title: normal tissue from patient 219

description: normal tissue from patient 219

source_name: normal tissue from patient 219

tag: patient id

value: female

tag: alcohol use

value: II

value: normal tissue from patient 219


title: Liver_high forage allowance_crossbred_-15 days_replicate 3

status: Public on Mar 07 2014

type: RNA

city: Montevideo

first: Mariana

last: Carriquiry

address: Ave Garzon 780

department: Department of Animal Sciences and Pastures

country: Uruguay

institute: Facultad de Agronomía, UdelaR

description:
Liver gene expression of mature cow in , high forage allowance, crossbred, -15 days, replicate 3
2034 -15

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 023647_D_F_20090518) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

molecule: total RNA

organism: Bos taurus

source_name: Liver, high forage allowance, crossbred, -15 days, replicate 3

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was isolated using TRIZOL (Invitrogen, Life Technologies, Carlsbad, CA, USA) followed by precipitation with lithium chloride and DNase-treatment (Applied Biosystems/Ambion, Austin,TX, USA). RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Liver biopsies were collected using a 14-gauge biopsy needle (Tru-Core-II Automatic Biopsy Instrument; Angiotech, Lausanne, Switzerland), at -165 and -15 ± 8 (gestation), +15 and +60 ± 3 (early lactation) days ± SD. Samples were immediately frozen in liquid nitrogen and stored at -80°C until analyzed.

tag: genotype

value: HA

tag: tissue

value: liver

tag: developmental stage

value: mature cow

tag: herbage allowance

value: high forage allowance

tag: time

value: -15 days (gestation)


title: normal tissue from patient 210

city: Beijing

first: Jiagen

last: Li

address: 17 Panjiayuannanli Chaoyang District

country: China

institute: Cancer Institute, CAMS

description: normal tissue from patient 210

hyb_protocol: The labeled RNA was purified and hybridized to microarrays according to the Agilent manufacturer's instructions.

scan_protocol: Images were scanned with the Agilent microarray scanner (Agilent), gridded, and analyzed using Agilent feature extraction software version 10.10.

data_processing: The lncRNA+mRNA array data were analyzed for data summarization, quantile normalization and quality control by using the GeneSpring software V11.5 (Agilent).

organism: Homo sapiens

source_name: normal tissue from patient 210

label_protocol: cDNA labeled with a fluorescent dye (Cy5 and Cy3-dCTP) was produced by Eberwine’s linear RNA amplification method and subsequent enzymatic reaction.

extract_protocol: Total RNA was extracted from the specimens using Trizol reagent (Invitrogen) and purified with mirVana miRNA Isolation Kit (Ambion, Austin, TX, USA). RNA purity and concentration were determined from OD260/280 readings using spectrophotometer (NanoDrop ND-1000) and RNA integrity was determined by 1% formaldehyde denaturing gel electrophoresis.

tag: age

tag: Sex

value: male

tag: tobacco use

value: no

value: yes

tag: tumor loation

value: lower

tag: tumor grade

value: well

tag: t stage

tag: n stage

tag: tnm stage

value: III

tag: arrhythmia

tag: pneumonia

tag: anastomotic leak

tag: adjuvant therapy

value: unknown

tag: death at fu

tag: survival time(months)

tag: disease state

value: esophageal squamous cell carcinoma

value: normal tissue from patient 210


title: cancer tissue from patient 210

description: cancer tissue from patient 210

source_name: cancer tissue from patient 210

tag: patient id

tag: alcohol use

tag: tissue

value: cancer tissue from patient 210


title: Liver_high forage allowance_crossbred_+15 days_replicate 3

description:
Liver gene expression of mature cow in , high forage allowance, crossbred, +15 days, replicate 3
2034 +15

source_name: Liver, high forage allowance, crossbred, +15 days, replicate 3

tag: genotype

tag: developmental stage

tag: herbage allowance

tag: time

value: +15 days (early lactation)


title: normal tissue from patient 215

description: normal tissue from patient 215

source_name: normal tissue from patient 215

tag: age

tag: Sex

tag: tobacco use

tag: tumor loation

value: middle

tag: tumor grade

value: moderately

tag: t stage

value: normal tissue from patient 215


title: Liver_low forage allowance_crossbred_-15 days_replicate 3

description:
Liver gene expression of mature cow in , low forage allowance, crossbred, -15 days, replicate 3
2151 -15

source_name: Liver, low forage allowance, crossbred, -15 days, replicate 3

value: HA

value: liver

value: mature cow

value: low forage allowance


title: Liver_high forage allowance_crossbred_+60 days_replicate 3

description:
Liver gene expression of mature cow in , high forage allowance, crossbred, +60 days, replicate 3
2034 +60

source_name: Liver, high forage allowance, crossbred, +60 days, replicate 3

value: high forage allowance

value: +60 days (early lactation)


title: Liver_high forage allowance_purebred_-165 days_replicate 3

description:
Liver gene expression of mature cow in , high forage allowance, purebred, -165 days, replicate 3
3178 -165

source_name: Liver, high forage allowance, purebred, -165 days, replicate 3

value: HH

value: -165 days (gestation)


title: Liver_high forage allowance_crossbred_-165 days_replicate 3

description:
Liver gene expression of mature cow in , high forage allowance, crossbred, -165 days, replicate 3
2034 -165

source_name: Liver, high forage allowance, crossbred, -165 days, replicate 3


title: normal tissue from patient 211

description: normal tissue from patient 211

source_name: normal tissue from patient 211

value: male

value: yes

value: poorly

tag: n stage

tag: tnm stage

value: III

tag: arrhythmia

value: no

tag: pneumonia

tag: anastomotic leak

tag: adjuvant therapy

value: normal tissue from patient 211


title: cancer tissue from patient 214

description: cancer tissue from patient 214

source_name: cancer tissue from patient 214

tag: patient id

tag: alcohol use

value: middle

tag: death at fu

tag: survival time(months)

tag: disease state

value: esophageal squamous cell carcinoma

tag: tissue

value: cancer tissue from patient 214


title: normal tissue from patient 208

description: normal tissue from patient 208

source_name: normal tissue from patient 208

tag: age

tag: Sex

value: lower

value: well

value: normal tissue from patient 208


title: Liver_high forage allowance_purebred_-15 days_replicate 3

description:
Liver gene expression of mature cow in , high forage allowance, purebred, -15 days, replicate 3
3178 -15

source_name: Liver, high forage allowance, purebred, -15 days, replicate 3

tag: genotype

value: liver

tag: developmental stage

value: mature cow

tag: herbage allowance

tag: time

value: -15 days (gestation)


title: normal tissue from patient 206

description: normal tissue from patient 206

source_name: normal tissue from patient 206

tag: tobacco use

tag: tumor loation

tag: tumor grade

tag: t stage

tag: n stage

tag: tnm stage

value: II

value: normal tissue from patient 206


title: cancer tissue from patient 212

description: cancer tissue from patient 212

source_name: cancer tissue from patient 212

tag: patient id

value: male

tag: alcohol use

tag: arrhythmia

tag: pneumonia

tag: anastomotic leak

tag: adjuvant therapy

value: cancer tissue from patient 212


title: cancer tissue from patient 208

description: cancer tissue from patient 208

source_name: cancer tissue from patient 208

tag: age

tag: Sex

value: yes

tag: death at fu

tag: survival time(months)

tag: disease state

tag: tissue

value: cancer tissue from patient 208


title: cancer tissue from patient 207

description: cancer tissue from patient 207

source_name: cancer tissue from patient 207

tag: tobacco use

tag: tumor loation

value: poorly

value: III

value: no

value: cancer tissue from patient 207


title: normal tissue from patient 212

description: normal tissue from patient 212

source_name: normal tissue from patient 212

tag: tumor grade

tag: t stage

value: esophageal squamous cell carcinoma

value: normal tissue from patient 212


title: normal tissue from patient 214

description: normal tissue from patient 214

source_name: normal tissue from patient 214

value: middle

tag: n stage

tag: tnm stage

value: normal tissue from patient 214


title: normal tissue from patient 207

description: normal tissue from patient 207

source_name: normal tissue from patient 207

tag: patient id

tag: alcohol use

value: normal tissue from patient 207


title: Liver_low forage allowance_purebred_+60 days_replicate 2

description:
Liver gene expression of mature cow in , low forage allowance, purebred, +60 days, replicate 2
3100 +60

source_name: Liver, low forage allowance, purebred, +60 days, replicate 2

tag: genotype

value: AA

value: liver

tag: developmental stage

value: mature cow

tag: herbage allowance

value: low forage allowance

tag: time

value: +60 days (early lactation)


title: cancer tissue from patient 206

description: cancer tissue from patient 206

source_name: cancer tissue from patient 206

tag: age

tag: Sex

value: male

value: well

value: II

tag: arrhythmia

tag: pneumonia

tag: anastomotic leak

tag: adjuvant therapy

value: cancer tissue from patient 206


title: Liver_low forage allowance_purebred_-165 days_replicate 2

description:
Liver gene expression of mature cow in , low forage allowance, purebred, -165 days, replicate 2
3100 -165

source_name: Liver, low forage allowance, purebred, -165 days, replicate 2

tag: tissue

value: -165 days (gestation)


title: cancer tissue from patient 142

description: cancer tissue from patient 142

source_name: cancer tissue from patient 142

tag: tobacco use

value: yes

value: no

tag: tumor loation

value: upper

tag: tumor grade

value: moderately

value: III

value: unknown

tag: death at fu

tag: survival time(months)

tag: disease state

value: cancer tissue from patient 142


title: normal tissue from patient 205

description: normal tissue from patient 205

source_name: normal tissue from patient 205

tag: patient id

tag: alcohol use

tag: t stage

tag: n stage

tag: tnm stage

value: esophageal squamous cell carcinoma

value: normal tissue from patient 205


title: cancer tissue from patient 148

description: cancer tissue from patient 148

source_name: cancer tissue from patient 148

tag: age

tag: Sex

value: middle

value: cancer tissue from patient 148


title: normal tissue from patient 148

description: normal tissue from patient 148

source_name: normal tissue from patient 148

tag: arrhythmia

tag: pneumonia

value: normal tissue from patient 148


title: normal tissue from patient 135

description: normal tissue from patient 135

source_name: normal tissue from patient 135

value: male

value: lower

value: poorly

tag: anastomotic leak

tag: adjuvant therapy

value: normal tissue from patient 135


title: normal tissue from patient 142

description: normal tissue from patient 142

source_name: normal tissue from patient 142

tag: tobacco use

tag: tissue

value: normal tissue from patient 142


title: cancer tissue from patient 205

description: cancer tissue from patient 205

source_name: cancer tissue from patient 205

value: yes

tag: tumor loation

tag: tumor grade

value: II

value: cancer tissue from patient 205


title: normal tissue from patient 146

description: normal tissue from patient 146

source_name: normal tissue from patient 146

value: no

tag: death at fu

tag: survival time(months)

value: normal tissue from patient 146


title: normal tissue from patient 136

description: normal tissue from patient 136

source_name: normal tissue from patient 136

tag: patient id

value: female

value: moderately

value: III

tag: disease state

value: normal tissue from patient 136


title: cancer tissue from patient 146

description: cancer tissue from patient 146

source_name: cancer tissue from patient 146

tag: alcohol use

value: middle

tag: t stage

value: esophageal squamous cell carcinoma

value: cancer tissue from patient 146


title: Liver_low forage allowance_crossbred_+60 days_replicate 2

description:
Liver gene expression of mature cow in , low forage allowance, crossbred, +60 days, replicate 2
2154 +60

source_name: Liver, low forage allowance, crossbred, +60 days, replicate 2

tag: genotype

value: HA

value: liver

tag: developmental stage

value: mature cow

tag: herbage allowance

value: low forage allowance

tag: time

value: +60 days (early lactation)


title: cancer tissue from patient 136

description: cancer tissue from patient 136

source_name: cancer tissue from patient 136

tag: age

tag: Sex

value: lower

tag: n stage

tag: tnm stage

tag: arrhythmia

value: yes

tag: pneumonia

value: cancer tissue from patient 136


title: Liver_low forage allowance_purebred_+15 days_replicate 2

description:
Liver gene expression of mature cow in , low forage allowance, purebred, +15 days, replicate 2
3100 +15

source_name: Liver, low forage allowance, purebred, +15 days, replicate 2

value: AA

tag: tissue

value: +15 days (early lactation)


title: Liver_low forage allowance_crossbred_+15 days_replicate 2

description:
Liver gene expression of mature cow in , low forage allowance, crossbred, +15 days, replicate 2
2154 +15

source_name: Liver, low forage allowance, crossbred, +15 days, replicate 2


title: Liver_low forage allowance_purebred_-15 days_replicate 2

description:
Liver gene expression of mature cow in , low forage allowance, purebred, -15 days, replicate 2
3100 -15

source_name: Liver, low forage allowance, purebred, -15 days, replicate 2

value: -15 days (gestation)


title: Liver_low forage allowance_crossbred_-15 days_replicate 2

description:
Liver gene expression of mature cow in , low forage allowance, crossbred, -15 days, replicate 2
2154 -15

source_name: Liver, low forage allowance, crossbred, -15 days, replicate 2


title: Liver_low forage allowance_crossbred_-165 days_replicate 2

description:
Liver gene expression of mature cow in , low forage allowance, crossbred, -165 days, replicate 2
2154 -165

source_name: Liver, low forage allowance, crossbred, -165 days, replicate 2

value: -165 days (gestation)


title: Liver_high forage allowance_purebred_+60 days_replicate 2

description:
Liver gene expression of mature cow in , high forage allowance, purebred, +60 days, replicate 2
1073 +60

source_name: Liver, high forage allowance, purebred, +60 days, replicate 2

value: high forage allowance


title: cancer tissue from patient 134

description: cancer tissue from patient 134

source_name: cancer tissue from patient 134

value: female

tag: tobacco use

value: no

tag: tumor loation

tag: tumor grade

value: moderately

value: II

tag: anastomotic leak

tag: adjuvant therapy

tag: death at fu

value: cancer tissue from patient 134


title: normal tissue from patient 134

description: normal tissue from patient 134

source_name: normal tissue from patient 134

tag: patient id

tag: alcohol use

value: middle

tag: t stage

tag: survival time(months)

tag: disease state

value: esophageal squamous cell carcinoma

value: normal tissue from patient 134


title: cancer tissue from patient 132

description: cancer tissue from patient 132

source_name: cancer tissue from patient 132

tag: age

tag: Sex

value: male

value: III

value: cancer tissue from patient 132


title: normal tissue from patient 132

description: normal tissue from patient 132

source_name: normal tissue from patient 132

value: yes

tag: n stage

tag: tnm stage

value: normal tissue from patient 132


title: cancer tissue from patient 131

description: cancer tissue from patient 131

source_name: cancer tissue from patient 131

value: poorly

tag: arrhythmia

tag: pneumonia

value: cancer tissue from patient 131


title: Liver_high forage allowance_purebred_+15 days_replicate 2

description:
Liver gene expression of mature cow in , high forage allowance, purebred, +15 days, replicate 2
1073 +15

source_name: Liver, high forage allowance, purebred, +15 days, replicate 2

tag: genotype

value: AA

tag: tissue

value: liver

tag: developmental stage

value: mature cow

tag: herbage allowance

tag: time

value: +15 days (early lactation)


title: cancer tissue from patient 135

description: cancer tissue from patient 135

source_name: cancer tissue from patient 135

tag: tobacco use

tag: tumor loation

value: lower

tag: tumor grade

value: no

tag: anastomotic leak

tag: adjuvant therapy

value: unknown

tag: death at fu

value: cancer tissue from patient 135


title: normal tissue from patient 131

description: normal tissue from patient 131

source_name: normal tissue from patient 131

tag: patient id

tag: age

tag: alcohol use

value: middle

tag: t stage

value: II

tag: survival time(months)

tag: disease state

value: esophageal squamous cell carcinoma

value: normal tissue from patient 131


title: normal tissue from patient 122

description: normal tissue from patient 122

source_name: normal tissue from patient 122

tag: Sex

value: male

value: upper

tag: n stage

tag: tnm stage

tag: arrhythmia

tag: pneumonia

value: normal tissue from patient 122


title: Liver_high forage allowance_purebred_-15 days_replicate 2

description:
Liver gene expression of mature cow in , high forage allowance, purebred, -15 days, replicate 2
1073 -15

source_name: Liver, high forage allowance, purebred, -15 days, replicate 2

tag: genotype

tag: tissue

tag: developmental stage

tag: herbage allowance

value: high forage allowance

tag: time

value: -15 days (gestation)


title: cancer tissue from patient 122

description: cancer tissue from patient 122

source_name: cancer tissue from patient 122

tag: tobacco use

value: yes

tag: tumor loation

tag: tumor grade

value: poorly

tag: anastomotic leak

tag: adjuvant therapy

tag: death at fu

value: cancer tissue from patient 122


title: normal tissue from patient 119

description: normal tissue from patient 119

source_name: normal tissue from patient 119

tag: patient id

tag: age

value: female

tag: alcohol use

value: well

tag: t stage

value: III

tag: survival time(months)

tag: disease state

value: normal tissue from patient 119


title: Liver_high forage allowance_crossbred_+60 days_replicate 2

description:
Liver gene expression of mature cow in , high forage allowance, crossbred, +60 days, replicate 2
2011 +60

source_name: Liver, high forage allowance, crossbred, +60 days, replicate 2

tag: genotype

value: HA

value: liver

value: mature cow

value: +60 days (early lactation)


title: normal tissue from patient 120

description: normal tissue from patient 120

source_name: normal tissue from patient 120

tag: Sex

value: moderately

tag: n stage

tag: tnm stage

tag: arrhythmia

value: no

tag: pneumonia

value: esophageal squamous cell carcinoma

tag: tissue

value: normal tissue from patient 120


title: normal tissue from patient 108

description: normal tissue from patient 108

source_name: normal tissue from patient 108

tag: tobacco use

tag: tumor loation

value: upper

tag: tumor grade

value: normal tissue from patient 108


title: Liver_high forage allowance_crossbred_+15 days_replicate 2

description:
Liver gene expression of mature cow in , high forage allowance, crossbred, +15 days, replicate 2
2011 +15

source_name: Liver, high forage allowance, crossbred, +15 days, replicate 2

tag: developmental stage

tag: herbage allowance

value: high forage allowance

tag: time

value: +15 days (early lactation)


title: cancer tissue from patient 108

description: cancer tissue from patient 108

source_name: cancer tissue from patient 108

tag: patient id

tag: age

tag: alcohol use

value: poorly

tag: anastomotic leak

tag: adjuvant therapy

value: yes

tag: death at fu

value: cancer tissue from patient 108


title: cancer tissue from patient 119

description: cancer tissue from patient 119

source_name: cancer tissue from patient 119

tag: Sex

value: female

value: middle

value: well

tag: t stage

tag: n stage

value: III

tag: survival time(months)

tag: disease state

value: cancer tissue from patient 119


title: Liver_high forage allowance_crossbred_-165 days_replicate 2

description:
Liver gene expression of mature cow in , high forage allowance, crossbred, -165 days, replicate 2
2011 -165

source_name: Liver, high forage allowance, crossbred, -165 days, replicate 2

tag: genotype

value: HA

tag: tissue

value: liver

value: mature cow

value: -165 days (gestation)


title: normal tissue from patient 81

description: normal tissue from patient 81

source_name: normal tissue from patient 81

value: male

tag: tobacco use

tag: tumor loation

value: lower

tag: tumor grade

tag: tnm stage

value: II

tag: arrhythmia

value: no

tag: pneumonia

value: unknown

value: esophageal squamous cell carcinoma

value: normal tissue from patient 81


title: normal tissue from patient 68

description: normal tissue from patient 68

source_name: normal tissue from patient 68

tag: patient id

tag: age

value: yes

tag: alcohol use

value: upper

value: poorly

value: normal tissue from patient 68


title: cancer tissue from patient 68

description: cancer tissue from patient 68

source_name: cancer tissue from patient 68

value: III

tag: anastomotic leak

tag: adjuvant therapy

tag: death at fu

value: cancer tissue from patient 68


title: Liver_high forage allowance_purebred_-165 days_replicate 2

description:
Liver gene expression of mature cow in , high forage allowance, purebred, -165 days, replicate 2
1073 -165

source_name: Liver, high forage allowance, purebred, -165 days, replicate 2

value: AA

tag: developmental stage

tag: herbage allowance

value: high forage allowance

tag: time


title: normal tissue from patient 80

description: normal tissue from patient 80

source_name: normal tissue from patient 80

tag: Sex

value: well

tag: t stage

tag: n stage

tag: survival time(months)

tag: disease state

value: normal tissue from patient 80


title: cancer tissue from patient 120

description: cancer tissue from patient 120

source_name: cancer tissue from patient 120

value: male

tag: tobacco use

tag: tumor loation

tag: tumor grade

value: moderately

tag: tnm stage

tag: tissue

value: cancer tissue from patient 120


title: cancer tissue from patient 81

description: cancer tissue from patient 81

source_name: cancer tissue from patient 81

tag: patient id

tag: age

tag: alcohol use

value: lower

value: II

tag: arrhythmia

value: no

tag: pneumonia

value: cancer tissue from patient 81


title: cancer tissue from patient 30

description: cancer tissue from patient 30

source_name: cancer tissue from patient 30

value: yes

value: middle

tag: anastomotic leak

tag: adjuvant therapy

tag: death at fu

value: esophageal squamous cell carcinoma

value: cancer tissue from patient 30


title: Liver_high forage allowance_crossbred_-15 days_replicate 2

description:
Liver gene expression of mature cow in , high forage allowance, crossbred, -15 days, replicate 2
2011 -15

source_name: Liver, high forage allowance, crossbred, -15 days, replicate 2

tag: genotype

value: HA

value: liver

tag: developmental stage

value: mature cow

tag: herbage allowance

tag: time

value: -15 days (gestation)


title: normal tissue from patient 30

description: normal tissue from patient 30

source_name: normal tissue from patient 30

tag: Sex

tag: tobacco use

value: poorly

tag: t stage

tag: n stage

value: III

tag: survival time(months)

tag: disease state

value: normal tissue from patient 30


title: Liver_low forage allowance_purebred_+60 days_replicate 1

description:
Liver gene expression of mature cow in , low forage allowance, purebred, +60 days, replicate 1
1212 +60

source_name: Liver, low forage allowance, purebred, +60 days, replicate 1

value: HH

tag: tissue

value: low forage allowance

value: +60 days (early lactation)


title: Liver_low forage allowance_purebred_+15 days_replicate 1

description:
Liver gene expression of mature cow in , low forage allowance, purebred, +15 days, replicate 1
1212 +15

source_name: Liver, low forage allowance, purebred, +15 days, replicate 1

value: +15 days (early lactation)


title: normal tissue from patient 29

description: normal tissue from patient 29

source_name: normal tissue from patient 29

tag: patient id

tag: age

value: male

value: no

tag: alcohol use

tag: tumor loation

value: lower

tag: tumor grade

value: well

tag: tnm stage

value: normal tissue from patient 29


title: Liver_low forage allowance_purebred_-15 days_replicate 1

description:
Liver gene expression of mature cow in , low forage allowance, purebred, -15 days, replicate 1
1212 -15

source_name: Liver, low forage allowance, purebred, -15 days, replicate 1

tag: genotype


title: normal tissue from patient 288

description: normal tissue from patient 288

source_name: normal tissue from patient 288

value: yes

value: middle

value: moderately

tag: arrhythmia

tag: pneumonia

tag: anastomotic leak

tag: adjuvant therapy

tag: death at fu

value: esophageal squamous cell carcinoma

value: normal tissue from patient 288


title: cancer tissue from patient 288

description: cancer tissue from patient 288

source_name: cancer tissue from patient 288

tag: Sex

tag: tobacco use

tag: t stage

value: cancer tissue from patient 288


title: cancer tissue from patient 29

description: cancer tissue from patient 29

source_name: cancer tissue from patient 29

tag: n stage

value: III

tag: survival time(months)

tag: disease state

value: cancer tissue from patient 29


title: normal tissue from patient 285

description: normal tissue from patient 285

source_name: normal tissue from patient 285

tag: patient id

tag: age

value: female

value: II

tag: tissue

value: normal tissue from patient 285


title: Liver_low forage allowance_purebred_-165 days_replicate 1

description:
Liver gene expression of mature cow in , low forage allowance, purebred, -165 days, replicate 1
1212 -165

source_name: Liver, low forage allowance, purebred, -165 days, replicate 1

value: HH

value: liver

tag: developmental stage

value: mature cow

tag: herbage allowance

value: low forage allowance

tag: time

value: -165 days (gestation)


title: normal tissue from patient 287

description: normal tissue from patient 287

source_name: normal tissue from patient 287

value: male

tag: alcohol use

tag: tumor loation

tag: tumor grade

tag: tnm stage

tag: arrhythmia

value: no

value: normal tissue from patient 287


title: normal tissue from patient 279

description: normal tissue from patient 279

source_name: normal tissue from patient 279

tag: Sex

value: yes

value: middle

value: moderately

tag: pneumonia

tag: anastomotic leak

tag: adjuvant therapy

tag: death at fu

value: normal tissue from patient 279


title: Liver_low forage allowance_crossbred_+15 days_replicate 1

description:
Liver gene expression of mature cow in , low forage allowance, crossbred, +15 days, replicate 1
2006 +15

source_name: Liver, low forage allowance, crossbred, +15 days, replicate 1

tag: genotype

value: AH

value: +15 days (early lactation)


title: Liver_low forage allowance_crossbred_-165 days_replicate 1

description:
Liver gene expression of mature cow in , low forage allowance, crossbred, -165 days, replicate 1
2006 -165

source_name: Liver, low forage allowance, crossbred, -165 days, replicate 1


title: cancer tissue from patient 287

description: cancer tissue from patient 287

source_name: cancer tissue from patient 287

tag: patient id

tag: tobacco use

tag: t stage

tag: n stage

tag: survival time(months)

tag: disease state

value: esophageal squamous cell carcinoma

value: cancer tissue from patient 287


title: normal tissue from patient 281

description: normal tissue from patient 281

source_name: normal tissue from patient 281

tag: age

tag: alcohol use

value: III

tag: tissue

value: normal tissue from patient 281


title: Liver_low forage allowance_crossbred_+60 days_replicate 1

description:
Liver gene expression of mature cow in , low forage allowance, crossbred, +60 days, replicate 1
2006 +60

source_name: Liver, low forage allowance, crossbred, +60 days, replicate 1

value: liver

tag: developmental stage

tag: herbage allowance

tag: time

value: +60 days (early lactation)


title: cancer tissue from patient 280

description: cancer tissue from patient 280

source_name: cancer tissue from patient 280

tag: Sex

tag: tumor loation

tag: tumor grade

tag: tnm stage

tag: arrhythmia

tag: pneumonia

value: cancer tissue from patient 280


title: normal tissue from patient 284

description: normal tissue from patient 284

source_name: normal tissue from patient 284

tag: patient id

tag: tobacco use

value: I

tag: anastomotic leak

tag: adjuvant therapy

tag: death at fu

value: normal tissue from patient 284


title: cancer tissue from patient 285

description: cancer tissue from patient 285

source_name: cancer tissue from patient 285

tag: age

value: female

value: no

tag: t stage

tag: n stage

value: II

tag: survival time(months)

tag: disease state

value: cancer tissue from patient 285


title: cancer tissue from patient 284

description: cancer tissue from patient 284

source_name: cancer tissue from patient 284

value: male

value: yes

tag: alcohol use

value: middle

value: moderately

tag: tissue

value: cancer tissue from patient 284


title: cancer tissue from patient 281

description: cancer tissue from patient 281

source_name: cancer tissue from patient 281

tag: Sex

tag: tumor loation

value: esophageal squamous cell carcinoma

value: cancer tissue from patient 281


title: Liver_high forage allowance_purebred_+60 days_replicate 1

description:
Liver gene expression of mature cow in  gene expression of mature cow in , high forage allowance, purebred, +60 days, replicate 1
3240 +60

source_name: Liver, high forage allowance, purebred, +60 days, replicate 1

tag: genotype

value: HH

tag: developmental stage

value: mature cow

tag: herbage allowance

value: high forage allowance

tag: time


title: Liver_low forage allowance_crossbred_-15 days_replicate 1

description:
Liver gene expression of mature cow in , low forage allowance, crossbred, -15 days, replicate 1
2006 -15

source_name: Liver, low forage allowance, crossbred, -15 days, replicate 1

value: AH

value: liver

value: low forage allowance

value: -15 days (gestation)


title: Late_lesion_patient_17

city: Philadelphia

first: daniel

last: beiting

state: PA

address: 380 S. University Ave

department: Pathobiology

country: USA

institute: University of Pennsylvania

description:
9224523042_C
Patient 25

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: The data were quantile normalized without background subtraction using Illumina GenomeStudio V1.8.

label: biotin

source_name: biopsy of late cutaneous Leishmania braziliensis lesion

label_protocol: Biotin-labeled complementary RNA (cRNA) was made using the Illumina TotalPrep RNA Amplification Kit.

growth_protocol: Biopsies were directly preserved in RNAlater (Qiagen) and stored at -80c until the time of extraction.

extract_protocol: Each biopsy was immersed in 1ml of Buffer RLT (Qiagen) and homogenized, on ice, using brief pulses with a rotor-stator. Total RNA was isolated using the Qiagen RNeasy Plus kit.

value: Leishmania braziliensis lesion

tag: lesion stage

value: late

tag: lesion size (mm^2)

tag: illness duration at time of biopsy (days)

tag: patient age (years)

tag: patient sex

value: M

tag: batch


title: normal tissue from patient 280

description: normal tissue from patient 280

source_name: normal tissue from patient 280

tag: patient id

tag: age

value: male

tag: tobacco use

value: no

tag: tumor grade

tag: t stage

tag: n stage

tag: tnm stage

value: III

tag: arrhythmia

tag: pneumonia

tag: anastomotic leak

tag: adjuvant therapy

tag: death at fu

value: normal tissue from patient 280


title: normal tissue from patient 277

description: normal tissue from patient 277

source_name: normal tissue from patient 277

tag: Sex

value: female

value: yes

tag: alcohol use

tag: tumor loation

value: middle

value: poorly

tag: survival time(months)

tag: disease state

tag: tissue

value: normal tissue from patient 277


title: cancer tissue from patient 279

description: cancer tissue from patient 279

source_name: cancer tissue from patient 279

tag: patient id

tag: age

value: moderately

value: II

value: esophageal squamous cell carcinoma

value: cancer tissue from patient 279


title: cancer tissue from patient 277

description: cancer tissue from patient 277

source_name: cancer tissue from patient 277

tag: tobacco use

tag: tumor grade

value: cancer tissue from patient 277


title: Late_lesion_patient_15

description:
9224523042_A
Patient 23

value: Leishmania braziliensis lesion

tag: lesion stage

tag: lesion size (mm^2)

tag: illness duration at time of biopsy (days)

tag: patient age (years)

tag: patient sex

tag: batch


title: cancer tissue from patient 80

description: cancer tissue from patient 80

source_name: cancer tissue from patient 80

value: upper

value: well

tag: t stage

tag: n stage

tag: tnm stage

tag: arrhythmia

tag: pneumonia

tag: anastomotic leak

tag: adjuvant therapy

tag: death at fu

value: cancer tissue from patient 80


title: Late_lesion_patient_16

description:
7680491091_K
Patient 24

tag: tissue

value: late

value: F


title: Late_lesion_patient_14

description:
9224523042_D
Patient 22


title: Liver_high forage allowance_purebred_-15 days_replicate 1

description:
Liver gene expression of mature cow in  gene expression of mature cow in , high forage allowance, purebred, -15 days, replicate 1
3240 -15

source_name: Liver, high forage allowance, purebred, -15 days, replicate 1

tag: genotype

value: HH

value: liver

tag: developmental stage

value: mature cow

tag: herbage allowance

value: high forage allowance

tag: time

value: -15 days (gestation)


title: normal tissue from patient 275

description: normal tissue from patient 275

source_name: normal tissue from patient 275

tag: patient id

tag: age

tag: Sex

value: male

tag: tobacco use

value: yes

tag: alcohol use

tag: tumor loation

value: middle

tag: tumor grade

value: no

tag: survival time(months)

tag: disease state

value: normal tissue from patient 275


title: Liver_high forage allowance_purebred_+15 days_replicate 1

description:
Liver gene expression of mature cow in  gene expression of mature cow in , high forage allowance, purebred, +15 days, replicate 1
3240 +15

source_name: Liver, high forage allowance, purebred, +15 days, replicate 1

value: +15 days (early lactation)


title: Late_lesion_patient_13

description:
9224523042_J
Patient 21

value: Leishmania braziliensis lesion

tag: lesion stage

tag: lesion size (mm^2)

tag: illness duration at time of biopsy (days)

tag: patient age (years)

tag: patient sex

value: M

tag: batch


title: Liver_high forage allowance_purebred_-165 days_replicate 1

description:
Liver gene expression of mature cow in , high forage allowance, purebred, -165 days, replicate 1
3240 -165

source_name: Liver, high forage allowance, purebred, -165 days, replicate 1

tag: genotype

tag: tissue

tag: developmental stage

tag: herbage allowance

value: -165 days (gestation)


title: normal tissue from patient 273

description: normal tissue from patient 273

source_name: normal tissue from patient 273

tag: patient id

tag: age

tag: Sex

value: moderately

tag: t stage

tag: n stage

tag: tnm stage

value: II

tag: arrhythmia

tag: pneumonia

tag: anastomotic leak

tag: adjuvant therapy

tag: death at fu

value: esophageal squamous cell carcinoma

value: normal tissue from patient 273


title: cancer tissue from patient 274

description: cancer tissue from patient 274

source_name: cancer tissue from patient 274

tag: tobacco use

tag: alcohol use

tag: tumor loation

value: lower

tag: tumor grade

value: I

tag: survival time(months)

tag: disease state

value: cancer tissue from patient 274


title: cancer tissue from patient 275

description: cancer tissue from patient 275

source_name: cancer tissue from patient 275

tag: patient id

tag: tissue

value: cancer tissue from patient 275


title: normal tissue from patient 274

description: normal tissue from patient 274

source_name: normal tissue from patient 274

tag: age

tag: Sex

value: male

value: normal tissue from patient 274


title: Late_lesion_patient_12

description:
9224523027_L
Patient 20

tag: lesion stage

value: late

tag: lesion size (mm^2)

tag: illness duration at time of biopsy (days)

tag: patient age (years)

tag: patient sex

value: F

tag: batch


title: Liver_high forage allowance_crossbred_+60 days_replicate 1

description:
Liver gene expression of mature cow in , high forage allowance, crossbred, +60 days, replicate 1
3060 +60

source_name: Liver, high forage allowance, crossbred, +60 days, replicate 1

tag: genotype

value: AH

value: liver

tag: developmental stage

value: mature cow

tag: herbage allowance

value: high forage allowance

tag: time

value: +60 days (early lactation)


title: Late_lesion_patient_11

description:
9224523027_F
Patient 19

value: Leishmania braziliensis lesion

value: M


title: normal tissue from patient 269

description: normal tissue from patient 269

source_name: normal tissue from patient 269

tag: tobacco use

value: yes

tag: alcohol use

tag: tumor loation

value: middle

tag: tumor grade

value: poorly

tag: t stage

tag: n stage

tag: tnm stage

value: III

tag: arrhythmia

value: no

tag: pneumonia

tag: anastomotic leak

tag: adjuvant therapy

tag: death at fu

value: esophageal squamous cell carcinoma

value: normal tissue from patient 269


title: cancer tissue from patient 269

description: cancer tissue from patient 269

source_name: cancer tissue from patient 269

tag: patient id

tag: age

tag: Sex

value: male

tag: survival time(months)

tag: disease state

tag: tissue

value: cancer tissue from patient 269


title: cancer tissue from patient 273

description: cancer tissue from patient 273

source_name: cancer tissue from patient 273

tag: tobacco use

tag: alcohol use

value: moderately

value: II

value: cancer tissue from patient 273


title: Liver_high forage allowance_crossbred_+15 days_replicate 1

description:
Liver gene expression of mature cow in , high forage allowance, crossbred, +15 days, replicate 1
3060 +15

source_name: Liver, high forage allowance, crossbred, +15 days, replicate 1

tag: genotype

value: AH

value: liver

tag: developmental stage

value: mature cow

tag: herbage allowance

tag: time

value: +15 days (early lactation)


title: Late_lesion_patient_9

description:
9224523027_D
Patient 17

source_name: biopsy of late cutaneous Leishmania braziliensis lesion

value: Leishmania braziliensis lesion

tag: lesion stage

value: late

tag: lesion size (mm^2)

tag: illness duration at time of biopsy (days)

tag: patient age (years)

tag: patient sex

value: M

tag: batch


title: Late_lesion_patient_10

description:
9224523027_E
Patient 18


title: cancer tissue from patient 266

description: cancer tissue from patient 266

source_name: cancer tissue from patient 266

tag: patient id

tag: age

value: yes

tag: tumor loation

value: middle

tag: tumor grade

tag: t stage

tag: n stage

tag: tnm stage

tag: arrhythmia

tag: pneumonia

tag: anastomotic leak

tag: adjuvant therapy

tag: death at fu

value: cancer tissue from patient 266


title: normal tissue from patient 266

description: normal tissue from patient 266

source_name: normal tissue from patient 266

tag: Sex

tag: tobacco use

tag: alcohol use

value: no

tag: survival time(months)

tag: disease state

value: esophageal squamous cell carcinoma

tag: tissue

value: normal tissue from patient 266


title: cancer tissue from patient 265

description: cancer tissue from patient 265

source_name: cancer tissue from patient 265

tag: patient id

tag: age

value: male

value: cancer tissue from patient 265


title: Liver_high forage allowance_crossbred_-15 days_replicate 1

description:
Liver gene expression of mature cow in , high forage allowance, crossbred, -15 days, replicate 1
3060 -15

source_name: Liver, high forage allowance, crossbred, -15 days, replicate 1

tag: genotype

tag: developmental stage

tag: herbage allowance

value: high forage allowance

tag: time

value: -15 days (gestation)


title: normal tissue from patient 265

description: normal tissue from patient 265

source_name: normal tissue from patient 265

tag: tumor loation

tag: tumor grade

value: moderately

tag: t stage

tag: n stage

tag: tnm stage

value: II

tag: arrhythmia

value: normal tissue from patient 265


title: Late_lesion_patient_8

description:
7680491091_H
Patient 16

tag: lesion stage

tag: lesion size (mm^2)

tag: illness duration at time of biopsy (days)

tag: patient age (years)

tag: patient sex

tag: batch


title: normal tissue from patient 264

description: normal tissue from patient 264

source_name: normal tissue from patient 264

tag: patient id

tag: age

tag: Sex

tag: tobacco use

tag: alcohol use

value: poorly

value: III

tag: pneumonia

tag: anastomotic leak

tag: adjuvant therapy

tag: death at fu

tag: survival time(months)

tag: disease state

tag: tissue

value: normal tissue from patient 264


title: cancer tissue from patient 264

description: cancer tissue from patient 264

source_name: cancer tissue from patient 264

tag: tumor loation

tag: tumor grade

tag: t stage

tag: n stage

tag: tnm stage

tag: arrhythmia

value: cancer tissue from patient 264


title: Late_lesion_patient_7

description:
7680491091_J
Patient 15

value: Leishmania braziliensis lesion

tag: lesion stage

value: late

tag: lesion size (mm^2)

tag: illness duration at time of biopsy (days)

tag: patient age (years)

tag: patient sex

value: F

tag: batch


title: normal tissue from patient 262

description: normal tissue from patient 262

source_name: normal tissue from patient 262

tag: patient id

tag: age

tag: Sex

value: female

tag: tobacco use

value: no

tag: alcohol use

value: middle

tag: pneumonia

tag: anastomotic leak

tag: adjuvant therapy

value: yes

value: normal tissue from patient 262


title: normal tissue from patient 260

description: normal tissue from patient 260

source_name: normal tissue from patient 260

tag: tumor loation

tag: tumor grade

value: well

tag: t stage

tag: n stage

tag: death at fu

tag: survival time(months)

tag: disease state

value: esophageal squamous cell carcinoma

tag: tissue

value: normal tissue from patient 260


title: cancer tissue from patient 262

description: cancer tissue from patient 262

source_name: cancer tissue from patient 262

value: moderately

tag: tnm stage

value: II

tag: arrhythmia

value: cancer tissue from patient 262


title: Late_lesion_patient_6

description:
7680491091_G
Patient 14

tag: lesion stage

tag: lesion size (mm^2)

tag: illness duration at time of biopsy (days)

tag: patient age (years)

tag: patient sex

value: M

tag: batch


title: cancer tissue from patient 261

description: cancer tissue from patient 261

source_name: cancer tissue from patient 261

tag: patient id

tag: age

tag: Sex

value: male

tag: tobacco use

tag: alcohol use

value: III

tag: pneumonia

tag: anastomotic leak

tag: adjuvant therapy

value: cancer tissue from patient 261


title: Liver_high forage allowance_crossbred_-165 days_replicate 1

description:
Liver gene expression of mature cow in , high forage allowance, crossbred, -165 days, replicate 1
3060 -165

source_name: Liver, high forage allowance, crossbred, -165 days, replicate 1

tag: genotype

value: AH

tag: tissue

value: liver

tag: developmental stage

value: mature cow

tag: herbage allowance

value: high forage allowance

tag: time

value: -165 days (gestation)


title: normal tissue from patient 261

description: normal tissue from patient 261

source_name: normal tissue from patient 261

value: yes

tag: tumor loation

value: middle

tag: tumor grade

tag: t stage

tag: n stage

tag: tnm stage

tag: arrhythmia

value: no

tag: death at fu

tag: survival time(months)

tag: disease state

value: normal tissue from patient 261


title: Late_lesion_patient_4

description:
7680491091_F
Patient 12

value: Leishmania braziliensis lesion

tag: lesion stage

value: late

tag: lesion size (mm^2)

tag: illness duration at time of biopsy (days)

tag: patient age (years)

tag: patient sex

value: F

tag: batch


title: cancer tissue from patient 260

description: cancer tissue from patient 260

source_name: cancer tissue from patient 260

tag: patient id

tag: age

tag: Sex

value: female

tag: tobacco use

tag: alcohol use

value: well

tag: pneumonia

tag: anastomotic leak

tag: adjuvant therapy

value: esophageal squamous cell carcinoma

tag: tissue

value: cancer tissue from patient 260


title: normal tissue from patient 259

description: normal tissue from patient 259

source_name: normal tissue from patient 259

tag: tumor loation

tag: tumor grade

value: moderately

tag: t stage

tag: n stage

tag: tnm stage

value: III

tag: arrhythmia

tag: death at fu

tag: survival time(months)

value: normal tissue from patient 259


title: cancer tissue from patient 258

description: cancer tissue from patient 258

source_name: cancer tissue from patient 258

tag: patient id

value: poorly

value: II

tag: disease state

value: cancer tissue from patient 258


title: cancer tissue from patient 259

description: cancer tissue from patient 259

source_name: cancer tissue from patient 259

tag: age

tag: Sex

value: yes

value: cancer tissue from patient 259


title: normal tissue from patient 258

description: normal tissue from patient 258

source_name: normal tissue from patient 258

tag: tobacco use

value: no

tag: alcohol use

value: middle

value: normal tissue from patient 258


title: SPT4-R3 seedlings 10 DAS, biological rep2

city: Regensburg

first: Klaus

last: Grasser

address: Universtitätsstr. 51

country: Germany

institute: University of Regensburg

description: Gene expression data from Spt4-R3 mutant

hyb_protocol: Following fragmentation, cRNA was hybridized for 16 hr at 45C on GeneChip Arabidopsis ATH1 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affimetrix Genechip Scanner 3000

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

organism: Arabidopsis thaliana

source_name: 10 DAS seedlings of SPT4 RNAi line 3

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

growth_protocol: seeds were stratified for 2 days and grown for 10 days on solid (0.8% Agar) MS in an plant incubator only the aerial part was harvested

extract_protocol: RNeasy Mini Plant kit supplied with RNase-Free DNase set (Qiagen)

value: seedlings

tag: genetic background

value: Columbia -0

value: 10 days after statification

tag: genotype

value: Spt4-R3 mutant


title: normal tissue from patient 256

description: normal tissue from patient 256

source_name: normal tissue from patient 256

value: male

value: lower

tag: pneumonia

tag: anastomotic leak

tag: adjuvant therapy

value: esophageal squamous cell carcinoma

tag: tissue

value: normal tissue from patient 256


title: Late_lesion_patient_5

description:
7680491091_D
Patient 13

source_name: biopsy of late cutaneous Leishmania braziliensis lesion

value: Leishmania braziliensis lesion

tag: lesion stage

value: late

tag: lesion size (mm^2)

tag: illness duration at time of biopsy (days)

tag: patient age (years)

tag: patient sex

value: M

tag: batch


title: Late_lesion_patient_3

description:
7680491091_I
Patient 11


title: SPT4-R3 seedlings 10 DAS, biological rep3


title: Late_lesion_patient_1

description:
7680491091_E
Patient 9


title: Col-0 seedlings 10 DAS, biological rep2

description: Gene expression data from WT

source_name: 10 DAS seedlings of wild-type

value: wild type


title: Late_lesion_patient_2

description:
7680491091_C
Patient 10


title: normal tissue from patient 253

description: normal tissue from patient 253

source_name: normal tissue from patient 253

tag: patient id

value: female

tag: tumor loation

tag: tumor grade

value: poorly

tag: t stage

tag: n stage

tag: tnm stage

value: II

tag: arrhythmia

value: yes

tag: death at fu

tag: survival time(months)

tag: disease state

value: normal tissue from patient 253


title: cancer tissue from patient 256

description: cancer tissue from patient 256

source_name: cancer tissue from patient 256

tag: age

tag: Sex

tag: tobacco use

tag: alcohol use

value: moderately

value: III

value: no

tag: pneumonia

tag: anastomotic leak

tag: adjuvant therapy

tag: tissue

value: cancer tissue from patient 256


title: Early_lesion_patient_8

description:
9224523027_B
Patient 8

source_name: biopsy of early cutaneous Leishmania braziliensis lesion

tag: lesion stage

value: early

tag: lesion size (mm^2)

tag: illness duration at time of biopsy (days)

tag: patient age (years)

tag: patient sex

tag: batch


title: normal tissue from patient 251

description: normal tissue from patient 251

source_name: normal tissue from patient 251

tag: patient id

value: male

tag: tumor loation

value: lower

tag: tumor grade

tag: t stage

tag: n stage

tag: tnm stage

tag: arrhythmia

tag: death at fu

value: normal tissue from patient 251


title: SPT4-R3 seedlings 10 DAS, biological rep1

value: seedlings

tag: genetic background

value: Columbia -0

tag: age

value: 10 days after statification

tag: genotype

value: Spt4-R3 mutant


title: cancer tissue from patient 253

description: cancer tissue from patient 253

source_name: cancer tissue from patient 253

tag: Sex

value: female

tag: tobacco use

tag: alcohol use

value: middle

tag: pneumonia

tag: anastomotic leak

tag: adjuvant therapy

tag: survival time(months)

tag: disease state

value: esophageal squamous cell carcinoma

tag: tissue

value: cancer tissue from patient 253


title: Col-0 seedlings 10 DAS, biological rep3

description: Gene expression data from WT

value: wild type


title: Early_lesion_patient_7

description:
9224523027_C
Patient 7

value: Leishmania braziliensis lesion

tag: lesion stage

tag: lesion size (mm^2)

tag: illness duration at time of biopsy (days)

tag: patient age (years)

tag: patient sex

value: F

tag: batch


title: cancer tissue from patient 251

description: cancer tissue from patient 251

source_name: cancer tissue from patient 251

tag: patient id

tag: age

value: no

value: yes

tag: tumor loation

tag: tumor grade

value: moderately

tag: t stage

tag: n stage

tag: tnm stage

value: III

tag: arrhythmia

tag: death at fu

value: cancer tissue from patient 251


title: Early_lesion_patient_6

description:
9224523027_A
Patient 6

value: early


title: normal tissue from patient 227

description: normal tissue from patient 227

source_name: normal tissue from patient 227

tag: Sex

value: male

tag: tobacco use

tag: alcohol use

value: II

tag: pneumonia

tag: anastomotic leak

tag: adjuvant therapy

tag: survival time(months)

tag: disease state

value: normal tissue from patient 227


title: cancer tissue from patient 227

description: cancer tissue from patient 227

source_name: cancer tissue from patient 227

tag: patient id

tag: tissue

value: cancer tissue from patient 227


title: normal tissue from patient 226

description: normal tissue from patient 226

source_name: normal tissue from patient 226

tag: age

value: female

tag: tumor loation

value: normal tissue from patient 226


title: cancer tissue from patient 226

description: cancer tissue from patient 226

source_name: cancer tissue from patient 226

value: middle

tag: tumor grade

tag: t stage

value: esophageal squamous cell carcinoma

value: cancer tissue from patient 226


title: Early_lesion_patient_5

description:
9224523027_K
Patient 5

value: Leishmania braziliensis lesion

tag: lesion stage

tag: lesion size (mm^2)

tag: illness duration at time of biopsy (days)

tag: patient age (years)

tag: patient sex

value: M

tag: batch


title: PPC-1 sh184 #2

city: La Jolla

first: Roy

middle: M

last: Williams

state: CA

address: 3030 Science Park Road

department: Regenerative Medicine

institute: The Scripps Research Institute

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were filtered for p< 0.05 and normalised using quantile normalisation with GeneSpring, and log2 transformed.

source_name: PPC-1 sh184

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: cell line

tag: cell type

value: primary prostatic tumor cells

tag: genotype/variation

value: lacking NWD1 expression (sh184)


title: normal tissue from patient 224

description: normal tissue from patient 224

source_name: normal tissue from patient 224

tag: Sex

tag: tobacco use

value: yes

tag: alcohol use

value: moderately

tag: n stage

tag: tnm stage

tag: arrhythmia

tag: pneumonia

value: no

tag: anastomotic leak

tag: adjuvant therapy

tag: death at fu

tag: survival time(months)

value: normal tissue from patient 224


title: normal tissue from patient 225

description: normal tissue from patient 225

source_name: normal tissue from patient 225

tag: patient id

tag: age

value: male

tag: tumor loation

value: lower

tag: tumor grade

tag: t stage

tag: disease state

tag: tissue

value: normal tissue from patient 225


title: PPC-1 sh3922 #2

tag: cell line

tag: cell type

tag: genotype/variation

value: lacking NWD1 expression (sh3922)


title: Early_lesion_patient_4

description:
9224523027_I
Patient 4

tag: lesion stage

value: early

tag: lesion size (mm^2)

tag: illness duration at time of biopsy (days)

tag: patient age (years)

tag: patient sex

value: F

tag: batch


title: cancer tissue from patient 225

description: cancer tissue from patient 225

source_name: cancer tissue from patient 225

tag: Sex

tag: tobacco use

tag: alcohol use

tag: n stage

tag: tnm stage

value: II

tag: arrhythmia

tag: pneumonia

tag: anastomotic leak

tag: adjuvant therapy

tag: death at fu

tag: survival time(months)

value: cancer tissue from patient 225


title: PPC-1 sh3922 #1

tag: cell line

tag: cell type

tag: genotype/variation


title: Early_lesion_patient_2

description:
7680491091_L
Patient 2

tag: tissue

tag: lesion stage

tag: lesion size (mm^2)

tag: illness duration at time of biopsy (days)

tag: patient age (years)


title: cancer tissue from patient 224

description: cancer tissue from patient 224

source_name: cancer tissue from patient 224

tag: patient id

tag: age

tag: Sex

tag: tobacco use

tag: alcohol use

tag: tumor loation

value: middle

tag: tumor grade

tag: t stage

value: III

tag: disease state

value: esophageal squamous cell carcinoma

value: cancer tissue from patient 224


title: Early_lesion_patient_3

description:
9224523027_G
Patient 3

value: Leishmania braziliensis lesion

tag: patient sex

tag: batch


title: cancer tissue from patient 405

description: cancer tissue from patient 405

source_name: cancer tissue from patient 405

tag: n stage

tag: tnm stage

tag: arrhythmia

value: yes

tag: pneumonia

tag: anastomotic leak

tag: adjuvant therapy

tag: death at fu

tag: survival time(months)

value: cancer tissue from patient 405


title: LM10403S ClO2 exposure rep4

city: West Lafayette

first: Aaron

middle: Mark

last: Pleitner

state: IN

address: 745 Agriculture Mall Drive

department: Food Science

institute: Purdue University

description: Sample 4

hyb_protocol: Briefly, microarray slides were blocked in a prehybridization buffer supplemented with bovine serum albumen (BSA) (Sigma-Aldrich), washed with deionized water then isopropyl alcohol. Dried Cy3- and Cy5-labeled cDNA was hydrated with hybridization buffer containing 0.6 mg/ml sheared salmon sperm DNA (Invitrogen), denatured twice at 95ºC for 5 minutes and briefly centrifuged. cDNA was hybridized to the microarray at 42ºC for 16 hours. Following hybridization, slides were washed according to the PFGRC/JCVI M008 protocol and dried by centrifugation.

scan_protocol: Images were scanned using a GenePix 4000B scanner (Molecular Devices Corp.) using the following general scanning parameters: pixel size=10, focus position=20, lines to average=1, laser power=100%. The auto-PMT function was used to scan the slides with an acceptable PMT range of 400-900. Raw TIFF images were automatically gridded and analyzed using GenePix Pro 6.0 software.

data_processing:
Analyses of microarray data were performed in R with Bioconductor using LIMMA software (Smyth, 2005). Background correction was performed using the “normexp” method. For normalization within arrays, the data were weighted for the genomic DNA controls and normalized using print-tip loess method (Smyth & Speed, 2003). The data were then scale normalized between arrays. The correlation between duplicate spots was calculated (Smyth et al., 2005) and a linear model was fitted to the normalized log ratios and empirical Bayes statistics were applied for differential expression analysis. EGD-e locus names were used in lieu of 10403S locus names to facilitate comparisons exposure and control in this study. Genes with higher transcript levels in the ClO2 exposed cultures compared to its control group (1/fold change>1.5) and adjusted p-values < 0.05 were considered positively differentially expressed, and thus increased activity by ClO2 exposure.  Genes with higher transcript levels in the control cultures compared to the ClO2 exposed culture groups (fold change>1.5) and adjusted p-values <0.05 were considered negatively differentially expressed, and thus had decreased activity by ClO2 exposure. For the oligo spots that were either blank (in the case of the empty spots), over-saturated or had print tip issues, the values are designated as null. The final averaged, normalized values containing the following data columns are provided in the 'avrg_fold.txt' supplementary file;
A: (Log2(CH1)+Log2(CH2))/2
M: Log2-transformed (CH1/CH2) ratio
Fold Change: 2^M-value; (representing reference/test)
1/Fold Change: 1/(2^M-value); (representing test/reference)
adj. p-value: p-value statistic with multiple comparison adjustment

organism: Listeria monocytogenes

label_protocol: The Pathogen Functional Genomics Resource Center/J. Craig Venter Institute (PFGRC/JCVI) L. monocytogenes microarray version 2 was used to identify mRNA transcript level differences between wildtype strains and their respective ClO2 exposed samples. The PFGRC/JCVI microbial RNA aminoallyl labeling for microarray standard operating procedure M007 (publicly available at: http://pfgrc.jcvi.org/index.php/microarray/protocols.html) was used to reverse transcribe and label the total RNA. Spectrophotometry was used to quantify cDNA and total picomoles of Cy3 or Cy5 (Amersham Biosciences, Piscataway, NJ) incorporation. Cy3- and Cy5-labeled cDNA was combined and thoroughly dehydrated prior to hybridization. PFGRC/JCVI standard operating procedure M008 (publicly available at: http://pfgrc.jcvi.org/index.php/microarray/protocols.html) was used to hybridize the Cy-dye labeled cDNA to the microarray.

growth_protocol: Bacteria were initially grown in 5 ml of BHI broth at 37°C, 230rpm shaking for 15 h. A 1% inoculum was transferred to 5 ml of prewarmed BHI broth and grown to an OD600 of ∼0.4. After growth to an OD600 of ∼0.4, a ∼1% (vol/vol) inoculum was transferred to 50 ml of prewarmed (37°C) BHI broth in a 300-ml nephelo flask (Bellco, Vineland, NJ) to obtain a calculated OD600 of 0.004 (the volume transferred was adjusted based on the actual OD600 of the starting inoculum). After growth to an OD600 of ∼0.4, early log phase, the experimental culture was then exposed to ClO2.

extract_protocol: Following exposure, samples were added to ice cold stop solution of 10% acid-phenol chloroform (Life Technologies, Grand Island, NY) in ethanol (10:1 ratio culture to stop solution).  Bacterial cells were then collected by centrifugation at 15,300 x g for 20 min at 4°C.  Cells were re-suspended in 1mL TRI Reagent® (Life Technologies, Grand Island, NY) and added to a 2 mL phase lock tube with 0.1 mm zirconium beads.  Cell lysis was performed through bead beating for 5 cycles of 30 sec each at speed setting 4 in the FastPrep FP120 (BIO101/Savant, Santa Ana, CA).  Samples were chilled on ice between each cycle.  Following centrifugation at 1,700 x g for 10 min at 4°C, 0.1 mL of 1-bromo-3-chloropropane was added to the supernatant and incubated at room temperature for 10 min.  RNA was precipitated in isopropanol at -20°C overnight.  DNase treatment and further RNA purification was performed as outlined previously (Raengpradub et al. 2008).  RNA quantity and quality was assessed by spectroscopy on NanoDrop 2000c (ThermoScientific, Wilmington, DE) and using the 2100 Bioanalyzer system (Agilent, Foster City, CA), respectively.

treatment_protocol: The experimental sample was exposed to 300mg/L aqueous ClO2 (CDG Environmental, Bethlehem, PA) for 15min at 37C, 230rpm.  The same volume of phosphate buffered saline (PBS) was added to the control samples to correct for volume addition and headspace alteration.   Both ClO2 and PBS were pre-warmed to 37C prior to addition.

tag: strain

tag: genotype/variation

value: wild type

tag: exposed to

value: PBS (no treatment control)

tag: treated with

value: 300mg/L aqueous ClO2 for 15min


title: normal tissue from patient 404

description: normal tissue from patient 404

source_name: normal tissue from patient 404

tag: patient id

tag: age

tag: Sex

value: male

tag: tobacco use

value: no

tag: alcohol use

tag: tumor loation

value: lower

tag: tumor grade

value: poorly

tag: tissue

value: normal tissue from patient 404


title: PPC-1 sh184 #1

tag: cell line

tag: cell type

value: primary prostatic tumor cells

value: lacking NWD1 expression (sh184)


title: LM10403S ClO2 exposure rep3

description: Sample 3


title: cancer tissue from patient 404

description: cancer tissue from patient 404

source_name: cancer tissue from patient 404

tag: t stage

tag: n stage

tag: tnm stage

tag: arrhythmia

tag: pneumonia

tag: anastomotic leak

tag: adjuvant therapy

tag: disease state

value: cancer tissue from patient 404


title: PPC-1 shGFP #1

source_name: PPC-1 shGFP

tag: genotype/variation

value: control cells (shGFP)


title: normal tissue from patient 405

description: normal tissue from patient 405

source_name: normal tissue from patient 405

tag: patient id

tag: age

tag: Sex

value: middle

value: moderately

value: II

tag: death at fu

tag: survival time(months)

value: esophageal squamous cell carcinoma

value: normal tissue from patient 405


title: LM10403S ClO2 exposure rep2

description: Sample 2

tag: strain

value: wild type

tag: exposed to

tag: treated with


title: LM10403S ClO2 exposure rep1

description: Sample 1

value: PBS (no treatment control)


title: normal tissue from patient 402

description: normal tissue from patient 402

source_name: normal tissue from patient 402

tag: tobacco use

value: yes

tag: alcohol use

tag: tumor loation

tag: tumor grade

tag: t stage

tag: tissue

value: normal tissue from patient 402


title: cancer tissue from patient 402

description: cancer tissue from patient 402

source_name: cancer tissue from patient 402

value: male

value: no

tag: n stage

tag: tnm stage

tag: arrhythmia

tag: pneumonia

tag: anastomotic leak

tag: adjuvant therapy

value: cancer tissue from patient 402


title: Norm_skin_control_10

description:
9224523042_F
Control 10

source_name: biopsy of normal skin

value: normal skin

tag: lesion stage

tag: lesion size (mm^2)

tag: illness duration at time of biopsy (days)

tag: patient age (years)

tag: patient sex

tag: batch


title: Early_lesion_patient_1

description:
9224523042_I
Patient 1

source_name: biopsy of early cutaneous Leishmania braziliensis lesion

value: Leishmania braziliensis lesion

value: early

value: F


title: Norm_skin_control_9

description:
9224523042_B
Control 9


title: PPC-1 shGFP #2

tag: cell line

tag: cell type

value: primary prostatic tumor cells

tag: genotype/variation

value: control cells (shGFP)


title: normal tissue from patient 398

description: normal tissue from patient 398

source_name: normal tissue from patient 398

tag: patient id

tag: age

tag: Sex

tag: tobacco use

tag: alcohol use

tag: tumor loation

value: lower

tag: tumor grade

value: moderately

tag: t stage

tag: death at fu

tag: survival time(months)

tag: disease state

value: normal tissue from patient 398


title: Norm_skin_control_8

description:
9224523042_H
Control 8

tag: tissue

tag: lesion stage

tag: lesion size (mm^2)

tag: illness duration at time of biopsy (days)

tag: patient age (years)


title: cancer tissue from patient 400

description: cancer tissue from patient 400

source_name: cancer tissue from patient 400

tag: n stage

tag: tnm stage

value: II

tag: arrhythmia

tag: pneumonia

tag: anastomotic leak

tag: adjuvant therapy

value: esophageal squamous cell carcinoma

value: cancer tissue from patient 400


title: cancer tissue from patient 403

description: cancer tissue from patient 403

source_name: cancer tissue from patient 403

tag: patient id

tag: age

tag: Sex

tag: tobacco use

tag: alcohol use

tag: tumor loation

value: middle

value: poorly

value: yes

value: cancer tissue from patient 403


title: Norm_skin_control_7

description:
9224523042_G
Control 7

tag: tissue

tag: patient sex

tag: batch


title: normal tissue from patient 400

description: normal tissue from patient 400

source_name: normal tissue from patient 400

value: male

value: no

tag: tumor grade

tag: t stage

tag: death at fu

tag: survival time(months)

tag: disease state

value: normal tissue from patient 400


title: cancer tissue from patient 398

description: cancer tissue from patient 398

source_name: cancer tissue from patient 398

tag: n stage

tag: tnm stage

tag: arrhythmia

tag: pneumonia

value: cancer tissue from patient 398


title: normal tissue from patient 396

description: normal tissue from patient 396

source_name: normal tissue from patient 396

tag: patient id

tag: age

tag: anastomotic leak

tag: adjuvant therapy

value: normal tissue from patient 396


title: Norm_skin_control_6

description:
9224523042_L
Control 6

value: normal skin

tag: lesion stage

tag: lesion size (mm^2)

tag: illness duration at time of biopsy (days)

tag: patient age (years)


title: cancer tissue from patient 392

description: cancer tissue from patient 392

source_name: cancer tissue from patient 392

tag: Sex

tag: tobacco use

tag: alcohol use

tag: tumor loation

tag: tumor grade

value: III

tag: tissue

value: cancer tissue from patient 392


title: Norm_skin_control_3

description:
9224523027_H
Control 3

tag: patient sex

tag: batch


title: normal tissue from patient 393

description: normal tissue from patient 393

source_name: normal tissue from patient 393

value: female

value: lower

tag: t stage

tag: n stage

tag: tnm stage

tag: arrhythmia

tag: pneumonia

tag: death at fu

tag: survival time(months)

tag: disease state

value: normal tissue from patient 393


title: cancer tissue from patient 393

description: cancer tissue from patient 393

source_name: cancer tissue from patient 393

tag: patient id

tag: age

tag: anastomotic leak

tag: adjuvant therapy

value: esophageal squamous cell carcinoma

value: cancer tissue from patient 393


title: cancer tissue from patient 396

description: cancer tissue from patient 396

source_name: cancer tissue from patient 396

tag: Sex

tag: tobacco use

tag: alcohol use

tag: tumor loation

value: moderately

value: II

value: cancer tissue from patient 396


title: normal tissue from patient 392

description: normal tissue from patient 392

source_name: normal tissue from patient 392

value: yes

tag: tumor grade

tag: tissue

value: normal tissue from patient 392


title: Norm_skin_control_2

description:
7680491091_B
Control 2

tag: lesion stage

tag: lesion size (mm^2)

tag: illness duration at time of biopsy (days)

tag: patient age (years)

tag: patient sex

tag: batch


title: normal tissue from patient 385

description: normal tissue from patient 385

source_name: normal tissue from patient 385

value: no

value: middle

tag: t stage

tag: n stage

tag: tnm stage

tag: arrhythmia

tag: pneumonia

tag: death at fu

tag: survival time(months)

tag: disease state

value: normal tissue from patient 385


title: cancer tissue from patient 385

description: cancer tissue from patient 385

source_name: cancer tissue from patient 385

tag: patient id

tag: age

tag: Sex

tag: tobacco use

tag: alcohol use

tag: tumor loation

tag: anastomotic leak

tag: adjuvant therapy

value: cancer tissue from patient 385


title: normal tissue from patient 382

description: normal tissue from patient 382

source_name: normal tissue from patient 382

value: male

tag: tumor grade

tag: tissue

value: normal tissue from patient 382


title: Norm_skin_control_4

description:
9224523042_E
Control 4

value: normal skin

tag: lesion stage

tag: lesion size (mm^2)

tag: illness duration at time of biopsy (days)

tag: patient age (years)

tag: patient sex

tag: batch


title: cancer tissue from patient 391

description: cancer tissue from patient 391

source_name: cancer tissue from patient 391

value: female

value: upper

tag: t stage

tag: n stage

tag: tnm stage

value: III

tag: arrhythmia

tag: pneumonia

tag: death at fu

tag: survival time(months)

tag: disease state

value: cancer tissue from patient 391


title: Moderate dysplasia 5

type: genomic

city: Aurora

first: Ichiro

last: Nakachi

state: CO

address: 12700 East 19th Avenue, RC2 9th floor

department: Division of Pulmonary Sciences and Critical Care Medicine, Department of Medicine

institute: University of Colorado Denver

description: Genomic DNA extracted from bronchial biopsy was genotyped using Human 660W-Quad chip (Illumina).

scan_protocol: standard Illumina protocols for Human 660w-Quad chip and HumanOmni2.5-Quad chips using iScan

data_processing: Genotyped data, Log R ratio (LRR) and B allele frequency (BAF) were generated using GenomeStudio (Illumina). All samples (bronchial biopsies/brushings) examined were analyzed as pairs with matched reference blood samples.

label: C-Bio and A-DNP

molecule: genomic DNA

source_name: preinvasive lesion

extract_protocol: Biopsies were homogenized in TRIzol reagent and after chloroform addition, the interface layer was saved. Protein was precipitated from the interface using sodium citrate, followed by ethanol precipitation of the supernatant. The DNA pellet was dissolved in low-EDTA TE buffer. For brushings, after overnight digestion with Proteinase-K, DNA was isolated from protein using sodium chloride (salting out), precipitated by ethanol, and dissolved in TE buffer. For reference blood samples, the column-based extraction protocol was conducted using QuickGene-601. Extracted DNA was quantified, verified to be of high molecular weight.

value: moderate dysplasia

tag: bronchial location

value: Right Upper Lung

value: Bronchial biopsy

tag: representation

tag: patient

value: Patient 11


title: Norm_skin_control_5

description:
9224523042_K
Control 5

source_name: biopsy of normal skin

tag: tissue

tag: lesion stage


title: cancer tissue from patient 382

description: cancer tissue from patient 382

source_name: cancer tissue from patient 382

tag: patient id

tag: age

tag: Sex

tag: tobacco use

value: yes

tag: alcohol use

tag: tumor loation

value: lower

tag: tumor grade

value: moderately

tag: anastomotic leak

tag: adjuvant therapy

value: esophageal squamous cell carcinoma

value: cancer tissue from patient 382


title: Patient 11_blood 660w array

description: Genomic DNA extracted from blood was genotyped using Human 660W-Quad chip (Illumina), and used as a reference of PI-6 RUL

hyb_protocol: standard Illumina protocols for Human 660w-Quad chip and HumanOmni2.5-Quad chips

source_name: blood (normal reference)

value: blood (normal reference)

value: Blood

value: Patient11 Blood


title: Invasive cancer 6

source_name: invasive lung cancer

label_protocol: standard Illumina protocols for Human 660w-Quad chip and HumanOmni2.5-Quad chips

value: large cell carcinoma

value: Left Upper Divisional Lung

value: Patient 4


title: normal tissue from patient 381

description: normal tissue from patient 381

source_name: normal tissue from patient 381

value: male

tag: t stage

tag: n stage

tag: tnm stage

value: III

tag: arrhythmia

tag: pneumonia

value: no

tag: death at fu

value: normal tissue from patient 381


title: normal tissue from patient 391

description: normal tissue from patient 391

source_name: normal tissue from patient 391

value: female

value: upper

tag: survival time(months)

tag: disease state

tag: tissue

value: normal tissue from patient 391


title: cancer tissue from patient 381

description: cancer tissue from patient 381

source_name: cancer tissue from patient 381

tag: patient id

tag: age

value: yes

value: lower

value: cancer tissue from patient 381


title: Norm_skin_control_1

description:
7680491091_A
Control 1

value: normal skin

tag: lesion stage

tag: lesion size (mm^2)

tag: illness duration at time of biopsy (days)

tag: patient age (years)

tag: patient sex

tag: batch


title: normal tissue from patient 403

description: normal tissue from patient 403

source_name: normal tissue from patient 403

tag: Sex

tag: tobacco use

tag: alcohol use

tag: tumor loation

value: middle

tag: tumor grade

value: poorly

tag: t stage

value: II

tag: anastomotic leak

tag: adjuvant therapy

value: esophageal squamous cell carcinoma

value: normal tissue from patient 403


title: cancer tissue from patient 380

description: cancer tissue from patient 380

source_name: cancer tissue from patient 380

value: moderately

tag: n stage

tag: tnm stage

tag: arrhythmia

tag: pneumonia

tag: death at fu

tag: survival time(months)

tag: disease state

tag: tissue

value: cancer tissue from patient 380


title: cancer tissue from patient 376

description: cancer tissue from patient 376

source_name: cancer tissue from patient 376

tag: patient id

tag: age

value: male

value: cancer tissue from patient 376


title: normal tissue from patient 378

description: normal tissue from patient 378

source_name: normal tissue from patient 378

tag: Sex

tag: tobacco use

value: well

value: I

value: no

value: normal tissue from patient 378


title: Col-0 seedlings 10 DAS, biological rep1

description: Gene expression data from WT

source_name: 10 DAS seedlings of wild-type

value: seedlings

tag: genetic background

value: Columbia -0

value: 10 days after statification

tag: genotype

value: wild type


title: normal tissue from patient 380

description: normal tissue from patient 380

source_name: normal tissue from patient 380

tag: alcohol use

tag: tumor loation

value: middle

tag: tumor grade

tag: t stage

value: yes

value: normal tissue from patient 380


title: normal tissue from patient 376

description: normal tissue from patient 376

source_name: normal tissue from patient 376

tag: n stage

tag: tnm stage

value: II

tag: anastomotic leak

tag: adjuvant therapy

value: esophageal squamous cell carcinoma

value: normal tissue from patient 376


title: cancer tissue from patient 378

description: cancer tissue from patient 378

source_name: cancer tissue from patient 378

value: lower

tag: arrhythmia

tag: pneumonia

tag: death at fu

tag: survival time(months)

value: cancer tissue from patient 378


title: Patient 4_blood

description: Genomic DNA extracted from blood was genotyped using Human 660W-Quad chip (Illumina), and used as a reference of IC-4 LUDB

tag: disease state

value: blood (normal reference)

tag: tissue

value: Blood

tag: representation

value: Patient4 Blood

tag: patient

value: Patient 4


title: normal tissue from patient 409

description: normal tissue from patient 409

source_name: normal tissue from patient 409

tag: patient id

tag: age

tag: Sex

value: male

tag: tobacco use

value: upper

value: moderately

value: III

value: no

value: normal tissue from patient 409


title: normal tissue from patient 408

description: normal tissue from patient 408

source_name: normal tissue from patient 408

tag: alcohol use

tag: tumor loation

tag: tumor grade

tag: t stage

value: yes

value: normal tissue from patient 408


title: cancer tissue from patient 409

description: cancer tissue from patient 409

source_name: cancer tissue from patient 409

tag: n stage

tag: tnm stage

tag: anastomotic leak

tag: adjuvant therapy

value: cancer tissue from patient 409


title: normal tissue from patient 407

description: normal tissue from patient 407

source_name: normal tissue from patient 407

tag: arrhythmia

tag: pneumonia

tag: death at fu

tag: survival time(months)

value: esophageal squamous cell carcinoma

value: normal tissue from patient 407


title: cancer tissue from patient 407

description: cancer tissue from patient 407

source_name: cancer tissue from patient 407

tag: disease state

tag: tissue

value: cancer tissue from patient 407


title: cancer tissue from patient 373

description: cancer tissue from patient 373

source_name: cancer tissue from patient 373

tag: patient id

tag: age

value: lower

value: poorly

value: cancer tissue from patient 373


title: cancer tissue from patient 375

description: cancer tissue from patient 375

source_name: cancer tissue from patient 375

tag: Sex

tag: tobacco use

value: middle

value: cancer tissue from patient 375


title: cancer tissue from patient 406

description: cancer tissue from patient 406

source_name: cancer tissue from patient 406

value: male

tag: alcohol use

tag: tumor loation

value: cancer tissue from patient 406


title: cancer tissue from patient 374

description: cancer tissue from patient 374

source_name: cancer tissue from patient 374

tag: tumor grade

value: well

tag: t stage

value: II

value: cancer tissue from patient 374


title: normal tissue from patient 374

description: normal tissue from patient 374

source_name: normal tissue from patient 374

tag: n stage

tag: tnm stage

value: no

value: normal tissue from patient 374


title: cancer tissue from patient 408

description: cancer tissue from patient 408

source_name: cancer tissue from patient 408

value: moderately

value: III

tag: anastomotic leak

tag: adjuvant therapy

value: yes

value: cancer tissue from patient 408


title: normal tissue from patient 375

description: normal tissue from patient 375

source_name: normal tissue from patient 375

tag: arrhythmia

tag: pneumonia

value: esophageal squamous cell carcinoma

value: normal tissue from patient 375


title: normal tissue from patient 406

description: normal tissue from patient 406

source_name: normal tissue from patient 406

tag: death at fu

tag: survival time(months)

value: normal tissue from patient 406


title: cancer tissue from patient 371

description: cancer tissue from patient 371

source_name: cancer tissue from patient 371

tag: disease state

tag: tissue

value: cancer tissue from patient 371


title: cancer tissue from patient 370

description: cancer tissue from patient 370

source_name: cancer tissue from patient 370

tag: patient id

tag: age

value: middle

value: cancer tissue from patient 370


title: normal tissue from patient 366

description: normal tissue from patient 366

source_name: normal tissue from patient 366

tag: Sex

value: male

tag: tobacco use

value: poorly

value: I

value: normal tissue from patient 366


title: normal tissue from patient 370

description: normal tissue from patient 370

source_name: normal tissue from patient 370

tag: alcohol use

tag: tumor loation

value: II

value: normal tissue from patient 370


title: normal tissue from patient 367

description: normal tissue from patient 367

source_name: normal tissue from patient 367

value: female

value: no

tag: tumor grade

tag: t stage

value: normal tissue from patient 367


title: cancer tissue from patient 366

description: cancer tissue from patient 366

source_name: cancer tissue from patient 366

value: yes

tag: n stage

tag: tnm stage

value: cancer tissue from patient 366


title: normal tissue from patient 365

description: normal tissue from patient 365

source_name: normal tissue from patient 365

value: III

tag: anastomotic leak

tag: adjuvant therapy

value: esophageal squamous cell carcinoma

value: normal tissue from patient 365


title: normal tissue from patient 373

description: normal tissue from patient 373

source_name: normal tissue from patient 373

value: lower

tag: arrhythmia

tag: pneumonia

value: normal tissue from patient 373


title: cancer tissue from patient 365

description: cancer tissue from patient 365

source_name: cancer tissue from patient 365

value: middle

tag: death at fu

tag: survival time(months)

value: cancer tissue from patient 365


title: normal tissue from patient 362

description: normal tissue from patient 362

source_name: normal tissue from patient 362

value: male

value: poorly

value: unknown

tag: disease state

tag: tissue

value: normal tissue from patient 362


title: normal tissue from patient 361

description: normal tissue from patient 361

source_name: normal tissue from patient 361

tag: patient id

tag: age

value: well

value: II

value: normal tissue from patient 361


title: cancer tissue from patient 362

description: cancer tissue from patient 362

source_name: cancer tissue from patient 362

tag: Sex

tag: tobacco use

value: no

value: cancer tissue from patient 362


title: cancer tissue from patient 367

description: cancer tissue from patient 367

source_name: cancer tissue from patient 367

value: female

tag: alcohol use

tag: tumor loation

value: yes

value: cancer tissue from patient 367


title: normal tissue from patient 355

description: normal tissue from patient 355

source_name: normal tissue from patient 355

value: upper

tag: tumor grade

value: moderately

tag: t stage

value: I

value: esophageal squamous cell carcinoma

value: normal tissue from patient 355


title: 0% tumor content

description: Genomic DNA extracted from blood was genotyped using HumanOmni2.5-Quad chip (Illumina), and used as a reference of PI-12 RML

data_processing: Genotyped data, Log R ratio (LRR) and B allele frequency (BAF) were generated using GenomeStudio (Illumina). All samples (bronchial biopsies/brushings) examined were analyzed as pairs with mathched reference blood samples.

source_name: lymphoblastoid cell line (NCI-BL1395)

extract_protocol: Biopsies were homogenized in TRIzol reagent and after chloroform addition, the interface layer was saved. Protein was precipitated from the interface using sodium citrate, followed by ethanol precipitation of the supernatant. The DNA pellet was dissolved in low-EDTA TE buffer. For brushings, after overnight digestion with Proteinase-K, DNA was isolated from protein using sodium chloride (salting out), precipitated by ethanol, and dissolved in TE buffer. For reference blood samples, the column-based extraction protocol was conducted using QuickGene-601. Extracted DNA was quantified, verified to be of high molecular weight. For cell line pair, genomic DNA was purchased from cell bank (ATCC).

value: lymphoblastoid cell (normal reference)

value: Blood

tag: representation

value: 0% tumor


title: 12.5% tumor content

source_name: H1395 mixed with BL1395

value: non-small cell lung cancer

value: Tumor tissue

value: 12% tumor


title: cancer tissue from patient 361

description: cancer tissue from patient 361

source_name: cancer tissue from patient 361

value: male

value: middle

value: well

tag: n stage

tag: tnm stage

value: II

tag: anastomotic leak

value: cancer tissue from patient 361


title: 1.6% tumor content

value: 1% tumor


title: Hyperplasia 1

source_name: preinvasive lesion

value: hyperplasia

tag: bronchial location

value: Right Lower Lung

value: Bronchial biopsy

tag: patient

value: Patient 5


title: normal tissue from patient 353

description: normal tissue from patient 353

source_name: normal tissue from patient 353

value: no

value: yes

value: poorly

value: III

tag: arrhythmia

tag: pneumonia

tag: adjuvant therapy

tag: death at fu

tag: survival time(months)

value: esophageal squamous cell carcinoma

value: normal tissue from patient 353


title: cancer tissue from patient 355

description: cancer tissue from patient 355

source_name: cancer tissue from patient 355

tag: patient id

tag: age

tag: Sex

value: female

value: upper

value: moderately

value: I

tag: disease state

tag: tissue

value: cancer tissue from patient 355


title: 25% tumor content

value: non-small cell lung cancer

value: Tumor tissue

value: 25% tumor


title: cancer tissue from patient 353

description: cancer tissue from patient 353

source_name: cancer tissue from patient 353

value: male

tag: tobacco use

tag: alcohol use

tag: tumor loation

value: middle

tag: tumor grade

tag: t stage

value: cancer tissue from patient 353


title: Patient 12_blood

source_name: blood

value: blood (normal reference)

value: Blood

tag: representation

value: Patient 12 blood

value: Patient 12


title: normal tissue from patient 342

description: normal tissue from patient 342

source_name: normal tissue from patient 342

value: yes

value: lower

value: well

tag: n stage

tag: tnm stage

value: III

value: no

tag: anastomotic leak

value: esophageal squamous cell carcinoma

value: normal tissue from patient 342


title: cancer tissue from patient 347

description: cancer tissue from patient 347

source_name: cancer tissue from patient 347

value: moderately

value: II

tag: arrhythmia

tag: pneumonia

tag: adjuvant therapy

value: cancer tissue from patient 347


title: day12 Corin+ day42_3

city: Kyoto

first: Daisuke

last: Doi

address: 53 Kawahara-cho, Shogoin, Sakyoku

department: Clinical Application

country: Japan

institute: Center for iPS Cell Research and Application

hyb_protocol: Following fragmentation, 5.5 ug of cDNA were hybridized for 17 hr at 45C on GeneChip Human Gene-1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The data were analyzed with GeneSpring version 12.5 using default analysis settings and global scaling as normalization method (RMA16).

source_name: iPSC-derived cells (day12 Corin+, day42)

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 200 ng total RNA (Ambion WT Expression Kit, 2011, Affymetrix).

growth_protocol: The iPSCs were cultured on chemically definced matrix before cell sorting, and then the cells were cultured on aggregative sphere.

extract_protocol: Total RNA was extracted by Rneasy mini Kit by Qiagen, accoring to manufucture's protocol.

treatment_protocol: Cultured cells were harvested after an enzymatic dissociation. At least 1 million cells were harvested.

tag: tisuue

value: cultured cells

tag: cell type


title: normal tissue from patient 347

description: normal tissue from patient 347

source_name: normal tissue from patient 347

tag: patient id

tag: age

tag: Sex

value: male

tag: death at fu

tag: survival time(months)

value: normal tissue from patient 347


title: 6.3% tumor content

tag: disease state

value: non-small cell lung cancer

tag: tissue

value: Tumor tissue

value: 6% tumor


title: day12 Corin+ day42_2

value: iPSC-derived cells (day12 Corin+, day42)


title: cancer tissue from patient 342

description: cancer tissue from patient 342

source_name: cancer tissue from patient 342

tag: tobacco use

value: yes

tag: alcohol use

tag: tumor loation

tag: tumor grade

tag: t stage

value: cancer tissue from patient 342


title: Mild dysplasia 4

value: mild dysplasia

tag: bronchial location

value: Right Middle Lung

value: Bronchial brushing

tag: representation

tag: patient

value: Patient 15


title: normal tissue from patient 341

description: normal tissue from patient 341

source_name: normal tissue from patient 341

value: no

value: lower

value: poorly

tag: n stage

tag: tnm stage

value: III

tag: arrhythmia

tag: pneumonia

tag: anastomotic leak

tag: adjuvant therapy

value: unknown

value: esophageal squamous cell carcinoma

value: normal tissue from patient 341


title: 3.1% tumor content

value: non-small cell lung cancer

value: 3% tumor


title: day12 Corin+ day42_1

tag: tisuue

value: cultured cells

tag: cell type


title: cancer tissue from patient 341

description: cancer tissue from patient 341

source_name: cancer tissue from patient 341

tag: patient id

tag: age

tag: Sex

value: male

tag: death at fu

tag: survival time(months)

tag: disease state

tag: tissue

value: cancer tissue from patient 341


title: cancer tissue from patient 340

description: cancer tissue from patient 340

source_name: cancer tissue from patient 340

tag: tobacco use

value: yes

tag: alcohol use

tag: tumor loation

tag: tumor grade

value: moderately

tag: t stage

value: II

value: cancer tissue from patient 340


title: normal tissue from patient 340

description: normal tissue from patient 340

source_name: normal tissue from patient 340

tag: n stage

tag: tnm stage

tag: arrhythmia

tag: pneumonia

value: normal tissue from patient 340


title: Moderate dysplasia 2

value: moderate dysplasia

tag: bronchial location

value: Right Upper Lung

value: Bronchial brushing

tag: representation

tag: patient

value: Patient 6


title: day12 unsorted day42_2

source_name: iPSC-derived cells (day12 unsorted, day42)

tag: tisuue

tag: cell type


title: Moderate dysplasia 6

value: Left Upper Lung

value: Patient 12


title: normal tissue from patient 338

description: normal tissue from patient 338

source_name: normal tissue from patient 338

tag: patient id

tag: age

tag: Sex

value: middle

value: poorly

value: III

value: no

tag: anastomotic leak

tag: adjuvant therapy

tag: death at fu

tag: survival time(months)

value: esophageal squamous cell carcinoma

value: normal tissue from patient 338


title: Severe dysplasia 2

tag: disease state

value: severe dysplasia

value: Left Lower Lung

tag: tissue

value: Patient 8


title: Mild dysplasia 1

value: mild dysplasia


title: Patient 8_blood

value: blood (normal reference)

value: Blood

value: Patient 8 blood


title: normal tissue from patient 337

description: normal tissue from patient 337

source_name: normal tissue from patient 337

value: male

tag: tobacco use

tag: alcohol use

tag: tumor loation

value: lower

tag: tumor grade

value: well

tag: t stage

tag: n stage

tag: tnm stage

value: yes

value: normal tissue from patient 337


title: cancer tissue from patient 337

description: cancer tissue from patient 337

source_name: cancer tissue from patient 337

tag: arrhythmia

tag: pneumonia

value: cancer tissue from patient 337


title: cancer tissue from patient 338

description: cancer tissue from patient 338

source_name: cancer tissue from patient 338

tag: patient id

tag: age

value: middle

value: poorly

value: III

value: cancer tissue from patient 338


title: day12 unsorted day42_1

tag: tisuue

value: cultured cells

tag: cell type

value: iPSC-derived cells (day12 unsorted, day42)


title: day12 Corin+ day28_3

source_name: iPSC-derived cells (day12 Corin+, day28)


title: Moderate dysplasia 7

source_name: preinvasive lesion

value: moderate dysplasia

tag: bronchial location

value: Right Middle Lung

value: Bronchial brushing

tag: representation

tag: patient

value: Patient 12


title: normal tissue from patient 371

description: normal tissue from patient 371

source_name: normal tissue from patient 371

tag: Sex

value: no

tag: anastomotic leak

tag: adjuvant therapy

tag: death at fu

tag: survival time(months)

tag: disease state

value: esophageal squamous cell carcinoma

tag: tissue

value: normal tissue from patient 371


title: 100% tumor content

source_name: pure cancer cell line (NCI-H1395)

value: non-small cell lung cancer

value: Tumor tissue

value: 100% tumor


title: normal tissue from patient 334

description: normal tissue from patient 334

source_name: normal tissue from patient 334

value: male

tag: tobacco use

value: yes

tag: alcohol use

tag: tumor loation

value: lower

tag: tumor grade

tag: t stage

tag: n stage

tag: tnm stage

value: II

value: normal tissue from patient 334


title: cancer tissue from patient 334

description: cancer tissue from patient 334

source_name: cancer tissue from patient 334

tag: patient id

tag: age

value: poorly

tag: arrhythmia

tag: pneumonia

value: cancer tissue from patient 334


title: day12 Corin+ day28_2

tag: tisuue

value: cultured cells

tag: cell type

value: iPSC-derived cells (day12 Corin+, day28)


title: Normal histology 3

description: Genomic DNA extracted from bronchial brushing was genotyped using HumanOmni2.5-Quad chip (Illumina).

value: normal histology

tag: bronchial location

value: Right Middle Lung

value: Bronchial brushing

tag: representation

tag: patient

value: Patient 18


title: Patient 18_blood

source_name: blood (normal reference)

tag: disease state

value: blood (normal reference)

tag: tissue

value: Blood

value: Patient 18 Blood


title: cancer tissue from patient 333

description: cancer tissue from patient 333

source_name: cancer tissue from patient 333

tag: Sex

tag: tobacco use

tag: alcohol use

value: no

value: upper

tag: anastomotic leak

tag: adjuvant therapy

tag: death at fu

tag: survival time(months)

value: esophageal squamous cell carcinoma

value: cancer tissue from patient 333


title: normal tissue from patient 333

description: normal tissue from patient 333

source_name: normal tissue from patient 333

tag: patient id

tag: age

value: male

value: yes

tag: tumor loation

tag: tumor grade

tag: t stage

tag: n stage

tag: tnm stage

value: II

value: normal tissue from patient 333


title: day12 unsorted day28_3

source_name: iPSC-derived cells (day12 unsorted, day28)

tag: tisuue

value: cultured cells

tag: cell type


title: Carcinoma in situ 3

tag: disease state

value: carcinoma in situ

tag: bronchial location

value: Left Upper Lung

tag: tissue

tag: representation

tag: patient

value: Patient 7


title: normal tissue from patient 322

description: normal tissue from patient 322

source_name: normal tissue from patient 322

tag: Sex

value: female

tag: tobacco use

tag: alcohol use

value: lower

value: well

value: I

tag: arrhythmia

tag: pneumonia

tag: anastomotic leak

tag: adjuvant therapy

value: normal tissue from patient 322


title: cancer tissue from patient 324

description: cancer tissue from patient 324

source_name: cancer tissue from patient 324

tag: patient id

tag: age

value: no

tag: tumor loation

value: middle

tag: tumor grade

tag: t stage

tag: death at fu

tag: survival time(months)

value: cancer tissue from patient 324


title: day12 Corin+ day28_1

tag: tisuue

tag: cell type

value: iPSC-derived cells (day12 Corin+, day28)


title: cancer tissue from patient 322

description: cancer tissue from patient 322

source_name: cancer tissue from patient 322

tag: n stage

tag: tnm stage

tag: disease state

value: esophageal squamous cell carcinoma

tag: tissue

value: cancer tissue from patient 322


title: normal tissue from patient 324

description: normal tissue from patient 324

source_name: normal tissue from patient 324

tag: Sex

tag: tobacco use

tag: alcohol use

value: II

tag: arrhythmia

value: normal tissue from patient 324


title: normal tissue from patient 321

description: normal tissue from patient 321

source_name: normal tissue from patient 321

tag: patient id

value: male

value: yes

value: moderately

tag: pneumonia

tag: anastomotic leak

tag: adjuvant therapy

value: unknown

value: normal tissue from patient 321


title: day12 unsorted day28_1

value: cultured cells

value: iPSC-derived cells (day12 unsorted, day28)


title: cancer tissue from patient 321

description: cancer tissue from patient 321

source_name: cancer tissue from patient 321

tag: age

tag: tumor loation

value: lower

tag: tumor grade

tag: t stage

value: cancer tissue from patient 321


title: Moderate dysplasia 4

value: moderate dysplasia

tag: bronchial location

value: Right Lower Lung

value: Bronchial brushing

tag: representation

tag: patient

value: Patient 7


title: day12 unsorted day28_2

tag: tisuue

tag: cell type


title: Patient 15_blood

description: Genomic DNA extracted from blood was genotyped using HumanOmni2.5-Quad chip (Illumina), and used as a reference of PI-10 RUL

tag: disease state

value: blood (normal reference)

tag: tissue

value: Blood

value: Patient 15 Blood

value: Patient 15