title: Colony_D-M_7vs.M_8

description: Colony_D-M_7vs.M_8 Microarray batch: G

value: Male

value: 7 days

value: pooled mRNA from 4 developing males

value: 8 days


title: CCA_Tumor_Sample [W039T]

status: Public on Oct 20 2013

type: genomic

city: Singapore

first: Weng Khong

last: Lim

state: Singapore

address: 11 Hospital Drive

department: Department of Medical Sciences

country: Singapore

institute: National Cancer Centre Singapore

description: Methylation profiling on IDH1/2 wild-type and mutant CCA tumors

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation540 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using recommended Illumina scanner settings

data_processing: GenomeStudio software was used to analyze raw Illumina BeadChip data and generate summary files containing average beta avalues.

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

label_protocol: According to manufacturer's protocol

extract_protocol: Genomic DNA was extracted from cells using Qiagen Blood and Cell Culture DNA kit (Qiagen, CA)

tag: tissue type

value: CCA Tumor

tag: idh1/2 mutation status

value: WildType

tag: cca-type (ov or non-ov)

value: OV


title: Technical_Control [MetControl]


title: Technical_Control [Met_Ctrl]


title: Colony_A-M_13vs.M_14

type: RNA

city: Lausanne

first: Yannick

last: Wurm

address: Biophore

department: Ecology and Evolution

country: Switzerland

institute: University of Lausanne

description: Colony_A-M_13vs.M_14 Microarray batch: G

hyb_protocol: Hybridization buffer (3x SSC, 0.18% SDS, 200 ng/μl yeast tRNA, 200 ng/µl polyA DNA; final concentration) was added to samples; samples were denatured, applied to microarrays, and hybridized overnight at 64°C. After hybridization, slides were washed sequential.

scan_protocol: Scanner: Agilent Technologies microarray scanner. Image quantification GenePix 5.1

data_processing:
Median signal and background intensities for each cDNA probe were extracted from scanned microarray images using Axon Genepix Pro 6.0. The limma 2.16 package (Smyth 2004) in R 2.8.1 (The R Development Core Team 2007) was used for Normexp background correction, Print-tip Loess normalization within arrays, and Aquantile normalization between arrays (Smyth & Speed 2003). The arrayQualityMetrics package (Kauffmann et al. 2009) and custom R scripts were used for quality control. We determined during this step that a 384-well plate containing four 96-well sub plates, namely ABE ABF, ABG and ABH, was upside down when printing the G series, so the gene positions in the .GPRs for the "G" arrays are incorrect for 384 positions (those that end in "ABE", "ABF", "ABG" or "ABH"). This was corrected by reversing the order of the values on each of the sub-plates prior to analysis in R with the following code ("RG" represents all raw data):

clonesFromABEtoABH = substr(RG$genes$ID, 8,10) %in% c("ABE", "ABF", "ABG", "ABH")
gBatchChips = unlist(strsplit(RG$targets$FileName[RG$targets$Batch=="G"], ".gpr"))
for (gChip in gBatchChips) {
RG$R[clonesFromABEtoABH, gChip] = rev(RG$R[clonesFromABEtoABH, gChip])
RG$G[clonesFromABEtoABH, gChip] = rev(RG$G[clonesFromABEtoABH, gChip])
}
rm(gBatchChips, gChip, clonesFromABEtoABH)

We constructed a design matrix incorporating effects for each of the 21 timepoints for males, 20 timepoints for queens, and 19 timepoints for workers, as well as effects for replicate (confounded with colony of origin) and microarray batch (the large number of hybridizations required splitting the experiment across two microarray batches). The linear model applied to each gene may thus be represented as 'expression = caste_timepoint+replicate+microarray_batch'. The limma package was used for fitting of the model and computation of moderated t-statistics using empirical Bayes shrinkage for five sets of contrasts. A first set of contrasts determined gene expression differences between all pairs of castes at the first and last timepoint (three contrasts at T0, three at Tlast). Three additional sets of contrasts, one for each caste, determined gene expression differences between neighboring timepoints (respectively 20, 19 and 18 contrasts for males, queens and workers). P-values for differential expression were globally adjusted within each of these first four sets of contrasts for 0.1% False Discovery Rate (FDR; Benjamini Hochberg 1995). A final set of contrasts was used to combine information from replicates into single gene expression level estimates for each caste and timepoint relative to reference RNA.

molecule: total RNA

organism: Solenopsis invicta

label_protocol: Total RNA was amplified using the Ambion Message Amp II kit. Amplified RNA plus Alien spike control RNAs (Stratagene) were labeled using the indirect aa-dUTP labeling method. Reverse transcription primers: random 9mers.

growth_protocol: 12 monogyne S. invicta fire ant colonies were collected from a single population around Athens GA, USA. All colonies were returned to the laboratory and reared for two month under standard conditions (Jouvenaz et al., 1977). Four colonies produced many males, four colonies produced many queens, and four colonies produced only workers. There is genetic variability between colonies, however it is moderate because only few queens founded the North American S. invicta population when they were introduced from South America in the 1930s (Ross et al., 1993; Ross and Shoemaker, 2008).

extract_protocol: Samples were ground using 500 mg of 1.4 mm ceramic beads (Quackenbush) and a Fastprep bead shaker. Tissue was then homogenized in Trizol (invitrogen) and RNA extracted using the manufacturer's recommended protocol. Caste could not be visually determined unambiguously for male- and queen-destined brood within the first days of voiding the meconium. In this case DNA was extracted from the organic hase of the Trizol extraction, and sex was determined based on heterozygosity at six microsatellite markers (male ants are haploid, queens are diploid). Subsequently, extracted RNA was pooled to obtain for each replicate, caste and time point a single pool of either 10 workers, 4 queens, or 4 males.

treatment_protocol: Three castes: Worker, queen & male; four colonies used for each caste (12 colonies total). To synchronize development, colony queens were isolated for eight hours in small boxes with ten adult workers. Larvae reaching the L4 stage were visually inspected either every hour (for hour timepoints) or every eight hours (for day timepoints); developing individuals that had voided their meconium were isolated with adult workers until collection. After 0h, 3h, 6h, 12h, 18h, 24h, 36h and 48h (hour timepoints) and once every 24hours until eclosion (day timepoints),  a group of five workers, a single male or a single queen were placed in 2ml screwcap tubes and immediately flash-frozen in liquid nitrogen. Eclosion occured after 15 days for male, 14 days for queen and 12 days for worker larvae. Only media workers, approximately 2mm long were retained.

tag: caste

tag: colony

value: A

tag: timepoint

value: 13 days

tag: biomaterial

value: 14 days


title: Colony_D-M_6vs.M_7

description: Colony_D-M_6vs.M_7 Microarray batch: G

value: D

value: 6 days


title: Normal Bile Duct [31823989N]

source_name: Normal Bile Duct

value: Normal Tissue

value: Non-OV


title: Colony_D-M_10vs.M_11

description: Colony_D-M_10vs.M_11 Microarray batch: G

value: 10 days

value: 11 days


title: Colony_D-M_12hvs.M_18h

description: Colony_D-M_12hvs.M_18h Microarray batch: I

value: 12 hours

value: 18 hours


title: CCA_Tumor_Sample [45070804T]

value: Mutant


title: CCA_Tumor_Sample [29150572T]


title: Normal Bile Duct [Z1102N]


title: CCA_Tumor_Sample [31215286T]


title: Colony_D-M_11vs.M_12

description: Colony_D-M_11vs.M_12 Microarray batch: G

value: Male

value: pooled mRNA from 4 developing males

value: 12 days


title: CCA_Tumor_Sample [23474504T]

value: CCA Tumor


title: Colony_D-M_8vs.M_9

description: Colony_D-M_8vs.M_9 Microarray batch: G

value: 8 days

value: 9 days


title: CCA_Tumor_Sample [77071507T]


title: Colony_D-M_3hvs.M_6h

description: Colony_D-M_3hvs.M_6h Microarray batch: G

value: 3 hours

value: 6 hours


title: CCA_Tumor_Sample [T-94]

value: WildType


title: Colony_D-M_24hvs.M_36h

description: Colony_D-M_24hvs.M_36h Microarray batch: G

value: D

value: 24 hours

value: 36 hours


title: Insm1 control #7

city: Berlin

first: Jochen

last: Welcker

address: Robert-Rössle-Str. 10

country: Germany

institute: MDC Berlin

description:
Sample name: 5003391030_f
replicate 7

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with Illumina Genome Studio

label: biotin

organism: Mus musculus

source_name: Insm1 control #7_pituitary gland

label_protocol: Biotinylated cRNA were prepared with the Ambion Illumina TotalPrep RNA Amplif Kit

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit.

tag: strain

value: C57/BL6;129Ola mixed

tag: genotype/variation

value: Insm1 +/-

tag: developmental stage

value: embryo

tag: age

tag: tissue

value: pituitary gland


title: Insm1 control #9

description:
Sample name: 5003391030_a
replicate 9

source_name: Insm1 control #9_pituitary gland


title: Insm1 control #6

description:
Sample name: 5003391030_d
replicate 6

source_name: Insm1 control #6_pituitary gland


title: Colony_D-M_3vs.M_4

description: Colony_D-M_3vs.M_4 Microarray batch: G

value: 3 days

value: 4 days


title: Colony_D-M_15vs.M_0h

description: Colony_D-M_15vs.M_0h Microarray batch: G

value: Male

value: 15 days

value: pooled mRNA from 4 developing males

value: 0 hours


title: CCA_Tumor_Sample [33587479T]

value: CCA Tumor

value: Non-OV


title: Insm1 control #8

description:
Sample name: 5003391030_h
replicate 8

source_name: Insm1 control #8_pituitary gland


title: Insm1 control #4

description:
Sample name: 5003391025_h
replicate 4

source_name: Insm1 control #4_pituitary gland


title: Insm1 control #5

description:
Sample name: 5003391030_b
replicate 5

source_name: Insm1 control #5_pituitary gland


title: Insm1 control #2

description:
Sample name: 5003391025_d
replicate 2

source_name: Insm1 control #2_pituitary gland


title: Insm1 control #1

description:
Sample name: 5003391025_b
replicate 1

source_name: Insm1 control #1_pituitary gland


title: Insm1 control #3

description:
Sample name: 5003391025_f
replicate 3

source_name: Insm1 control #3_pituitary gland


title: Insm1 control #10

description:
Sample name: 5003391030_c
replicate 10

source_name: Insm1 control #10_pituitary gland


title: CCA_Tumor_Sample [T-1331]


title: CCA_Tumor_Sample [T-1202]


title: Insm1 mutant #6

description:
Sample name: 5003391030_g
replicate 6

source_name: Insm1 mutant #6_pituitary gland

value: Insm1 -/-


title: Colony_D-M_13vs.M_14

description: Colony_D-M_13vs.M_14 Microarray batch: G

value: 13 days

value: 14 days


title: CCA_Tumor_Sample [17231203T]

value: WildType


title: Colony_D-M_14vs.M_15

description: Colony_D-M_14vs.M_15 Microarray batch: G

value: D


title: Colony_D-M_36hvs.M_48h

description: Colony_D-M_36hvs.M_48h Microarray batch: G

value: 36 hours

value: 48 hours


title: Colony_D-M_12vs.M_13

description: Colony_D-M_12vs.M_13 Microarray batch: G

value: 12 days


title: Normal Bile Duct [37417607N]

value: Normal Tissue


title: CCA_Tumor_Sample [86014838T]


title: CCA_Tumor_Sample [97203223T]


title: CCA_Tumor_Sample [90866096T]


title: CCA_Tumor_Sample [17137053T]

value: Mutant


title: CCA_Tumor_Sample [T-2284]


title: CCA_Tumor_Sample [T-3001]


title: Insm1 mutant #1

description:
Sample name: 5003391025_a
replicate 1

source_name: Insm1 mutant #1_pituitary gland

value: C57/BL6;129Ola mixed

value: embryo

value: pituitary gland


title: Insm1 mutant #2

description:
Sample name: 5003391025_c
replicate 2

source_name: Insm1 mutant #2_pituitary gland


title: Insm1 mutant #5

description:
Sample name: 5003391030_e
replicate 5

source_name: Insm1 mutant #5_pituitary gland


title: Colony_D-M_48hvs.M_3

description: Colony_D-M_48hvs.M_3 Microarray batch: G

value: Male

value: pooled mRNA from 4 developing males

value: 3 days


title: Colony_D-M_18hvs.M_24h

description: Colony_D-M_18hvs.M_24h Microarray batch: G

value: 18 hours

value: 24 hours


title: CCA_Tumor_Sample [19286759T]

value: CCA Tumor

value: Non-OV


title: Insm1 mutant #4

description:
Sample name: 5003391025_g
replicate 4

source_name: Insm1 mutant #4_pituitary gland

value: Insm1 -/-


title: 62CD31+TEC

status: Public on Oct 19 2013

city: shanghai

first: ling-qun

last: Kong

address: 180# Fenglin Road, Shanghai

country: China

institute: Zhongshan hospital affiliated to fudan university

description: Gene expression data from CD31+TEC

hyb_protocol: Array hybridization and wash was performed using GeneChip® Hybridization,  Wash and Stain Kit (Cat#900720, Affymetrix, Santa Clara, CA, US)in Hybridization  Oven 645 (Cat#00‐0331‐220V, Affymetrix, Santa Clara, CA, US)and Fluidics Station  450 (Cat#00‐0079, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s  instructions

scan_protocol: Slides were scanned by GeneChip® Scanner 3000 (Cat#00‐00212, Affymetrix,  Santa Clara, CA, US)

data_processing: Slides were  Command Console Software 3.1 (Affymetrix, Santa Clara, CA, US) with default settings. Raw data were normalized by MAS 5.0 algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US).

source_name: CD31+ tumor endothelial cells (TEC) isolated from tumor tissue of hepatocellular carcinoma (HCC) patients (Case Number 16)

label_protocol: Total RNA were amplified, labeled and purified by using GeneChip 3’IVT Express  Kit (Cat#901229, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s  instructions to obtain biotin labeled cRNA.

growth_protocol: Patient specimens were collected immediately after removal from patients with pathologically proven HCC and positive -fetoprotein (AFP), then washed 3 times by phosphate buffer solution (PBS) ,and then processing into a single cell suspension

extract_protocol: Lysis/Binding Bufferextraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Single cell suspension was obtained from separated tumor and non-tumor liver tissues of surgical specimens following the protocol (http://www.miltenyibiotec.com), then CD31+ cells or CD105+ cells were isolated using CD31 antibody or CD105 antibody conjugated magnetic beads in autoMACSpro (Meltenyi biotec).

value: tumor tissue of HCC

tag: age (year)

tag: gender (male or female)

value: M


title: 46NTC

description: Gene expression data from NTC

source_name: remnant cells after isolated TEC from adjacent non-tumor tissue (NTC) of hepatocellular carcinoma (HCC) patients (Case Number 14)

value: adjacent non-tumor tissue of HCC


title: 18NTC

description: Gene expression data from NTC

source_name: remnant cells after isolated TEC from adjacent non-tumor tissue (NTC) of hepatocellular carcinoma (HCC) patients (Case Number 12)


title: 58CD31+NEC

description: Gene expression data from CD31+NEC

source_name: CD31+non-tumor endothelial cells (NEC) isolated from adjacent non-tumor tissue of hepatocellular carcinoma (HCC) patients (Case Number 15)


title: 46CD31+NEC

description: Gene expression data from CD31+NEC

source_name: CD31+non-tumor endothelial cells (NEC) isolated from adjacent non-tumor tissue of hepatocellular carcinoma (HCC) patients (Case Number 14)


title: 20CD31+NEC

description: Gene expression data from CD31+NEC

source_name: CD31+non-tumor endothelial cells (NEC) isolated from adjacent non-tumor tissue of hepatocellular carcinoma (HCC) patients (Case Number 13)


title: 18TC

description: Gene expression data from TC

source_name: remnant cells after isolated TEC from tumor tissue (TC) of hepatocellular carcinoma (HCC) patients (Case Number 12)


title: 46CD31+TEC

description: Gene expression data from CD31+TEC

source_name: CD31+ tumor endothelial cells (TEC) isolated from tumor tissue of hepatocellular carcinoma (HCC) patients (Case Number 14)


title: 18CD31+NEC

description: Gene expression data from CD31+NEC

source_name: CD31+non-tumor endothelial cells (NEC) isolated from adjacent non-tumor tissue of hepatocellular carcinoma (HCC) patients (Case Number 12)


title: Normal Bile Duct [210776N]

source_name: Normal Bile Duct

value: WildType


title: 58TC

description: Gene expression data from TC

source_name: remnant cells after isolated TEC from tumor tissue (TC) of hepatocellular carcinoma (HCC) patients (Case Number 15)


title: 20CD31+TEC

description: Gene expression data from CD31+TEC

source_name: CD31+ tumor endothelial cells (TEC) isolated from tumor tissue of hepatocellular carcinoma (HCC) patients (Case Number 13)


title: 16CD31+TEC

description: Gene expression data from CD31+TEC

source_name: CD31+ tumor endothelial cells (TEC) isolated from tumor tissue of hepatocellular carcinoma (HCC) patients (Case Number 11)

value: F


title: 18CD31+TEC

description: Gene expression data from CD31+TEC

source_name: CD31+ tumor endothelial cells (TEC) isolated from tumor tissue of hepatocellular carcinoma (HCC) patients (Case Number 12)


title: 20TC

description: Gene expression data from TC

source_name: remnant cells after isolated TEC from tumor tissue (TC) of hepatocellular carcinoma (HCC) patients (Case Number 13)


title: 20NTC

description: Gene expression data from NTC

source_name: remnant cells after isolated TEC from adjacent non-tumor tissue (NTC) of hepatocellular carcinoma (HCC) patients (Case Number 13)


title: 16CD31+NEC

description: Gene expression data from CD31+NEC

source_name: CD31+non-tumor endothelial cells (NEC) isolated from adjacent non-tumor tissue of hepatocellular carcinoma (HCC) patients (Case Number 11)


title: Colony_D-M_9vs.M_10

description: Colony_D-M_9vs.M_10 Microarray batch: G

value: D

value: 9 days

value: 10 days


title: 46TC

description: Gene expression data from TC

source_name: remnant cells after isolated TEC from tumor tissue (TC) of hepatocellular carcinoma (HCC) patients (Case Number 14)


title: 58NTC

description: Gene expression data from NTC

source_name: remnant cells after isolated TEC from adjacent non-tumor tissue (NTC) of hepatocellular carcinoma (HCC) patients (Case Number 15)


title: Insm1 mutant #3

description:
Sample name: 5003391025_e
replicate 3

source_name: Insm1 mutant #3_pituitary gland

value: C57/BL6;129Ola mixed

value: embryo

value: pituitary gland


title: Colony_D-M_0hvs.M_3h

description: Colony_D-M_0hvs.M_3h Microarray batch: G

value: Male

value: 0 hours

value: pooled mRNA from 4 developing males

value: 3 hours


title: 16TC

description: Gene expression data from TC

source_name: remnant cells after isolated TEC from tumor tissue (TC) of hepatocellular carcinoma (HCC) patients (Case Number 11)


title: 16NTC

description: Gene expression data from NTC

source_name: remnant cells after isolated TEC from adjacent non-tumor tissue (NTC) of hepatocellular carcinoma (HCC) patients (Case Number 11)


title: 62CD31+NEC

description: Gene expression data from CD31+NEC

source_name: CD31+non-tumor endothelial cells (NEC) isolated from adjacent non-tumor tissue of hepatocellular carcinoma (HCC) patients (Case Number 16)


title: 62NTC

description: Gene expression data from NTC

source_name: remnant cells after isolated TEC from adjacent non-tumor tissue (NTC) of hepatocellular carcinoma (HCC) patients (Case Number 16)


title: 10TC

description: Gene expression data from TC

source_name: remnant cells after isolated TEC from tumor tissue (TC) of hepatocellular carcinoma (HCC) patients (Case Number 10)


title: 8CD31+NEC

description: Gene expression data from CD31+NEC

source_name: CD31+non-tumor endothelial cells (NEC) isolated from adjacent non-tumor tissue of hepatocellular carcinoma (HCC) patients (Case Number 9)


title: 8TC

description: Gene expression data from TC

source_name: remnant cells after isolated TEC from tumor tissue (TC) of hepatocellular carcinoma (HCC) patients (Case Number 9)


title: 4CD31+TEC

description: Gene expression data from CD31+TEC

source_name: CD31+ tumor endothelial cells (TEC) isolated from tumor tissue of hepatocellular carcinoma (HCC) patients (Case Number 7)


title: 10CD31+TEC

description: Gene expression data from CD31+TEC

source_name: CD31+ tumor endothelial cells (TEC) isolated from tumor tissue of hepatocellular carcinoma (HCC) patients (Case Number 10)


title: 5CD31+NEC

description: Gene expression data from CD31+NEC

source_name: CD31+non-tumor endothelial cells (NEC) isolated from adjacent non-tumor tissue of hepatocellular carcinoma (HCC) patients (Case Number 8)


title: 58CD31+TEC

description: Gene expression data from CD31+TEC

source_name: CD31+ tumor endothelial cells (TEC) isolated from tumor tissue of hepatocellular carcinoma (HCC) patients (Case Number 15)


title: 4CD105+TEC

description: Gene expression data from CD105+TEC

source_name: CD105+ tumor endothelial cells (TEC) isolated from tumor tissue of hepatocellular carcinoma (HCC) patients (Case Number 7)


title: 4CD105+NEC

description: Gene expression data from CD105+NEC

source_name: CD105+non-tumor endothelial cells (NEC) isolated from adjacent non-tumor tissue of hepatocellular carcinoma (HCC) patients (Case Number 7)


title: 5CD105+NEC

description: Gene expression data from CD105+NEC

source_name: CD105+non-tumor endothelial cells (NEC) isolated from adjacent non-tumor tissue of hepatocellular carcinoma (HCC) patients (Case Number 8)


title: 4CD31+NEC

description: Gene expression data from CD31+NEC

source_name: CD31+non-tumor endothelial cells (NEC) isolated from adjacent non-tumor tissue of hepatocellular carcinoma (HCC) patients (Case Number 7)


title: 5CD105+TEC

description: Gene expression data from CD105+TEC

source_name: CD105+ tumor endothelial cells (TEC) isolated from tumor tissue of hepatocellular carcinoma (HCC) patients (Case Number 8)


title: 62TC

description: Gene expression data from TC

source_name: remnant cells after isolated TEC from tumor tissue (TC) of hepatocellular carcinoma (HCC) patients (Case Number 16)


title: 10CD31+NEC

description: Gene expression data from CD31+NEC

source_name: CD31+non-tumor endothelial cells (NEC) isolated from adjacent non-tumor tissue of hepatocellular carcinoma (HCC) patients (Case Number 10)


title: 2CD105+NEC

description: Gene expression data from CD105+NEC

source_name: CD105+non-tumor endothelial cells (NEC) isolated from adjacent non-tumor tissue of hepatocellular carcinoma (HCC) patients (Case Number 6)


title: 2CD31+NEC

description: Gene expression data from CD31+NEC

source_name: CD31+non-tumor endothelial cells (NEC) isolated from adjacent non-tumor tissue of hepatocellular carcinoma (HCC) patients (Case Number 6)


title: 8CD31+TEC

description: Gene expression data from CD31+TEC

source_name: CD31+ tumor endothelial cells (TEC) isolated from tumor tissue of hepatocellular carcinoma (HCC) patients (Case Number 9)


title: 2CD31+TEC

description: Gene expression data from CD31+TEC

source_name: CD31+ tumor endothelial cells (TEC) isolated from tumor tissue of hepatocellular carcinoma (HCC) patients (Case Number 6)


title: 2CD105+TEC

description: Gene expression data from CD105+TEC

source_name: CD105+ tumor endothelial cells (TEC) isolated from tumor tissue of hepatocellular carcinoma (HCC) patients (Case Number 6)


title: 10NTC

description: Gene expression data from NTC

source_name: remnant cells after isolated TEC from adjacent non-tumor tissue (NTC) of hepatocellular carcinoma (HCC) patients (Case Number 10)


title: 5CD31+TEC

description: Gene expression data from CD31+TEC

source_name: CD31+ tumor endothelial cells (TEC) isolated from tumor tissue of hepatocellular carcinoma (HCC) patients (Case Number 8)


title: 1CD105+NEC

description: Gene expression data from CD105+NEC

source_name: CD105+non-tumor endothelial cells (NEC) isolated from adjacent non-tumor tissue of hepatocellular carcinoma (HCC) patients (Case Number 5)


title: RCD105+NEC

description: Gene expression data from CD105+NEC

source_name: CD105+non-tumor endothelial cells (NEC) isolated from adjacent non-tumor tissue of hepatocellular carcinoma (HCC) patients (Case Number 4)


title: RCD105+TEC

description: Gene expression data from CD105+TEC

source_name: CD105+ tumor endothelial cells (TEC) isolated from tumor tissue of hepatocellular carcinoma (HCC) patients (Case Number 4)


title: OCD31+NEC

description: Gene expression data from CD31+NEC

source_name: CD31+non-tumor endothelial cells (NEC) isolated from adjacent non-tumor tissue of hepatocellular carcinoma (HCC) patients (Case Number 2)


title: 1CD31+NEC

description: Gene expression data from CD31+NEC

source_name: CD31+non-tumor endothelial cells (NEC) isolated from adjacent non-tumor tissue of hepatocellular carcinoma (HCC) patients (Case Number 5)


title: 1CD105+TEC

description: Gene expression data from CD105+TEC

source_name: CD105+ tumor endothelial cells (TEC) isolated from tumor tissue of hepatocellular carcinoma (HCC) patients (Case Number 5)


title: QCD105+NEC

description: Gene expression data from CD105+NEC

source_name: CD105+non-tumor endothelial cells (NEC) isolated from adjacent non-tumor tissue of hepatocellular carcinoma (HCC) patients (Case Number 3)


title: QCD105+TEC

description: Gene expression data from CD105+TEC

source_name: CD105+ tumor endothelial cells (TEC) isolated from tumor tissue of hepatocellular carcinoma (HCC) patients (Case Number 3)


title: OCD105+TEC

description: Gene expression data from CD105+TEC

source_name: CD105+ tumor endothelial cells (TEC) isolated from tumor tissue of hepatocellular carcinoma (HCC) patients (Case Number 2)


title: RCD31+NEC

description: Gene expression data from CD31+NEC

source_name: CD31+non-tumor endothelial cells (NEC) isolated from adjacent non-tumor tissue of hepatocellular carcinoma (HCC) patients (Case Number 4)


title: QCD31+TEC

description: Gene expression data from CD31+TEC

source_name: CD31+ tumor endothelial cells (TEC) isolated from tumor tissue of hepatocellular carcinoma (HCC) patients (Case Number 3)


title: 1CD31+TEC

description: Gene expression data from CD31+TEC

source_name: CD31+ tumor endothelial cells (TEC) isolated from tumor tissue of hepatocellular carcinoma (HCC) patients (Case Number 5)


title: RCD31+TEC

description: Gene expression data from CD31+TEC

source_name: CD31+ tumor endothelial cells (TEC) isolated from tumor tissue of hepatocellular carcinoma (HCC) patients (Case Number 4)


title: OCD31+TEC

description: Gene expression data from CD31+TEC

source_name: CD31+ tumor endothelial cells (TEC) isolated from tumor tissue of hepatocellular carcinoma (HCC) patients (Case Number 2)


title: QCD31+NEC

description: Gene expression data from CD31+NEC

source_name: CD31+non-tumor endothelial cells (NEC) isolated from adjacent non-tumor tissue of hepatocellular carcinoma (HCC) patients (Case Number 3)


title: OCD105+NEC

description: Gene expression data from CD105+NEC

source_name: CD105+non-tumor endothelial cells (NEC) isolated from adjacent non-tumor tissue of hepatocellular carcinoma (HCC) patients (Case Number 2)


title: NCD105+TEC

description: Gene expression data from CD105+TEC

source_name: CD105+ tumor endothelial cells (TEC) isolated from tumor tissue of hepatocellular carcinoma (HCC) patients (Case Number 1)


title: NCD105+NEC

description: Gene expression data from CD105+NEC

source_name: CD105+non-tumor endothelial cells (NEC) isolated from adjacent non-tumor tissue of hepatocellular carcinoma (HCC) patients (Case Number 1)


title: NCD31+NEC

description: Gene expression data from CD31+NEC

source_name: CD31+non-tumor endothelial cells (NEC) isolated from adjacent non-tumor tissue of hepatocellular carcinoma (HCC) patients (Case Number 1)


title: 05 Knockout (miR-1-1)

city: San Francisco

first: Gladstone

last: Bioinformatics

state: CA

address: 1650 Owens St

department: Data Science and Biotechnology

country: USA

institute: Gladstone Institutes

hyb_protocol: Samples were hybridized to Affymetrix mouse genechip ST 2.0 arrays: GeneChip Expression Analysis Technical Manual 702232 Rev. 3

scan_protocol: Affymetrix GCS3000

data_processing: CEL files were generated using AGCC 4.0.0.1567G. The values in the CEL files were then normalized with the RMA normalization method, using the Affymetrix Power Tools suite, version 1.12.0.

source_name: Knockout (miR-1-1)

label_protocol: Genomic DNA was removed using a gDNA eliminator column (Qiagen)

growth_protocol: Samples are from neonatal hearts (P2) from wildtype, miR-1-1 null and miR-1-2 +/-: miR-1-1 +/- double heterozygote mice

extract_protocol:
Total RNA was extracted with TRIzol (Invitrogen), following the manufacturer’s suggested protocol.
amplication protocol: NuGen Ovation pico WTA system v2

treatment_protocol: Neonatal hearts (P2) from wildtype, miR-1-1 null and miR-1-2 +/-: miR-1-1 +/- double heterozygote animals were isolated

value: Mixed 129 x C57BL/6

value: Neonatal hearts (P2)

value: miR-1-1 Knockout


title: 08 Heterozygous Deletion (miR-1)

source_name: Heterozygous Deletion (miR-1)

value: miR-1 DOUBLE HETEROZYGOUS DELETION


title: 09 Heterozygous Deletion (miR-1)


title: 06 Knockout (miR-1-1)


title: 07 Heterozygous Deletion (miR-1)


title: K562 pTRE ERG CL9 no dox

first: Claudia

middle: D

last: Baldus

state: Berlin

address: Hindenburgdamm 30

department: Hematology and Oncology

institute: Charite

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

scan_protocol: GeneChips were scanned using the  Affymetrix GeneChip Scanner3000

data_processing: The data were analyzed with Gene Spring using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 1.

source_name: CL9 no dox

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: K562 pTRE ERG3 cells were cultured in 10%RMPI 5%CO2

extract_protocol: RNA was purified with Qiagen Rneasy Minikit according to manufacturer's conditions

treatment_protocol: K562 pTRE ERG3 cells were induced with 1µg/ml doxycycline daily for 8 days

tag: cell line

tag: treatment

value: unstimulated


title: K562 pTRE ERG CL46 no dox

source_name: CL46 no dox


title: NCD31+TEC

description: Gene expression data from CD31+TEC

source_name: CD31+ tumor endothelial cells (TEC) isolated from tumor tissue of hepatocellular carcinoma (HCC) patients (Case Number 1)

value: tumor tissue of HCC


title: 02 Wildtype

source_name: Wildtype

value: WILDTYPE


title: ST_KO−2

first: Julius

last: Müller

address: 61 Biopolis Drive

department: IMCB

institute: A*Star Singapore

description: replicate 2

data_processing: The data were normalised using quantile normalisation with beadarray in R

source_name: spermatid

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

tag: genotype

tag: cell type

value: spermatid


title: ST_KO−3

description: replicate 3


title: ST_KO_het−2

description: replicate 2


title: K562 pTRE ERG CL9 dox

source_name: CL9 dox

value: 8-day dox stimulation


title: 01 Wildtype


title: 04 Knockout (miR-1-1)


title: K562 pTRE ERG CL46 dox

source_name: CL46 dox


title: ST_KO_het−3

description: replicate 3


title: K562 pTRE ERG CL4 no dox

source_name: CL4 no dox


title: K562 pTRE ERG CL4 dox

source_name: CL4 dox


title: ST_KO_het−1

description: replicate 1


title: Gene expression difference between control and apocynin-treatment

status: Public on Oct 18 2013

city: Nagoya

first: Shugo

last: Suzuki

state: Aichi

address: 1 Kawasumi, Mizuho-Cho, Mizuho-Ku

department: Experimental Pathology and Tumor Biology

country: Japan

institute: Nagoya City University Graduate School of Medical Sciences

hyb_protocol: 1 µg of labeled probe was used for hybridization with TaKaRa Hybridization Chamber at 37°C for 16 hours. After hybridization, slides were washed sequential

scan_protocol: Scanned on 3D-gene Scanner 3000 (TORAY)

data_processing: LOWESS normalized, background subtracted data obtained.

organism: Rattus norvegicus

source_name: Control ventral prostate lobe

label_protocol: １ µg of total RNA were amplified with Ambion Amino Allyl aRNA kit, then 10 µg of amlified RNA labelded with Amersham Cy5 or Cy3 Mono-Reactive Dye.

extract_protocol: Total RNA extracted using ISOGEN following manufacturer's instructions

treatment_protocol: Six-week-old TRAP rats were treated with/without apocynin 500 mg/L in drinking water for 8 weeks, then, sacrificed.

value: Ventral prostate lobe

source_name: Apocynin-treated ventral prostate lobe

value: with apocynin 500 mg/L


title: 03 Wildtype


title: ST_KO−1

description: replicate 1


title: ST_WT−2

description: replicate 2


title: ST_WT−3

description: replicate 3


title: ST_WT−1

description: replicate 1


title: WT ProB_1

city: Huddinge

first: HONG

last: QIAN

state: Stockholms Lan

address: Neo, HERM, Floor 7, Hälsovägen 7,

department: Department of Medicine

country: Sweden

institute: Karolinska Institute

description: Cells sorted as B220+CD19+CD43highIgM-

hyb_protocol: cRNA fragments hybridized against MOE430 2.0 Affymetrix gene expression arrays chip according to manufacturer instructions

scan_protocol: Chips were scanned using a GeneChip TM Scanner 3000

data_processing: Expression values were acquired using RMA and Mouse430_2.cdf file

source_name: mouse bone marrow

label_protocol: RNA was labelled and amplified according to Affymetrix TM GeneChip Expression Analysis Technical Manual 2011

growth_protocol: Cells obtained fresh from the bone marrow of mice.

extract_protocol: RNeasy Micro kit (Qiagen) has been used to extract RNA according to manufacturer instruction

treatment_protocol: No treatment has been used.

value: wild-type

tag: genetic background


title: WT PreB_1

description: Cells sorted as B220+CD19+CD43low/negIgM-


title: WT ProB_2

description: Cells sorted as B220+CD19+CD43highIgM-


title: Ebf1 hetero ProB_1

description: Cells sorted as B220+CD19+CD43highIgM-

value: Ebf1 heterozygote


title: WT PreB_2


title: BRAIN|ORF73|SC017

city: Boston

first: Ramnik

middle: J

last: Xavier

state: MA

address: 185 Cambridge Street

institute: Massachusetts General Hospital

description: mice harvested midday

hyb_protocol: Following fragmentation, 20 ug (samples 16xxx) or 12.5 ug (samples 21xxx) of cRNA were hybridized for 16 hr at 45C on Mouse 430 2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneArray Scanner 7G06.

data_processing: The data were analyzed with Affymetrix GeneChip Command Console using Affymetrix default analysis settings and global scaling as normalization method. Target intensity of arrays was set to 1500 (for samples 16xxx) or 100 (for samples 21xxx). Data were normalized using Robust Multi-array Average normalization routine in Affymetrix’s Expression Console software.

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug (samples 16xxx) or 100 ng (samples 21xxx) total RNA (Expression Analysis Technical Manual, 2008, Affymetrix). RNA was labeled at the Multiplexed Gene Analysis Core Facility at Washington University in St. Louis.

growth_protocol: 7-9 week old male C57BL/6J mice were infected intranasally with wild-type (WT) MHV68, ORF73.stop mutant virus or mockulum.

extract_protocol: RNA was extracted using the ToTALLY RNA kit (Ambion) from tissues incubated in RNAlater-ICE (Ambion) and purified by lithium chloride precipitation and RNeasy column. Equal amounts of RNA were pooled from three to four mice per condition for each microarray chip.

treatment_protocol: After cardiac perfusion with PBS, brains, livers and spleens were harvested at 28 days post infection (dpi) and immediately snap frozen.

value: BRAIN

tag: infectious agent


title: SPLEEN|ORF73|SC019

description: mice harvested midday

value: SPLEEN


title: 8NTC

description: Gene expression data from NTC

source_name: remnant cells after isolated TEC from adjacent non-tumor tissue (NTC) of hepatocellular carcinoma (HCC) patients (Case Number 9)

value: adjacent non-tumor tissue of HCC

value: M


title: SPLEEN|ORF73|SC2

description: mice harvested midday


title: BRAIN|MOCK|SC017

description: mice harvested midday

source_name: MOCK

value: MOCK


title: BRAIN|ORF73|SC019

description: mice harvested midday


title: BRAIN|MOCK|SC018

description: mice harvested midday


title: Ebf1 hetero ProB_2

description: Cells sorted as B220+CD19+CD43highIgM-


title: SPLEEN|MHV-68|SC2

description: mice harvested in afternoon


title: SPLEEN|MHV-68|SC3

description: mice harvested in afternoon


title: SPLEEN|MHV-68|SC019

description: mice harvested midday


title: SPLEEN|MOCK|SC3

description: mice harvested in morning


title: SPLEEN|MOCK|SC019

description: mice harvested midday


title: BRAIN|MHV-68|SC018

description: mice harvested midday


title: Ebf1 hetero PreB_1


title: LIVER|ORF73|SC2

description: mice harvested midday

value: LIVER


title: LIVER|ORF73|SC3

description: mice harvested midday


title: BRAIN|MOCK|SC019

description: mice harvested midday


title: BRAIN|MHV-68|SC017

description: mice harvested midday


title: SPLEEN|ORF73|SC3

description: mice harvested midday


title: BRAIN|MHV-68|SC019

description: mice harvested midday


title: SPLEEN|MOCK|SC2

description: mice harvested in morning


title: LIVER|ORF73|SC019

description: mice harvested midday


title: BRAIN|ORF73|SC018

description: mice harvested midday


title: LIVER|MHV-68|SC3

description: mice harvested in afternoon


title: LIVER|MOCK|SC019

description: mice harvested midday


title: LIVER|MHV-68|SC019

description: mice harvested midday


title: LIVER|MHV-68|SC2

description: mice harvested in afternoon


title: LIVER|MOCK|SC2

description: mice harvested in morning


title: LIVER|MOCK|SC1

description: mice harvested in morning


title: Huvec_CTRL_3

city: Candiolo

first: Enzo

last: Medico

state: TO

address: Strada Prov. 142, km 3,95

department: Oncology

country: Italy

institute: Candiolo Cancer Institute, University of Torino

description: HUVECs transduced with control oligonucleotide and GFP, sorted for fluorescence positive population

hyb_protocol: 0.85 microgram of biotin-labeled cRNA was hybridized to Illumina HumanRef8 V2 at 55 °C overnight. BeadChips were incubated with Cy3 streptavidin and washed according to the manufacturer’s protocol.

scan_protocol: The hybridized BeadChips were scanned by Illumina BeadScan confocal scanner and analyzed by Illumina's BeadStudio version 1.5.1.3

data_processing: Data were normalized by Illumina's BeadStudio version 1.5.1.3 with ranbk invariant normalization

label: Biotin

source_name: Human Umbilical Vein Endothelial Cells

label_protocol: Five hundred ng of total RNA was reverse transcribed and amplified overnight with T7 RNA polymerase and labeled with biotin following the manufacturer’s protocol.

growth_protocol: M199 containing 20% FBS

extract_protocol: RNA extraction was performed using Trizol plus RNA purification kit (Invitrogen). RNA qualitative and quantitative assessment was performed using the Bioanalyzer 2100 (Agilent Tecnologies).

value: HUVECs

tag: tranducer


title: Huvec_CTRL_2

value: control oligonucleotide and GFP, sorted for fluorescence positive population


title: Huvec_LNA_mir126_3

description: HUVECs transduced with mir-126 antisense oligonucleotide and GFP, sorted for fluorescence positive population


title: Huvec_GFP_2

description: HUVECs transduced with GFP, sorted for fluorescence positive population


title: Huvec_CTRL_1


title: Great Basin woodrat fed Juniper Replicate 2

city: Banyuls sur Mer

first: Elodie

last: Magnanou

address: Avenue du Fontaulé

department: BIOM Biologie Intégrative des Organismes Marins CNRS  - UPMC

country: France

institute: Laboratoire Arago

description: Wild woodrats acclimated to captivity for 3 month then fed juniper for 5 days (increasing doses in the rabbit chow diet)

hyb_protocol: The fluorescently labelled amplified RNA were hybridized to Agilent Technologies 60mer oligonucleotide rat microarrays (G4131F) per the manufacturer's instructions.

scan_protocol: Microarrays were scanned on an Agilent Technologies G2565BA Microarray Scanner System

data_processing: Agilent Feature Extraction Software (v 9.1.3.1) was used for background subtraction and LOWESS normalization.

organism: Neotoma lepida

source_name: Liver from Great Basin Neotoma lepida fed Juniper

label_protocol: Total RNA (500ng/sample) was labelled with Cyanine-3 CTP or Cyanine-5 CTP using an Agilent Low RNA Input Linear Amplification kit as specified by the manufacturer

growth_protocol: Woodrats were housed in individual cages and were acclimated to captivity for 3 months before the experiment. Woodrats were fed standard rabbit chow (Harlan Teklad formula 2031); water was provided ad libitum

extract_protocol: Total RNA from the liver sections was extracted using Tri Reagent (Sigma) per the manufacturer's protocol

treatment_protocol: Experimental animals were fed a gradually increasing amount of plant components over a five-day period to allow induction of biotransformation pathways

tag: sample type

value: Wild caught

tag: gender

value: Female

value: liver

tag: diet

value: Juniper

tag: population

value: Great Basin

source_name: Reference : equimolar pool of liver tRNA of the 16 samples

value: reference


title: Mojave woodrat fed Juniper Replicate 4

source_name: Liver from Mojave Neotoma lepida fed Juniper

value: Mojave


title: Huvec_LNA_mir126_2

value: mir-126 antisense oligonucleotide and GFP, sorted for fluorescence positive population


title: Huvec_GFP_1

value: GFP, sorted for fluorescence positive population


title: Mojave woodrat fed Creosote Replicate 3

description: Wild woodrats acclimated to captivity for 3 month then fed creosote for 5 days (increasing doses in the rabbit chow diet)

source_name: Liver from Mojave Neotoma lepida fed Creosote

value: male

value: creosote


title: Great Basin woodrat fed Juniper Replicate 3


title: Great Basin woodrat fed Juniper Replicate 4


title: Mojave woodrat fed Juniper Replicate 3


title: Mojave woodrat fed Juniper Replicate 2


title: Mojave woodrat fed Juniper Replicate 1


title: LIVER|MOCK|SC3

description: mice harvested in morning

tag: strain


title: Mojave woodrat fed Creosote Replicate 4


title: Mojave woodrat fed Creosote Replicate 2


title: Mojave woodrat fed Creosote Replicate 1


title: Great Basin woodrat fed Creosote Replicate 4

source_name: Liver from Great Basin Neotoma lepida fed Creosote


title: Great Basin woodrat fed Juniper Replicate 1


title: premir467c-2_Mouse Lung Epithelial Cells MLE-12_rep2

first: christian

middle: lacks

last: lino cardenas

state: Massachusetts

address: 185 Cambridge st Room 3224

department: division of cardiovascular

institute: Massachusetts general hospital-Harvard medical school

description: Gene expression data from MLE-12 after 24h transfection

hyb_protocol: Labeled RNA was hybridized for 17 hr at 75C on Agilent 8X15K gene expression array. Arrays were washed according to the manufacturer's protocol.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 8x15K array slides

data_processing:
The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters.
Cyclic lowess, data was normalized with AFFY package in R and was transformed to log2.

source_name: Mouse Lung Epithelial cell MLE-12, biological rep 2

label_protocol: Cy3 labeled RNA was prepared according to the standard Agilent protocol from 100ng total RNA

extract_protocol: Total RNA extracted using miRNeasy mini kit (Qiagen) according to the manufacturer's instructions.

value: Lung Epithelial cell line MLE-12

tag: transfection

tag: passage


title: Great Basin woodrat fed Creosote Replicate 1

tag: tissue


title: Great Basin woodrat fed Creosote Replicate 2


title: premir467c-3_Mouse Lung Epithelial Cells MLE-12_rep3

source_name: Mouse Lung Epithelial cell MLE-12, biological rep 3


title: premir467c-1_Mouse Lung Epithelial Cells MLE-12_rep1

source_name: Mouse Lung Epithelial cell MLE-12, biological rep 1


title: Huvec_LNA_mir126_1


title: premir467c-4_Mouse Lung Epithelial Cells MLE-12_rep4

source_name: Mouse Lung Epithelial cell MLE-12, biological rep 4


title: premir466d-3_Mouse Lung Epithelial Cells MLE-12_rep3


title: Great Basin woodrat fed Creosote Replicate 3


title: premir466d-4_Mouse Lung Epithelial Cells MLE-12_rep4


title: premir466d-1_Mouse Lung Epithelial Cells MLE-12_rep1


title: premir466a-4_Mouse Lung Epithelial Cells MLE-12_rep4


title: premir466d-2_Mouse Lung Epithelial Cells MLE-12_rep2


title: premir466a-3_Mouse Lung Epithelial Cells MLE-12_rep3


title: premir466a-1_Mouse Lung Epithelial Cells MLE-12_rep1


title: prectrl-1_Mouse Lung Epithelial Cells MLE-12_rep1

value: prectrl


title: premir466a-2_Mouse Lung Epithelial Cells MLE-12_rep2


title: prectrl-3_Mouse Lung Epithelial Cells MLE-12_rep3


title: premir337-2_Mouse Lung Epithelial Cells MLE-12_rep2


title: prectrl-2_Mouse Lung Epithelial Cells MLE-12_rep2


title: premir337-3_Mouse Lung Epithelial Cells MLE-12_rep3


title: premir337-4_Mouse Lung Epithelial Cells MLE-12_rep4


title: antmir125a-4_Mouse Lung Epithelial Cells MLE-12_rep4


title: prectrl-4_Mouse Lung Epithelial Cells MLE-12_rep4


title: antmir125a-3_Mouse Lung Epithelial Cells MLE-12_rep3


title: antmir125a-2_Mouse Lung Epithelial Cells MLE-12_rep2


title: antmir30d-3_Mouse Lung Epithelial Cells MLE-12_rep3


title: premir337-1_Mouse Lung Epithelial Cells MLE-12_rep1


title: antmir30a-2_Mouse Lung Epithelial Cells MLE-12_rep2


title: antmir30a-3_Mouse Lung Epithelial Cells MLE-12_rep3


title: antmir125a-1_Mouse Lung Epithelial Cells MLE-12_rep1


title: Ebf1 hetero PreB_2

value: Ebf1 heterozygote


title: antmir30d-1_Mouse Lung Epithelial Cells MLE-12_rep1


title: antmir30d-2_Mouse Lung Epithelial Cells MLE-12_rep2


title: antmir30a-4_Mouse Lung Epithelial Cells MLE-12_rep4


title: antmir30a-1_Mouse Lung Epithelial Cells MLE-12_rep1


title: antmir23b-4_Mouse Lung Epithelial Cells MLE-12_rep4


title: antctrl-4_Mouse Lung Epithelial Cells MLE-12_rep4

value: antctrl


title: antmir30d-4_Mouse Lung Epithelial Cells MLE-12_rep4


title: antmir23b-1_Mouse Lung Epithelial Cells MLE-12_rep1


title: antctrl-3_Mouse Lung Epithelial Cells MLE-12_rep3


title: antctrl-1_Mouse Lung Epithelial Cells MLE-12_rep1


title: antctrl-2_Mouse Lung Epithelial Cells MLE-12_rep2


title: C44P

city: Valencia

first: Dolors

last: Sanchez-Izquierdo

state: Valencia

address: Avda. Campanar 21

department: Genomics Unit

country: Spain

institute: IIS La Fe

data_processing: RMA-DABG,background substraction, log2 data transformation

source_name: Control plasma

label_protocol: Biotinylated RNA were prepared according to the standard Affymetrix protocol

growth_protocol: not applicable

extract_protocol: RNA extracted with miRNeasy Qiagen kit for plasma samples and mirVana (Life Technologies) for biopsies. RNA was analyzed by NanoDrop and Bioanalyzer.

treatment_protocol: not applicable

value: plasma


title: D101PC

source_name: Patient plasma plus carrier at low concentration

value: plasma with carrier


title: C44PC

source_name: Control plasma plus carrier at low concentration


title: D101PC+

source_name: Patient plasma plus carrier at high concentration

value: plasma with carrier at high


title: antmir23b-2_Mouse Lung Epithelial Cells MLE-12_rep2


title: VC6P


title: polyI:C_nasal_epithelium_healthy_subject (142_H07)

city: Amsterdam

first: Ariane

last: Wagener

address: Meibergdreef 9

country: Netherlands

institute: Academic Medical Center

hyb_protocol: According to standard Affymetrix protocol.

data_processing:
Array images were analyzed by Affymetrix Expression Console using the robust multichip analysis (RMA) algorithm. The normalized data were further analysed using R (version 2.9) and the Bioconductor Limma package version 3.14.1. Probesets without a known geneID were excluded for further analyses.
The data was further normalized in R by quantile normalization between the arrays

source_name: isolated and cultured nasal epithelial cells, stimulated with Poly(I:C) for 24 hours

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

growth_protocol: Isolated airway epithelial cells were grown in fully humidified air containing 5% CO2 at 37°C, and culture medium was replaced every other day.

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

treatment_protocol: Cells were cultured to 80% confluence and were pre-incubated with BEBM for 24 hours prior to the the stimulation with BEBM containing 20µg/ml of Poly(I:C) or BEBM alone (controls) for 24 hours. Next, removement of supernatant and RNA extraction.

tag: disease state (condition)

value: healthy

tag: paired samples

value: Male

tag: agent


title: D61PC+

value: plasma with carriet at high


title: baseline_nasal_epithelium_healthy_subject (144_G07)

scan_protocol: According to standard Affymetrix protocol.

source_name: isolated and cultured nasal epithelial cells, not stimulated

value: control


title: baseline_nasal_epithelium_asthma_subject (138_C05)

value: asthma

value: Female


title: baseline_nasal_epithelium_asthma_subject (129_H07)


title: baseline_nasal_epithelium_rhinitis_subject (132_B09)

value: rhinitis


title: polyI:C_nasal_epithelium_rhinitis_subject (130_F09)


title: VC6B

source_name: Control biopsy

value: biopsy


title: D61PC


title: D61P

source_name: Patient plasma


title: D101P


title: D61B

source_name: Patient biopsy


title: baseline_nasal_epithelium_asthma_subject (126_A09)


title: polyI:C_bronchial_epithelium_rhinitis_subject (140_C07)

source_name: isolated and cultured bronchial epithelial cells, stimulated with Poly(I:C) for 24 hours


title: baseline_bronchial_epithelium_rhinitis_subject (139_F05)

source_name: isolated and cultured bronchial epithelial cells, not stimulated


title: C44B


title: D101B


title: polyI:C_nasal_epithelium_asthma_subject (137_G07)


title: VC6PC


title: polyI:C_nasal_epithelium_asthma_subject (124_H07)


title: polyI:C_nasal_epithelium_asthma_subject (128_C05)


title: polyI:C_bronchial_epithelium_healthy_subject (119_E07)


title: polyI:C_nasal_epithelium_rhinitis_subject (104_G07)


title: polyI:C_bronchial_epithelium_healthy_subject (90_F05)


title: polyI:C_bronchial_epithelium_healthy_subject (112_F05)


title: baseline_bronchial_epithelium_healthy_subject (88_A05)


title: baseline_bronchial_epithelium_healthy_subject (120_G05)


title: baseline_nasal_epithelium_healthy_subject (79_A07)


title: polyI:C_bronchial_epithelium_asthma_subject (115_A07)


title: polyI:C_nasal_epithelium_rhinitis_subject (97_A05)


title: baseline_nasal_epithelium_healthy_subject (108_E09)


title: baseline_bronchial_epithelium_asthma_subject (117_H05)


title: baseline_nasal_epithelium_rhinitis_subject (103_B07)


title: polyI:C_nasal_epithelium_healthy_subject (81_B07)


title: baseline_bronchial_epithelium_healthy_subject (114_C05)


title: baseline_nasal_epithelium_rhinitis_subject (98_E07)


title: baseline_nasal_epithelium_healthy_subject (87_E05)


title: baseline_nasal_epithelium_asthma_subject (59_C09)


title: polyI:C_bronchial_epithelium_asthma_subject (69_E05)


title: polyI:C_nasal_epithelium_healthy_subject (61_A05)


title: baseline_bronchial_epithelium_asthma_subject (101_A05)


title: polyI:C_nasal_epithelium_healthy_subject (106_C09)


title: polyI:C_nasal_epithelium_healthy_subject (86_F07)


title: baseline_bronchial_epithelium_asthma_subject (55_H09)


title: polyI:C_bronchial_epithelium_asthma_subject (102_F05)


title: polyI:C_nasal_epithelium_asthma_subject (58_G09)


title: polyI:C_bronchial_epithelium_asthma_subject (57_G05)


title: baseline_bronchial_epithelium_asthma_subject (68_C05)


title: polyI:C_bronchial_epithelium_asthma_subject (47_G09)


title: baseline_nasal_epithelium_asthma_subject (43_B07)


title: baseline_nasal_epithelium_healthy_subject (62_D09)


title: polyI:C_bronchial_epithelium_healthy_subject (50_G05)


title: polyI:C_nasal_epithelium_asthma_subject (44_B05)


title: polyI:C_bronchial_epithelium_rhinitis_subject (36_F07)


title: polyI:C_nasal_epithelium_rhinitis_subject (28_B09)


title: baseline_bronchial_epithelium_healthy_subject (49_G09)


title: baseline_bronchial_epithelium_asthma_subject (48_D05)


title: baseline_bronchial_epithelium_rhinitis_subject (34_E05)


title: baseline_nasal_epithelium_asthma_subject (26_E09)


title: baseline_nasal_epithelium_rhinitis_subject (30_H09)


title: polyI:C_nasal_epithelium_asthma_subject (25_A07)


title: antmir23b-3_Mouse Lung Epithelial Cells MLE-12_rep3

tag: cell line


title: baseline_nasal_epithelium_rhinitis_subject (6_D05)


title: polyI:C_nasal_epithelium_rhinitis_subject (5_D07)


title: polyI:C_bronchial_epithelium_healthy_subject (21_D07)


title: polyI:C_bronchial_epithelium_healthy_subject (3_H05)


title: baseline_bronchial_epithelium_rhinitis_subject (9_H07)


title: polyI:C_bronchial_epithelium_rhinitis_subject (8_E05)


title: baseline_bronchial_epithelium_healthy_subject (20_F05)


title: baseline_bronchial_epithelium_healthy_subject (1_G07)


title: polyI:C_bronchial_epithelium_asthma_subject (24_E07)


title: baseline_bronchial_epithelium_asthma_subject (22_A09)


title: baseline_nasal_epithelium_healthy_subject (13_F09)


title: baseline_bronchial_epithelium_rhinitis_subject (16_D09)


title: polyI:C_nasal_epithelium_healthy_subject (15_A07)


title: deoR_0-2_2

city: Baltimore

first: David

middle: A

last: Rasko

state: MD

address: 801 W. Baltimore Street, Room 619

department: Istitute for Genome Sciences/Microbiology and Immunology

institute: University of Maryland School of Medicine

hyb_protocol: All protocols were done according to manufacturer's specifications: http://www.affymetrix.com/support/technical/manual/expression_manual.affx

data_processing: Data has not been processed other than those protocols within GCOSv1.4

organism: Shigella flexneri 2a str. 2457T

source_name: deoR at OD600=0.2

growth_protocol: bacteria grown in tryptic soy broth

extract_protocol: phenol/chlorofom followed by LiCl precipitation

tag: genotype/variation


title: deoR_1-0_2

scan_protocol: All protocols were done according to manufacturer's specifications: http://www.affymetrix.com/support/technical/manual/expression_manual.affx

source_name: deoR at OD600=1.0


title: deoR_1-0_1

label_protocol: All protocols were done according to manufacturer's specifications: http://www.affymetrix.com/support/technical/manual/expression_manual.affx


title: deoR_0-2_1


title: baseline_bronchial_epithelium_rhinitis_subject (10_B05)


title: deoR_0-5_1

source_name: deoR at OD600=0.5


title: 2457T_0-5_1

value: wild type


title: 2457T_broth

source_name: broth growth

growth_protocol: bacteria grown in LB


title: 2457T_0-2_1


title: polyI:C_bronchial_epithelium_rhinitis_subject (12_D07)


title: deoR_0-5_2


title: 2457T_invasion

source_name: invasion growth

growth_protocol: intracellular bacteria, 3 hours post invasion of HCT-8 cell (colonic epithelial cell line)

extract_protocol: phenol/chlorofom followed by LiCl precipitation. Eukaryotic RNA was removed with MICROBEnrich kit (invitrogen)


title: 2457T_0-5_2


title: 2457T_0-2_2


title: 2457T_1-0_1


title: 2457T_1-0_2


title: polyI:C_bronchial_epithelium_rhinitis_subject (18_H05)


title: PE/CAPJ15, replicate 1

city: Manchester

first: John

middle: S

last: Hall

state: Greater Manchester

address: WMIC, 27 Palatine Road

department: Faculty Institute of Cancer Sciences

country: United Kingdom

institute: The University of Manchester

description: Baseline cell line expression

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Human U133 plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Affymetrix GeneChip scanner 3000 running GCOS software

data_processing: The data were analyzed with Affymetrix Expression Console 1.3.1 using RMA using Affymetrix default analysis settings and global scaling as normalization method.

source_name: Baseline expression of PE/CAPJ15 cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Cell lines were grown in standard conditions (described on the ATCC website).

extract_protocol: Qiagen RNAeasy tissue protocol

treatment_protocol: No treatment (baseline expression)

tag: surviving fraction at 2gy


title: PE/CAPJ34, replicate 1

description: Baseline cell line expression

source_name: Baseline expression of PE/CAPJ34 cells


title: PE/CAPJ49, replicate 1

description: Baseline cell line expression

source_name: Baseline expression of PE/CAPJ49 cells


title: CD34-TGF-β1-LCs biological rep 3

city: Graz

first: Karin

last: Wagner

state: Styria

address: Stiftingtalstrasse 24

department: Molecular Biology

country: Austria

institute: Medical University Graz

hyb_protocol: Affymetrix GeneChip Human Genome U133 Plus 2.0 Array (Cat No. 900470); Affymetrix GeneChip® HT hybridization, Wash and Stain Kit (Cat No. 900720); Affymetrix Genechip®  fluidics station 450: protocol FS450_0001 for Cartridge Arrays

scan_protocol: Affymetrix Scanner: GCS3000; AGCC (Command Console Software  AGCC 3.2)

data_processing:
Affymetrix Geneexpression Console (Expression Console EC1.2.1.20) using Affymetrix default analysis settings for generation of CEL-files.
Data Pre-Processing and Filtering (Partek Software, v.6.6): RMA  (background correction, quantile normalization across all chips in the experiment, log2 transformation, median polish summarization); 2way-Anova
The Series supplementary file additional_processed_data.txt includes the following data: [1] RMA for comparison with external files, [2] RMA for analysis BMP7 and TGFb only and [3] mas5-Signal; no log

source_name: cord blood isolated CD34 cells

label_protocol: Affymetrix GeneChip® 3’ IVT Express Kit (P/N 702646 Rev. ; Cat.No. 901228

growth_protocol: in vitro generated LCs in the presence of  TGF-β1 or BMP-7 from CD34+ cells

extract_protocol: Total RNA was isolated from sorted cells by using RNeasy Micro Kit (QIAGEN) according to the manufacturer recommendations.

treatment_protocol: CD34+ hematopoietic stem cells were isolated from freshly obtained cord blood and cultured in the presence of GM-CSF, SCF, Flt3L, TNFa and either TGF-β1 or BMP-7 for 7 days to get immature LCs.

tag: cell type

value: CD34+ hematopoietic stem cells

tag: treatment

tag: patient

value: C


title: RPMI2650, replicate 1

description: Baseline cell line expression

source_name: Baseline expression of RPMI2650 cells


title: FaDu, replicate 1

description: Baseline cell line expression

source_name: Baseline expression of FaDu cells


title: CD34-BMP-7-LCs biological rep 2

value: B


title: CAL27, replicate 1

description: Baseline cell line expression

source_name: Baseline expression of CAL27 cells


title: SW579, replicate 1

description: Baseline cell line expression

source_name: Baseline expression of SW579 cells


title: CD34-TGF-β1-LCs biological rep 1

value: A


title: Detroit562, replicate 1

description: Baseline cell line expression

source_name: Baseline expression of Detroit562 cells


title: Lung_tumor_AC_stage_2_rep36

city: Neuchatel

first: Sam

last: Ansari

state: Neuchatel

address: Quai Jeanrenaud 5

department: Research & Development

institute: Philip Morris Products SA

hyb_protocol: Ten µg of biotinylated fragmented cRNA were hybridized to Affymetrix GeneChip® HG U133 Plus 2.0 for 16 hours.

scan_protocol: Cartridges were scanned using the GeneChip Scanner 3000 (Affymetrix). Scanned image files were visually inspected for artifacts and the generated Cel files was used as input for data analysis. The Affymetrix Command Console Software (AGCC, Affymetrix, Santa Clara, CA) was used to control the fluidics station and the scanner.

data_processing: Data were normalized using the Mas5 algorithm and made available as test dataset for the participants of the SBV improver Diagnostic Signature Challenge.

source_name: Adenocarcinoma, stage 2

label_protocol: After synthesis of double-stranded cDNA using 100ng total RNA as starting material, biotinylated cRNA was generated and fragmented. The degree of fragmentation and the length distribution of this fragmented biotinylated cRNA was checked by capillary electrophoresis using the Agilent 2100 Bioanalyzer.

extract_protocol: 50-100mg of tissue was lyzed using Trizol and TissueLyser Tissue Disruptor (Qiagen) followed by chloroform extraction. An equal volume of 70% ethanol was added to the aqueous phase and the sample was bound to RNeasy® Mini column (Qiagen 74104). The sample was treated with DNAse while on the column and washed, followed by elution from the column with 0.1mM EDTA.  RNA concentration and quality were assessed using spectrophotometer and Agilent Bio-analyzer, respectively.

treatment_protocol: Frozen Tissue Sample

value: male

tag: age at excision (years)

tag: ethnicity

value: Caucasian

tag: clinical diagnosis patient

value: Car accident with multiple injuries (Status Past), Coma  (as a result of car accident) (Status Past), Adenocarcinoma of the lung (Status New)

tag: bmi

tag: height (cm)

tag: weight (kg)

tag: smoking status

value: Previous Use

tag: smoking duration (years)

tag: smoking dose (cigarettes/day)

tag: excision year

tag: sample recovery type

value: Surgical

value: Lung Tumor

tag: tnm stage

tag: ajcc uicc stage

value: IIB

tag: biosample confirmed diagnosis

value: Non-Small Cell Carcinoma

tag: biosample confirmed sub-diagnosis

value: Adenocarcinoma

tag: clinical diagnosis specimen

value: Adenocarcinoma of the lung

tag: tumor grade

value: Poorly differentiated

tag: rin

tag: sbv challenge gold standard


title: Lung_tumor_SCC_stage_1_rep33

source_name: Squamous Cell Carcinoma, stage 1

tag: gender

tag: age at excision (years)

tag: ethnicity

tag: clinical diagnosis patient

value: Squamous cell carcinoma of the lung (Status New)

value: Current Use

tag: tissue

value: IB

value: Non-small cell carcinoma

value: Squamous cell carcinoma

value: Squamous cell carcinoma of the lung


title: Lung_tumor_AC_stage_1_rep40

source_name: Adenocarcinoma, stage 1

value: male

value: Adenocarcinoma of the lung (Status New)

tag: bmi

tag: height (cm)

tag: weight (kg)

tag: smoking status

tag: smoking duration (years)

value: IA

value: Moderate to poorly differentiated


title: CD34-TGF-β1-LCs biological rep 2

tag: cell type

value: CD34+ hematopoietic stem cells

tag: treatment

tag: patient

value: B


title: Lung_tumor_AC_stage_1_rep41

value: female

value: Asian/Pacific Islander

value: Diabetes (Status Ongoing), High blood pressure (Status Ongoing), Bronchiolo-alveolar adenocarcinoma of the lung (Status New)

value: Never Used

tag: smoking dose (cigarettes/day)

tag: excision year

tag: sample recovery type

value: Surgical

value: Lung Tumor

tag: tnm stage

tag: ajcc uicc stage

tag: clinical diagnosis specimen


title: Lung_tumor_AC_stage_1_rep39

tag: gender

tag: age at excision (years)

tag: ethnicity

value: Caucasian

tag: biosample confirmed diagnosis

value: Non-Small Cell Carcinoma

tag: biosample confirmed sub-diagnosis

value: Adenocarcinoma

value: Adenocarcinoma of the lung

tag: tumor grade

value: Well to moderately differentiated

tag: rin

tag: sbv challenge gold standard


title: OE21, replicate 1

description: Baseline cell line expression

source_name: Baseline expression of OE21 cells

tag: surviving fraction at 2gy


title: Lung_tumor_SCC_stage_1_rep34

value: male

tag: clinical diagnosis patient

value: Squamous cell carcinoma of the lung (Status New)

tag: bmi

tag: height (cm)

tag: weight (kg)

tag: smoking status

tag: smoking duration (years)

tag: tissue

value: IB

value: Squamous Cell Carcinoma

value: Squamous cell carcinoma of the lung

value: Moderately differentiated


title: PE/CAPJ41, replicate 1

description: Baseline cell line expression

source_name: Baseline expression of PE/CAPJ41 cells


title: CD34-BMP-7-LCs biological rep 1

tag: cell type

value: CD34+ hematopoietic stem cells

tag: treatment

tag: patient

value: A


title: Lung_tumor_SCC_stage_2_rep39

source_name: Squamous Cell Carcinoma, stage 2

tag: gender

tag: age at excision (years)

tag: ethnicity

value: Squamous cell carcinoma, keratinizing of the lung (Status New)

value: Current Use

tag: smoking dose (cigarettes/day)

tag: excision year

tag: sample recovery type

value: Bronchus Tumor

tag: tnm stage

tag: ajcc uicc stage

value: IIA

tag: clinical diagnosis specimen


title: CD34-BMP-7-LCs biological rep 3

value: C


title: Lung_tumor_AC_stage_2_rep33

value: Caucasian

tag: clinical diagnosis patient

value: Ischemic heart disease (Status Ongoing), Hypertension (Status Ongoing), Colorectal cancer (Status ), Adenocarcinoma of the lung (Status New)

tag: bmi

tag: height (cm)

value: Surgical

value: Lung Tumor

tag: biosample confirmed diagnosis

value: Non-small cell carcinoma

tag: biosample confirmed sub-diagnosis

tag: tumor grade

value: Moderate to poorly differentiated

tag: rin

tag: sbv challenge gold standard


title: Lung_tumor_AC_stage_2_rep32

tag: gender

value: female

value: Chronic pancreatitis  (Status Ongoing), Adenocarcinoma of the lung (Status New)

tag: weight (kg)

tag: smoking status

value: Never Used

tag: smoking duration (years)

tag: tissue

value: Non-small Cell Carcinoma

value: Adenocarcinoma

value: Adenocarcinoma of the lung

value: Well to moderately differentiated


title: Lung_tumor_AC_stage_1_rep38

value: male

tag: age at excision (years)

tag: ethnicity

value: Adenocarcinoma of the lung (Status New)

tag: smoking dose (cigarettes/day)

tag: excision year

tag: sample recovery type

value: IA


title: Lung_tumor_AC_stage_2_rep34

tag: clinical diagnosis patient

tag: bmi

value: Current Use

tag: tnm stage

tag: ajcc uicc stage

value: IIB

tag: clinical diagnosis specimen


title: Lung_tumor_AC_stage_2_rep35

value: Caucasian

value: Chronic bronchitis (Status Ongoing), Adenocarcinoma of the lung (Status New)

tag: height (cm)

value: Occasional Use

tag: biosample confirmed diagnosis

tag: biosample confirmed sub-diagnosis

tag: tumor grade

value: Moderately differentiated

tag: rin


title: KYSE30, replicate 1

description: Baseline cell line expression

source_name: Baseline expression of KYSE30 cells

tag: surviving fraction at 2gy


title: Lung_tumor_SCC_stage_1_rep31

tag: gender

value: Simple chronic bronchitis   (Status Ongoing), Unspecified gastritis and gastroduodenitis  (Status Ongoing), Duodenal ulcer  (Status Past), Squamous cell carcinoma of the lung (Status New)

tag: weight (kg)

tag: smoking status

tag: smoking duration (years)

value: Surgical

tag: tissue

value: Lung Tumor

value: IB

value: Non-Small Cell Carcinoma

value: Squamous Cell Carcinoma

value: Squamous cell carcinoma of the lung

value: Poorly differentiated

tag: sbv challenge gold standard


title: Lung_tumor_AC_stage_1_rep37

value: female

tag: age at excision (years)

tag: ethnicity

value: Asian/Pacific Islander

tag: clinical diagnosis patient

value: Never Used

tag: smoking dose (cigarettes/day)

tag: excision year

tag: sample recovery type

value: Adenocarcinoma of the lung


title: Lung_tumor_SCC_stage_2_rep38

value: male

value: Squamous cell carcinoma of the lung (Status New)

tag: bmi

tag: height (cm)

value: Current Use

tag: tnm stage

tag: ajcc uicc stage

value: IIA

tag: biosample confirmed diagnosis

value: Non-small cell carcinoma

value: Squamous cell carcinoma

tag: clinical diagnosis specimen


title: Lung_tumor_AC_stage_2_rep31

value: Adenocarcinoma of the lung (Status New)

tag: weight (kg)

value: Surgical

value: Lung Diseased

value: IIB

tag: rin


title: Lung_tumor_SCC_stage_1_rep32

tag: gender

value: Caucasian

value: Chronic bronchitis (Status Ongoing), Squamous cell carcinoma of the lung (Status New)

tag: smoking status

tag: smoking duration (years)

value: Lung Tumor

value: IB

value: Squamous Cell Carcinoma

tag: tumor grade

value: Moderately differentiated


title: Lung_tumor_AC_stage_2_rep30

value: female

tag: age at excision (years)

tag: ethnicity

value: Adenocarcinoma of lung (Status New)

value: Never Used

tag: tissue

value: Adenocarcinoma of lung

tag: sbv challenge gold standard


title: Lung_tumor_AC_stage_1_rep36

tag: clinical diagnosis patient

tag: smoking dose (cigarettes/day)

tag: excision year

tag: sample recovery type

value: IA

tag: biosample confirmed sub-diagnosis

value: Adenocarcinoma

value: Adenocarcinoma of the lung

value: Moderate to poorly differentiated


title: Lung_tumor_SCC_stage_2_rep31

value: male

value: Acute duodenal ulcer (Status Past), Acute gastritis with hemorrhage (Status Past), Squamous cell carcinoma of the lung (Status New)

tag: bmi

tag: height (cm)

value: Current Use

value: Surgical

tag: tnm stage

tag: ajcc uicc stage

value: Squamous cell carcinoma of the lung


title: Lung_tumor_AC_stage_2_rep29

tag: gender

value: Caucasian

value: Adenocarcinoma of the lung (Status New)

tag: weight (kg)

value: Lung Normal

value: IIA

tag: clinical diagnosis specimen

tag: rin


title: Lung_tumor_SCC_stage_1_rep30

tag: age at excision (years)

value: Duodenal ulcer (Status Past), Squamous cell carcinoma of the lung (Status New)

tag: smoking status

tag: smoking duration (years)

value: Lung Tumor

value: IB


title: Lung_tumor_SCC_stage_2_rep36

tag: ethnicity

value: Squamous cell carcinoma, keratinizing of the lung (Status New)

tag: tissue

value: Bronchus Tumor

value: IIB

tag: sbv challenge gold standard


title: Lung_tumor_AC_stage_1_rep35

value: Asian/Pacific Islander

tag: clinical diagnosis patient

tag: smoking dose (cigarettes/day)

tag: excision year

value: IA

tag: biosample confirmed diagnosis

value: Non-Small Cell Carcinoma

value: Adenocarcinoma

value: Adenocarcinoma of the lung

tag: tumor grade

value: Moderately differentiated


title: Lung_tumor_SCC_stage_2_rep33

value: male

tag: bmi

tag: height (cm)

value: Current Use

tag: sample recovery type

value: Surgical

tag: tnm stage

value: Squamous cell carcinoma, keratinizing of the lung


title: Lung_tumor_SCC_stage_2_rep35

tag: gender

value: Caucasian

value: Hypertension (Status Ongoing), Squamous cell carcinoma, keratinizing of the lung (Status New)

tag: weight (kg)

tag: ajcc uicc stage

value: Squamous cell carcinoma

tag: biosample confirmed sub-diagnosis

value: Acute leukemia

tag: clinical diagnosis specimen


title: Lung_tumor_SCC_stage_1_rep28

tag: age at excision (years)

tag: ethnicity

value: Squamous cell carcinoma of the lung (Status New)

tag: smoking status

tag: smoking duration (years)

value: Lung Tumor

value: Squamous Cell Carcinoma

value: Squamous cell carcinoma of the lung

value: Moderate to poorly differentiated

tag: rin


title: Lung_tumor_SCC_stage_2_rep32

tag: clinical diagnosis patient

tag: smoking dose (cigarettes/day)

tag: excision year

tag: tissue

value: IIA

tag: sbv challenge gold standard


title: Lung_tumor_AC_stage_2_rep28

value: female

value: Adenocarcinoma of the lung (Status New)

tag: bmi

tag: height (cm)

tag: sample recovery type

tag: biosample confirmed diagnosis

value: Non-small cell carcinoma

value: Adenocarcinoma

tag: tumor grade

value: Well to moderately differentiated


title: Lung_tumor_AC_stage_1_rep34

tag: gender

value: male

tag: weight (kg)

value: Previous Use

value: Surgical

tag: tnm stage

tag: ajcc uicc stage

value: IB

value: Non-Small Cell Carcinoma

tag: biosample confirmed sub-diagnosis

value: Adenocarcinoma of the lung

value: Moderately differentiated


title: Lung_tumor_SCC_stage_2_rep30

tag: age at excision (years)

tag: ethnicity

value: Caucasian

value: Arthritis (Status Past), Squamous cell carcinoma, keratinizing of the lung (Status New)

tag: smoking status

tag: smoking duration (years)

value: Bronchus Tumor

value: IIB

value: Squamous Cell Carcinoma, Keratinizing

tag: clinical diagnosis specimen


title: Lung_tumor_SCC_stage_1_rep26

tag: clinical diagnosis patient

value: Bronchitis (Status Ongoing), Ischemic cardiomyopathy (Status Ongoing), Squamous cell carcinoma of the upper lobe of right lung (Status New)

value: Current Use

tag: smoking dose (cigarettes/day)

tag: excision year

tag: tissue

value: Lung Tumor

value: Squamous cell carcinoma

value: Moderate to poorly differentiated

tag: rin


title: Lung_tumor_AC_stage_2_rep23

value: male

value: White

value: Adenocarcinoma of the lung (Status New)

tag: bmi

tag: height (cm)

tag: sample recovery type

value: IIA

tag: biosample confirmed diagnosis

value: Non-small cell carcinoma

value: Adenocarcinoma

tag: sbv challenge gold standard


title: Lung_tumor_AC_stage_1_rep31

tag: gender

tag: weight (kg)

value: Surgical

tag: tnm stage

tag: ajcc uicc stage

value: IB

value: Adenocarcinoma of the lung

tag: tumor grade

value: Moderately differentiated


title: Lung_tumor_AC_stage_1_rep33

tag: age at excision (years)

tag: ethnicity

value: Caucasian

value: Large cell carcinoma of the lung (Status New)

tag: smoking status

tag: smoking duration (years)

value: Non-Small Cell Carcinoma

tag: biosample confirmed sub-diagnosis

value: Large cell carcinoma of the lung

value: Poorly differentiated


title: Lung_tumor_SCC_stage_1_rep25

tag: clinical diagnosis patient

value: Squamous cell carcinoma of the lung (Status New)

value: Never Used

tag: smoking dose (cigarettes/day)

tag: excision year

tag: tissue

value: Lung Tumor

value: Squamous cell carcinoma

tag: clinical diagnosis specimen

value: Squamous cell carcinoma of the lung


title: Lung_tumor_AC_stage_2_rep27

value: male

value: Essential hypertension  (Status Ongoing), Adenocarcinoma of the lung (Status New)

tag: bmi

tag: height (cm)

tag: sample recovery type

value: IIA

tag: biosample confirmed diagnosis

value: Well to moderately differentiated

tag: rin


title: Lung_tumor_AC_stage_1_rep32

tag: gender

value: female

value: Adenocarcinoma of the lung (Status New)

tag: weight (kg)

value: Surgical

tag: tnm stage

tag: ajcc uicc stage

value: IB

value: Non-small cell carcinoma

value: Adenocarcinoma

tag: sbv challenge gold standard


title: Lung_tumor_AC_stage_2_rep26

tag: age at excision (years)

tag: ethnicity

value: Caucasian

value: Obesity (Status Ongoing), Adenocarcinoma of the lung (Status New)

tag: smoking status

tag: smoking duration (years)

value: Adenocarcinoma of the lung

tag: tumor grade


title: Lung_tumor_SCC_stage_2_rep37

tag: clinical diagnosis patient

value: Chronic obstructive pulmonary disease (Status Ongoing), Squamous cell carcinoma of the lung (Status New)

value: Current Use

tag: smoking dose (cigarettes/day)

tag: excision year

tag: tissue

tag: biosample confirmed sub-diagnosis

value: Moderate to poorly differentiated


title: Lung_tumor_SCC_stage_1_rep24

value: Chronic bronchitis (Status Ongoing), Gastritis (Status Ongoing), Squamous cell carcinoma of the lung (Status New)

tag: bmi

tag: height (cm)

tag: sample recovery type

value: Lung Tumor

value: IA

tag: biosample confirmed diagnosis

value: Squamous cell carcinoma, keratinizing

tag: clinical diagnosis specimen

value: Squamous cell carcinoma of the lung

value: Moderately differentiated


title: Lung_tumor_SCC_stage_2_rep29

tag: gender

value: male

value: White

value: Squamous cell carcinoma, keratinizing of the lung (Status New)

tag: weight (kg)

tag: tnm stage

tag: ajcc uicc stage

value: IIA

tag: rin


title: Lung_tumor_SCC_stage_2_rep34

tag: age at excision (years)

tag: ethnicity

value: Arterial hypertension (Status Ongoing), Squamous cell carcinoma, keratinizing of the lung (Status New)

tag: smoking status

tag: smoking duration (years)

value: Surgical

value: Non-small cell carcinoma

value: Squamous cell carcinoma

tag: sbv challenge gold standard


title: Lung_tumor_SCC_stage_1_rep27

value: Caucasian

tag: clinical diagnosis patient

value: Alkylosing spondylitis (Status Ongoing), Squamous cell carcinoma of the lung (Status Ongoing)

tag: smoking dose (cigarettes/day)

tag: excision year

tag: tissue

value: IB

tag: tumor grade


title: Lung_tumor_AC_stage_2_rep24

value: Adenocarcinoma of the lung (Status New)

tag: bmi

tag: height (cm)

value: Current Use

tag: sample recovery type

tag: biosample confirmed diagnosis

tag: biosample confirmed sub-diagnosis

value: Adenocarcinoma

value: Adenocarcinoma of the lung

value: Poorly differentiated


title: Lung_tumor_SCC_stage_1_rep29

tag: gender

value: Cancer of the lung (Status New), Hypertension (Status Ongoing), Nocardia pnemonia (Status Past), Chronic obstructive pulmonary disease (Status Ongoing), Squamous cell carcinoma of the lung (Status New)

tag: weight (kg)

value: Lung Tumor

tag: tnm stage

tag: ajcc uicc stage

value: Non-Small Cell Carcinoma

value: Squamous Cell Carcinoma

tag: clinical diagnosis specimen

value: Squamous cell carcinoma of the lung


title: Lung_tumor_AC_stage_2_rep25

value: male

tag: age at excision (years)

tag: ethnicity

value: Arterial hypertension (Status Ongoing), Adenocarcinoma of the lung (Status New)

tag: smoking status

value: Never Used

tag: smoking duration (years)

value: IIB

value: Moderately differentiated

tag: rin


title: Lung_tumor_AC_stage_1_rep30

value: female

value: Caucasian

tag: clinical diagnosis patient

tag: smoking dose (cigarettes/day)

tag: excision year

value: Surgical

tag: tissue

value: IA

value: Non-small cell carcinoma

tag: sbv challenge gold standard


title: Lung_tumor_AC_stage_2_rep22

value: Adenocarcinoma of the lung (Status New)

tag: bmi

tag: height (cm)

value: Current Use

tag: sample recovery type

tag: biosample confirmed diagnosis

value: Adenocarcinoma

value: Adenocarcinoma of the lung

tag: tumor grade


title: Lung_tumor_SCC_stage_1_rep21

tag: gender

value: Squamous cell carcinoma of the lung (Status New)

tag: weight (kg)

value: Lung Tumor

tag: tnm stage

tag: ajcc uicc stage

tag: biosample confirmed sub-diagnosis

value: Squamous cell carcinoma

value: Moderate to poorly differentiated


title: Lung_tumor_SCC_stage_2_rep28

value: male

tag: age at excision (years)

tag: ethnicity

value: Essential hypertension (Status Ongoing), Chronic bronchitis (Status Ongoing), Squamous cell carcinoma of the lung (Status New)

tag: smoking status

tag: smoking duration (years)

value: Squamous Cell Carcinoma

tag: clinical diagnosis specimen

value: Squamous cell carcinoma of the lung

value: Poorly differentiated


title: Lung_tumor_SCC_stage_1_rep23

value: female

value: Caucasian

tag: clinical diagnosis patient

tag: smoking dose (cigarettes/day)

tag: excision year

tag: tissue

value: IB

tag: rin


title: Lung_tumor_AC_stage_1_rep29

value: White

value: Bronchiolo-alveolar adenocarcinoma of the lung (Status New)

tag: bmi

tag: height (cm)

tag: sample recovery type

value: Surgical

tag: biosample confirmed diagnosis

value: Bronchiolo-alveolar adenocarcinoma

tag: sbv challenge gold standard


title: Lung_tumor_SCC_stage_2_rep26

tag: gender

value: Squamous cell carcinoma, large cell, non-keratinizing of the lung (Status New)

tag: weight (kg)

value: Never Used

tag: tnm stage

tag: ajcc uicc stage

value: IIB


title: Lung_tumor_AC_stage_2_rep20

tag: age at excision (years)

tag: ethnicity

value: Cancer of the bladder (Status Past), Adenocarcinoma of the lung (Status New)

tag: smoking status

value: Current Use

value: Lung Tumor

value: IIA

value: Adenocarcinoma

value: Adenocarcinoma of the lung

tag: tumor grade

value: Well to moderately differentiated


title: Lung_tumor_AC_stage_1_rep27

value: male

tag: clinical diagnosis patient

value: Angina (Status Ongoing), Arteriopathy (Status Ongoing), Adenocarcinoma of the lung (Status New)

tag: smoking duration (years)

tag: smoking dose (cigarettes/day)

tag: clinical diagnosis specimen


title: Lung_tumor_SCC_stage_1_rep20

value: Caucasian

value: Duodenal ulcer  (Status Past), Essential hypertension (Status Ongoing), Squamous cell carcinoma of the lung (Status New)

tag: bmi

tag: excision year

tag: tissue

value: IB

value: Non-Small Cell Carcinoma

tag: biosample confirmed sub-diagnosis

value: Squamous cell carcinoma

value: Squamous cell carcinoma of the lung

tag: rin


title: Lung_tumor_SCC_stage_1_rep19

tag: gender

value: Essential hypertension (Status Ongoing), Squamous cell carcinoma, keratinizing of the lung (Status New)

tag: height (cm)

value: Occasional Use

tag: sample recovery type

value: Surgical

value: IA

tag: biosample confirmed diagnosis

value: Non-small cell carcinoma

value: Squamous cell carcinoma, keratinizing

tag: sbv challenge gold standard


title: Lung_tumor_AC_stage_1_rep26

tag: age at excision (years)

tag: ethnicity

value: Hypertension (Status Ongoing), Chronic bronchitis (Status Ongoing), Bronchiolo-alveolar adenocarcinoma of the lung (Status New)

tag: weight (kg)

value: Current Use

value: Lung Tumor

tag: tnm stage

tag: ajcc uicc stage

value: Bronchiolo-alveolar adenocarcinoma

value: Well differentiated


title: Lung_tumor_AC_stage_2_rep19

value: male

value: Caucasian

tag: clinical diagnosis patient

value: Alcoholism (Status Ongoing), Large cell carcinoma of the lung (Status New)

tag: smoking status

tag: smoking duration (years)

tag: smoking dose (cigarettes/day)

value: IIB

value: Adenocarcinoma

value: Large cell carcinoma of the lung

tag: tumor grade

value: Moderate to poorly differentiated


title: Lung_tumor_AC_stage_2_rep18

value: Unspecified gastritis and gastroduodenitis (Status Ongoing), Adenocarcinoma of the lung (Status New)

tag: bmi

tag: excision year

tag: tissue

tag: clinical diagnosis specimen

value: Adenocarcinoma of the lung


title: Lung_tumor_AC_stage_2_rep21

tag: gender

value: female

value: Adenocarcinoma of the lung (Status New)

tag: height (cm)

value: Never Used

tag: sample recovery type

value: Surgical

tag: rin


title: Lung_tumor_SCC_stage_2_rep27

tag: age at excision (years)

tag: ethnicity

value: Arterial hypertension (Status Ongoing), Squamous cell carcinoma of the lung (Status New)

value: IIA

tag: biosample confirmed diagnosis

value: Non-small cell carcinoma

tag: biosample confirmed sub-diagnosis

value: Squamous cell carcinoma

value: Squamous cell carcinoma of the lung

tag: sbv challenge gold standard


title: Lung_tumor_SCC_stage_1_rep22

value: male

value: Caucasian

tag: clinical diagnosis patient

value: Chronic bronchitis (Status Ongoing), Squamous cell carcinoma, keratinizing of the lung (Status New)

tag: weight (kg)

tag: smoking status

value: Current Use

value: Lung Tumor

tag: tnm stage

tag: ajcc uicc stage

value: IB

value: Moderately differentiated


title: Lung_tumor_SCC_stage_1_rep18

value: Coronary atherosclerosis     (Status Ongoing), Simple chronic bronchitis (Status Ongoing), Squamous cell carcinoma  of the lung (Status New)

tag: bmi

value: Occasional Use

tag: smoking duration (years)

tag: smoking dose (cigarettes/day)

tag: excision year

value: Non-Small Cell Carcinoma

value: Squamous Cell Carcinoma

value: Squamous cell carcinoma  of the lung

tag: tumor grade

value: Moderate to poorly differentiated


title: Lung_tumor_SCC_stage_2_rep24

tag: gender

value: female

value: Chronic obstructive pulmonary disease (Status Ongoing), Hypertension (Status Ongoing), Squamous cell carcinoma of the lung (Status New)

tag: height (cm)

tag: sample recovery type

value: Surgical

tag: tissue

value: IIB

tag: clinical diagnosis specimen


title: Lung_tumor_AC_stage_2_rep17

value: male

tag: age at excision (years)

tag: ethnicity

value: Pneumonia (Status New), Adenocarcinoma of lung (Status New)

value: Adenocarcinoma of lung

tag: rin


title: Lung_tumor_AC_stage_1_rep28

tag: clinical diagnosis patient

value: Adenocarcinoma of the lung (Status New)

tag: weight (kg)

value: Lung Diseased

value: Adenocarcinoma of the lung

tag: sbv challenge gold standard


title: Lung_tumor_SCC_stage_2_rep25

value: Caucasian

value: Essential hypertension (Status Ongoing), Squamous cell carcinoma, keratinizing of the skin (Status New)

tag: smoking status

value: Previous Use

value: Lung Tumor

tag: tnm stage

tag: ajcc uicc stage

value: II


title: Lung_tumor_AC_stage_1_rep22

tag: bmi

value: Current Use

tag: smoking duration (years)

tag: smoking dose (cigarettes/day)

value: IB

tag: biosample confirmed diagnosis

value: Non-small cell carcinoma

tag: biosample confirmed sub-diagnosis

value: Adenocarcinoma

value: Moderately differentiated


title: Lung_tumor_AC_stage_1_rep23

tag: gender

value: female

value: Bronchiolo-alveolar adenocarcinoma of the lung (Status New)

tag: height (cm)

value: Never Used

tag: excision year

tag: sample recovery type

value: Surgical

value: Non-Small Cell Carcinoma

tag: tumor grade


title: Lung_tumor_SCC_stage_2_rep22

value: male

tag: age at excision (years)

tag: ethnicity

value: Squamous cell carcinoma of the lung (Status New)

tag: tissue

value: IIA

value: Squamous cell carcinoma

tag: clinical diagnosis specimen

value: Squamous cell carcinoma of the lung

tag: rin


title: Lung_tumor_SCC_stage_2_rep23

value: Caucasian

tag: clinical diagnosis patient

value: Hypertension (Status Ongoing), Squamous cell carcinoma of the lung (Status New)

tag: weight (kg)

tag: smoking status

value: Occasional Use

value: Lung Tumor

tag: tnm stage

tag: sbv challenge gold standard


title: Lung_tumor_SCC_stage_1_rep17

value: Simple chronic bronchitis (Status Ongoing), Squamous cell carcinoma of the lung (Status New)

tag: bmi

value: Current Use

tag: smoking duration (years)

tag: smoking dose (cigarettes/day)

tag: ajcc uicc stage

value: IB

tag: biosample confirmed diagnosis

value: Squamous Cell Carcinoma

value: Moderate to poorly differentiated


title: Lung_tumor_AC_stage_1_rep24

tag: gender

value: female

value: Simple chronic bronchitis  (Status Ongoing), Adenocarcinoma of the lung (Status New)

tag: height (cm)

value: Never Used

tag: excision year

tag: sample recovery type

value: IA

value: Adenocarcinoma

value: Adenocarcinoma of the lung

value: Well to moderately differentiated


title: Lung_tumor_AC_stage_2_rep16

value: male

tag: age at excision (years)

tag: ethnicity

value: Simple chronic bronchitis   (Status Ongoing), Alveolar adenocarcinoma of the lung (Status New)

value: Surgical

tag: tissue

value: IIA

value: Non-small cell carcinoma

tag: biosample confirmed sub-diagnosis

value: Alveolar adenocarcinoma of the lung

tag: tumor grade


title: Lung_tumor_AC_stage_1_rep25

value: White

tag: clinical diagnosis patient

value: Adenocarcinoma of the lung (Status New)

tag: weight (kg)

tag: smoking status

value: Current Use

value: Lung Tumor

value: Mucinous adenocarcinoma

tag: clinical diagnosis specimen

tag: rin


title: Lung_tumor_AC_stage_1_rep20

value: Caucasian

value: Hypertension (Status Ongoing), Chronic bronchitis (Status Ongoing), Adenocarcinoma of the lung (Status New)

tag: bmi

tag: smoking duration (years)

tag: smoking dose (cigarettes/day)

tag: tnm stage

value: IB

value: Non-Small Cell Carcinoma

tag: sbv challenge gold standard


title: Lung_tumor_SCC_stage_1_rep16

tag: gender

value: Ischemic and dismethabolic cardiopathy (Status Ongoing), Carcinoma of the lung (Status New)

tag: height (cm)

tag: excision year

tag: ajcc uicc stage

tag: biosample confirmed diagnosis

value: Squamous Cell Carcinoma

value: Carcinoma of the lung


title: Lung_tumor_SCC_stage_2_rep20

value: male

tag: age at excision (years)

tag: ethnicity

value: Squamous cell carcinoma of the lung (Status New)

tag: sample recovery type

tag: tissue

value: IIB

tag: biosample confirmed sub-diagnosis

value: Squamous cell carcinoma of the lung

value: Moderately differentiated


title: Lung_tumor_SCC_stage_2_rep21

tag: clinical diagnosis patient

tag: weight (kg)

tag: smoking status

value: Surgical

value: IIA

value: Non-small cell carcinoma

value: Squamous cell carcinoma

tag: clinical diagnosis specimen

tag: tumor grade

value: Poorly differentiated


title: Lung_tumor_AC_stage_2_rep13

value: Caucasian

value: Adenocarcinoma of the lung (Status New)

tag: bmi

value: Previous Use

tag: smoking duration (years)

tag: smoking dose (cigarettes/day)

value: Lung Tumor

tag: tnm stage

value: Adenocarcinoma

value: Adenocarcinoma of the lung

tag: rin


title: Lung_tumor_AC_stage_1_rep14

tag: gender

tag: height (cm)

value: Current Use

tag: excision year

tag: ajcc uicc stage

value: IB

value: Moderate to poorly differentiated

tag: sbv challenge gold standard


title: Lung_tumor_SCC_stage_1_rep12

value: male

tag: age at excision (years)

tag: ethnicity

value: Squamous cell carcinoma of the lung (Status New)

value: Occasional Use

tag: sample recovery type

tag: tissue

tag: biosample confirmed diagnosis


title: Lung_tumor_AC_stage_1_rep19

tag: clinical diagnosis patient

tag: weight (kg)

tag: smoking status

value: Surgical

tag: biosample confirmed sub-diagnosis

tag: clinical diagnosis specimen


title: Lung_tumor_AC_stage_1_rep21

value: Hypertension (Status Ongoing), Chronic bronchitis (Status Ongoing), Adenocarcinoma of the lung (Status New)

tag: bmi

tag: smoking duration (years)

tag: smoking dose (cigarettes/day)

tag: tnm stage

tag: tumor grade


title: Lung_tumor_SCC_stage_2_rep19

tag: gender

value: Squamous cell carcinoma, keratinizing of the lung (Status New)

tag: height (cm)

tag: excision year

tag: ajcc uicc stage

value: IIB

tag: rin


title: Lung_tumor_SCC_stage_2_rep16

tag: age at excision (years)

tag: ethnicity

tag: sample recovery type

tag: tissue

value: Squamous cell carcinoma, keratinizing of the lung

tag: sbv challenge gold standard


title: Lung_tumor_SCC_stage_2_rep18

value: Caucasian

tag: clinical diagnosis patient

value: Diabetes  (Status Ongoing), Squamous cell carcinoma of the lung (Status New)

tag: weight (kg)

tag: smoking status

tag: biosample confirmed diagnosis

value: Non-small cell carcinoma

tag: biosample confirmed sub-diagnosis

value: Squamous cell carcinoma

value: Squamous cell carcinoma of the lung


title: Lung_tumor_AC_stage_1_rep13

value: Adenocarcinoma of the lung (Status New)

tag: bmi

tag: smoking duration (years)

tag: smoking dose (cigarettes/day)

value: Lung Tumor

tag: tnm stage

value: Adenocarcinoma

tag: clinical diagnosis specimen

value: Adenocarcinoma of the lung

value: Moderately differentiated


title: Lung_tumor_AC_stage_2_rep11

tag: gender

value: female

tag: height (cm)

value: Never Used

tag: excision year

tag: ajcc uicc stage

value: IIA

tag: tumor grade


title: Lung_tumor_AC_stage_2_rep12

value: male

tag: age at excision (years)

tag: ethnicity

value: Previous Use

tag: sample recovery type

value: Surgical

tag: tissue

tag: rin


title: Lung_tumor_SCC_stage_1_rep15

tag: clinical diagnosis patient

value: Squamous cell carcinoma of the lung (Status New)

tag: weight (kg)

tag: smoking status

value: Current Use

value: IB

tag: biosample confirmed diagnosis

value: Squamous cell carcinoma, keratinizing

tag: sbv challenge gold standard


title: Lung_tumor_AC_stage_1_rep18

value: Caucasian

tag: bmi

tag: smoking duration (years)

tag: smoking dose (cigarettes/day)

tag: tnm stage

value: IA

value: Non-small cell carcinoma

tag: biosample confirmed sub-diagnosis

value: Moderate to poorly differentiated


title: Lung_tumor_AC_stage_1_rep17

tag: gender

value: Adenocarcinoma of the lung (Status New)

tag: height (cm)

tag: excision year

value: Lung Tumor

tag: ajcc uicc stage

tag: clinical diagnosis specimen


title: Lung_tumor_SCC_stage_2_rep17

tag: age at excision (years)

tag: ethnicity

value: Malignant neoplasm of the lung (Status New)

tag: sample recovery type

tag: tissue

value: IIB

value: Malignant neoplasm of the lung

tag: tumor grade


title: Lung_tumor_SCC_stage_1_rep13

tag: clinical diagnosis patient

value: Arterial hypertension (Status Ongoing), Squamous cell carcinoma, keratinizing of the lung (Status New)

tag: weight (kg)

tag: smoking status

tag: biosample confirmed diagnosis

value: Non-Small Cell Carcinoma

value: Squamous Cell Carcinoma

value: Poorly differentiated

tag: rin


title: Lung_tumor_AC_stage_2_rep9

value: male

value: Hypertension (Status Ongoing), Diabetes (Status Ongoing), Adenocarcinoma of the lung (Status New)

tag: bmi

value: Previous Use

tag: smoking dose (cigarettes/day)

value: Surgical

tag: tnm stage

value: Adenocarcinoma

value: Adenocarcinoma of the lung

tag: sbv challenge gold standard


title: Lung_tumor_AC_stage_1_rep15

tag: gender

value: female

value: Caucasian

value: Appendicitis with appendectomy (Status Past), Viral hepatitis a (Status Past), Gastric ulcer (Status Recurrent), Thyroidectomy (Status Past), Adenocarcinoma of the lung (Status New)

tag: height (cm)

value: Never Used

tag: smoking duration (years)

tag: excision year

value: IB


title: Lung_tumor_AC_stage_2_rep14

tag: age at excision (years)

tag: ethnicity

value: Cancer of the lung (Status New), Gastroesophageal reflux disease (Status Ongoing), Hypertension (Status Ongoing), Laparotomy for liver injury (Status Past), Hemorrhoids (Status Past), Adenocarcinoma of the lung (Status New)

value: Lung Tumor

tag: ajcc uicc stage

value: IIA

tag: clinical diagnosis specimen

value: Moderately differentiated


title: Lung_tumor_AC_stage_1_rep16

tag: clinical diagnosis patient

value: Adenocarcinoma of the lung (Status New)

value: Current Use

tag: sample recovery type

tag: tissue

value: Non-Small Cell Carcinoma

tag: biosample confirmed sub-diagnosis

tag: tumor grade


title: Lung_tumor_SCC_stage_1_rep14

value: male

value: Squamous cell carcinoma of the lung (Status New)

tag: bmi

tag: weight (kg)

tag: smoking status

value: IA

tag: biosample confirmed diagnosis

value: Non-small cell carcinoma

value: Squamous cell carcinoma

value: Squamous cell carcinoma of the lung

tag: rin


title: Lung_tumor_AC_stage_2_rep10

tag: gender

value: Caucasian

value: Hypertension (Status Ongoing), Gastritis (Status Ongoing), Adenocarcinoma of the lung (Status New)

tag: height (cm)

tag: smoking dose (cigarettes/day)

value: Surgical

tag: tnm stage

value: Adenocarcinoma

value: Adenocarcinoma of the lung

value: Moderate to poorly differentiated

tag: sbv challenge gold standard


title: Lung_tumor_SCC_stage_1_rep10

tag: age at excision (years)

tag: ethnicity

value: Arterial hypertension (Status Ongoing), Squamous cell carcinoma, keratinizing of the lung (Status New)

tag: smoking duration (years)

tag: excision year

value: Lung Tumor

tag: ajcc uicc stage

value: IB

value: Squamous cell carcinoma, keratinizing

value: Well to moderately differentiated


title: Lung_tumor_SCC_stage_1_rep11

value: male

tag: clinical diagnosis patient

value: Coronary atherosclerosis    (Status Ongoing), Essential hypertension (Status Ongoing), Malignant neoplasm of lip (Status Past), Squamous cell carcinoma  of the lung (Status New)

value: Current Use

tag: sample recovery type

tag: tissue

value: Non-Small Cell Carcinoma

tag: biosample confirmed sub-diagnosis

value: Squamous Cell Carcinoma

tag: clinical diagnosis specimen

value: Squamous cell carcinoma  of the lung

value: Moderately differentiated


title: Lung_tumor_AC_stage_2_rep8

value: Caucasian

value: Chronic bronchitis (Status Ongoing), Adenocarcinoma of the lung (Status New)

tag: bmi

tag: weight (kg)

tag: smoking status

value: IIA

tag: biosample confirmed diagnosis

value: Non-small cell carcinoma


title: Lung_tumor_SCC_stage_2_rep15

tag: gender

value: female

value: Appendicitis with appendectomy (Status Past), Tonsillitis with tonsillectomy (Status Past), Squamous cell carcinoma of the lung (Status New)

tag: height (cm)

value: Previous Use

tag: smoking dose (cigarettes/day)

value: Surgical

value: IIB

value: Squamous cell carcinoma of the lung

tag: rin


title: Lung_tumor_AC_stage_2_rep15

value: male

tag: age at excision (years)

tag: ethnicity

value: Asian/Pacific Islander

value: Gastritis (Status Past), Adenocarcinoma of the lung (Status New)

value: Lung Tumor

tag: tnm stage

value: Adenocarcinoma

value: Adenocarcinoma of the lung

tag: tumor grade

tag: sbv challenge gold standard


title: Lung_tumor_AC_stage_2_rep6

tag: clinical diagnosis patient

value: Adenocarcinoma of the lung (Status New)

value: Current Use

tag: smoking duration (years)

tag: excision year

tag: sample recovery type

tag: ajcc uicc stage

value: Poorly differentiated


title: Lung_tumor_SCC_stage_2_rep14

value: Caucasian

value: Squamous cell carcinoma, keratinizing of the lung (Status New)

tag: bmi

tag: weight (kg)

value: Never Used

tag: tissue

value: IIA

tag: clinical diagnosis specimen


title: Lung_tumor_AC_stage_2_rep7

tag: gender

value: female

value: Lesion on the left lung (Status New), Stomach ulcer (Status Past), Sinus problems (Status Ongoing), Psoriasis (Status Ongoing), Chronic obstructive pulmonary disease (Status New), Glaucoma (Status Ongoing), Anxiety (Status New), Cataract (Status New), Hypertension (Status Ongoing), Adenocarcinoma of the lung (Status New)

tag: height (cm)

tag: smoking status

tag: biosample confirmed diagnosis

value: Non-small cell carcinoma

tag: biosample confirmed sub-diagnosis


title: Lung_tumor_SCC_stage_2_rep13

tag: age at excision (years)

tag: ethnicity

value: Malignant neoplasm of the lung (Status New)

value: Previous Use

tag: smoking dose (cigarettes/day)

value: Surgical

tag: tnm stage

value: Squamous cell carcinoma

value: Malignant neoplasm of the lung

tag: rin


title: Lung_tumor_AC_stage_1_rep11

value: male

tag: clinical diagnosis patient

value: Chronic bronchitis (Status Ongoing), Hypertension (Status Ongoing), Adenocarcinoma of the lung (Status New)

tag: smoking duration (years)

tag: excision year

value: Lung Tumor

value: IB

value: Adenocarcinoma

tag: tumor grade

tag: sbv challenge gold standard