title: PBMC from Stable  154.2 at T0

description: STA, Biological replicate  154 of 190, Technical replicate 2 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA154.2

value: PBMC from STA154

tag: time point


title: PBMC from Stable  154.1 at T0

status: Public on Feb 09 2017

type: RNA

city: Nantes

first: Daniel

last: BARON

state: Loire-Atlantique (44)

address: 30 Bd Jean Monnet

department: UMR1064 - Centre de Recherche en Transplantation & Immunologie

country: France

institute: Institut national de la santé et de la recherche médicale-INSERM

description: STA, Biological replicate  154 of 190, Technical replicate 1 of 2

hyb_protocol: 1 mg of Cy5-labeled reference aRNA and 1 mg of Cy3-labeled sample aRNA were hybridized on the array for 16 h at 428C in a sealed chamber (Telechem Int., Sunnyval, CA).

scan_protocol: Hybridized slides were scanned by fluorescence confocal microscopy (ScanArray 3000,GSI-Lumonics) using independent laser excitation of the two fluorescent dyes at 532 and 633 nm at a 10 mm/pixel resolution. Fluorescence values and ratios were extracted with the GenePix Pro 5.1 software.

data_processing: The data were normalized using a lowest fit approach independently applied to each log ratio distributions.

molecule: total RNA

organism: Homo sapiens

source_name: Total RNA from PBMC of 169 kidney graft recipients with stable graft function and under standard immunosuppressive treatment

label_protocol: All aRNA samples were fragmented using RNA fragmentation Reagents (Ambion) according to the manufacturer’s protocols. Fragmented aRNA  were labeled with Cyanine 3 (Cy3; Amersham Biosciences, Buckinghamshire, UK). As the reference for the hybridization, aRNA were prepared as described from PBMC of 169 kidney graft recipients with stable graft function and under standard immunosuppressive treatment. This referential aRNA was pooled and labeled with Cyanine 5 (Cy5). Cyanine incorporation and aRNA quantities were confirmed using a Nanodrop ND1000 spectrometer.

extract_protocol: Ten milliliters of peripheral blood were collected in EDTA tubes. Peripheral Blood Mononuclear Cells (PBMC) were separated on a Ficoll layer (Eurobio, Les Ulis, France) and frozen in Trizol1 reagent (Invitrogen, Life Technologies, CA). One microgram of total RNA (tRNA) of each sample was subjected to amplification using the Amino Allyl MessageAmp TM II aRNA Amplification Kit (Ambion, Austin, TX) according to the manufacturer’s protocols. Quality and quantity of tRNA and amplified RNA (aRNA) was tested by an Agilent 2100 Bioanalyser.

tag: sample type

value: pool of 169 PBMC samples from Stable patients (STA)

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA154.1

tag: tissue

tag: individual replicate

tag: techical replicate

value: Replicate 1 of 2


title: PBMC from Stable  155.2 at T0

description: STA, Biological replicate  155 of 190, Technical replicate 2 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA155.2

value: PBMC from STA155

value: Replicate 2 of 2


title: ESCC_Biopsy_ES02202

city: Chuo-ku

first: Hiroki

last: Sasaki

state: Tokyo

country: Japan

institute: National Cancer Center Reseach Institute

description: Gene expression data from biopsy of esophageal squamous cell carcinoma

hyb_protocol: Following fragmentation, 10µg of cRNA were hybridized for 16 hr at 45ﾟC on GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner 3000 7G.

data_processing: The data were analyzed with GeneSpring version 12.6 using affymetrix expression analysis settings (Summarization algorithm: MAS5).

label: biotin

source_name: Esophageal squamous cell carcinoma

label_protocol: Biotinylated cRNA were prepared from 100 ng total RNA by GeneChip 3' IVT Express Kit. The procedure was according to the standard Affymetrix protocol.

growth_protocol: All esophageal squamous cell carcionma specimens were provided by the National Cancer Center Hospital and National Cancer Center Hospital East after obtaining written informed consent from each patient and approval by the Center’s Ethics Committee.

extract_protocol: Frozen biopsy specimens were placed in the ISOGEN solution and homogenised. Extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: All biopsy specimens were obtained before therapy and immediately frozen at -80 ﾟC until use.

tag: disease state

value: ESCC

value: Biopsy before therapy

tag: therapy

value: Chemoradiotherapy


title: PBMC from Stable  153.2 at T0

description: STA, Biological replicate  153 of 190, Technical replicate 2 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA153.2

value: PBMC from STA153


title: 76WD2

city: Chicago

first: Yinan

last: Zheng

state: Illinois

address: 680 N Lake Shore Drive, Suite 1400

department: Department of Preventive Medicine

country: USA

institute: Northwestern University

description: Participant 76 measured at day 2

hyb_protocol: See manufacturer's website: http://www.nanostring.com/

data_processing: The raw data were first quantile normalized (without controls), then log2 transformed.

source_name: Whole blood

extract_protocol: A total of 240 peripheral blood samples from 120 participants on both examination days were collected in PAXgene Blood RNA Tubes.  We collected 24 ml of blood at the end of each study day (between 4-6 p.m.) from each participant at each participant’s workplace.  All samples were frozen at -80ºC and sent to the laboratory.  Total RNA was extracted from whole blood according to the manufacturer’s protocols using the PAXgene Blood RNA Kit Qiagen-763134 (Qiagen, Valencia, California).  RNA samples were quantified and quality controlled using absorbance measurements, following NanoString’s technical guidelines.  The mean RNA concentration was 104.4 µg/ml.  All samples had an optical density (OD) 280/260 ratio of 1.9 or greater and an OD 260/230 ratio of 1.8 or greater.

tag: group

value: Office Worker

tag: Sex

value: Female

tag: age

tag: bmi

tag: regular drinker

tag: smoker

tag: cigarettes smoked

tag: temperature

tag: dew point

tag: initial sbp

tag: initial dbp

tag: final sbp

tag: final dbp

tag: fvc

tag: pef


title: ESCC_Biopsy_ES03501

tag: disease state

tag: tissue


title: ESCC_Biopsy_ES01701

tag: therapy


title: 92WD2

description: Participant 92 measured at day 2

scan_protocol: See manufacturer's website: http://www.nanostring.com/

tag: group

tag: Sex


title: ESCC_Biopsy_ES02301


title: 75WD1

description: Participant 75 measured at day 1

label_protocol: See manufacturer's website: http://www.nanostring.com/

tag: age

tag: bmi


title: 77WD1

description: Participant 77 measured at day 1

tag: regular drinker

tag: smoker


title: 73WD2

description: Participant 73 measured at day 2

value: Truck Driver

value: Male

tag: cigarettes smoked

tag: temperature


title: 74WD1

description: Participant 74 measured at day 1

tag: dew point

tag: initial sbp


title: 75WD2

description: Participant 75 measured at day 2

tag: initial dbp

tag: final sbp


title: 74WD2

description: Participant 74 measured at day 2

tag: final dbp

tag: fvc


title: PBMC from Stable  153.1 at T0

description: STA, Biological replicate  153 of 190, Technical replicate 1 of 2

tag: sample type

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA153.1

tag: individual replicate

tag: techical replicate

tag: time point


title: 76WD1

description: Participant 76 measured at day 1

tag: group

tag: Sex

tag: pef


title: 72WD2

description: Participant 72 measured at day 2

tag: age

tag: bmi

tag: regular drinker


title: 71WD2

description: Participant 71 measured at day 2

tag: smoker

tag: cigarettes smoked

tag: temperature


title: 71WD1

description: Participant 71 measured at day 1

tag: dew point

tag: initial sbp

tag: initial dbp


title: PBMC from Stable  152.2 at T0

description: STA, Biological replicate  152 of 190, Technical replicate 2 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA152.2

tag: tissue

value: PBMC from STA152


title: PBMC from Stable  152.1 at T0

description: STA, Biological replicate  152 of 190, Technical replicate 1 of 2

tag: sample type

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA152.1


title: 70WD2

description: Participant 70 measured at day 2

tag: final sbp

tag: final dbp

tag: fvc


title: 70WD1

description: Participant 70 measured at day 1

tag: group


title: ESCC_Biopsy_ES01102

tag: disease state

tag: therapy


title: ESCC_Biopsy_ES01402


title: PBMC from Stable  151.2 at T0

description: STA, Biological replicate  151 of 190, Technical replicate 2 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA151.2

value: PBMC from STA151

tag: individual replicate

tag: techical replicate

tag: time point


title: PBMC from Stable  150.1 at T0

description: STA, Biological replicate  150 of 190, Technical replicate 1 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA150.1

value: PBMC from STA150


title: ESCC_Biopsy_ES00802


title: 73WD1

description: Participant 73 measured at day 1

tag: Sex

tag: age

tag: bmi

tag: regular drinker

tag: smoker

tag: pef


title: PBMC from Stable  151.1 at T0

description: STA, Biological replicate  151 of 190, Technical replicate 1 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA151.1

tag: tissue


title: PBMC from Stable  150.2 at T0

description: STA, Biological replicate  150 of 190, Technical replicate 2 of 2

tag: sample type

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA150.2


title: ESCC_Biopsy_ES00402


title: ESCC_Biopsy_ES00302


title: 69WD2

description: Participant 69 measured at day 2

tag: cigarettes smoked

tag: temperature

tag: dew point

tag: initial sbp

tag: initial dbp

tag: final sbp


title: ESCC_Biopsy_ES00202

tag: disease state

tag: therapy


title: ESCC_Biopsy_ES00102


title: 67WD2

description: Participant 67 measured at day 2

tag: group

tag: final dbp

tag: fvc


title: 69WD1

description: Participant 69 measured at day 1

tag: Sex

tag: age

tag: bmi


title: 68WD2

description: Participant 68 measured at day 2

tag: regular drinker

tag: smoker

tag: pef


title: 68WD1

description: Participant 68 measured at day 1

tag: cigarettes smoked


title: 66WD2

description: Participant 66 measured at day 2

tag: temperature


title: 67WD1

description: Participant 67 measured at day 1

tag: dew point


title: 72WD1

description: Participant 72 measured at day 1

tag: initial sbp


title: 65WD2

description: Participant 65 measured at day 2

tag: initial dbp


title: 65WD1

description: Participant 65 measured at day 1

tag: final sbp


title: PBMC from Stable  149.1 at T0

description: STA, Biological replicate  149 of 190, Technical replicate 1 of 2

tag: sample type

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA149.1

tag: tissue

value: PBMC from STA149

tag: individual replicate

tag: techical replicate

tag: time point


title: PBMC from Stable  148.2 at T0

description: STA, Biological replicate  148 of 190, Technical replicate 2 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA148.2

value: PBMC from STA148


title: 64WD2

description: Participant 64 measured at day 2

tag: group

tag: Sex

tag: final dbp

tag: fvc


title: PBMC from Stable  148.1 at T0

description: STA, Biological replicate  148 of 190, Technical replicate 1 of 2

value: pool of 169 PBMC samples from Stable patients (STA)

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA148.1


title: 63WD2

description: Participant 63 measured at day 2

tag: age

tag: bmi

tag: regular drinker

tag: smoker


title: 64WD1

description: Participant 64 measured at day 1

tag: cigarettes smoked

tag: temperature

tag: dew point

tag: pef


title: PBMC from Stable  149.2 at T0

description: STA, Biological replicate  149 of 190, Technical replicate 2 of 2

tag: sample type

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA149.2


title: ESCC_Biopsy_BPY257

tag: disease state

tag: tissue

tag: therapy


title: 66WD1

description: Participant 66 measured at day 1

tag: initial sbp

tag: initial dbp

tag: final sbp


title: ESCC_Biopsy_BPY258


title: 63WD1

description: Participant 63 measured at day 1

tag: group

tag: Sex

tag: final dbp


title: ESCC_Biopsy_BPY256

tag: tumor stage

value: StageIII

tag: tnm stage


title: PBMC from Stable  147.1 at T0

description: STA, Biological replicate  147 of 190, Technical replicate 1 of 2

source_name: Total RNA from PBMC of 169 kidney graft recipients with stable graft function and under standard immunosuppressive treatment

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA147.1

value: PBMC from STA147

tag: individual replicate

tag: techical replicate

value: Replicate 1 of 2

tag: time point


title: ESCC_Biopsy_BPY266

value: ESCC


title: 61WD2

description: Participant 61 measured at day 2

tag: age

tag: bmi

tag: regular drinker

tag: smoker

tag: cigarettes smoked

tag: temperature

tag: dew point

tag: fvc


title: 62WD1

description: Participant 62 measured at day 1

tag: initial sbp

tag: initial dbp

tag: final sbp

tag: pef


title: 62WD2

description: Participant 62 measured at day 2

tag: group

tag: Sex

tag: final dbp


title: PBMC from Stable  146.2 at T0

description: STA, Biological replicate  146 of 190, Technical replicate 2 of 2

tag: sample type

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA146.2

tag: tissue

value: PBMC from STA146

tag: individual replicate

tag: techical replicate

value: Replicate 2 of 2


title: 61WD1

description: Participant 61 measured at day 1

tag: age

tag: bmi

tag: regular drinker


title: PBMC from Stable  147.2 at T0

description: STA, Biological replicate  147 of 190, Technical replicate 2 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA147.2

tag: time point


title: 60WD2

description: Participant 60 measured at day 2

tag: smoker

tag: cigarettes smoked

tag: temperature

tag: dew point


title: 60WD1

description: Participant 60 measured at day 1

tag: initial sbp

tag: initial dbp

tag: final sbp

tag: fvc


title: 59WD2

description: Participant 59 measured at day 2

tag: group

tag: Sex

tag: final dbp

tag: pef


title: ESCC_Biopsy_BPY253

source_name: Esophageal squamous cell carcinoma

tag: disease state

tag: tissue

value: Biopsy before therapy

tag: therapy

value: Chemoradiotherapy


title: ESCC_Biopsy_BPY250


title: PBMC from Stable  146.1 at T0

description: STA, Biological replicate  146 of 190, Technical replicate 1 of 2

tag: sample type

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA146.1

tag: individual replicate

tag: techical replicate


title: PBMC from Stable  145.2 at T0

description: STA, Biological replicate  145 of 190, Technical replicate 2 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA145.2

value: PBMC from STA145

tag: time point


title: PBMC from Stable  145.1 at T0

description: STA, Biological replicate  145 of 190, Technical replicate 1 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA145.1


title: 58WD1

description: Participant 58 measured at day 1

source_name: Whole blood

value: Truck Driver

tag: age

tag: bmi

tag: regular drinker

tag: smoker

tag: cigarettes smoked

tag: temperature


title: ESCC_Biopsy_BPY252

description: Gene expression data from biopsy of esophageal squamous cell carcinoma


title: ESCC_Biopsy_ES00702


title: 58WD2

description: Participant 58 measured at day 2

tag: group

value: Male

tag: dew point

tag: initial sbp

tag: initial dbp

tag: final sbp

tag: fvc


title: ESCC_Biopsy_BPY255

tag: disease state

tag: tissue

tag: therapy


title: ESCC_Biopsy_BPY247


title: 57WD1

description: Participant 57 measured at day 1

tag: Sex

tag: final dbp

tag: pef


title: 57WD2

description: Participant 57 measured at day 2

tag: age

tag: bmi


title: ESCC_Biopsy_BPY246


title: 55WD2

description: Participant 55 measured at day 2

value: Office Worker

tag: regular drinker

tag: smoker


title: ESCC_Biopsy_BPY237


title: 55WD1

description: Participant 55 measured at day 1

tag: cigarettes smoked

tag: temperature


title: PBMC from Stable  143.2 at T0

description: STA, Biological replicate  143 of 190, Technical replicate 2 of 2

tag: sample type

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA143.2

value: PBMC from STA143

tag: individual replicate

tag: techical replicate

tag: time point


title: ESCC_Biopsy_BPY232


title: 54WD2

description: Participant 54 measured at day 2

tag: group

tag: dew point

tag: initial sbp

tag: initial dbp

tag: final sbp

tag: fvc


title: 53WD2

description: Participant 53 measured at day 2

tag: Sex

tag: final dbp

tag: pef


title: 52WD2

description: Participant 52 measured at day 2

tag: age

tag: bmi

tag: regular drinker


title: 53WD1

description: Participant 53 measured at day 1

tag: smoker

tag: cigarettes smoked

tag: temperature


title: PBMC from Stable  144.1 at T0

description: STA, Biological replicate  144 of 190, Technical replicate 1 of 2

tag: sample type

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA144.1

tag: tissue

value: PBMC from STA144

tag: individual replicate

tag: techical replicate


title: 52WD1

description: Participant 52 measured at day 1

tag: group

tag: dew point

tag: initial sbp


title: PBMC from Stable  144.2 at T0

description: STA, Biological replicate  144 of 190, Technical replicate 2 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA144.2

tag: time point


title: ESCC_Biopsy_BPY230

tag: disease state

tag: therapy


title: PBMC from Stable  143.1 at T0

description: STA, Biological replicate  143 of 190, Technical replicate 1 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA143.1


title: ESCC_Biopsy_BPY228


title: PBMC from Stable  142.2 at T0

description: STA, Biological replicate  142 of 190, Technical replicate 2 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA142.2

value: PBMC from STA142


title: 51WD2

description: Participant 51 measured at day 2

tag: Sex

tag: initial dbp

tag: final sbp

tag: final dbp

tag: fvc

tag: pef


title: PBMC from Stable  142.1 at T0

description: STA, Biological replicate  142 of 190, Technical replicate 1 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA142.1


title: 54WD1

description: Participant 54 measured at day 1

tag: age

tag: bmi

tag: regular drinker

tag: smoker

tag: cigarettes smoked

tag: temperature


title: ESCC_Biopsy_BPY226

tag: tissue

tag: tumor stage

tag: tnm stage


title: PBMC from Stable  141.2 at T0

description: STA, Biological replicate  141 of 190, Technical replicate 2 of 2

tag: sample type

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA141.2

value: PBMC from STA141

tag: individual replicate

tag: techical replicate

tag: time point


title: ESCC_Biopsy_BPY219

tag: disease state

tag: therapy


title: 51WD1

description: Participant 51 measured at day 1

tag: group

tag: Sex

tag: dew point

tag: initial sbp

tag: initial dbp

tag: final sbp

tag: final dbp

tag: fvc


title: 50WD2

description: Participant 50 measured at day 2

tag: age

tag: bmi

tag: regular drinker

tag: smoker

tag: cigarettes smoked

tag: temperature

tag: pef


title: 49WD2

description: Participant 49 measured at day 2


title: 49WD1

description: Participant 49 measured at day 1


title: 48WD1

description: Participant 48 measured at day 1


title: PBMC from Stable  140.2 at T0

description: STA, Biological replicate  140 of 190, Technical replicate 2 of 2

tag: sample type

value: pool of 169 PBMC samples from Stable patients (STA)

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA140.2

tag: tissue

value: PBMC from STA140

tag: individual replicate

tag: techical replicate

tag: time point


title: PBMC from Stable  141.1 at T0

description: STA, Biological replicate  141 of 190, Technical replicate 1 of 2

source_name: Total RNA from PBMC of 169 kidney graft recipients with stable graft function and under standard immunosuppressive treatment

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA141.1


title: 47WD2

description: Participant 47 measured at day 2

tag: group

tag: Sex

tag: dew point

tag: initial sbp


title: ESCC_Biopsy_BPY207

tag: disease state

tag: therapy


title: 47WD1

description: Participant 47 measured at day 1

tag: age

tag: bmi

tag: initial dbp

tag: final sbp

tag: final dbp

tag: fvc


title: ESCC_Biopsy_BPY202


title: PBMC from Stable  139.2 at T0

description: STA, Biological replicate  139 of 190, Technical replicate 2 of 2

tag: sample type

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA139.2

value: PBMC from STA139


title: ESCC_Biopsy_BPY206

tag: tissue


title: 46WD2

description: Participant 46 measured at day 2

tag: regular drinker

tag: smoker

tag: cigarettes smoked

tag: temperature

tag: pef


title: 48WD2

description: Participant 48 measured at day 2

tag: group

tag: Sex

tag: dew point


title: pericarp WT_TU_rep2

city: Chania

first: Panagiotis

last: Kalaitzis

address: Alsyllio Agrokepio, 1 Makedonias str

department: Horticultural Genetics and Biotechnology

country: Greece

institute: Mediterranean Agronomic Institute of Chania (MAICh)

hyb_protocol: GeneAtlas Hybridization, Wash and Stain Kit for WT Array Strips  #901667

scan_protocol: Affymetrix GeneAtlas Imaging Station

data_processing: Affymetrix Expression Console, RMA and Transcriptome Analysis Console v2.0

organism: Solanum lycopersicum

source_name: Turning 2

label_protocol: Affymetrix GeneChip WT Terminal Labeling Kit  #900671

growth_protocol: lines were grown under standard open greenhouse hydroponic conditions until plants reached desired developmental stage

extract_protocol: Εach sample we analyzed 500 ng total RNA extracted with the PureLink® RNA Mini Kit (Ambion)

tag: developmental stage

value: Turning


title: PBMC from Stable  138.1 at T0

description: STA, Biological replicate  138 of 190, Technical replicate 1 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA138.1

value: PBMC from STA138

tag: individual replicate

tag: techical replicate

value: Replicate 1 of 2

tag: time point


title: PBMC from Stable  140.1 at T0

description: STA, Biological replicate  140 of 190, Technical replicate 1 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA140.1


title: ESCC_Biopsy_BPY189

source_name: Esophageal squamous cell carcinoma

tag: disease state

value: ESCC

tag: therapy


title: 46WD1

description: Participant 46 measured at day 1

tag: age

tag: bmi

tag: initial sbp

tag: initial dbp

tag: final sbp

tag: final dbp

tag: fvc


title: ESCC_Biopsy_BPY190

tag: tissue

value: Biopsy before therapy


title: PBMC from Stable  139.1 at T0

description: STA, Biological replicate  139 of 190, Technical replicate 1 of 2

tag: sample type

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA139.1


title: pericarp WT_PK_rep2

source_name: Pink 2

value: Pink


title: ESCC_Biopsy_BPY210

value: Chemoradiotherapy


title: pericarp WT_TU_rep1

source_name: Turning 1


title: PBMC from Stable  138.2 at T0

description: STA, Biological replicate  138 of 190, Technical replicate 2 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA138.2

value: Replicate 2 of 2


title: PBMC from Stable  137.1 at T0

description: STA, Biological replicate  137 of 190, Technical replicate 1 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA137.1

value: PBMC from STA137


title: PBMC from Stable  137.2 at T0

description: STA, Biological replicate  137 of 190, Technical replicate 2 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA137.2


title: 59WD1

description: Participant 59 measured at day 1

source_name: Whole blood

tag: group

value: Truck Driver

tag: Sex

value: Male

tag: regular drinker

tag: smoker

tag: cigarettes smoked

tag: temperature

tag: pef


title: ESCC_Biopsy_BPY191

description: Gene expression data from biopsy of esophageal squamous cell carcinoma

tag: disease state

tag: therapy


title: pericarp WT_RR_rep3

source_name: Red Ripe 3

tag: developmental stage

value: Red Ripe


title: ESCC_Biopsy_BPY187


title: ESCC_Biopsy_BPY186

tag: tumor stage

value: StageIII

tag: tnm stage


title: pericarp WT_RR_rep2

source_name: Red Ripe 2


title: 45WD2

description: Participant 45 measured at day 2

value: Office Worker

tag: age

tag: bmi

tag: dew point

tag: initial sbp

tag: initial dbp

tag: final sbp


title: 45WD1

description: Participant 45 measured at day 1

tag: group

tag: Sex

tag: final dbp

tag: fvc


title: 44WD2

description: Participant 44 measured at day 2

tag: regular drinker

tag: smoker

tag: cigarettes smoked

tag: temperature


title: pericarp WT_RR_rep1

source_name: Red Ripe 1

tag: developmental stage


title: PBMC from Stable  136.2 at T0

description: STA, Biological replicate  136 of 190, Technical replicate 2 of 2

source_name: Total RNA from PBMC of 169 kidney graft recipients with stable graft function and under standard immunosuppressive treatment

tag: sample type

value: pool of 169 PBMC samples from Stable patients (STA)

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA136.2

tag: tissue

value: PBMC from STA136

tag: individual replicate

tag: techical replicate

tag: time point


title: 44WD1

description: Participant 44 measured at day 1

tag: age

tag: bmi

tag: dew point

tag: initial sbp

tag: pef


title: PBMC from Stable  135.2 at T0

description: STA, Biological replicate  135 of 190, Technical replicate 2 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA135.2

value: PBMC from STA135


title: 43WD2

description: Participant 43 measured at day 2

tag: group

tag: Sex

tag: initial dbp

tag: final sbp

tag: final dbp


title: ESCC_Biopsy_BPY183

tag: disease state

tag: therapy


title: 43WD1

description: Participant 43 measured at day 1

tag: regular drinker

tag: smoker

tag: cigarettes smoked

tag: temperature

tag: fvc


title: 42WD2

description: Participant 42 measured at day 2

tag: age


title: ESCC_Biopsy_BPY184

tag: tissue


title: ESCC_Biopsy_BPY185

tag: tumor stage

tag: tnm stage


title: ESCC_Biopsy_BPY173


title: 42WD1

description: Participant 42 measured at day 1

tag: bmi

tag: dew point

tag: initial sbp

tag: pef


title: PBMC from Stable  135.1 at T0

description: STA, Biological replicate  135 of 190, Technical replicate 1 of 2

tag: sample type

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA135.1

tag: individual replicate

tag: techical replicate

tag: time point


title: PBMC from Stable  134.2 at T0

description: STA, Biological replicate  134 of 190, Technical replicate 2 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA134.2

value: PBMC from STA134


title: pericarp WT_BR_rep2

source_name: Breaker 2

tag: developmental stage

value: Breaker


title: 41WD1

description: Participant 41 measured at day 1

tag: group

tag: Sex

tag: regular drinker

tag: smoker

tag: initial dbp

tag: final sbp

tag: final dbp


title: 41WD2

description: Participant 41 measured at day 2

tag: age

tag: cigarettes smoked

tag: temperature

tag: fvc


title: 50WD1

description: Participant 50 measured at day 1

tag: bmi

tag: dew point

tag: initial sbp

tag: pef


title: PBMC from Stable  136.1 at T0

description: STA, Biological replicate  136 of 190, Technical replicate 1 of 2

tag: sample type

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA136.1

tag: tissue

tag: individual replicate

tag: techical replicate

value: Replicate 1 of 2

tag: time point


title: PBMC from Stable  134.1 at T0

description: STA, Biological replicate  134 of 190, Technical replicate 1 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA134.1


title: ESCC_Biopsy_BPY166

source_name: Esophageal squamous cell carcinoma

tag: disease state

value: ESCC

tag: therapy


title: ESCC_Biopsy_BPY170

value: Biopsy before therapy


title: ESCC_Biopsy_BPY161


title: PBMC from Stable  132.2 at T0

description: STA, Biological replicate  132 of 190, Technical replicate 2 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA132.2

value: PBMC from STA132


title: pericarp WT_PK_rep1

source_name: Pink 1

tag: developmental stage

value: Pink


title: 40WD2

description: Participant 40 measured at day 2

tag: group

tag: Sex

tag: regular drinker

tag: smoker

tag: initial dbp

tag: final sbp

tag: final dbp


title: 40WD1

description: Participant 40 measured at day 1

tag: age

tag: bmi

tag: cigarettes smoked

tag: temperature

tag: dew point

tag: initial sbp

tag: fvc


title: 39WD2

description: Participant 39 measured at day 2

tag: pef


title: PBMC from Stable  133.2 at T0

description: STA, Biological replicate  133 of 190, Technical replicate 2 of 2

tag: sample type

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA133.2

tag: tissue

value: PBMC from STA133

tag: individual replicate

tag: techical replicate

value: Replicate 2 of 2

tag: time point


title: PBMC from Stable  133.1 at T0

description: STA, Biological replicate  133 of 190, Technical replicate 1 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA133.1


title: 39WD1

description: Participant 39 measured at day 1

source_name: Whole blood

tag: group

tag: Sex

tag: regular drinker

tag: smoker


title: ESCC_Biopsy_BPY156

tag: disease state

tag: tumor stage

tag: tnm stage

tag: therapy

value: Chemoradiotherapy


title: 38WD2

description: Participant 38 measured at day 2

value: Male

tag: age

tag: bmi

tag: cigarettes smoked

tag: temperature

tag: dew point

tag: initial dbp

tag: final sbp

tag: final dbp


title: ESCC_Biopsy_BPY177

tag: tissue


title: PBMC from Stable  132.1 at T0

description: STA, Biological replicate  132 of 190, Technical replicate 1 of 2

tag: sample type

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA132.1

tag: individual replicate

tag: techical replicate

tag: time point


title: anti-C10orf10

type: protein

city: Chongqing

first: jianjun

last: li

address: No. 29, Gaotanyan Street, Shapingba District

country: China

institute: Department of Oncology, Southwest Hospital

hyb_protocol: not applicable

scan_protocol: not applicable

data_processing: The percentage of positive cells, as the extent of immunostaining, was quantified classified into 5 groups under microscope: <10% positive cells for 0; 10% to 25% for 1; 26% to 50% for 2; 51% to 75% for 3 and ≥ 76% for 4. The intensity of staining was graded as negative (scored as 0), weak (1), moderate (2) or strong (3) positivity. The two pathologists independently reviewed all core biopsies. The sum of the percentage of positive staining and the intensity was used to define expression levels.

label: DAB

molecule: protein

source_name: Breast cancer

label_protocol: Immunohistochemical staining was performed using the antibody against C10orf10  (1:50; Santa Cruz Biotechnology) as described previously

extract_protocol: not applicable

tag: target molecule

tag: antibody source

value: Santa Cruz Biotechnology

tag: antibody catalog number

tag: antibody dilution


title: ESCC_Biopsy_BPY151-2

tag: disease state

tag: therapy


title: PBMC from Stable  131.2 at T0

description: STA, Biological replicate  131 of 190, Technical replicate 2 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA131.2

value: PBMC from STA131


title: PBMC from Stable  130.2 at T0

description: STA, Biological replicate  130 of 190, Technical replicate 2 of 2

source_name: Total RNA from PBMC of 169 kidney graft recipients with stable graft function and under standard immunosuppressive treatment

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA130.2

value: PBMC from STA130


title: 37WD2

description: Participant 37 measured at day 2

tag: group

value: Office Worker

tag: Sex

tag: age

tag: bmi

tag: regular drinker

tag: smoker

tag: cigarettes smoked

tag: initial sbp

tag: fvc

tag: pef


title: ESCC_Biopsy_BPY144

tag: tissue


title: ESCC_Biopsy_BPY146

tag: tumor stage

value: StageIII

tag: tnm stage


title: 37WD1

description: Participant 37 measured at day 1

tag: temperature

tag: dew point

tag: initial dbp

tag: final sbp

tag: final dbp


title: ESCC_Biopsy_BPY139

tag: disease state

tag: therapy


title: PBMC from Stable  130.1 at T0

description: STA, Biological replicate  130 of 190, Technical replicate 1 of 2

tag: sample type

value: pool of 169 PBMC samples from Stable patients (STA)

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA130.1

tag: individual replicate

tag: techical replicate

tag: time point


title: ESCC_Biopsy_BPY149


title: 38WD1

description: Participant 38 measured at day 1

tag: group

tag: Sex

tag: age

tag: bmi

tag: regular drinker

tag: smoker

tag: cigarettes smoked

tag: initial sbp


title: PBMC from Stable  131.1 at T0

description: STA, Biological replicate  131 of 190, Technical replicate 1 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA131.1

tag: tissue


title: 36WD2

description: Participant 36 measured at day 2

value: Truck Driver

tag: temperature

tag: dew point

tag: initial dbp

tag: final sbp

tag: fvc

tag: pef


title: pericarp WT_BR_rep1

source_name: Breaker 1

tag: developmental stage

value: Breaker


title: PBMC from Stable  129.2 at T0

description: STA, Biological replicate  129 of 190, Technical replicate 2 of 2

tag: sample type

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA129.2

value: PBMC from STA129

tag: individual replicate

tag: techical replicate

tag: time point


title: ESCC_Biopsy_BPY135

tag: disease state

value: ESCC

tag: therapy


title: ESCC_Biopsy_BPY140

value: Biopsy before therapy


title: Camarosa infected vs. Non-infected crown tissue replicate 1

city: Valencia

first: Jose

last: Gadea

address: Ingeniero Fausto Elio

department: Stress

country: Spain

institute: IBMCP

description: Crown tissue from strawberry cv. Camarosa, C. acutatum infected vs. Mock treated. Replicate 1.

hyb_protocol: One microgram (120 pmol of incorporated dye) from each fluorescently labeled cDNA sample was added to a final volume of 250 μl of the hybridization solution (25% of Microarray Hybridization Solution v.2.0, from GE Healthcare; and 25% of formamide). Hybridizations were performed in a Lucidea Slide Pro Automatic Hybridization Station (Amersham Pharmacia Biotech).

scan_protocol: Slides were scanned using a GenePix 4000B reader (Axon Instruments) at 5 micron resolution.

data_processing: LOWESS normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal.

organism: Fragaria x ananassa

source_name: infected camarosa

label_protocol: The MessageAmp II aRNA amplification kit (Ambion, Austin, TX, USA) was used for RNA amplification using 7 μg of total purified RNA following the manufacturer’s instructions. Quantity and quality of the amplified RNA (aRNA) was performed by capillary-based separation using an Experion Automated Electrophoresis Station (Biorad) and its integrity was assessed to have a distribution of sizes from 250-3000 nt with most of the aRNA between 800-1400 nt. The aRNA was used for generating fluorescently labeled cDNA using the SuperScript Plus Indirect Labeling System kit with the Alexa Fluor 555 and Alexa Fluor 647 dyes (Invitrogen) following the manufacturer’s recommendation.

growth_protocol: 8-week-old strawberry plantlets were placed in 20-cm diameter plastic pots containing sterilized peat (Klansmann-Deilmann, Geeste, Germany) and grown for a minimum of six additional weeks prior pathogen inoculation.

extract_protocol: Total RNA was isolated according to Medina-Escobar et al. (1997) from crowns of strawberry plants (‘Camarosa’ ) inoculated under controlled conditions with C. acutatum or sprayed with solvent as a control. Total RNA samples were treated with  RNase-free DNase (Invitrogen, Burlington, ON, Canada) to remove any DNA contamination prior to cDNA synthesis. An additional step of column purification with RNeasy Mini kit (Qiagen, Valencia, CA, USA) was added to ensure the purity of the RNA.

treatment_protocol: Conidia of C. acutatum isolate CECT 20240 were suspended in sterile water at a density of 104 CFU ml-1 and sprayed onto strawberry plants as earlier described (Casado-Díaz et al., 2006). Mock treatments were done by spraying or adding the solvent only.

tag: cultivar

value: Camarosa

value: Colletotrichum acutatum infected

source_name: mock camarosa

value: mock


title: Camarosa infected vs. Non-infected crown tissue replicate 3

description: Crown tissue from strawberry cv. Camarosa, C. acutatum infected vs. Mock treated. Replicate 3.


title: Camarosa infected vs. Non-infected crown tissue replicate 2

description: Crown tissue from strawberry cv. Camarosa, C. acutatum infected vs. Mock treated. Replicate 2.


title: ESCC_Biopsy_BPY133

description: Gene expression data from biopsy of esophageal squamous cell carcinoma

source_name: Esophageal squamous cell carcinoma


title: PBMC from Stable  128.2 at T0

description: STA, Biological replicate  128 of 190, Technical replicate 2 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA128.2

value: PBMC from STA128

value: Replicate 2 of 2


title: 36WD1

description: Participant 36 measured at day 1

tag: group

tag: Sex

value: Male

tag: age

tag: bmi

tag: regular drinker

tag: smoker

tag: cigarettes smoked

tag: final dbp


title: PBMC from Stable  127.2 at T0

description: STA, Biological replicate  127 of 190, Technical replicate 2 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA127.2

tag: tissue

value: PBMC from STA127


title: PBMC from Stable  129.1 at T0

description: STA, Biological replicate  129 of 190, Technical replicate 1 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA129.1

value: Replicate 1 of 2


title: ESCC_Biopsy_BPY125

value: Chemoradiotherapy


title: ESCC_Biopsy_BPY132


title: PBMC from Stable  128.1 at T0

description: STA, Biological replicate  128 of 190, Technical replicate 1 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA128.1


title: 34WD2

description: Participant 34 measured at day 2

source_name: Whole blood

tag: temperature

tag: dew point

tag: initial sbp

tag: initial dbp

tag: final sbp

tag: fvc

tag: pef


title: 35WD1

description: Participant 35 measured at day 1


title: 35WD2

description: Participant 35 measured at day 2


title: PBMC from Stable  127.1 at T0

description: STA, Biological replicate  127 of 190, Technical replicate 1 of 2

tag: sample type

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA127.1

tag: individual replicate

tag: techical replicate

tag: time point


title: 33WD2

description: Participant 33 measured at day 2

tag: group

tag: Sex

tag: age

tag: bmi


title: 33WD1

description: Participant 33 measured at day 1

tag: regular drinker

tag: smoker

tag: cigarettes smoked

tag: final dbp


title: PBMC from Stable  126.2 at T0

description: STA, Biological replicate  126 of 190, Technical replicate 2 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA126.2

tag: tissue

value: PBMC from STA126


title: 32WD2

description: Participant 32 measured at day 2

value: Office Worker

tag: temperature

tag: dew point

tag: initial sbp

tag: initial dbp


title: 34WD1

description: Participant 34 measured at day 1

tag: final sbp

tag: fvc

tag: pef


title: ESCC_Biopsy_BPY121

tag: disease state

tag: tumor stage

value: StageIII

tag: tnm stage

tag: therapy


title: ESCC_Biopsy_BPY119


title: PBMC from Stable  124.1 at T0

description: STA, Biological replicate  124 of 190, Technical replicate 1 of 2

tag: sample type

value: pool of 169 PBMC samples from Stable patients (STA)

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA124.1

value: PBMC from STA124

tag: individual replicate

tag: techical replicate

tag: time point


title: PBMC from Stable  124.2 at T0

description: STA, Biological replicate  124 of 190, Technical replicate 2 of 2

source_name: Total RNA from PBMC of 169 kidney graft recipients with stable graft function and under standard immunosuppressive treatment

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA124.2


title: PBMC from Stable  126.1 at T0

description: STA, Biological replicate  126 of 190, Technical replicate 1 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA126.1


title: 31WD2

description: Participant 31 measured at day 2

tag: group

tag: Sex

tag: age

tag: bmi

tag: regular drinker

tag: smoker

tag: cigarettes smoked

tag: final dbp


title: 32WD1

description: Participant 32 measured at day 1

tag: temperature

tag: dew point

tag: initial sbp

tag: initial dbp

tag: final sbp

tag: fvc

tag: pef


title: ESCC_Biopsy_BPY122

tag: disease state

tag: tissue

tag: therapy


title: PBMC from Stable  125.1 at T0

description: STA, Biological replicate  125 of 190, Technical replicate 1 of 2

tag: sample type

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA125.1

value: PBMC from STA125

tag: individual replicate

tag: techical replicate

tag: time point


title: 30WD1

description: Participant 30 measured at day 1

tag: group

tag: Sex

tag: age

tag: bmi

tag: regular drinker

tag: smoker


title: 31WD1

description: Participant 31 measured at day 1

tag: cigarettes smoked

tag: temperature

tag: dew point

tag: initial sbp

tag: initial dbp

tag: final dbp


title: 30WD2

description: Participant 30 measured at day 2

tag: final sbp

tag: fvc

tag: pef


title: PBMC from Stable  125.2 at T0

description: STA, Biological replicate  125 of 190, Technical replicate 2 of 2

tag: sample type

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA125.2

tag: tissue

tag: individual replicate

tag: techical replicate


title: ESCC_Biopsy_BPY117

tag: disease state

value: ESCC

tag: therapy


title: PBMC from Stable  122.1 at T0

description: STA, Biological replicate  122 of 190, Technical replicate 1 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA122.1

value: PBMC from STA122

tag: time point


title: PBMC from Stable  121.2 at T0

description: STA, Biological replicate  121 of 190, Technical replicate 2 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA121.2

value: PBMC from STA121


title: PBMC from Stable  123.1 at T0

description: STA, Biological replicate  123 of 190, Technical replicate 1 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA123.1

value: PBMC from STA123


title: PBMC from Stable  122.2 at T0

description: STA, Biological replicate  122 of 190, Technical replicate 2 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA122.2


title: ESCC_Biopsy_BPY105

source_name: Esophageal squamous cell carcinoma

value: Biopsy before therapy

tag: tumor stage

tag: tnm stage


title: PBMC from Stable  121.1 at T0

description: STA, Biological replicate  121 of 190, Technical replicate 1 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA121.1


title: ESCC_Biopsy_BPY112

description: Gene expression data from biopsy of esophageal squamous cell carcinoma


title: ESCC_Biopsy_BPY106


title: PBMC from Stable  123.2 at T0

description: STA, Biological replicate  123 of 190, Technical replicate 2 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA123.2


title: ESCC_Biopsy_BPY109


title: ESCC_Biopsy_BPY115


title: F2

city: Beijing

first: Shuai

last: Liu

address: Dong Dan San Tiao 9, Beijing, China

institute: Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College

description: This sample is the second of three adult female worm biological replicates used in this experiment. Adult female worms were isolated from separate infected rabbits at 6 weeks post-infection.

hyb_protocol: Array hybridization, washing, scanning, and data acquisition were carried out according to the NimbleGen Arrays user’s guide.

scan_protocol: The arrays were scanned using MS200 scanner (NimbleGen Systems) with 2 µm resolution, and NimbleScan software (NimbleGen) was used to extract fluorescent intensity raw data from the scanned images.

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

organism: Schistosoma japonicum

source_name: adult female worm

label_protocol: cDNA labeled with a fluorescent dye (Cy3-dCTP) was produced by Eberwine’s linear RNA amplification method and subsequent enzymatic reaction, and the procedure has been improved by using CapitalBio cRNA Amplification and Labeling Kit (CapitalBio, Beijing, China) for producing higher yields of labeled cDNA.

growth_protocol: The freshly released cercariae were harvested from S. japonicum-infected Oncomelania hupensis purchased from Hunan Institute of Parasitic Diseases, Yueyang, China. Hepatic schistosomula were isolated from infected New Zealand rabbits at 2 weeks post-infection. Adult worms were isolated from infected rabbits at 6 weeks post-infection and manually separated under a light microscope. Eggs were purified from liver tissues of infected rabbits by enzyme digestion method.

extract_protocol: Total RNA was extracted using RNeasy Mini kit (QIAGEN) and the contaminating genomic DNA were removed from RNA samples with Tubro DNA-free kit (Ambion, CA, USA).  The quantity and quality of the RNA samples were assessed by NanoDropND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE) and denaturing agarose gel electrophoresis.

treatment_protocol: Parasites of all stages were soaked in RNAlater Solution (Ambion, CA, USA), and stored at -80°C until total RNA was isolated.

tag: developmental stage

value: adult female


title: F1-1

description: This sample is the first of three  adult female worm biological replicates (the first of two adult female worm technical replicates) used in this experiment. Adult female worms were isolated from separate infected rabbits at 6 weeks post-infection.


title: 29WD2

description: Participant 29 measured at day 2

source_name: Whole blood

tag: group

tag: Sex

tag: age

tag: bmi

tag: regular drinker

tag: smoker

tag: cigarettes smoked

tag: temperature

tag: dew point


title: 29WD1

description: Participant 29 measured at day 1

tag: initial sbp

tag: initial dbp

tag: final sbp

tag: final dbp

tag: fvc

tag: pef


title: ESCC_Biopsy_BPY101

tag: disease state

tag: tissue

tag: therapy


title: PBMC from Stable  120.2 at T0

description: STA, Biological replicate  120 of 190, Technical replicate 2 of 2

tag: sample type

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA120.2

value: PBMC from STA120

tag: individual replicate

tag: techical replicate

value: Replicate 2 of 2

tag: time point


title: F1-2

description: This sample is the first of three adult female worm biological replicates (the second of two adult female worm technical replicates) used in this experiment. Adult female worms were isolated from separate infected rabbits at 6 weeks post-infection.

tag: developmental stage


title: 27WD2

description: Participant 27 measured at day 2

tag: group

value: Truck Driver

tag: Sex

value: Male

tag: age

tag: bmi

tag: regular drinker

tag: smoker

tag: cigarettes smoked


title: ESCC_Biopsy_BPY118

value: Chemoradiotherapy


title: ESCC_Biopsy_BPY102

tag: tumor stage

tag: tnm stage


title: M1-2

description: This sample is the first of three adult male worm biological replicates (the second of two  adult male worm technical replicates) used in this experiment. Adult male worms were isolated from separate infected rabbits at 6 weeks post-infection.

source_name: adult male worm

value: adult male


title: PBMC from Stable  120.1 at T0

description: STA, Biological replicate  120 of 190, Technical replicate 1 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA120.1

value: Replicate 1 of 2


title: ESCC_Biopsy_BPY116

tag: disease state

value: StageIII


title: M3

description: This sample is the third of three  adult male worm biological replicates used in this experiment. Adult male worms were isolated from separate infected rabbits at 6 weeks post-infection.


title: F3

description: This sample is the third of three adult female worm biological replicates used in this experiment. Adult female worms were isolated from separate infected rabbits at 6 weeks post-infection.


title: ESCC_Biopsy_BPY104

tag: tissue


title: M2

description: This sample is the second of three  adult male worm biological replicates used in this experiment. Adult male worms were isolated from separate infected rabbits at 6 weeks post-infection.


title: 27WD1

description: Participant 27 measured at day 1

tag: temperature

tag: dew point

tag: initial sbp

tag: initial dbp

tag: final sbp

tag: final dbp

tag: fvc

tag: pef


title: 25WD2

description: Participant 25 measured at day 2

tag: group

tag: Sex

tag: age


title: PBMC from Stable  119.2 at T0

description: STA, Biological replicate  119 of 190, Technical replicate 2 of 2

source_name: Total RNA from PBMC of 169 kidney graft recipients with stable graft function and under standard immunosuppressive treatment

tag: sample type

value: pool of 169 PBMC samples from Stable patients (STA)

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA119.2

value: PBMC from STA119

tag: individual replicate

tag: techical replicate

tag: time point


title: 26WD2

description: Participant 26 measured at day 2

tag: bmi

tag: regular drinker

tag: smoker

tag: cigarettes smoked


title: 26WD1

description: Participant 26 measured at day 1

tag: temperature

tag: dew point

tag: initial sbp


title: 25WD1

description: Participant 25 measured at day 1

tag: initial dbp

tag: final sbp

tag: final dbp


title: PBMC from Stable  119.1 at T0

description: STA, Biological replicate  119 of 190, Technical replicate 1 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA119.1

tag: tissue


title: 24WD1

description: Participant 24 measured at day 1

tag: group

value: Office Worker

tag: Sex

tag: fvc

tag: pef


title: PBMC from Stable  118.1 at T0

description: STA, Biological replicate  118 of 190, Technical replicate 1 of 2

tag: sample type

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA118.1

value: PBMC from STA118

tag: individual replicate

tag: techical replicate


title: PBMC from Stable  116.2 at T0

description: STA, Biological replicate  116 of 190, Technical replicate 2 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA116.2

value: PBMC from STA116

tag: time point


title: ESCC_Biopsy_BPY089

tag: disease state

value: ESCC

tag: therapy


title: PBMC from Stable  117.1 at T0

description: STA, Biological replicate  117 of 190, Technical replicate 1 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA117.1

value: PBMC from STA117


title: ESCC_Biopsy_BPY086

value: Biopsy before therapy


title: PBMC from Stable  117.2 at T0

description: STA, Biological replicate  117 of 190, Technical replicate 2 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA117.2


title: ESCC_Biopsy_BPY096

description: Gene expression data from biopsy of esophageal squamous cell carcinoma


title: ESCC_Biopsy_BPY087

tag: tumor stage

tag: tnm stage


title: ESCC_Biopsy_BPY093


title: 23WD2

description: Participant 23 measured at day 2

tag: age

tag: bmi

tag: regular drinker

tag: smoker

tag: cigarettes smoked

tag: temperature

tag: dew point

tag: initial sbp


title: ESCC_Biopsy_BPY088

tag: tissue


title: PBMC from Stable  116.1 at T0

description: STA, Biological replicate  116 of 190, Technical replicate 1 of 2

tag: sample type

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA116.1


title: ESCC_Biopsy_BPY092


title: PBMC from Stable  118.2 at T0

description: STA, Biological replicate  118 of 190, Technical replicate 2 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA118.2

tag: individual replicate


title: 24WD2

description: Participant 24 measured at day 2

tag: group

tag: Sex

tag: initial dbp

tag: final sbp

tag: final dbp

tag: fvc

tag: pef


title: ESCC_Biopsy_BPY095

source_name: Esophageal squamous cell carcinoma

tag: disease state

tag: therapy


title: 23WD1

description: Participant 23 measured at day 1

tag: age

tag: bmi

tag: regular drinker

tag: smoker


title: ESCC_Biopsy_BPY084


title: PBMC from Stable  115.2 at T0

description: STA, Biological replicate  115 of 190, Technical replicate 2 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA115.2

value: PBMC from STA115

tag: techical replicate

tag: time point


title: ESCC_Biopsy_BPY083

tag: tissue


title: Day01_ZT20-Day01_ZT16

city: Notre Dame

first: Jacqueline

last: Lopez

state: Indiana

address: 019 Galvin Life Science Center

department: Biology

institute: University of Notre Dame

hyb_protocol: Dual-colour hybridization, post-hybridization washing, and scanning were done according to manufacturer's instructions (Roche NimbleGen, Madison, WI).

scan_protocol: Images were acquired using a NimbleGen MS 200 with 2μm resolution (Roche NimbleGen, Madison, WI).

data_processing: The image data from these arrays were processed using the software NimbleScan v2.5 (Roche NimbleGen, Madison, WI).

organism: Daphnia pulex

source_name: whole body, 8hrs, dark period

label_protocol: Beginning with 1.0 μg of total RNA, a single round of amplification using MessageAmpTM II aRNA kit (Ambion, Austin, TX) was performed for each RNA sample.  The cRNA (10 μg) was converted to double strand cDNA with random primers using the Invitrogen SuperScript Double-Stranded cDNA Synthesis kit (Invitrogen, Carlsbad, CA).  From 1 μg double-stranded cDNA, labeled cDNA was generated with NimbleGen’s Dual-colour Labeling Kit (Roche NimbleGen, Inc.).

growth_protocol: Daphnia cultures of genotype, Roughwood 40-11, were maintained for three generations at 18°C in 750mL of COMBO medium  (Kilham, Kreeger, Lynn, Goulden, & Herrera, 1998) with a 12L:12D photoperiod (with abrupt transitions). Every second day, culture media containing Scenedesmus acutus algae (200,000 cells/ml) was replaced, and individuals were culled to maintain a density of 50 individuals per 750mL.

extract_protocol: Samples were homogenized in TRIzol Reagent (Invitrogen, Carlsbad, CA).  The homogenate was purified using Qiagen’s RNeasy Mini Kit (Qiagen,Venlo, Netherlands) with on-column DNAse treatment to isolate total RNA (Lopez & Colbourne 2011).

treatment_protocol: Third generation females (7–9 day old) were maintained at 18˚C in 750mL of COMBO medium with a 12L:12D photoperiod (with abrupt transitions).  Replicates of 30 individuals were collected and immediately frozen every 4 hours over a 48 hour time course. Period measurements are labeled as hour of collection and phase of the light cycle.

tag: strain

value: Roughwood 40-11

tag: elapsed time (hours)

tag: day

tag: zeitgeber time

tag: light cycle phase

value: dark period

source_name: whole body, 4hrs, dark period


title: Day03_ZT8-Day02_ZT20

source_name: whole body, 44hrs, light period

value: light period

source_name: whole body, 32hrs, dark period


title: Day02_ZT20-Day02_ZT8

source_name: whole body, 20hrs, light period


title: Day01_ZT20-Day03_ZT8


title: Day03_ZT4-Day02_ZT16

source_name: whole body, 40hrs, light period

source_name: whole body, 28hrs, dark period


title: Day01_ZT16-Day03_ZT12

source_name: whole body, 48hrs, dark period


title: Day02_ZT12-Day02_ZT0

source_name: whole body, 24hrs, dark period

source_name: whole body, 12hrs, light period


title: Day02_ZT0-Day01_ZT20


title: PBMC from Stable  115.1 at T0

description: STA, Biological replicate  115 of 190, Technical replicate 1 of 2

source_name: Total RNA from PBMC of 169 kidney graft recipients with stable graft function and under standard immunosuppressive treatment

tag: sample type

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA115.1

tag: individual replicate


title: 22WD2

description: Participant 22 measured at day 2

source_name: Whole blood

tag: group

tag: Sex

value: Male

tag: cigarettes smoked

tag: temperature

tag: dew point

tag: initial sbp

tag: initial dbp

tag: final sbp

tag: final dbp

tag: fvc

tag: pef


title: 21WD2

description: Participant 21 measured at day 2

tag: age

tag: bmi

tag: regular drinker

tag: smoker


title: 22WD1

description: Participant 22 measured at day 1


title: ESCC_Biopsy_BPY080

tag: disease state

tag: tissue

tag: therapy

value: Chemoradiotherapy


title: 20WD2

description: Participant 20 measured at day 2

tag: group

value: Truck Driver

tag: Sex


title: PBMC from Stable  114.2 at T0

description: STA, Biological replicate  114 of 190, Technical replicate 2 of 2

tag: sample type

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA114.2

value: PBMC from STA114

tag: individual replicate

tag: techical replicate

value: Replicate 2 of 2

tag: time point


title: PBMC from Stable  114.1 at T0

description: STA, Biological replicate  114 of 190, Technical replicate 1 of 2

value: pool of 169 PBMC samples from Stable patients (STA)

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA114.1

value: Replicate 1 of 2


title: PBMC from Stable  113.2 at T0

description: STA, Biological replicate  113 of 190, Technical replicate 2 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA113.2

value: PBMC from STA113


title: ESCC_Biopsy_BPY079

source_name: Esophageal squamous cell carcinoma


title: Day03_ZT0-Day02_ZT12

source_name: whole body, 36hrs, light period

tag: strain

tag: elapsed time (hours)

tag: day

tag: zeitgeber time

tag: light cycle phase


title: ESCC_Biopsy_BPY081


title: PBMC from Stable  113.1 at T0

description: STA, Biological replicate  113 of 190, Technical replicate 1 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA113.1


title: ESCC_Biopsy_BPY077


title: 20WD1

description: Participant 20 measured at day 1

tag: age

tag: bmi

tag: cigarettes smoked

tag: temperature

tag: dew point

tag: initial sbp

tag: initial dbp

tag: final sbp

tag: final dbp

tag: fvc

tag: pef


title: Day02_ZT20-Day02_ZT16


title: Day03_ZT4-Day03_ZT0


title: PBMC from Stable  112.2 at T0

description: STA, Biological replicate  112 of 190, Technical replicate 2 of 2

tag: sample type

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA112.2

tag: tissue

value: PBMC from STA112

tag: individual replicate

tag: techical replicate

tag: time point


title: ESCC_Biopsy_BPY075

tag: disease state

tag: therapy


title: Day03_ZT12-Day03_ZT0

tag: strain

tag: elapsed time (hours)

tag: day

tag: zeitgeber time

tag: light cycle phase


title: ESCC_Biopsy_BPY074


title: Day02_ZT4-Day01_ZT16

source_name: whole body, 16hrs, light period

source_name: whole body, 4hrs, dark period


title: Day02_ZT16-Day02_ZT12


title: 19WD2

description: Participant 19 measured at day 2

tag: group

tag: Sex

tag: age

tag: bmi

tag: regular drinker

tag: smoker

tag: cigarettes smoked

tag: temperature

tag: dew point

tag: initial sbp

tag: initial dbp


title: 19WD1

description: Participant 19 measured at day 1

tag: final sbp

tag: final dbp

tag: fvc

tag: pef


title: Day02_ZT8-Day02_ZT4

source_name: whole body, 20hrs, light period

tag: strain

tag: elapsed time (hours)

tag: day

tag: zeitgeber time


title: 18WD2

description: Participant 18 measured at day 2

tag: group

tag: Sex

tag: age


title: 18WD1

description: Participant 18 measured at day 1

tag: bmi

tag: regular drinker

tag: smoker


title: PBMC from Stable  111.2 at T0

description: STA, Biological replicate  111 of 190, Technical replicate 2 of 2

tag: sample type

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA111.2

tag: tissue

value: PBMC from STA111

tag: individual replicate

tag: techical replicate

tag: time point


title: PBMC from Stable  110.2 at T0

description: STA, Biological replicate  110 of 190, Technical replicate 2 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA110.2

value: PBMC from STA110


title: PBMC from Stable  112.1 at T0

description: STA, Biological replicate  112 of 190, Technical replicate 1 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA112.1


title: PBMC from Stable  111.1 at T0

description: STA, Biological replicate  111 of 190, Technical replicate 1 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA111.1


title: 17WD1

description: Participant 17 measured at day 1

tag: cigarettes smoked

tag: temperature

tag: dew point

tag: initial sbp

tag: initial dbp

tag: final sbp

tag: final dbp

tag: fvc


title: Day02_ZT8-Day01_ZT20

tag: strain

tag: elapsed time (hours)

tag: day

tag: zeitgeber time

tag: light cycle phase

source_name: whole body, 8hrs, dark period


title: ESCC_Biopsy_BPY069

tag: disease state

value: ESCC

tag: tissue

tag: tumor stage

value: StageIII

tag: tnm stage

tag: therapy


title: PBMC from Stable  110.1 at T0

description: STA, Biological replicate  110 of 190, Technical replicate 1 of 2

source_name: Total RNA from PBMC of 169 kidney graft recipients with stable graft function and under standard immunosuppressive treatment

tag: sample type

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA110.1

tag: individual replicate

tag: techical replicate

tag: time point


title: 17WD2

description: Participant 17 measured at day 2

source_name: Whole blood

tag: group

tag: Sex

tag: age

tag: bmi

tag: regular drinker

tag: smoker

tag: cigarettes smoked

tag: temperature

tag: dew point

tag: initial sbp

tag: initial dbp

tag: final sbp

tag: pef


title: Day03_ZT8-Day03_ZT4

source_name: whole body, 44hrs, light period

tag: strain

tag: elapsed time (hours)

tag: day

tag: zeitgeber time

tag: light cycle phase

source_name: whole body, 40hrs, light period


title: ESCC_Biopsy_BPY062

source_name: Esophageal squamous cell carcinoma

tag: disease state

tag: tissue

value: Biopsy before therapy

tag: therapy


title: ESCC_Biopsy_BPY068


title: Day02_ZT12-Day02_ZT8

source_name: whole body, 24hrs, dark period

value: Roughwood 40-11


title: ESCC_Biopsy_BPY060


title: Day02_ZT0-Day03_ZT12

source_name: whole body, 12hrs, light period

source_name: whole body, 48hrs, dark period

value: dark period


title: PBMC from Stable  109.1 at T0

description: STA, Biological replicate  109 of 190, Technical replicate 1 of 2

tag: sample type

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA109.1

value: PBMC from STA109

tag: individual replicate

tag: techical replicate

tag: time point


title: Day02_ZT16-Day02_ZT4

source_name: whole body, 28hrs, dark period

source_name: whole body, 16hrs, light period

value: light period


title: PBMC from Stable  108.2 at T0

description: STA, Biological replicate  108 of 190, Technical replicate 2 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA108.2

value: PBMC from STA108


title: ESCC_Biopsy_BPY058

description: Gene expression data from biopsy of esophageal squamous cell carcinoma

tag: tumor stage

tag: tnm stage

value: Chemoradiotherapy


title: ESCC_Biopsy_BPY072


title: PBMC from Stable  109.2 at T0

description: STA, Biological replicate  109 of 190, Technical replicate 2 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA109.2


title: 16WD1

description: Participant 16 measured at day 1

tag: group

value: Office Worker

tag: Sex

value: Male

tag: age

tag: bmi

tag: regular drinker

tag: smoker

tag: cigarettes smoked

tag: temperature

tag: dew point

tag: initial sbp

tag: initial dbp

tag: final dbp

tag: fvc


title: 16WD2

description: Participant 16 measured at day 2

tag: final sbp

tag: pef


title: ESCC_Biopsy_BPY061

tag: disease state

tag: tissue

tag: therapy


title: Day01_ZT16-Day03_ZT4

source_name: whole body, 4hrs, dark period

tag: strain

tag: elapsed time (hours)

tag: day

tag: zeitgeber time

tag: light cycle phase


title: Day03_ZT0-Day02_ZT20

source_name: whole body, 36hrs, light period

source_name: whole body, 32hrs, dark period


title: ESCC_Biopsy_BPY054


title: 15WD1

description: Participant 15 measured at day 1

tag: group

tag: Sex

tag: age

tag: bmi

tag: regular drinker

tag: smoker

tag: cigarettes smoked


title: 15WD2

description: Participant 15 measured at day 2

tag: temperature

tag: dew point

tag: initial sbp

tag: initial dbp

tag: final sbp

tag: final dbp

tag: fvc


title: 14WD2

description: Participant 14 measured at day 2

tag: pef


title: ESCC_Biopsy_BPY052

tag: disease state

tag: tissue

tag: therapy


title: Day03_ZT12-Day03_ZT8

tag: strain

tag: elapsed time (hours)

tag: day

tag: zeitgeber time

tag: light cycle phase


title: 14WD1

description: Participant 14 measured at day 1

tag: group

tag: Sex

tag: age

tag: bmi

tag: regular drinker

tag: smoker

tag: cigarettes smoked


title: 13WD2

description: Participant 13 measured at day 2

tag: temperature

tag: dew point

tag: initial sbp

tag: initial dbp

tag: final sbp

tag: final dbp

tag: fvc


title: PBMC from Stable  108.1 at T0

description: STA, Biological replicate  108 of 190, Technical replicate 1 of 2

source_name: Total RNA from PBMC of 169 kidney graft recipients with stable graft function and under standard immunosuppressive treatment

tag: sample type

value: pool of 169 PBMC samples from Stable patients (STA)

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA108.1

tag: tissue

tag: individual replicate

tag: techical replicate

tag: time point


title: PBMC from Stable  107.2 at T0

description: STA, Biological replicate  107 of 190, Technical replicate 2 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA107.2

value: PBMC from STA107

value: Replicate 2 of 2


title: ESCC_Biopsy_BPY047

tag: disease state

tag: therapy


title: PBMC from Stable  107.1 at T0

description: STA, Biological replicate  107 of 190, Technical replicate 1 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA107.1

value: Replicate 1 of 2


title: ESCC_Biopsy_BPY048

tag: tumor stage

tag: tnm stage


title: Day02_ZT4-Day02_ZT0

tag: strain

tag: elapsed time (hours)

tag: day

tag: zeitgeber time

tag: light cycle phase


title: PBMC from Stable  105.2 at T0

description: STA, Biological replicate  105 of 190, Technical replicate 2 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA105.2

value: PBMC from STA105


title: 13WD1

description: Participant 13 measured at day 1

source_name: Whole blood

tag: group

tag: Sex

tag: age

tag: bmi

tag: regular drinker

tag: smoker

tag: cigarettes smoked

tag: temperature

tag: dew point

tag: initial sbp

tag: initial dbp

tag: final sbp

tag: pef


title: PBMC from Stable  106.1 at T0

description: STA, Biological replicate  106 of 190, Technical replicate 1 of 2

tag: sample type

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA106.1

tag: tissue

value: PBMC from STA106

tag: individual replicate

tag: techical replicate

tag: time point


title: 12WD1

description: Participant 12 measured at day 1

tag: group

value: Truck Driver

tag: Sex

tag: final dbp

tag: fvc


title: 12WD2

description: Participant 12 measured at day 2

tag: age

tag: bmi

tag: regular drinker

tag: smoker


title: ESCC_Biopsy_BPY051

source_name: Esophageal squamous cell carcinoma

tag: disease state

value: ESCC

tag: therapy


title: PBMC from Stable  106.2 at T0

description: STA, Biological replicate  106 of 190, Technical replicate 2 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA106.2


title: ESCC_Biopsy_BPY045

value: Biopsy before therapy


title: Edoardo_251914810017-4_1.txt #1 target

city: Wageningen

first: Peter

last: van Baarlen

address: De Elst 1

department: Animal Sciences

country: Netherlands

institute: Wageningen University

hyb_protocol: Agilent hybridization protocol for Two-color microarray-based Gene expression analysis. Version 5.5

scan_protocol: Scanned on an ScanArray Express 4000 scanner (Perkin Elmer, Wellesley, MA). Images were quantified using ImaGene Version 7.5 software (BioDiscovery Inc., Marina Del Rey, CA, USA).

data_processing:
scanned slides were Lowess normalised using Prep (van Hijum, Applied Bioinformatics 2003 2(4):241-244).
Background subtracted, Lowess normalised, Cy5/Cy3 ratios (no log transformation); interslide scaling was performed using PostPrep (van Hijum, Applied Bioinformatics 2003 2(4):241-244). The raw numbers from this analysis were multiplied by 10000 yielding the numbers that are now in the Matrix sheet.

organism: Streptococcus suis

source_name: suis WT O.D. 0.04 + 45 minutes of incubation with the competence peptide and DNA

label_protocol: RNA (1 μg) from S. suis samples was labeled using the Cyanine 5 (Cy5) labeling reaction (indirect labeling of synthesized cDNA with the CyScribe Post-Labeling and Purification kit; Amersham Biosciences, Buckinghamshire, United Kingdom).

growth_protocol: S. suis was grown in Todd-Hewitt broth (THB) (Difco) at 37°C under 5% CO2 for 18 hr.

extract_protocol: RNA extraction was preceded by induction of competence as described in [7]. Briefly S. suis S10 was grown to OD600nm 0.04. Thirty five ml of culture was collected and donor DNA (pNZ8048, 350 µg) in EB buffer (10 mM Tris-Cl, pH 8.5) was added to the bacteria along with synthetic XIP (GNWGTWVEE) at a final concentration of 250 µM [6]. Control extracts were obtained using same quantities of culture with donor DNA added but without XIP stimulation. Ten ml of the induced culture were collected after 5, 15 and 45 minutes following XIP exposure. Ten ml of uninduced cultures were collected at 15 and 45 minutes, spun down and the pellets were resuspended in 2.5 mL PBS plus 5 mL RNAprotect buffer (Promega). After 5 minutes of incubation the bacteria were collected via centrifugation and immediately frozen in liquid nitrogen until further handling. The frozen pellet was dissolved in 110 µl of TE containing proteinase K and lysozymes (1.25 µg/mL and 15 ug/ml respectively) and incubated for 10 minutes. The bacterial pellet was dissolved in 700 µL RLT buffer (Promega) containing 7 µl of freshly added β-mercaptoethanol and the bacteria were disrupted using a FastPrep-24 (MP. Biomedicals, Solon, OH) for 20 sec at 6.0 m/sec. Total RNA was purified using the RNeasy Mini Kit (Qiagen). The quality and the concentration of RNA were assessed with an Experion System (Bio-Rad) and by analysis of the A260/A280 ratio (NanoDrop 8000 UV-Vis Spectrophotometer). cDNA was synthesized with a SuperScript III Reverse Transcriptase kit (Invitrogen) using Aminoallyl-dUTP as dUTPs source and purified with the Illustra CyScribe GFX Purification Kit (GE Healthcare). The cDNA was labelled with CyDye Post-Labeling Reactive Dye Pack (GE Healthcare).

treatment_protocol: RNA was extracted at the start of the experiment and after 5, 10 and 45 minutes after induction of competence (t=0 for all conditions)

tag: strain


title: ESCC_Biopsy_BPY044


title: ESCC_Biopsy_BPY040


title: 11WD2

description: Participant 11 measured at day 2

tag: cigarettes smoked

tag: temperature

tag: dew point

tag: initial sbp

tag: initial dbp

tag: final sbp

tag: pef


title: Edoardo_251914810017-4_1.txt #1 control

source_name: suis WT O.D. 0.04 + 15 minutes of incubation with competence peptide and DNA


title: Edoardo_251914810017-4_2.txt #1 target

source_name: suis WT O.D. 0.04 + 5 minutes of incubation with competence peptide and DNA


title: 21WD1

description: Participant 21 measured at day 1

tag: group

tag: Sex


title: Edoardo_251914810017-4_2.txt #1 control


title: PBMC from Stable  105.1 at T0

description: STA, Biological replicate  105 of 190, Technical replicate 1 of 2

tag: sample type

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA105.1

tag: tissue

tag: individual replicate

tag: techical replicate

tag: time point


title: PBMC from Stable  104.2 at T0

description: STA, Biological replicate  104 of 190, Technical replicate 2 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA104.2

value: PBMC from STA104


title: 11WD1

description: Participant 11 measured at day 1

tag: age

tag: bmi

tag: regular drinker

tag: smoker

tag: final dbp

tag: fvc


title: Edoardo_251914810017-3_2.txt #1 target

source_name: suis WT O.D. 0.04 + DNA 15’ (No peptide)

tag: strain


title: PBMC from Stable  104.1 at T0

description: STA, Biological replicate  104 of 190, Technical replicate 1 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA104.1


title: ESCC_Biopsy_BPY043

tag: disease state

tag: therapy


title: 9WD2

description: Participant 9 measured at day 2

tag: cigarettes smoked

tag: temperature

tag: dew point

tag: initial sbp

tag: initial dbp

tag: final sbp

tag: pef


title: ESCC_Biopsy_BPY274

tag: tissue

value: Surgery


title: 9WD1

description: Participant 9 measured at day 1

tag: group

tag: Sex

tag: age


title: ESCC_Biopsy_BPY273


title: ESCC_Biopsy_BPY270


title: Edoardo_251914810017-3_1.txt #1 target

source_name: suis WT O.D. 0.04 + Pep 15’ (no DNA)


title: Edoardo_251914810017-3_2.txt #1 control

source_name: suis WT O.D. 0.04 + DNA 45’ (No peptide)


title: Edoardo_251914810017-3_1.txt #1 control


title: 8WD1

description: Participant 8 measured at day 1

tag: bmi

tag: regular drinker

tag: smoker


title: PBMC from Stable  103.2 at T0

description: STA, Biological replicate  103 of 190, Technical replicate 2 of 2

source_name: Total RNA from PBMC of 169 kidney graft recipients with stable graft function and under standard immunosuppressive treatment

tag: sample type

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA103.2

value: PBMC from STA103

tag: individual replicate

tag: techical replicate

tag: time point


title: 8WD2

description: Participant 8 measured at day 2

tag: cigarettes smoked

tag: temperature

tag: final dbp

tag: fvc


title: PBMC from Stable  102.2 at T0

description: STA, Biological replicate  102 of 190, Technical replicate 2 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA102.2

value: PBMC from STA102


title: PBMC from Stable  103.1 at T0

description: STA, Biological replicate  103 of 190, Technical replicate 1 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA103.1


title: Edoardo_251914810017-2_2.txt #1 target

tag: strain


title: Edoardo_251914810017-2_2.txt #1 control


title: 7WD2

description: Participant 7 measured at day 2

source_name: Whole blood

tag: dew point

tag: initial sbp

tag: initial dbp

tag: final sbp

tag: pef


title: 7WD1

description: Participant 7 measured at day 1

tag: group

tag: Sex

tag: age

tag: bmi


title: Edoardo_251914810017-2_1.txt #1 target


title: 6WD2

description: Participant 6 measured at day 2

tag: regular drinker

tag: smoker


title: ESCC_Biopsy_BPY267

tag: disease state

tag: tissue

tag: therapy

value: Neo-adjuvant chemotherapy


title: ESCC_Biopsy_BPY265


title: PBMC from Stable  101.2 at T0

description: STA, Biological replicate  101 of 190, Technical replicate 2 of 2

tag: sample type

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA101.2

value: PBMC from STA101

tag: individual replicate

tag: techical replicate

tag: time point


title: PBMC from Stable  101.1 at T0

description: STA, Biological replicate  101 of 190, Technical replicate 1 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA101.1


title: ESCC_Biopsy_BPY269

source_name: Esophageal squamous cell carcinoma


title: PBMC from Stable  100.2 at T0

description: STA, Biological replicate  100 of 190, Technical replicate 2 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA100.2

value: PBMC from STA100


title: Edoardo_251914810017-2_1.txt #1 control

source_name: suis WT O.D. 0.04 + 45 minutes of incubation with the competence peptide and DNA

tag: strain


title: 6WD1

description: Participant 6 measured at day 1

value: Office Worker

value: Male

tag: cigarettes smoked

tag: temperature

tag: dew point

tag: initial sbp

tag: initial dbp

tag: final dbp

tag: fvc


title: PBMC from Stable  100.1 at T0

description: STA, Biological replicate  100 of 190, Technical replicate 1 of 2

value: pool of 169 PBMC samples from Stable patients (STA)

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA100.1


title: PBMC from Stable  102.1 at T0

description: STA, Biological replicate  102 of 190, Technical replicate 1 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA102.1


title: 5WD2

description: Participant 5 measured at day 2

tag: group

tag: Sex

tag: age

tag: bmi

tag: regular drinker

tag: final sbp

tag: pef


title: ESCC_Biopsy_BPY254

description: Gene expression data from biopsy of esophageal squamous cell carcinoma

tag: disease state

tag: tissue

tag: therapy


title: PBMC from Stable  99.2 at T0

description: STA, Biological replicate  99 of 190, Technical replicate 2 of 2

tag: sample type

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA099.2

value: PBMC from STA099

tag: individual replicate

value: STA 99 of 190

tag: techical replicate

value: Replicate 2 of 2

tag: time point


title: 5WD1

description: Participant 5 measured at day 1

tag: smoker

tag: cigarettes smoked

tag: temperature

tag: dew point

tag: initial sbp

tag: initial dbp


title: Edoardo_251914810017-1_2.txt #1 target

source_name: suis WT O.D. 0.04 + DNA 15’ (No peptide)

tag: strain


title: ESCC_Biopsy_BPY262


title: ESCC_Biopsy_BPY251


title: Edoardo_251914810017-1_2.txt #1 control

source_name: suis WT O.D. 0.04 + 15 minutes of incubation with competence peptide (No DNA)


title: 4WD2

description: Participant 4 measured at day 2

tag: group

tag: Sex

tag: age

tag: bmi

tag: regular drinker

tag: final dbp

tag: fvc


title: ESCC_Biopsy_BPY259

tag: disease state

tag: tissue

tag: therapy


title: Edoardo_251914810017-1_1.txt #1 target

source_name: suis WT O.D. 0.04 + 15 minutes of incubation with competence peptide and DNA


title: PBMC from Stable  99.1 at T0

description: STA, Biological replicate  99 of 190, Technical replicate 1 of 2

tag: sample type

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA099.1

tag: individual replicate

tag: techical replicate

value: Replicate 1 of 2

tag: time point


title: Edoardo_251914810017-1_1.txt #1 control

source_name: suis WT O.D. 0.04 + 5 minutes of incubation with competence peptide and DNA


title: ESCC_Biopsy_BPY245


title: 4WD1

description: Participant 4 measured at day 1

value: Truck Driver

tag: smoker

tag: cigarettes smoked

tag: temperature

tag: dew point

tag: initial sbp

tag: final sbp

tag: pef


title: PBMC from Stable  98.1 at T0

description: STA, Biological replicate  98 of 190, Technical replicate 1 of 2

source_name: Total RNA from PBMC of 169 kidney graft recipients with stable graft function and under standard immunosuppressive treatment

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA098.1

value: PBMC from STA098

value: STA 98 of 190


title: PBMC from Stable  98.2 at T0

description: STA, Biological replicate  98 of 190, Technical replicate 2 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA098.2


title: ESCC_Biopsy_BPY243

value: ESCC

value: Biopsy before therapy


title: ESCC_Biopsy_BPY241


title: 3WD2

description: Participant 3 measured at day 2

source_name: Whole blood

tag: group

tag: Sex

tag: age

tag: bmi

tag: regular drinker

tag: initial dbp


title: 3WD1

description: Participant 3 measured at day 1

tag: final dbp

tag: fvc


title: PBMC from Stable  97.2 at T0

description: STA, Biological replicate  97 of 190, Technical replicate 2 of 2

tag: sample type

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA097.2

tag: tissue

value: PBMC from STA097

tag: individual replicate

value: STA 97 of 190

tag: techical replicate


title: PBMC from Stable  97.1 at T0

description: STA, Biological replicate  97 of 190, Technical replicate 1 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA097.1

tag: time point


title: ESCC_Biopsy_BPY240

source_name: Esophageal squamous cell carcinoma

tag: disease state

tag: therapy

value: Neo-adjuvant chemotherapy


title: shDab2 LPS 6 h-rep2

city: Taoyuan

first: Ching-Ping

last: Tseng

address: No.259, Wenhua 1st Rd., Guishan Dist.

country: Taiwan

institute: Chang Gung University

hyb_protocol: Fluorescent targets were hybridized to the Mouse Whole Genome OneArray® with Phalanx hybridization buffer using Phalanx Hybridization System. After 16 hrs hybridization at 50 ℃, non-speciﬁc binding targets were washed away by three different washing steps (WashⅠ 42 ℃ 5 mins；Wash Ⅱ 42 ℃, 5 mins, 25 ℃ 5 mins; Wash Ⅲ rinse 20 times)

scan_protocol: The arrays were scanned by Agilent Technologies G2505C scanner (635nm power 100  PMT 0 ; 532nm power n/a, PMT n/a ) and quantify the fluoresence intensity.

data_processing:
The signal intensity of each spot was loaded into Rosetta Resolver System® (Rosetta Biosoftware) to process data analysis. The error model of Rosetta Resolver System® could remove both systematic and random errors form the data. We ﬁltered out spots that the ﬂag is less than 0. Spots that passed the criteria were normalized by 50% media scaling normalization method.
Normalize intensities: Median scaling performed on data set without flagged and control data.
Merge technical replicate data: Average intensity values calculated on technical replicates (average_intensity_values.txt).
Calculate average ratios of the hybridization replicates and find significant values for each gene by pairwise comparision (Ranking and hypothesis testing).

organism: Mus musculus

source_name: shDab2 LPS 6 h

label_protocol: 1 µg of total RNA was reverse-transcribed and amplified using Amino Allyl aRNA Amplification Kit (Phalanx Biotech Group, Taiwan) and Cy5 dyes (Amersham Pharmacia, Piscataway, NJ, USA).

extract_protocol: RNA extraction by Trizol. RNA purity was checked by optical density of NanoDrop ND-1000 and agarose electrophoresis with the result of A260/A280≧1.8, no gDNA contamination. RNA integrity was measured by Agilent RNA 6000 Nano Assay (RIN≧8).

tag: cell line

tag: cell type

value: macrophage-like cells

tag: shRNA

tag: treated with

value: LPS


title: ESCC_Biopsy_BPY242


title: shDab2 CTL-rep2

source_name: shDab2 CTL

value: PBS


title: PBMC from Stable  96.2 at T0

description: STA, Biological replicate  96 of 190, Technical replicate 2 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA096.2

value: PBMC from STA096

value: STA 96 of 190


title: 2WD1

description: Participant 2 measured at day 1

tag: group

tag: Sex

value: Male

tag: age

tag: smoker

tag: cigarettes smoked

tag: temperature

tag: dew point

tag: initial sbp

tag: final sbp

tag: pef


title: shDab2 LPS 6 h-rep1


title: shDab2 CTL-rep1


title: 1WD2

description: Participant 1 measured at day 2

tag: bmi

tag: regular drinker

tag: initial dbp

tag: final dbp

tag: fvc


title: PBMC from Stable  96.1 at T0

description: STA, Biological replicate  96 of 190, Technical replicate 1 of 2

tag: sample type

value: pool of 169 PBMC samples from Stable patients (STA)

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA096.1

tag: tissue

tag: individual replicate

tag: techical replicate

tag: time point


title: ESCC_Biopsy_BPY224

tag: disease state

tag: therapy

value: Surgery


title: 1WD1

description: Participant 1 measured at day 1

tag: group

tag: Sex

tag: age

tag: smoker

tag: cigarettes smoked

tag: temperature


title: 2WD2

description: Participant 2 measured at day 2

tag: bmi

tag: regular drinker

tag: dew point

tag: initial sbp

tag: final sbp

tag: pef


title: ESCC_Biopsy_BPY236

tag: tissue


title: ESCC_Biopsy_BPY227


title: PBMC from Stable  95.2 at T0

description: STA, Biological replicate  95 of 190, Technical replicate 2 of 2

tag: sample type

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA095.2

value: PBMC from STA095

tag: individual replicate

value: STA 95 of 190

tag: techical replicate

value: Replicate 2 of 2


title: PBMC from Stable  95.1 at T0

description: STA, Biological replicate  95 of 190, Technical replicate 1 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA095.1

value: Replicate 1 of 2

tag: time point


title: shLuc LPS 6 h-rep2

source_name: shLuc LPS 6 h

tag: cell line

tag: cell type

tag: shRNA

value: shLuc

tag: treated with


title: ESCC_Biopsy_BPY220

tag: disease state

value: ESCC

value: Biopsy before therapy

tag: therapy


title: PBMC from Stable  94.2 at T0

description: STA, Biological replicate  94 of 190, Technical replicate 2 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA094.2

value: PBMC from STA094

value: STA 94 of 190


title: ESCC_Biopsy_BPY223

value: Neo-adjuvant chemotherapy


title: shLuc LPS 6 h-rep1

value: macrophage-like cells

value: LPS


title: Individual 21 before exposure to high altitude

first: bao

last: liu

address: 30 Gaotanyan street

department: Institute of Medicine and Hygienic Equipment for High Altitude Region

institute: 3rd Military Medical University

hyb_protocol: After stopping the labeling procedure, the Hy3™-labeled samples were hybridized on the miRCURYTM LNA Array (v.18.0) (Exiqon) according to array manual.  a, The total 25 μL mixture from Hy3™-labeled samples with 25 μL hybridization buffer were first denatured for 2 min at 95°C, incubated on ice for 2 min. b, Then hybridized to the microarray for 16–20 h at 56°C in a 12-Bay Hybridization Systems (Hybridization System - Nimblegen Systems, Inc., Madison, WI, USA). c, Following hybridization, the slides were achieved, washed several times using Wash buffer kit (Exiqon)

scan_protocol: Then the slides were scanned using the Axon GenePix 4000B microarray scanner (Axon Instruments, Foster City, CA).Scanned images were then imported into GenePix Pro 6.0 software (Axon) for grid alignment and data extraction.

data_processing: Replicated miRNAs were averaged and miRNAs that intensities>=30 in all samples were chosen for calculating normalization factor. Expressed data were normalized using the Median normalization. After normalization, significant differentially expressed miRNAs between two groups were identified through Fold change and P-value. Differentially expressed miRNAs between two samples were filtered through fold change. Finally, hierarchical clustering was performed to show distinguishable miRNA expression profiling among samples.

source_name: Plasma

label_protocol: After quality control, the miRCURY™ Hy3™/Hy5™ Power labeling kit (Exiqon, Vedbaek, Denmark) was used according to the manufacturer’s guideline for miRNA labelling by following steps:a, 1μLRNA in 2.0 μL of water was combined with 1.0 μL of CIP buffer and CIP (Exiqon). The mixture was incubated for 30 min at 37°C. b, The Reaction was terminated by incubation for 5 min at 95°C. Then 3.0 μL of labeling buffer, 1.5 μL of fluorescent label (Hy3TM), 2.0 μL of DMSO, 2.0 μL of labeling enzyme were added into the mixture.The labeling reaction was incubated for 1 h at 16°C c, Terminated by incubation for 15 min at 65°C.

extract_protocol: Total RNA was isolated using TRIzol (Invitrogen) and purified with RNeasy mini kit (QIAGEN) according to manufacturer’s instructions. RNA quality and quantity was measured by using nanodrop spectrophotometer (ND-1000, Nanodrop Technologies) and RNA Integrity was determined by gel electrophoresis.  Total RNA was isolated using TRIzol (Invitrogen) and purified with RNeasy mini kit (QIAGEN) according to manufacturer’s instructions. RNA quality and quantity was measured by using nanodrop spectrophotometer (ND-1000, Nanodrop Technologies) and RNA Integrity was determined by gel electrophoresis.

value: Plasma

tag: age

tag: bmi

tag: Sex


title: Individual 22 before exposure to high altitude


title: shLuc CTL-rep1

source_name: shLuc CTL

value: PBS


title: shLuc CTL-rep2


title: PBMC from Stable  94.1 at T0

description: STA, Biological replicate  94 of 190, Technical replicate 1 of 2

source_name: Total RNA from PBMC of 169 kidney graft recipients with stable graft function and under standard immunosuppressive treatment

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA094.1


title: ESCC_Biopsy_BPY217


title: ESCC_Biopsy_BPY218


title: Individual 20 before exposure to high altitude

value: Male


title: Individual 18 before exposure to high altitude


title: Individual 19 before exposure to high altitude


title: PBMC from Stable  93.2 at T0

description: STA, Biological replicate  93 of 190, Technical replicate 2 of 2

value: pool of 169 PBMC samples from Stable patients (STA)

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA093.2

value: PBMC from STA093

value: STA 93 of 190


title: PBMC from Stable  93.1 at T0

description: STA, Biological replicate  93 of 190, Technical replicate 1 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA093.1


title: ESCC_Biopsy_BPY214


title: PBMC from Stable  92.2 at T0

description: STA, Biological replicate  92 of 190, Technical replicate 2 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA092.2

value: PBMC from STA092

value: STA 92 of 190


title: chondrocytes Gal-3 rep3

city: Vienna

first: Markus

last: Jeitler

address: Lazarettgasse 14

country: Austria

institute: Medical University Vienna

description: Isolated osteoarthritic chondrocytes were cultured to 90% confluency, starved overnight and treated with 50 µg/ml Galectin-3 for 24h in starvation medium.

hyb_protocol: Affymetrix GeneChip® Human PrimeView arrays were washed, stained and scanned according to the protocol described in GeneChip® 3` IVT Plus Labeling Assay User Manual (Fluidics Protocol FS450_0002)

scan_protocol: Scanning was done on an Affymetrix GeneChip Scanner 3000 7G, software AGCC 3.1.1

data_processing: RMA (Robust Multiarray average) Signal extraction using Affymetrix Expression Console Version 1.1

source_name: chondrocytes, Gal-3, 50 µg/ml

label_protocol: 200ng of total RNA were amplified and labeled using the Affymetrix 3` IVT Express Kit (Catalog Number 901229, Affymetrix, Santa Clara, CA)

growth_protocol: Osteoarthritic chondrocytes were isolated from femoral condyles and tibial plateaus of articular cartilage. Isolated chondrocytes were cultured in Dulbecco’s modified Eagle’s medium (DMEM; Gibco) containing 10% fetal calf serum (Biochrom) and 100 µg/ml gentamicin (Gibco) in a humidified atmosphere of 5% CO2/95% air at 37°C. To preserve the chondrocyte phenotype, only freshly isolated and seeded cells without subculturing were used for all assays.

extract_protocol: Total RNA was extracted using the innuPREP RNA Mini Kit (Analytik Jena, Jena, Germany). For quality control and quantification of total RNA, each sample was run on the Agilent 2100 Bioanalyzer Nano LabChip (Agilent Technologies, Santa Clara, CA, USA).

treatment_protocol: Upon 90% confluency, chondrocyte cultures were starved overnight using DMEM supplemented with gentamicin and treated with 50 µg/ml recombinant Galectin-3 in starvation medium for 24 h.

value: osteoarthritis

value: chondrocytes

tag: tissue location

value: knee

tag: gender

value: female


title: chondrocytes untreated control rep4

description: Isolated osteoarthritic chondrocytes were cultured to 90% confluency, starved overnight and cultured for 24h in starvation medium.

source_name: chondrocytes, untreated


title: ESCC_Biopsy_BPY209

description: Gene expression data from biopsy of esophageal squamous cell carcinoma

source_name: Esophageal squamous cell carcinoma

value: ESCC

value: Biopsy before therapy


title: Individual 17 before exposure to high altitude


title: chondrocytes untreated control rep3


title: ESCC_Biopsy_BPY205

value: Surgery


title: ESCC_Biopsy_BPY211

value: Neo-adjuvant chemotherapy


title: PBMC from Stable  91.2 at T0

description: STA, Biological replicate  91 of 190, Technical replicate 2 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA091.2

value: PBMC from STA091

value: STA 91 of 190

value: Replicate 2 of 2


title: chondrocytes Gal-3 rep2


title: chondrocytes Gal-3 rep4


title: ESCC_Biopsy_BPY208


title: PBMC from Stable  92.1 at T0

description: STA, Biological replicate  92 of 190, Technical replicate 1 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA092.1

value: Replicate 1 of 2


title: ESCC_Biopsy_BPY204


title: Individual 16 before exposure to high altitude

value: Plasma

value: Male


title: Individual 13 before exposure to high altitude


title: PBMC from Stable  90.1 at T0

description: STA, Biological replicate  90 of 190, Technical replicate 1 of 2

value: pool of 169 PBMC samples from Stable patients (STA)

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA090.1

value: PBMC from STA090

value: STA 90 of 190


title: PBMC from Stable  90.2 at T0

description: STA, Biological replicate  90 of 190, Technical replicate 2 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA090.2


title: Individual 12 before exposure to high altitude


title: PBMC from Stable  91.1 at T0

description: STA, Biological replicate  91 of 190, Technical replicate 1 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA091.1


title: chondrocytes untreated control  rep2

value: osteoarthritis


title: Individual 14 before exposure to high altitude


title: ESCC_Biopsy_BPY199


title: chondrocytes Gal-3 rep1

value: chondrocytes


title: PBMC from Stable  89.2 at T0

description: STA, Biological replicate  89 of 190, Technical replicate 2 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA089.2

value: PBMC from STA089

value: STA 89 of 190


title: PBMC from Stable  89.1 at T0

description: STA, Biological replicate  89 of 190, Technical replicate 1 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA089.1


title: ESCC_Biopsy_BPY201

value: ESCC


title: chondrocytes untreated control rep1

value: knee

value: female


title: ESCC_Biopsy_BPY198

value: Biopsy before therapy

value: Neo-adjuvant chemotherapy


title: Individual 11 before exposure to high altitude

source_name: Plasma


title: PBMC from Stable  88.2 at T0

description: STA, Biological replicate  88 of 190, Technical replicate 2 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA088.2

value: PBMC from STA088

value: STA 88 of 190


title: Individual 9 before exposure to high altitude


title: ESCC_Biopsy_BPY195


title: ESCC_Biopsy_BPY196


title: Individual 10 before exposure to high altitude


title: Individual 8 before exposure to high altitude


title: Individual 6 before exposure to high altitude


title: Individual 7 before exposure to high altitude


title: ESCC_Biopsy_BPY194


title: PBMC from Stable  87.1 at T0

description: STA, Biological replicate  87 of 190, Technical replicate 1 of 2

source_name: Total RNA from PBMC of 169 kidney graft recipients with stable graft function and under standard immunosuppressive treatment

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA087.1

value: PBMC from STA087

value: STA 87 of 190

value: Replicate 1 of 2


title: PBMC from Stable  87.2 at T0

description: STA, Biological replicate  87 of 190, Technical replicate 2 of 2

value: pool of 169 PBMC samples from Stable patients (STA)

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA087.2

value: Replicate 2 of 2


title: PBMC from Stable  86.2 at T0

description: STA, Biological replicate  86 of 190, Technical replicate 2 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA086.2

value: PBMC from STA086

value: STA 86 of 190


title: Individual 5 before exposure to high altitude

value: Plasma

value: Male


title: ESCC_Biopsy_BPY188


title: Individual 4 before exposure to high altitude


title: ESCC_Biopsy_BPY193


title: Individual 3 before exposure to high altitude


title: PBMC from Stable  88.1 at T0

description: STA, Biological replicate  88 of 190, Technical replicate 1 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA088.1


title: PBMC from Stable  86.1 at T0

description: STA, Biological replicate  86 of 190, Technical replicate 1 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA086.1


title: Individual 2 before exposure to high altitude


title: PBMC from Stable  85.1 at T0

description: STA, Biological replicate  85 of 190, Technical replicate 1 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA085.1

value: PBMC from STA085

value: STA 85 of 190


title: ESCC_Biopsy_BPY160

source_name: Esophageal squamous cell carcinoma

value: ESCC