title: AE126_vs_AE126_ZnResist3_rep3

city: Mol

first: Rob

last: Van Houdt

address: Boeretang 200

department: Interdisciplinary Biosciences

country: Belgium

institute: SCK-CEN

description: Comparison of AE126 with AE126 zinc resistant strain 3 from lab evolution experiment

hyb_protocol: Labeled cDNA was re-suspended in the universal hybridization buffer (Pronto kit), mixed and added to the spotted slide for overnight hybridization at 42 C in a Tecan HS4800 Pro hybridization station (Tecan Group Ltd, Switzerland). Afterwards, the slide was washed according to Pronto kit’s protocol.

scan_protocol: Slides were scanned (at 532 and 635 nm) using the GenePix Personal 4100A microarray scanner (Molecular Devices, USA).

data_processing: Micro-array spot-signals were analyzed using the GenePix Pro v.6.0.1 software and flagged according to build-in quality criteria. Raw median intensity data were imported into R version 2.7.0 for statistical analysis using the LIMMA package version 2.15.15 (Smyth 2005) as available from BioConductor. Raw data were background-corrected based on convolution of normal and exponential distributions with an offset of 50 (Ritchie et al. 2007). Data were normalized within each array using the printing-tip loess normalization algorithm (Smyth and Speed 2003). The in-slide replicate correlations were calculated using the Duplicate correlation function in the LIMMA package (Smyth 2005). The log expression values were fitted to al linear model and moderated t-statistics were calculated using empirical Bayes method (Smyth 2004). P-values were corrected for multiple testing using the Benjamin and Hochberg’s method to control the false discovery rate (Benjamini and Hochberg 1995).

organism: Cupriavidus metallidurans

label_protocol: Ten micrograms of RNA were reverse transcribed following the instructions provided with the Pronto kit (Promega, United States). Two color labeling, green for control samples and red for condition (metal challenge) samples, was performed using respectively CyTM3-dCTP and CyTM5-dCTP nucleotides (Amersham BioSciences, United Kingdom).

growth_protocol: The strains were cultivated by  inoculating 30 ml of MM284 in biological triplicates with 300 μL of a stationary phase culture at 30 °C. These subcultures were allowed to grow until an OD600 value of around 0.6 was reached. Next, cells were harvested by centrifugation for 2 min at 10000 rpm and the bacterial pellets were flash frozen by immersion into liquid nitrogen.

extract_protocol: The bacterial pellets were kept frozen at -80 °C until total RNA extraction was performed using the SV Total RNA Isolation system (Promega Corporation). The quantity of extracted RNA was measured using a NanoDropTM 1000 spectrophotometer (Thermo Scientific). The RNA quality was determined with a Bioanalyzer (Agilent 2100 Electrophoresis Bioanalyzer Agilent Technologies).

treatment_protocol: All strains were grown in normal conditions, as the aim of this study was to compare the general gene expression of two different strains.


title: Human Mammary Epithelial Cells_Rheb_transfected_6

status: Public on Dec 31 2016

type: RNA

city: Durham

first: David

last: Hsu

state: NC

address: 905 S. LaSalle St. Rm 3008

department: Medical Oncology

country: USA

institute: Duke University

hyb_protocol: The resulting biotin-labeled RNA samples were then hybridized with Affymetrix U133A 2.0 GeneChip arrays according to the manufacturer's instructions (Affymetrix, Santa Clara, CA).

scan_protocol: GeneChips were scanned using the Gene Array Scanner (Affymetrix) following the manufacturer’s instructions (Affymetrix, Santa Clara, CA).

data_processing: The data were analyzed using the R statistical platform with the Bioconductor affymetrix package [R version 2.13.1 (2011-07-08) and Bioconductor version 2.9].

label: biotin

molecule: total RNA

organism: Homo sapiens

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3-4 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Mammary epithelial cells were isolated from a breast reductive surgery at Duke University and grown at 37 degrees C in mammary epithelial cell growth medium (MEGM) containing a MEGM Bullet Kit, human transferrin and isopenterol.

extract_protocol: Total RNA was isolated using a Qiagen Rneasy kit.

treatment_protocol: Cells were brought to quisecence by serum starvation and treated with adenovirus to over-express the Rheb oncogene (10 replicates) or GFP (10 replicates).  Eighteen hours after infection, activation of oncogenes and secondary targets were confirmed by western blotting.

tag: cell type

value: Human Mammary Epithelial cells (HMECs)

tag: genotype/variation

value: over-expressing Rheb oncogene


title: Basophils_1

city: Suita

first: Takashi

last: Satoh

state: Osaka

address: 3-1 Yamada-oka

department: RIMD

country: Japan

institute: Osaka university

hyb_protocol: Following fragmentation,  cDNA were hybridized for 16 hr at 45C on GeneChip mouse genome 430 2.0 array. GeneChips were washed and stained in the Affymetrix Fluidics Station.

scan_protocol: GeneChips were scanned using  Genechip Scanner.

data_processing: The data were analyzed by R

organism: Mus musculus

source_name: hematopoietic cells

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

growth_protocol: Mice were housed in individually ventilated cages in a temperature and light regulated room in a SPF facility and received food and water ad libitum. All studies received local ethics review board approval and were performed in accordance with the guidelines of the animal care and use committee of the Research Institute for Microbial Diseases at Osaka University.

extract_protocol: Total RNA was isolated from each cell sample using a RNA isolation kit (Roche) and further purified using a RNeasy kit (Qiagen, Hilden, Germany) according to the manufacturer's instructions.

treatment_protocol: Cells were washed in ice-cold FACS buffer (2% FCS, 2 mM EDTA in PBS), then incubated with each antibody for 15 min and washed twice with FACS buffer. Then these cells were prepared by using FACS ARIA

tag: strain

tag: gender

value: male

tag: age

value: 8 weeks old

tag: tissue

value: spleen

value: basophils


title: Human Mammary Epithelial Cells_Rheb_transfected_3


title: DS#30

type: genomic

city: Madrid

first: Mercedes

last: Robledo

state: Madrid

address: C/ Melchor Fernández Almagro, 3

department: Human Cancer Genetics Program

country: Spain

institute: Spanish National Cancer Research Centre (CNIO)

description: tumoral tissue 30

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

source_name: tumoral tissue

label_protocol: Standard Illumina Protocol

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

tag: tissue type

value: medullary thyroid carcinoma


title: F480 posi_BAL

value: Lung

value: residential macrophage


title: Human Mammary Epithelial Cells_Rheb_transfected_4


title: SatM_BAL

value: novel monocyte SatM involved in fibrosis


title: mSR1dullCC1dull_BAL


title: DS#29

description: tumoral tissue 29


title: DS#32

description: tumoral tissue 32


title: AE126_vs_AE126_ZnResist3_rep2


title: MP_BAL


title: Human Mammary Epithelial Cells_Rheb_transfected_1


title: other Ly6c-_Blood

value: blood

value: Ly6c- monocyte excluding SatM, msr1-cc1-monocyte and msr1 dull cc1 dull monocyte


title: DS#27

description: tumoral tissue 27


title: DS#28

description: tumoral tissue 28


title: MP1, biological rep3

city: Thiruvananthapuram

first: Vinitha

last: Richard

state: Kerala

address: Thycaud P.O.

department: Cancer Research Program

country: India

institute: Rajiv Gandhi Centre for Biotechnology

description: Differential expression analysis of genes in MP1.

hyb_protocol: Labeled cRNA was fragmented in a 0.5ug/uL reaction and used for array hybridization and washing according to the standard Affymetrix protocol on an Affymetrix FS450 Fluidics station.

scan_protocol: The arrays were scanned on an Affymetrix GeneChip Scanner 3000 7G using the Affymetrix Statistical Algorithm MAS 5.0 (GCOS v1.3) algorithm.

data_processing: Softwares used for analysis were Partek Genomic Solutions 6.2 (Partek Inc., St. Charles, MO), Matlab 7 (Mathworks Inc., MA) and GCOS 1.3 (Affymetrix Inc., CA).

label: Biotin

source_name: SCC172, MP1 fraction

label_protocol: 100ng of total RNA were used for preparation of biotin-labeled targets (cRNA) using modified MessageAmp™ -based protocols (Ambion Inc., Austin, TX).

growth_protocol: The OSCC cell line SCC172 were adherent cells maintained in Dulbecco’s Modified Eagle’s Medium (Sigma, D1152) containing 25mM HEPES and 3.6g/L sodium bicarbonate supplemented with 10% Foetal Bovine Serum (FBS, Sigma) and 1% antibiotic antimycotic cocktail (Invitrogen). Cells were incubated at 37C with 5% CO2 in a humidified incubator.

extract_protocol: Total RNA was isolated using Qiagen’s All Prep DNA/RNA Mini Kit (Cat. No. 80204) following the manufacturer’s instructions.

treatment_protocol: Side population analysis was based on the previously described method (Goodell et al., 1997) with slight modifications. Briefly, cells were incubated (1x10^6cells/ml) in pre-warmed DMEM supplemented with 2% fetal bovine serum (FBS) (Sigma) and 10Mm HEPES (Sigma) containing 5 µg/ml Hoechst 33342 for 45 minutes at 37C (water-bath) with intermittent mixing. After incubation, stained cells were washed and re-suspended in ice-cold HBSS (Sigma) supplemented with 2% FBS. Propidium iodide (1µg/ml) was added immediately before analysis to label dead cells. Analysis and sorting was performed on FACS Aria II (BD Biosciences) using Diva Software.

tag: cell line

tag: fraction

value: oral squamous cell carcinoma (OSCC) cells


title: AE126_vs_AE126_ZnResist2_rep3

description: Comparison of AE126 with AE126 zinc resistant strain 2 from lab evolution experiment


title: Human Mammary Epithelial Cells_Rheb_transfected_2


title: DS#33

description: tumoral tissue 33


title: mSR1-CC-_Blood


title: AE126_vs_AE126_ZnResist2_rep2


title: AE126_vs_AE126_ZnResist3_rep1


title: DS#25

description: tumoral tissue 25


title: SatM_Blood


title: AE126_cnrH_vs_AE126_cnrH_ZnResist_rep3

description: Comparison of AE126 cnrH mutant with zinc resistant strain from lab evolution experiment


title: mSR1-CC-_BM

value: bone marrow


title: MP1, biological rep1


title: SP1, biological rep2

description: Differential expression analysis of genes in SP1.

source_name: SCC172, SP1 fraction


title: CB_SW480-R

city: Berlin

first: Lars

last: Bullinger

address: Augustenburger Platz 1

department: Hematology, Oncology and Tumorimmunology

country: Germany

institute: Charité

hyb_protocol: according to manufactor's instructions  (Genome-Wide Human SNP  6.0 User Guide, Affymetrix)

scan_protocol: Chips were scanned using the Gene Chip Scanner 3000

data_processing:
CEL-files were generated using Affymetrix Command console software.
CHP files were generated using the birdseed-v2 algorithm in Genotyping Console Version 4.2

source_name: cell line

growth_protocol: All cell lines were maintained under standard conditions. Cell line identity and purity were verified using the Multiplex Cell Authentication and Contamination Tests (Multiplexion).

extract_protocol: DNA was isolated using the PureLink Genomic DNA Mini Kit (Invitrogen) from the respective cell lines.

treatment_protocol: PU-H71 was generated and provided by the laboratory of G. Chiosis as previously described [Moulick K, Ahn JH, Zong H, Rodina A, Cerchietti L, Gomes DaGama EM, et al. Affinity-based proteomics reveal cancer-specific networks coordinated by Hsp90. Nature chemical biology 2011;7(11):818-26]. Puromycin was obtained from Sigma-Aldrich.From each PU-H71-resistant cell line, clones were generated by seeding single cells into 96-well plates.

tag: phenotype

value: resistant


title: DS#24

description: tumoral tissue 24


title: CB_A549-P

label_protocol: according to manufactor's instructions  (Genome-Wide Human SNP  6.0 User Guide, Affymetrix)

value: sensitive


title: AE126_vs_AE126_ZnResist2_rep1


title: SP1, biological rep1


title: csc1_sc3__snp6.0

city: Daejeon

first: sujin

last: Baek

address: Gwahank-ro 125

department: MGRC

country: South Korea

institute: KRIBB

description: gastric cancer stem cell (csc1-clone3)

hyb_protocol: Each array according to the manufacturer`s instruction

data_processing: Copy number values for individual SNPs were extracted and converted from CEL files into signal intensities using Genotypeing Console software. Circular Binary segmentation was applied using DNAcopy package for R Bioconductor on raw data.

source_name: gastric cancer stem cell (csc1-clone3)

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: Standard DNA preparation protocol using Qiagen's DNA prep kit

value: gastric cancer stem cell


title: CB_A549-R


title: AE126_cnrH_vs_AE126_cnrH_ZnResist_rep2


title: MP1, biological rep2


title: mSR1dullCC1dull_BM


title: CB_SW480-P


title: DS#22

description: tumoral tissue 22


title: tissue resident M2-like macrophage_BM

value: tissue residential macrophage


title: DS#31

description: tumoral tissue 31


title: AE126_cnrH_vs_AE126_cnrH_ZnResist_rep1


title: root +glu, biological rep 2

city: Taipei

first: Ming-Hsiun

last: Hsieh

address: 128 Academia Road, Section 2

department: Institute of Plant and Microbial Biology

country: Taiwan

institute: Academia Sinica

description: Gene expression data from rice roots with Glu treatment for 0.5 hour

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Rice Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: The arrays were scanned on the Affymetrix GeneChip Scanner 3000.

data_processing: The Affymetrix CEL data were generated from GCOS and normalized using RMA algorithm in Genespring 11.5 software. Baselines were transformed to median of control samples. Expression value of probeset that >100 was defined as present. Unpaired t-test was performed to examine the reproducibility of the data sets. Probesets with P-value <0.05 and at least two-fold change between control and treatment groups were selected into the final list.

organism: Oryza sativa Japonica Group

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Rice (Oryza sativa L. ssp. Japonica cv. TNG67) seeds were germinated in continuous dark at 30°C for 3 days and then transferred to hydroponic solution (Yoshida et al., 1976) without NH4NO3 (-N) and grown under controlled conditions (30°C, 12-h photoperiod, 200 µmol photons m-2 s-1, 70% relative humidity) for 2 weeks.

extract_protocol: Total RNA from –N and + Glu-treated roots was extracted using a phenol extraction protocol.

treatment_protocol: 17-day-old rice seedlings grown in –N hydroponic solution were transferred to -N or +2.5 mM Glu solution for 30 min.

tag: variety

value: root

tag: growth stage

value: seedling


title: DS#21

description: tumoral tissue 21


title: DS#20

description: tumoral tissue 20


title: csc3-sc_snp6.0

description: gastric cancer stem cell

scan_protocol: Each array according to the manufacturer`s instruction


title: mSR1-CC-_SP

value: male

value: 8 weeks old


title: root (-N), biological rep 2

description: Gene expression data from rice roots without Glu treatment

source_name: rice roots without Glu treatment


title: DS#19

description: tumoral tissue 19


title: other Ly6c-_SP

value: spleen


title: OT-1_DC_replicate_3

city: Montréal

first: Mélissa

last: Mathieu

state: Québec

address: 900 rue Saint Denis

department: CRCHUM

country: Canada

institute: University of Montreal

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Raw data were pre-processed by log2 transformation, quantile normalisation and exclusion of genes where the average signal was smaller or equal to the background and/or the standard deviation was smaller or equal to 0.1.

source_name: Sorted OT-1 activated by dendritic cells

label_protocol: Biotinylated cRNA were prepared with the Ambion TotalPrep RNA Amplification

growth_protocol: OT-1 CD8+ T lymphocytes were cocultured for 24h with CD40-B LPS OVA or with DC LPS OVA (ratio 5:1).

extract_protocol: RNA extraction by TRIZOL followed by purification with a Quiagen RNeasy CleanUp Kit

treatment_protocol: Cells were stained, resuspended in PBS containing 0.5mM EDTA and activated OT-1 T cells (CD8+ CD69+) were sorted with a BD FACSAria III

tag: cell population

value: dendritic cells


title: root +glu, biological rep 1

source_name: rice roots with Glu treatment for 0.5 hour


title: csc2-sc_snp6.0

description: gastric cancer stem cell


title: OT-1_DC_replicate_2


title: csc3-dc_snp6.0

description: differentiated cell

value: differentiated cell


title: SatM_spleen


title: root (-N), biological rep 1


title: csc1-dc_snp6.0

description: differentiated cell


title: OT-1_DC_replicate_1


title: DS#26

description: tumoral tissue 26

value: medullary thyroid carcinoma


title: tissue resident M2-like macrophage_spleen

value: tissue residential macrophages


title: DS#18

description: tumoral tissue 18


title: SMP_WT_2

value: novel monocyte progenitor of SatM


title: OT-1_cB_replicate_4

source_name: Sorted OT-1 activated by CD40-activated B cells

value: CD40-activated B cells


title: DS#17

description: tumoral tissue 17


title: csc1-sc_snp6.0

description: gastric cancer stem cell


title: DS#16

description: tumoral tissue 16


title: csc2-dc_snp6.0

description: differentiated cell


title: csc2-n_snp6.0

description: normal

value: normal


title: csc3-n_snp6.0

description: normal


title: OT-1_cB_replicate_3


title: DS#14

description: tumoral tissue 14


title: OT-1_cB_replicate_2


title: DS#12

description: tumoral tissue 12


title: OT-1_cB_replicate_1


title: DS#13

description: tumoral tissue 13


title: SMP_2

value: bone marrow


title: MDP

value: monocyte/ macrophage DC progenitor


title: DS#15

description: tumoral tissue 15


title: cMoP_WT_1

value: common monocyte progenitor


title: Strain_α522_CSF replicate2

city: Wuerzburg

first: Biju Joseph

last: Ampattu

address: Josef-Schneider Str 2

department: Department of Microbiology

institute: University of Wuerzburg

description: replicate 2 of 3

hyb_protocol: The labelled DNA were mixed together in hybridization buffer (3 x SSC and 0.1% SDS) and hybridized onto prehybridized microarray slides using a Tecan Hybridization station.

scan_protocol: The slides were scanned using a Genepix Pro scanner with settings to avoid more than 10% of the spots being saturated.

data_processing: Raw data generated after flagging for obvious cases of stray background and spots with a signal to noise ratio of less than 3 were further analyses using the R package limma. Loess normalization was used for within slide and Rquantile normalization was used for between slide normalization.

organism: Neisseria meningitidis

source_name: RNA from strain α522 grown in PPM+ and exposed to human csf

label_protocol: 10 µg of test RNA and 10 µg of common reference RNA were labelled with Cy3 dCTP and Cy5 dCTP using reverse transcriptase (Invitrogen)and random nonamers and the labelled DNA was precipitated and purified.

growth_protocol: The strains were grown in PPM+ medium to a mid log phase and harvested for RNA isolation. For isolation of RNA from the strains on exposure to human material, the cells were harvested and exposed to human saliva, blood or csf for 30 minutes and cells were harvested for RNA isolation.

extract_protocol: Total RNA extracted using RNeasy kit from Qiagen following manufacturer's instructions

tag: exposure

value: PPM+ grown  and exposed to human csf strain using Trizol

source_name: Common Reference

tag: reference

value: Pool of all individual RNA´s


title: OT-1_DC_replicate_4


title: Strain_α522_CSF replicate3

description: replicate 3 of 3


title: GMP

value: granulocyte- monocyte progenitor


title: Strain_α522_CSF replicate1

description: replicate 1 of 3


title: Strain_α522_blood replicate2

description: replicate 2 of 3

source_name: RNA from strain α522 grown in PPM+ and exposed to human whole blood

value: PPM+ grown  and exposed to human blood strain using Trizol


title: cMoP_2

value: male


title: SatM_BM

value: 8 weeks old

value: novel monocyte SatM involved in fibrosis


title: Strain_α522_blood replicate3

description: replicate 3 of 3


title: DS#10

description: tumoral tissue 10


title: SMP_1


title: DS#9

description: tumoral tissue 9


title: DS#11

description: tumoral tissue 11


title: SMP_WT_1


title: DS#7

description: tumoral tissue 7


title: DS#8

description: tumoral tissue 8


title: CB_MDA-R

description: MDA-R

value: resistant


title: Strain_α522_Saliva replicate3

description: replicate 3 of 3

source_name: RNA from strain α522 grown in PPM+ and exposed to human saliva

value: PPM+ grown  and exposed to human saliva strain using Trizol


title: Strain_α522_blood replicate1

description: replicate 1 of 3


title: Strain_α522_Saliva replicate2

description: replicate 2 of 3


title: CB_MDA-P

description: MDA-P

value: sensitive


title: DS#5

description: tumoral tissue 5

value: medullary thyroid carcinoma


title: SatM_2


title: DS#6

description: tumoral tissue 6


title: Strain_α522_PPM+ replicate3

description: replicate 3 of 3

source_name: RNA from strain α522 grown in PPM+

value: PPM+ grown strain using Trizol


title: Strain_α522_Saliva replicate1

description: replicate 1 of 3


title: DS#3

description: tumoral tissue 3


title: cMoP_1


title: inflammatory monocyte_1

value: inflammatory monocytes


title: Strain_α522_PPM+ replicate2

description: replicate 2 of 3


title: Xenopus laevis expression data from larval inner ear tissue 50_2

city: Cleveland

first: Selene

last: Virk

state: OH

address: 2103 Cornell Road

institute: Case Western Reserve University

description: Gene expression data from larval animals ranging from stage 50 to stage 52 based on Nieuwkoop and Faber (1994) Normal Table of Xenopus laevis (Daudin). Garland Publishing Inc, New York ISBN 0-8153-1896-0.

hyb_protocol: Fragmented cDNA was hybridized according to manufacture's protocol (Affymetrix)

scan_protocol: GeneChip Xenopus laevis 2.0 were scanned using the GeneChip Scanner 3000 7G (Affymetrix)

data_processing: Data processed using JMP Genomics software

organism: Xenopus laevis

source_name: Xenopus laevis larvae

label_protocol: Labeled antisense single-stranded cDNA was prepared from each RNA replicate (1 ug total RNA) using the Ovation RNA Amplification System V2 in conjunction with the FL-Ovation cDNA Biotin Module V2 (both from NuGEN)

growth_protocol: Larval Xenopus laevis (n=38) were aged 15-21 days post-fertilization with an average weight of 0.14 ± 0.03 g and an average length of 3.07 ± 0.25 cm and obtained from Nasco (Fort Atkinson, WI). Animal procedures and protocols were approved by the Institutional Animal Care and Use Committee (IACUC) of New Mexico State University.

extract_protocol: Total RNA was extracted using the RNeasy Mini Kit (Qiagen, Valencia, CA) as per Trujillo-Provencio C, Powers T, Sultemeier D, Serrano E: RNA isolation from Xenopus inner ear sensory endorgans for transcriptional profiling and molecular cloning. Methods Mol Biol 2009, 493:3-20.

value: inner ear

tag: developmental stage

value: larval stages 50-52

value: larval animals 15-21 days post-fertilization


title: inflammatory monocyte_2

value: bone marrow


title: DS#2

description: tumoral tissue 2


title: Xenopus laevis expression data from larval inner ear tissue 50_3

label_protocol: Labeled antisense single-stranded cDNA was prepared from each RNA replicate (0.7 ug total RNA) using the Ovation RNA Amplification System V2 in conjunction with the FL-Ovation cDNA Biotin Module V2 (both from NuGEN)

growth_protocol: Larval Xenopus laevis (n=24) were aged 15-21 days post-fertilization with an average weight of 0.16 ± 0.03 g and an average length of 3.19 ± 0.27 cm and obtained from Nasco (Fort Atkinson, WI). Animal procedures and protocols were approved by the Institutional Animal Care and Use Committee (IACUC) of New Mexico State University.


title: SatM_1


title: Xenopus laevis expression data from larval inner ear tissue 50_1

growth_protocol: Larval Xenopus laevis (n=15) were aged 15-21 days post-fertilization with an average weight of 0.15 ± 0.04 g and an average length of 2.99 ± 0.28 cm and obtained from Nasco (Fort Atkinson, WI). Animal procedures and protocols were approved by the Institutional Animal Care and Use Committee (IACUC) of New Mexico State University.


title: Strain_α522_PPM+ replicate1

description: replicate 1 of 3


title: DS#1

description: tumoral tissue 1


title: zrf1a-2 zrf1b-1 seedlings, replicate 2

city: Strasbourg

first: Wen-Hui

last: Shen

address: 12 rue du General Zimmer

country: France

institute: IBMP-CNRS

description:
zrf1ab-2_2 seedlings
Biological replicate 2 of zrf1a-2 zrf1b-1 seedlings.

hyb_protocol: Hybridized to Agilent-021169 arrays. Please see manufacturer's web site at: http://www.agilent.com/

scan_protocol: Scanned on an Agilent G2565CA scanner. Images were quantified using Agilent Feature Extraction Software.

data_processing: Agilent Feature Extraction Software was used for background subtraction. Signal intensity were normalized using Quantile method. Signal: Raw Cy3 signal intensity; Log2NormSignal: Log2 transformed normalized signal.

organism: Arabidopsis thaliana

source_name: seedlings, zrf1a-2 zrf1b-1

label_protocol: 2 µg of total RNA were labeled according to Agilent's instructions. Please see manufacturer's web site at: http://www.agilent.com/

growth_protocol: Plants were grown in the greenhouse under 12h light and 12h dark at 22°C.

extract_protocol: Total RNA was extracted using the Trizol reagent (Invitrogen) followed by RNeasy mini kit (Qiagen) clean-up according to manufacturer's instructions.

tag: ecotype

value: Columbia

value: zrf1a-2 zrf1b-1

value: seedlings

value: 6 days


title: KR Primary

city: Frederick

first: NA-YOUNG

last: SONG

state: MD

address: 1050 Boyles Street

institute: NCI

hyb_protocol: 15 ug of biotinylated cRNA were fragmented and hybridized for 16 hr at 45C on mouse Genome Array mo430 2.0.

scan_protocol: GeneChips were washed and stained in the Affymetrix Fluidics Station 450,  were scanned using the Affymetrix Scanner 7G.

data_processing: The data were analyzed using Affymetrix Expression Console and normalized to 150.

source_name: KR tumor-derived cell line

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 150ng total RNA (IVT Express 15402 or IVT Plus 18737)

growth_protocol: Cells were maintained in RPMI1640 media with 10% FBS.

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

treatment_protocol: Cells were collected at 80-90% confluency.

tag: sample type

value: KR tumor-derived cell line

tag: cell type

value: lung cancer cells


title: KR 1

source_name: Cell line derived from KR Primary cell-induced lung tumor (Kras IKKa low cells)

tag: strain


title: DS#4

description: tumoral tissue 4

source_name: tumoral tissue


title: DS#23

description: tumoral tissue 23


title: zrf1a-2 zrf1b-1 seedlings, replicate 1

description:
zrf1ab-2_1 seedlings
Biological replicate 1 of zrf1a-2 zrf1b-1 seedlings.

tag: genotype/variation


title: Strain_MC58_CSF replicate3

description: replicate 3 of 3

source_name: RNA from strain MC58 grown in PPM+ and exposed to human csf

value: PPM+ grown  and exposed to human csf strain using Trizol

value: Pool of all individual RNA´s


title: zrf1a-1 zrf1b-1 seedlings, replicate 3

description:
zrf1ab-1_3 seedlings
Biological replicate 3 of zrf1a-1 zrf1b-1 seedlings.

source_name: seedlings, zrf1a-1 zrf1b-1

value: zrf1a-1 zrf1b-1

tag: age


title: csc1_sc2__snp6.0

description: gastric cancer stem cell (csc1-clone2)

source_name: gastric cancer stem cell (csc1-clone2)

value: gastric cancer stem cell


title: Kras;IKKa floxed 2

source_name: Kras;IKKa floxed mice at 4m post adeno cre

growth_protocol: All mice used in this study were cared for in accordance with the guidelines of the Institutional Animal Care and Use Committee (IACUC) of the National Institute of Health (NIH).

treatment_protocol: The mice were intratracheally treated with adeno virus containing cre recombinase. At 4 months post injection, the mice were euthnized and lung tissues were collected.

value: Kras;IKKa floxed

tag: ttissue

value: lung


title: Strain_MC58_blood replicate3

description: replicate 3 of 3

source_name: RNA from strain MC58 grown in PPM+ and exposed to human whole blood

value: PPM+ grown  and exposed to human blood strain using Trizol


title: Kras;IKKa floxed 1


title: Strain_MC58_CSF replicate2

description: replicate 2 of 3


title: Kras 2

source_name: Kras mice at 4m post adeno cre

value: Kras


title: zrf1a-1 zrf1b-1 seedlings, replicate 2

description:
zrf1ab-1_2 seedlings
Biological replicate 2 of zrf1a-1 zrf1b-1 seedlings.

tag: tissue


title: Wild-type seedlings, replicate 2

description:
WT_2 seedlings
Biological replicate 2 of wild-type seedlings.

source_name: seedlings, wild-type

value: wild type


title: 5504494024_K

first: Liang-Chuan

last: Lai

state: Taiwan

address: 1 Jen-Ai Road, Sec 1

department: Physiology

institute: National Taiwan University

description: SAMPLE 87

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

extract_protocol: Genomic DNAs were extracted and purified from normal and tumor lung samples using Qiagen DNeasy Kit according to standard instructions

tag: gender

value: Female

tag: disease stage

value: Normal

value: normal adjacent lung tissue


title: 5504494024_J

description: SAMPLE 86

value: lung adenocarcinoma tissue


title: Strain_MC58_blood replicate2

description: replicate 2 of 3


title: 5504494024_L

description: SAMPLE 88


title: IKKa floxed 2

source_name: IKKa floxed mice at 4m post adeno cre

value: IKKa floxed


title: Kras 1


title: zrf1a-1 zrf1b-1 seedlings, replicate 1

description:
zrf1ab-1_1 seedlings
Biological replicate 1 of zrf1a-1 zrf1b-1 seedlings.

value: Columbia

value: seedlings

value: 6 days


title: Wild-type seedlings, replicate 3

description:
WT_3 seedlings
Biological replicate 3 of wild-type seedlings.


title: Wild-type seedlings, replicate 1

description:
WT_1 seedlings
Biological replicate 1 of wild-type seedlings.


title: 5504494024_H

description: SAMPLE 84


title: 5504494024_I

description: SAMPLE 85


title: Strain_MC58_Saliva replicate3

description: replicate 3 of 3

source_name: RNA from strain MC58 grown in PPM+ and exposed to human saliva

value: PPM+ grown  and exposed to human saliva strain using Trizol

source_name: Common Reference


title: 5504494024_G

description: SAMPLE 83


title: wild type 2

source_name: WT mice at 4m post adeno cre


title: cMoP_WT_2

source_name: hematopoietic cells

value: male

value: 8 weeks old

value: bone marrow

value: common monocyte progenitor


title: IKKa floxed 1

value: lung


title: 5504494024_F

description: SAMPLE 82


title: wild type 1


title: Strain_MC58_Saliva replicate2

description: replicate 2 of 3

value: Pool of all individual RNA´s


title: CACO2_OV-ESRP1_rep1

city: Turin

first: Fiorella

last: Altruda

address: Via Nizza 52

country: Italy

institute: University of Turin

description:
CRC cell line
3998720029_C

hyb_protocol: Hybridization of cRNAs (750 ng) was carried out using Illumina Human 48 k gene chips (Human HT-12 V4 BeadChip). Array washing was performed using Illumina High Temp Wash Buffer for 10′ at 55 °C, followed by staining using streptavidin-Cy3 dyes (Amersham Biosciences).

scan_protocol: Probe intensity data were obtained and normalized using the Illumina Genome Studio software (Genome Studio V2011.1) and further processed with Excel software

data_processing: Subsequent data processing, carried out with Excel (Microsoft), included: (i) scaling, Log2 transformation and detection filtering; (ii) removal of redundant probes (>average); (iii) Log2Ratio transformation and selection of genes differentially expressed; Log2Ratio expression data were clustered and visualized using the GEDAS software

source_name: CACO2 ESRP1 A +

label_protocol: Synthesis of cDNA and biotinylated cRNAwas performed using the IlluminaTotalPrep RNA Amplification Kit (Ambion), according to the manufacturer’s protocol using 500 ng of total RNA. Quality assessment and quantification of cRNAswere performed with Agilent RNA kits on Bioanalyzer 2100.

growth_protocol: Standard culture conditions for Caco2 cell line

extract_protocol: RNA was extracted using miRNeasy Mini Kit (Qiagen). The quantification and quality analysis of RNA was performed on a Bioanalyzer 2100 (Agilent), using RNA 6000 nano Kit (Agilent)

treatment_protocol: ShRNA-mediated knockdown (Sh) and cDNA-mediated overexpression (OV) of ESRP1 were obtained using PLKO.1 and pLX304 lentiviruses, respectively.

tag: cell line

value: CRC cell line

tag: condition

value: oveexpressing ESRP1


title: Strain_MC58_CSF replicate1

description: replicate 1 of 3

value: PPM+ grown  and exposed to human csf strain using Trizol


title: CACO2_OV-ESRP1_rep2

description:
CRC cell line
3998720029_D

source_name: CACO2 ESRP1 B +


title: Strain_MC58_Saliva replicate1

description: replicate 1 of 3


title: CACO2_EV_rep2

description:
CRC cell line
3998720029_B

source_name: CACO2 EMPTY B

value: control overexpression


title: Male treatment, biological rep3

city: Shanghai

first: Qian

last: Ba

address: 320 Yueyang Rd

country: China

institute: Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences

description: Gene expression data from liver of male mice received CdCl2

hyb_protocol: Array hybridization and wash was performed using GeneChip® Hybridization, Wash and Stain Kit (Cat#900720, Affymetrix) in Hybridization Oven 645 and Fluidics Station 450 followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by GeneChip® Scanner 3000.

data_processing: Raw data were normalized by MAS 5.0 algorithm, Gene Spring Software12.6.1.

source_name: Liver of male mice received 100nM CdCl2

label_protocol: Biotin labeled cRNA were obtained by using GeneChip 3' IVT PLUS Reagent Kit (Cat#902416, Affymetrix) followed the manufacturer’s instructions.

growth_protocol: Female mice were caged individually during mating, pregnancy and lactation. And the offsprings were separately housed after weaning.

extract_protocol: Total RNA was extracted using Takara RNAiso Plus Kit (Cat#9109, Takara) following the manufacturer’s instructions.

treatment_protocol: Female mice were exposed by water or 100nM cadmium chloride in water continually from 1 week before copulation. After weaning, the offsprings were seperately housed with the supply of water or 100nM cadmium chloride in water continually untill 30 weeks of age, when they were sacrificed and the liver were sampled.

value: Liver

value: Male

value: Cadmium Chloride 100nM


title: 5504494024_D

description: SAMPLE 80

value: Female

value: lung adenocarcinoma tissue


title: Strain_MC58_PPM+ replicate1

description: replicate 1 of 3

source_name: RNA from strain MC58 grown in PPM+

value: PPM+ grown strain using Trizol


title: sh50(Ñ)

first: Fatima

last: Sanchez-Cabo

address: Melchor Fernandez Almagro

institute: CNIC

description:
CPC-shB, cell culture #(Ñ)
Expression of miRNAs from Sca1+CPC inhibiting Bmi1

hyb_protocol: 100 ng of Cy3 labelled RNA were hybridized for 20 hours at 55ºC in a hybridization oven  (G2545A, Agilent) set to 15 rpm in a final concentration of 1X GE Blocking Agent and 1X Hi-RPM Hybridization Buffer, according to manufacturer's instructions (miRNA Microarray System Protocol, Agilent Technologies).

scan_protocol: Arrays were scanned at 5mm resolution on an Agilent DNA Microarray Scanner (G2565BA, Agilent Technologies) using the default settings for miRNA Microarray v2.0 (miRNA Microarray System Protocol, Agilent Technologies).

data_processing: Images provided by the scanner were analyzed using Agilent´s software Feature Extraction version 10.7.3.1 and protocol miRNA_105_Jan09

source_name: CPC-shB cell culture

label_protocol: miRNA Labeling Kit (Agilent Technologies) was used to label RNA. Basically, 100 ng of total RNA were dephosphorylated and Cyanine 3-pCp molecule was ligated to the 3´ end of each RNA molecule by using T4 RNA ligase.

growth_protocol: Sca1+ CPC were plated in culture plates pre-coated with 0.1% gelatin and were maintained at 37°C, 3% oxygen with the corresponding medium (IMDM, 10% FCS, 1% penicillin and streptomycin and 1% L-glutamine, supplemented with 10 ng/ml EGF (E9644, Sigma), 20 ng/ml FGF (450-33, Prepotech) and LIF (103 U; ESG1107, Millipore). Medium was refreshed every 2 days. Cells were passaged at 70%-80% confluency by tripsinization.

extract_protocol: Total RNA was isolated using the mirVana kit (Ambion). RNA was quantified and integrity was checked by agarose gel electrophoresis.

treatment_protocol: Cells were transduced with respectives lentivirus at a MOI of 10 with the appropriate dilution of the stock in 3 ml of culture medium and polybrene (SIGMA) at 8 ug/ml, for seven to eight hours. Then, inoculum was removed and cell cultures were refreshed with medium before assay.

value: Sca1+ Cardiac Protenitor Cells (CPC)

value: inhibiting Bmi1


title: Strain_MC58_PPM+ replicate3

description: replicate 3 of 3


title: Strain_MC58_PPM+ replicate2

description: replicate 2 of 3


title: CACO2_EV_rep1

description:
CRC cell line
3998720029_A

source_name: CACO2 EMPTY A


title: Strain_MC58_blood replicate1

description: replicate 1 of 3

value: PPM+ grown  and exposed to human blood strain using Trizol


title: 5504494024_E

description: SAMPLE 81

value: Normal

value: normal adjacent lung tissue


title: sh50(2)

description:
CPC-shB, cell culture #2
Expression of miRNAs from Sca1+CPC inhibiting Bmi1


title: Male treatment, biological rep2


title: sh50(1)

description:
CPC-shB, cell culture #1
Expression of miRNAs from Sca1+CPC inhibiting Bmi1


title: sh69(Ñ)

description:
CPC-shScramble, cell culture #(Ñ)
Expression of miRNAs from Sca1+CPC overexpressing sh-Scramble

source_name: CPC-shScramble cell culture

value: overexpressing sh-Scramble


title: sh69(2)

description:
CPC-shScramble, cell culture #(2)
Expression of miRNAs from Sca1+CPC overexpressing sh-Scramble


title: CMV(3)

description:
CPC-B+, cell culture #3
Expression of miRNAs from Sca1+CPC overexpressing Bmi1

source_name: CPC-B+  cell culture

value: overexpressing Bmi


title: Male treatment, biological rep1


title: CACO2_ShESRP1_rep2

description:
CRC cell line
9371242085_L

source_name: CACO2 sh4 300ul

value: CRC cell line

value: ESRP1 silenced


title: CMV(2)

description:
CPC-B+, cell culture #2
Expression of miRNAs from Sca1+CPC overexpressing Bmi1

value: overexpressing Bmi1


title: 5504494024_C

description: SAMPLE 79


title: 5504494024_A

description: SAMPLE 77


title: CACO2_scr_rep2

description:
CRC cell line
9371242085_H

source_name: CACO2 scramble 300ul

value: control Sh


title: CACO2_ShESRP1_rep1

description:
CRC cell line
9371242085_K


title: 5504494023_L

description: SAMPLE 76


title: Female treatment, biological rep3

description: Gene expression data from liver of female mice received CdCl2

source_name: Liver of female mice received 100nM CdCl2

value: Liver


title: SKOV3 Hyperthermia-1

city: Houston

first: Sangbae

last: Kim

state: TX

address: 1 Baylor plaza

department: HGSC

institute: Baylor Colleage of Medicine

description: To export to gene expression data based on unique gene, we used Sample Gene Profile option of Illumina BeadStudio software.

hyb_protocol: Labeled, amplified material (750 ng per array) was hybridized to the Illumina HumanHT-12 V3.0 expression beadchip according to the Manufacturer's instructions (Illumina, Inc., San Diego, CA).

scan_protocol: Arrays were scanned with an Illumina Bead array Reader confocal scanner (BeadStation 500GXDW; Illumina, Inc., San Diego, CA) according to the Manufacturer's instructions

data_processing: Array data processing were performed on Illumina BeadStudio software. We normalized gene expression data using Quantile normalization and log2 transformatoin. To export to a data matrix, Group probe profile option of this software was used.

source_name: Ovarian cancer cells

label_protocol: Biotin-labeled cRNA samples for hybridization were prepared according to Illumina's recommended sample labeling procedure: 500 ng of total RNA was used for cDNA synthesis, followed by an amplification/labeling step (in vitro transcription) to synthesize biotin-labeled cRNA using the Illumina. TotalPrep RNA Amplification kit (Ambion Inc., Austin, TX). cRNA concentrations using spectrophotometer (Nanodrop, ND-1000)

extract_protocol: Total RNA was isolated from tissues with mirVana RNA Isolation labeling kit (Ambion Inc) according to the manufacturer protocol. RNA quality and integrity were confirmed by ExperionTM Automated Electrophoresis System (BIO-RAD)

value: ovarian cancer

tag: treatment


title: 5504494023_E

description: SAMPLE 69


title: Male con trol, biological rep3

description: Gene expression data from liver of male mice received water

source_name: Liver of male mice received water

value: Male

value: Water


title: Female con trol, biological rep3

description: Gene expression data from liver of female mice received water

source_name: Liver of female mice received water

value: Female


title: Female con trol, biological rep2


title: 5504494023_I

description: SAMPLE 73


title: 5504494023_K

description: SAMPLE 75


title: SKOV3 Control-2


title: Male con trol, biological rep1


title: A2780 Hyperthermia-2


title: Female treatment, biological rep1

value: Cadmium Chloride 100nM


title: Female treatment, biological rep2


title: 5504494023_G

description: SAMPLE 71


title: SKOV3 Control-1


title: Female con trol, biological rep1


title: 5504494023_F

description: SAMPLE 70

value: lung adenocarcinoma tissue


title: 5504494023_J

description: SAMPLE 74


title: SKOV3 Hyperthermia-2


title: NET47 soluble transfected, rep3

city: Edinburgh

first: Jose

middle: Ignacio

last: de las Heras

address: Max Born Crescent

department: Wellcome Trust Centre

country: United Kingdom

institute: University of Edinburgh

description: replicate 3

scan_protocol: Standard Protocols (Clinical Research Facility Edinburgh), Scanner: HiScan H166

data_processing: Data were log2 transformed and quantile normalised using the BioConductor package Limma.

source_name: HT1080 cell line

label_protocol: Ambion Illumina TotalPrep kit

growth_protocol: HT1080 fibroblasts were grown in Dulbecco's modified Eagle's medium (DMEM) supplemented with 10% fetal calf serum (FBS), 100 units/ml penicillin and 100 μg/ml streptomycin.

extract_protocol: total RNA extraction was performed using Trizol reagent (Invitrogen) according to the manufacturer's instructions

treatment_protocol: For the full length NETs, NET-GFP fusions were transfected into HT1080 using Lipofectamine2000, and stable cell lines selected with Geneticin at 500ug/ml. Correct localisation was verified by FISH. For the soluble nucleoplasmic fragments, transient transfections were used with a NLS-GFP fusion as control.

value: soluble fragment NET, nucleoplasmic


title: Male con trol, biological rep2


title: A2780 Hyperthermia-1


title: 5504494024_B

description: SAMPLE 78


title: 5504494023_H

description: SAMPLE 72


title: CACO2_scr_rep1

description:
CRC cell line
9371242085_G


title: A2780 Control-2


title: 5504494023_A

description: SAMPLE 65


title: NET47 soluble transfected, rep2

description: replicate 2

hyb_protocol: Standard Protocols (Clinical Research Facility Edinburgh)


title: HSCs sorted from Lig4mut mouse, rep 1

city: Singapore

first: Henry

last: Yang

address: 28 Medical Drive

country: Singapore

institute: Cancer Science Institute of Singapore

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

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

data_processing: The data were analyzed using RMA in the bioconducter and normalized using cross correlation.  The trimmed mean target intensity of each array was set to 8.

source_name: BM slam+ HSC

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Lig4mut/+ mice were intercrossed to generate Lig4mut and littermate wild-type control (WT - Lig4+/+) mice

treatment_protocol: Lig4mut HSCs compared with those WT HSCs from normal mice


title: 5504494023_D

description: SAMPLE 68

label_protocol: Standard Illumina Protocol


title: HSCs sorted from Lig4mut mouse, rep 3


title: 5504494023_B

description: SAMPLE 66


title: NET39 soluble transfected, rep3

description: replicate 3


title: 5504494022_J

description: SAMPLE 64


title: A2780 Control-1


title: H1299_T18_GSK-J4_rep2

city: Dallas

first: Luc

last: Girard

address: 5323 Harry Hines Blvd

department: Hamon Center for Therapeutic Oncology Research

institute: UT Southwestern Medical Center

hyb_protocol: 1.5 ug of the amplified and labeled cRNA probes was hybridized to the chip overnight at 58 degree C, then washed, blocked and detected by streptavidin-Cy3 per manufacturer's protocol.

scan_protocol: The chips were scanned by Illumina iScan system.

data_processing: Bead-level data were processed with the MBCB algorithm (Ding et al, Nucl Acids Res, 36:e58, 2008), which is a background-correction and summarization method, then quantile-normalized and log2-transformed

label_protocol: 500 ng of total RNA was used to label the cRNA probes by Ambion Illumina TotalPrep RNA Amplification kit (Cat# IL1791)

growth_protocol: NSCLC cell lines were maintained in RPMI-1640 (Life Technologies Inc.) with 5% FBS.

extract_protocol: Total RNA was extracted using RNeasy Plus Mini kit (Qiagen). Quality control was performed with Agilent Bioanalyzer.

treatment_protocol: NSCLC lines were treated with increasing doses of paclitaxel + carboplatin combination (2:3), given in cycles of drug on/drug off treatment scheme. Each cycle consisted of 4-5 days of drug treatment and drug-free culturing for 1-2 weeks.

value: 1 µM GSK-J4, 24 h

tag: histology

value: Large Cell

value: M

tag: race

value: Caucasian

tag: smoker

value: Smoker

tag: pack-years


title: HSCs sorted from Lig4mut mouse, rep 2


title: H1299_GSK-J4_rep2


title: HSCs sorted from normal mouse, rep 1

value: wild type


title: H1299_T18_DMSO_rep2

value: DMSO control, 24 h


title: HSCs sorted from normal mouse, rep 2


title: NET39 soluble transfected, rep2

description: replicate 2


title: H1299_T18_JIB-04_rep2


title: NET47 soluble transfected, rep1

description: replicate 1


title: H1299_JIB-04_rep2


title: HSCs sorted from normal mouse, rep 3


title: 5504494022_I

description: SAMPLE 63

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

data_processing: BeadStudio software v3.2

value: Normal

value: normal adjacent lung tissue


title: NET29 soluble transfected, rep2

description: replicate 2


title: NET29 soluble transfected, rep3

description: replicate 3


title: NET39 soluble transfected, rep1

description: replicate 1


title: NET29 soluble transfected, rep1

description: replicate 1


title: 5504494022_H

description: SAMPLE 62


title: 5504494023_C

description: SAMPLE 67


title: A2C12_SP2_Replicate2

city: Hannover

first: Astrid

last: Rohrbeck

state: Niedersachsen

address: Carl-Neuberg-Straße 1

department: Department of Toxicology

institute: Medizinische Hochschule Hannover

hyb_protocol: Following fragmentation, labeled cRNA of each sample was hybridized to Affymetrix GeneChip® Mouse Genome -430 2.0 Array covering over 34.000 genes and stained according to the manufacturer's instructions.

scan_protocol: The arrays were scanned using the GeneChip® Scanner 3000.

data_processing:
Array data was normalized using scaling or per-chip normalization to adjust the total or average intensity of each array to be approximately the same. Following experimental normalization of each chip we defined intensity signals < 75 as background. Software program: Expression Console, program version:  1.1.2800.19935, algorithm: rma.
Expression values were calculated as the ratio of SP vs non-SP signals. Genes that were at least 30% up- or downregulated in all three replicates were defined as differentially expressed.

source_name: lung tumor cell line

label_protocol: Total RNA (200ng) was used to generate biotin-labeled cRNA (10 µg) by means of GeneChip® 3´IVT Express Kit (Affymetrix). Sample processing was performed exactly as described by the microarray manufacturer (Affymetrix). Quality control of cRNA was performed using a bioanalyzer (Agilent 2001 Biosizing, Agilent Technologies).

growth_protocol: The spontaneously transformed mouse lung carcinoma cell lines A2C12, cRAF_cMYC and betaD5 was isolated from lung tumors of double c-myc and c-raf transgenic mice. Cells were isolated from lung tumors of eight-months-old transgenic mice using the protocol for the isolation and culture of rodent primary respiratory cells (Hansen T, 2006). The mouse cell lines A2C12, cRAF_cMYC and betaD5 were cultured in Dulbecco's Modified Eagle's Medium (DMEM, PAA, Cölbe, Germany) supplemented with 10% fetal calf serum, 2 mM L-glutamine, 100 units/ml streptomycin, and 100 µg/ml penicillin in a humidified atmosphere containing 5% CO2 at 37 °C.

extract_protocol: RNA-extraction was performed with the RNeasy Micro Kit (RNeasy MicroKit Qiagen, Santa Clarita, CA, USA) according to the manufacturer’s instruction.  The RNA concentration of the samples was then measured with the NanoDrop ND-1000 (Kisker Produkte für die Biotechnology, Steinfurt, Germany).

tag: disease state

value: lung cancer

value: SP


title: H1299_DMSO_rep2


title: 5504494022_G

description: SAMPLE 61


title: 5504494022_D

description: SAMPLE 58


title: H1299_T18_GSK-J4_rep1


title: H1299_T18_JIB-04_rep1


title: 5504494022_F

description: SAMPLE 60


title: NLS-GFP transfected, rep2

description: replicate 2

value: soluble NLS-GFP control, nucleoplasmic


title: 5504494022_E

description: SAMPLE 59


title: NET47-GFP overexpression, rep2

description: replicate 2

value: full length NET, transmembrane


title: H1299_T18_DMSO_rep1


title: H1299_JIB-04_rep1


title: A2C12_nonSP3_Replicate3

description: The spontaneously transformed mouse lung carcinoma cell lines A2C12, cRAF_cMYC and betaD5 was isolated from lung tumors of double c-myc and c-raf transgenic mice. Cells were isolated from lung tumors of eight-months-old transgenic mice using the protocol for the isolation and culture of rodent primary respiratory cells (Hansen T, 2006).

value: nonSP


title: NET47-GFP overexpression, rep3

description: replicate 3


title: NLS-GFP transfected, rep1

description: replicate 1


title: A2C12_SP4_Replicate1


title: H1299_DMSO_rep1


title: 5504494015_L

description: SAMPLE 56

value: Female


title: 5504494022_C

description: SAMPLE 57


title: cRAF_cMYC_SP2_Replicate2


title: A2C12_SP3_Replicate3


title: NET47-GFP overexpression, rep1

description: replicate 1


title: A2C12_nonSP4_Replicate1


title: cRAF_cMYC_SP3_Replicate3


title: 5504494015_K

description: SAMPLE 55


title: 5504494015_J

description: SAMPLE 54

value: lung adenocarcinoma tissue


title: H1299_T18_Xenograft_rep2

value: H1299_T18 mouse xenograft, untreated


title: H1299_T18_Xenograft_rep3


title: cRAF_cMYC_nonSP2_Replicate2


title: NLS-GFP transfected, rep3

description: replicate 3


title: 5504494015_G

description: SAMPLE 51


title: 5504494015_H

description: SAMPLE 52


title: NET39-GFP overexpression, rep4

description: replicate 4


title: H1299_Xenograft_rep3

value: H1299 mouse xenograft, untreated


title: 5504494015_I

description: SAMPLE 53


title: cRAF_cMYC_SP_Replicate1


title: H1299_GSK-J4_rep1

value: 1 µM GSK-J4, 24 h

value: Large Cell


title: NET29-GFP overexpression, rep4

description: replicate 4


title: cRAF_cMYC_nonSP_Replicate1


title: H1299_Xenograft_rep2

value: M

value: Caucasian


title: cRAF_cMYC_nonSP3_Replicate3


title: NET39-GFP overexpression, rep2

description: replicate 2


title: H1299_Xenograft_rep1

value: Smoker


title: H1299_T18_Xenograft_rep1


title: NET39-GFP overexpression, rep3

description: replicate 3


title: NET39-GFP overexpression, rep1

description: replicate 1


title: betaD5_SP2_Replicate2


title: H1355_T16_rep3

value: 16 cycles of paclitaxel+carboplatin

value: Adenocarcinoma


title: 5504494015_F

description: SAMPLE 50


title: H1355_T16_rep2


title: NET29-GFP overexpression, rep3

description: replicate 3


title: betaD5_SP3_Replicate3


title: H1355_T16_rep1


title: 5504494015_E

description: SAMPLE 49

value: Normal

value: normal adjacent lung tissue


title: 5504494015_C

description: SAMPLE 47


title: NET29-GFP overexpression, rep2

description: replicate 2


title: betaD5_nonSP3_Replicate3

value: lung cancer


title: A2C12_nonSP2_Replicate2


title: untreated control, rep3

description: replicate 3

value: untreated


title: 5504494015_B

description: SAMPLE 46


title: H1355_rep4

value: Untreated


title: betaD5_nonSP2_Replicate2

value: nonSP


title: H1355_rep3


title: 5495321014_L

description: SAMPLE 44

value: Female


title: betaD5_SP_Replicate1

value: SP


title: H1355_rep5


title: NET29-GFP overexpression, rep1

description: replicate 1

value: full length NET, transmembrane


title: H1299_T18_rep3

value: 18 cycles of paclitaxel+carboplatin


title: untreated control, rep4

description: replicate 4


title: 5495321014_K

description: SAMPLE 43


title: untreated control, rep2

description: replicate 2


title: CS3155_gal_2

city: Kgs. Lyngby

first: Jun

last: Chen

state: Denmark

address: Søltofts Plads Building 221

department: Food

country: Denmark

institute: The Technical University of Denmark

description: control spots have eliminated

hyb_protocol: For hybridization standard Agilent's kits, reagents and equipment were used according to manufacturers' specifications. See (http://www.chem.agilent.com/Library/usermanuals/Public/G4813-90000_OneColor_Prokaryote_Protocol_1.3.pdf)

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565BA) using one color scan setting for 8x15k array slides (Scan Area 61x21.6 mm, Scan resolution 5 µm, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: Data processing was conducted using limma package on R (Smyth GK, 2005; RDC Team 2005). Backgroundcorrection: ( backgroundCorrect ( x, method = normexp, offset = 16 ) ); normalization: ( normalizeBetweenArrays (x, method = quantile) ).

organism: Lactococcus cremoris subsp. cremoris MG1363

source_name: CS3155 grows on galactose

label_protocol: Cyanine-3 (Cy3) labeled cDNA was prepared from 5 ug total RNA using the FairPlay III Microarray Labeling Kit (Agilent Technologies, Santa Clara, CA) according to the manufacturer's instructions, followed by purification procedure in the kit. Dye incorporation and cDNA yield were checked with the NanoDrop ND-1000 Spectrophotometer (Agilent Technologies, Santa Clara, CA).

growth_protocol: Growth temperature: 30°C. Growth medium: SALN medium + 0.2% glucose, maltose or galactose. SALN media was described by Chen J et al., Oxidative stress at high temperatures in Lactococcus lactis due to an insufficient supply of Riboflavin. Appl Environ Microbiol. 2013 Oct; 79(19): 6140-7.

extract_protocol: Cells mixed with 200 µl Solution I (0.3M sucrose; 0.01M NaAC, pH = 4.8) and Solution II (2% SDS; 0.01M NaAC, pH = 4.8) were disrupted by acid washed glass beads (106 microns; sigma) in 400 µl hot phenol (equilibrated with acetate; Sigma). After centrifuge at full speed for 5 mins at room temperature, supernatant was extracted with hot phenol twice and followed by a extraction with 400 µ hot phenol and chloroform (1:1). Then, RNA was precipitated and washed by ethanol. RNA was dissolved in 25 µl DEPC-treated water. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: no additional treatments

value: mutant

tag: carbon source

value: galactose


title: 5504494015_D

description: SAMPLE 48

value: lung adenocarcinoma tissue


title: H1299_T18_rep1

value: Large Cell

value: M

value: Caucasian


title: 5504494015_A

description: SAMPLE 45


title: CS3155_gal_3

description: control spots have eliminated


title: 5495321014_H

description: SAMPLE 40


title: 5495321014_I

description: SAMPLE 41


title: CS3155_gal_1

description: control spots have eliminated


title: 5495321014_J

description: SAMPLE 42


title: 5495321014_G

description: SAMPLE 39


title: H1299_rep5

value: Smoker


title: MG1363_gal_1

description: control spots have eliminated

source_name: MG1363 grows on galactose

value: wild type


title: untreated control, rep1

description: replicate 1


title: H1299_rep3


title: H1355_T13_rep2

value: 13 cycles of paclitaxel+carboplatin

value: Adenocarcinoma


title: MG1363_gal_3

description: control spots have eliminated


title: betaD5_nonSP_Replicate1

value: lung cancer

tag: cell type


title: H1299_rep4

value: Untreated


title: MG1363_gal_2

description: control spots have eliminated

tag: strain


title: 5495321014_F

description: SAMPLE 38


title: H1299_T15_rep2

value: 15 cycles of paclitaxel+carboplatin


title: H1299_T18_rep2


title: CS3155_mal_2

description: control spots have eliminated

source_name: CS3155 grows on maltose

tag: genotype/variation

value: maltose


title: 5495321014_E

description: SAMPLE 37

value: Female

value: Normal

tag: age

value: normal adjacent lung tissue


title: CS3155_mal_1

description: control spots have eliminated

value: mutant


title: 5495321014_D

description: SAMPLE 36


title: MG1363_mal_3

description: control spots have eliminated

source_name: MG1363 grows on maltose


title: CS3155_mal_3

description: control spots have eliminated


title: H1299_T15_rep1


title: 5495321014_C

description: SAMPLE 35


title: MG1363_mal_1

description: control spots have eliminated


title: 5495321014_B

description: SAMPLE 34


title: CS3155_glu_3

description: control spots have eliminated

source_name: CS3155 grows on glucose

value: glucose


title: H1355_T13_rep1


title: 5495321012_L

description: SAMPLE 32

value: lung adenocarcinoma tissue


title: 5495321014_A

description: SAMPLE 33


title: H1355_rep2


title: 5495321012_K

description: SAMPLE 31


title: H1355_T8_rep2

value: 8 cycles of paclitaxel+carboplatin


title: 5495321012_I

description: SAMPLE 29


title: CS3155_glu_2

description: control spots have eliminated


title: CS3155_glu_1

description: control spots have eliminated


title: H1299_T10_rep2

value: 10 cycles of paclitaxel+carboplatin

value: Large Cell

value: M


title: MG1363_glu_3

description: control spots have eliminated

source_name: MG1363 grows on glucose

value: wild type


title: 5495321012_H

description: SAMPLE 28


title: MG1363_glu_2

description: control spots have eliminated


title: 5495321012_G

description: SAMPLE 27


title: 5495321012_J

description: SAMPLE 30


title: H1355_T8_rep1

value: Caucasian

value: Smoker


title: HVBD29

city: Kyoto

first: Natsue

last: Uehiro

address: 54 Kawaharacho, Shogoin, Sakyo-ku

department: Department of Breast Surgery

institute: Kyoto University

description: SAMPLE 119

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

data_processing:
Genome Studio Methylation Module and NIMBL software for MATLAB
The 'Matrix processed.txt' contains peak based corrected Average Beta
The 'Matrix signal intensities.txt' contains unmethylated and methylated signal intensities

source_name: blood of a healthy individual

extract_protocol: QIAmp DNA Blood Maxi Kit (QIAGEN)

tag: sample type

value: Blood

tag: ffpe restoration

value: no


title: HVBD26

description: SAMPLE 116


title: HVBD28

description: SAMPLE 118


title: HVBD27

description: SAMPLE 117


title: H1355_T4_rep1

value: 4 cycles of paclitaxel+carboplatin

value: Adenocarcinoma

tag: gender


title: 5495321012_E

description: SAMPLE 25

value: Female

tag: disease stage

tag: tissue


title: 5495321012_D

description: SAMPLE 24


title: H1299_rep2

value: Untreated


title: H1299_T5_rep2

value: 5 cycles of paclitaxel+carboplatin


title: H1299_T5_rep1


title: H1299_T10_rep1


title: HVBD25

description: SAMPLE 115


title: MG1363_glu_1

description: control spots have eliminated


title: 5495321012_F

description: SAMPLE 26


title: HVBD21

description: SAMPLE 111


title: 5495321012_C

description: SAMPLE 23

value: Normal

value: normal adjacent lung tissue


title: HVBD23

description: SAMPLE 113


title: HVBD24

description: SAMPLE 114


title: 5495321012_B

description: SAMPLE 22

value: lung adenocarcinoma tissue


title: HVBD22

description: SAMPLE 112


title: HVBD19

description: SAMPLE 109


title: HVBD20

description: SAMPLE 110


title: 5374669024_K

description: SAMPLE 20


title: HVBD18

description: SAMPLE 108


title: H1355_rep1


title: 5374669024_H

description: SAMPLE 17


title: 5374669024_F

description: SAMPLE 15


title: 143B_rep2

city: Clayton

first: Justin

middle: C

last: St. John

state: Vic

address: 27-31 Wright St

department: Centre for Genetic Diseases

country: Australia

institute: Hudson Institute of Medical Research

description:
SAMPLE 16
replicate 2
143B2

hyb_protocol: 143B cell line was labelled, amplified and hybridized to HumanHT-12 v4 Expression BeadChip Kit, according to manufacturer's instructions

data_processing: Data was preprocessed with quantile normalization with ‘lumi’ R package (BeadArray Specific Methods for Illumina Methylation and Expression Microarrays). Raw signal intensity values were subjected to normalization procedure: including background correction, log2 transformation and variance stabilization by using the lumiR package of R Bioconductor project

source_name: 143B late tumor

growth_protocol: All 143B cell lines were routinely cultured in standard DMEM (SD-DMEM) consisting of DMEM, 10% (v/v) FBS, 10mM Sodium Pyruvate, 2mM Glutamax and 1 % (v/v) Penicillin/Streptomycin (Life Technologies). 143B0 (Rho0) cells were supplemented with uridine (Sigma-Aldrich, NSW, Australia) at a final concentration of 50 µg/ml. All cell lines were cultured at 37 °C in 5% CO2 and 95% humidity.

extract_protocol: Total RNA was extracted using RNeasy Mini Kit (Qiagen), according to manufacturer's instructions. All RNA samples were treated with DNase I (Qiagen) for 20 minutes at room temperature to remove DNA contamination

value: 143B osteosarcoma tumor

tag: tumor size

value: Late stage (800mm^3)

tag: mtdna content

value: with its own mtDNA


title: 143B_rep3

description:
SAMPLE 17
replicate 3
143B3

label_protocol: 143B cell line was labelled, amplified and hybridized to HumanHT-12 v4 Expression BeadChip Kit, according to manufacturer's instructions


title: HVBD17

description: SAMPLE 107


title: 5495321012_A

description: SAMPLE 21


title: 143B_GBM_rep2

description:
SAMPLE 14
replicate 2
GBM3

source_name: 143B GBM late tumor

value: harbors mtDNA from glioblastoma multiforme (HSR-GBM1) cells


title: 143B_rep1

description:
SAMPLE 15
replicate 1
143B1


title: 143B_GBM_rep1

description:
SAMPLE 13
replicate 1
GBM1


title: 143B_NSC_rep3

description:
SAMPLE 12
replicate 3
NSC4

source_name: 143B NSC late tumor

value: harbors mtDNA from neural stem cells


title: HVBD16

description: SAMPLE 106


title: 5374669024_I

description: SAMPLE 18


title: 5374669024_J

description: SAMPLE 19


title: 5374669024_E

description: SAMPLE 14


title: H1299_rep1

tag: treatment

tag: histology

value: Large Cell

value: M

value: Caucasian


title: HVBD15

description: SAMPLE 105

value: Blood

value: no


title: 5374669024_G

description: SAMPLE 16


title: 5374669024_D

description: SAMPLE 13


title: 143B_GBM_E_rep3

description:
SAMPLE 9
replicate 3
143B_GBM E5

source_name: 143B GBM early tumor

value: Early stage (50mm^3)


title: 143B_NSC_rep2

description:
SAMPLE 11
replicate 2
NSC3


title: MG1363_mal_2

description: control spots have eliminated

value: wild type

value: maltose


title: 5374669019_L

description: SAMPLE 12

value: Female


title: HVBD13

description: SAMPLE 103


title: HVBD12

description: SAMPLE 102


title: 5374669019_J

description: SAMPLE 10


title: 143B_GBM_E_rep1

description:
SAMPLE 7
replicate 1
143B_GBM E2


title: 143B_GBM_E_rep2

description:
SAMPLE 8
replicate 2
143B_GBM E3


title: HVBD9

description: SAMPLE 99


title: HVBD10

description: SAMPLE 100


title: HVBD14

description: SAMPLE 104


title: HVBD8

description: SAMPLE 98


title: 5374669019_K

description: SAMPLE 11

value: Normal


title: HVBD7

description: SAMPLE 97


title: 5374669019_I

description: SAMPLE 9

value: normal adjacent lung tissue


title: 5374669019_H

description: SAMPLE 8

value: lung adenocarcinoma tissue


title: 143B_NSC_E_rep1

description:
SAMPLE 4
replicate 1
143B_NSC E2

source_name: 143B NSC early tumor

value: 143B osteosarcoma tumor


title: 143B_NSC_E_rep3

description:
SAMPLE 6
replicate 3
143B_NSC E4


title: 143B_NSC_E_rep2

description:
SAMPLE 5
replicate 2
143B_NSC E3


title: HVBD11

description: SAMPLE 101


title: HVBD6

description: SAMPLE 96


title: 5374669019_G

description: SAMPLE 7


title: HVBD5

description: SAMPLE 95


title: 143B_Rho0_rep2

description:
SAMPLE 2
replicate 2
Rho 0#2

source_name: 143B Rho0 late tumor

value: Late stage (800mm^3)

value: without mtDNA


title: HVBD4

description: SAMPLE 94


title: 143B_Rho0_rep1

description:
SAMPLE 1
replicate 1
Rho 0#1


title: 5374669019_E

description: SAMPLE 5


title: HVBD3

description: SAMPLE 93


title: 143B_Rho0_rep3

description:
SAMPLE 3
replicate 3
Rho 0#4


title: FFPE54

description: SAMPLE 90

source_name: breast cancer tissue

extract_protocol: NucleoSpin FFPE DNA Kit (Macherey Nagel)

value: formalin-fixed paraffin-embedded breast cancer tissue

value: yes


title: 5374669019_F

description: SAMPLE 6


title: FFPE53

description: SAMPLE 88


title: 5374669019_C

description: SAMPLE 3


title: FFPE52

description: SAMPLE 87


title: Me13 + AZD6244 0.1 uM + AZD8055 0.3 uM 8h_rep3

city: Milan

first: Loris

last: De Cecco

address: via Venezian 1

institute: IRCSS Istituto Nazionale Tumori

hyb_protocol: Standard Illumina hybridization protocol

data_processing: The data were processed and normalised using quantile normalisation with BeadStudio software

source_name: melanoma

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

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

tag: cell line

value: melanoma

tag: drug concentration

tag: time exposure


title: Me13 + AZD6244 0.1 uM + AZD8055 0.3 uM 8h_rep2


title: Papilloma

description: SAMPLE 89

source_name: benign breast tumor tissue

value: formalin-fixed paraffin-embedded papilloma tissue of the breast


title: 5374669019_D

city: Taipei

description: SAMPLE 4


title: Me13 + PLX4720 0.5 uM + BEZ235 0.1 uM 8h_rep3


title: H1355_T4_rep2

value: 4 cycles of paclitaxel+carboplatin

value: Adenocarcinoma

value: M

tag: race

value: Caucasian

tag: smoker

value: Smoker

tag: pack-years


title: 5374669019_B

description: SAMPLE 2


title: 5374669019_A

description: SAMPLE 1


title: FFPE51

description: SAMPLE 86


title: Me13 + PLX4720 0.5 uM + BEZ235 0.1 uM 8h_rep1

tag: cell type


title: HVBD1

description: SAMPLE 91

value: Blood

value: no


title: FFPE50

description: SAMPLE 85


title: FFPE49

description: SAMPLE 84


title: HVBD2

description: SAMPLE 92


title: Me13 + AZD6244 0.1 uM + AZD8055 0.3 uM 8h_rep1


title: FFPE48

description: SAMPLE 83


title: Me13 + AZD6244 0.1 uM + BEZ235 0.1 uM 8h_rep3


title: FFPE47

description: SAMPLE 82


title: FFPE45

description: SAMPLE 80


title: Me13 + PLX4720 0.5 uM + BEZ235 0.1 uM 8h_rep2


title: FFPE46

description: SAMPLE 81


title: Me13 + PLX4720 0.5 uM 8h_rep2


title: Me13 + AZD6244 0.1 uM + BEZ235 0.1 uM 8h_rep1


title: Me13 + PLX4720 0.5 uM 8h_rep3


title: Pool of adjacent normal epithelia

description: SAMPLE 79

source_name: adjacent normal breast tissue

value: pooled sample of formalin-fixed paraffin-embedded adjacent normal breast tissue


title: Me13 + AZD6244 0.1 uM + BEZ235 0.1 uM 8h_rep2


title: FFPE44

description: SAMPLE 78


title: FFPE43

description: SAMPLE 77


title: Me13 + AZD8055 0.3 uM 8h_rep3


title: FFPE41

description: SAMPLE 75


title: FFPE40

description: SAMPLE 74


title: FFPE42

description: SAMPLE 76


title: FFPE39

description: SAMPLE 73


title: FFPE38

description: SAMPLE 72


title: FFPE35

description: SAMPLE 69


title: FFPE37

description: SAMPLE 71


title: FFPE33

description: SAMPLE 67


title: FFPE32

description: SAMPLE 66


title: FFPE34

description: SAMPLE 68


title: Me13 + PLX4720 0.5 uM 8h_rep1


title: FFPE30

description: SAMPLE 64


title: Me13 + AZD6244 0.1 uM 8h_rep2


title: Me13 + BEZ235 0.1 uM 8h_rep1


title: FFPE28

description: SAMPLE 62


title: Me13 + AZD8055 0.3 uM 8h_rep2


title: Me13 + BEZ235 0.1 uM 8h_rep3


title: FFPE27

description: SAMPLE 61


title: Me13 + BEZ235 0.1 uM 8h_rep2


title: Me13 8h_rep3

value: Untreated


title: Me13 + AZD8055 0.3 uM 8h_rep1


title: FFPE25

description: SAMPLE 59


title: FFPE26

description: SAMPLE 60


title: Me13 + AZD6244 0.1 uM 8h_rep3


title: FFPE36

description: SAMPLE 70


title: FFPE24

description: SAMPLE 58


title: Me13 + AZD6244 0.1 uM 8h_rep1


title: FFPE29

description: SAMPLE 63


title: FFPE31

description: SAMPLE 65


title: FFPE23

description: SAMPLE 57


title: Me13 8h_rep1


title: Me13 8h_rep2


title: FFPE21

description: SAMPLE 55


title: FFPE19

description: SAMPLE 53


title: FFPE17

description: SAMPLE 51


title: FFPE16

description: SAMPLE 50


title: FFPE15

description: SAMPLE 49


title: FFPE18

description: SAMPLE 52


title: FFPE22

description: SAMPLE 56


title: FFPE13

description: SAMPLE 47


title: FFPE14

description: SAMPLE 48


title: FFPE11

description: SAMPLE 45


title: FFPE12

description: SAMPLE 46


title: Tailbud Rep 1

city: Brisbane

first: Charles

middle: Cameron

last: Bell

state: Queensland

address: 37 Kent Street

institute: Mater Research

hyb_protocol: The labeled material was hydrolyzed and used for microarray hybridization with hybridization at 42ºC

scan_protocol: Hybridized microarrays were scanned on a 600B Scanner (Agilent Technologies Inc.).

data_processing: The images were analyzed using Imagene 5.6.0 (BioDiscovery) to determine mean foreground and background signal intensities for both channels. All primary data, including images, were then imported into the comprehensive microarray relational database, Bio-Array Software Environment (BASE). In the case of all direct comparisons, the raw data for each hybridization was compiled into an experiment and subjected to print tip Loess normalization using R functions from Bioconductor (Linear models for Microarray Data, LIMMA) and Statistics for Microarray Analysis (SMA).

organism: Danio rerio

source_name: STD-MO tailbud 13_01_06a

label_protocol: Total RNA from each sample was linearly amplified from 800ng of total RNA using the Amino Allyl MessageAmp amplification kit (Ambion Inc/GeneWorks), yielding a minimum of 20µg amino-allyl-labeled antisense aRNA per reaction. The quantity and size distribution of the aRNA products was assessed using the Agilent Bioanalyzer 2100. Five micrograms of each aRNA sample was fluorescently labeled by covalent coupling to either Cy5- or Cy3-NHS ester dyes (Amersham).

growth_protocol: Outbred wild type zebrafish stocks were reared and embryos obtained. Embryos were incubated at 28.5°C

extract_protocol: Zebrafish embryos were homogenized in RLT buffer (Qiagen) using a 21 gauge needle and 1ml syringe. Total RNA extracted by RNeasy column purification (QIAGEN) was assessed for quantity and integrity on the Bioanalyzer 2100 (Agilent Technologies).

treatment_protocol: 30-50 embryos were collected from clutches at three different time points: 30% epiboly, shield and tailbud stage

value: Tailbud embryos

source_name: MTX2-MO tailbud 13_01_06a


title: Tailbud Rep 2

source_name: STD-MO tailbud 13_1_06b

source_name: MTX2-MO tailbud 13_1_06b


title: 143B_NSC_rep1

description:
SAMPLE 10
replicate 1
NSC2

value: 143B osteosarcoma tumor

value: harbors mtDNA from neural stem cells


title: 30% Epiboly Rep 12

source_name: STD-MO 30% epiboly 30_05_04

value: 30% epiboly embryos

source_name: MTX2-MO 30% epiboly 30_05_04


title: Tailbud Rep 3

source_name: MTX2-MO tailbud 16_11_05

source_name: STD-MO tailbud 16_11_05


title: Shield Rep 5

source_name: MTX2-MO shield 13_11_05

value: Shield stage embryos

source_name: STD-MO shield 13_11_05


title: FFPE8

description: SAMPLE 42

value: formalin-fixed paraffin-embedded breast cancer tissue

value: yes


title: FFPE9

description: SAMPLE 43


title: Shield Rep 1

source_name: STD-MO shield 13_1_06a

source_name: MTX2-MO shield 13_1_06a


title: Shield Rep 2

source_name: STD-MO shield 13_01_06b

source_name: MTX2-MO shield 13_01_06b


title: Tailbud Rep 4

source_name: STD-MO tailbud 23_10_05

source_name: MTX2-MO tailbud 23_10_05


title: FFPE7

description: SAMPLE 41

source_name: breast cancer tissue


title: Shield Rep 3

source_name: MTX2-MO shield 16_11_05

source_name: STD-MO shield 16_11_05


title: FFPE10

description: SAMPLE 44


title: 30% Epiboly Rep 8

source_name: STD-MO 30% epiboly 19_05_04 #1


title: Shield Rep 4

source_name: STD-MO shield 23_10_05

source_name: MTX2-MO shield 23_10_05


title: FFPE6

description: SAMPLE 40


title: 30% Epiboly Rep 10

source_name: STD-MO 30% epiboly 19_05_04 #3


title: Tailbud Rep 5

source_name: MTX2-MO tailbud 13_11_05

source_name: STD-MO tailbud 13_11_05


title: 30% Epiboly Rep 6

source_name: STD-MO 30% epiboly 29_05_04 #3


title: 30% Epiboly Rep 9

source_name: STD-MO 30% epiboly 19_05_04 #2


title: FFPE4

description: SAMPLE 38


title: FFPE5

description: SAMPLE 39


title: 30% Epiboly Rep 4

source_name: MTX2-MO 30% epiboly 29_05_04

source_name: STD-MO 30% epiboly 29_05_04


title: 30% Epiboly Rep 5

source_name: STD-MO 30% epiboly 29_05_04 #2


title: 30% Epiboly Rep 11

source_name: STD-MO 30% epiboly 19_05_04 #4


title: FFPE2

description: SAMPLE 36


title: FFPE3

description: SAMPLE 37


title: 30% Epiboly Rep 7

source_name: STD-MO 30% epiboly 29_05_04 #4


title: MFP-Rep4

city: Charlestown

first: Kamila

last: Naxerova

state: MA

address: 149 13th Street

department: Center For Systems Biology

institute: Massachusetts General Hospital / Harvard Medical School

hyb_protocol: According to manufacturer's instructions (Affymetrix)

data_processing: RMA (Bioconductor's Affy package)

source_name: xenograft

extract_protocol: Tumors were snap frozen, RNA was extracted with the RNeasy Mini kit (Qiagen)

tag: microenvironment

value: Mammary fat pad


title: MFP-Rep3

scan_protocol: According to manufacturer's instructions (Affymetrix)


title: 30% Epiboly Rep 3

source_name: STD-MO 30% epiboly 13_11_05


title: FFPE1

description: SAMPLE 35

source_name: breast cancer tissue

tag: sample type


title: MFP-Rep2

label_protocol: According to manufacturer's instructions (Affymetrix)


title: Brain-Rep4

value: Brain


title: 30% Epiboly Rep 1

source_name: STD-MO 30% epiboly 16_11_05


title: HMMEC

description: SAMPLE 34

source_name: endothelial cell line

extract_protocol: PureLink Genomic DNA Mini kit (Life Technologies)

value: cultured cell line

tag: ffpe restoration


title: 30% Epiboly Rep 2

source_name: STD-MO 30% epiboly 23_10_05


title: Brain-Rep1


title: Brain-Rep3


title: HMEC

description: SAMPLE 32

source_name: mammary epithelial cell line


title: 75% epiboly stage

data_processing: The images were analyzed using Imagene 5.6.0 (BioDiscovery) to determine mean foreground and background signal intensities for both channels. All primary data, including images, were then imported into the comprehensive microarray relational database, Bio-Array Software Environment (BASE). Data were exported from BASE into GeneSpring 7.3 (Agilent Technologies) for further analysis and visualization. The data was then transformed by applying a per chip normalization to the 50th percentile, and per gene normalization to the median whereby the ratio of each gene is divided by the median of its measurement across all samples. This transformation resulted in clearer visualization of the relative expression changes for each gene across the entire time course

source_name: 75% epiboly stage embryos DVTC4

growth_protocol: Outbred wild type zebrafish stocks were reared and embryos obtained. Embryos were incubated at 28.5°C.

treatment_protocol: 30-50 uninjected embryos were collected from a single clutch of eggs at 9 time points: 64-cell, high, sphere, 30% and 50% epiboly, shield, 75% and 90% epiboly and tailbud staged.

value: 75% epiboly stage embryos

source_name: REFERENCE

value: Reference RNA pool was generated by combining equal amounts of total RNA from each of the nine representative time points


title: Tailbud stage

source_name: Tailbud stage embryos DVTC4

value: Tailbud stage embryos


title: Brain-Rep2


title: 90% epiboly stage

source_name: 90% epiboly stage embryos DVTC4

value: 90% epiboly stage embryos


title: DU4475

description: SAMPLE 31

source_name: breast cancer cell line

value: no


title: MFP-Rep1


title: Shield stage

source_name: Shield stage embryos DVTC4


title: A549-Day0

city: Berlin

first: Lars

last: Bullinger

address: Augustenburger Platz 1

institute: Charité

hyb_protocol: Hybridization, washing, and staining protocols, respectively, were performed on Affymetrix GeneChip instruments (Hybridization Oven 640, Fluidics Station FS450) as recommended by the manufacturer.

scan_protocol: Scanning was performed on Affymetrix GeneChip Scanner GCS3000 instruments as recommended by the manufacturer using default settings. The software used was GCOS 1.2 or higher.

data_processing: The data were analyzed with BRB ArrayTools using RMA. Intensity values were log2 transformed

source_name: cell line

label_protocol: For each sample preparation, total RNA was converted into double-stranded cDNA by reverse transcription using the 3' IVT Express Kit from Affymetrix according to the manufacturer's recommendations.

growth_protocol: All cell lines were maintained under standard conditions. Cell line identity and purity were verified using the Multiplex Cell Authentication and Contamination Tests (Multiplexion).

extract_protocol: The total RNA was purified with a TRIzol-based protocol.

tag: phenotype

value: sensitive


title: HUVEC

description: SAMPLE 33


title: JIMT-1

description: SAMPLE 30


title: SW480-R clone1

description: SW480-R clone1

value: resistant


title: SW480-Day0


title: SW480-R clone2

description: SW480-R clone2


title: Sphere stage

source_name: Sphere stage embryos DVTC4

value: Sphere stage embryos


title: ZR75-1

description: SAMPLE 27


title: MDA-MB-453

description: SAMPLE 29


title: A549-R clone2

description: A549-R clone2


title: MRK-nu-1

description: SAMPLE 28


title: 64 cell stage

source_name: 64 cell stage embryos DVTC4

value: 64 cell stage embryos


title: T47D

description: SAMPLE 26


title: MCF7

description: SAMPLE 25


title: 30% epiboly stage

source_name: 30% epiboly stage embryos DVTC4

value: 30% epiboly stage embryos


title: SKBR3

description: SAMPLE 24


title: A549-R clone5

description: A549-R clone5


title: BT474

description: SAMPLE 23


title: High stage

source_name: High stage embryos DVTC4

value: High stage embryos


title: HCC2218

description: SAMPLE 22


title: Printex90 2 days 17

city: Ottawa

first: Mainul

last: Husain

address: 50 Colombine Driveway

institute: Health Canada

description: Biological replicate Day 2, Treated

scan_protocol: Scanned on an Agilent G2565AA scanner.

data_processing: Images were quantified using Agilent Feature Extraction Software (version A.8.5.1.1). Non background subtracted median signal intensities were LOWESS normalized using the maanova library in R. Probes with technical replicates were averaged using the median.

source_name: Lung

label_protocol: Complementary DNA (cDNA) and cyanine labelled complementary RNA (cRNA) were synthesized from 200 ng of total RNA from individual mice from each of the CBNP exposed experimental (N = 5) and control groups (N = 5), and universal reference total RNA (Agilent Technologies, Inc., Mississauga, ON, Canada), using Low Input Quick Amp Labeling Kit (Agilent Technologies Inc., Mississauga, ON, Canada) according to the manufacturer’s instruction. Cyanine-labelled cRNAs were synthesized using T7 RNA polymerase in vitro transcription kits (Agilent Technologies Inc., Mississauga, ON, Canada) and later purified using RNeasy Mini Kits (Qiagen, Mississauga, ON, Canada); experimental and control cRNAs were labelled with Cyanine 5-CTP, and reference RNAs were labelled with Cyanine 3-CTP. Each experimental or control Cy-5 labelled cRNA sample (300 ng) was mixed with equimolar amounts of Cy-3 labelled reference cRNA and hybridized to Agilent SurePrint G3 Mouse GE 8x60K oligonucleotide microarrays (Agilent Technologies Inc., Mississauga, ON, Canada) for 17 h in a hybridization chamber at 65°C with a rotation speed of 10 rpm. Microarray slides were washed twice according to the manufacturer’s instructions (1X with wash buffer 1 and 1X with wash buffer 2; Agilent Technologies Inc., Mississauga, ON, Canada), and were scanned on an Agilent G2505C scanner at 3 µm resolution. Data from the scanned images were extracted using Agilent Feature Extraction software version 11.0.1.1.

growth_protocol: Six-to-seven week old female C57BL/6BomTac mice were purchased from Taconic (Ry, Denmark) and were allowed 1-2 weeks to acclimate. A total of 112 mice were divided into 8 experimental (N = 8 per group) and 8 control groups (N = 6 per group), and were maintained in polypropylene cages with sawdust bedding and enrichment, at 20-22°C temperature and relative humidity of 40-60% with a 12 h light-to-dark cycle. All mice received food and water ad libitum during the period of the whole experiment. All animal experiments were approved by the Danish “Animal Experiments Inspectorate” and performed according to their guidelines for ethical conduct and care for animals in research (The Danish Ministry of Justice, Animal Experiments Inspectorate, permission 2010/561-1779).

extract_protocol: Total RNA was isolated from random sections of lung tissues from 80 mice in total (n = 5 per exposed and control group) using TRIzol (Invitrogen, Carlsbad, CA, USA) and purified using RNeasy Plus Mini Kit (Qiagen, Mississauga, ON, Canada) according to the manufacturer’s instructions. Total RNA concentration was measured using NanoDrop 2000 spectrophotometer (Thermo Fisher Scientific Inc., Wilmington, DE, USA) and RNA quality and integrity were assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies, Inc., Mississauga, ON, Canada) according to the manufacturer’s instruction. All RNA samples showed A260/280 ratios between 2.0 and 2.15, and RNA integrity numbers (RIN) of 7 and above, and were used to conduct microarray and real-time RT-qPCR experiments. Total RNA samples were stored at -80°C until analysed.

treatment_protocol: Briefly, printex 90 was suspended in 0.2 µm filtered, ɤ-irradiated Nanopure Diamond UV water (Pyrogens: ˂0,001 EU/ml, total organic carbon: ˂3.0 ppb), for 16 min without pause, using a Branson Sonifier S-450D (Branson Ultrasonics Corp., Danbury, CT, USA), and was subjected to sonication using a Branson Sonifier S-450D (Branson Ultrasonics Corp., Danbury, CT, USA) equipped with a disruptor horn (model number 101-147-037(Jackson et al., 2011a)). Total sonication time was 16 min without pause; samples were kept cool on ice during the sonication procedure. Vehicle control solutions contained only Nanopure Diamond UV water was also sonicated as described above. A total of 112 C57BL/6 mice were divided into 8 experimental (N = 8 per group) and 8 control (N = 6 per group) groups. Prior to intratracheal instillation, mice were anesthetized with 4% Isofluoran. Mice from the experimental groups received a single dose of 0.162 mg/50 µl (162 µg per mouse) of CBNP suspension following by 200 µl air by intratracheal instillation. Mice from matching control groups received the same volume of control vehicle. Mice were anesthetized with subcutaneous injection of Hypnorm® (fentanyl citrate 0.315 mg/ml and fluanisone 10 mg/ml from Janssen Pharma) and Dormicum® (Midazolam 5 mg/mL from Roche) at 3 hrs, 1, 2, 3, 4, 5, 14 and 42 d following CBNP or control vehicle exposure. Blood was collected by cardiac puncture and was stabilized in 36 µl of 0.17M potassium-EDTA and kept on ice until plasma was isolated by centrifugation at 2500 x g for 10 min at 4°C. Lungs were flushed twice with 0.8ml sterile 0.9% NaCl through the trachea to obtain BAL fluid. BAL fluids were stored on ice until centrifugation at 400 x g for 10 min at 4°C. The BAL cells were re-suspended in 100 µl medium (HAM F-12 with 1% penicillin/streptomycin and 10% fetal bovine serum). Acellular BAL fluid was recovered and stored at -80°C. The total number of living and dead cells in BAL was determined by NucleoCounter NC-200TM (Chemometec, Denmark) from diluted cell suspension following manufacturer’s protocol, the total cell counts were calculated for each mouse. Lung and liver were collected immediately, were snap frozen in liquid nitrogen and stored at -80°C until analyzed.

value: lung

tag: strain

value: C57BL/6BomTac Mouse

tag: sampleID

tag: time point

value: 2 days

tag: dose

source_name: Agilent Universal Mouse Reference RNA (UMRR)

value: Reference

value: 11 mouse cell lines


title: 53-05PB407

city: Ulm

first: Stephan

middle: Rainer

last: Bohl

address: Alber Einstein Allee 23

department: Internal Medicine III

institute: University Hospital of Ulm

source_name: mononuclear cells from peripheral blood

treatment_protocol: Primary AML samples were taken at the time of diagnosis prior to treatment with DAC. For the analysis patients were then grouped based on the response to DAC which was given later during the course of the disease. In this study, DAC was given three times daily on 3 consecutive days (total dose 135mg/m², repeated every 6 weeks).

tag: age

tag: gender

value: male

tag: genetic risk group

tag: dnmt3a status

value: MUT

tag: npm1 status

value: WT

tag: response to dac

value: no response


title: Neg. Control (H2O) 3 days 72

description: Biological replicate Day 3, Control

hyb_protocol: Each experimental or control Cy-5 labelled cRNA sample (300 ng) was mixed with equimolar amounts of Cy-3 labelled reference cRNA and hybridized to Agilent SurePrint G3 Mouse GE 8x60K oligonucleotide microarrays (Agilent Technologies Inc., Mississauga, ON, Canada) for 17 h in a hybridization chamber at 65°C with a rotation speed of 10 rpm. Microarray slides were washed twice according to the manufacturer’s instructions (1X with wash buffer 1 and 1X with wash buffer 2; Agilent Technologies Inc., Mississauga, ON, Canada), and were scanned on an Agilent G2505C scanner at 3 µm resolution. Data from the scanned images were extracted using Agilent Feature Extraction software version 11.0.1.1.

tag: tissue

tag: treatment

value: Neg. Control (H2O)

value: 3 days


title: HMC1-8

description: SAMPLE 21

value: cultured cell line

value: no


title: 52-07KM0159

source_name: mononuclear cells from bone marrow

value: female

value: intermediate

value: yes response


title: 50-07PB0850


title: Neg. Control (H2O) 3hours 49

description: Biological replicate 3 hours, Control

tag: cell type


title: Printex90 5 days 44

description: Biological replicate Day 5, Treated

value: 5 days


title: 51-05PB870


title: Printex90 3 days 30

description: Biological replicate Day 3, Treated

value: lung


title: A549-Parental

tag: cell line

value: sensitive


title: FFPE20

description: SAMPLE 54

source_name: breast cancer tissue

tag: sample type

value: formalin-fixed paraffin-embedded breast cancer tissue

value: yes


title: HCC1954

description: SAMPLE 20

tag: ffpe restoration


title: 9-05KM4110-2


title: HCC1395

description: SAMPLE 19


title: Printex90 3hours 6

description: Biological replicate 3 Hours, Treated

value: C57BL/6BomTac Mouse

value: Reference

value: 11 mouse cell lines


title: Neg. Control (H2O) 2 days 63

description: Biological replicate Day 2, Control

value: 2 days


title: SW480-Parental

tag: phenotype


title: 50% epiboly stage

source_name: 50% epiboly stage embryos DVTC4

value: 50% epiboly stage embryos

value: Reference RNA pool was generated by combining equal amounts of total RNA from each of the nine representative time points


title: 48-07PB0955

value: MUT

value: WT

value: no response


title: 49-06KM5392

value: male


title: BT549

description: SAMPLE 17

value: cultured cell line

value: no


title: 46-06PB5461

value: intermediate


title: Printex90 4 days 38

description: Biological replicate Day 4, Treated

value: lung

tag: strain

value: 4 days


title: Neg. Control (H2O) 5 days 80

description: Biological replicate Day 5, Control

value: Neg. Control (H2O)

tag: sampleID

value: 5 days


title: 44-06PB3295

value: high

value: yes response


title: MCF10A

description: SAMPLE 18


title: Hs578T-array A6

description: SAMPLE 14


title: MDA-MB-231-array C6

description: SAMPLE 13


title: Hs578T-array E2

description: SAMPLE 15


title: Printex90 14 days 116

description: Biological replicate Day 14, Treated

value: C57BL/6BomTac Mouse

tag: time point

value: 14 days

value: Reference

value: 11 mouse cell lines


title: MDA-MB-231-array A3

description: SAMPLE 12


title: BT20

description: SAMPLE 11


title: MDA-MB-436

description: SAMPLE 16


title: HCC1187

description: SAMPLE 10


title: Neg. Control (H2O) 4 days 78

description: Biological replicate Day 4, Control

tag: dose


title: HCC70

description: SAMPLE 9


title: 45-06PB4872

tag: age


title: 42-06KM7407

tag: gender

value: female


title: 41-06KM7242-02

tag: genetic risk group

value: WT

value: MUT


title: 33-07PB6409-02

tag: dnmt3a status


title: 36-06PB1262-02

value: male

tag: npm1 status


title: 39-06KM5405-02

tag: response to dac

value: no response


title: MDA-MB-468-array C2

description: SAMPLE 7

value: cultured cell line

value: no


title: HCC1806

description: SAMPLE 8


title: 35-06KM2327-02

value: intermediate


title: MDA-MB-468-array B6

description: SAMPLE 6


title: 32-07PB5807-02


title: HCC2157

description: SAMPLE 5


title: Neg. Control (H2O) 1 day 58

description: Biological replicate Day 1, Control

tag: tissue

value: lung

value: 1 day


title: HCC1937

description: SAMPLE 4


title: HCC1599

description: SAMPLE 3


title: Neg. Control (H2O) 14 days 134

description: Biological replicate Day 14, Control

tag: treatment

value: Neg. Control (H2O)


title: Neg. Control (H2O) 1 day 56

description: Biological replicate Day 1, Control

tag: cell type


title: 43-06PB1902


title: 34-05PB1394-02

value: high


title: 26-07KM4026


title: Neg. Control (H2O) 14 days 132

description: Biological replicate Day 14, Control


title: Neg. Control (H2O) 42 days 138

description: Biological replicate Day 42, Control

value: 42 days


title: 31-07PB4984-02


title: HCC1143

description: SAMPLE 2


title: HCC38

description: SAMPLE 1


title: 27-07KM5863

value: yes response


title: Printex90 1 day 13

description: Biological replicate Day 1, Treated

value: C57BL/6BomTac Mouse


title: Printex90 3hours 8

description: Biological replicate 3 Hours, Treated

value: Reference


title: 24-07KM2584


title: Printex90 5 days 41

description: Biological replicate Day 5, Treated

value: 5 days

value: 11 mouse cell lines


title: 22-07PB2989

value: WT


title: Neg. Control (H2O) 4 days 74

description: Biological replicate Day 4, Control

value: 4 days


title: 21-05KM2202

value: female


title: Printex90 1 day 16

description: Biological replicate Day 1, Treated


title: 25-07KM3939

value: male


title: Printex90 42 days 127

description: Biological replicate Day 42, Treated


title: Neg. Control (H2O) 3 days 71

description: Biological replicate Day 3, Control

value: 3 days


title: Neg. Control (H2O) 5 days 79

description: Biological replicate Day 5, Control


title: Printex90 3 days 28

description: Biological replicate Day 3, Treated


title: Printex90 2 days 22

description: Biological replicate Day 2, Treated

value: 2 days


title: 19-05PB966


title: Printex90 14 days 113

description: Biological replicate Day 14, Treated

value: 14 days


title: 20-06KM0007

value: intermediate


title: Neg. Control (H2O) 3hours 52

description: Biological replicate 3 hours, Control

value: lung


title: 18-05PB4991

value: MUT

value: no response


title: 16-05PB2678


title: Neg. Control (H2O) 42 days 136

description: Biological replicate Day 42, Control

value: Neg. Control (H2O)

value: 42 days


title: Neg. Control (H2O) 2 days 64

description: Biological replicate Day 2, Control

value: C57BL/6BomTac Mouse


title: 17-05PB4406


title: Neg. Control (H2O) 3 days 70

description: Biological replicate Day 3, Control

value: Reference


title: Printex90 4 days 40

description: Biological replicate Day 4, Treated


title: Printex90 5 days 48

description: Biological replicate Day 5, Treated

value: 5 days


title: Printex90 42 days 128

description: Biological replicate Day 42, Treated

value: 11 mouse cell lines


title: Neg. Control (H2O) 1 day 55

description: Biological replicate Day 1, Control

value: 1 day


title: 14-05PB1842

value: high

value: WT


title: Neg. Control (H2O) 5 days 81

description: Biological replicate Day 5, Control


title: Printex90 1 day 10

description: Biological replicate Day 1, Treated


title: Neg. Control (H2O) 42 days 139

description: Biological replicate Day 42, Control


title: 15-05PB2290

value: female

value: yes response


title: 10-05KM4989

value: male


title: 11-05KM5249


title: 13-05KM784


title: Printex90 3 days 27

description: Biological replicate Day 3, Treated

value: 3 days


title: Printex90 42 days 124

description: Biological replicate Day 42, Treated


title: 06-05KM3432


title: Printex90 14 days 119

description: Biological replicate Day 14, Treated

value: 14 days


title: Neg. Control (H2O) 2 days 65

description: Biological replicate Day 2, Control

value: lung

value: 2 days


title: 05-05KM3241

value: no response


title: 07-05KM369

value: intermediate

value: MUT


title: KD607

city: Kaohsiung

first: Kuang-Den

address: 123, Ta-Pei Rd., Niao-Sung Dist.

department: Translational Research Center in Biomedical Sicences

institute: Kaohsiung Chang Gung Memorial Hospital

description: Kawasaki disease sample from KD607

data_processing: GenomeStudio methylation module v.1.9.0

source_name: Genomic DNA from KD607

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

value: PBMC

tag: Sex

tag: disease

value: Kawasaki disease

tag: cal


title: Neg. Control (H2O) 14 days 129

description: Biological replicate Day 14, Control

value: C57BL/6BomTac Mouse

value: Neg. Control (H2O)

tag: sample type

value: Reference


title: KD661

description: Kawasaki disease sample from KD661

source_name: Genomic DNA from KD661


title: KD622

description: Kawasaki disease sample from KD622

source_name: Genomic DNA from KD622


title: Neg. Control (H2O) 4 days 77

description: Biological replicate Day 4, Control

tag: strain

value: 4 days

value: 11 mouse cell lines


title: 08-05KM4036

value: WT


title: KD628

description: Kawasaki disease sample from KD628

source_name: Genomic DNA from KD628


title: KD600

description: Kawasaki disease sample from KD600

source_name: Genomic DNA from KD600


title: KD630

description: Kawasaki disease sample from KD630

source_name: Genomic DNA from KD630


title: KD580

description: Kawasaki disease sample from KD580

source_name: Genomic DNA from KD580


title: Printex90 42 days 125

description: Biological replicate Day 42, Treated

tag: sampleID

value: 42 days


title: 01-05KM1921

value: male

value: high


title: 04-05KM2989

value: female

value: yes response


title: 02-07KM1602


title: KD574

description: Kawasaki disease sample from KD574

source_name: Genomic DNA from KD574


title: 03-05KM2650


title: KD603

description: Kawasaki disease sample from KD603

source_name: Genomic DNA from KD603


title: Printex90 4 days 34

description: Biological replicate Day 4, Treated

value: lung

tag: time point


title: KD548

description: Kawasaki disease sample from KD548

source_name: Genomic DNA from KD548


title: Neg. Control (H2O) 2 days 61

description: Biological replicate Day 2, Control

value: 2 days

tag: dose


title: Neg. Control (H2O) 14 days 133

description: Biological replicate Day 14, Control

value: 14 days


title: KD551

description: Kawasaki disease sample from KD551

source_name: Genomic DNA from KD551

tag: age


title: Printex90 3hours 3

description: Biological replicate 3 Hours, Treated

source_name: Lung


title: KD536

description: Kawasaki disease sample from KD536

source_name: Genomic DNA from KD536


title: Neg. Control (H2O) 3 days 68

description: Biological replicate Day 3, Control

value: 3 days

source_name: Agilent Universal Mouse Reference RNA (UMRR)


title: Printex90 2 days 21

description: Biological replicate Day 2, Treated


title: Printex90 4 days 36

description: Biological replicate Day 4, Treated


title: Neg. Control (H2O) 3hours 53

description: Biological replicate 3 hours, Control