title: NSCLC 19

first: Magdalena

middle: B

last: Wozniak

address: 150 cours Albert Thomas

department: Genetic Epidemiology

institute: International Agency for Research on Cancer

description: Case

data_processing:
The data were analysed in HTqPCR package using R Bioconductor. miRNAs with undetermined Ct values in more than 120 samples were filtered out. Data were quantile normalized. Following normalization Ct values with an interquartile range (IQR) of less than 1.5 and endogenous controls were removed from subsequent analysis, and limma analysis was performed to identify differentially regulated miRNA between cases and controls. With limma, a one-factorial linear model is fitted for each miRNA and the standard errors (SE) are moderated using an empirical Bayes model resulting in moderated t-statistics for each miRNA. These analysis were performed separately for CARD A and CARD B.
Matrix normalized worksheet reports normalized signal (quantile normalization).  Fold Change worksheet reports fold changes across all cases and controls.

label: FAM

source_name: plasma

label_protocol: Expression levels of 754 miRNAs (Sanger miRBase v14) were quantified using the TaqMan Human MicroRNA Array A + B Card Set v3.0 (Applied Biosystems, Foster City, CA) as per the manufacturer's instructions (including pre-amplification).

extract_protocol: Total RNA was isolated from 300L of plasma using NucleoSpin® miRNA Plasma kit (Macherey-Nagel, Düren, Germany) according to the manufacturer’s protocol with Proteinase K digest, addition of 2μg of glycogen carrier and DNAse digest steps. All samples were spiked-in with 10pmol of Arabidopsis thaliana synthetic miR-159a (synthesized by Eurofins MWG Operon, Ebersberg, Germany) to control for variations in the RNA preparation step.

treatment_protocol: Peripheral blood was collected in EDTA tubes at the time of interview.

tag: age at interview

tag: smoking status

value: Ever smoker

tag: morphology (for patients only)

value: Non-small cell lung cancer patient


title: NSCLC 18

status: Public on Dec 31 2015

type: RNA

city: Lyon

country: France

description: Case

molecule: total RNA

organism: Homo sapiens

tag: gender

value: Male

tag: disease state


title: NSCLC 17

description: Case

value: Female

value: Never smoker


title: blood-high-36

city: Newcastle

first: Simon

last: Cockell

address: Framlington Place

country: United Kingdom

institute: Newcastle University

hyb_protocol: 50 ng of the obtained biotinylated cRNA samples was hybridized onto the Illumina HumanHT-12 v4 as per manufacturer's instructions.

scan_protocol: The samples were scanned using the Illumina iScan array scanner. There were no deviations from the Illumina protocol  The samples were scanned using the Illumina iScan array scanner.  The samples were scanned using the Illumina iScan array scanner. There were no deviations from the Illumina protocol.  The samples were scanned using the Illumina iScan array scanner.  The samples were scanned using the Illumina iScan array scanner. There were no deviations from the Illumina protocol.

data_processing: Data were processed using R/Bioconductor (the lumi package), Raw data were transformed using a Variance Stabilizing Transformation, and normalized with the robust spline normalization algorithm. Probes were selected which fulfilled the criteria of Illumina probe detection p-value of <0.01.

label: biotin

source_name: whole blood, fatigue level: High

label_protocol: The Illumina TotalPrep-96 RNA Amplification Kit was used to generate Biotin labeled (biotin-16-UTP), amplified cRNA starting from 200ng total RNA.

extract_protocol: Total RNA isolated from peripheral whole blood using PAXgene Blood miRNA kit [PreAnalytix GmbH, Switzerland] following manufacturer’s protocol, RNA integrity checked using Agilent Bioanalyser.

tag: tissue

value: whole blood

tag: fatigue status

value: High

tag: patient group

value: Patient


title: Caco-2_4h_50µg/mL_of_polymeric nanoparticles (Eudragit® RLPO)_rep1

city: nancy

first: Olivier

last: Joubert

address: 2 allée guinier

department: Dpt 4

institute: Université de lorraine

description:
Gene expression in Caco-2 cells after 4 h in presence of polymeric nanoparticles exposure (Eudragit® RL PO, 50µg/mL)
S46_1_2

hyb_protocol: Six hundred ng of CTP-Cy3-labelled cRNA (specific activity > 10 pmol Cy3 / µg cRNA) was fragmented at 60°C for 30 min in a reaction volume of 25 µL containing 25 x Agilent fragmentation buffer and 10 x Agilent blocking agent following the manufacturer’s instructions. On cRNA fragmentation completion, 25 µL of 2 x Agilent hybridization buffer were added to the fragmentation mixture and cRNA were hybridized to SurePrint G3 Human GE v2 8x60K (Agilent Technologies, Santa Clara, CA, USA) for 17 h at 65°C in a rotating hybridization oven. After hybridization, microarrays were washed 1 min at room temperature with GE Wash Buffer 1TM and 1 min with 37°C GE Wash buffer 2TM (Agilent Technologies, Santa Clara, CA, USA), and immediately dried by brief immersion in acetonitrile.

scan_protocol: Slides were scanned immediately after washing using Agilent DNA Microarray Scanner (G2505C) by setting: (i) one color scan channel for 8x60k array slides, (ii) scan area of 61x21.6 mm, (iii) scan resolution of 3 µm, (iv) dye channel to Green, (v) Tiff file dynamic range of 20 bits and (vi) Green PMT to 100 %.

data_processing:
The scanned images were analyzed by Feature Extraction version 11.0.1.1 (Agilent Technologies, Santa Clara, CA, USA) using default parameters (protocol GE1_1100_Jul11 and Grid: 039494_D_F_20140326) to subtract background and to obtain spatially detrended processed signal intensities. Features flagged in Feature Extraction as Non-uniform outliers Feature were excluded.
Normalized signal intensity by Genespring (version 13.0, Agilent Technologies, Santa Clara, CA, USA)

source_name: Caco-2, 4 h, 50µg/mL of polymeric nanoparticles (Eudragit® RLPO), replicate 1

label_protocol: CTP-cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng RNA using the One-Color Microarray-Based Gene Expression Analysis (version 6.6, Agilent Technologies, Santa Clara, CA, USA) according to manufacturer's instructions, followed by chromatographic purification (RNeasy Mini kit, QIAGEN, Venlo, NL). Dye incorporation and cRNA yield and quality were checked by spectrophotometry (BioSpec-nano, Shimadzu) and by electrophoresis (Agilent 2100 Bioanalyzer).

growth_protocol: Caco-2 human colon epithelial-like cell line is derived from a sample of a 72 years old man suffering from colorectal adenocarcinoma and was obtained from American Type Culture Collection (ATCC, HTB-37™, Manassas, VA, USA). Cells were grown in EMEM culture medium (Sigma Aldrich, Saint Quentin Fallavier, France) supplemented with 20% of heat-inactivated fetal bovine serum (Eurobio, Les Ullis, France) and 1% non-essential amino acids, as well as penicillin (100U/mL) and 1mM sodium pyruvate (all from Sigma Aldrich, Saint Quentin Fallavier, France). Cells were incubated at 37°C under a 5 % CO2 atmosphere, and diluted by half once a week and medium was change every 3 days. Passage 39 was used.

extract_protocol: The quality of RNA extracted by RNeasy® Mini Kit (Qiagen, Venlo, NL) was determined by spectrophotometry (A260nm/A280nm > 1.8, BioSpec-nano, Shimadzu) and by capillary electrophoresis using RNA 6000 Nano® (RIN > 8, Agilent 2100 Bioanalyzer, Santa Clara, CA, USA).

treatment_protocol: Caco-2 cells at a density of 3x105 cells/mL were incubated without (control) or with S-nitrosoglutathione (GSNO, 1.4 µM), or with Eudragit RL PO polymeric nanoparticles (NP-ERL, 50 μg/mL), or with GSNO loaded Eudragit RL PO polymeric nanoparticles (NP-GSNO, 50 μg/mL, corresponding 1.4 µM GSNO) for 4h. GSNO and nanoparticles was prepared by W. Wu and Professor R. Schneider in LRGP UPR-CNRS 3349 and EA 3452 CITHEFOR laboratories (Lorraine University, France).

value: Colon

tag: age

value: 72 years

tag: cell line

value: Caco-2 colon epithelial-like cell line

tag: agent

value: nanoparticles


title: Caco-2_4h_50µg/mL_of_GSNO (1.4 µM) loaded polymeric nanoparticles (Eudragit® RLPO)_rep3

description:
Gene expression in Caco-2 cells after 4 h in presence of GSNO loaded nanoparticles exposure (GSNO 1.4 µM - Eudragit® RL PO 50 µg/mL)
S35_2_4

source_name: Caco-2, 4 h, 50µg/mL of GSNO (1.4 µM) loaded polymeric nanoparticles (Eudragit® RLPO), replicate 3

value: GSNO loaded nanoparticles


title: NSCLC 16

description: Case


title: Caco-2_4h_50µg/mL_of_GSNO (1.4 µM) loaded polymeric nanoparticles (Eudragit® RLPO)_rep4

description:
Gene expression in Caco-2 cells after 4 h in presence of GSNO loaded nanoparticles exposure (GSNO 1.4 µM - Eudragit® RL PO 50 µg/mL)
S35_2_3

source_name: Caco-2, 4 h, 50µg/mL of GSNO (1.4 µM) loaded polymeric nanoparticles (Eudragit® RLPO), replicate 4


title: NSCLC 14

description: Case


title: Caco-2_4h_50µg/mL_of_GSNO (1.4 µM) loaded polymeric nanoparticles (Eudragit® RLPO)_rep1

description:
Gene expression in Caco-2 cells after 4 h in presence of GSNO loaded nanoparticles exposure (GSNO 1.4 µM - Eudragit® RL PO 50 µg/mL)
S46_2_4

source_name: Caco-2, 4 h, 50µg/mL of GSNO (1.4 µM) loaded polymeric nanoparticles (Eudragit® RLPO), replicate 1


title: MCL 1135

type: genomic

city: Barcelona

first: Pedro

last: Jares

state: Barcelona

address: c/ Villarroel 170

department: Genomics Unit

country: Spain

institute: IDIBAPS

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

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

data_processing: BeadStudio software v3.2

label: Cy5 and Cy3

molecule: genomic DNA

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted using Qiagen DNeasy Kit according to standard instructions

tag: disease

value: primary MCL


title: Caco-2_4h_50µg/mL_of_GSNO (1.4 µM) loaded polymeric nanoparticles (Eudragit® RLPO)_rep2

description:
Gene expression in Caco-2 cells after 4 h in presence of GSNO loaded nanoparticles exposure (GSNO 1.4 µM - Eudragit® RL PO 50 µg/mL)
S46_2_3

source_name: Caco-2, 4 h, 50µg/mL of GSNO (1.4 µM) loaded polymeric nanoparticles (Eudragit® RLPO), replicate 2


title: Caco-2_4h_1.4 µM_of_GSNO_rep4

description:
Gene expression in Caco-2 cells after 4 h in presence of GSNO exposure (1.4 ÂµM)
S35_2_1

source_name: Caco-2, 4 h, 1.4 µM of GSNO, replicate 4

value: GSNO


title: blood-high-35


title: MCL 1131


title: MCL 1134


title: NSCLC 13

description: Case


title: blood-low-20

source_name: whole blood, fatigue level: Low

value: Low


title: MCL 1133


title: NSCLC 15

description: Case


title: Caco-2_4h_1.4 µM_of_GSNO_rep2

description:
Gene expression in Caco-2 cells after 4 h in presence of GSNO exposure (1.4 ÂµM)
S46_2_1

source_name: Caco-2, 4 h, 1.4 µM of GSNO, replicate 2


title: MCL 1132


title: NSCLC 12

description: Case


title: blood-mid-73

source_name: whole blood, fatigue level: Mid

value: Mid


title: blood-mid-72


title: Caco-2_4h_1.4 µM_of_GSNO_rep3

description:
Gene expression in Caco-2 cells after 4 h in presence of GSNO exposure (1.4 ÂµM)
S35_2_2

source_name: Caco-2, 4 h, 1.4 µM of GSNO, replicate 3


title: Caco-2_4h_1.4 µM_of_GSNO_rep1

description:
Gene expression in Caco-2 cells after 4 h in presence of GSNO exposure (1.4 µM)
S46_2_2

source_name: Caco-2, 4 h, 1.4 µM of GSNO, replicate 1


title: blood-mid-71


title: NSCLC 10

description: Case


title: NSCLC 11

description: Case

value: Ever smoker


title: MCL 1128


title: MCL 1129


title: Caco-2_Control_rep4

description:
Gene expression in Caco-2 cells after 4 h in absence of treatment
S35_1_3

source_name: Caco-2, 4 h, Control, replicate 4

value: Control


title: blood-high-34


title: MCL 1126


title: MCL 1130


title: Caco-2_Control_rep3

description:
Gene expression in Caco-2 cells after 4 h in absence of treatment
S35_1_4

source_name: Caco-2, 4 h, Control, replicate 3

value: Male


title: Caco-2_Control_rep2

description:
Gene expression in Caco-2 cells after 4 h in absence of treatment
S46_1_3

source_name: Caco-2, 4 h, Control, replicate 2


title: MCL153


title: blood-control-29

source_name: whole blood, fatigue level: Control

value: Female


title: blood-mid-70


title: blood-high-33


title: NSCLC 9

description: Case

source_name: plasma

value: Never smoker

value: Non-small cell lung cancer patient


title: NSCLC 8

description: Case


title: MCL 1123


title: NSCLC 7

description: Case


title: NSCLC 6

description: Case


title: NSCLC 5

description: Case


title: NSCLC 4

description: Case


title: MCL 1114


title: blood-high-31

source_name: whole blood, fatigue level: High

value: whole blood

value: High


title: NSCLC 3

description: Case


title: blood-low-19

value: Patient


title: blood-high-30


title: THP-1_4h_ 6µM_of_GSNO_rep3

description: Gene expression in THP-1 cells after 4 h in presence of GSNO exposure (6 µM)

hyb_protocol: Six hundred ng of CTP-Cy3-labelled cRNA was fragmented at 60°C for 30 min in a reaction volume of 25 µL containing 25 x Agilent fragmentation buffer and 10 x Agilent blocking agent following the manufacturer’s instructions. On cRNA fragmentation completion, 25 µL of 2 x Agilent hybridization buffer were added to the fragmentation mixture and cRNA were hybridized to SurePrint G3 Human GE v2 8x60K (Agilent) for 17 h at 65°C in a rotating hybridization oven. After hybridization, microarrays were washed 1 min at room temperature with GE Wash Buffer 1TM and 1 min with 37°C GE Wash buffer 2TM (Agilent), and immediately dried by brief immersion in acetonitrile.

data_processing: The scanned images were analyzed by Feature Extraction version 11.0.1.1 (Agilent) using default parameters (protocol GE1_1100_Jul11 and Grid: 039494_D_F_20140326) to subtract background and to obtain spatially detrended processed signal intensities. Features flagged in Feature Extraction as Non-uniform outliers Feature were excluded.

source_name: THP-1, 4 h, 6 µM of GSNO, replicate 3

label_protocol: CTP-cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng RNA using the One-Color Microarray-Based Gene Expression Analysis (Agilent, version 6.6) according to manufacturer's instructions, followed by chromatographic purification (RNeasy Mini kit, QIAGEN). Dye incorporation and cRNA yield and quality were checked by spectrophotometry (specific activity > 10 pmol Cy3 / µg cRNA, BioSpec-nano, Shimadzu) and by electrophoresis (Agilent 2100 Bioanalyzer).

growth_protocol: THP-1 human monocyte cell line is derived from a blood sample of a one-year old child suffering from acute monocytic leukemia and was obtained from American Type Culture Collection (ATCC, TIB-202TM, Manassas, VA, USA). Cells were grown in RPMI 1640 medium (GIBCO, Invitrogen, Cergy Pontoise, France) supplemented with 10 % of heat-inactivated fetal bovine serum (Eurobio, Les Ullis, France), as well as 100 U/mL of penicillin, 100 µg/mL of streptomycin and 0.25 µg/mL of amphotericin B (all from Sigma, Saint Quentin Fallavier, France). Cells were incubated at 37°C to an atmosphere composed of 95 % air, 5 % CO2 and diluted by half every 3 days.

extract_protocol: The quality of the RNA extracted by TRIzol® Reagent (Invitrogen, La Jolla, CA) was determined by spectrophotometry (A260nm/A280nm, A260nm/A230nm > 1.8, BioSpec-nano, Shimadzu) and by capillary electrophoresis using RNA 6000 Nano® (RIN > 9, Agilent 2100 Bioanalyzer, Santa Clara, CA, USA).

treatment_protocol: THP-1 cells at a density of 3 x 105 cells / mL were incubated without (control) or with S-Nitrosoglutathione (GSNO, 1.4 or 6 µM) for 4 h. GSNO [CAS number: 57564-91-7] was synthesized by Dr W.Wu and Prof. R. Schneider in LRGP UPR-CNRS 3349 laboratories (Lorraine University, France).

value: peripheral blood

value: male


title: MCL 1072


title: blood-high-32


title: THP-1_4h_ 6µM_of_GSNO_rep1

source_name: THP-1, 4 h, 6 µM of GSNO, replicate 1


title: THP-1_4h_ 6µM_of_GSNO_rep4

source_name: THP-1, 4 h, 6 µM of GSNO, replicate 4


title: MCL 1115


title: MCL 1029


title: MCL 982

source_name: MCL 982


title: MCL 1013


title: NSCLC 2

description: Case


title: THP-1_4h_1.4µM_of_GSNO_rep3

description: Gene expression in THP-1 cells after 4 h in presence of GSNO exposure (1.4 µM)

source_name: THP-1, 4 h, 1.4 µM of GSNO, replicate 3


title: THP-1_4h_1.4µM_of_GSNO_rep4

source_name: THP-1, 4 h, 1.4 µM of GSNO, replicate 4


title: blood-mid-69


title: MCL 983

source_name: MCL 983


title: Caco-2_Control_rep1

description:
Gene expression in Caco-2 cells after 4 h in absence of treatment
S46_1_4

source_name: Caco-2, 4 h, Control, replicate 1

value: Colon

value: 72 years

value: Caco-2 colon epithelial-like cell line


title: NSCLC 1

description: Case


title: THP-1_4h_ 6µM_of_GSNO_rep2

description: Gene expression in THP-1 cells after 4 h in presence of GSNO exposure (6 µM)

source_name: THP-1, 4 h, 6 µM of GSNO, replicate 2


title: blood-mid-68

source_name: whole blood, fatigue level: Mid


title: MCL 980

source_name: MCL 980

value: primary MCL


title: THP-1_4h_1.4µM_of_GSNO_rep2

source_name: THP-1, 4 h, 1.4 µM of GSNO, replicate 2


title: blood-high-29


title: CRTL 100

description: Control

value: Non-cancer


title: THP-1_4h_1.4µM_of_GSNO_rep1

source_name: THP-1, 4 h, 1.4 µM of GSNO, replicate 1


title: blood-mid-67

value: Mid


title: THP-1_4h_0µM_of_GSNO_rep4

description: Gene expression in THP-1 cells after 4 h in absence of GSNO exposure (0 µM)

source_name: THP-1, 4 h, 0 µM of GSNO, replicate 4


title: MCL 975

source_name: MCL 975


title: blood-control-28

source_name: whole blood, fatigue level: Control


title: blood-mid-65


title: CRTL 98

description: Control

source_name: plasma


title: CRTL 97

description: Control

value: Ever smoker


title: CRTL 99

description: Control


title: CRTL 95

description: Control


title: MCL 972

source_name: MCL 972


title: MCL212


title: blood-mid-64


title: THP-1_4h_0µM_of_GSNO_rep1

source_name: THP-1, 4 h, 0 µM of GSNO, replicate 1


title: MCL 974

source_name: MCL 974


title: blood-control-27

value: Control


title: blood-mid-63


title: MCL 957

source_name: MCL 957


title: MCL 959

source_name: MCL 959


title: THP-1_4h_0µM_of_GSNO_rep3

source_name: THP-1, 4 h, 0 µM of GSNO, replicate 3


title: CRTL 94

description: Control

value: Male


title: THP-1_4h_0µM_of_GSNO_rep2

source_name: THP-1, 4 h, 0 µM of GSNO, replicate 2


title: blood-high-28

source_name: whole blood, fatigue level: High

value: Female


title: CRTL 93

description: Control


title: MCL 981

source_name: MCL 981


title: blood-mid-62

source_name: whole blood, fatigue level: Mid


title: blood-mid-61


title: CRTL 92

description: Control

value: Never smoker


title: CRTL 96

description: Control


title: CRTL 91

description: Control


title: CRTL 90

description: Control


title: CRTL 89

description: Control


title: CRTL 86

description: Control


title: CRTL 88

description: Control


title: CRTL 85

description: Control


title: blood-control-26


title: blood-high-26


title: MCL 954

source_name: MCL 954


title: MCL211


title: blood-control-25


title: MCL 944

source_name: MCL 944


title: MCL 953

source_name: MCL 953


title: blood-high-25


title: MCL 933

source_name: MCL 933


title: MCL 943

source_name: MCL 943


title: blood-high-27


title: blood-mid-59


title: MCL 928

source_name: MCL 928


title: MCL 931

source_name: MCL 931


title: blood-mid-58


title: CRTL 84

description: Control

source_name: plasma


title: MCL 942

source_name: MCL 942


title: CRTL 83

description: Control


title: MCL 937

source_name: MCL 937


title: CRTL 82

description: Control


title: blood-mid-60


title: CRTL 81

description: Control


title: blood-control-24

source_name: whole blood, fatigue level: Control


title: blood-low-18

source_name: whole blood, fatigue level: Low

value: Low


title: CRTL 80

description: Control


title: CRTL 87

description: Control


title: MCL 938

source_name: MCL 938


title: MCL 920

source_name: MCL 920


title: MCL 924

source_name: MCL 924


title: CRTL 79

description: Control


title: MCL 921

source_name: MCL 921


title: MCL 922

source_name: MCL 922


title: blood-high-24

source_name: whole blood, fatigue level: High

value: whole blood


title: blood-control-23


title: CRTL 77

description: Control


title: CRTL 78

description: Control


title: CRTL 76

description: Control


title: CRTL 75

description: Control


title: CRTL 74

description: Control


title: CRTL 73

description: Control


title: blood-mid-56

source_name: whole blood, fatigue level: Mid


title: blood-mid-57


title: MCL 918

source_name: MCL 918


title: blood-mid-66


title: MCL 956

source_name: MCL 956


title: blood-high-23

value: High


title: blood-mid-55

value: Patient


title: MCL 881

source_name: MCL 881


title: CRTL 72

description: Control


title: blastocyst_13_2_High_G5_ 35

city: Amsterdam

first: Martijs

last: Jonker

address: Science Park 904

department: Microarray Department

country: Netherlands

institute: University of Amsterdam

hyb_protocol: 825 ng of labeled sample aRNA and 825 ng labeled reference aRNA were hybridized to 4x 180k custom designed Agilent arrays (Agilent technologies). The 180k microarray (design ID:028004) contained ~42.000 probes in quadruplet and 11.200 control probes (ref Mantikou, et al., 2013, PLOS). The hybridization mixture was prepared according to the Two-Color Microarray-Based Gene Expression Analysis protocol (Agilent technologies). The aRNA was allowed to hybridize for 17 hours at 650C and 10 rpm.

scan_protocol: Afterwards, the slides were washed and scanned in an ozone-free room with the Agilent scanner GA2505C (Agilent Technologies). Slides were scanned at 3 μm resolution.

data_processing: Microarray data were extracted with Feature Extraction software 10.7.1 (Agilent Technologies). The data were analyzed in R-2.14.1 (http://cran.r-project.org/). All arrays were subjected to a set of quality control checks, such as visual inspection of the scans, checking for spatial effects through pseudo-color plots, and inspection of pre- and post-normalized data with box plots, density plots, ratio-intensity plots and principal component analysis First the data were normalized using lowess normalization using both the test and reference channels then expression values were calculated by using the robust multi-array average (RMA) algorithm (Irizarry et al.). When multiple embryos per woman were correlated only one of those samples was selected to avoid effects of pseudoreplication. For each experimental condition mean expression values were calculated. The conditions were compared using Spearman correlation coefficients.

source_name: blastocyst_13_2_High_G5_ 35

label_protocol: 10 µl of CyDye (Cy3 for test samples and Cy5 for reference samples) diluted in DMSO was added to each reaction. Then, the samples were incubated in the dark at room temperature for 60 min. The reactions were quenched by 5 µl of 4 M hydroxylamine for 15 min at room temperature in the dark. The labeled RNA was purified according to the MicroElute RNA Cleanup protocol (Omega). The RNA was finally eluted in 15 µl Rnase/DNase free water. Pooled aRNA from the amplified samples was used as a reference in all experiments. The yield and CyDye incorporation of labeled aRNA were measured with the NanoDrop ND-1000 (Thermo Scientific).

growth_protocol: All embryos were cultured in HTF (Lonza, Verviers, Belgium) supplemented with 10% GPO (XX) under 5% CO2 and 20% O2 as part of normal patient treatment until day 4 when they were cryopreserved. Forty women (23 undergoing IVF and 17 undergoing ICSI) were randomised to have their embryos cultured for two additional days after thawing (till embryonic day 6) in one of the following groups: (i) HTF-medium and 20% O2, (ii) HTF-medium and 5% O2, (iii) G5-medium and 20% O2 and (iv) G5-medium and 5% O2.

extract_protocol: For sample preparation we used a protocol that was recently developed and validated for analysis of picogram amounts of RNA (Mantikou, et al. 2013, PLOS). Briefly, RNA isolation was performed using the Arcturus PicoPure isolation kit (Applied biosystems) following the instructions of the manufacturer. RNA extraction was performed with 50μl extraction buffer and the recommended DNase treatment was performed. The RNA was then amplified using the Arcturus RiboAmp HS Plus (Applied Biosystems). The concentration of the aRNA was measured on the Nano-drop ND-1000 (Thermo Scientific) and the quality of the amplified product was investigated with the BioAnalyzer (Agilent Technologies) using the RNA Nano 6000 kit (Agilent Technologies). 5 µg of amplified RNA was dried in a speedvac and then dissolved in 5 µl 50 mM carbonate buffer (pH 8.5) and placed at 370C for 10 min.

treatment_protocol: During the experimental culture, the two culture media were prepared according to the manufacturers’ instructions. HTF-medium was supplemented with 10% GPO and was equilibrated in 5% CO2, while G5-medium (Vitrolife, Göteborg, Sweden) was supplemented with HSA (5 mg/ml) and was equilibrated in 6% CO2.   Randomization of the women to the four experimental groups was performed in the morning before thawing using sealed envelopes and stratification was performed for maternal age (≤ 35 and >35 years). The embryos were morphologically assessed according to the Gardner criteria, by two (SR, SM) embryologists that were blinded for the culture conditions used, right after thawing, at the end of the first day of culture and at the end of the second day of culture just before freezing and parameters like cell number, percentage of fragmentation and presence of dead cells were noted (ref Gardner, et al., 2000). At the end of the culture, individual embryos (n=89) were transferred in PCR-tubes, flash frozen in liquid nitrogen and stored at -80oC until RNA extraction. Only embryos that had developed to the morula and blastocyst stage (n=41) were further analysed.

tag: score

value: blastocyst

tag: oxygen concentration

tag: embryoid

tag: medium

tag: age mother

source_name: Common Reference

tag: common reference

value: Pooled samples


title: morula_40_2_Low_G5_ 30

value: morula


title: MCL 916

source_name: MCL 916


title: CRTL 71

description: Control

source_name: plasma

tag: age at interview

tag: smoking status


title: blood-control-22

tag: gender


title: MCL 781

source_name: MCL 781


title: morula_17_3_Low_HTF_ 32

source_name: morula_17_3_Low_HTF_ 32

value: HTF


title: MCL 868

source_name: MCL 868


title: blood-mid-52


title: early_bl_24_2_High_G5_ 40

source_name: early_bl_24_2_High_G5_ 40


title: CRTL 70

description: Control

tag: disease state


title: morula_3_2_High_HTF_ 31

source_name: morula_3_2_High_HTF_ 31


title: blood-high-22

tag: tissue


title: blood-mid-54

tag: fatigue status


title: MCL 741

source_name: MCL 741


title: MCL210


title: blood-mid-51

tag: patient group


title: early_bl_8_1_Low_G5_ 30

source_name: early_bl_8_1_Low_G5_ 30


title: blood-mid-53


title: CRTL 69

description: Control


title: blastocyst_22_1_Low_HTF_ 38

source_name: blastocyst_22_1_Low_HTF_ 38


title: MLN151


title: morula_3_3_High_HTF_ 31

source_name: morula_3_3_High_HTF_ 31


title: blood-low-17

source_name: whole blood, fatigue level: Low


title: CRTL 68

description: Control


title: CRTL 67

description: Control


title: CRTL 66

description: Control


title: CRTL 65

description: Control


title: MCL209


title: blood-high-21

source_name: whole blood, fatigue level: High


title: morula_2_3_Low_HTF_ 38

source_name: morula_2_3_Low_HTF_ 38


title: MCL207


title: morula_19_3_High_HTF_ 39

source_name: morula_19_3_High_HTF_ 39


title: MCL205


title: MCL208


title: blood-mid-50

source_name: whole blood, fatigue level: Mid


title: CRTL 64

description: Control


title: blood-low-16


title: early_bl_18_1_Low_G5_ 34

source_name: Common Reference


title: blood-control-21

source_name: whole blood, fatigue level: Control


title: blood-mid-49


title: MCL206


title: CRTL 63

description: Control

source_name: plasma


title: morula_32_2_High_G5_ 35

source_name: morula_32_2_High_G5_ 35


title: morula_9_2_High_G5_ 37

source_name: morula_9_2_High_G5_ 37


title: morula_35_1_High_HTF_ 30

source_name: morula_35_1_High_HTF_ 30


title: CRTL 62

description: Control


title: blood-high-20


title: MCL203


title: MCL201


title: CRTL 61

description: Control


title: blood-mid-48


title: MCL202


title: morula_32_4_High_G5_ 35

source_name: morula_32_4_High_G5_ 35


title: MCL204


title: early_bl_27_1_Low_HTF_ 33

source_name: early_bl_27_1_Low_HTF_ 33


title: blastocyst_5_3_Low_HTF_ 32

source_name: blastocyst_5_3_Low_HTF_ 32


title: MCL150


title: morula_34_1_High_G5_ 35

source_name: morula_34_1_High_G5_ 35


title: blood-low-15


title: blood-mid-46


title: early_bl_21_1_Low_G5_ 39


title: CRTL 59

description: Control


title: CRTL 60

description: Control


title: blood-mid-47


title: CRTL 58

description: Control


title: CRTL 57

description: Control


title: MCL149


title: CRTL 56

description: Control


title: CRTL 55

description: Control


title: MCL148


title: MCL146


title: CRTL 54

description: Control


title: morula_6_2_High_G5_ 37

source_name: morula_6_2_High_G5_ 37


title: blastocyst_20_2_High_HTF_ 27

source_name: blastocyst_20_2_High_HTF_ 27


title: CRTL 53

description: Control


title: MCL145


title: blood-high-19


title: blood-mid-45


title: MCL147


title: MCL144


title: blood-mid-43


title: blood-mid-44


title: blood-control-20


title: morula_19_2_High_HTF_ 39

source_name: morula_19_2_High_HTF_ 39


title: blood-high-18

source_name: whole blood, fatigue level: High


title: morula_2_2_Low_HTF_ 38

source_name: morula_2_2_Low_HTF_ 38


title: morula_40_4_Low_G5_ 30


title: blastocyst_7_2_Low_G5_ 40

source_name: blastocyst_7_2_Low_G5_ 40


title: MCL141


title: CRTL 52

description: Control


title: blood-mid-42

source_name: whole blood, fatigue level: Mid


title: CRTL 51

description: Control


title: morula_10_2_Low_HTF_ 37

source_name: morula_10_2_Low_HTF_ 37

source_name: Common Reference


title: CRTL 50

description: Control

source_name: plasma


title: MCL143


title: CRTL 49

description: Control


title: CRTL 48

description: Control


title: morula_39_2_High_HTF_ 42

source_name: morula_39_2_High_HTF_ 42


title: blood-low-14

source_name: whole blood, fatigue level: Low


title: blood-mid-41


title: MCL142


title: morula_11_3_High_HTF_ 30

source_name: morula_11_3_High_HTF_ 30


title: MCL140


title: MCL138


title: CRTL 47

description: Control


title: blood-mid-39


title: morula_30_2_High_G5_ 36

source_name: morula_30_2_High_G5_ 36


title: morula_37_2_High_G5_ 39

source_name: morula_37_2_High_G5_ 39


title: MCL139


title: MCL137


title: morula_5_1_Low_HTF_ 32

source_name: morula_5_1_Low_HTF_ 32


title: CRTL 45

description: Control


title: blood-mid-40


title: CRTL 44

description: Control


title: CRTL 46

description: Control


title: blood-high-17


title: CRTL 43

description: Control


title: early_bl_23_2_High_G5_ 28

source_name: early_bl_23_2_High_G5_ 28


title: MCL135


title: blood-mid-38


title: blood-mid-36


title: CRTL 42

description: Control


title: MCL134


title: morula_25_1_High_HTF_ 34

source_name: morula_25_1_High_HTF_ 34


title: blastocyst_15_2_Low_G5_ 31

source_name: blastocyst_15_2_Low_G5_ 31


title: blood-low-11


title: MCL136


title: cDNA wt-UPF1 YPD

city: Burjassot

first: Jose

middle: E.

last: Perez-Ortin

state: Valencia

address: Dr. Moliner 50

department: Bioquimica y Biologia Molecular

institute: Universitat de Valencia

description: mRNA Amount: Processed data of cDNA triplicate experiment, [mRNA/cell volume] adjusted and Median Absolute Deviation normalized.

hyb_protocol: Hybridization Solution was: 0.5M Na-Phosphate buffer, 1mM EDTA and 7% SDS, pH 7.2. The hybridization protocol used was as follows. Filters were inserted in 12.5X 2.5-cm flat-bottom plastic tubes and pre-hybridized in a rotator oven with 5 ml pre-hybridization solution (the same as used for hybridization but without the radioactive sample) at 65ºC. The pre-hybridization solution was then replaced with 5 ml of the same solution containing 1-5X10exp6 dpm/mL of radioactive sample and hybridized for 48h. Washing conditions were: 20 min at 65ºC in 1X SSC, 0.5% SDS, and twice at 65ºC for 10 min in 0.5X SSC, 0.1% SDS. After quantification, filters were stripped by washing them once with 50 mM NaOH at 45ºC, once with 50 mM Tris-HCl, pH 7.5, 0.1x SSC, 0.1% SDS and once pouring with boiling stripping buffer (5 mM sodium phosphate, pH 7.5, 0.1% SDS) over the membrane and left to cool at room temperature. To ensure that radioactivity had been eliminated, the filters were either checked with a Geiger counter.

scan_protocol: Images were acquired using a FujiFilm FLA3000 Phosphorimager. After the washing step, membranes were kept humid, sealed in Saran wrap, avoiding any bubbles, and exposed to an imaging plate (BAS-MP, FujiFilm) for various times.

data_processing:
Raw image quantization with background subtracted and Median Absolute Desviation normalization of each triplicate.
Value was the result of the local background sustraction to the raw data. In Processed data, we normalized using ArrayStat software (Median Absolute Deviation). For RA, average values were corrected by percentage of guanines and for nTR the average value for each gene was corrected by percentage of uridines present in each probe-coding strand. The mRNA levels was adjusted using the concentration of mRNA/cell for each strain regard the wild type strain.

organism: Saccharomyces cerevisiae

source_name: Wild type cells grown in YPD to exponential phase.

label_protocol: In vivo labeling by run-on (GRO) was done using 33P-UTP. Around 6 x 10exp8 yeast cells were used to perform in vivo transcription. After spinning down cells, they were permeabilized with 20 mL of 0.5% sarkosyl and cells were recovered by low-speed centrifugation and the supernatant was removed. In vivo transcription was performed by resuspending cells in 115 µl of RNA water and adding 162 µL of Run On Mix (120 µl of 2.5x transcription buffer [50 mM Tris-HCl pH 7.7, 500 mM KCl, 80 mM MgCl2], 20 µl of AGC mix [10 mM each of CTP, ATP and GTP], 6 µl of DTT [0.1 M] and 13 µl of [α-33P]UTP [3000 Ci/mmol, 10 Ci/µL]). The mix was incubated for 5 minutes at 30ºC to allow transcription elongation. The reaction was stopped by adding 1 ml of cold distilled water to the mix.

growth_protocol: Exponential growth in YPD (or YPGal) at 28ºC.

extract_protocol: Total RNA isolated from yeast cells was prepared as described by Sherman et al. [1986], but using a multiple-sample automated device (Fast-Prep, BIO101) to break the cells. Sherman F, Fink GR, Hicks JB (1986) Methods in yeast genetics. Spring Harbor Cold Laboratory Press, Cold Spring Harbor, New York.

tag: genotype/variation

value: wild type

tag: strain

tag: media

value: YPD


title: CRTL 41

description: Control

value: Non-cancer


title: blood-low-12


title: blastocyst_30_6_High_G5_ 36

source_name: blastocyst_30_6_High_G5_ 36


title: blastocyst_36_3_Low_HTF_ 34

source_name: blastocyst_36_3_Low_HTF_ 34


title: cDNA upf1 YPD

source_name: upf1Δ cells grown in YPD to exponential phase

value: upf1Δ deletion mutant


title: MCL131

tag: disease

value: primary MCL


title: MCL133


title: MCL130


title: blood-mid-35

source_name: whole blood, fatigue level: Mid

value: Mid


title: MCL132


title: blood-mid-34


title: CRTL 40

description: Control

value: Male

value: Ever smoker


title: CRTL 39

description: Control


title: CRTL 38

description: Control


title: blood-mid-37

value: Female


title: blood-low-13

value: Low


title: cDNA rai1 YPD

source_name: rai1Δ cells grown in YPD to exponential phase

value: rai1Δ deletion mutant


title: cDNA dst1 YPD

source_name: dst1Δ cells grown in YPD to exponential phase

value: dst1Δ deletion mutant


title: CRTL 37

description: Control

source_name: plasma

value: Never smoker


title: CRTL 36

description: Control


title: CRTL 35

description: Control


title: cDNA sfp1 YPD

source_name: sfp1Δ cells grown in YPD to exponential phase

value: sfp1Δ deletion mutant


title: CRTL 34

description: Control


title: MCL128


title: GRO upf1 YPD

description: nascent Transcriptional Rate: Processed data of Genomic Run On triplicate experiment, Median Absolute Deviation normalized.


title: blood-high-15

source_name: whole blood, fatigue level: High

value: whole blood

value: High

value: Patient


title: MCL123


title: blood-high-14


title: cDNA wt YPD

value: wild type


title: MCL127


title: GRO wt-UPF1 YPD

value: YPD


title: MCL124


title: cDNA rpb4 YPD

source_name: rpb4Δ cells grown in YPD to exponential phase

value: rpb4Δ deletion mutant


title: blood-mid-33


title: MCL125


title: CRTL 32

description: Control

value: Non-cancer


title: blood-low-10

source_name: whole blood, fatigue level: Low


title: GRO dst1 YPGal

value: YPGal


title: GRO rai1 YPD


title: CRTL 33

description: Control


title: CRTL 31

description: Control


title: blood-high-16


title: CRTL 30

description: Control


title: MCL129

value: primary MCL


title: CRTL 29

description: Control

value: Male


title: blood-control-19

source_name: whole blood, fatigue level: Control

value: Control


title: blood-low-9

value: Female


title: blood-low-8

value: Low


title: MCL121_2


title: GRO sfp1 YPGal


title: MCL122


title: MCL120


title: GRO wt YPGal


title: GRO rpb4 YPGal


title: CRTL 28

description: Control

value: Ever smoker


title: CRTL 27

description: Control


title: MCL119


title: blood-mid-31

value: Mid


title: CRTL 26

description: Control

value: Never smoker


title: blood-low-7


title: GRO dst1 YPD

value: dst1Δ deletion mutant


title: CRTL 25

description: Control


title: MCL117


title: blood-mid-30

value: whole blood


title: blood-low-6


title: GRO sfp1 YPD

value: sfp1Δ deletion mutant


title: GRO rpb4 YPD


title: CRTL 24

description: Control


title: MCL116


title: blood-mid-32

value: Patient


title: CRTL 23

description: Control


title: GRO Hpr1 degron t30 on filter V9-L1-x

description: Run-on labelling for hpr1degron strain t30 on filter V9-L1-x

scan_protocol: Images were acquired using a FujiFilm FLA3000 Phosphorimager. After the washing step, membranes were kept humid, sealed in Saran wrap, avoiding any bubbles, and exposed to an imaging plate (BAS-MP, FujiFilm) for variable times.

data_processing: Raw image quantization with background subtraction. This experiment is a single repeat. No elaborated data were generated.

source_name: hpr1degron 30 min at 30ºC

growth_protocol: Cells were grown in YP-Raffinose +Ade+ 0.1 mM CuSO4  at 26ºC to 0.5 OD600. At that cells were spun-down and changed to YP-Galactose+Ade without CuSO4 for 30 min at 26ºC. Then cells were shifted to 37ºC to induce degron-mediated proteolysis and recovered after 30 min. Samples include wt, as a control, hpr1delta and hpr1-degron after 0 or 30 min growth at 37ºC.


title: MCL118


title: blood-mid-29


title: CRTL 22

description: Control


title: GRO wt YPD

value: wild type


title: CRTL 21

description: Control


title: GRO Hpr1 degron t0 on filter V9-L1-x

description: Run-on labelling for hpr1degron strain t0 on filter V9-L1-x

source_name: hpr1degron at 26ºC


title: GRO Hpr1 delta t30 on filter V9-L1-x

description: Run-on labelling for hpr1delta strain t30 on filter V9-L1-x

source_name: hpr1delta 30 min at 30ºC

value: hpr1 delta


title: blood-control-18


title: GRO Hpr1 delta t0 on filter V9-L1-x

description: Run-on labelling for hpr1delta strain t0 on filter V9-L1-x

source_name: hpr1delta at 26ºC


title: MCL113


title: MCL115


title: MCL114


title: MCL126


title: blood-mid-27


title: CRTL 20

description: Control


title: MCL112


title: morula_35_2_High_HTF_ 30

source_name: morula_35_2_High_HTF_ 30

tag: score

value: morula

value: High

value: HTF

source_name: Common Reference

value: Pooled samples


title: blood-high-13


title: blood-control-17


title: blood-control-16


title: CRTL 18

description: Control

value: Male

value: Non-cancer


title: blood-high-12

value: Female


title: GRO wt t0 on filter V9-L1-x

description: Run-on labelling for WT strain t0 on filter V9-L1-x

source_name: wt at 26ºC

value: W303-1a wild type


title: CRTL 17

description: Control

value: Ever smoker


title: CRTL 19

description: Control


title: GRO wt t30 on filter V9-L1-x

description: Run-on labelling for WT strain t30 on filter V9-L1-x

source_name: wt 30 min at 30ºC


title: B. bifidum PRL2010 growth in MRS-oxgall-cholestrol medium 2

city: Parma

first: Marco

last: Ventura

address: Viale delle Scienze 11/A

department: Dept. Life Sciences

country: Italy

institute: University of Parma

hyb_protocol: Prehybridization was performed by incubating the arrays with prehybridization solution (6X SSPE, 0.05% Tween-20, 20mM EDTA, 5x Denhardt's solution, 100 ng/ul Salmon Sperm DNA, 0.05% SDS) for 60 minutes at 45 °C.  5 ug of Labeled aRNA were fragmented by incubation with Fragmentation Solution (40mM Tris Acetate pH 8.1, 100 mM KOAc, 30 mM MgOAc) for 20' at 95°C. Hybridization was performed at 45Â°C for 16 hours in hybridization solution (6X SSPE, 0.05% Tween-20, 20mM EDTA, 25% DiFormamide, 100 ng/ul Salmon Sperm DNA, 0.04% SDS).         Hybridization washings were performed as following:         - wash with 6X SSPET wash solution (6X SSPE, 0.05% Tween-20).         - wash with 3X SSPET wash solution (3X SSPE, 0.05% Tween-20).         - wash with 0.5X SSPET wash solution (0.5X SSPE, 0.05% Tween-20).         - wash with PBST was solution (2X PBS, 0.1% Tween-20).         - 2 washes with 2X PBS

scan_protocol: Scanning was performed on InnoScan 700 (Innopsys) scanner. Laser was set at 33% power and PMT at 650.

data_processing: Data extraction was carried out using CombiMstrix Microarray Imager software and a quantile normalization of data was performed using Combimatrix Blist v0.6 software. All teh procedures provided were performed as indicated by Combimatrix protocols available at Combimatrix website (www.combimatrix.com).

organism: Bifidobacterium bifidum PRL2010

source_name: B.bifidum PRL2010 growth in a cholesterol-oxgall rich environment

label_protocol: Five µg of the same pool of total RNA were labeled using RNA Ampulse amplification and labeling kit with Cy5 for Combimatrix arrays (Kreatech Diagnostics, The Netherlands) according to manufacturer instructions.

growth_protocol: B. bifidum PRL2010 was grown anaerobically in the Man-Rogosa-Sharp (MRS) supplemented with 0.05% (w/v) L-cysteine hydrochloride. B. bifidum PRL2010 cells that were grown to an OD of 0.6 supplemented of 5% oxgall and 100µg/ml cholesterol and subsequent incubation for 180 minutes at 37°C.

extract_protocol: Total RNA was isolated using the macaloid acid method and then treated with DNase. Briefly, cell pellets were resuspended in 1 ml of QUIAZOL and placed in a tube containing 0.8 g of glass beads (diameter, 106 um). The cells were lysed by shaking the mix on a BioSpec homogenizer at 4°C for 2 min (maximum setting). The mixture was then centrifuged at 12,000 rpm for 15 min, and the upper phase containing the RNA-containing sample was recovered. The RNA sample was further purified by phenol extraction and ethanol precipitation according to a previously described method (Sambrook et al., 1989).

tag: protocol

value: MRS-oxgall-cholestrol medium


title: MCL109

value: primary MCL


title: CRTL 16

description: Control


title: MCL110


title: blood-high-11


title: CRTL 15

description: Control


title: B. bifidum PRL2010 growth in MRS-cholestrol medium 2

source_name: B.bifidum PRL2010 growth in a cholesterol rich environment

growth_protocol: B. bifidum PRL2010 was grown anaerobically in the Man-Rogosa-Sharp (MRS) supplemented with 0.05% (w/v) L-cysteine hydrochloride. B. bifidum PRL2010 cells that were grown to an OD of 0.6 supplemented with 100µg/ml cholesterol and subsequent incubation for 180 minutes at 37°C.

value: MRS-cholestrol medium


title: MCL108


title: B. bifidum PRL2010 growth in MRS-oxgall-cholestrol medium 1


title: CRTL 14

description: Control


title: B. bifidum PRL2010 growth in MRS-cholestrol medium 1


title: MCL106


title: MCL107


title: blood-mid-26

source_name: whole blood, fatigue level: Mid

value: whole blood

value: Mid


title: CRTL 13

description: Control

source_name: plasma


title: blood-high-10

value: Patient


title: MCL105


title: CRTL 12

description: Control


title: blood-mid-25


title: MCL103


title: MCL104


title: blood-high-9


title: MCL102


title: CRTL 11

description: Control


title: blood-mid-23


title: MCL101


title: blood-mid-24


title: blood-control-15

value: Control


title: blood-low-5

value: Low


title: CRTL 10

description: Control

value: Never smoker


title: B. bifidum PRL2010 growth in MRS medium 2

source_name: B.bifidum PRL2010 growth in MRS broth

growth_protocol: B. bifidum PRL2010 was grown anaerobically in the Man-Rogosa-Sharp (MRS) supplemented with 0.05% (w/v) L-cysteine hydrochloride incubated at 37°C.

value: MRS medium


title: B. bifidum PRL2010 growth in MRS medium 1


title: MCL009


title: MCL008


title: MCL007


title: CRTL 5

description: Control


title: CRTL 9

description: Control


title: blood-mid-21


title: MCL004


title: blood-control-14


title: MCL006


title: Zebrafish_self_to_self_9cRA_rep1

first: Eva

middle: Lima

last: Oliveira

address: Carrer Jordi Girona 18-26

department: Environmental Chemistry

institute: IDAEA CSIC

description: 9cRA embryo treated vs 9cRA embryo treated at 5 dpf. Self to self 1

hyb_protocol: These following components were added in this order: 825ng of Cy3 labeled cRNA, 825 of Cy5 labeled cRNA, 11ul of 10x blocking Reagent, a volume of nuclease free water up to 52.8ul and 2.2ul of 25x fragmentation buffer. Incubate at 60ºC for exactly 30 minuts. Immediately cool on ice. Stop reaction by adding 55ul of 2x GEx Hybridization Buffer.  100ml of hybridization cocktail was used to each array. Set the Agilent hybridization oven at 65ºC and rotation speed to 10rpm, during 17hours. After hybridization, slides were washed. One last Acetonitrile wash was perform, followed by a stabilization and dry solution wash.

scan_protocol: Microarrays were scanned using an Agilent DNA Microarray Scanner G2505C, and data were acquired using Agilent's Feature Extraction Software version 10.5.1.1

data_processing: The scanned images were analyzed with Feature Extraction Software v 10.5.1.1 (Agilent) using default parameters (protocol GE2_105_jan09 and Grid: 026437_D_F_20110614) to obtain background subtracted and spatially detrended Processed Signal intensities

organism: Danio rerio

source_name: embryos treated with 9cRA

label_protocol: Cyanine 3-CTP samples and Cyanine 5-CTP samples were prepare from 200ng of total RNA using the Two-Color Microarray-Based Gene Expression Analysis Low Input Quick Amp Labeling kit (Agilent), followed by the purification of the labelled/amplified RNA using Qiagen RNeasy mini kit.

growth_protocol: Zebrafish (D. rerio) embryos and eleutheroembryos were obtained by natural mating and raised at 28.5 ◦C (Kimmel et al., 1995) with a 12L:12D photoperiod in embryo water [90  g/mL of Instant Ocean (Aquarium Systems, Sarrebourg, France; http://zfin.org/), 0.58 mM CaSO4·2H2O, dissolved in reverse osmosis purified water]. Animal stages were recorded as days or hours postfertilization (dpf or hpf).

extract_protocol: Total RNA was isolated from 50 embryos per replicate using Trizol reagent protocol (Invitrogen). RNA concentration was measured by spectrophotometric absorption at 260nm in Nanodrop ND-800 (nanodrop technologies, Wilmington, DE) and their integrity checked by Agilent 2100 bioanalyzer (agilent technologies, Santa Clara CA).

treatment_protocol: Three treated embryo replicates and three control replicates with 50 fertilized eggs from the 2 day post fertilization to the 5 day post fertilization were exposed during 72h in a 100ml glass. Treated solutions were prepared with 100nM of Retinoic Acid dissolved in water for fish and the control solutions treatments were prepared and directly prepared in embryo water with DMSO (0.1%). All the solutions were prepared on the same day of the experiment and renewal each day. Three treated embryo replicates and three control replicates with 50 fertilized eggs from the 4 day post fertilization to the 5 day post fertilization were exposed during 24h in a 100ml glass. Treated solutions were prepared with 100nM of Retinoic Acid dissolved in water for fish and the control solutions treatments were prepared and directly prepared in embryo water with DMSO (0.1%). All the solutions were prepared on the same day of the experiment and renewal each day. Three treated embryo replicates and three control replicates with 50 fertilized eggs from the 2 day post fertilization to the 5 day post fertilization were exposed during 72h in a 100ml glass. Treated solutions were prepared with 100nM of 9-cis Retinoic Acid dissolved in water for fish and the control solutions treatments were prepared and directly prepared in embryo water with DMSO (0.1%). All the solutions were prepared on the same day of the experiment and renewal each day. Three treated embryo replicates and three control replicates with 50 fertilized eggs from the 4 day post fertilization to the 5 day post fertilization were exposed during 24h in a 100ml glass. Treated solutions were prepared with 100nM of 9-cis Retinoic Acid dissolved in water for fish and the control solutions treatments were prepared and directly prepared in embryo water with DMSO (0.1%). All the solutions were prepared on the same day of the experiment and renewal each day.

tag: developmental stage

value: 5 dpf embryo

tag: agent

value: 100nM of 9cRA


title: Zebrafish_RA_72h_rep2

description: Biological replicate 2 of 3. RA embryo treated (72h) vs water control embryo treated at 5 dpf

source_name: embryos treated with RA

value: 100nM of RA

source_name: pooled embryos control DMSO 0.1%

value: DMSO water control


title: Zebrafish_RA_72h_rep1

description: Biological replicate 1 of 3. RA embryo treated (72h) vs water control embryo treated at 5 dpf


title: blood-control-13

source_name: whole blood, fatigue level: Control

value: Female


title: Zebrafish_self_to_self_9cRA_rep2

description: 9cRA embryo treated vs 9cRA embryo treated at 5 dpf. Self to self 2


title: CRTL 7

description: Control

value: Male

value: Non-cancer


title: Zebrafish_RA_72h_rep3

description: Biological replicate 3 of 3. RA embryo treated (72h) vs water control embryo treated at 5 dpf


title: MCL005


title: CRTL 6

description: Control

value: Ever smoker


title: blood-mid-20


title: blood-mid-22


title: Zebrafish_RA_24h_rep1

description: Biological replicate 1 of 3. RA embryo treated (24h) vs water control embryo treated at 5 dpf


title: MCL002

value: primary MCL


title: blood-mid-19


title: MCL003


title: blood-mid-18


title: CRTL 8

description: Control


title: CRTL 3

description: Control


title: CRTL 4

description: Control


title: Zebrafish_RA_24h_rep3

description: Biological replicate 3 of 3. RA embryo treated (24h) vs water control embryo treated at 5 dpf


title: CRTL 1

description: Control


title: CRTL 2

description: Control


title: Zebrafish_RA_24h_rep2

description: Biological replicate 2 of 3. RA embryo treated (24h) vs water control embryo treated at 5 dpf


title: NSCLC 100

description: Case

tag: morphology (for patients only)

value: Non-small cell lung cancer patient


title: NSCLC 99

description: Case


title: NSCLC 98

description: Case


title: NSCLC 97

description: Case


title: Zebrafish_9cRA_72h_rep2

description: Biological replicate 2 of 3. 9cRA embryo treated (72h) vs water control embryo treated at 5 dpf


title: blood-mid-17

value: whole blood


title: NOA POST 10 (exon)

city: Bergen

first: Tomasz

last: Stokowy

address: Nygardsgaten 5

department: IT Division

country: Norway

institute: University of Bergen

description: Biomarkers project

hyb_protocol: Array hybridization, washing, and scanning were performed according to manufacturer’s recommendations by using GeneChip® Hybridization, Wash and Stain Kit (Affymetrix, Santa Clara, CA).

scan_protocol: Microarrays scanned using Affymetrix 3000 Scanner according to the instructions of the manufacturer

data_processing: Raw data were normalized with RMA method using Affymetrix software delivered to the scanner.

source_name: testicular biopsy with nonobstructive azoospermia

label_protocol: The sense-strand cDNA was fragmentized and labeled using the Affymetrix GeneChip® WT Terminal Labeling Kit (Affymetrix, Santa Clara, CA).

growth_protocol: Not applicable, total RNA extracted from testicular biopsy cells

extract_protocol:
Tri-Reagent (Sigma-Aldrich, St. Louis, USA)  and post-purification using RNeasy Plus Mini Kit (Qiagen, Hilden, Germany)
Testicular biopsy

treatment_protocol: Not applicable, samples extracted from untreated patients with various stages of azoospermia

tag: Sex

value: male

value: testis

tag: testis

value: left

tag: age

tag: histopatological desription

value: postmeiotic arrest

tag: response to the hormonal therapy

value: positive response (sperm cells appered in ejaculate


title: MCL111


title: Zebrafish_9cRA_72h_rep3

description: Biological replicate 3 of 3. 9cRA embryo treated (72h) vs water control embryo treated at 5 dpf


title: MCL001


title: Zebrafish_9cRA_72h_rep1

description: Biological replicate 1 of 3. 9cRA embryo treated (72h) vs water control embryo treated at 5 dpf


title: NOA POST 6 (exon)

description: Biomarkers project

tag: tissue


title: blood-mid-15

tag: fatigue status

value: Mid

value: Patient

tag: gender


title: blood-high-8

source_name: whole blood, fatigue level: High

value: High

tag: patient group


title: blood-control-11

value: Control


title: blood-mid-16


title: Zebrafish_9cRA_24h_rep3

description: Biological replicate 3 of 3. 9cRA embryo treated (24h) vs water control embryo treated at 5 dpf

value: 5 dpf embryo

value: 100nM of 9cRA

value: DMSO water control


title: blood-mid-28

value: Female


title: Zebrafish_9cRA_24h_rep2

description: Biological replicate 2 of 3. 9cRA embryo treated (24h) vs water control embryo treated at 5 dpf


title: Zebrafish_9cRA_72h_rep2.1

description: Biological replicate 2 of 3. 9cRA embryo treated (72h) vs water control embryo treated at 5 dpf (technical replicate)


title: blood-control-12


title: Zebrafish_9cRA_24h_rep1

description: Biological replicate 1 of 3. 9cRA embryo treated (24h) vs water control embryo treated at 5 dpf


title: blood-low-4

source_name: whole blood, fatigue level: Low

value: Low


title: Zebrafish_self_to_self_rep1_2

description: DMSO control embryo vs DMSO control embryo at 2 dpf. Self to self 1

source_name: pooled embryos solvent control bNF

treatment_protocol: Four different treatments were done. Zebrafish embryos were treated with Benzo(a)pyrene, B-Naphthoflavone and Benzo(k)fluoranthene. 3 biological replicates were donne in each treatment. All the solutions were prepared on the same day of the experiment and renewal every day. Each biological replicate corresponds to 50 fertilized embryos exposed to each treatment, with their own dmso control sample.

value: 2 dpf embryo

value: DMSO control


title: NSCLC 96

description: Case

value: Male

tag: age at interview

tag: smoking status

value: Ever smoker

tag: disease state

value: Non-small cell lung cancer patient


title: NSCLC 95

description: Case


title: NSCLC 94

description: Case


title: SP-1

city: Shanghai

first: Juan

last: Du

state: Shanghai

address: NO.415 Fengyang Road

country: China

institute: Changzheng Hospital

description: Sample name: F

hyb_protocol: Labeled RNA was hybridized to the microarray slide for 16-20 hr at 56 degrees C and washed with miRCURY LNA microRNA Power Labeling kit (Exiqon) according to manufacture's protocol.

scan_protocol: Array were scanned using the Axon GenePix 4000B microarray scanner.Scanned images were then imported into GenePix Pro 6.0 software (Axon) for grid alignment and data extraction.

data_processing:
Each signal value of unique probe ID was calculated from average of Hy3 signal intensities of replicated probes. and miRNAs that intensities>50 in all samples were chosen for calculating normalization factor. Expressed data were normalized using the Median normalization.
Only human microRNAs analyzed.

source_name: multiple myeloma

label_protocol: Total RNA was labeled with miRCURY LNA microRNA Power Labeling kit (Exiqon) according to manufacture's protocol.

extract_protocol: Total RNA was harvested using TRIzol (Invitrogen) and miRNeasy mini kit (QIAGEN) according to manufacturer’s instructions.

tag: individual

value: multiple myeloma

tag: status after 5 years

value: Dead

tag: histology

value: λlight chain

value: 68 years

tag: Stage

value: IIIB

tag: cell type

value: Side population (SP) cells


title: SP-2

description: Sample name: D

value: IgG-κ

value: 65 years

value: IIIA


title: MP-1

description: Sample name: E

value: Main population (MP) cells


title: MP-2

description: Sample name: C


title: Zebrafish_self_to_self_rep2_2

description: Benzo(a)pyrene embryo treated vs Benzo(a)pyrene embryo treated at 5 dpf. Self to self 2

source_name: embryos treated with BaP

tag: developmental stage

value: 5 dpf embryo

tag: agent

value: 0.1mg/L of Benzo(a)pyrene


title: NSCLC 93

description: Case

tag: morphology (for patients only)


title: NOA POST 7 (exon)

description: Biomarkers project

tag: Sex

value: male

value: testis

tag: testis

value: left

tag: age

tag: histopatological desription

value: postmeiotic arrest

value: no response


title: NSCLC 92

description: Case

tag: gender

value: Male

value: Ever smoker

value: Non-small cell lung cancer patient


title: NOA POST 2 (exon)

description: Biomarkers project

tag: tissue

tag: response to the hormonal therapy


title: NOA POST 4 (exon)

description: Biomarkers project

value: right

value: positive response (sperm cells appered in ejaculate


title: NSCLC 91

description: Case

tag: age at interview

tag: smoking status


title: blood-control-10

value: whole blood

tag: fatigue status

value: Control

tag: patient group

value: Female


title: Zebrafish_BkF_rep3

description: Biological replicate 3 of 3. benzo(k)fluoranthene embryo treated vs solvent control embryo treated at 2 dpf

source_name: embryos treated with BkF

value: 2 dpf embryo

value: 12.7ug/L of Benzo(k)Fluoranthene

source_name: pooled embryos control solvent

value: DMSO control


title: NOA POST 3 (exon)

description: Biomarkers project


title: NSCLC 90

description: Case

value: Never smoker

tag: disease state


title: Zebrafish_BkF_rep2

description: Biological replicate 2 of 3. benzo(k)fluoranthene embryo treated vs solvent control embryo treated at 2 dpf


title: Zebrafish_BkF_rep1

description: Biological replicate 1 of 3. benzo(k)fluoranthene embryo treated vs solvent control embryo treated at 2 dpf


title: NSCLC 89

description: Case


title: blood-mid-14

value: Mid

value: Patient


title: blood-mid-12


title: Zebrafish_large_BaP_rep3

description: Biological replicate 3 of 3. Benzo(a)pyrene embryo treated vs dmso control embryo treated at 5 dpf

value: 5 dpf embryo

value: 0.1mg/L of Benzo(a)pyrene


title: BA11 sample #210

city: Pittsburgh

first: Etienne

last: Sibille

state: PA

address: 450 Technology Drive, Suite 231

department: Psychiatry

country: USA

institute: University of Pittsburgh

description: dissected from frozen coronal blocks ~2–3 cm caudal to the temporal pole

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials: • Heat the hybridization cocktail to 99°C for 5 minutes in a heat block • Incubate the probe array filled with Pre-Hybridization Mix at 45°C for 10 minutes with rotation • Transfer the hybridization cocktail that has been heated at 99°C, to a 45°C heat block for 5 minutes • Spin the hybridization cocktail at maximum speed in a microcentrifuge for 5 minutes to collect any insoluble material from the hybridization mixture • Remove the array from the hybridization oven. Vent the array with a clean pipette tip and extract the Pre-Hybridization Mix from the array with a micropipettor. Refill the array with the appropriate volume of the clarified hybridization cocktail, avoiding any insoluble matter at the bottom of the tube • Place probe array into the hybridization oven, set to 45°C • To avoid stress to the motor, load probe arrays in a balanced configuration around the axis. Rotate at 60 rpm • Hybridize for 16 hours • During the latter part of the 16-hour hybridization, proceed to the GeneChip® Expression Wash, Stain and Scan User Manual, P/N 702731, to prepare reagents for the washing and staining steps required immediately after completion of hybridization

scan_protocol: Affymetrix GeneChIP Scanner 3000 7G

data_processing: All samples were analyzed using the Affymetrix Human Gene 1.1 ST microarray platform. Gene expression values were corrected, quantile-normalized, and log2-transformed via Affymetrix Expression Console software (build 1.2.1.20) using RMA algorithm. A total of 33,297 probe sets were available on each array; only those probe sets with annotated gene symbols were selected (20,237 gene symbols). If a gene was represented by multiple probe sets, the one with the largest intensity interquartile region was selected to represent that gene. Microarray data for each brain region were analyzed separately.

source_name: Brain prefrontal cortex, broadman areas 11

label_protocol: According to standard affymetrix protocol: • 10ul  Purified cDNA10ul • DEPC H2O • 4ul  10x IVT Labeling Buffer • 12ul  IVT Labeling NTP mix • 4ul  IVT Labeling Enzyme mix - Incubate at 37C 16 hour in an incubating oven or thermal cycler with heated lid to avoid condensation. - Purify labeled cRNA generated from either IVT labeling reaction using RNeasy RNA Purification Mini kit (Qiagen) using the RNA Cleanup Protocol according to manufacturers instructions. - Quantitate Biotin labeled cRNA using 260nm/280nm spectrophotometric assay.

growth_protocol: not applicable

extract_protocol: Total RNA was extracted from frozen samples stored in TRIzol (Invitrogen, Carlsbad, Calif.) and processed for microarray analysis according to the microarray manufacturer’s protocol (Affymetrix, Santa Clara, Calif.)

treatment_protocol: not applicable

value: brain

tag: pmi

tag: ph

tag: rin

value: F

tag: race

value: B

tag: tod


title: BA11 sample #208

tag: Sex

value: M


title: Zebrafish_large_BaP_rep1

description: Biological replicate 1 of 3. Benzo(a)pyrene embryo treated vs dmso control embryo treated at 5 dpf

tag: developmental stage

tag: agent


title: blood-mid-13


title: blood-mid-11


title: Zebrafish_large_BaP_rep2

description: Biological replicate 2 of 3. Benzo(a)pyrene embryo treated vs dmso control embryo treated at 5 dpf


title: blood-mid-10


title: NSCLC 88

description: Case

tag: morphology (for patients only)

value: Non-small cell lung cancer patient


title: NSCLC 87

description: Case

tag: gender

value: Male

value: Ever smoker


title: NSCLC 86

description: Case


title: BA11 sample #207

tag: tissue

tag: age

value: W


title: blood-control-9

value: whole blood

value: Control

value: Female


title: NSCLC 84

description: Case

tag: age at interview


title: blood-mid-9


title: Zebrafish_short_BaP_rep2

description: Biological replicate 2 of 3. Benzo(a)pyrene embryo treated vs dmso control embryo treated at 2 dpf

value: 2 dpf embryo

value: 33.2ug/L of Benzo(a)pyrene

value: DMSO control


title: BA11 sample #209


title: BA11 sample #204


title: blood-high-7

value: High

value: Patient


title: BA11 sample #206


title: Zebrafish_bNF_rep3

description: Biological replicate 3 of 3. b-naphtoflavone embryo treated vs solvent control embryo treated at 2 dpf

source_name: embryos treated with bNF

value: 38.5ug/L of b-Naphthoflavone


title: NSCLC 83

description: Case

tag: smoking status


title: Zebrafish_short_BaP_rep1

description: Biological replicate 1 of 3. Benzo(a)pyrene embryo treated vs dmso control embryo treated at 2 dpf


title: blood-low-2

tag: fatigue status

value: Low


title: blood-low-3

tag: patient group


title: Zebrafish_short_BaP_rep3

description: Biological replicate 3 of 3. Benzo(a)pyrene embryo treated vs dmso control embryo treated at 2 dpf


title: blood-mid-8

source_name: whole blood, fatigue level: Mid

value: Mid


title: BA11 sample #203

value: brain


title: BA11 sample #202

value: M


title: BA11 sample #205


title: BA11 sample #201


title: Zebrafish_bNF_rep2

description: Biological replicate 2 of 3. b-naphtoflavone embryo treated vs solvent control embryo treated at 2 dpf


title: BA11 sample #200


title: NSCLC 82

description: Case

source_name: plasma

tag: disease state

value: Non-small cell lung cancer patient


title: Zebrafish_bNF_rep1

description: Biological replicate 1 of 3. b-naphtoflavone embryo treated vs solvent control embryo treated at 2 dpf


title: fibroblast_BRCA1wt_4

city: Mainz

first: Anna

last: Etzold

state: Germany (Deutschland)

address: Langenbeckstr. 1

country: Germany

institute: Universität Mainz

hyb_protocol: conducted by Affymetrix company

scan_protocol: conducted by Affymetrix company

data_processing: The data were analyzed with Affymetrix Expression  Console with RMA normalization.

label_protocol: conducted by Affymetrix company

growth_protocol: grown in DMEM + 10% FCS to subconfluency

extract_protocol: TriZol RNA extraction

treatment_protocol: untreated

tag: disease

value: healthy

value: dermal fibroblast, untreated


title: blood-mid-7


title: blood-high-6


title: blood-low-1


title: BA11 sample #199

tag: pmi

tag: ph

value: W


title: NSCLC 80

description: Case

value: Male

value: Ever smoker


title: fibroblast_BRCA1wt_3


title: NSCLC 81

description: Case


title: NSCLC 79

description: Case


title: blood-control-8

value: whole blood

value: Control

value: Female


title: NSCLC 78

description: Case


title: NSCLC 76

description: Case


title: NSCLC 77

description: Case


title: NSCLC 75

description: Case

value: Never smoker


title: NSCLC 74

description: Case


title: fibroblast_BRCA1mosMe_3

value: cancers


title: BA11 sample #198

tag: rin

tag: race


title: fibroblast_BRCA1mosMe_4


title: fibroblast_BRCA1wt_2


title: blood-mid-4

value: Patient


title: BA11 sample #193

tag: Sex

tag: tod


title: NSCLC 73

description: Case


title: blood-mid-6


title: BA11 sample #197


title: fibroblast_BRCA1mosMe_2


title: blood-control-7


title: BA11 sample #191

value: F


title: blood-mid-5


title: blood-high-5

value: High


title: blood-high-3


title: blood-mid-3

value: Mid


title: blood-high-4


title: HighCO2_2W_rep3

city: Iizuka

first: Kousuke

last: Hanada

state: Fukuoka

address: 680-4 Kawazu

department: Department of Bioscience and Bioinformatics

country: Japan

institute: Kyushu Institute Technology

hyb_protocol: Hybridization was performed using the in situ Hybridization Kit Plus (Agilent Technologies, Tokyo, Japan)

scan_protocol: Hybridized and washed material on each glass slide was scanned by an Agilent G2505 B DNA microarray scanner (Agilent Technologies)

data_processing:
Data analysis was performed by Feature Extraction and Image Analysis software (Agilent Technologies, Tokyo, Japan).
The array intensities were processed using the Bioconductor (www.bioconductor.org) affy package in the R software environment (www.r-project.org). Hybridization intensities in our arrays were simply normalized among different arrays by quantile normalization.

organism: Arabidopsis thaliana

label_protocol: cRNA amplification and fluorescence labeling were performed using the Agilent Low RNA Input Linear Amplification Kit (Agilent Technology, Tokyo, Japan) according to the manufacturer's protocol. A primer containing poly dT and a T7 polymerase promoter was annealed to the poly A+ RNA. First and second strands of cDNA were reverse transcribed from 500 ng total RNA using MMLV-RT enzyme. Cyanine 3- labeled cRNA was synthesized using T7 RNA polymerase. Labeled cRNA was purified by RNeasy Mini Kit (Qiagen, Tokyo, Japan).

extract_protocol: Approximately 500 μg of total RNA was three times extracted from each sample using TRIzol (Invitrogen).

tag: cultivar

value: Col-0; wild type

value: 14-d-old seedlings

tag: exposed to

value: elevated (780 μmol mol-1) CO2 for 14 days

tag: chamber id

value: ChamberA


title: BA11 sample #192

tag: tissue

value: brain

value: M


title: HighCO2_2W_rep2

value: ChamberB


title: BA11 sample #195

tag: age

value: W


title: fibroblast_BRCA1mosMe_1

value: dermal fibroblast, untreated


title: NSCLC 72

description: Case

tag: gender

value: Male

tag: age at interview

value: Ever smoker

tag: morphology (for patients only)

value: Non-small cell lung cancer patient


title: BA11 sample #190


title: blood-control-6

value: whole blood

tag: fatigue status

value: Control

tag: patient group

value: Female


title: NSCLC 71

description: Case

tag: smoking status

tag: disease state


title: HighCO2_2W_rep4


title: NSCLC 70

description: Case


title: HighCO2_2W_rep1


title: BA11 sample #189

tag: pmi

tag: ph


title: NSCLC 69

description: Case


title: HighCO2_1W_rep4

value: elevated (780 μmol mol-1) CO2 for 7 days


title: BA11 sample #194

tag: rin

tag: race


title: BA11 sample #188

tag: Sex

tag: tod


title: HighCO2_1W_rep3

tag: cultivar

tag: exposed to


title: BA11 sample #187

tag: tissue

value: F


title: blood-control-5


title: NSCLC 68

description: Case


title: blood-high-2

value: High

value: Patient


title: HighCO2_1W_rep2

value: Col-0; wild type

value: 14-d-old seedlings

tag: chamber id


title: blood-mid-2

value: Mid

tag: gender


title: BA11 sample #196

value: brain

tag: age

value: M


title: HighCO2_1W_rep1

value: ChamberA


title: fibroblast_BRCA1wt_1

tag: disease

value: healthy

value: dermal fibroblast, untreated


title: blood-high-1

tag: fatigue status


title: BA11 sample #186

value: W


title: HighCO2_3D_rep4

value: elevated (780 μmol mol-1) CO2 for 3 days

value: ChamberB


title: NSCLC 64

description: Case

tag: age at interview

value: Ever smoker

tag: morphology (for patients only)

value: Non-small cell lung cancer patient


title: NSCLC 65

description: Case

value: Male

tag: smoking status

tag: disease state


title: blood-control-4

value: whole blood

value: Control

tag: patient group

value: Female


title: NSCLC 66

description: Case


title: NSCLC 63

description: Case


title: NSCLC 62

description: Case


title: HighCO2_3D_rep2

value: Col-0; wild type


title: HighCO2_1D_rep3

value: 14-d-old seedlings

value: elevated (780 μmol mol-1) CO2 for 1 day


title: BA11 sample #181

value: brain

tag: pmi

tag: ph

tag: rin


title: BA11 sample #185

tag: Sex

value: M

tag: race

tag: tod


title: HighCO2_3D_rep3

tag: cultivar

tag: tissue

tag: exposed to

value: ChamberA


title: blood-mid-1

value: Mid

value: Patient

tag: gender


title: BA11 sample #180

tag: age

value: W


title: HighCO2_1D_rep2

tag: chamber id


title: BA11 sample #183

value: B


title: blood-control-1

tag: fatigue status


title: NSCLC 60

description: Case

tag: age at interview

tag: morphology (for patients only)


title: NSCLC 67

description: Case

tag: smoking status

tag: disease state


title: BA11 sample #178

tag: pmi


title: blood-control-2

tag: patient group


title: NSCLC 61

description: Case


title: DHT_Flutamide_1

city: Houston

first: Paul

last: Webb

address: 6670 Bertner Ave

department: Genomic Medicine

institute: Houston Methodist Research Institute

description: replicate 2

hyb_protocol: Biotinylated cRNA samples were hybridized to MouseWG-6v2 arrays at 58°C for 18 h according to manufacturer's protocol.

scan_protocol: Standard Illumina protocol with the iScan reader.

data_processing: Raw data was obtained from GenomeStudio and subsequently background-subtracted and quantile-normalized using the lumi package in R.

source_name: LNCaP cells_DHT_Flutamide_1

label_protocol: cRNA synthesis and labeling were performed using Illumina® TotalPrep™-96 RNA Amplification Kit (Ambion). Biotin labeling in vitro transcription reaction was performed at 37°C for 14 h.

growth_protocol: LNCaP cells were purchased from ATCC and were maintained in RPMI 1640 supplemented with L-glutamine and 10% fetal bovine serum.

extract_protocol: Total RNA was extracted using Rneasy Mini kit (QIAGEN), in accordance with manufacturer's instructions.

treatment_protocol: LNCaP cells maintained in media harboring 10% charcoal-stripped serum DMSO (control), 10nM DHT, 1μM Flutamide, 1μM Flutamide + 10nM DHT, 30μM MJC13, or 30μM MJC13 + 10nM DHT for 24 hours.

tag: cell line

value: LNCaP


title: HighCO2_1D_rep4

value: ChamberB


title: BA11 sample #179

tag: ph

tag: rin

tag: Sex

value: F


title: BA11 sample #184

tag: race

tag: tod


title: HighCO2_1D_rep1

tag: cultivar

tag: tissue

tag: exposed to


title: NSCLC 59

description: Case

tag: gender

value: Male

value: Ever smoker

value: Non-small cell lung cancer patient


title: NSCLC 58

description: Case


title: NSCLC 85

description: Case


title: HighCO2_3D_rep1

value: elevated (780 μmol mol-1) CO2 for 3 days

tag: chamber id


title: BA11 sample #182

tag: age


title: NSCLC 57

description: Case

tag: age at interview

tag: morphology (for patients only)


title: Flutamide_1

description: replicate 1

source_name: LNCaP cells_Flutamide_1


title: DHT_MJC13_3

description: replicate 1

source_name: LNCaP cells_DHT_MJC13_3


title: BA11 sample #177


title: NSCLC 55

description: Case

tag: smoking status

tag: disease state


title: NSCLC 54

description: Case


title: BA11 sample #176

tag: pmi


title: blood-control-3

value: whole blood

tag: fatigue status

value: Control

tag: patient group

value: Female


title: MJC13_2

description: replicate 3

source_name: LNCaP cells_MJC13_2

tag: cell line


title: NSCLC 56

description: Case


title: HighCO2_12H_rep3

value: Col-0; wild type

value: 14-d-old seedlings

value: elevated (780 μmol mol-1) CO2 for 12hr


title: BA11 sample #173

value: brain

tag: ph

tag: rin

tag: Sex

value: M


title: NSCLC 53

description: Case


title: HighCO2_12H_rep2

tag: cultivar


title: DHT_MJC13_2

description: replicate 1

source_name: LNCaP cells_DHT_MJC13_2


title: DMSO_3

description: replicate 2

source_name: LNCaP cells_DMSO_3


title: HighCO2_12H_rep4

tag: tissue


title: DHT_1

description: replicate 1

source_name: LNCaP cells_DHT_1


title: HighCO2_6H_rep4

tag: exposed to

value: elevated (780 μmol mol-1) CO2 for 6hr


title: NSCLC 52

description: Case

tag: gender


title: HighCO2_6H_rep2

tag: chamber id


title: HighCO2_12H_rep1

value: ChamberA


title: BA11 sample #170

tag: age

tag: race

value: W

tag: tod


title: BA11 sample #172


title: BA11 sample #171

value: B


title: HighCO2_6H_rep3


title: NSCLC 51

description: Case

tag: age at interview

tag: smoking status

tag: morphology (for patients only)


title: HighCO2_6H_rep1


title: DHT_MJC13_1

description: replicate 1

source_name: LNCaP cells_DHT_MJC13_1

value: LNCaP


title: DMSO_2

description: replicate 3

source_name: LNCaP cells_DMSO_2


title: MJC13_1

description: replicate 3

source_name: LNCaP cells_MJC13_1


title: BA11 sample #169

tag: pmi


title: HighCO2_2H_rep4

value: elevated (780 μmol mol-1) CO2 for 2hr

value: ChamberB


title: NSCLC 49

description: Case

value: Male

value: Ever smoker

tag: disease state

value: Non-small cell lung cancer patient


title: MJC13_3

description: replicate 1

source_name: LNCaP cells_MJC13_3

tag: cell line


title: Flutamide_3

description: replicate 2

source_name: LNCaP cells_Flutamide_3


title: DHT_Flutamide_3

description: replicate 3

source_name: LNCaP cells_DHT_Flutamide_3


title: Flutamide_2

description: replicate 2

source_name: LNCaP cells_Flutamide_2


title: NSCLC 48

description: Case


title: NSCLC 47

description: Case


title: BA11 sample #165

source_name: Brain prefrontal cortex, broadman areas 11

tag: ph


title: BA11 sample #166

tag: rin


title: BA11 sample #168

tag: Sex


title: NSCLC 50

description: Case


title: NSCLC 46

description: Case


title: BA11 sample #174


title: NSCLC 44

description: Case


title: NSCLC 43

description: Case


title: BA11 sample #167


title: BA11 sample #163

value: F


title: HighCO2_0H_rep4

tag: cultivar

value: elevated (780 μmol mol-1) CO2 for 0hr


title: HighCO2_2H_rep2

value: Col-0; wild type

tag: tissue


title: BA11 sample #164


title: HighCO2_0H_rep3

value: 14-d-old seedlings

tag: exposed to


title: HighCO2_2H_rep1


title: DHT_2

description: replicate 2

source_name: LNCaP cells_DHT_2


title: NSCLC 45

description: Case

source_name: plasma

tag: gender


title: HighCO2_0H_rep1

tag: chamber id


title: DHT_Flutamide_2

description: replicate 3

source_name: LNCaP cells_DHT_Flutamide_2


title: BA11 sample #160

tag: age


title: BA11 sample #162

tag: race


title: BA11 sample #161

tag: tod


title: MDA-MB-231 transfected with Negative Controls oligonucleotide, replicate 2

city: Oslo

first: Leonardo

middle: A.

last: Meza-Zepeda

address: Ullernchausseen 70

department: Department of Tumor Biology

institute: Oslo University Hospital

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Raw data was exported from GenomeStudio (Illumina) and quantile normalised in J-Express

label: Biotin

source_name: MDA-MB-231 ATCC® HTB-26™

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

growth_protocol: The osteosarcoma cells were grown in RPMI1640 (Lonza, Basel, Switzerland) or DMEM (Lonza) supplemented with 10 % foetal calf serum (PAA Laboratories GmbH, Pasching,  Austria), GlutaMAX (Invitrogen, California, USA) and penicillin/streptomycin (Lonza), at 37°C with 5 % CO2. All cells were split when reaching 80 % confluency. The osteoblast cells were maintained in medium provided by the manufacturer, split when reaching 80 % confluency, and harvested when enough cells for DNA and RNA isolation were obtained.

extract_protocol: RNA was isolated using the standard TRIzol procedure (Invitrogen), and further purified with an RNeasy mini column (Qiagen GmbH, Hilden, Germany), according to the manufacturers’ instructions.

tag: cell type

value: Triple-negative breast cancer

tag: sample origin

value: Pleural effusion

value: Female


title: BA11 sample #159

value: brain


title: MDA-MB-231 transfected with Negative Controls oligonucleotide, replicate 3


title: HighCO2_0H_rep2


title: MDA-MB-231 transfected with Negative Controls oligonucleotide, replicate 1


title: NSCLC 42

description: Case

data_processing:
The data were analysed in HTqPCR package using R Bioconductor. miRNAs with undetermined Ct values in more than 120 samples were filtered out. Data were quantile normalized. Following normalization Ct values with an interquartile range (IQR) of less than 1.5 and endogenous controls were removed from subsequent analysis, and limma analysis was performed to identify differentially regulated miRNA between cases and controls. With limma, a one-factorial linear model is fitted for each miRNA and the standard errors (SE) are moderated using an empirical Bayes model resulting in moderated t-statistics for each miRNA. These analysis were performed separately for CARD A and CARD B.
Matrix normalized worksheet reports normalized signal (quantile normalization).  Fold Change worksheet reports fold changes across all cases and controls.

tag: age at interview

tag: smoking status

tag: morphology (for patients only)


title: DMSO_1

description: replicate 2

source_name: LNCaP cells_DMSO_1

tag: cell line


title: BA11 sample #158

tag: pmi

tag: ph

value: M


title: MDA-MB-231 transfected with Let7a mimic, replicate 3


title: NSCLC 41

description: Case

tag: disease state


title: NSCLC 40

description: Case


title: NSCLC 39

description: Case


title: NSCLC 38

description: Case


title: NSCLC 35

description: Case


title: NSCLC 37

description: Case


title: BA11 sample #156

tag: rin

tag: Sex

value: W


title: BA11 sample #155

tag: tissue

value: B


title: NSCLC 36

description: Case

tag: gender


title: MDA-MB-231 transfected with Let7a mimic, replicate 1


title: BA11 sample #154


title: MDA-MB-231 transfected with Let7a mimic, replicate 2


title: BA11 sample #157


title: BA11 sample #153


title: NSCLC 34

description: Case


title: BA11 sample #152


title: Pitts1 curcumin 3

first: Jens

middle: U.

last: Marquardt

address: Langenbeckstrasse 1

department: Department of Medicine I

institute: University of Mainz

hyb_protocol: Illumina protocol

scan_protocol: Illumina protocol

data_processing: We used Illumina Genome Studio for the Quantile data normalization (standard pipeline).

source_name: Hepatoma cell line

label_protocol: Illumina protocol

growth_protocol: Human hepatoma cells were cultured with DMEM and 10% FCS

extract_protocol: Qiagen Rneasy Kit

treatment_protocol: 72h of treatment with 25uM of curcmumin

tag: agent

value: curcumin


title: Pitts1 curcumin 1


title: BA11 sample #175

tag: age


title: Pitts1 control 2


title: NSCLC 33

description: Case

label_protocol: Expression levels of 754 miRNAs (Sanger miRBase v14) were quantified using the TaqMan Human MicroRNA Array A + B Card Set v3.0 (Applied Biosystems, Foster City, CA) as per the manufacturer's instructions (including pre-amplification).

extract_protocol: Total RNA was isolated from 300L of plasma using NucleoSpin® miRNA Plasma kit (Macherey-Nagel, Düren, Germany) according to the manufacturer’s protocol with Proteinase K digest, addition of 2μg of glycogen carrier and DNAse digest steps. All samples were spiked-in with 10pmol of Arabidopsis thaliana synthetic miR-159a (synthesized by Eurofins MWG Operon, Ebersberg, Germany) to control for variations in the RNA preparation step.


title: BA11 sample #149

tag: race


title: BA11 sample #150

tag: tod


title: Pitts1 control 3


title: BA11 sample #151


title: Pitts1 curcumin 2


title: PLC curcumin 3

value: PLC


title: NSCLC 31

description: Case


title: Pitts1 control 1


title: PLC curcumin 2


title: HMEC TGFb 8 d Sss I

city: Los Angeles

first: Xiaojing

last: Yang

state: CA

address: 1441 Eastlake Ave, Room 7336

institute: USC/Norris Comprehensive Cancer Center

description: Freshly prepared nuclei (2x10^5 cells) were resuspended in 1X M.SssI reaction buffer (NEB), then treated with 50U of M.SssI (NEB) in 15µL 10X reaction buffer, 45µL 1M sucrose and 0.75µL SAM in a volume of 150uL. Reactions were quenched by the addition of an equal volume of Stop Solution (20nM Tris-HCl [pH 7.9], 600mM NaCl, 1% SDS, 10mM EDTA, 400µg/ml Proteinase K) and incubated at 55°C overnight (Gal-Yam et al., 2006).

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation HM450 Beadchip using standard Illumina protocol

source_name: Human mammary epithelial cell TGFb treated 8 d, M. Sss I treat

growth_protocol: The immortalized human mammary epithelial cell line (HMLE) and the derivative cell line HMLE-Twist-ER were kindly provided by the Robert Weinberg laboratory (MIT). The culture of the cells was carried out as described previously (Elenbaas et al., 2001; Mani et al., 2008)

extract_protocol: DNA was purified by phenol/chloroform extraction and ethanol precipitation. Bisulfite conversion was performed using the EZ DNA methylation Kit (Zymo Research). All samples passed bisulfite conversion quality control and were subsequently processed for the Illumina Infinium DNA methylation platform (Human Methylation 450 Bead Chip).

treatment_protocol: To induce the expression of Twist, HMLE-Twist-ER cells were exposed to 4-hydroxy tamoxifen (4-OHT) at a concentration of 20 nM continuously until change in morphology was observed, typically 12 days. TGF-beta1 at a concentration of 2.5 ng/ml was used to treat HMLE cells for 12 days.

value: HMLE

tag: time point


title: BA11 sample #148


title: HMEC TGFb 12 d NoE

description: Freshly prepared nuclei (2x10^5 cells) were resuspended in 1X M.SssI reaction buffer (NEB), then treated with 45µL 1M sucrose and 0.75µL SAM in 10X reaction buffer,  in a volume of 150uL. Reactions were quenched by the addition of an equal volume of Stop Solution (20nM Tris-HCl [pH 7.9], 600mM NaCl, 1% SDS, 10mM EDTA, 400µg/ml Proteinase K) and incubated at 55°C overnight (Gal-Yam et al., 2006).

source_name: Human mammary epithelial cell TGFb treated 12 d


title: NSCLC 32

first: Magdalena

last: Wozniak

address: 150 cours Albert Thomas

institute: International Agency for Research on Cancer

description: Case

value: Male


title: HMEC TGFb 12 d Sss I

source_name: Human mammary epithelial cell TGFb treated 12 d, M. Sss I treat


title: PLC curcumin 1


title: DHT_3

description: replicate 3

source_name: LNCaP cells_DHT_3

value: LNCaP


title: HMEC TGFb 2 d Sss I

source_name: Human mammary epithelial cell TGFb treated 2 d, M. Sss I treat


title: NSCLC 29

description: Case

value: Ever smoker

value: Non-small cell lung cancer patient


title: HMEC TGFb 0 d Sss I

source_name: Human mammary epithelial cell TGFb treated 0 d, M. Sss I treat


title: HMEC TGFb 2 d NoE

source_name: Human mammary epithelial cell TGFb treated 2 d


title: NSCLC 30

description: Case


title: HMEC TWIST 12 d Sss I

source_name: Human mammary epithelial cell TWIST overexpression 12 d, M. Sss I treat

value: HMLE-Twist-ER


title: HMEC TGFb 0 d NoE

source_name: Human mammary epithelial cell TGFb treated 0 d


title: NSCLC 28

description: Case


title: HMEC TGFb 8 d NoE

source_name: Human mammary epithelial cell TGFb treated 8 d


title: BA11 sample #147

source_name: Brain prefrontal cortex, broadman areas 11


title: HighCO2_2H_rep3

tag: cultivar

value: Col-0; wild type

tag: exposed to

value: elevated (780 μmol mol-1) CO2 for 2hr

tag: chamber id

value: ChamberA


title: PLC control 3


title: NSCLC 27

description: Case

tag: age at interview

tag: smoking status

tag: morphology (for patients only)


title: MSOD_rep1a

city: Roma

first: Camilla

last: Bernardini

address: L.go F.Vito 1

institute: Università Cattolica del Sacro Cuore

description: Test

data_processing:
SDS RQ Manager version 2.4 (Applied Biosystems) was used to calculate Ct values
For the normalization it uses the average value of U6 snRNA-001973 wells to calculate dCt values (Ct_target-Ct_U6)
Fold change worksheet reports test/control (i.e., MSOD/FVB) ratios, expressed as 2^-deltadeltaCt

organism: Mus musculus

source_name: MSOD_lumbar spinal cord ventral

label_protocol: From each sample, 600 ng of total RNA was reverse transcribed using Taqman MicroRNA Reverse Transcription Kit with Megaplex Primer Pools A & B (Applied Biosystems, Foster City, CA, USA).

extract_protocol: Extraction of total RNA was performed according to the manufacturer's instructions. Total RNA was isolated from frozen lumbar spinal ventral tissue specimens using pestel homogenization and TRIzol reagent (Invitrogen, Carlsbad, CA, USA), therefore purified using the RNAeasy mini purification kit (QIAGEN) according to the RNA cleanup protocol

tag: strain background

value: FVB

tag: genotype/variation

value: 4 months

value: Lumbar Spinal Cord Ventral


title: BA11 sample #146

value: brain

tag: pmi

tag: ph

tag: rin

value: M


title: MSOD_rep3a

description: Test

tag: tissue


title: HMEC TWIST 8 d Sss I

data_processing: BeadStudio software v3.2

source_name: Human mammary epithelial cell TWIST overexpression 8 d, M. Sss I treat

tag: cell line


title: PLC control 1

tag: agent


title: NSCLC 24

description: Case

source_name: plasma

tag: gender

tag: disease state


title: PLC control 2


title: FVB_rep4a

description: Control

source_name: WT_lumbar spinal cord ventral

value: wild type

tag: age


title: Huh7 curcumin 3

value: curcumin


title: BA11 sample #144

tag: Sex

tag: race

value: W

tag: tod


title: MSOD_rep4a

description: Test


title: MSOD_rep2a

description: Test


title: NSCLC 25

description: Case

tag: age at interview


title: Huh7 curcumin 1


title: BA11 sample #145


title: HMEC TWIST 12 d NoE

source_name: Human mammary epithelial cell TWIST overexpression 12 d

tag: time point


title: HMEC TWIST 2 d NoE

source_name: Human mammary epithelial cell TWIST overexpression 2 d


title: Huh7 control 3

source_name: Hepatoma cell line


title: HMEC TWIST 8 d NoE

source_name: Human mammary epithelial cell TWIST overexpression 8 d


title: BA11 sample #140


title: NSCLC 22

description: Case

value: Female

tag: smoking status

value: Never smoker

tag: morphology (for patients only)


title: NSCLC 23

description: Case


title: NSCLC 26

description: Case

value: Male


title: Huh7 curcumin 2


title: Huh7 control 2


title: BA11 sample #141

value: F


title: NSCLC 21

description: Case

value: Ever smoker

value: Non-small cell lung cancer patient


title: FVB_rep1a

description: Control

tag: strain background

tag: genotype/variation


title: HMEC TWIST 2 d Sss I

source_name: Human mammary epithelial cell TWIST overexpression 2 d, M. Sss I treat

value: HMLE-Twist-ER


title: BA11 sample #139

tag: pmi

tag: ph


title: BA11 sample #142

tag: tissue

tag: rin


title: FVB_rep3a

description: Control


title: FVB_rep2a

description: Control


title: NSCLC 20

description: Case


title: HMEC TWIST 0 d Sss I

source_name: Human mammary epithelial cell TWIST overexpression 0 d, M. Sss I treat

tag: cell line


title: HMEC TWIST 0 d NoE

source_name: Human mammary epithelial cell TWIST overexpression 0 d


title: BA11 sample #138

value: B


title: BA11 sample #134


title: WRL68 curcumin 2

tag: agent


title: Huh7 control 1


title: BA11 sample #137


title: BA11 sample #136


title: BA11 sample #135


title: WRL68 control 3


title: BA11 sample #133


title: BA11 sample #132


title: WRL68 curcumin 3


title: WRL68 control 1


title: BA11 sample #129


title: BA11 sample #130


title: WRL68 curcumin 1


title: BA11 sample #131


title: WRL68 control 2


title: LCL_truncating10

city: Madrid

first: Tereza

last: Vaclova

address: C/ Melchor Fernández Almagro, 3

department: Human Cancer Genetics

institute: CNIO - Spanish National Cancer Research Centre

description: miRNA expression at basal conditions

hyb_protocol: Total RNA was hybridized on LNA based miRNA microarrays 7th generation (miRNAs from miRBase Release 19.0; GAL File used for identification of miRNAs was created on 2013-02-21, 11:09). Labeled RNA was hybridized to miRCURY LNA™ microRNA Arrays over 16 hours at 56ºC using Agilent Hybridization chambers SureHyb and a rotating oven.

scan_protocol: Arrays were washed, dried and scanned with Agilent G2565AA Microarray Scanner System (Agilent Technologies). Fluorescence intensities on scanned images were measured with Agilent Feature Extraction software, version 10.7 (Agilent Technologies), using a modified Exiqon protocol.

data_processing: The raw data were extracted from scanned slides with Feature Extraction software (Agilent; version 10.7). The microarray background correction was performed using normexp method and normalization between arrays was carried out via quantiles method in R statistical software (version 2.13.0). Human miRNAs were filtered and replicate probes were merged by their mean profile.

source_name: LCL, truncating BRCA1

label_protocol: 300 ng of RNA was CIP treated and Hy3-labeled using miRCURY LNA™ microRNA Hi-Power Labeling Kit (Exiqon)

extract_protocol: Total RNA was extracted using TRIzol Reagent (Invitrogen) according to the manufacturer´s instructions. Ten million cells from each LCL was used for RNA isolation. RNA quality and quantity was determined using LabChip technology on an Agilent 2100 BioAnalyser (Agilent Technologies).

value: lymphoblastoid cell line

value: truncating BRCA1

tag: gender

value: female


title: LCL_truncating9

description: miRNA expression at basal conditions

tag: age


title: KMCH control 3

value: KMCH


title: KMCH curcumin 2


title: KMCH curcumin 3


title: BA11 sample #126

value: brain

tag: Sex


title: LCL_truncating8

description: miRNA expression at basal conditions


title: KMCH curcumin 1


title: BA11 sample #127

tag: race


title: plasma of HIRI mouse

city: Beijing

first: Qinghua

last: Cui

address: 38 Xueyuan Road

institute: Peking University

hyb_protocol: The labeled cRNAs were hybridized onto the Mouse LncRNA Array v2.0 (8 x 60K, Arraystar).

scan_protocol: After having washed the slides, the arrays were scanned by the Agilent Scanner G2505C.

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed using the GeneSpring GX v12.0 software package (Agilent Technologies). After quantile normalization of the raw data, LncRNAs and mRNAs that at least 1 out of 6 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis.

source_name: mosue plasma of IRI

label_protocol: The sample preparation and microarray hybridization were performed based on the manufacturer’s standard protocols with minor modifications. Briefly, mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). Then, each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3’ bias utilizing a random priming method.

extract_protocol: Total RNA from each sample was quantified by the NanoDrop ND-1000 and RNA integrity was assessed by standard denaturing agarose gel electrophoresis.

value: Plasma


title: LCL_truncating7

description: miRNA expression at basal conditions