title: Primary ATII cells_vehicle_24h_rep.4


title: Huh751_NTCP_C3

status: Public on Oct 25 2016

type: RNA

city: Dallas

first: Yujin

last: Hoshida

state: TX

address: 5323 Harry Hines Blvd

country: USA

institute: University of Texas Southwestern Medical Center

hyb_protocol: Refer to the Illumina BeadArray Assay System Manual.

data_processing: For each probe, replicated measurements (beads) were averaged after removing outliers by GenomeStudio software v.3 (Illumina). Data were then normalized using cubic spline algorithm implemented in GenePattern Illumina normalizer module (www.broadinstitute.org/genepattern) after setting a floor value of 1.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Huh7.5.1-NTCP cells treated with control (scrambled) peptide

growth_protocol: Huh7.5.1 cells were seeded in 6-well plates at 50% confluency one day prior to transduction with human NTCP-expressing vesicular stomatitis virus pseudoparticles (VSVpp) (GeneCopoeia). After three days, the cells were expanded and selected for NTCP expression with 1.8 µg/mL puromycin (Huh7.5.1-NTCP).

extract_protocol: RNA was isolated using RNeasy kit (Qiagen) according to manufacturer's protocol.

treatment_protocol: Huh7.5.1-NTCP cells were treated with either control (scrambled) or HBV preS1 peptide (200 nM) for 48 h.

tag: cell line

tag: cell type

value: Huh7.5.1 cells expressing NTCP

tag: treatment

value: control (scrambled) peptide


title: Huh751_NTCP_C1

scan_protocol: Refer to the Illumina BeadArray Assay System Manual.


title: primary lung fibroblasts_BAPN_24h_rep.4

city: Bad Nauheim

first: Rory

last: Morty

address: Parkstr. 1

department: W.G. Kerckhoff-Institut

country: Germany

institute: MPI für Herz- und Lungenforschung

description: Gene expression after 24 hours BAPN treatment

hyb_protocol: 0.6 ug of Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent-028005 SurePrint G3 Mouse GE 8x60K Microarray (GPL10787) for 18 hours at 65°C in a rotating hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 028005_D_F_20121126 for RS-284 samples or Grid: : 028005_D_F_ 20120201 for RS-266 samples ) to obtain background subtracted and spatially detrended Processed Signal intensities. Features which were not positive and significant, not above background or were population outliers were flagged as “Compromised”. If features were flagged “Compromised” in all samples of either one of the experiments RS-266 or RS-284, than they were excluded.

organism: Mus musculus

source_name: primary lung fibroblasts

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1 ug RNA using the One-Color Low Input Quick-Amp Labeling kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Following the isolation protocol of Corti et al. 1996, ATII cells were isolated and cultured in an air-liquid interface six well plate and kept in the incubator for 3 days until a monolayer of cells was formed. Afterwards, either vehicle (1x PBS) or 1mM β-aminopropionitrile (BAPN) was added to the cells for duration of 24 h. Total RNA from the cells was isolated using a peqlab total RNA extraction kit.

treatment_protocol: Following the isolation protocol, primary murine lung fibroblasts were cultured and passaged at least 3 times before the experiment. Following seeding in 6-well plate, cells were starved for 24h prior to treatment. Afterwards, either vehicle (1x PBS) or 1mM β-aminopropionitrile (BAPN) was added to the cells for duration of 24 h.

tag: tissue

value: primary lung fibroblasts

value: 1mM BAPN


title: Huh751_NTCP_P1

source_name: Huh7.5.1-NTCP cells treated with HBV preS1 peptide

label_protocol: Refer to the Illumina BeadArray Assay System Manual.

value: HBV preS1 peptide


title: Huh751_NTCP_C2


title: primary lung fibroblasts_BAPN_24h_rep.2


title: 3969

type: genomic

city: Seattle

first: William

middle: M

last: Grady

state: WASHINGTON

address: 1100 Fairview N.Ave

department: Department of Clinical Research

institute: Fred Hutchinson Cancer Research Center

description: esophagus sample

hyb_protocol: per Illumina Infinium protocol

scan_protocol: per Illumina Infinium protocol

data_processing:
Filtered out probes with detection p-value > 0.05, probes on the X chromosome, and probes containing at least one SNP with low minor allele frequency (MAF=0) in the probe body. The background noise is corrected and SWAN normalization is performed by using the functions provided by the Bioconductor minfi package. Batch effects across three batch runs are corrected using the Combat algorithm from the R sva package.
MatrixSignalIntensities.csv: Unmethylated and methylated signal intensities and detection p-value

label: Cy5 and Cy3

molecule: genomic DNA

source_name: esophagus

label_protocol: per Illumina Infinium protocol

extract_protocol: formalin-fixed, paraffin-embedded samples were extracted using the DNAeasy blood and tissue kit (Qiagen)

tag: run

tag: histology

value: BE

tag: age

tag: gender

value: M

tag: be status


title: 3972

description: esophagus sample

value: EAC

tag: Stage

value: III

tag: smokecigarettes

value: Yes

tag: alcoholicrinksperweek

value: 6 to 10 drinks a week


title: primary lung fibroblasts_vehicle_24h_rep.1

description: Gene expression after 24 hours vehicle treatment

value: vehicle


title: set_2 MV-4-11 500 nM OF1 Treatment Replicate 3

city: Oxford

first: Panagis

last: Filippakopoulos

state: Oxfordshire

address: ORCRB - Roosevelt Drive

department: Nuffield Department of Medicine

country: United Kingdom

institute: Oxford University

description:
SAMPLE 42
MV4;11 500 nM OF1 Treatment Replicate 3

hyb_protocol: Standard Illumina hybridization protocol on Illumina HumanHT-12 v4 beadchips

scan_protocol: Standard Illumina scanning protocol on an Illumina iScan Scanner. The Illumina GenomeStudio (v.1.9.0, Illumina Inc.) was used to generate bead files

data_processing: GenomeStudio data were processed in R (v.3.2) (Ihaka and Gentleman, 1996) using Bioconductor (v.3.1) (Gentleman et al., 2004) and the lumi package (v.2.20.2) (Du et al., 2008). Quality controls were carried out using the arrayQualityMetrics package (v.3.24.0) (Kauffmann et al., 2009) taking into account array intensity distributions, distance between arrays and variance mean-dependence. Principal component analysis was used to decide which arrays to process together. Background correction followed by variance stabilizing transform (Lin et al., 2008) and quantile between microarrays normalization were carried out with the lumi package. From the 47231 probe sets available on the HumanHT12 V4 chip, removal of un-expressed probes resulted in 24019 probesets. A linear model was applied employing the limma package (v.3.24.13) (Ritchie et al., 2015) followed by empirical Bayesian analysis to determine differential expression between not-treated and treated samples. Genes were considered differentially expressed if the adjusted P-value, calculated using the Benjamini–Hochberg method (Benjamini and Hochberg, 1995) in order to minimize false discovery rate, was less than 0.05 and the mean level of expression was greater than 1.5-fold.

source_name: MV-4-11 Cells

label_protocol: mRNA samples were processed using the Illumina TotalPrep-96 RNA Amplification Kit followed by the Illumina Whole-Genome Gene Expression Direct Hybridisation Assay

growth_protocol: Human cell lines (K562 and MV-4-11) were obtained from ATCC and the Leibnitz Institute DSMZ-German Collection of Microorganisms and cell cultures (www.dsmz.de). Cell lines were cultured in RPMI-1640 medium (Cat.#61870-044, Gibco) containing 10% fetal calf serum (Cat.#2-01F10-I, BioConcept), 100 U/ml penicillin and 100 U/ml streptomycin (Cat.#15140-122, Gibco). Cells were grown at 37 °C in a humidified cabinet at 5 % CO2 (Heraeus Function Line).

extract_protocol: Total RNA was isolated using a standard TRIzol (Invitrogen) protocol and prepared using RNeasy columns (Cat.#74106 plus; Qiagen). RNA was quantified using a Nanodrop spectrophotometer (model ND1000; Thermo Fisher) and integrity assessed on a BioAnalyzer (2100; Agilent Laboratories, USA). All samples had a RNA Integrity Number (RIN) ≥ 9.

treatment_protocol: Cells were seeded the day prior to treatment at 2x105 per ml. Treatments were performed so that a final concentration of 0.1 % DMSO (Cat.#D1435; Sigma) was achieved and cells were incubated with DMSO or 500 nM (final concentration) of test compound (BSP, JQ1, LP99, GSK2801, iCBP112 or OF1) for 6 h prior to isolation of RNA.


title: 3968

description: esophagus sample

value: HGD


title: 3970

description: esophagus sample


title: primary lung fibroblasts_vehicle_24h_rep.4


title: set_2 MV-4-11 500 nM GSK2801 Treatment Replicate 3

description:
SAMPLE 36
MV4;11 500 nM GSK2801 Treatment Replicate 3
sample failed quality control; no processed data


title: set_2 MV-4-11 500 nM iCBP112 Treatment Replicate 3

description:
SAMPLE 39
MV4;11 500 nM iCBP112 Treatment Replicate 3


title: 3971

description: esophagus sample


title: set_2 MV-4-11 500 nM OF1 Treatment Replicate 1

description:
SAMPLE 40
MV4;11 500 nM OF1 Treatment Replicate 1


title: set_2 MV-4-11 500 nM iCBP112 Treatment Replicate 2

description:
SAMPLE 38
MV4;11 500 nM iCBP112 Treatment Replicate 2


title: set_2 MV-4-11 500 nM iCBP112 Treatment Replicate 1

description:
SAMPLE 37
MV4;11 500 nM iCBP112 Treatment Replicate 1


title: 3967

description: esophagus sample

value: Fundus


title: primary lung fibroblasts_vehicle_24h_rep.2


title: 3964

description: esophagus sample


title: primary lung fibroblasts_vehicle_24h_rep.3


title: set_2 MV-4-11 500 nM GSK2801 Treatment Replicate 2

description:
SAMPLE 35
MV4;11 500 nM GSK2801 Treatment Replicate 2


title: set_2 MV-4-11 500 nM LP99 Treatment Replicate 1

description:
SAMPLE 31
MV4;11 500 nM LP99 Treatment Replicate 1


title: set_2 MV-4-11 500 nM LP99 Treatment Replicate 2

description:
SAMPLE 32
MV4;11 500 nM LP99 Treatment Replicate 2


title: set_2 MV-4-11 500 nM GSK2801 Treatment Replicate 1

description:
SAMPLE 34
MV4;11 500 nM GSK2801 Treatment Replicate 1


title: 3963

description: esophagus sample


title: set_2 MV-4-11 500 nM LP99 Treatment Replicate 3

description:
SAMPLE 33
MV4;11 500 nM LP99 Treatment Replicate 3


title: set_2 MV-4-11 500 nM JQ1 Treatment Replicate 2

description:
SAMPLE 29
MV4;11 500 nM JQ1 Treatment Replicate 2


title: set_2 MV-4-11 500 nM OF1 Treatment Replicate 2

description:
SAMPLE 41
MV4;11 500 nM OF1 Treatment Replicate 2


title: 4032

description: esophagus sample

value: F

tag: bmi

value: No


title: set_2 MV-4-11 500 nM BSP Treatment Replicate 2

description:
SAMPLE 26
MV4;11 500 nM BSP Treatment Replicate 2

value: BSP


title: 3965

description: esophagus sample


title: set_2 MV-4-11 500 nM BSP Treatment Replicate 3

description:
SAMPLE 27
MV4;11 500 nM BSP Treatment Replicate 3


title: set_2 MV-4-11 DMSO Replicate 3

description:
SAMPLE 24
MV4;11 DMSO Replicate 3

value: DMSO


title: set_2 MV-4-11 500 nM BSP Treatment Replicate 1

description:
SAMPLE 25
MV4;11 500 nM BSP Treatment Replicate 1


title: 3962

description: esophagus sample

value: Cardia


title: 3951

description: esophagus sample

value: LGD


title: 3943

description: esophagus sample

value: I


title: 3950

description: esophagus sample


title: 3961

description: esophagus sample

value: SQ


title: set_2 K562 500 nM OF1 Treatment Replicate 2

description:
SAMPLE 20
K562 500 nM OF1 Treatment Replicate 2

source_name: K562 Cells


title: set_2 K562 500 nM OF1 Treatment Replicate 1

description:
SAMPLE 19
K562 500 nM OF1 Treatment Replicate 1


title: set_2 MV-4-11 DMSO Replicate 2

description:
SAMPLE 23
MV4;11 DMSO Replicate 2


title: set_2 MV-4-11 500 nM JQ1 Treatment Replicate 1

description:
SAMPLE 28
MV4;11 500 nM JQ1 Treatment Replicate 1


title: set_2 MV-4-11 500 nM JQ1 Treatment Replicate 3

description:
SAMPLE 30
MV4;11 500 nM JQ1 Treatment Replicate 3


title: 4029

description: esophagus sample

value: II


title: 3946

description: esophagus sample

value: M


title: set_2 K562 500 nM iCBP112 Treatment Replicate 3

description:
SAMPLE 18
K562 500 nM iCBP112 Treatment Replicate 3


title: set_2 K562 500 nM iCBP112 Treatment Replicate 2

description:
SAMPLE 17
K562 500 nM iCBP112 Treatment Replicate 2


title: 4212

description: esophagus sample

value: EAC

value: Less than one drink a week


title: 4216

description: esophagus sample

value: Yes


title: 3949

description: esophagus sample


title: 4226

description: esophagus sample


title: 4210

description: esophagus sample

value: 1 to 5 drinks a week


title: 3947

description: esophagus sample


title: 3966

description: esophagus sample


title: set_2 K562 500 nM iCBP112 Treatment Replicate 1

description:
SAMPLE 16
K562 500 nM iCBP112 Treatment Replicate 1


title: set_2 K562 500 nM GSK2801 Treatment Replicate 3

description:
SAMPLE 15
K562 500 nM GSK2801 Treatment Replicate 3


title: 3959

description: esophagus sample


title: 4221

description: esophagus sample

value: BE


title: 4240

description: esophagus sample

value: Unknown


title: 4250

description: esophagus sample

value: FBE

value: III

value: 6 to 10 drinks a week


title: 4224

description: esophagus sample


title: 4223

description: esophagus sample

value: F


title: set_2 K562 500 nM GSK2801 Treatment Replicate 2

description:
SAMPLE 14
K562 500 nM GSK2801 Treatment Replicate 2


title: set_2 K562 500 nM OF1 Treatment Replicate 3

description:
SAMPLE 21
K562 500 nM OF1 Treatment Replicate 3


title: set_2 K562 500 nM GSK2801 Treatment Replicate 1

description:
SAMPLE 13
K562 500 nM GSK2801 Treatment Replicate 1


title: set_2 K562 500 nM LP99 Treatment Replicate 3

description:
SAMPLE 12
K562 500 nM LP99 Treatment Replicate 3


title: set_2 K562 500 nM LP99 Treatment Replicate 2

description:
SAMPLE 11
K562 500 nM LP99 Treatment Replicate 2


title: set_2 K562 500 nM JQ1 Treatment Replicate 3

description:
SAMPLE 9
K562 500 nM JQ1 Treatment Replicate 3


title: set_2 K562 500 nM LP99 Treatment Replicate 1

description:
SAMPLE 10
K562 500 nM LP99 Treatment Replicate 1


title: 4211

description: esophagus sample


title: set_2 MV-4-11 DMSO Replicate 1

description:
SAMPLE 22
MV4;11 DMSO Replicate 1

value: DMSO


title: set_2 K562 500 nM JQ1 Treatment Replicate 2

description:
SAMPLE 8
K562 500 nM JQ1 Treatment Replicate 2


title: 4235

description: esophagus sample


title: set_2 K562 500 nM JQ1 Treatment Replicate 1

description:
SAMPLE 7
K562 500 nM JQ1 Treatment Replicate 1


title: set_2 K562 DMSO Replicate 3

description:
SAMPLE 3
K562 DMSO Replicate 3
sample failed quality control; no processed data


title: set_2 K562 500 nM BSP Treatment Replicate 3

description:
SAMPLE 6
K562 500 nM BSP Treatment Replicate 3

value: BSP


title: set_2 K562 500 nM BSP Treatment Replicate 2

description:
SAMPLE 5
K562 500 nM BSP Treatment Replicate 2


title: 4237

description: esophagus sample

value: HGD


title: set_2 K562 DMSO Replicate 1

description:
SAMPLE 1
K562 DMSO Replicate 1


title: 4213

description: esophagus sample

value: LGD

value: I


title: 4231

description: esophagus sample


title: set_1 OCI-AML3 500 nM JQ1 Treatment Replicate 2

description:
OCI-AML3 500 nM JQ1 Treatment Replicate 2
SAMPLE 35

data_processing: GenomeStudio data were processed in R (v.3.2) (Ihaka and Gentleman, 1996) using Bioconductor (v.3.1) (Gentleman et al., 2004) and the lumi package (v.2.20.2) (Du et al., 2008). Quality controls were carried out using the arrayQualityMetrics package (v.3.24.0) (Kauffmann et al., 2009) taking into account array intensity distributions, distance between arrays and variance mean-dependence. Principal component analysis was used to decide which arrays to process together. Background correction followed by variance stabilizing transform (Lin et al., 2008) and quantile between microarrays normalization were carried out with the lumi package. From the 47231 probe sets available on the HumanHT12 V4 chip, removal of un-expressed probes resulted in 24283 probesets. A linear model was applied employing the limma package (v.3.24.13) (Ritchie et al., 2015) followed by empirical Bayesian analysis to determine differential expression between not-treated and treated samples. Genes were considered differentially expressed if the adjusted P-value, calculated using the Benjamini–Hochberg method (Benjamini and Hochberg, 1995) in order to minimize false discovery rate, was less than 0.05 and the mean level of expression was greater than 1.5-fold.

source_name: OCI-AML3 Cells

growth_protocol: Human cell lines (K562, KASUMI-1, and MV4;11) were obtained from ATCC and the Leibnitz Institute DSMZ-German Collection of Microorganisms and cell cultures (www.dsmz.de). Cell lines were cultured in RPMI-1640 medium (Cat.#61870-044, Gibco) containing 10% fetal calf serum (Cat.#2-01F10-I, BioConcept), 100 U/ml penicillin and 100 U/ml streptomycin (Cat.#15140-122, Gibco). The OCI/AML3 cell line (19) was maintained in α-MEM (Cat.#BE12-169F; BioWhittaker) supplemented with 20 % heat-inactivated foetal calf serum (PAA #A15-152). Cells were grown at 37 °C in a humidified cabinet at 5 % CO2 (Heraeus Function Line).

treatment_protocol: Cells were seeded the day prior to treatment at 2x105 per ml. Treatments were performed so that a final concentration of 0.1 % DMSO (Cat.#D1435; Sigma) was achieved and cells were incubated with DMSO or test compound (500 nM BSP or JQ1 final concentration) for 6 h prior to isolation of RNA.


title: 4230

description: esophagus sample


title: 4248

description: esophagus sample


title: 4254

description: esophagus sample

value: No


title: set_1 OCI-AML3 500 nM JQ1 Treatment Replicate 1

description:
OCI-AML3 500 nM JQ1 Treatment Replicate 1
SAMPLE 34


title: set_1 OCI-AML3 500 nM BSP Treatment Replicate 1

description:
OCI-AML3 500 nM BSP Treatment Replicate 1
SAMPLE 31


title: set_1 OCI-AML3 500 nM BSP Treatment Replicate 3

description:
OCI-AML3 500 nM BSP Treatment Replicate 3
SAMPLE 33


title: 4282

description: esophagus sample

value: M


title: 4218

description: esophagus sample


title: set_1 OCI-AML3 500 nM BSP Treatment Replicate 2

description:
OCI-AML3 500 nM BSP Treatment Replicate 2
SAMPLE 32


title: set_2 K562 DMSO Replicate 2

description:
SAMPLE 2
K562 DMSO Replicate 2


title: 4232

description: esophagus sample


title: set_1 OCI-AML3 500 nM JQ1 Treatment Replicate 3

description:
OCI-AML3 500 nM JQ1 Treatment Replicate 3
SAMPLE 36


title: 4256

description: esophagus sample


title: 4220

description: esophagus sample


title: 4252

description: esophagus sample


title: 4245

description: esophagus sample


title: 4255

description: esophagus sample


title: set_1 OCI-AML3 DMSO Replicate 3

description:
OCI-AML3 DMSO Control Replicate 3
SAMPLE 30


title: 4281

description: esophagus sample


title: set_2 K562 500 nM BSP Treatment Replicate 1

description:
SAMPLE 4
K562 500 nM BSP Treatment Replicate 1


title: set_1 OCI-AML3 DMSO Replicate 2

description:
OCI-AML3 DMSO Control Replicate 2
SAMPLE 29


title: 4215

description: esophagus sample


title: set_1 OCI-AML3 DMSO Replicate 1

description:
OCI-AML3 DMSO Control Replicate 1
SAMPLE 28


title: set_1 MV-4-11 500 nM JQ1 Treatment Replicate 2

description:
MV4;11 500 nM JQ1 Treatment Replicate 2
SAMPLE 26


title: 4233

description: esophagus sample


title: 4251

description: esophagus sample


title: 4253

description: esophagus sample


title: set_1 MV-4-11 500 nM JQ1 Treatment Replicate 3

description:
MV4;11 500 nM JQ1 Treatment Replicate 3
SAMPLE 27


title: 4283

description: esophagus sample

value: More than 10 drinks a week


title: set_1 MV-4-11 500 nM BSP Treatment Replicate 3

description:
MV4;11 500 nM BSP Treatment Replicate 3
SAMPLE 24


title: set_1 MV-4-11 DMSO Replicate 3

description:
MV4;11 DMSO Control Replicate 3
SAMPLE 21


title: 4238

description: esophagus sample

value: Less than one drink a week


title: set_1 MV-4-11 DMSO Replicate 1

description:
MV4;11 DMSO Control Replicate 1
SAMPLE 19


title: set_1 MV-4-11 500 nM BSP Treatment Replicate 1

description:
MV4;11 500 nM BSP Treatment Replicate 1
SAMPLE 22


title: 4247

description: esophagus sample


title: set_1 MV-4-11 DMSO Replicate 2

description:
MV4;11 DMSO Control Replicate 2
SAMPLE 20


title: set_1 KASUMI-1 500 nM JQ1 Treatment Replicate 2

description:
KASUMI-1 500 nM JQ1 Treatment Replicate 2
SAMPLE 17

source_name: KASUMI-1 Cells


title: set_1 KASUMI-1 500 nM JQ1 Treatment Replicate 3

description:
KASUMI-1 500 nM JQ1 Treatment Replicate 3
SAMPLE 18


title: set_1 KASUMI-1 500 nM JQ1 Treatment Replicate 1

description:
KASUMI-1 500 nM JQ1 Treatment Replicate 1
SAMPLE 16


title: 4279

description: esophagus sample

value: Yes


title: 4241

description: esophagus sample


title: set_1 MV-4-11 500 nM BSP Treatment Replicate 2

description:
MV4;11 500 nM BSP Treatment Replicate 2
SAMPLE 23


title: genomic DNA from peripheral blood 90

city: London

first: Tim

last: Spector

address: Westminster Bridge road

department: Twin Research and Genetic Epidemiology

institute: King's College London

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

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

data_processing: The raw Intensity Data files (*.idat) were uploaded into R (version 3.1.1) using Minfi (source(https://bioconductor.org/biocLite.R)). The methylation values were calculated as: beta = methylated signal/(methylated signal + unmethylated signal + 100). Further data quality control was all performed in R. Probes were removed that: 1) failed detection (p > 0.01) in one or more samples and/or had a bead count less than 3 in more than 5% of samples (n = 3,325), 2) aligned to more than one location in the human genome with their 50 bp sequence, 3) located on the sex chromosomes, 4) harboured common genetic variants occurring in European Caucasians (MAF > 1%) within 10 bp on the probe at the interrogated CpG site, and 5) contained variants at any MAF at the interrogated CpG site (Butcher, L. Illumina450ProbeVariants.db: Annotation Package combining variant data from 1000 Genomes Project for Illumina HumanMethylation450 Bead Chip probes. R package version 1.3.1). The remaining number of probes was 453,627.

source_name: peripheral blood 90

label_protocol: Illumina protocol

extract_protocol: Genomic DNA was extracted and purified from peripheral blood samples

value: peripheral blood

tag: twin pair id

tag: age at blood sample

value: female

tag: beadchip and order on beadchip (sentrix id)

tag: cancer status

value: healthy

tag: age at blood sampling vs age at diagnosis

value: Before

tag: age at diagnosis minus age at blood sampling


title: genomic DNA from peripheral blood 91

source_name: peripheral blood 91

value: cancer-diagnosis

tag: cancer location

value: breast

tag: icd information

value: Malignt neoplasm of upper-outer quadrant of breast

value: Infiltrating duct carcinoma, NOS


title: genomic DNA from peripheral blood 89

source_name: peripheral blood 89

tag: tissue


title: set_1 MV-4-11 500 nM JQ1 Treatment Replicate 1

description:
MV4;11 500 nM JQ1 Treatment Replicate 1
SAMPLE 25

tag: cell line

tag: treatment


title: 4244

description: esophagus sample

tag: run

tag: histology

tag: age

tag: gender


title: genomic DNA from peripheral blood 88

source_name: peripheral blood 88


title: genomic DNA from peripheral blood 92

source_name: peripheral blood 92

value: colon

value: Malignt neoplasm of colon, unspecified

value: Adenocarcinoma NOS


title: set_1 K562 500 nM JQ1 Treatment Replicate 3

description:
K562 500 nM JQ1 Treatment Replicate 3
SAMPLE 9
sample failed quality control; no processed data


title: set_1 KASUMI-1 500 nM BSP Treatment Replicate 3

description:
KASUMI-1 500 nM BSP Treatment Replicate 3
SAMPLE 15

value: BSP


title: set_1 KASUMI-1 DMSO Replicate 2

description:
KASUMI-1 DMSO Control Replicate 2
SAMPLE 11

value: DMSO


title: set_1 KASUMI-1 DMSO Replicate 1

description:
KASUMI-1 DMSO Control Replicate 1
SAMPLE 10


title: genomic DNA from peripheral blood 86

source_name: peripheral blood 86

value: After

value: Malignt neoplasm of overlapping sites of breast

value: Lobular carcinoma, NOS


title: genomic DNA from peripheral blood 77

source_name: peripheral blood 77


title: set_1 KASUMI-1 DMSO Replicate 3

description:
KASUMI-1 DMSO Control Replicate 3
SAMPLE 12


title: set_1 KASUMI-1 500 nM BSP Treatment Replicate 1

description:
KASUMI-1 500 nM BSP Treatment Replicate 1
SAMPLE 13


title: genomic DNA from peripheral blood 82

source_name: peripheral blood 82


title: genomic DNA from peripheral blood 87

source_name: peripheral blood 87


title: genomic DNA from peripheral blood 81

source_name: peripheral blood 81


title: set_1 KASUMI-1 500 nM BSP Treatment Replicate 2

description:
KASUMI-1 500 nM BSP Treatment Replicate 2
SAMPLE 14


title: genomic DNA from peripheral blood 84

source_name: peripheral blood 84

value: Intraductal carcinoma in situ of breast

value: Carcinoma in situ NOS


title: genomic DNA from peripheral blood 83

source_name: peripheral blood 83

value: peripheral blood

value: female


title: set_1 K562 500 nM BSP Treatment Replicate 3

description:
K562 500 nM BSP Treatment Replicate 3
SAMPLE 6


title: genomic DNA from peripheral blood 79

source_name: peripheral blood 79

value: Malignt neoplasm of breast of unspecified site


title: genomic DNA from peripheral blood 78

source_name: peripheral blood 78

value: healthy


title: genomic DNA from peripheral blood 85

source_name: peripheral blood 85


title: genomic DNA from peripheral blood 76

source_name: peripheral blood 76

value: cancer-diagnosis

value: Before

value: breast

value: Infiltrating duct and lobular carcinoma


title: genomic DNA from peripheral blood 80

source_name: peripheral blood 80

value: Intraductal carcinoma, noninfiltrating


title: set_1 K562 DMSO Replicate 3

description:
K562 DMSO Control Replicate 3
SAMPLE 3

source_name: K562 Cells


title: set_1 K562 500 nM JQ1 Treatment Replicate 2

description:
K562 500 nM JQ1 Treatment Replicate 2
SAMPLE 8


title: genomic DNA from peripheral blood 73

source_name: peripheral blood 73


title: genomic DNA from peripheral blood 74

source_name: peripheral blood 74

value: Malignt neoplasm of lower-outer quadrant of breast

value: Infiltrating duct carcinoma, NOS


title: Treated patient_8

city: Ribeirao Preto

first: Luiz Gustavo

middle: Araujo

last: Gardinassi

state: Sao Paulo

address: Av. dos Bandeirantes, 3900

country: Brazil

institute: Ribeirao Preto Nursing School/ University of São Paulo

description: SAMPLE 45

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Log2 transformation and RSN normalization was performed using Lumi package for R.

source_name: Human peripheral blood

label_protocol: Biotinylated cRNA were prepared with the Illumina TotalPrep Amplification kit (Ambion, Austin, TX, USA)

extract_protocol: Total RNA was extracted from  from peripheral blood collected to PaxGene RNA blood tubes using PAXgene Blood RNA Kit (PreAnalyticX).

tag: age (years)

tag: Sex

value: M

tag: disease state/treatment

value: VL patient 5 months after treatment with pentavalent antimonial


title: Treated patient_6

description: SAMPLE 43

value: VL patient 2 months after treatment with pentavalent antimonial


title: set_1 K562 DMSO Replicate 2

description:
K562 DMSO Control Replicate 2
SAMPLE 2

value: DMSO


title: set_1 K562 500 nM BSP Treatment Replicate 2

description:
K562 500 nM BSP Treatment Replicate 2
SAMPLE 5

value: BSP


title: Treated patient_7

description: SAMPLE 44

value: F

value: VL patient 3 months after treatment with pentavalent antimonial


title: Treated patient_5

description: SAMPLE 42

value: peripheral blood


title: set_1 K562 500 nM BSP Treatment Replicate 1

description:
K562 500 nM BSP Treatment Replicate 1
SAMPLE 4


title: set_1 K562 500 nM JQ1 Treatment Replicate 1

description:
K562 500 nM JQ1 Treatment Replicate 1
SAMPLE 7


title: genomic DNA from peripheral blood 71

source_name: peripheral blood 71

tag: twin pair id

tag: age at blood sample

value: female

value: After


title: Treated patient_4

description: SAMPLE 41

value: VL patient 4 months after treatment with pentavalent antimonial


title: genomic DNA from peripheral blood 75

source_name: peripheral blood 75

tag: beadchip and order on beadchip (sentrix id)

tag: cancer status

value: healthy

value: Before


title: Control_15

description: SAMPLE 37

value: healthy, Montenegro negative


title: genomic DNA from peripheral blood 68

source_name: peripheral blood 68

value: cancer-diagnosis

tag: age at blood sampling vs age at diagnosis

tag: age at diagnosis minus age at blood sampling

value: colon

value: Malignt neoplasm of sigmoid colon

value: Adenocarcinoma NOS


title: Treated patient_1

description: SAMPLE 38

value: M


title: set_1 K562 DMSO Replicate 1

description:
K562 DMSO Control Replicate 1
SAMPLE 1


title: Treated patient_2

description: SAMPLE 39


title: Control_14

description: SAMPLE 36


title: genomic DNA from peripheral blood 66

source_name: peripheral blood 66

tag: cancer location

value: breast

tag: icd information

value: Malignt neoplasm of upper-outer quadrant of breast

value: Infiltrating duct carcinoma, NOS


title: Control_11

description: SAMPLE 33

tag: tissue

value: F


title: genomic DNA from peripheral blood 64

source_name: peripheral blood 64


title: Control_9

description: SAMPLE 31


title: Control_12

description: SAMPLE 34


title: genomic DNA from peripheral blood 65

source_name: peripheral blood 65


title: Treated patient_3

description: SAMPLE 40

value: VL patient 5 months after treatment with pentavalent antimonial


title: genomic DNA from peripheral blood 63

source_name: peripheral blood 63

value: peripheral blood


title: genomic DNA from peripheral blood 69

source_name: peripheral blood 69

value: female


title: genomic DNA from peripheral blood 58

source_name: peripheral blood 58


title: Control_13

description: SAMPLE 35


title: Control_10

description: SAMPLE 32


title: genomic DNA from peripheral blood 60

source_name: peripheral blood 60

value: After


title: genomic DNA from peripheral blood 67

source_name: peripheral blood 67

value: Malignt neoplasm of breast of unspecified site


title: Control_8

description: SAMPLE 30


title: genomic DNA from peripheral blood 62

source_name: peripheral blood 62

value: Malignt neoplasm of rectosigmoid junction


title: genomic DNA from peripheral blood 61

source_name: peripheral blood 61


title: genomic DNA from peripheral blood 72

source_name: peripheral blood 72

value: Before

value: ovary

value: Malignt neoplasm of ovary

value: Serous cystadenocarcinoma, NOS


title: genomic DNA from peripheral blood 55

source_name: peripheral blood 55

value: healthy


title: genomic DNA from peripheral blood 59

source_name: peripheral blood 59

value: cancer-diagnosis

value: colon

value: Malignt neoplasm of rectum

value: Mucinous adenocarcinoma


title: genomic DNA from peripheral blood 70

source_name: peripheral blood 70

value: breast

value: Neoplasm, malignt


title: Control_6

description: SAMPLE 28

source_name: Human peripheral blood

value: M

value: healthy, Montenegro negative


title: Control_4

description: SAMPLE 26

value: peripheral blood

value: F


title: genomic DNA from peripheral blood 57

source_name: peripheral blood 57

value: female

value: Intraductal carcinoma in situ of breast

value: Carcinoma in situ NOS


title: genomic DNA from peripheral blood 51

source_name: peripheral blood 51

value: After


title: Control_7

description: SAMPLE 29


title: genomic DNA from peripheral blood 52

source_name: peripheral blood 52

value: Malignt neoplasm of upper-inner quadrant of breast

value: Infiltrating duct carcinoma, NOS


title: genomic DNA from peripheral blood 54

source_name: peripheral blood 54

value: Malignt neoplasm of sigmoid colon

value: Adenocarcinoma NOS


title: Asymptomatic_13

description: SAMPLE 21

value: healthy, Montenegro positive


title: genomic DNA from peripheral blood 53

source_name: peripheral blood 53

value: healthy


title: genomic DNA from peripheral blood 50

source_name: peripheral blood 50

value: cancer-diagnosis

value: Before

value: pancreas

value: Malignt neoplasm of head of pancreas

value: Carcinoma, NOS


title: genomic DNA from peripheral blood 49

source_name: peripheral blood 49

value: peripheral blood


title: Control_5

description: SAMPLE 27

value: F

value: healthy, Montenegro negative


title: Asymptomatic_11

description: SAMPLE 19


title: genomic DNA from peripheral blood 48

source_name: peripheral blood 48

value: female

value: Malignt neoplasm of thyroid gland

value: Papillary adenocarcinoma


title: Control_2

description: SAMPLE 24

value: M


title: Control_1

description: SAMPLE 23


title: genomic DNA from peripheral blood 45

source_name: peripheral blood 45

value: breast

value: Malignt neoplasm of breast of unspecified site

value: Infiltrating duct carcinoma, NOS


title: genomic DNA from peripheral blood 46

source_name: peripheral blood 46


title: genomic DNA from peripheral blood 56

source_name: peripheral blood 56

value: After


title: Asymptomatic_9

description: SAMPLE 17

value: healthy, Montenegro positive


title: Asymptomatic_14

description: SAMPLE 22


title: Asymptomatic_8

description: SAMPLE 16


title: Control_3

description: SAMPLE 25


title: Asymptomatic_10

description: SAMPLE 18


title: Asymptomatic_12

description: SAMPLE 20


title: genomic DNA from peripheral blood 42

source_name: peripheral blood 42

value: cancer-diagnosis

value: melanoma

value: Malignt melanoma of upper limb, including shoulder

value: Superficial spreading melanoma


title: genomic DNA from peripheral blood 44

source_name: peripheral blood 44

value: healthy


title: genomic DNA from peripheral blood 43

source_name: peripheral blood 43

value: peripheral blood

value: Malignt neoplasm of upper-outer quadrant of breast

value: Tubular adenocarcinoma


title: Asymptomatic_5

description: SAMPLE 13


title: Asymptomatic_4

description: SAMPLE 12

value: F


title: Asymptomatic_1

description: SAMPLE 9


title: Asymptomatic_3

description: SAMPLE 11


title: genomic DNA from peripheral blood 36

source_name: peripheral blood 36

value: female

value: Before


title: VL patient_7

description: SAMPLE 7

value: M

value: VL patient before treatment with pentavalent antimonial


title: Asymptomatic_6

description: SAMPLE 14


title: genomic DNA from peripheral blood 41

source_name: peripheral blood 41


title: VL patient_8

description: SAMPLE 8

source_name: Human peripheral blood


title: genomic DNA from peripheral blood 37

source_name: peripheral blood 37

value: colon

value: Malignt neoplasm of sigmoid colon

value: Adenocarcinoma NOS


title: genomic DNA from peripheral blood 47

source_name: peripheral blood 47

value: After


title: genomic DNA from peripheral blood 39

source_name: peripheral blood 39


title: genomic DNA from peripheral blood 38

source_name: peripheral blood 38

value: cancer-diagnosis

value: breast

value: Malignt neoplasm of central portion of breast

value: Infiltrating duct carcinoma, NOS


title: genomic DNA from peripheral blood 34

source_name: peripheral blood 34

value: healthy


title: VL patient_5

description: SAMPLE 5

value: peripheral blood


title: VL patient_3

description: SAMPLE 3


title: VL patient_2

description: SAMPLE 2


title: genomic DNA from peripheral blood 30

source_name: peripheral blood 30


title: VL patient_4

description: SAMPLE 4


title: genomic DNA from peripheral blood 32

source_name: peripheral blood 32


title: VL patient_6

description: SAMPLE 6


title: Asymptomatic_7

description: SAMPLE 15

value: healthy, Montenegro positive


title: VL patient_1

description: SAMPLE 1


title: genomic DNA from peripheral blood 31

source_name: peripheral blood 31


title: genomic DNA from peripheral blood 40

source_name: peripheral blood 40

value: Malignt neoplasm of breast of unspecified site


title: genomic DNA from peripheral blood 35

source_name: peripheral blood 35

value: Carcinoma, NOS


title: Asymptomatic_2

description: SAMPLE 10


title: genomic DNA from peripheral blood 23

source_name: peripheral blood 23

value: female


title: genomic DNA from peripheral blood 33

source_name: peripheral blood 33

value: Before


title: genomic DNA from peripheral blood 28

source_name: peripheral blood 28

value: Intraductal papillary adenocarcinoma with invasion


title: genomic DNA from peripheral blood 24

source_name: peripheral blood 24

value: melanoma

value: Malignt melanoma of upper limb, including shoulder

value: Malignt melanoma, NOS


title: genomic DNA from peripheral blood 27

source_name: peripheral blood 27

value: colon

value: Malignt neoplasm of splenic flexure

value: Mucinous adenocarcinoma


title: genomic DNA from peripheral blood 29

source_name: peripheral blood 29


title: genomic DNA from peripheral blood 26

source_name: peripheral blood 26


title: genomic DNA from peripheral blood 25

source_name: peripheral blood 25


title: A3_Birch_Treg

city: Bergisch Gladbach

first: Jutta

last: Kollet

address: Friedrich-Ebert-Str. 68

department: Bioinformatics

institute: Miltenyibiotec GmbH

hyb_protocol: Cy3 labeled cDNAs were hybridized overnight (17 hours, 65°C) to Agilent Whole Human Genome Oligo Microarrays (8x60K v2, Design ID 039494) using Agilent’s recommended hybridization chamber and oven. Finally, microarrays were washed once with wash buffer 1 for 1 min at RT followed by a second wash with wash buffer 2 for 1 min at 37°C.

scan_protocol: Fluorescence signals of the hybridized Agilent Microarrays were detected using Agilent’s Microarray Scanner System (G2505C, Agilent Technologies, Palo Alto, USA).

data_processing: The Agilent Feature Extraction Software (FES 10.7.3.1 ) was used to read out and process the microarray image files.

source_name: Allergic 3 Birch Treg

label_protocol: 250 ng of each of the amplified cDNAs were used as template for Cy3 labeling which was performed according to Miltenyi Biotec’s undisclosed protocol.

growth_protocol: Peripheral blood mononuclear cells were isolated from fresh peripheral EDTA blood samples by by density gradient centrifugation. All blood donors gave informed consent. PBMCs were resuspended in RPMI-1640 (Gibco, Life Technologies, Darmstadt, Germany), supplemented with 5% (v/v) human AB-serum (GemCell, Gemini-Bioproducts, West Sacramento, CA, USA) and stimulated for 7 hours in presence of 1µg/ml CD40 and CD28 pur antibody.Cells were labeled with CD154-Biotin, CD137-PE, followed by anti-Biotin and anti-PE MicroBeads (CD154 and CD137 MircoBead Kit; both Miltenyi Biotec, Bergisch Gladbach, Germany) and magnetically enriched by two sequential MS columns (Miltenyi Biotec).MACS enriched CD154+ and CD137+ cells were further FACS purified on a FACS Aria II (Becton-Dickenson). 4000 FACS purified antigen-specific CD154+ and CD137+ CD4+ T cells were used for microarray experiments.

extract_protocol: Cell samples were lysed using SuperAmp Lysis Buffer following manufacturer’s instructions. SuperAmplification was performed according to Miltenyi Biotec’s undisclosed protocol. Briefly, the amplification is based on a global PCR protocol of mRNA-derived cDNA. mRNA was isolated via magnetic bead technology.

tag: condition

value: allergic

tag: allergen

value: Birch

tag: tcell population

value: regulatory T cell

tag: donor

tag: group


title: A4_Birch_Tcon

source_name: Allergic 4 Birch Tcon

value: conventional T cell

tag: age


title: A2_Birch_Treg

source_name: Allergic 2 Birch Treg

tag: Sex


title: A4_Birch_Treg

source_name: Allergic 4 Birch Treg


title: A1_Birch_Treg

source_name: Allergic 1 Birch Treg


title: genomic DNA from peripheral blood 22

source_name: peripheral blood 22

value: peripheral blood

tag: gender

value: healthy

value: After


title: genomic DNA from peripheral blood 20

source_name: peripheral blood 20

tag: twin pair id

value: cancer-diagnosis

value: breast

value: Malignt neoplasm of breast of unspecified site

tag: histology

value: Infiltrating duct carcinoma, NOS


title: A2_Birch_Tcon

source_name: Allergic 2 Birch Tcon

value: female


title: genomic DNA from peripheral blood 17

source_name: peripheral blood 17

tag: age at blood sample

tag: beadchip and order on beadchip (sentrix id)

value: Malignt neoplasm of rectosigmoid junction

value: Adenocarcinoma NOS


title: A3_Birch_Tcon

source_name: Allergic 3 Birch Tcon


title: genomic DNA from peripheral blood 21

source_name: peripheral blood 21

tag: cancer status

tag: age at blood sampling vs age at diagnosis

value: Malignt neoplasm of upper-outer quadrant of breast


title: genomic DNA from peripheral blood 18

source_name: peripheral blood 18

tag: age at diagnosis minus age at blood sampling


title: cooled 6

city: Ann Arbor

first: Christopher

middle: Louis

last: Mendias

state: Michigan

address: 109 Zina Pitcher Place

department: Orthopaedic Surgery

institute: University of Michigan

hyb_protocol: Following Labeling procedure, 3.75 ug of biotinylated cDNA were hybridized at 48C – WT on Human Gene ST 2.1 strip arrays, and were washed and stained using the Affymetrix Gene Atlas system (software version 1.0.4.267)

scan_protocol: Arrays were scanned using the Affymetrix Gene Atlas system (software version 1.0.4.267)

data_processing: Data was analyzed using the limma and oligo Bioconductor packages implemented in the R-statistical environment version 3.3.0. RMA was used to fit log2 transformed expression values

source_name: vastus lateralis_cooled

label_protocol: cDNA were prepared according to the Nugen Ovation PicoSL WTA System V2 kit protocol from 10 ng total RNA (Ovation PicoSL WTA System V2 Manual, P/N M01226 v4).  Subsequently, Biotinylated cDNA were prepared according to the Nugen Encore Biotin Module from 3.75 ug of cDNA (Encore Biotin Module Manual, P/N M01111 v6)

extract_protocol: Qiazol RNA extraction

tag: activity level

value: physically active

value: male

value: skeletal muscle

tag: muscle name

value: vastus lateralis


title: genomic DNA from peripheral blood 15

source_name: peripheral blood 15

tag: tissue

tag: cancer location

value: cervix

tag: icd information

value: Malignt neoplasm of endocervix


title: H3_Birch_Treg

source_name: Healthy 3 Birch Treg

tag: condition

tag: allergen

value: Birch

tag: tcell population

value: regulatory T cell

tag: donor


title: H7_Birch_Treg

source_name: Healthy 7 Birch Treg

value: healthy

tag: group

tag: Sex

tag: age


title: H5_Birch_Treg

source_name: Healthy 5 Birch Treg


title: genomic DNA from peripheral blood 16

source_name: peripheral blood 16

value: peripheral blood

tag: twin pair id

tag: age at blood sample

tag: gender

value: cancer-diagnosis

value: Before

value: Malignt neoplasm of central portion of breast

tag: histology


title: genomic DNA from peripheral blood 19

source_name: peripheral blood 19

value: female

tag: beadchip and order on beadchip (sentrix id)

tag: cancer status

tag: age at blood sampling vs age at diagnosis

value: After

tag: age at diagnosis minus age at blood sampling


title: H4_Birch_Treg

source_name: Healthy 4 Birch Treg


title: H7_Birch_Tcon

source_name: Healthy 7 Birch Tcon

value: conventional T cell


title: H2_Birch_Treg

source_name: Healthy 2 Birch Treg


title: cooled 5

tag: activity level

tag: tissue

tag: muscle name


title: genomic DNA from peripheral blood 1

source_name: peripheral blood 1


title: genomic DNA from peripheral blood 2

source_name: peripheral blood 2

tag: cancer location

value: endometrium

tag: icd information

value: Malignt neoplasm of endometrium

value: Adenocarcinoma NOS


title: genomic DNA from peripheral blood 8

source_name: peripheral blood 8

value: colon

value: Malignt neoplasm of colon, unspecified


title: genomic DNA from peripheral blood 11

source_name: peripheral blood 11

value: Malignt neoplasm of rectum

value: Mucin-producing adenocarcinoma


title: A1_Birch_Tcon

source_name: Allergic 1 Birch Tcon

tag: condition

value: allergic

tag: allergen

value: Birch

tag: tcell population

tag: donor


title: H5_Birch_Tcon

source_name: Healthy 5 Birch Tcon

value: healthy

tag: group

tag: Sex

tag: age


title: control 5

source_name: vastus lateralis_control

value: physically active

tag: gender

value: male

value: skeletal muscle

value: vastus lateralis


title: genomic DNA from peripheral blood 13

source_name: peripheral blood 13

value: peripheral blood

tag: twin pair id

tag: age at blood sample

value: female

tag: beadchip and order on beadchip (sentrix id)


title: control 6


title: genomic DNA from peripheral blood 6

source_name: peripheral blood 6

tag: cancer status

tag: age at blood sampling vs age at diagnosis

value: Before

tag: age at diagnosis minus age at blood sampling


title: genomic DNA from peripheral blood 12

source_name: peripheral blood 12

tag: tissue

value: After


title: genomic DNA from peripheral blood 5

source_name: peripheral blood 5

value: cancer-diagnosis

tag: cancer location

value: breast

value: Malignt neoplasm of lower-outer quadrant of breast

tag: histology

value: Infiltrating duct carcinoma, NOS


title: cooled 4

source_name: vastus lateralis_cooled

tag: activity level

tag: muscle name


title: genomic DNA from peripheral blood 10

source_name: peripheral blood 10


title: control 4


title: H4_Birch_Tcon

source_name: Healthy 4 Birch Tcon

tag: condition

tag: allergen

tag: tcell population

value: conventional T cell


title: H3_Birch_Tcon

source_name: Healthy 3 Birch Tcon

tag: donor

tag: group

tag: Sex


title: genomic DNA from peripheral blood 14

source_name: peripheral blood 14

tag: twin pair id

tag: gender


title: genomic DNA from peripheral blood 9

source_name: peripheral blood 9

tag: age at blood sample

tag: beadchip and order on beadchip (sentrix id)

tag: icd information

value: Malignt neoplasm of overlapping sites of breast


title: genomic DNA from peripheral blood 3

source_name: peripheral blood 3

tag: cancer status

tag: age at blood sampling vs age at diagnosis

tag: age at diagnosis minus age at blood sampling


title: cooled 3

tag: tissue


title: cooled 1

tag: activity level


title: control 1

tag: muscle name


title: cooled 2


title: control 3


title: A3_Asp_Treg

source_name: Allergic 3 Asp Treg

tag: condition

value: allergic

value: Asp

value: regulatory T cell

tag: age


title: H2_Birch_Tcon

source_name: Healthy 2 Birch Tcon

value: healthy

tag: allergen

value: Birch

tag: tcell population


title: A4_Asp_Treg

source_name: Allergic 4 Asp Treg

tag: donor

tag: group


title: tissue_normal 459

city: Chongqing

first: Yuanyuan

last: Wu

address: Sha ping ba

country: China

institute: Third Military Medical University

description: mRNA and lncRNA expressison inadjacent normal esophageal tissue

hyb_protocol: 1.0 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B).

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v11.5.1 software package (Agilent Technologies). After quantile normalization of the raw data, LncRNAs and mRNAs that at least 5 out of 10 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis.

source_name: adjacent normal esophageal tissue

label_protocol: Each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3’ bias utilizing a random priming method. The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

extract_protocol: Total RNA was extracted from human esophageal cancers and their matched adjacent normal tissues using Trizol following manufacturer's instructions.RNA quantity and quality were measured by NanoDrop ND-1000. RNA integrity was assessed by standard denaturing agarose gel electrophoresis.

value: esophagus

value: male

tag: tnm stage

value: Normal tissue


title: H1_Birch_Tcon

source_name: Healthy 1 Birch Tcon

tag: Sex

value: female


title: tissue_normal 482

tag: gender


title: control 2

source_name: vastus lateralis_control

value: physically active

value: skeletal muscle

value: vastus lateralis


title: tissue_normal 478


title: A1_Asp_Treg

source_name: Allergic 1 Asp Treg


title: A5_Asp_Treg

source_name: Allergic 5 Asp Treg


title: A6_Asp_Tcon

source_name: Allergic 6 Asp Tcon


title: tissue_normal 480


title: A4_Asp_Tcon

source_name: Allergic 4 Asp Tcon


title: tissue_cancer 482

description: mRNA and lncRNA expressison in esophageal tumor tissues

source_name: esophageal tumor


title: A2_Asp_Treg

source_name: Allergic 2 Asp Treg


title: A5_Asp_Tcon

source_name: Allergic 5 Asp Tcon


title: H1_Birch_Treg

source_name: Healthy 1 Birch Treg


title: tissue_normal 471


title: tissue_cancer 480


title: A3_Asp_Tcon

source_name: Allergic 3 Asp Tcon


title: Adeno-GFP injection of p53 fl/fl mice/ad libitum feeding, 3

city: Graz

first: Andreas

last: Prokesch

state: Styria

address: Harrachgasse 21/7

department: Institute of Cell Biology, Histology, and Embryology

country: Austria

institute: Medical University Graz

description: gene expression of GFP control fed

hyb_protocol: Genechip hybridization, wash, stain and scan were performed using standard Affymetrix procedures.

scan_protocol: GeneTitan instrument was used for scanning.

data_processing: Raw array data were normalized using RMA method implemented in CarmaWeb (https://carmaweb.genome.tugraz.at/carma/). A moderate t-test was used to compare ntc and siAspa. The p-values  were corrected for multiple testing using Benjamini-Hochberg's method. Corrected p-values <0.05 were considered differentially expressed.

source_name: liver from p53 fl/fl mice

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 200ng total RNA.

growth_protocol: Male floxed p53 C57Bl/6N mice were housed under standard 12 hour light/ 12 hour dark cycles and fed a standard chow (ssniff R/M-H) diet ad libitum.

extract_protocol: Total RNA was isolated with miRNeasy RNA isolation kit (Qiagen) according to manufacturers recommendations yielding a RIN of greater than 7.

treatment_protocol: Adenoviruses expressing GFP and CRE were generated using the Adeno-X Expression System 2 (Clontech) as described previously44 and purified by standard CsCl gradients. Titers were determined by the Adeno-X Rapid Titer Kit (Clontech). Equal titers (~ 1.7*10^9 infectious units diluted in 250 µl sterile saline) were injected via the tail vein into 2 months old, male C57BL/6 Trp53tm1Brn/J mice45, after dilating the tail vein in a 42oC water bath for 1 min. Mice were fed standard chow (ssniff R/M-H). Three days later, mice were fed ad libitum or fasted for 24 hours and sacrificed.

tag: strain

value: Male

tag: diet

value: ad libitum feeding


title: genomic DNA from peripheral blood 4

source_name: peripheral blood 4

value: peripheral blood

tag: twin pair id

tag: age at blood sample

tag: beadchip and order on beadchip (sentrix id)

tag: cancer status

value: After


title: tissue_cancer 471

tag: tissue


title: Adeno-GFP injection of p53 fl/fl mice/ad libitum feeding, 2

description: gene expression of GFP control fed


title: no overload control  [Mendias_009_09]

description: prepared using the GeneChip WT PLUS Reagent Kit and hybridized to Mouse Gene 2.1 ST Array Strips

source_name: plantaris muscle, no synergist ablation, no PDGF inhibitor

value: no overload control


title: A2_Asp_Tcon

source_name: Allergic 2 Asp Tcon

value: allergic

value: conventional T cell


title: Adeno-GFP injection of p53 fl/fl mice/ad libitum feeding, 1

description: gene expression of GFP control fed


title: A1_Asp_Tcon

source_name: Allergic 1 Asp Tcon

value: Asp


title: no overload control  [Mendias_010_10]


title: tissue_cancer 478


title: genomic DNA from peripheral blood 7

source_name: peripheral blood 7

value: cancer-diagnosis

tag: age at blood sampling vs age at diagnosis

value: Before

tag: age at diagnosis minus age at blood sampling

tag: cancer location

value: melanoma

tag: icd information

value: Malignt melanoma of trunk

tag: histology

value: Malignt melanoma, NOS


title: 10 day control  [Mendias_006_06]

source_name: plantaris muscle, synergist ablation, no PDGF inhibitor

tag: time point

value: 10 day

value: control

value: male


title: TH_T

city: Bareillly

first: SANJEEV

middle: KUMAR

last: SHUKLA

state: UTTAR PRADESH

address: IZATNAGAR

department: Division of Animal Genetics

country: India

institute: Indian Veterinary Research Institute

description: Gene Expression after 6 hr infection of M.Bovis in cattle blood

hyb_protocol: Samples that pass the QC for specific activity were taken for hybridization. 600ng of labeled cRNA were hybridized on the array (AMADID: 29411) using the Gene Expression Hybridization kit (Part Number 5190-0404; Agilent) in Sure hybridization Chambers (Agilent) at 65ºC for 16 hours. Hybridized slides were washed using wash buffers (Part No: 5188-5327; Agilent)

scan_protocol: scanned using the Agilent Microarray Scanner (Agilent Technologies, Part Number G2600D)

data_processing: Images were quantified using Feature Extraction Software ( Agilent). Feature extracted raw data was analyzed using GeneSpring GX Version  software from Agilent. Normalization of the data was done in GeneSpring GX using the 75th percentile shift

organism: Bos indicus

source_name: macrophages cells

label_protocol: The samples were labeled using Agilent Quick-Amp labeling kit (Part number: 5190-0442). 500ng of total RNA was reverse transcribed using oligo dT based method. mRNA was primed with oligo dT primer tagged to T7 promoter sequence and converted into double stranded cDNA using MMLV-RT reverse transcriptase. Further, in the same reaction cDNA was in-vitro transcribed to cRNA using T7 RNA polymerase enzyme. During cRNA synthesis, Cy3 labeled Cytosine nucleotide was incorporated into the newly synthesized strands. Labeled cRNA thus obtained was cleaned up using Qiagen RNeasy columns (Qiagen, Cat No: 74106). Concentration and amount of dye incorporated were determined using Nanodrop ND-1000.

growth_protocol: Blood from the jugular vein was collected into lithium heparin and in 15 ml clean centrifuge tube, equal amount of blood and Histopaque 1077 (Sigma-Aldrich Ireland Ltd., Dublin, Ireland)  centri. at 850 × g for 20 min., buffy coats were harvested, diluted 1:3 in PBS, centri. at 1200 × g for 30 min. PBMC were then washed twice in PBS at 500 × g for 10 min  and in RPMI 1640 with 10% foetal calf serum and penicillin/streptomycin) placed at 5 × 106 PBMC in 50 ml teflon flasks. Non-adherent cells were removed by washes with pre-warmed PBS, and adhered monocyte cells were cultured for 6 days at 370C, with 5% CO2 to obtain MDMs.

extract_protocol: RNA isolation was performed using Qiagen RNeasy Mini Kit (CAT# 74106 ) following the manufacturer's recommendations.

treatment_protocol: Monocyte cells were harvested for treatments of M.Bovis  6 h post stimulation and stored at -80 0C in 1 ml of Trizol1 reagent (Invitrogen Ltd.).

value: Blood

value: 6 hr infection

tag: infection

value: Mycobacterium bovis


title: 10 day treatment  [Mendias_007_07]

source_name: plantaris muscle, synergist ablation, PDGF inhibitor used

tag: group

value: treatment


title: 10 day treatment  [Mendias_008_08]

tag: Sex


title: H5_Asp_Treg

source_name: Healthy 5 Asp Treg

tag: condition

value: healthy

tag: allergen

tag: tcell population

value: regulatory T cell

tag: donor

value: female

tag: age


title: H9_Asp_Treg

source_name: Healthy 9 Asp Treg


title: Adeno-GFP injection of p53 fl/fl mice/fasting for 24 hours, 3

description: gene expression of GFP control fasted

tag: strain

value: Male

tag: diet

value: fasting for 24 hours


title: tissue_cancer 459

tag: tissue

value: esophagus

tag: gender

tag: tnm stage


title: Adeno-GFP injection of p53 fl/fl mice/fasting for 24 hours, 2

description: gene expression of GFP control fasted


title: Adeno-GFP injection of p53 fl/fl mice/fasting for 24 hours, 1

description: gene expression of GFP control fasted


title: Adeno-cre injection of p53 fl/fl mice/ad libitum feeding, 3

description: gene expression of p53KO fed

value: ad libitum feeding


title: H8_Asp_Treg

source_name: Healthy 8 Asp Treg

value: Asp


title: TH_C


title: H4_Asp_Treg

source_name: Healthy 4 Asp Treg


title: H3_Asp_Treg

source_name: Healthy 3 Asp Treg


title: 10 day control  [Mendias_005_05]


title: BU_T

description: Gene Expression after 6  hr infection of M.Bovis in cattle blood

organism: Bubalus bubalis

value: 6  hr infection


title: 3 day treatment  [Mendias_004_04]

value: 3 day


title: H9_Asp_Tcon

source_name: Healthy 9 Asp Tcon

value: conventional T cell


title: 3 day control  [Mendias_002_02]

value: control


title: BU_C


title: CB_C

organism: Bos taurus


title: H8_Asp_Tcon

source_name: Healthy 8 Asp Tcon


title: CB_T


title: Adeno-cre injection of p53 fl/fl mice/fasting for 24 hours, 3

description: gene expression of p53KO fasted


title: 3 day treatment  [Mendias_003_03]

value: male


title: Adeno-cre injection of p53 fl/fl mice/fasting for 24 hours, 2

description: gene expression of p53KO fasted


title: H4_Asp_Tcon

source_name: Healthy 4 Asp Tcon


title: HF_T

organism: Bos primigenius

value: Blood


title: Adeno-cre injection of p53 fl/fl mice/ad libitum feeding, 1

description: gene expression of p53KO fed

source_name: liver from p53 fl/fl mice


title: H5_Asp_Tcon

source_name: Healthy 5 Asp Tcon


title: Adeno-cre injection of p53 fl/fl mice/ad libitum feeding, 2

description: gene expression of p53KO fed


title: MPCshTug1_clone3_rep2

status: Public on Oct 24 2016

city: Houston

first: Shawn

middle: Samson

last: Badal

address: 2121 W. Holcombe Blvd

department: Nephrology

institute: MD Anderson Cancer Center

description: gene expression after Tug1 knockdown in differentiated podocytes

hyb_protocol: The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000. 1 μg of each labeled cRNA was fragmented by adding 11 μl 10 × Blocking Agent and 2.2 μl of 25×Fragmentation Buffer, then heated at 60 °C for 30 min, and finally 55 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 100μl of hybridization solution was dispensed into the gasket slide and assembled to the gene expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: After washing, slides were scanned with the Agilent DNA Microarray Scanner. Data was extracted using Agilent Feature Extraction software. Normalization was performed using Agilent GeneSpring GX 12.1 software.

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

source_name: Cultured cells

label_protocol: Sample labeling and array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology). Briefly, total RNA from each sample was linearly amplified and labeled with Cy3-UTP.

growth_protocol: Temperature Sensitive SV40-T antigen Immortalized podocytes were cultured first at 33 degrees in RPMI-1040 supplemented with 10% FBS and 1% Antibiotics, cells were thermoswitched to 37 degrees to induce differentiation and cultured for 10 days in DMEM (1g glucose/L) supplemented with 5% FBS and 1% Antibiotics.

extract_protocol: Cells were lysed and RNA extracted using Trizol Reagent and column purified over the PureLink RNA Easy Kit (LifeTech). RNA quantity and quality were measured by NanoDrop ND-1000. RNA integrity was assessed by standard denaturing agarose gel electrophoresis.

treatment_protocol: Cells were transduced with a lentiviral shRNA constructs (pGIPZ) harboring either shScramble control shRNA or shRNA directed against Tug1 RNA.

tag: cell type

value: Kidney Podocyte

value: Epithelial

tag: immortilization technique

value: SV40-Temperature sensitive T antigen


title: MPCshTug1_clone3_rep1


title: MPCshTug1_clone2_rep2


title: Adeno-cre injection of p53 fl/fl mice/fasting for 24 hours, 1

description: gene expression of p53KO fasted


title: A6_Asp_Treg

source_name: Allergic 6 Asp Treg

value: allergic


title: MPCshTug1_clone2_rep1


title: MPCshCtrl_rep1


title: MPCshCtrl_rep2


title: PBMC_p053_t3w_Young

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

hyb_protocol: Hybridisation of 10ug cRNA was done overnight for 16 hours at 45ºC in a Hybridisation Oven 640 (Affymetrix). The protocol is conducted as described in the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 2 (Eukaryotic Target Hybridization) (P/N 701027, revision 5).

scan_protocol: Arrays were scanned on an Affymetrix 3000 7G scanner, as described n the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 2 (Eukaryotic Arrays: Washing, Staining and Scanning (P/N 701028, revision 5).

data_processing: Expression estimates were calculated applying the robust microarray analysis (RMA) algorithm.

source_name: Peripheral blood mononuclear cells (PBMCs), isolated from subject 053, three weeks after treatment with a 30% Caloric Restriction diet (T2=t3w)

label_protocol: The Ambion MessageAmp aRNA Amplification Kit was used to prepare labelled cRNA from 500ng of total RNA. The protocol was conducted using the reagents provided by Ambion (P/N 1751), as per the manufacturer's instructions.

growth_protocol: Subjects were recruited by publishing advertisements in local newspapers and by sending out general e-mails to an e-mail list of persons who had indicated their interest in participating in studies of our university. Only men were included, because of hormonal fluctuations in young women may influence outcomes. During a screening visit, subjects donated a fasting blood sample and gave written informed consent. In the fasting blood sample, glucose, hemoglobin, and hematocrit were measured. Subjects were excluded based on the following exclusion criteria: body mass index (BMI in kg/m2) less than 20 or higher than 30, adherence to a weight-reduction or medically prescribed diet, dementia (Mini-Mental State Examination score < 21), diabetes, anemia, gastrointestinal disorders, use of drugs known to interfere with energy ballance, or a history of medical or surgical events known to affect the study outcome. The study was approved by the Medical Ethical Committe of Wageningen University.

extract_protocol: PBMCs were isolated from whole blood using BD Vacutainer Cell Preparation Tubes according to the manufacturer’s instructions. Total RNA was isolated from PBMC samples using Trizol reagent (Invitrogen, Breda, The Netherlands) and purified using Qiagen RNeasy Micro Kit (Qiagen, Venlo, The Netherlands). RNA integrity was checked on chip analysis (Agilent 2100 bioanalyzer, Agilent Technologies, Amsterdam, the Netherlands) according to the manufacturer's instructions. RNA was judged as suitable for array hybridization only if samples exhibited intact bands corresponding to the 18S and 28S ribosomal RNA subunits, and displayed no chromosomal peaks or RNA degradation products (RNA Integrity Number > 8.0).

treatment_protocol: The study design consisted of two phases. Phase 1 (days 1-14): controlled dietary intervention in which each of participants had to remain weight stable. Each of the participants was provided with a diet containing approximately 90% of their estimated total daily energy requirement. The remaining 10% was chosen from a list of choice items. In phase 2 (days 15-35): each of the participants was provided with a diet containing 70% of the energy that each participant consumed during the last three days of phase 1. Composition of the diets was determined as described in (Winkels et al. 2011, PMID: 21527169). Blood samples were taken at the end of phase 1, before CR, and at the end of phase 2, after CR.

tag: time

value: 3 w

tag: subject

tag: age (yrs)

tag: bmi (kg/m2)

tag: body fat percentage (fm)

tag: physical activity level (pal)

tag: dutch eating behaviour questionarre (deqb)

tag: hemoglobin (hb)

tag: hematocrite (ht)

tag: glucose (mmol/l)

value: PBMC


title: PBMC_p053_t0w_Young

source_name: Peripheral blood mononuclear cells (PBMCs), isolated from subject 053, before treatment with a 30% Caloric Restriction diet (T0=t0w)

value: 0 w

tag: Sex

value: Male


title: HF_C

description: Gene Expression after 24 hr infection of M.Bovis in cattle blood

tag: time point

value: 24 hr infection

tag: infection

value: Mycobacterium bovis


title: PBMC_p048_t0w_Young

source_name: Peripheral blood mononuclear cells (PBMCs), isolated from subject 048, before treatment with a 30% Caloric Restriction diet (T0=t0w)


title: H3_Asp_Tcon

source_name: Healthy 3 Asp Tcon

tag: condition

value: healthy

tag: allergen

value: Asp

tag: tcell population

tag: donor

tag: group

value: female

tag: age


title: PBMC_p045_t0w_Old

source_name: Peripheral blood mononuclear cells (PBMCs), isolated from subject 045, before treatment with a 30% Caloric Restriction diet (T0=t0w)

tag: time

tag: subject

tag: age (yrs)

tag: cell type


title: U-2OS pmiR-206

city: Boston

first: Zhenfeng

last: Duan

state: Massachusetts

address: 55 Fruit Street Jackson Building

institute: Massachusetts General Hospital

description: osteosarcoma cell line with pmiR-206

hyb_protocol: Total RNA was processed and hybridized to Affymetrix Genechip HG-U95Av2 arrays (Affymetrix, Santa Clara, CA) by the Gene Array Technology Center at Harvard Medical School (http://genome.med.harvard.edu)

scan_protocol: The expression level of each mRNA is quantified by measuring its hybridization to these 23-mers in comparison to its hybridization to a one-base mismatch oligonucleotide

data_processing: The average expression value for each gene across the arrays was used to normalize the mRNA intensities. The CEL files were transformed into intensity information using the RMA normalization of Qlucore 3.2. Qlucore were used to analyze the microarray data (http://www.qlucore.com). Fold change in expression between miR-206 treated cell lines and control cell lines were evaluated using the Mann-Whitney test. A 1.2 foldchange or greater change in intensity combined with a Mann-Whitney associated P value less than 0.05 was used as the criterion for inclusion in our filtered data set.

source_name: osteosarcoma cell line with CDK11 siRNA

label_protocol: To account for and eliminate biologic noise, RNA was isolated from three distinct flasks of each cell line and pooled together. RNA quality was determined via ethidium bromide staining following agarose/formaldehyde gel electrophoresis

growth_protocol: The U-2OS and KHOS osteosarcoma cell lines were seeded onto the 100mm cell culture plate

extract_protocol: Total RNA was collected from these cells using TRIzol® Reagent (GIBCO Grand Island, NY) according to the manufacturer’s instructions

treatment_protocol: Cell were transfected miRSelect pEP-miR-206 or miRSelect pEP-miR-Null

tag: cell line

tag: tissue

value: osteosarcoma


title: PBMC_p045_t3w_Old

source_name: Peripheral blood mononuclear cells (PBMCs), isolated from subject 045, three weeks after treatment with a 30% Caloric Restriction diet (T2=t3w)

tag: bmi (kg/m2)

tag: body fat percentage (fm)

tag: physical activity level (pal)

tag: dutch eating behaviour questionarre (deqb)

tag: hemoglobin (hb)

tag: hematocrite (ht)


title: PBMC_p039_t0w_Young

source_name: Peripheral blood mononuclear cells (PBMCs), isolated from subject 039, before treatment with a 30% Caloric Restriction diet (T0=t0w)

tag: Sex

tag: glucose (mmol/l)


title: PBMC_p048_t3w_Young

source_name: Peripheral blood mononuclear cells (PBMCs), isolated from subject 048, three weeks after treatment with a 30% Caloric Restriction diet (T2=t3w)


title: PBMC_p044_t0w_Old

source_name: Peripheral blood mononuclear cells (PBMCs), isolated from subject 044, before treatment with a 30% Caloric Restriction diet (T0=t0w)


title: PBMC_p039_t3w_Young

source_name: Peripheral blood mononuclear cells (PBMCs), isolated from subject 039, three weeks after treatment with a 30% Caloric Restriction diet (T2=t3w)


title: 10w_Rat liver APAP/PB_2

city: Osaka

first: Ko

last: Omura

address: 2-1-6 Kashima yodogawa-ku

country: Japan

institute: Astellas Pharma Inc.

description: Gene expression data from liver obtained from 2-stage carcinogenesis model in rats

hyb_protocol: Following fragmentation, 20 ug of cRNA were hybridized for 18 hr at 45C on GeneChip Rat 230 2.0 array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.

data_processing: Microarray image data were processed using Affymetrics Microarray Suite, version 5.0 (MAS5.0).

organism: Rattus norvegicus

source_name: rat liver_1000mpk APAP-initiated and PB-promoted at euthanasia

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA.

growth_protocol: At first, rats were treated with each initiator for 1 or 2 weeks. After 2-week withdrawal, water containing 500 ppm of phenobarbital was given to animals for 6 weeks. Partial hepatectomy was performed 1-week after biginning of promotion. Therfore, 5w and 10w indicates each sampling timepoint.

extract_protocol: Total RNA was extracted by using an RNeasy® Mini Kit (Qiagen) according to the manufacturer's instructions.

tag: gender

tag: strain

value: liver


title: 10w_Rat liver APAP/PB_3

value: male


title: 10w_Rat liver MP/PB_4

source_name: rat liver_100mpk MP-initiated and PB-promoted at euthanasia


title: 10w_Rat liver APAP/PB_1


title: PBMC_p044_t3w_Old

source_name: Peripheral blood mononuclear cells (PBMCs), isolated from subject 044, three weeks after treatment with a 30% Caloric Restriction diet (T2=t3w)


title: 10w_Rat liver MP/PB_3


title: KHOS PmiR-206

description: osteosarcoma cell line with pmiR-206

value: KHOS


title: PBMC_p038_t0w_Young

source_name: Peripheral blood mononuclear cells (PBMCs), isolated from subject 038, before treatment with a 30% Caloric Restriction diet (T0=t0w)


title: 10w_Rat liver MP/PB_1


title: 10w_Rat liver APAP/PB_4


title: 10w_Rat liver MP/PB_2


title: 10w_Rat liver MP/PB_5


title: PBMC_p038_t3w_Young

source_name: Peripheral blood mononuclear cells (PBMCs), isolated from subject 038, 3\three weeks after treatment with a 30% Caloric Restriction diet (T2=t3w)


title: PBMC_p033_t0w_Young

source_name: Peripheral blood mononuclear cells (PBMCs), isolated from subject 033, before treatment with a 30% Caloric Restriction diet (T0=t0w)


title: 10w_Rat liver TAA/PB_3

source_name: rat liver_45mpk TAA-initiated and PB-promoted at euthanasia


title: 3 day control  [Mendias_001_01]

source_name: plantaris muscle, synergist ablation, no PDGF inhibitor

tag: time point

value: 3 day

tag: group

value: control


title: 10w_Rat liver TAA/PB_4


title: 10w_Rat liver TAA/PB_2


title: PBMC_p031_t3w_Young

source_name: Peripheral blood mononuclear cells (PBMCs), isolated from subject 031, three weeks after treatment with a 30% Caloric Restriction diet (T2=t3w)

tag: time

tag: subject


title: PBMC_p033_t3w_Young

source_name: Peripheral blood mononuclear cells (PBMCs), isolated from subject 033, three weeks after treatment with a 30% Caloric Restriction diet (T2=t3w)

tag: age (yrs)

tag: cell type


title: PBMC_p030_t3w_Old

source_name: Peripheral blood mononuclear cells (PBMCs), isolated from subject 030, 3\three weeks after treatment with a 30% Caloric Restriction diet (T2=t3w)


title: 10w_Rat liver DEN30/PB_2

source_name: rat liver_30mpk DEN-initiated and PB-promoted at euthanasia

tag: tissue


title: 10w_Rat liver DEN30/PB_4


title: 10w_Rat liver DEN30/PB_3


title: 10w_Rat liver TAA/PB_1


title: PBMC_p029_t3w_Young

source_name: Peripheral blood mononuclear cells (PBMCs), isolated from subject 029, three weeks after treatment with a 30% Caloric Restriction diet (T2=t3w)

tag: bmi (kg/m2)


title: 10w_Rat liver DEN30/PB_1


title: PBMC_p029_t0w_Young

source_name: Peripheral blood mononuclear cells (PBMCs), isolated from subject 029, before treatment with a 30% Caloric Restriction diet (T0=t0w)

tag: body fat percentage (fm)


title: 10w_Rat liver DEN3/PB_4

source_name: rat liver_3mpk DEN-initiated and PB-promoted at euthanasia


title: 10w_Rat liver DEN3/PB_3


title: 10w_Rat liver DEN3/PB_5


title: 10w_Rat liver TAA/PB_5


title: 10w_Rat liver DEN3/PB_2


title: 10w_Rat liver MC/PB_3

source_name: rat liver_non initiated and PB-promoted at euthanasia


title: 10w_Rat liver MC/water_4

source_name: rat liver_non initiated and non promoted at euthanasia


title: 10w_Rat liver MC/PB_1


title: PBMC_p031_t0w_Young

source_name: Peripheral blood mononuclear cells (PBMCs), isolated from subject 031, before treatment with a 30% Caloric Restriction diet (T0=t0w)

tag: physical activity level (pal)


title: PBMC_p024_t3w_Old

source_name: Peripheral blood mononuclear cells (PBMCs), isolated from subject 024, three weeks after treatment with a 30% Caloric Restriction diet (T2=t3w)

tag: dutch eating behaviour questionarre (deqb)


title: PBMC_p030_t0w_Old

source_name: Peripheral blood mononuclear cells (PBMCs), isolated from subject 030, before treatment with a 30% Caloric Restriction diet (T0=t0w)

tag: hemoglobin (hb)


title: PBMC_p024_t0w_Old

source_name: Peripheral blood mononuclear cells (PBMCs), isolated from subject 024, before treatment with a 30% Caloric Restriction diet (T0=t0w)

tag: hematocrite (ht)


title: 10w_Rat liver MC/PB_2


title: 10w_Rat liver MC/water_3


title: 10w_Rat liver DEN3/PB_1


title: PBMC_p020_t0w_Young

source_name: Peripheral blood mononuclear cells (PBMCs), isolated from subject 020, before treatment with a 30% Caloric Restriction diet (T0=t0w)

tag: Sex


title: 10w_Rat liver MC/water_2


title: 5w_Rat liver APAP/PB_2

source_name: rat liver_1000mpk APAP-initiated and PB-promoted at hepatectomy


title: PBMC_p020_t3w_Young

source_name: Peripheral blood mononuclear cells (PBMCs), isolated from subject 020, three weeks after treatment with a 30% Caloric Restriction diet (T2=t3w)

tag: glucose (mmol/l)


title: PBMC_p019_t3w_Young

source_name: Peripheral blood mononuclear cells (PBMCs), isolated from subject 019, three weeks after treatment with a 30% Caloric Restriction diet (T2=t3w)


title: 5w_Rat liver APAP/PB_4

tag: gender


title: 5w_Rat liver APAP/PB_3

tag: strain


title: 5w_Rat liver MP/PB_5

source_name: rat liver_100mpk MP-initiated and PB-promoted at hepatectomy


title: 10w_Rat liver MC/water_1


title: PBMC_p019_t0w_Young

source_name: Peripheral blood mononuclear cells (PBMCs), isolated from subject 019, before treatment with a 30% Caloric Restriction diet (T0=t0w)


title: 10w_Rat liver MC/PB_4


title: 5w_Rat liver MP/PB_3


title: PBMC_p018_t3w_Old

source_name: Peripheral blood mononuclear cells (PBMCs), isolated from subject 018, three weeks after treatment with a 30% Caloric Restriction diet (T2=t3w)


title: PBMC_p018_t0w_Old

source_name: Peripheral blood mononuclear cells (PBMCs), isolated from subject 018, before treatment with a 30% Caloric Restriction diet (T0=t0w)


title: PBMC_p017_t3w_Old

source_name: Peripheral blood mononuclear cells (PBMCs), isolated from subject 017, three weeks after treatment with a 30% Caloric Restriction diet (T2=t3w)


title: 5w_Rat liver MP/PB_4


title: 5w_Rat liver TAA/PB_4

source_name: rat liver_45mpk TAA-initiated and PB-promoted at hepatectomy


title: 5w_Rat liver TAA/PB_3


title: 5w_Rat liver APAP/PB_1


title: 5w_Rat liver MP/PB_2


title: 5w_Rat liver TAA/PB_2


title: 5w_Rat liver MP/PB_1


title: 5w_Rat liver TAA/PB_1


title: 5w_Rat liver DEN30/PB_4

source_name: rat liver_30mpk DEN-initiated and PB-promoted at hepatectomy


title: PBMC_p014_t3w_Old

source_name: Peripheral blood mononuclear cells (PBMCs), isolated from subject 014, three weeks after treatment with a 30% Caloric Restriction diet (T2=t3w)


title: 5w_Rat liver DEN30/PB_3


title: 5w_Rat liver DEN3/PB_4

source_name: rat liver_3mpk DEN-initiated and PB-promoted at hepatectomy


title: 5w_Rat liver DEN30/PB_2


title: 5w_Rat liver DEN3/PB_3


title: 5w_Rat liver TAA/PB_5


title: PBMC_p016_t0w_Old

source_name: Peripheral blood mononuclear cells (PBMCs), isolated from subject 016, before treatment with a 30% Caloric Restriction diet (T0=t0w)

value: Missing value


title: 5w_Rat liver MC/PB_4

source_name: rat liver_non initiated and PB-promoted at hepatectomy


title: PBMC_p017_t0w_Old

source_name: Peripheral blood mononuclear cells (PBMCs), isolated from subject 017, before treatment with a 30% Caloric Restriction diet (T0=t0w)


title: 5w_Rat liver DEN30/PB_1


title: 5w_Rat liver DEN3/PB_2


title: PBMC_p009_t3w_Young

source_name: Peripheral blood mononuclear cells (PBMCs), isolated from subject 009, three weeks after treatment with a 30% Caloric Restriction diet (T2=t3w)


title: 5w_Rat liver DEN3/PB_1


title: 5w_Rat liver MC/water_2

source_name: rat liver_non initiated and non promoted at hepatectomy


title: 5w_Rat liver MC/water_3


title: 5w_Rat liver MC/PB_2


title: KO_Ly6C+ F4/80low, biological rep2, non-treated, day 4

city: Debrecen

first: Szilard

last: Poliska

address: Egyetem ter 1.

department: Biochemistry and Molecular Biology

country: Hungary

institute: University of Debrecen

description: Gene expression data of muscle-derived macrophages

hyb_protocol: Samples were hybridized at 45 degrees Celsius for 16 hours and then standard washing protocol was performed using GeneChip Fluidics Station 450 (Affymetrix).

scan_protocol: Arrays were scanned on GeneChip Scanner 7G (Affymetrix), Affymetrix GeneChip Command Console (AGCC) was used to obtain image files.

data_processing:
CHP files were generated using Affymetrix Expression Control.
Downstream data analysis was performed in GeneSpring GX 12,  CEL files were imported using RMA algorithm and median normalization was performed.

source_name: muscle-derived tissue macrophage

label_protocol: Ambion WT Expression Kit (Applied Biosystems) and GeneChip WT Terminal Labeling and Control Kit (Affymetrix) were used for amplifying and labeling 150 ng of RNA samples.

growth_protocol: Muscle injury was caused by cardiotoxin ijection into the tibialis anterior muscle. Macrophages were separated after 1, 2 and 4 days post-injury from the regenerating muscle.

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

treatment_protocol: CD45+ hematopoietic cells from regenerating muscles were isolated with a magnetic bead selection (Miltenyi). Cells were labeled with PE-conjugated Ly6C and APC-conjugated F4/80 antibodies and then sorted into Ly6C+ F4/80low and Ly6C- F4/80high subsets.

value: KO (C57B6/J, PPARg fl/fl, LysM Cre+)

tag: cell surafce marker

value: Ly6C+ F4/80low

tag: treatment

value: non-treated

value: day 4


title: PBMC_p016_t3w_Old

source_name: Peripheral blood mononuclear cells (PBMCs), isolated from subject 016, three weeks after treatment with a 30% Caloric Restriction diet (T2=t3w)

tag: time

value: 3 w

value: Male

value: PBMC


title: 5w_Rat liver DEN3/PB_5


title: 5w_Rat liver MC/PB_3


title: PBMC_p014_t0w_Old

source_name: Peripheral blood mononuclear cells (PBMCs), isolated from subject 014, before treatment with a 30% Caloric Restriction diet (T0=t0w)

value: 0 w

tag: subject


title: PBMC_p001_t0w_Old

source_name: Peripheral blood mononuclear cells (PBMCs), isolated from subject 001, before treatment with a 30% Caloric Restriction diet (T0=t0w)

tag: age (yrs)


title: 5w_Rat liver MC/water_4


title: 5w_Rat liver MC/PB_1


title: CTL3

city: New Haven

first: Myles

middle: H

last: Alderman III

state: Ct

address: 10 Amistad St

department: Cell Biology

institute: Yale University School of Medicine

hyb_protocol: Labeled ChIP-DNA was hybridized using the NimbleGen Hybridization System per the users manual by the Yale Center for Genomic Analysis.

scan_protocol: Arrays were scanned on a NimbleGen scanner per the manufacturers protocol.

data_processing:
Arrays were processed using Nimblegen's standard protocol for Nimblescan 2.4 ChIP data extraction.
Data was log2 normalized and analyzed using Partek software. All GFF file scores are Log2 ChIP/input ratios.

source_name: Uterine ChIP DNA

label_protocol: 1 µg ChIP DNA was directly labeled by Klenow (New England Biolabs) random priming with Cy3 or Cy5 random nanomers per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

extract_protocol: Tissue samples were thawed on ice. Total DNA was purified using the Qiagen DNeasy Tissue Kit (Qiagen, Valencia, CA, USA), according to the manufacturer’s instructions. Genomic DNA samples were stored at -80°C until further use. Genomic DNA samples were fragmented and then enriched for methylated DNA as required for NimbleGen methylation arrays. 6 μg total genomic DNA was digested overnight in 24U Mse I supplemented with 100 ng/μl BSA. The reaction was stopped by heating to 65°C for 20 minutes, then samples were purified using a QIAquick PCR Purification Kit (Qiagen, Valencia, CA). The quality of digestion was assessed by running samples on a 2% agarose gel. Mse I digested DNA was heat-denatured and then incubated overnight at 4°C with monoclonal mouse anti 5-methyl cytidine (ab10805) purchased from Abcam (Cambridge, MA, USA). The DNA-antibody mixture was then incubated for 2 hours at 4°C with pre-washed Protein A agarose beads. The beads were washed three times, then resuspended in digestion buffer containing Proteinase K and incubated overnight at 55°C. DNA was extracted using organic extractions of phenol followed by chloroform:isoamyl alcohol. The aqueous layers were transferred to fresh tubes, and the DNA was precipitated with ethanol. The resulting pellet was air dried and resuspended in 10mM Tris-HCl at pH 8.5. Immunoprecipitated and input DNA were then amplified using a GenomePlex Complete Whole Genome Amplification (WGA) Kit (Sigma, Saint Louis, MO, USA) according to manufacturer’s instructions. Samples were then purified using a QIAquick PCR Purification Kit (Qiagen, Valencia, CA, USA).

treatment_protocol: Dams were exposed to DMSO control for days 9-21 of pregnancy. Offspring were euthenized at 2 weeks and their uteri harvested.

tag: age

value: 2 weeks

tag: in utero treatment

value: DMSO

tag: chip antibody

value: Monoclonal mouse anti-5-methyl-cytidine

source_name: Uterine Input DNA

value: None (Input DNA)


title: KO_Ly6C+ F4/80low, biological rep3, non-treated, day 4


title: PBMC_p009_t0w_Young

source_name: Peripheral blood mononuclear cells (PBMCs), isolated from subject 009, before treatment with a 30% Caloric Restriction diet (T0=t0w)

tag: bmi (kg/m2)

tag: body fat percentage (fm)

tag: cell type


title: KO_Ly6C+ F4/80low, biological rep4, non-treated, day 4


title: PBMC_p001_t3w_Old

source_name: Peripheral blood mononuclear cells (PBMCs), isolated from subject 001, three weeks after treatment with a 30% Caloric Restriction diet (T2=t3w)

tag: physical activity level (pal)

tag: dutch eating behaviour questionarre (deqb)

tag: hemoglobin (hb)


title: BPA1

treatment_protocol: Dams were exposed to 5 mg/kg/day BPA  for days 9-21 of pregnancy. Offspring were euthenized at 2 weeks and their uteri harvested.

value: BPA


title: CTL2


title: KO_Ly6C+ F4/80low, biological rep1, non-treated, day 4


title: CTL1


title: 5w_Rat liver MC/water_1

value: male

tag: tissue

value: liver


title: WT_Ly6C+ F4/80low, biological rep3, non-treated, day 4


title: WT_Ly6C+ F4/80low, biological rep1, non-treated, day 4


title: WT_Ly6C+ F4/80low, biological rep2, non-treated, day 4


title: WT_Ly6C- F4/80high, biological rep3, rosiglitazone, day 2

value: Ly6C- F4/80high

value: rosiglitazone

value: day 2


title: WT_Ly6C+ F4/80low, biological rep4, non-treated, day 4

value: Ly6C+ F4/80low


title: WT_Ly6C- F4/80high, biological rep2, rosiglitazone, day 2


title: WT_Ly6C+ F4/80low, biological rep3, rosiglitazone, day 2


title: WT_Ly6C+ F4/80low, biological rep1, rosiglitazone, day 2


title: KO_Ly6C- F4/80high, biological rep2, non-treated, day 2

value: KO (C57B6/J, PPARg fl/fl, LysM Cre+)

value: non-treated


title: WT_Ly6C+ F4/80low, biological rep2, rosiglitazone, day 2


title: KO_Ly6C+ F4/80low, biological rep5, non-treated, day 2


title: KO_Ly6C+ F4/80low, biological rep3, non-treated, day 2


title: KO_Ly6C+ F4/80low, biological rep2, non-treated, day 2


title: WT_Ly6C- F4/80high, biological rep1, rosiglitazone, day 2


title: KO_Ly6C+ F4/80low, biological rep4, non-treated, day 2


title: KO_Ly6C- F4/80high, biological rep4, non-treated, day 2


title: WT_Ly6C- F4/80high, biological rep5, non-treated, day 2


title: KO_Ly6C- F4/80high, biological rep3, non-treated, day 2


title: KO_Ly6C- F4/80high, biological rep5, non-treated, day 2


title: KO_Ly6C- F4/80high, biological rep1, non-treated, day 2


title: WT_Ly6C- F4/80high, biological rep6, non-treated, day 2


title: WT_Ly6C- F4/80high, biological rep2, non-treated, day 2


title: WT_Ly6C- F4/80high, biological rep1, non-treated, day 2


title: WT_Ly6C- F4/80high, biological rep3, non-treated, day 2


title: HUVEC Treated 1

city: Birmingham

first: Shishir

last: Shetty

address: Wolfson Drive

department: Institute of Immunology and Immunotherapy

institute: University of Birmingham

description: Gene expression in cytokine treated HUVEC

hyb_protocol: Hybridization sample was prepared as per manufacturer's protocol followed by 17-hour hybridization (65 degrees centigrade)

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner using one color scan setting.

data_processing:
Data were extracted through GeneSpring software, Agilent Technologies.
Threshold: 1
Logbase: 2
Technology: Agilent.SingleColor.39494
Normalization: Shift to 75.0 percentile
Baseline Transformation: median of all samples
FlagSettings:
Feature is not Uniform:A
Feature is a population outlier:A
Feature is Saturated:A
Feature is not above background:M
Feature is not positive and significant:M

source_name: TNFa and IFNg treated Human umbilical vein endothelial  cells replicate 1

label_protocol: Low-input Quick Amp Labeling Kit, One-Color generated fluorescent RNA (complimentary RNA). The method utilized a T7 RNA polymerase blend, which simultaneously amplified target material and incorporated Cyanine 3-CTP.

growth_protocol: Human liver sinusoidal endothelial cells  were grown  in medium composed of human endothelial basal growth medium (Invitrogen) supplemented with 10 % human serum (HD Supplies), 10 ng/ml vascular endothelial growth factor (VEGF; PeproTech), and 10 ng/ml hepatocyte growth factor (HGF; PeproTech)  Human umbilical vein endothelial cell. Human endothelial basal growth medium supplemented with 10 % human serum, 10 ng/ml epidermal growth factor (EGF; Peprotech) and 10 µg/ml hydrocortisone (Sigma).

extract_protocol: Total RNA was isolated and purified from cell pellets of HSEC and HUVEC using the RNeasy® Mini Kit (Qiagen) and RNase-Free DNase Set (Qiagen), following the manufacturer’s protocol

treatment_protocol: Cytokine stimulated endothelial cells were stimulated with TNFalpha (10ng/ml) and Interferon gamma (10ng/ml) for 24 hours and then underwent RNA extraction

value: umbilical vein endothelial cells


title: HUVEC Treated 2

source_name: TNFa and IFNg treated Human umbilical vein  endothelial cells replicate 2


title: HUVEC Untreated 2

description: Gene expression in untreated HUVEC

source_name: Cultured Human umbilical vein endothelial cells replicate 2


title: WT_Ly6C- F4/80high, biological rep4, non-treated, day 2


title: WT_Ly6C+ F4/80low, biological rep5, non-treated, day 2


title: WT_Ly6C+ F4/80low, biological rep4, non-treated, day 2


title: HSEC Treated 2

description: Gene expression in cytokine treated HSEC

source_name: TNFa and IFNg treated Human liver endothelial cells replicate 2

value: liver sinusoidal endothelial cells


title: KO_Ly6C+ F4/80low, biological rep3, non-treated, day 1

value: day 1


title: WT_Ly6C+ F4/80low, biological rep2, non-treated, day 2


title: 423798A01_M3125_BOA_exposed_rep1

city: Athens

first: Anthony

middle: E.

last: Glenn

state: GA

address: 950 College Station Rd

department: Toxicology & Mycotoxin Research Unit

institute: USDA, ARS, USNPRC, R.B. Russell Research Center

hyb_protocol: Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol.

scan_protocol: Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol.

data_processing: The normalized .calls files provided by NimbleGen (representing normalized gene expression values and accession numbers for each gene interrogated by the array) were imported into ArrayStar v.11 for comparative analysis.

organism: Fusarium verticillioides

source_name: M3125 BOA-Exposed

label_protocol: Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol.

growth_protocol: Wild-type F. verticillioides FRC M-3125 was grown for three days in PDB (50 ml) at 200 rpm in the dark at 27C. The fungus then was transferred (1 ml) to replicate flasks of fresh PDB (50 ml) and grown for three more days to synchronize cultures.

extract_protocol: Samples were ground with liquid nitrogen, and RNA was extracted with Ambion PureLink RNA Mini Kit (Life Technologies, Carlsbad, CA, USA) using homogenizers, followed by treatment with Turbo DNase (Life Technologies), all according to manufacturer’s instructions. RNA integrity was evaluated on an Agilent 2100 Bioanalyzer. Double stranded cDNA was generated using Roche cDNA Synthesis System (Indianapolis, IN, USA), again according to instructions.

treatment_protocol: For induction, ethanol-dissolved BOA (50 µg ml-1 final conc.; 1% ethanol) was added to cultures, while only ethanol (1%) was added for the BOA-unexposed treatment. After 2 hr incubation, the fungal growth was harvested by vacuum filtration, flash frozen in liquid nitrogen, and stored at -80C until ready for extraction.

tag: genotype/variation

value: wild-type

tag: exposed to

value: 50 ug/ml ethanolic BOA


title: HUVEC Untreated 1

description: Gene expression in untreated HUVEC

source_name: Cultured Human umbilical vein endothelial cells replicate 1


title: KO_Ly6C+ F4/80low, biological rep1, non-treated, day 2

tag: strain

tag: cell surafce marker


title: WT_Ly6C+ F4/80low, biological rep6, non-treated, day 2

tag: treatment

tag: time


title: WT_Ly6C+ F4/80low, biological rep3, non-treated, day 2


title: 423799A01_M3125_BOA_exposed_rep2


title: 423802A01_M3125_Control_rep2

source_name: M3125 BOA-Unexposed

value: 1% ethanol (vehicle control)


title: HSEC Treated 1

source_name: TNFa and IFNg treated Human liver endothelial cells replicate 1


title: HSEC Untreated 2

description: Gene expression in untreated HSEC

source_name: Cultured Human liver endothelial cells replicate 2


title: HSEC Untreated 1

description: Gene expression in untreated HSEC

source_name: Cultured Human liver endothelial cells replicate 1


title: KO_Ly6C+ F4/80low, biological rep2, non-treated, day 1

source_name: muscle-derived tissue macrophage


title: 423796A01_M3125_Control_rep1


title: KO_Ly6C+ F4/80low, biological rep1, non-treated, day 1


title: WT_Ly6C+ F4/80low, biological rep1, non-treated, day 2


title: WT_Ly6C+ F4/80low, biological rep4, non-treated, day 1


title: Removal salamander after 4 days: biological rep3

city: Fujisawa

first: Tsukasa

last: Mori

state: Kanagawa

address: Kameino 1866

department: Bioresource Sciences

institute: Nihon University

description: Gene expression data from tail tissues of Rana pirica tadpoles with larval salamanders and removal of the salamanders .

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

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000.  The data were analyzed with GeneChip Operating Software (GCOS) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

data_processing: The data were analyzed first with GCOS algorithm MAS 5 and then using GeneSpringGX11.5.1.

organism: Rana pirica

source_name: Tail tissues from reversion type tadpoles with Salamanders for 4 days

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Tadpoles before growing hind limb.

extract_protocol: Total RNA was obtained using the Qiagen RNA medium preparation system.  RNA yield was measured by absorbance at 260 nm and the quality was assessed by confirming the integrity of the rRNA bands by electrophoresis.

treatment_protocol: Tail tissue was dissected from each tadpole, cut into small pieces, and collected together in a single tube containing RNAlaterTM (QIAGEN RNA stabilization reagent) for subsequent use in producing RNA probes for the functional microarray analysis. The tissues were stored at -80°C until RNA extraction.

value: tail

tag: stress

value: larval salamanders for 4 days then removal


title: Removal dragon fly after 4 days: biological rep1

description: Gene expression data from tail tissues of Rana pirica tadpoles with Dragon fly and removal of the Dragon fly .

source_name: Tail tissues from reversion type tadpoles with Dragon fly for 4 days

value: Dragon fly for 4 days then removal


title: Removal dragon fly after 4 days: biological rep2


title: WT_Ly6C+ F4/80low, biological rep2, non-treated, day 1


title: KO_Ly6C+ F4/80low, biological rep4, non-treated, day 1


title: Removal dragon fly after 4 days: biological rep3


title: Removal salamander after 4 days: biological rep2


title: Dragon fly: biological rep1

description: Gene expression data from tail tissues of Rana pirica tadpoles with Dragon fly.

source_name: Tail tissues from tadpoles with Dragon fly for 8 days

value: Dragon fly for 8 days


title: Removal salamander after 4 days: biological rep1


title: WT_Ly6C+ F4/80low, biological rep1, non-treated, day 1


title: WT_Ly6C+ F4/80low, biological rep3, non-treated, day 1


title: Salamander: biological rep2

description: Gene expression data from tail tissues of Rana pirica tadpoles with larval salamanders.

source_name: Tail tissues from tadpoles with Salamanders for 8 days

value: larval salamanders for 8 days


title: Dragon fly: biological rep3


title: Salamander: biological rep3


title: Dragon fly: biological rep2


title: Control:biological rep1

description: Gene expression data from tail tissues of Rana pirica tadpoles without predators.

source_name: Tail tissues from tadpoles without predators for 8 days