_83


title: Chinese_sample_85


title: IGP20

value: Benign


title: IGP21

value: TMPRSS2-ERG Fusion-negative


title: Genotyping of Isolate CB92

description:
CGH-CB92
Genotyping of Isolate CB92 compare to NMI


title: dengue Patient_Timepoint1  7


title: dengue Patient_Timepoint1  8


title: dengue Patient_Timepoint1  6


title: Chinese_sample_84


title: Chinese_sample_80

value: female


title: Genotyping of Isolate CB114

description:
CGH-CB114
Genotyping of Isolate CB114 compare to NMI


title: IGP190

value: unclear


title: Genotyping of Isolate CB87

description:
CGH-CB87
Genotyping of Isolate CB87 compare to NMI

value: NMI


title: Genotyping of Isolate CB76

description:
CGH-CB76
Genotyping of Isolate CB76 compare to NMI


title: IGP188


title: IGP186


title: Genotyping of Isolate CB148

description:
CGH-CB148
Genotyping of Isolate CB148 compare to NMI


title: dengue Patient_Timepoint1  2


title: IGP185


title: dengue Patient_Timepoint1  4


title: dengue Patient_Timepoint1  1


title: Genotyping of Isolate CB64

description:
CGH-CB64
Genotyping of Isolate CB64 compare to NMI


title: Chinese_sample_79


title: IGP184


title: Genotyping of Isolate CB62

description:
CGH-CB62
Genotyping of Isolate CB62 compare to NMI


title: IGP183


title: Control_sample  26

value: Control


title: Genotyping of Isolate CB54

description:
CGH-CB54
Genotyping of Isolate CB54 compare to NMI


title: Chinese_sample_78


title: IGP182


title: Chinese_sample_77


title: Chinese_sample_76


title: Genotyping of Isolate CB149

description:
CGH-CB149
Genotyping of Isolate CB149 compare to NMI


title: IGP180

description: Large-scale gene expression profiles were investigated in 48 normal and 47 prostate tumor tissue samples using Affymetrix GeneChip Exon 1.0 ST microarrays. Gene expression profiles were compared among TMPRSS2-ERG fusion-positive and negative prostate tumors as well as benign samples.


title: Control_sample  24


title: dengue Patient_Timepoint1  5


title: Chinese_sample_75


title: Genotyping of Isolate CB63

description:
CGH-CB63
Genotyping of Isolate CB63 compare to NMI


title: IGP181


title: Control_sample  23


title: Chinese_sample_73


title: dengue Patient_Timepoint1  3


title: Control_sample  25


title: Control_sample  22


title: Control_sample  21


title: Genotyping of Isolate CB45

description:
CGH-CB45
Genotyping of Isolate CB45 compare to NMI


title: Chinese_sample_82


title: IGP18


title: IGP179


title: IGP178


title: Chinese_sample_69


title: Chinese_sample_74


title: Chinese_sample_71


title: Genotyping of Isolate S217

description:
CGH-S217
Genotyping of Isolate S217 compare to NMI


title: Genotyping of Isolate CB44

description:
CGH-CB44
Genotyping of Isolate CB44 compare to NMI


title: Genotyping of Isolate CB41

description:
CGH-CB41
Genotyping of Isolate CB41 compare to NMI


title: Control_sample  19


title: Control_sample  20


title: Chinese_sample_72


title: IGP176


title: Chinese_sample_70


title: Genotyping of Isolate Z3055

description:
CGH-Z3055
Genotyping of Isolate Z3055 compare to NMI


title: Control_sample  18


title: IGP174


title: Genotyping of Isolate Z2775

description:
CGH-Z2775
Genotyping of Isolate Z2775 compare to NMI


title: IGP177


title: Chinese_sample_64


title: Chinese_sample_66


title: Chinese_sample_67


title: Genotyping of Isolate NM

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


title: Control_sample  17


title: Chinese_sample_65


title: Genotyping of Isolate Luga

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

source_name: Luga

value: Luga


title: Control_sample  14


title: Genotyping of Isolate PCat

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

source_name: Pcat

value: Pcat


title: Control_sample  16

source_name: Human whole blood


title: IGP16


title: IGP145


title: Control_sample  15


title: Chinese_sample_63


title: Genotyping of Isolate Derma

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

source_name: Derma

value: Derma


title: IGP144


title: Control_sample  13


title: Chinese_sample_60


title: Genotyping of Isolate CB151

description:
CGH-CB151
Genotyping of Isolate CB151 compare to NMI


title: IGP143


title: Control_sample  12


title: IGP175


title: IGP17


title: Genotyping of Isolate CB120

description:
CGH-CB120
Genotyping of Isolate CB120 compare to NMI


title: Control_sample  11


title: Chinese_sample_68


title: Chinese_sample_61


title: IGP142


title: Control_sample  10


title: Genotyping of Isolate CB74

description:
CGH-CB74
Genotyping of Isolate CB74 compare to NMI


title: IGP141


title: IGP139


title: Genotyping of Isolate CB96

description:
CGH-CB96
Genotyping of Isolate CB96 compare to NMI


title: Genotyping of Isolate CB72

description:
CGH-CB72
Genotyping of Isolate CB72 compare to NMI


title: Chinese_sample_56


title: Chinese_sample_58


title: Genotyping of Isolate CB71

description:
CGH-CB71
Genotyping of Isolate CB71 compare to NMI


title: Control_sample  7


title: Chinese_sample_57


title: IGP137

description: Large-scale gene expression profiles were investigated in 48 normal and 47 prostate tumor tissue samples using Affymetrix GeneChip Exon 1.0 ST microarrays. Gene expression profiles were compared among TMPRSS2-ERG fusion-positive and negative prostate tumors as well as benign samples.


title: IGP138


title: Control_sample  9


title: Control_sample  6


title: IGP127


title: Chinese_sample_55


title: Genotyping of Isolate CB70

description:
CGH-CB70
Genotyping of Isolate CB70 compare to NMI


title: Control_sample  8


title: Control_sample  5


title: IGP126


title: Chinese_sample_62


title: Genotyping of Isolate CB69

description:
CGH-CB69
Genotyping of Isolate CB69 compare to NMI


title: Chinese_sample_59


title: Control_sample  4


title: Genotyping of Isolate CB68

description:
CGH-CB68
Genotyping of Isolate CB68  compare to NMI


title: Chinese_sample_54


title: Genotyping of Isolate CB154

description:
CGH-CB154
Genotyping of Isolate CB154 compare to NMI


title: Control_sample  3


title: Chinese_sample_50


title: IGP123


title: Chinese_sample_53


title: Control_sample  2


title: IGP120


title: IGP124


title: Genotyping of Isolate CB56

description:
CGH-CB56
Genotyping of Isolate CB56 compare to NMI


title: ELF74CL

description: qRT-PCR gene expression data of human endobronchial epithelial lining fluid ELF74CL

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

source_name: human endobronchial lining fluid, contralateral 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: contralateral site

tag: disease state

value: benign


title: Control_sample  1


title: Genotyping of Isolate CB52

description:
CGH-CB52
Genotyping of Isolate CB52 compare to NMI


title: Chinese_sample_52

value: blood

value: Chinese


title: ELF68CL

description: qRT-PCR gene expression data of human endobronchial epithelial lining fluid ELF68CL


title: ELF67CL

description: qRT-PCR gene expression data of human endobronchial epithelial lining fluid ELF67CL


title: IGP122

source_name: Human prostate epithelium


title: ELF66CL

description: qRT-PCR gene expression data of human endobronchial epithelial lining fluid ELF66CL


title: Genotyping of Isolate CB61

description:
CGH-CB61
Genotyping of Isolate CB61 compare to NMI


title: Genotyping of Isolate CB51

description:
CGH-CB51
Genotyping of Isolate CB51 compare to NMI


title: Genotyping of Isolate CB65

description:
CGH-CB65
Genotyping of Isolate CB65 compare to NMI


title: Genotyping of Isolate CB50

description:
CGH-CB50
Genotyping of Isolate CB50 compare to NMI


title: IGP119


title: IGP118


title: IGP117


title: Chinese_sample_48

value: male


title: ELF57CL

description: qRT-PCR gene expression data of human endobronchial epithelial lining fluid ELF57CL


title: IGP116


title: Genotyping of Isolate CB48

description:
CGH-CB48
Genotyping of Isolate CB48 compare to NMI


title: Chinese_sample_51


title: Genotyping of Isolate CB43

description:
CGH-CB43
Genotyping of Isolate CB43 compare to NMI


title: Chinese_sample_49


title: Genotyping of Isolate CB42

description:
CGH-CB42
Genotyping of Isolate CB42 compare to NMI


title: IGP115

description: Large-scale gene expression profiles were investigated in 48 normal and 47 prostate tumor tissue samples using Affymetrix GeneChip Exon 1.0 ST microarrays. Gene expression profiles were compared among TMPRSS2-ERG fusion-positive and negative prostate tumors as well as benign samples.

value: TMPRSS2-ERG Fusion-positive


title: ELF55CL

description: qRT-PCR gene expression data of human endobronchial epithelial lining fluid ELF55CL


title: ELF62CL

description: qRT-PCR gene expression data of human endobronchial epithelial lining fluid ELF62CL


title: ELF50CL

description: qRT-PCR gene expression data of human endobronchial epithelial lining fluid ELF50CL


title: IGP113


title: Genotyping of Isolate CB40

description:
CGH-CB40
Genotyping of Isolate CB40 compare to NMI


title: IGP111


title: Chinese_sample_44


title: IGP110


title: Chinese_sample_47


title: Chinese_sample_45


title: IGP108


title: ELF37CL

description: qRT-PCR gene expression data of human endobronchial epithelial lining fluid ELF37CL


title: Chinese_sample_41


title: Chinese_sample_42


title: phoP-F134-F335-60 h

city: Tübingen

first: Kay

last: Nieselt

state: DE

address: Sand 14

department: Department for Computer Science

institute: Institute for Bioinformatics and Medical Informatics

description: Medium F134

hyb_protocol: 3 µg of cDNA were hybridized for 16 hr at 50°C on Array Platform GPL9471. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G.

data_processing: RMA (Bolstad, 2002) as implemented in the affy package of Bioconductor.

organism: Streptomyces coelicolor

label_protocol: Biotinylated cDNA were prepared after fragmentation according to the standard Affymetrix protocol from 3 µg total RNA (Prokaryotic Sample and Array Processing, Technical Manual 701030 Rev. 5, 2004, Affymetrix).

growth_protocol: Fermentations were performed using the S. coelicolor INB201 (phoP mutant, Santos-Beneit et al., 2009) strain. As described previously (Nieselt et al., 2010), 5x10^8 CFU/l of germinated spores were used to inoculate 1.8 L of growth medium in 3-liter Applikon fermenters. The growth medium led to phosphate depletion after about 41 h of cultivation, with all other components remaining in excess until the end of the fermentation trials. Dissolved oxygen levels were maintained at a minimum of 50 % by the automatic adjustment of agitation (minimal stirrer speed 300 rpm) at a constant aeration rate of 0.9 l/l-min sterile air. The medium is referred to as F134.

extract_protocol: Total RNA isolation was performed via phenol extraction and RNeasy Midi Kit (Qiagen, 2001) according to manufacturer's instruction.

tag: genotype/variation

value: delta phoP mutant

tag: time point


title: phoP-F134-F335-58 h

description: Medium F134


title: ELF14CL

description: qRT-PCR gene expression data of human endobronchial epithelial lining fluid ELF14CL


title: Chinese_sample_43

tag: population


title: IGP105

value: Tumor


title: ELF40CL

description: qRT-PCR gene expression data of human endobronchial epithelial lining fluid ELF40CL


title: Chinese_sample_46


title: ELF13CL

description: qRT-PCR gene expression data of human endobronchial epithelial lining fluid ELF13CL


title: Chinese_sample_39


title: phoP-F134-F335-54 h

description: Medium F134


title: ELF11CL

description: qRT-PCR gene expression data of human endobronchial epithelial lining fluid ELF11CL


title: ELF2CL

description: qRT-PCR gene expression data of human endobronchial epithelial lining fluid ELF2CL


title: phoP-F134-F335-52 h

description: Medium F134


title: phoP-F134-F335-56 h

description: Medium F134


title: Chinese_sample_40


title: phoP-F134-F335-50 h

description: Medium F134


title: ELF72CL

description: qRT-PCR gene expression data of human endobronchial epithelial lining fluid ELF72CL

source_name: human endobronchial lining fluid, contralateral site, NSCLC

value: NSCLC


title: ELF26CL

description: qRT-PCR gene expression data of human endobronchial epithelial lining fluid ELF26CL


title: phoP-F134-F335-48 h

description: Medium F134


title: Chinese_sample_37


title: Chinese_sample_34


title: 13852772 - Col0_4d_2 vs upp-1_4d_2

city: evry

first: Soubigou-Taconnat

last: Ludivine

address: 2 rue gaston crémieux

department: URGV

institute: INRA

description: Impact on gene expression of the UPP loss-of-function at early development stage

hyb_protocol: upp-1_4d_2 Cy5 / Col0_4d_2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

scan_protocol: GenePix Pro 3.0, Cy3:pmt voltage 532nm,480V,laser power 35%, Cy5:635nm,pmt voltage 480V,laser power 30%

data_processing: The raw data comprised the logarithm of median feature pixel intensity at wavelength 635 nm (red) and 532 nm (green). No background was subtracted. An array-by-array normalization was performed to remove systematic biases. First, we excluded spots that were considered badly formed features by the experimenter (Flags=-100). Then we performed a global intensity-dependent normalization using the loess procedure (see Yang et al., 2002) to correct the dye bias. Finally, on each block, the log-ratio median is subtracted from each value of the log-ratio of the block to correct a print-tip effect on each metablock.

organism: Arabidopsis thaliana

label_protocol: labelling Cy3 and Cy5 direct, amplification=yes, aRNA 5 ug. Labelling protocol: 5 µg of aRNA (8µl) mixed with 2 µl of random nonamers 1µg/µl and 0.5 µl of RNAse Out 40 U/µl, denatured 10 min at 70 °C and chilled on ice. The followig components were added to the sample 4 µl of first strand buffer 5 X, 1 µl of 10 mM dNTP/2mM dCTP, 2 µl of 0.1 M DTT, 1.5 µl of Cy3-dCTP or Cy5-dCTP (Amersham Pharmacia Biotech, 25nmol tube, PA5502), 1 µl of SuperScript II RT 200U/µl. Then it was incubated at 42°C for 2.5 hours and chilled on ice. The sample was denaturated by adding 2 µl of NaOH 2.5M and incubated at 37 °C for exactly 15 min, then was added 10 µl of 2M MOPS and put on ice. The dyes were purified with the QIAquick PCR Purification Kit (QIAGEN).

growth_protocol: whole plant - A. thaliana medium (Estelle and Somerville 1987) / 50% hygrometry / 21°C / 16h light - 8h dark cycle

treatment_protocol: no treatment

tag: cultivar

value: mutant (upp-1)

tag: development stage

value: wild type


title: 13852773 - upp-1_4d_2 vs Col0_4d_2

hyb_protocol: Col0_4d_2 Cy5 / upp-1_4d_2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: IGP102

value: Benign


title: 13852763 - Col0_4d_1 vs upp-1_4d_1

hyb_protocol: upp-1_4d_1 Cy5 / Col0_4d_1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13852771 - upp-1_4d_1 vs Col0_4d_1

hyb_protocol: Col0_4d_1 Cy5 / upp-1_4d_1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: phoP-F134-F335-47 h

description: Medium F134

tag: strain


title: Chinese_sample_35

value: female


title: Genotyping of Isolate 5116

description:
CGH-5116
Genotyping of Isolate 5116 compare to NMI

value: NMI


title: ELF43CL

description: qRT-PCR gene expression data of human endobronchial epithelial lining fluid ELF43CL

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

value: large cell lung carcinoma


title: ELF42CL

description: qRT-PCR gene expression data of human endobronchial epithelial lining fluid ELF42CL


title: 13852271 - WS_8d_2 vs upp-2_8d_2

hyb_protocol: upp-2_8d_2 Cy5 / WS_8d_2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

value: wassilewskija

value: mutant (upp-2)


title: 13852270 - upp-2_8d_2 vs WS_8d_2

hyb_protocol: WS_8d_2 Cy5 / upp-2_8d_2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: Chinese_sample_36


title: Chinese_sample_31


title: Chinese_sample_38


title: 13852268 - upp-2_8d_1 vs WS_8d_1

hyb_protocol: WS_8d_1 Cy5 / upp-2_8d_1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: phoP-F134-F335-45 h

description: Medium F134


title: phoP-F134-F335-46 h

description: Medium F134


title: phoP-F134-F335-44 h

description: Medium F134


title: phoP-F134-F335-43 h

description: Medium F134


title: ELF3CL

description: qRT-PCR gene expression data of human endobronchial epithelial lining fluid ELF3CL

value: contralateral site


title: 13852256 - Col0_7d_2 vs upp-1_7d_2

hyb_protocol: upp-1_7d_2 Cy5 / Col0_7d_2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: ELF17CL

description: qRT-PCR gene expression data of human endobronchial epithelial lining fluid ELF17CL

source_name: human endobronchial lining fluid, contralateral site, carcinoid

value: carcinoid


title: ELF71CL

description: qRT-PCR gene expression data of human endobronchial epithelial lining fluid ELF71CL

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

value: squamous cell carcinoma


title: ELF20CL

description: qRT-PCR gene expression data of human endobronchial epithelial lining fluid ELF20CL


title: ELF48CL

description: qRT-PCR gene expression data of human endobronchial epithelial lining fluid ELF48CL


title: 13852252 - upp-1_7d_2 vs Col0_7d_2

hyb_protocol: Col0_7d_2 Cy5 / upp-1_7d_2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13852269 - WS_8d_1 vs upp-2_8d_1

hyb_protocol: upp-2_8d_1 Cy5 / WS_8d_1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: Chinese_sample_32

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

value: blood

value: Chinese


title: phoP-F134-F335-41 h

description: Medium F134


title: ELF30CL

description: qRT-PCR gene expression data of human endobronchial epithelial lining fluid ELF30CL


title: Chinese_sample_29


title: ELF29CL

description: qRT-PCR gene expression data of human endobronchial epithelial lining fluid ELF29CL


title: Chinese_sample_27

value: male


title: Chinese_sample_28


title: ELF24CL

description: qRT-PCR gene expression data of human endobronchial epithelial lining fluid ELF24CL


title: 13852250 - upp-1_7d_1 vs Col0_7d_1

hyb_protocol: Col0_7d_1 Cy5 / upp-1_7d_1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: phoP-F134-F335-40 h

description: Medium F134

value: delta phoP mutant


title: Chinese_sample_30


title: phoP-F134-F335-40.5 h

description: Medium F134


title: Chinese_sample_25


title: phoP-F134-F335-42 h

description: Medium F134


title: 13852251 - Col0_7d_1 vs upp-1_7d_1

hyb_protocol: upp-1_7d_1 Cy5 / Col0_7d_1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: phoP-F134-F335-39.5 h

description: Medium F134


title: 13852094 - upp-2_5d_2 vs WS_5d_2

hyb_protocol: WS_5d_2 Cy5 / upp-2_5d_2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13852085 - WS_5d_2 vs upp-2_5d_2

hyb_protocol: upp-2_5d_2 Cy5 / WS_5d_2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: ELF10CL

description: qRT-PCR gene expression data of human endobronchial epithelial lining fluid ELF10CL


title: Chinese_sample_33


title: ELF5CL

description: qRT-PCR gene expression data of human endobronchial epithelial lining fluid ELF5CL


title: 13852082 - WS_5d_1 vs upp-2_5d_1

hyb_protocol: upp-2_5d_1 Cy5 / WS_5d_1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: phoP-F134-F335-39 h

description: Medium F134

hyb_protocol: 3 µg of cDNA were hybridized for 16 hr at 50°C on Array Platform GPL9471. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.


title: Chinese_sample_26


title: Chinese_sample_23


title: 13852083 - upp-2_5d_1 vs WS_5d_1

hyb_protocol: WS_5d_1 Cy5 / upp-2_5d_1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: ELF4CL

description: qRT-PCR gene expression data of human endobronchial epithelial lining fluid ELF4CL


title: Chinese_sample_24


title: phoP-F134-F335-38.5 h

description: Medium F134


title: phoP-F134-F335-37.5 h

description: Medium F134


title: ELF77CL

description: qRT-PCR gene expression data of human endobronchial epithelial lining fluid ELF77CL

source_name: human endobronchial lining fluid, contralateral site, adenocarcinoma

value: adenocarcinoma


title: Chinese_sample_21


title: knockout rep4

first: Pei-wen

last: Pan

address: Biokatu 6

institute: Institute of Medical Technology, University of Tampere

hyb_protocol: 1.50 ug each sample was hybridized to Illumina’s SentrixÒ Mouse-6 Expression BeadChips (cat no BD-26-101) at 55 °C overnight (19 h) according to Illumina BeadStation 500X –protocol, Revision F.

scan_protocol: Chips were scanned with Illumina BeadArray Reader and the numerical results were extracted with Bead Studio v1.5.1.34

data_processing: Bead Studio v1.5.1.34

source_name: mouse brain

label_protocol: Using Illumina TotalPrep RNA Amplification kit (#IL1791, Ambion), following the manufacturer's protocol. Input amount: 200ng of total RNA. Incubation of labeling reaction: 14h.

extract_protocol: Total RNAs were purified using the RNeasy Mini Kit (Qiagen, Basel, Switzerland). On-column DNase digestion was performed during RNA purification process. RNA concentrations, A260/280, and A260/230 ratios were determined using the ND-1000 spectrophotometer (Nanodrop Technologies, Wilmington, USA).

tag: genetic background

tag: genotype

tag: age

value: 8 months

value: brain


title: ELF1CL

description: qRT-PCR gene expression data of human endobronchial epithelial lining fluid ELF1CL


title: ELF76CL

description: qRT-PCR gene expression data of human endobronchial epithelial lining fluid ELF76CL


title: phoP-F134-F335-38 h

description: Medium F134


title: wild type rep5

value: CAIX ko

tag: tissue


title: phoP-F134-F335-37 h

description: Medium F134


title: ELF75CL

description: qRT-PCR gene expression data of human endobronchial epithelial lining fluid ELF75CL


title: knockout rep3

value: wild type


title: ELF73CL

description: qRT-PCR gene expression data of human endobronchial epithelial lining fluid ELF73CL


title: phoP-F134-F335-36 h

description: Medium F134


title: Chinese_sample_20

tag: gender


title: wild type rep4


title: phoP-F134-F335-35 h

description: Medium F134


title: Chinese_sample_19


title: ELF70CL

description: qRT-PCR gene expression data of human endobronchial epithelial lining fluid ELF70CL


title: knockout rep2


title: phoP-F134-F335-33 h

description: Medium F134


title: phoP-F134-F335-36.5 h

description: Medium F134


title: wild type rep3


title: Chinese_sample_22


title: ELF69CL

description: qRT-PCR gene expression data of human endobronchial epithelial lining fluid ELF69CL


title: wild type rep2


title: Chinese_sample_17


title: ELF64CL

description: qRT-PCR gene expression data of human endobronchial epithelial lining fluid ELF64CL


title: phoP-F134-F335-32 h

description: Medium F134


title: knockout rep1


title: phoP-F134-F335-30 h

description: Medium F134


title: Chinese_sample_18

value: female


title: Chinese_sample_16


title: Chinese_sample_15


title: phoP-F134-F335-31 h

description: Medium F134


title: ELF61CL

description: qRT-PCR gene expression data of human endobronchial epithelial lining fluid ELF61CL


title: phoP-F134-F335-29 h

description: Medium F134


title: wild type rep1


title: ELF60CL

description: qRT-PCR gene expression data of human endobronchial epithelial lining fluid ELF60CL


title: phoP-F134-F335-28 h

description: Medium F134


title: Chinese_sample_14


title: phoP-F134-F335-27 h

description: Medium F134


title: ELF39CL

description: qRT-PCR gene expression data of human endobronchial epithelial lining fluid ELF39CL


title: phoP-F134-F335-26 h

description: Medium F134


title: Chinese_sample_13


title: Chinese_sample_10


title: Chinese_sample_12


title: phoP-F134-F335-25 h

description: Medium F134


title: ELF35CL

description: qRT-PCR gene expression data of human endobronchial epithelial lining fluid ELF35CL


title: phoP-F134-F335-24 h

description: Medium F134


title: Chinese_sample_11


title: ELF54CL

description: qRT-PCR gene expression data of human endobronchial epithelial lining fluid ELF54CL


title: ELF52CL

description: qRT-PCR gene expression data of human endobronchial epithelial lining fluid ELF52CL


title: ELF31CL

description: qRT-PCR gene expression data of human endobronchial epithelial lining fluid ELF31CL


title: ELF28CL

description: qRT-PCR gene expression data of human endobronchial epithelial lining fluid ELF28CL


title: ELF27CL

description: qRT-PCR gene expression data of human endobronchial epithelial lining fluid ELF27CL


title: phoP-F134-F335-23 h

description: Medium F134


title: Chinese_sample_8


title: Chinese_sample_9


title: ELF65CL

description: qRT-PCR gene expression data of human endobronchial epithelial lining fluid ELF65CL


title: unstable angina 1

city: Beijing

first: Xiaojuan

last: Ma

address: 1 Xiyuan Caochang, Haidian District

department: Department of Cardiovascular Disease

institute: Xiyuan Hospital, China Academy of Chinese Medicine Sciences

description: Gene expression data from unstable angina patient

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 with constant rotation at the speed of 60 rpm. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings

source_name: unstable angina patient of blood sample

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100ng total RNA (Ambion，AM1791).

extract_protocol: RNA was isolated with Trizol Reagent (Invitrogen Life Technologies, P/N 15596-018), according to the manufacturer’s instruction.

treatment_protocol: White blood cell was isolated from blood sample with the method of lymphocyte separation medium.

tag: cell type

value: white blood cell of venous blood

tag: symptom

value: unstable angina


title: Chinese_sample_1


title: ELF19CL

description: qRT-PCR gene expression data of human endobronchial epithelial lining fluid ELF19CL


title: Chinese_sample_7


title: ELF16CL

description: qRT-PCR gene expression data of human endobronchial epithelial lining fluid ELF16CL


title: ELF25CL

description: qRT-PCR gene expression data of human endobronchial epithelial lining fluid ELF25CL


title: ELF21CL

description: qRT-PCR gene expression data of human endobronchial epithelial lining fluid ELF21CL


title: unstable angina 2


title: ELF15CL

description: qRT-PCR gene expression data of human endobronchial epithelial lining fluid ELF15CL


title: ELF59IPN_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 59.0 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.

data_processing: Bioconductor [Gentleman et al. Genome Biology 59004] and R language [Ihaka and Gentleman. Journal of Computational and Graphical Statistics 159596] 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 59004].

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.

treatment_protocol: endobronchial epithelial lining fluid collected by bronchoscopic microsampling [Kahn&Kuner et al. 590059]

value: endobronchial epithelial lining fluid

value: nodule site

tag: patient

value: control patient

value: benign diagnosis


title: control

description: Gene expression data from normal human

source_name: normal human

value: control


title: SH17-T2 prostate tumour

description: SNP genotype data from prostate cancer patient at diagnosis

label_protocol: standard Affymetrix protocol

tag: individual


title: ELF59CL_contralateral_site

source_name: human endobronchial epithelial lining fluid

tag: site

value: contralateral site


title: ELF53CL_contralateral_site

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip« U133 Plus 53.0 in the Affymetrix GeneChip« Hybridization Oven 640. GeneChips were washed and stained in the Affymetrix GeneChip« Fluidics Station 450.

data_processing: Bioconductor [Gentleman et al. Genome Biology 53004] and R language [Ihaka and Gentleman. Journal of Computational and Graphical Statistics 153536] 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 53004].

treatment_protocol: endobronchial epithelial lining fluid collected by bronchoscopic microsampling [Kahn&Kuner et al. 530053]

tag: disease state


title: Chinese_sample_6

source_name: blood

value: blood

value: Chinese


title: ELF53IPN_nodule_site


title: ELF12CL

description: qRT-PCR gene expression data of human endobronchial epithelial lining fluid ELF12CL


title: ELF8CL

description: qRT-PCR gene expression data of human endobronchial epithelial lining fluid ELF8CL


title: Chinese_sample_3


title: ELF7CL

description: qRT-PCR gene expression data of human endobronchial epithelial lining fluid ELF7CL


title: SH12-N normal prostate

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.

value: normal prostate


title: ELF6CL

description: qRT-PCR gene expression data of human endobronchial epithelial lining fluid ELF6CL

value: adenocarcinoma


title: ELF23CL_contralateral_site

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip« U133 Plus 23.0 in the Affymetrix GeneChip« Hybridization Oven 640. GeneChips were washed and stained in the Affymetrix GeneChip« Fluidics Station 450.

data_processing: Bioconductor [Gentleman et al. Genome Biology 23004] and R language [Ihaka and Gentleman. Journal of Computational and Graphical Statistics 123236] 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 23004].

treatment_protocol: endobronchial epithelial lining fluid collected by bronchoscopic microsampling [Kahn&Kuner et al. 230023]


title: ELF51IPN_nodule_site

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip« U133 Plus 51.0 in the Affymetrix GeneChip« Hybridization Oven 640. GeneChips were washed and stained in the Affymetrix GeneChip« Fluidics Station 450.

data_processing: Bioconductor [Gentleman et al. Genome Biology 51004] and R language [Ihaka and Gentleman. Journal of Computational and Graphical Statistics 151516] 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 51004].

treatment_protocol: endobronchial epithelial lining fluid collected by bronchoscopic microsampling [Kahn&Kuner et al. 510051]


title: Chinese_sample_2

value: male


title: ELF74IPN

description: qRT-PCR gene expression data of human endobronchial epithelial lining fluid ELF74IPN

source_name: human endobronchial lining fluid, nodule site, benign

value: benign


title: Chinese_sample_4


title: ELF68IPN

description: qRT-PCR gene expression data of human endobronchial epithelial lining fluid ELF68IPN


title: ELF67IPN

description: qRT-PCR gene expression data of human endobronchial epithelial lining fluid ELF67IPN


title: SH17-T1 prostate tumour


title: ELF66IPN

description: qRT-PCR gene expression data of human endobronchial epithelial lining fluid ELF66IPN


title: Chinese_sample_5


title: ELF2CL_contralateral_site

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.

data_processing: Bioconductor [Gentleman et al. Genome Biology 2004] and R language [Ihaka and Gentleman. Journal of Computational and Graphical Statistics 1226] 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. 2002]


title: SH14-N normal prostate


title: SH12-T1 prostate tumour


title: ELF2IPN_nodule_site


title: ELF51CL_contralateral_site


title: ELF56CL_contralateral_site

data_processing: Bioconductor [Gentleman et al. Genome Biology 2004] and R language [Ihaka and Gentleman. Journal of Computational and Graphical Statistics 156566] 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. 20056]

value: tumor patient

value: squamous cell carcinoma


title: SH12-T2 prostate tumour


title: P107-TM1 prostate tumour


title: ELF62IPN

description: qRT-PCR gene expression data of human endobronchial epithelial lining fluid ELF62IPN


title: ELF57IPN

description: qRT-PCR gene expression data of human endobronchial epithelial lining fluid ELF57IPN


title: ELF41CL_contralateral_site

data_processing: Bioconductor [Gentleman et al. Genome Biology 2004] and R language [Ihaka and Gentleman. Journal of Computational and Graphical Statistics 141416] 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. 20041]


title: ELF41IPN_nodule_site


title: ELF23IPN_nodule_site


title: ELF56IPN_nodule_site


title: SH14-T2 prostate tumour


title: ELF50IPN

description: qRT-PCR gene expression data of human endobronchial epithelial lining fluid ELF50IPN


title: ELF40IPN

description: qRT-PCR gene expression data of human endobronchial epithelial lining fluid ELF40IPN


title: ELF55IPN

description: qRT-PCR gene expression data of human endobronchial epithelial lining fluid ELF55IPN


title: P107-N normal prostate


title: ELF38CL_contralateral_site

data_processing: Bioconductor [Gentleman et al. Genome Biology 2004] and R language [Ihaka and Gentleman. Journal of Computational and Graphical Statistics 138386] 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. 20038]


title: ELF38IPN_nodule_site


title: WX92-TM1 prostate tumour