title: thiowt_2 signal

description: raw data: slide10.txt (rows 20821 to 41557)


title: A2C12 SP cells biological replicate 1

status: Public on Aug 08 2012

type: RNA

city: Hannover

first: Thomas

last: Krüwel

address: Nikolai-Fuchs-Str. 1

country: Germany

institute: Fraunhofer Institute for Toxicology and Experimental Medicine

description: lung tumour cell line from a c-myc/c-raf double transgenic mouse model

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome-430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G.

data_processing: Data were normalized with the Robust Microarray Averaging (RMA) algorithm. Following experimental normalization signals < 50 were defined as background. Expression values were calculated as the ratio of non-stimulated (control) and anti-EpCAM stimulated SP vs. non-SP signals. Gene expression that was at least 25% increased or decreased in replicate experiments was considered as differentially expressed.

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: A2C12 SP cells

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

growth_protocol: Cells were cultured in Dulbecco's Modified Eagle's Medium (DMEM; PAA, Cölbe, Germany) supplemented with 10% foetal calf serum, 2 mmol/l L-glutamine, 100 units/ml streptomycin and 100 µg/ml penicillin in a humidified atmosphere containing 5% CO2 at 37°C. Cells were plated in 96well microtiter plates at a density of 5000 cells/well 24 h prior treatment.

extract_protocol: RNA-extraction was done with the RNeasy Micro Kit (Qiagen, Hilden, Germany) according to the manufacturer’s instruction.

treatment_protocol: Cells were treated with a monoclonal anti-mouse EpCAM antibody at concentrations of 100 µg/ml for 48 h. Subsequently, 10^6 cells/ml were resuspended in warm DMEM containing 2% FCS and 10 mmol/l HEPES buffer (Sigma-Aldrich, Munich, Germany). Hoechst 33342 dye was added to a final concentration of 5 µg/ml in the presence or absence of reserpine (50 µmol/l; Sigma-Aldrich, Munich, Germany) and incubated at 37°C for 90 min with gentle shaking. Afterwards, the cells were centrifuged at 4°C and resuspended in ice-cold Hank's balanced salt solution (HBSS, Invitrogen, Karlsruhe, Germany) containing 2% FCS and 10 mmol/l HEPES. Viable cells were visualized by propidium iodide staining (Invitrogen, Karlsruhe, Germany) and was added to a final concentration of 2 µg/ml. The cells were filtered by a 40 µm cell strainer to obtain a single cell suspension before sorting. Analyses and sorting were carried out on a FACSAria cytometer (Becton Dickinson, Heidelberg, Germany). Emissions of Hoechst 33342 (Hoechst-red and Hoechst-blue) were detected using 695/40 nm band-pass and 450/40 nm band-pass filters, respectively.

tag: background strain

tag: cell line

tag: cell fraction

value: SP

tag: treatment


title: KO_rep1

city: Milan

first: Francesca

middle: R.

last: Santoni de Sio

address: via Olgettina 58

department: SR-TIGET

country: Italy

institute: San Raffaele Scientific Institute

hyb_protocol: Hybridization on Mouse WG 6 v2 expression arrays (Illumina) was carried out according to the manufacturer’s instructions

scan_protocol: Scanning was carried out according to the manufacturer’s instructions

data_processing:
Data were normalized and analyzed using Illumina Beadstudio 3.1.3 (background correction and quantile normalization)
Expression profiles of each sample were imported into GeneSpringGX 7.3.1 (Agilent Technologies, USA).
In addition to expression values, Illumina BeadStudio software computes a detection p-value. Based on this, each probe was assigned a detection flag (P (present): p < 0.045; M (Marginal): p between 0.050 and 0.045, A (Absent): p>0.05). Expression values below a defined threshold (i.e. 20) are set to the threshold in order to remove negative values after background correction. To identify dysregulated genes in KO mice, t-test and/or ANOVA and additional steps of filtering were carried out.

source_name: Thymus

label_protocol: 100 ng of RNA was amplified and labeled using the Illumina TotalPrep RNA Amplification kit (Ambion)

extract_protocol: 8-12 weeks old mouse lymphocytes from 3 KO and 3 littermate control C57/bl6-129sv mice were mechanically extracted from thymus. Total RNA was extracted by MirVana kit (Ambion) and treated with DNAse (Turbo DNA free kit, Ambion), following manufacturer instructions. Quality control for RNA integrity was performed by capillary electrophoresis on Agilent 2100 Bioanalyzer,

tag: age

value: 8-12 weeks

tag: strain

tag: genotype/variation

value: KAP1 KO


title: A549 SP cells biological replicate 2

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

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G

organism: Homo sapiens

source_name: A549 SP cells

tag: cell type

value: lung adenocarcinoma


title: A2C12 non-SP cells biological replicate 3

source_name: A2C12 non-SP cells

value: non-SP


title: NIH-3T3_miR-378mimic-transfected_48h_rep3

city: Manchester

first: Dominik

middle: Andreas

last: Rückerl

address: Oxford Road

department: Faculty of Biology, Medicine and Health

country: United Kingdom

institute: The University of Manchester

description:
miR-378 m_3
gene expression data from cells transfected with a mmu-miR-378-3p mimic.

hyb_protocol: Following fragmentation, 5.5 ug of sscDNA were hybridized for 16 hr at 45C on Affymetrix GeneChip ® Mouse Gene 1.0 ST Array.

scan_protocol: GeneChips were scanned using the Agilent Technologies Micro Array Scanner #G2505B.

data_processing: The data were analyzed with Partek Genomics Suite version 6.5 using Affymetrix default analysis settings and RMA as normalization method. Based on the log 2 value of negative control probes of each chip, the background fluorescence was calculated in StatPlus and used to eliminate the microarray's background noise.

label_protocol: Total RNA was converted to cDNA using the GeneChip WT cDNA Synthesis and Amplification Kit (Affymetrix) and biotinylated using the GeneChip® WT Terminal Labeling Kit (Affymetrix).

growth_protocol: NIH-3T3 fibroblasts were grown in RPMI supplemented with 10% FCS, 2mM L-glutamine, 0.25U/ml penicillin and 100U/ml streptomycin at 37C 5%CO2.

extract_protocol: Total RNA was extracted using the Qiagen miRNeasy kit as described by the manufacturer.

treatment_protocol: Cells were transfected with 25nM RNA complexed to DharmaFECT 1 and analysed after 48 hours.

value: murine fibroblast cells

tag: transfectant

value: miR-378 mimic


title: A2C12 non-SP cells biological replicate 1


title: A549 anti-EpCAM treated non-SP cells biological replicate 2

source_name: A549 anti-EpCAM treated non-SP cells


title: A2C12 anti-EpCAM treated non-SP cells biological replicate 1

source_name: A2C12 anti-EpCAM treated non-SP cells

value: anti-EpCAM


title: A549 SP cells biological replicate 1


title: A2C12 non-SP cells biological replicate 2


title: NIH-3T3_miR-378inhibitor-transfected_48h_rep1

description:
miR-378 I_1
gene expression data from cells transfected with a mmu-miR-378-3p inhibitor.

value: miR-378 inhibitor


title: NIH-3T3_miR-378inhibitor-transfected_48h_rep3

description:
miR-378 I_3
gene expression data from cells transfected with a mmu-miR-378-3p inhibitor.


title: A549 non-SP cells biological replicate 2

source_name: A549 non-SP cells


title: HUCPV siBRE rep3

city: Hong Kong

first: Ka Ho Kenneth

last: Lee

email: kaholee@cuhk.edu.hk, elve@cuhk.edu.hk

address: 126 Lo Kwee Seong Integrated Biomedical Science Building, CUHK, Shatin, N.T.

department: School of Biomedical Sciences

country: Hong Kong

institute: The Chinese University of Hong Kong

description: This sample is of BRE-siRNA transfected HUCPV progenitor cells. It is the third of three control biological replicates used in this experiment, each from separate cultures.

hyb_protocol: Hybridization was performed using NimbleGen Hybridization system 4 (Roche) following the manufacturer's manual.

scan_protocol: Scanning was performed using NimbleGen MS 200 Microarray Scanner (Roche) following the manufacturer's manual.

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

source_name: HUCPV siBRE

label_protocol: Labeling was performed using NimbleGen One-Color DNA labeling kit (Roche) following the manufacturer’s manual.

growth_protocol: HUCPV progenitor cells were grown to 50% confluent in DMEM/F12 medium containing 15% ES cell qualified-FBS. The cultures were maintained at 37 °C in a CO2 incubator.

extract_protocol: Total RNA was extracted using the NucleopSpin RNA II kit (Macherey-Nagel) and DNA was removed by on-column DNase digestion with the RNase-Free DNase provided in the kit. RNA quality and concentration was determined by analysis with a Nimblegen bioanalyzer (Roche) at the Core-facilities at Genome Sequencing Laboratory (The Chinese University of Hong Kong, Hong Kong).

treatment_protocol: Transfection using ctl-siRNA or BRE-siRNA accompanied with Lipofectamine(TM) RNAiMAX was done twice in 24 hours interval.

tag: knockdown

value: BRE-siRNA transfected

value: human umbilical cord perivasular (HUCPV) progenitor cells


title: NIH-3T3_miR-378mimic-transfected_48h_rep2

description:
miR-378 m_2
gene expression data from cells transfected with a mmu-miR-378-3p mimic.


title: HUCPV siBRE rep2

description: This sample is of BRE-siRNA transfected HUCPV progenitor cells. It is the second of three control biological replicates used in this experiment, each from separate cultures.


title: A549 SP cells biological replicate 3


title: NIH-3T3_miR-378inhibitor-transfected_48h_rep2

description:
miR-378 I_2
gene expression data from cells transfected with a mmu-miR-378-3p inhibitor.


title: A549 anti-EpCAM treated non-SP cells biological replicate 1


title: NIH-3T3_Risc-transfected_48h_rep2

description:
Risc_2
gene expression data from cells transfected with control RNA.

value: RISC-free siRNA (control)


title: A549 non-SP cells biological replicate 1


title: NIH-3T3_miR-378mimic-transfected_48h_rep1

description:
miR-378 m_1
gene expression data from cells transfected with a mmu-miR-378-3p mimic.


title: HUCPV siCtl rep3

description: This sample is of ctl-siRNA transfected HUCPV progenitor cells. It is the third of three control biological replicates used in this experiment, each from separate cultures.

source_name: HUCPV siCtl

value: ctl-siRNA transfected


title: NIH-3T3_Risc-transfected_48h_rep1

description:
Risc_1
gene expression data from cells transfected with control RNA.


title: Effect of ∆tpk1 mutation with CF rep4

status: Public on Aug 07 2012

city: Montreal

first: Andre

last: Nantel

state: QC

address: 6100 Royalmount

department: Biotechnology Research Institute

country: Canada

institute: National Research Council of Canada

description: ∆tpk1 vs TPK1 +CF (repl 4)

hyb_protocol: The microarray slides were pre-hybridized for 2 hours at 42°C with DIGeasy hybridization buffer (Roche) containing 0.5 ug/ul of yeast tRNA (Roche) and 0.5 ug/ul of salmon sperm DNA (Invitrogen) and subsequently washed with 0.1X SSC and air dried. The slides were then hybridized with labeled cDNAs overnight at 42°C in DIGeasy hybridization buffer with yeast tRNA and salmon sperm DNA. Hybridization was done with an Advalytix SlideBooster. The slides were washed twice with SSC-0.2% SDS, once with 0.1X SSC-0.2% SDS and 3 times with 0.1X SSC. A final wash with isopropanol was performed and slides were air-dried.

scan_protocol: Slides were scanned with a ScanArray 5000 scanner (Perkin Elmer) at 10-µm resolution.

data_processing: Signal intensity was quantified with QuantArray software (Perkin Elmer) and final Lowess normalization and inspection of the data was done with the GeneSpring package GX v.7.3 (Agilent Technologies).

organism: Candida albicans

source_name: JJH233 strain + CF

label_protocol: 20 µg of total RNA was reverse transcribed using oligo(dT)21 in the presence of Cy5-dCTP (Perkin-Elmer-Cetus/NEN) and Superscript III reverse transcriptase (Invitrogen). Thereafter, template RNA was degraded by adding 2.5 units of RNase H (USB) and 1 ug of RNase A (Pharmacia) followed by incubation for 15 min at 37°C. The labeled cDNAs were purified with QIAquick PCR Purification Kit (Qiagen).

extract_protocol: Total RNA was isolated from quadruplicate independent biological samples using the RNeasy mini kit (Qiagen). Briefly, frozen cells were thawed out in RNeasy buffer RLT at a ratio of 3:1 [vol/vol] buffer/pellet. Resuspended cells were divided into 1 ml aliquots in 2 ml screw cap microcentrifuge tubes containing 0.6 ml of 0.5 mm diameter acid-washed glass beads. Samples were homogenized 6 times, for 5 minutes each, in a BeadBeater set at maximum speed.

treatment_protocol: Overnight cultures of cells were diluted to an OD600nm of 0.2 in 100 ml fresh YPD medium (or other appropriate medium for the experiment). Cultures were grown at 30°C with shaking to an OD600nm of 1 or at 37C for 8 hours. CF-treated cells were further incubated with 125ng/ml of caspofungin for 30 min.

value: TPK1 reintegrant

tag: incubated with

value: 125ng/ml of caspofungin for 30 min.

source_name: JJH383 strain + CF

value: ∆tpk1 mutant


title: HUCPV siBRE rep1

description: This sample is of BRE-siRNA transfected HUCPV progenitor cells. It is the first of three control biological replicates used in this experiment, each from separate cultures.


title: Effect of ∆tpk1 mutation with CF rep1

description: ∆tpk1 vs TPK1 +CF (repl 1)


title: A549 anti-EpCAM treated non-SP cells biological replicate 3


title: Effect of ∆tpk1 mutation with CF rep3

description: ∆tpk1 vs TPK1 +CF (repl 3)


title: A549 non-SP cells biological replicate 3


title: Effect of ∆tpk1 mutation rep2

description: ∆tpk1 vs TPK1 (repl 2)

source_name: JJH383 strain

source_name: JJH233 strain


title: NIH-3T3_Risc-transfected_48h_rep3

description:
Risc_3
gene expression data from cells transfected with control RNA.


title: HUCPV siCtl rep1

description: This sample is of ctl-siRNA transfected HUCPV progenitor cells. It is the first of three control biological replicates used in this experiment, each from separate cultures.


title: Effect of ∆tpk1 mutation rep3

description: ∆tpk1 vs TPK1 (repl 3)


title: Effect of ∆tpk1 mutation rep1

description: ∆tpk1 vs TPK1 (repl 1)


title: CF in ∆tpk1 mutants rep2

description: ∆tpk1 + CF (repl 2)


title: CF in ∆tpk1 mutants rep3

description: ∆tpk1 + CF (repl 3)


title: Effect of ∆tpk1 mutation with CF rep2

description: ∆tpk1 vs TPK1 +CF (repl 2)


title: Effect of ∆tpk1 mutation rep4

description: ∆tpk1 vs TPK1 (repl 4)


title: HUCPV siCtl rep2

description: This sample is of ctl-siRNA transfected HUCPV progenitor cells. It is the second of three control biological replicates used in this experiment, each from separate cultures.


title: CF in TPK1 reintegrant rep1

description: TPK1 + CF (repl 1)


title: CF in ∆tpk1 mutants rep1

description: ∆tpk1 + CF (repl 1)


title: CF in TPK1 reintegrant rep4

description: TPK1 + CF (repl 4)


title: CF in ∆tpk1 mutants rep4

description: ∆tpk1 + CF (repl 4)


title: CF in TPK1 reintegrant rep2

description: TPK1 + CF (repl 2)


title: T2 during hacA MT triplicate 3/3

city: Leiden

first: Benjamin

middle: M.

last: Nitsche

state: The Netherlands

address: Sylviusweg 72

department: Institute of Biology

country: Netherlands

institute: Leiden University

description: strain nc2.1: homologous recombination of the wild-type hacA locus in strain MA70.15 (DkusA::amdS+ in AB4.1 pyrG-) with a construct carying the constitutively active hacA locus and the AopyrG gene as selection marker

hyb_protocol: The GeneChip Hybridization, Wash and Stain Kit (#900720) is used for the for the hybridizations, washing, staining and scanning of the chips. The Affymetrixprotocols are strictly followed. The Affymetrix custom Aspergilus niger Genome Arrays are used for hybridization. To the 270 μl hybridization cocktail, 30 μl labeled material is added according the manual of the Affymetrix One Cycle Target Labeling Kit.

scan_protocol: Standard Affymetrix protocol

data_processing: The RMA Bioconductor package was used for data processing

label: Biotin

organism: Aspergillus niger

source_name: Mycelial biomass, exponential growth, glucose-limited bioreactor batch cultures of hacA mt

label_protocol: The Affymetrix One-Cycle Target Labeling Kit and Control Reagents (#900493) are used to synthesize Biotin-labeled cRNA. From each RNA sample 2 μg is used for the labeling experiments.

growth_protocol: Conidia for inoculation of bioreactor cultures were harvested from solidified CM with a sterile detergent solution containing 0.05% (w/v) Tween80 and 0.9% (w/v) NaCl. Batch cultivation of HacAWT and HacACA was initiated by inoculating 5L MM with conidial suspension to give 109 conidia L-1. Glucose was sterilized separately and added to sterile MM to give a final concentration of 0.75% (w/v). During cultivation at 30 °C, pH 3 was maintained by computer-controlled addition of 2 M NaOH or 1 M HCl. Sterile air was supplied at 1 L min-1 through a ring-sparger. Dissolved oxygen tension was above 40% of air saturation at any time, ensuring sufficient oxygen for growth. After spore germination 0.01% (v/v) polypropyleneglycol P2000 was added as antifoam agent. Submerged cultivation was performed with 6.6 L BioFlo3000 bioreactors (New Brunswick Scientific, NJ, USA).

extract_protocol: Total RNA was isolated from homogenized mycelial samples using TRIzol reagent (Invitrogen).

treatment_protocol: Mid-exponential growth phase from bioreactor batch culture with carbon-limited (glucose) minimal medium

value: MA70.15 (DkusA::amdS+ in AB4.1 pyrG-)

value: hacA mutant

tag: phase

value: T2 exponential growth


title: CF in TPK1 reintegrant rep3

description: TPK1 + CF (repl 3)


title: T1 during hacA MT triplicate 3/3

value: T1 exponential growth


title: hacA wild-type triplicate 3/3

description: strain nc1.1: homologous recombination of the wild-type hacA locus in strain MA70.15 (DkusA::amdS+ in AB4.1 pyrG-) with a control construct carying the hacA wild-type locus and the AopyrG gene as selection marker

source_name: Mycelial biomass, exponential growth phase, glucose-limited bioreactor batch cultures of hacA wt

value: hacA wild type

value: exponential growth


title: T2 during hacA MT triplicate 2/3


title: T1 during hacA MT triplicate 1/3


title: hacA wild-type triplicate 2/3


title: T3 during hacA MT triplicate 3/3

value: T3 exponential growth


title: T3 during hacA MT triplicate 2/3


title: T2 during hacA MT triplicate 1/3


title: hacA wild-type triplicate 1/3


title: T3 during hacA MT triplicate 1/3


title: B cells spleen 3

city: Cambridge

first: Micah

middle: James

last: Benson

state: MA

address: 200 Cambridge Park Drive

country: USA

institute: Pfizer

description: Gene expression data from B220+ CD23+ spleen B cells

hyb_protocol: biotinylated cDNA is added to a hybridization solution containing several biotinylated control oligonucleotides for quality control, and hybridized to a microarry chip overnight at 45 deg celsius

scan_protocol: standard Affymetrix protocol

data_processing: Data analyzed by GenePattern software suite

source_name: mouse spleen B cells

label_protocol: NuGEN Ovation V2

extract_protocol: Ambion Rnaqueous micro

value: B220+ CD23+ spleen B cells


title: Plasma cells bone marrow 1

description: Gene expression data from B220- CD138+ bone marrow plasma cells

source_name: mouse bone marrow plasma cells

value: B220- CD138+ bone marrow plasma cells


title: Plasma cells bone marrow 2


title: B cells spleen 1


title: T1 during hacA MT triplicate 2/3


title: B cells spleen 2


title: miR122-KO-T2

city: Taipei

first: Ann-Ping

last: Tsou

address: 155, Li-Nong St., Sec.2

department: Inst. Biotechnology in Medicine

country: Taiwan

institute: National Yang-Ming University

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

scan_protocol: GeneChips were scanned using an Affymetrix GeneChip scanner 3000.

data_processing: The resulting image data was captured and converted to digital output using GeneChip Operating Software v.1.4.0.036. The absolute results (*.chp) from the different experiments (probe arrays of the same type) that were scaled to the same target signal using the All Probe Sets scaling option (scaling factor, 500) may be directly compared (Parameter: Alpha1=0.05, Alpha2=0.065, Tau=0.015). Gene expression was quantified by robust multi-array analysis (RMA) using the Genomic Suite software from Partek.

source_name: KO, Tumor, 14M

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

extract_protocol: Super RNApure (Geneisis Biotech Inc, Taiwan) was used to extract total RNA from the frozen liver samples.

value: mir-122 knockout

value: 14 Month

tag: tissue type

value: Tumor


title: miR122-KO-69-T


title: miR122-KO-105-T


title: miR122-WT

source_name: Control, Liver, 14M

value: wild type

value: Liver


title: miR122-KO-157-T

source_name: KO, Tumor, 11M

value: 11 Month


title: miR122-KO-T


title: miR122-WT-125

source_name: Control, Liver, 11M


title: miR122-WT-103

value: WT

tag: tissue

value: 2 Month


title: miR122-WT-27


title: miR122-KO-265-T


title: miR122-KO-266-T


title: miR122-WT-349


title: miR122-KO-03


title: Plasma cells bone marrow 3


title: miR122-KO-90


title: miR122-WT-258


title: miR122-KO-94


title: miR122-KO-318-T


title: miR122-WT-163


title: C28.3

city: Berlin

first: Philipp

middle: G

last: Maass

address: Robert-Rössle-Strasse 10

institute: Max Delbrück Center for Molecular Medicine

description: ctr

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

source_name: C28/I2 chondrocytes

label_protocol: Standard Illumina labeling

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment. Quality control was performed with Nanodrop and Agilent Bioanalyser.

value: C28/I2 chondrocytes

tag: transfection

value: Control

tag: sample id


title: liver tumor 8

city: Columbus

first: kalpana

last: ghoshal

state: OH

address: 420 W. 12th Avenue

department: Molecular and Cellular Biochemistry

institute: The Ohio State University

description: Biological Replicate 8

hyb_protocol: Arrays were hybridized for 17 hours at 65 degrees Celsius.

scan_protocol: Scanned with Agilent G2505C Microarray Scanner using the AgilentG3_GX_2Color protocol

data_processing: The information about each probe on the array was extracted from the image data using Agilent Feature Extraction 10.9 (FE). This data is stored in the FE “.txt” files. The raw intensity values from these files is imported into the mathematical software package “R”, which is used for all data input, diagnostic plots, normalization and quality checking steps of the analysis process using scripts developed in-house by Peter White specifically for this analysis.

source_name: HCC in miR-122 KO male mice

label_protocol: Two-Color Microarray-Based Gene Expression Analysis Low Input Quick Amp Labeling Version 6.5, May 2010

growth_protocol: Liver tumors from miR-122 knockout mice and  livers from age-matched WT mice

extract_protocol: RNA was extracted using miRVana kit (Invitrogen) followed by further purification using RNeasy kit (Aquagen).

value: HCC liver tumor

tag: genotype

value: miR-122 KO

tag: genetic background

value: C57BL/6J and 129S/Svj mixed

source_name: miR-122 floxed male mouse

value: liver

value: miR-122 floxed


title: miR122-KO-91

tag: background strain


title: liver tumor 6

description: Biological Replicate 6


title: C28.1

description: ctr


title: liver tumor 3

description: Biological Replicate 3


title: liver tumor 5

description: Biological Replicate 5


title: siDA125942.2

description: ovr

value: DA125942 overexpression


title: C28.2

description: ctr


title: liver tumor 4

description: Biological Replicate 4


title: siDA125942.3

description: ovr


title: siDA125942.1

description: ovr


title: scrambled2

description: scr

value: scrambled siRNA


title: DA125942.1

description: sil

value: DA125942 siRNA silencing


title: scrambled3

description: scr


title: scrambled1

description: scr


title: DA125942.3

description: sil


title: liver tumor 1

description: Biological Replicate 1


title: microaerobic_cjejuni_exposed_60min_to_diffusible_caecal_matter, rep1

city: Sheffield

first: Robert

last: Poole

state: South Yorkshire

address: Firth Court, Western Bank

department: Molecular Biology & Biotechnology

institute: University of Sheffield

description:
This Sample represents 2 dye-swapped samples.
Slide15: Cy3=control, Cy5=test
Slide16: Cy3=test, Cy5=control

hyb_protocol: The Cy3-dCTP-labelled sample was mixed with the Cy5-dCTP-labelled sample and re-suspended in 120 μl salt-based hybridization buffer (supplied with the microarray slides). This was heated at 95 ˚C for 3 min, then cooled on ice for 3 min. The mixture was pipetted onto a microarray slide, sealed with a GeneFrame and coverslip in a hybridization chamber and incubated 18 h at 42˚C. Following hybridization, microarray slides (minus GeneFrame and coverslip) were washed in a series of pre-warmed (37 ˚C) SSC buffers for 5 min each at 37˚C: 1 x SSC/0.01% SDS, 1x SSC, 0.2x SSC and 0.01x SSC. Microarray slides were dried by centrifugation at 500 xg for 2 min before scanning.

scan_protocol: Slides were scanned on an Affymetrix 428 scanner. The average signal intensity and local background correction were obtained using a commercially available software package from BioDiscovery, Inc (Imagene, v 4.0 and GeneSight v 3.5).

data_processing: Spots automatically flagged as bad, negative or poor in the ImaGene software were removed before the statistical analysis was carried out in GeneSight. The mean values from each channel were log2 transformed and normalised using the LOWESS method to remove intensity-dependent effects in the log2(ratios) values. The Cy3/Cy5 fluorescent ratios were calculated from the normalized values.

organism: Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819

source_name: Microaerobic log-phase cultured control sample, 60 min

label_protocol: Approximately 12μg RNA was annealed to 4.5μg pd(N)6 random hexamers (Amersham Biosciences) by heating at 65˚C for 10 min, followed by 10 min at 22˚C and cooling on ice for 2 min. This was supplemented with 6μl of 5X First-strand buffer (Invitrogen), 2.5μl dNTP mixture (5mM each dATP, dTTP, dGTP and 2mM dCTP), 3μl 0.1 M DDT, 2μl 1mM Cy3 or Cy5 (Perkin elmer) and 1.5 μl Superscript III reverse transcriptase (200 U) (Invitrogen). This was incubated at 42˚C for 3 hours. The reaction was terminated by the addition of NaOH (7.5 μl of 1M) and HCl (7.5 μl of 1M) before the addition of TE buffer (300 μl). Labelled cDNA was purified using a QIAquick purification kit (Qiagen).

growth_protocol: 3 to 5% of an overnight starter was inoculated into 200 ml of Mueller Hinton Broth supplemented with vancomycin (10 µg/ml) in a 500 ml conical flask. Placed in a microaerobic workstation (80% N2, 10%O2, 10% CO2) and shaken at 125 rpm.

extract_protocol: Samples (30 ml) were harvested using phenol/ethanol to stabilize RNA and total RNA was purified using Qiagen's RNeasy Mini kit as recommended by the suppliers. RNA was quantified using a BioPhotometer (Eppendorf).

treatment_protocol: Based on the device described previously by Pirt (Pirt 1971), a custom-made diffusion capsule was designed and built to be used for exposing C. jejuni to chicken caecum contents. Low molecular weight (3.5 kD) cut-off dialysis membrane (Thermo Scientific) was used to close the ends of the capsule. The device was tested for linearity using a glucose assay (Sigma): a standard glucose solution was placed inside the diffusion capsule and the capsule was placed in a conical flask containing 100 ml deionised water. The flask was placed in a 37 ⁰C incubator, shaking at 100 rpm. Samples were taken every 20 minutes for two hours and placed in microcentrifuge tubes and refrigerated. At the end of the experiment, the glucose concentration of each sample was determined following the manufacturer's instructions. A concentration versus time curve was constructed and linear regression analysis showed an r2 value greater than 0.999. Freshly sampled chicken caecal contents (from Standard Fast Growth birds, circa 3 weeks old) provided by Tom Humphrey et al., University of Bristol (frozen on collection site and kept at -70º C until the time of the experiment) was diluted with PBS (approximately 1.0 g chicken caecal contents in 1.5 ml PBS). The suspension was placed inside the diffusion capsule. The diffusion capsule was closed with dialysis membrane and placed inside a 500 ml conical flask containing a C. jejuni culture growth in 200 ml Mueller Hinton Broth, cultured to have an OD600~0.3. Then the flask was placed into a 42º C microaerophilic incubator with 125 rpm shaking. 60 ml samples were taken aseptically and RNA was harvested. An identical culture with no treatment was growth simultaneously to provide control RNA. Complementary DNA was synthesized from those RNA samples and used for microarrays as described above. This process was done for 10, 30 and 60 min time points.

value: wild-type

tag: treatment duration

value: 60 min

source_name: Microaerobic log-phase cultured, exposed to chicken caecal contents, 60 min

value: exposure to chicken caecal contents


title: liver tumor 7

description: Biological Replicate 7


title: microaerobic_cjejuni_exposed_60min_to_diffusible_caecal_matter, rep2

description:
This Sample represents 2 dye-swapped samples.
Slide96: Cy3=control, Cy5=test
Slide98: Cy3=test, Cy5=control

tag: treatment


title: microaerobic_cjejuni_exposed_30min_to_diffusible_caecal_matter, rep2

description:
This Sample represents 2 dye-swapped samples.
Slide25: Cy3=control, Cy5=test
Slide31: Cy3=test, Cy5=control

source_name: Microaerobic log-phase cultured control sample, 30 min

value: 30 min

source_name: Microaerobic log-phase cultured, exposed to chicken caecal contents, 30 min


title: microaerobic_cjejuni_exposed_30min_to_diffusible_caecal_matter, rep1

description:
This Sample represents 2 dye-swapped samples.
Slide13: Cy3=control, Cy5=test
Slide14: Cy3=test, Cy5=control


title: DA125942.2

description: sil


title: microaerobic_cjejuni_exposed_10min_to_diffusible_caecal_matter, rep1

description:
This Sample represents 2 dye-swapped samples.
Slide11: Cy3=control, Cy5=test
Slide12: Cy3=test, Cy5=control

source_name: Microaerobic log-phase cultured control sample, 10 min

value: 10 min

source_name: Microaerobic log-phase cultured, exposed to chicken caecal contents, 10 min


title: liver tumor 2

description: Biological Replicate 2


title: seed_mixed

city: Beijing

first: Mingming

last: Kang

address: No. 2 Yuanmingyuan West Rd,

country: China

institute: China Agricultural University

hyb_protocol: GeneChip® Hybridization Wash and Stain Kit (Affymetrix) was used for hybridization, washing and staining according to the supplier's instruction.

scan_protocol: GeneChips were scanned by GeneChip® Scanner 3000 (Affymetrix)

data_processing: Data was processed by Affymetrix Microarray Suit (version 5.0) with default settings

organism: Zea mays

source_name: mix of maize early seeds

label_protocol: Biotin labeling was performed using FlashTag™ Biotin RNA Labeling Kit for Affymetrix® GeneChip® miRNA Arrays (www.genisphere.com FlashTag for Affymetrix 20Aug09)

extract_protocol: Total RNAs were isolated using mirVana® RNA Isolation Kit (Ambion)

value: mix of early seeds

tag: age


title: uterus_P4_WT_4hrs_rep2

city: Houston

first: Scott

middle: Andrew

last: Ochsner

state: TX

address: One Baylor Plaza

department: Molecular and Cellular Biology

institute: Baylor College of Medicine

description: Uterus isolated from wild-type ovariectomized mice treated with progesterone for 4h.

hyb_protocol: The fragmented, labeled cRNA (15 μg) was hybridized to murine genome U74Av2 mouse oligonucleotide arrays (Affymetrix, Santa Clara, CA).

scan_protocol: The microarrays were stained in an Affymetrix Fluidics station with streptavidin-phycoerythrin conjugates, followed by staining with an antistreptavidin antibody and streptavidin-phycoerythrin. The arrays were scanned at 3 μm with a GeneArray scanner (Affymetrix).

data_processing: DNA-Chip Analyzer dChip (version 1.3) was used to adjust arrays to a common baseline using invariant set normalization and to estimate expression using the PM-only model. All 24 Genechips were normalized to the uterus_P4_WT_40hrs_rep1 sample and all were modeled together. Data quality was reviewed using present call rates from MAS5 (average, 54%; range, 50–58%), ratios of 3′ to 5′ glyceraldehyde 3-phosphate dehydrogenase probe sets from MAS5 (average, 0.94; range, 0.8 to 1.5), and array outlier rates (average, 0.43%; range, 0.024–2.7%; only two of 24 chips >1%) from dChip.

source_name: uterus

label_protocol: RT by oligo(deoxythymidine), followed by in vitro transcription and biotin labeling of cRNA, were performed (Enzo Biochem, Farmingdale, NY).

growth_protocol: Mice were maintained at the designated animal care facility at Baylor College of Medicine according to the institutional guidelines for the care and use of laboratory animals.

extract_protocol: Total RNA was extracted from uterine tissues using the RNeasy total RNA isolation kit (Qiagen, Valencia, CA). RNA was pooled from the uteri of five mice per genotype and treatment. All RNA samples were analyzed with a Bioanalyser 2100 (Agilent Technologies, Palo Alto, CA) before microarray hybridization.

treatment_protocol: PRKO and wild-type mice were ovariectomized at 6 wk of age. Two weeks later, ovariectomized mice were injected with either vehicle (sesame oil) or P4 (in sesame oil; Sigma-Aldrich Corp., St. Louis, MO; 1 mg/mouse in 100 μl). The injections were repeated every 12 h, and groups of mice were killed 4 h after the first injection (acute P4 treatment) or 4 h after the fourth injection (chronic P4 treatment). The mice were killed by cervical dislocation after placing them under anesthesia (Avertin, 2,2-tribromoethyl alcohol, Sigma-Aldrich Corp.). Uterine tissues were flash-frozen at the time of dissection and stored at −80 C.

value: progesterone

value: wild type

tag: treatement time

value: 4 hours


title: CD4-RNA_Latent TB_2

city: beijing

first: hyk

last: liu

address: beijing

institute: IPB

description: Latent individuals with high response to M.tb specific antigen-stimulus

hyb_protocol: For each microarray performing,1.65 μg of Cy3-labelled cRNA (specific activity >9.0 pmol Cy3/ug cRNA) was fragmented at 60℃ for 30 minutes in a reaction volume of 55μl containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. Then 55μl 2×GEx Hybridization Buffer HI-PRM were added to the array to stop the fragmentation reaction and hybridized to 4×44K Agilent Whole Human Genome Oligo Microarrays (G4112F) for 17 hours at 65℃ in a rotating Agilent hybridization oven. After hybridization, microarrays were washed with GE Wash Buffer 1 (Agilent) and GE Wash buffer 2 (Agilent) following the manufacturers instructions, then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent Microarray Scanner (G2565BA) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5μm, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Agilent Feature Extraction Software (version 9.5.3) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: peripheral CD4+T cell, LTB2

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 1 μg RNA using Quick Amp Labeling Kit, One-Color (Agilent p/n 5190-0442) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN,p/n 74104).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Peripheral CD4+ T cells were purified by positive selection using magnetic beads (BD IMagTM anti-human CD4 Particles-DM, BD Biosciences). Total RNA was extracted from CD4+ T cells (CD4-RNA) of LTB1, LTB2 and TB patients and healthy controls by RNeasy Mini Kit (QIAGEN).Then, RNA quality was checked and mixed with an equal quantity of each individuals. The number of included individuals in each group was 11 for HD, 11 for LTB1, 12 for LTB2 and 11 for TB.

value: peripheral CD4+T cell


title: CD4-RNA_Latent TB_1

description: Latent individuals with moderate response to M.tb specific antigen-stimulus

source_name: peripheral CD4+T cell, LTB1


title: uterus_P4_PRKO_4hrs_rep2

description: Uterus isolated from PRKO ovariectomized mice treated with progesterone for 4h.

value: progesterone receptor knockout


title: uterus_veh_WT_4hrs_rep1

description: Uterus isolated from wild-type ovariectomized mice treated with vehicle for 4h.

value: vehicle


title: CD4-RNA_Healthy donors

description: Healthy individuals with negative response to M.tb specific antigen-stimulus

source_name: peripheral CD4+T cell, HD


title: uterus_veh_PRKO_4hrs_rep3

description: Uterus isolated from PRKO ovariectomized mice treated with vehicle for 4h.


title: uterus_veh_PRKO_4hrs_rep2


title: bap-1-24h-Ex3 _16X

city: Maastricht

first: Daneida

last: Lizarraga

state: Limburg

address: Universiteitssingel 50

department: Toxicogenomics

institute: Maastricht University

description:
bap-1-24h-Ex3 _16X_ 14180333.gpr
cDNA was generated using 1 μg of total RNA per sample and hybridize in the miRCURY (locked-nuclei acid array) 5th generation arrays (Exiqon, Denmark) that contain 9360 reporters, each present four times on the microarray. In our analysis 1326 human and viral reporters were used, of which 880 are unique human mature microRNAs.

hyb_protocol: In a total volume of 100 μl the sample was incubated for 5 minutes at 95oC, spinned for 2 minutes at maximal speed and injected in the hybridization station. Hybridization was performed in a Tecan HS4800 Pro Hybridization station according to manufacturer protocol.

scan_protocol: After hybridization the microarray slides were washed accordingly Exiqon instructions. Then arrays were scanned using the GenePix 4000A scanner (Axon Instruments, Foster City, CA). To quantify the signals, the images were processed to TXT files through the GenePix Pro Sofware Suite version 3.0 by using the GAL file for probe annotation as obtained from Exiqon. The Gal file is based on miRBase version 15.0. These TXT files were then imported in R 2.11.0, for quality control and statistical analysis. R package is freely available for academic use from the Comprehensive R Archive Network (http://www.cran.r-project.org/).

data_processing: First, the quality of all arrays was inspected using arrayQC, an in-house quality control pipeline that generates virtual images, boxplots, correlation plots, clustering images, MvA and PCA plots. Spike-ins were used for all arrays as an extra quality check. Within this dataset, no arrays were technically deviating. Quantile normalization was applied.

source_name: HepG2 cells (ATCC: HB-8065)

label_protocol: cDNA was generated using 1 μg of total RNA per sample. RNA was labeled only with Hy3 containing dye using the microRNACURY LNA™ microRNA Hy3 Power labeling kit (Exiqon, Denmark) according to the manufacturer’s protocol in a total volume of 25 μl. To adjust the volume to 100 μl, a hybridization buffer provided in miRCURY LNA™ microRNA Array, 5th generation kit (Exiqon, Denmark) was used.

growth_protocol: Human hepatocellular carcinoma HepG2 cells (ATCC HB-6065) were used in all the experiments. HepG2 cells were maintained as a monolayer culture in 95% humidity, atmosphere with 5% of CO2 and 37 ºC. HepG2 cells were passaged at preconfluent densities by the use of trypsin-EDTA solution. Cells were cultured and passaged in Minimal Essential Medium (MEM) supplemented with 10% of Foetal Bovine serum, 1% penicillin/streptomycin, 1% sodium-pryruvate and 1% non-essential amino acids. All media compounds were obtained from Gibco BRL (Breda, the Netherlans). Three milliliters of cells (1x105/mL) were seeded into each well in a 6-wells microtiter plate.

extract_protocol: Total RNA was isolated after 6, 12, 24 and 48 hours of incubation with BaP or DMSO in HepG2 total RNA was isolated from cells using miRNeasy mini Kit (Qiagen Westburg bv, Leusden, the Netherlands) according to the manufacturer’s instructions and followed by a DNAse I (Qiagen Inc.) treatment. RNA quantity was measured on a spectrophotometer and quality was determined on a BioAnalyzer (Agilent Technologies, Breda, the Netherlands). Only RNA samples which showed clear 18S and 28S peaks and with a RIN level higher than 8 were used.

treatment_protocol: HepG2 cells were exposed to 2 μM of BaP and to a vehicle control (0.5% DMSO) during 6, 12, 24 and 48 hours in three independent experiments.

value: hepatocellular carcinoma

tag: cell line

value: HepG2 cells (ATCC:HB-8065)

value: bap

tag: time


title: ct-1-24h-Ex3 _15X

description:
ct-1-24h-Ex3 _15X_ 14180332.gpr
cDNA was generated using 1 μg of total RNA per sample and hybridize in the miRCURY (locked-nuclei acid array) 5th generation arrays (Exiqon, Denmark) that contain 9360 reporters, each present four times on the microarray. In our analysis 1326 human and viral reporters were used, of which 880 are unique human mature microRNAs.

tag: cell type

value: ct


title: ct-2-48h-Ex3 _17X

description:
ct-2-48h-Ex3 _17X_ 14180344.gpr
cDNA was generated using 1 μg of total RNA per sample and hybridize in the miRCURY (locked-nuclei acid array) 5th generation arrays (Exiqon, Denmark) that contain 9360 reporters, each present four times on the microarray. In our analysis 1326 human and viral reporters were used, of which 880 are unique human mature microRNAs.


title: bap-1-48h-Ex3 _18X

description:
bap-1-48h-Ex3 _18X_ 14180345.gpr
cDNA was generated using 1 μg of total RNA per sample and hybridize in the miRCURY (locked-nuclei acid array) 5th generation arrays (Exiqon, Denmark) that contain 9360 reporters, each present four times on the microarray. In our analysis 1326 human and viral reporters were used, of which 880 are unique human mature microRNAs.


title: uterus_P4_WT_4hrs_rep3


title: uterus_P4_PRKO_40hrs_rep1

description: Uterus isolated from PRKO ovariectomized mice treated with progesterone for 40h.

value: 40 hours


title: leaf_3weeks

source_name: maize leaves at 3 weeks after germination

value: leaves

value: 3 weeks after germination


title: uterus_P4_PRKO_4hrs_rep1


title: uterus_P4_WT_4hrs_rep1


title: uterus_P4_PRKO_4hrs_rep3


title: uterus_veh_PRKO_40hrs_rep1

description: Uterus isolated from PRKO ovariectomized mice treated with vehicle for 40h.


title: uterus_veh_PRKO_4hrs_rep1


title: uterus_veh_WT_4hrs_rep3


title: bap-1-12h-Ex3 _14X

description:
bap-1-12h-Ex3 _14X_ 14180323.gpr
cDNA was generated using 1 μg of total RNA per sample and hybridize in the miRCURY (locked-nuclei acid array) 5th generation arrays (Exiqon, Denmark) that contain 9360 reporters, each present four times on the microarray. In our analysis 1326 human and viral reporters were used, of which 880 are unique human mature microRNAs.


title: CD4-RNA_TB

description: Tuberculosis individuals with high response to M.tb specific antigen-stimulus

source_name: peripheral CD4+T cell, TB


title: ct-1-12h-Ex3 _13X

description:
ct-1-12h-Ex3 _13X_ 14180321.gpr
cDNA was generated using 1 μg of total RNA per sample and hybridize in the miRCURY (locked-nuclei acid array) 5th generation arrays (Exiqon, Denmark) that contain 9360 reporters, each present four times on the microarray. In our analysis 1326 human and viral reporters were used, of which 880 are unique human mature microRNAs.


title: bap-1-48h-Ex2 _12X

description:
bap-1-48h-Ex2 _12X_ 14180253.gpr
cDNA was generated using 1 μg of total RNA per sample and hybridize in the miRCURY (locked-nuclei acid array) 5th generation arrays (Exiqon, Denmark) that contain 9360 reporters, each present four times on the microarray. In our analysis 1326 human and viral reporters were used, of which 880 are unique human mature microRNAs.


title: uterus_P4_WT_40hrs_rep1

description: Uterus isolated from wild-type ovariectomized mice treated with progesterone for 40h.


title: uterus_veh_WT_40hrs_rep1

description: Uterus isolated from wild-type ovariectomized mice treated with vehicle for 40h.


title: ct-2-48h-Ex2 _11X

description:
ct-2-48h-Ex2 _11X_ 14180252.gpr
cDNA was generated using 1 μg of total RNA per sample and hybridize in the miRCURY (locked-nuclei acid array) 5th generation arrays (Exiqon, Denmark) that contain 9360 reporters, each present four times on the microarray. In our analysis 1326 human and viral reporters were used, of which 880 are unique human mature microRNAs.


title: uterus_veh_WT_4hrs_rep2


title: bap-1-12h-Ex2 _8X

description:
bap-1-12h-Ex2 _8X_ 14180316.gpr
cDNA was generated using 1 μg of total RNA per sample and hybridize in the miRCURY (locked-nuclei acid array) 5th generation arrays (Exiqon, Denmark) that contain 9360 reporters, each present four times on the microarray. In our analysis 1326 human and viral reporters were used, of which 880 are unique human mature microRNAs.


title: ct-1-12h-Ex2 _7X

description:
ct-1-12h-Ex2 _7X_ 14180315.gpr
cDNA was generated using 1 μg of total RNA per sample and hybridize in the miRCURY (locked-nuclei acid array) 5th generation arrays (Exiqon, Denmark) that contain 9360 reporters, each present four times on the microarray. In our analysis 1326 human and viral reporters were used, of which 880 are unique human mature microRNAs.


title: ct-1-24h-Ex2 _9X

description:
ct-1-24h-Ex2 _9X_ 14180239.gpr
cDNA was generated using 1 μg of total RNA per sample and hybridize in the miRCURY (locked-nuclei acid array) 5th generation arrays (Exiqon, Denmark) that contain 9360 reporters, each present four times on the microarray. In our analysis 1326 human and viral reporters were used, of which 880 are unique human mature microRNAs.


title: uterus_veh_WT_40hrs_rep3


title: uterus_P4_WT_40hrs_rep3


title: uterus_veh_PRKO_40hrs_rep3


title: uterus_veh_PRKO_40hrs_rep2


title: FR3  (CD62Llo CD69+ Klrg1+) biological replicate 1

city: Miami

middle: R

last: Malek

state: FL

address: 1600 NW 10th Avenue

department: Microbiology/Immunology

institute: University of Miami

description: FACS purified Treg subsets

hyb_protocol: Biotinylated cRNA was hybridized to Affymetrix Gene  ST1.0  arrays

scan_protocol: Image analysis was performed using the Affymetrix Command Console Software (AGCC).

data_processing: Resulting data were normalized with the RMA method using software at GeneSifter (Seattle, WA). Multi-group comparisons of the transformed data of at least 2 independent biological replicates were performed using ANOVA applying the Benjamini Hochberg correction for false positives.

source_name: FR3  (CD62Llo CD69+ Klrg1+)

label_protocol: 20 to 50 ng RNA was used in a single round of linear RNA probe amplification and labeling using NuGEN Ovation Pico WTA system, WT-Ovation Exon module and Encore Biotin Module (NuGEN, San Carlos, CA, USA)

extract_protocol: Total RNA was isolated using TRizol and further purified with RNAeasy Minikit (QIAGEN).

treatment_protocol: Treg subsets were FACS sorted by on the expression of CD4 and Foxp3/RFP-reporter and total RNA was prepared for microarray analysis using Affymetrix Mouse Gene ST 1.0 arrays

value: spleen

tag: strain

tag: Sex

value: female

value: 9-14 weeks old


title: bap-1-24h-Ex2 _10X

description:
bap-1-24h-Ex2 _10X_ 14180240.gpr
cDNA was generated using 1 μg of total RNA per sample and hybridize in the miRCURY (locked-nuclei acid array) 5th generation arrays (Exiqon, Denmark) that contain 9360 reporters, each present four times on the microarray. In our analysis 1326 human and viral reporters were used, of which 880 are unique human mature microRNAs.


title: uterus_P4_PRKO_40hrs_rep2


title: FR3  (CD62Lhi CD69- Klrg1-) biological replicate 10

description: FACS purified Treg subsets

source_name: FR3  (CD62Lhi CD69- Klrg1-)


title: FR3  (CD62Llo CD69+ Klrg1-) biological replicate 1

description: FACS purified Treg subsets

source_name: FR3  (CD62Llo CD69+ Klrg1-)


title: uterus_P4_PRKO_40hrs_rep3


title: FR3  (CD62Llo CD69+ Klrg1-) biological replicate 2

description: FACS purified Treg subsets


title: bap-1-48h-Ex1 _6X

description:
bap-1-48h-Ex1 _6X_ 14180397.gpr
cDNA was generated using 1 μg of total RNA per sample and hybridize in the miRCURY (locked-nuclei acid array) 5th generation arrays (Exiqon, Denmark) that contain 9360 reporters, each present four times on the microarray. In our analysis 1326 human and viral reporters were used, of which 880 are unique human mature microRNAs.


title: uterus_veh_WT_40hrs_rep2


title: FR2  (CD62Llo CD69- Klrg1-) biological replicate 1

description: FACS purified Treg subsets

source_name: FR2  (CD62Llo CD69- Klrg1-)


title: ct-1-48h-Ex1 _5X

description:
ct-1-48h-Ex1 _5X_ 14180396.gpr
cDNA was generated using 1 μg of total RNA per sample and hybridize in the miRCURY (locked-nuclei acid array) 5th generation arrays (Exiqon, Denmark) that contain 9360 reporters, each present four times on the microarray. In our analysis 1326 human and viral reporters were used, of which 880 are unique human mature microRNAs.


title: FR3  (CD62Llo CD69+ Klrg1-) biological replicate 4

description: FACS purified Treg subsets


title: ct-2-24h-Ex1 _3X

description:
ct-2-24h-Ex1 _3X_ 14180385.gpr
cDNA was generated using 1 μg of total RNA per sample and hybridize in the miRCURY (locked-nuclei acid array) 5th generation arrays (Exiqon, Denmark) that contain 9360 reporters, each present four times on the microarray. In our analysis 1326 human and viral reporters were used, of which 880 are unique human mature microRNAs.


title: bap-1-24h-Ex1 _4X

description:
bap-1-24h-Ex1 _4X_ 14180386.gpr
cDNA was generated using 1 μg of total RNA per sample and hybridize in the miRCURY (locked-nuclei acid array) 5th generation arrays (Exiqon, Denmark) that contain 9360 reporters, each present four times on the microarray. In our analysis 1326 human and viral reporters were used, of which 880 are unique human mature microRNAs.


title: BMDM siBcl3 8hr LPS #1

city: La Jolla

first: Vivien

middle: Ya-Fan

last: Wang

state: CA

address: 9500 Gilman Drive, NSB, 3325A

department: Chemistry and Biochemistry

institute: UCSD

description:
SAMPLE 7
replicate 1

data_processing: The data were normalised using quantile normalisation with Illumina Inc. BeadStudio (v.2010.3.0.30128).

label: Strepavidin Cy-3

source_name: BMDM siBcl3 8hr LPS

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

growth_protocol: BMDMs were cultured in RPMI 1640 medium supplemented with 25% FBS and 25% L cell-conditioned medium as a source of M-CSF.

extract_protocol: RNA was extracted QIAGEN RNeasy kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: BMDMs were transfected with siRNA and then stimulated with LPS

value: 5-7 weeks

value: bone marrow

value: bone marrow derived macrophage (BMDM)

tag: transfected with

value: Bcl3 siRNA (Bcl3 knockdown)

tag: stimulated with

value: LPS for 8hrs


title: FR2  (CD62Llo CD69- Klrg1-) biological replicate 2

description: FACS purified Treg subsets

tag: tissue


title: uterus_P4_WT_40hrs_rep2

value: progesterone

value: wild type


title: BMDM siBcl3 0hr LPS #2

description:
SAMPLE 6
replicate 2

source_name: BMDM siBcl3 0hr LPS (no stimulation)


title: FR1  (CD62Lhi CD69- Klrg1-) biological replicate 1

description: FACS purified Treg subsets

source_name: FR1  (CD62Lhi CD69- Klrg1-)


title: BMDM siBcl3 8hr LPS #2

description:
SAMPLE 8
replicate 2


title: FR3  (CD62Llo CD69+ Klrg1-) biological replicate 3

description: FACS purified Treg subsets


title: FR1  (CD62Lhi CD69- Klrg1-) biological replicate 2

description: FACS purified Treg subsets


title: bap-1-12h-Ex1 _2X_

description:
bap-1-12h-Ex1 _2X_ 14180304.gpr
cDNA was generated using 1 μg of total RNA per sample and hybridize in the miRCURY (locked-nuclei acid array) 5th generation arrays (Exiqon, Denmark) that contain 9360 reporters, each present four times on the microarray. In our analysis 1326 human and viral reporters were used, of which 880 are unique human mature microRNAs.

value: hepatocellular carcinoma


title: BMDM siBcl3 0hr LPS #1

description:
SAMPLE 5
replicate 1


title: bap-1-6h-Ex3 _24X

description:
bap-1-6h-Ex3 _24X_ 14201344.gpr
cDNA was generated using 1 μg of total RNA per sample and hybridize in the miRCURY (locked-nuclei acid array) 5th generation arrays (Exiqon, Denmark) that contain 9360 reporters, each present four times on the microarray. In our analysis 1326 human and viral reporters were used, of which 880 are unique human mature microRNAs.

value: HepG2 cells (ATCC:HB-8065)


title: bap-1-6h-Ex2 _22X

description:
bap-1-6h-Ex2 _22X_ 14201342.gpr
cDNA was generated using 1 μg of total RNA per sample and hybridize in the miRCURY (locked-nuclei acid array) 5th generation arrays (Exiqon, Denmark) that contain 9360 reporters, each present four times on the microarray. In our analysis 1326 human and viral reporters were used, of which 880 are unique human mature microRNAs.

value: bap


title: BMDM siCTL 8hr LPS #2

description:
SAMPLE 4
replicate 2

source_name: BMDM siCTL 8hr LPS

value: scramble siRNA (control)


title: ct-1-6h-Ex3 _23X

description:
ct-1-6h-Ex3 _23X_ 14201343.gpr
cDNA was generated using 1 μg of total RNA per sample and hybridize in the miRCURY (locked-nuclei acid array) 5th generation arrays (Exiqon, Denmark) that contain 9360 reporters, each present four times on the microarray. In our analysis 1326 human and viral reporters were used, of which 880 are unique human mature microRNAs.

value: ct


title: ct-1-6h-Ex2 _21X

description:
ct-1-6h-Ex2 _21X_ 14201339.gpr
cDNA was generated using 1 μg of total RNA per sample and hybridize in the miRCURY (locked-nuclei acid array) 5th generation arrays (Exiqon, Denmark) that contain 9360 reporters, each present four times on the microarray. In our analysis 1326 human and viral reporters were used, of which 880 are unique human mature microRNAs.


title: miR122-WT-104

tag: genotype/variation

value: WT

value: Liver

value: 2 Month


title: ct-2-12h-Ex1 _1X

description:
ct-2-12h-Ex1 _1X_ 14180303.gpr
cDNA was generated using 1 μg of total RNA per sample and hybridize in the miRCURY (locked-nuclei acid array) 5th generation arrays (Exiqon, Denmark) that contain 9360 reporters, each present four times on the microarray. In our analysis 1326 human and viral reporters were used, of which 880 are unique human mature microRNAs.


title: bap-1-6h-Ex1 _20X

description:
bap-1-6h-Ex1 _20X_ 14201338.gpr
cDNA was generated using 1 μg of total RNA per sample and hybridize in the miRCURY (locked-nuclei acid array) 5th generation arrays (Exiqon, Denmark) that contain 9360 reporters, each present four times on the microarray. In our analysis 1326 human and viral reporters were used, of which 880 are unique human mature microRNAs.


title: BMDM siCTL 0hr LPS #1

description:
SAMPLE 1
replicate 1

source_name: BMDM siCTL 0hr LPS (no stimulation)


title: BMDM siCTL 0hr LPS #2

description:
SAMPLE 2
replicate 2


title: BMDM siCTL 8hr LPS #1

description:
SAMPLE 3
replicate 1


title: ct-1-6h-Ex1 _19X

description:
ct-1-6h-Ex1 _19X_ 14201337.gpr
cDNA was generated using 1 μg of total RNA per sample and hybridize in the miRCURY (locked-nuclei acid array) 5th generation arrays (Exiqon, Denmark) that contain 9360 reporters, each present four times on the microarray. In our analysis 1326 human and viral reporters were used, of which 880 are unique human mature microRNAs.


title: epid_WT_HF

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

institute: Wageningen University

hyb_protocol: One hundred nanogram of RNA per sample was hybridized to an Affymetrix GeneChip Mouse Gene 1.1 ST 24-array plate (Santa Clara, CA) according to manufacturer's instructions.

scan_protocol: Arrays were scanned on an Affymetrix 3000 7G scanner according to standard protocol.

data_processing: Expression estimates were calculated using RMA using RMA using R version R-2.15.0 and Bioconductor 2.10

source_name: epididymal adipose tissue

label_protocol: One hundred nanogram of RNA was used for whole transcript cDNA synthesis with the Ambion WT expression kit (Applied Biosystems, Nieuwekerk a/d IJssel, The Netherlands).

growth_protocol: WT C57BL/6J mice (8 weeks; Charles River Laboratories) and CD1d-null mice that had been backcrossed to C57BL/6J for 10-12 generations were bred in our facility.

extract_protocol: Epididymal adipose tissue was excised and stored at −80C until analysis. RNA was extracted using Trizol (Invitrogen) and further purified on an RNeasy micro column (Qiagen). RNA samples from 4-6 mice per experimental group were pooled for microarray analysis.

treatment_protocol: Mice were age matched and fed standard chow until age 10-11 weeks, and subsequently fed LFD (10 kcal% fat, Research Diet D12450B) or HFD (45 kcal% fat, Research Diet D12451) for 18-19 weeks.

value: epididymal adipose tissue

value: wildtype

tag: diet

value: high fat


title: MCF7_siControl_E2_24h_rep2

status: Public on Aug 06 2012

city: Stockholm

first: Chunyan

last: Zhao

address: Hälsovägen 7-9

department: Biosciences and Nutrition

country: Sweden

institute: Karolinska Institute

description:
SiCtrl-E2_2
Gene expression after 24 h E2 treatment in si_control treated cells

hyb_protocol: 600 ng 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 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Human GE 8x60K Microarrays (G4851A) for 17 hours at 65°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 37°C GE Wash buffer 2 (Agilent).

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

data_processing: The scanned images were analyzed with Feature Extraction Software 10.10.1.1 (Agilent) using default parameters (protocol GE1-1010_Sep10 and Grid: 028004_D_F_20100430) to obtain background subtracted and spatially detrended Processed Signal intensities. Data were subsequently subjected to quantile normalization in Partek Genomics Suite (6.5).

source_name: MCF7 cells_siControl_E2 treated

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng RNA using the Low Input Quick Amp Labeling Kit, One-Color (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.

growth_protocol: The human breast cancer cell line MCF7 was maintained in Dulbecco's Modified Eagle's Medium (DMEM) supplemented with 10% fetal bovine serum (FBS) (Invitrogen) at 37°C, under a humidified atmosphere of 5% carbon dioxide.

extract_protocol: Total RNA was extracted using RNeasy Mini Kit (Qiagen) following the manufacturer's recommendations.  RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: MCF-7 cells were transfected with a control siRNA or with the pool of siRNAs targeting c-Fos. At 6h after transfection, the medium was changed into phenol  red-free DMEM plus 2% charcoal-dextran-treated calf serum for 72 h and were then treated with vehicle or E2 for 24 h.

value: breast cancer cells

value: control siRNA for 72hr

tag: treated with

value: E2 for 24hr


title: epid_KO_LF_1

tag: genotype

value: low fat


title: MCF7_siControl_E2_24h_rep1

description:
SiCtrl-E2_1
Gene expression after 24 h E2 treatment in si_control treated cells


title: epid_WT_LF

data_processing: Expression estimates were calculated using RMA using R version R-2.15.0 and Bioconductor 2.10


title: MCF7_siControl_E2_24h_rep3

description:
SiCtrl-E2_3
Gene expression after 24 h E2 treatment in si_control treated cells


title: epid_KO_LF_2


title: MCF7_siFos_E2_24h_rep2

description:
SiFos-E2_2
Gene expression after 24 h E2 treatment in si_c-Fos treated cells

source_name: MCF7 cells_c-Fos knockdown_E2 treated

value: pool of siRNAs targeting c-Fos for 72hr


title: MCF7_siFos_E2_24h_rep3

description:
SiFos-E2_3
Gene expression after 24 h E2 treatment in si_c-Fos treated cells


title: MCF7_siFos_vehicle_24h_rep3

description:
SiFos-EtOH_3
Gene expression after 24 h vehicle treatment in si_c-Fos treated cells

source_name: MCF7 cells_c-Fos knockdown_Vehicle treated

value: vehicle for 24hr


title: MCF7_siControl_vehicle_24h_rep3

description:
SiCtrl-EtOH_3
Gene expression after 24 h Vehicle treatment in si_control treated cells

source_name: MCF7 cells_siControl_Vehicle treated


title: MCF7_siControl_vehicle_24h_rep1

description:
SiCtrl-EtOH_1
Gene expression after 24 h Vehicle treatment in si_control treated cells


title: MCF7_siFos_vehicle_24h_rep4

description:
SiFos-EtOH_4
Gene expression after 24 h vehicle treatment in si_c-Fos treated cells


title: MCF7_siFos_E2_24h_rep1

description:
SiFos-E2_1
Gene expression after 24 h E2 treatment in si_c-Fos treated cells


title: MCF7_siFos_vehicle_24h_rep2

description:
SiFos-EtOH_2
Gene expression after 24 h vehicle treatment in si_c-Fos treated cells


title: MCF7_siControl_vehicle_24h_rep2

description:
SiCtrl-EtOH_2
Gene expression after 24 h Vehicle treatment in si_control treated cells


title: MCF7_siFos_vehicle_24h_rep1

description:
SiFos-EtOH_1
Gene expression after 24 h vehicle treatment in si_c-Fos treated cells


title: MCF7_siFos_E2_24h_rep4

description:
SiFos-E2_4
Gene expression after 24 h E2 treatment in si_c-Fos treated cells


title: Control lung tissue, biological replicate 3

city: Neuherberg

first: Johannes

last: Beckers

address: Ingolstaedter Landstr. 1

department: Institute of Experimental Genetics

institute: Helmholtz Zentrum Muenchen

description:
wt_03.CEL
Gene expression data from lung tissue of control mice

hyb_protocol: According to the Affymetrix expression protocol

data_processing: RMA gene level analysis with Expression Console (Affymetrix) using standard settings (Sketch-Quantile)

source_name: Lung tissue from male control mice

label_protocol: Whole transcript Sense Target Labeling kit - 100 ng protocol (Affymetrix)

growth_protocol: Animals housed under spf conditions

extract_protocol: RNeasy Mini Kit (Qiagen) including DNase treatment

treatment_protocol: No treatment

value: 4 months

tag: gender

value: male

value: lung

value: control


title: Control lung tissue, biological replicate 5

description:
wt_08.CEL
Gene expression data from lung tissue of control mice

scan_protocol: According to the Affymetrix expression protocol


title: Cp70sps 6

first: Hung-Cheng

last: Lai

address: No.250, Wuxing St.

department: Department of Obstetrics and Gynecology, School of Medicine, College of Medicine,

institute: Taipei Medical University

description: replicate 1

data_processing: The data were normalised using quantile normalisation with BeadStudio

source_name: Cp70 used Hoechst3334 exclusion phenotype

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

growth_protocol: In Ultra Low attachment plates with serum-free DMEM/F12 medium containing insulin, 0.4% BSA, 10 ng/ml bFGF, and 20 ng/ml EGF

extract_protocol: RNA was teated DNase I and isolated by QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: 3uM niclosamide treated 0, 2, 4 and 6 hours

value: niclosamide

tag: time point (hours)

value: ovarian tumor-initiating cells

tag: selected methods

value: Hoechst 3334 exclusion phenotype


title: Control lung tissue, biological replicate 1

description:
wt_01.CEL
Gene expression data from lung tissue of control mice

tag: age


title: Control lung tissue, biological replicate 2

description:
wt_02.CEL
Gene expression data from lung tissue of control mice


title: Cp70sps 4

description: replicate 1

tag: treatment


title: Control lung tissue, biological replicate 4

description:
wt_07.CEL
Gene expression data from lung tissue of control mice


title: 8.1 ug/L PVP coated AgNP, exposure 3, rep.5

status: Public on Aug 05 2012

city: Boston

first: Helen

middle: C

last: Poynton

address: 100 Morrissey Blvd.

department: School for the Environment

institute: UMass Boston

description: LC25 PVP coated AgNP exposure

hyb_protocol: Labeled cRNA was hybridized to a custom 15,000 sequence D. magna array using the protocols of Agilent Technologies (AMADID # 023710).

scan_protocol: DNA microarrays were scanned using an Agilent Technologies Scanner G2505B at five micron resolution, and feature extraction was performed using Feature Extraction Software 9.5.1 (Agilent Technologies).

data_processing: Feature extraction was performed using Feature Extraction Software 9.5.1 (Agilent Technologies) to obtain intensity values for each probe.  Intensity values were further processed as described below:  Agilent one color microarray probe intensity data sets were grouped as “Experiment vs. Control” pairs by comparing each exposure to the unexposed control performed on the same date to construct expression ratios, which were then log2 transformed.  There were 6 biological replicates per each exposure condition and 6 per each control resulting in 36 “Experiment vs. Control” pairs.  Log2 transformed expression ratios were corrected for non-linear trends with loess global normalization method and a variance estimation algorithm was used to take heteroscedasticity into consideration.  A multiple slide method was used to detect candidate genes.  The technique treated the differential gene expression outcomes in a series of biological replicates (here 36) as Bernoulli trials.  Then a modified Fisher’s method of meta-analysis was applied to combine adjusted p-values:  the resulting p-values were adjusted with a Bonferroni correction using the number of null-hypotheses tested. This method does not require the use of between-array normalization because it does not apply any scale estimator.  Following these steps, a list of candidate genes was identified for each treatment, applying an average false positive cut-off of 1.

organism: Daphnia magna

source_name: PVPcoated AgNP exposed, 24-h, whole organism

label_protocol: 1.5 ug of total RNA was prepared for microarray hybridization using the Quick Amp One Color Labeling kit and One Color RNA Spike-in kit following the manufacturer’s protocols (Agilent Technologies, Santa Clara, CA).

growth_protocol: Daphnia magna were cultured at the US EPA culture facility in Cincinnati OH in Moderately Hard Reconstituted water at 25 degrees C.  They were fed 3 times weekly a combination of Pseudokirchneriella subcapitata and alfalfa extract.

extract_protocol: D. magna were removed from the exposure vessels with a pipet and immersed immediately in Tri Reagent (Molecular Research Center, Cincinnati, OH).  Whole organism daphnid tissue was homogenized for 5 min. at 30 vibrations/s using a Retsch MM 300 mixer mill (Retsch, Newtown, PA) with 3.2 mm stainless steel beads (Biospec Products, Bartlesville, OK).  Following homogenization, RNA was isolated using Tri Reagent according to the manufacturer’s methods (Molecular Research Center, Cincinnati, OH) and treated with DNAse I using Ambion's DNAfree kit (Ambion, Austin, TX).

treatment_protocol: All exposures to the nanoparticles or Ag salt were conducted on adult female daphnids 10 days old and occurred at 25.0 C for 24 hours

tag: pooling

value: 10 days old

value: female


title: Ifitm1-deficient lung tissue, biological replicate 3

description:
ko_06.CEL
Gene expression data from lung tissue of Ifitm1-deficient mice

source_name: Lung tissue from male Ifitm1-deficient mice

value: Ifitm1 k.o.


title: 8.1 ug/L PVP coated AgNP, exposure 3, rep.4

description: LC25 PVP coated AgNP exposure


title: Ifitm1-deficient lung tissue, biological replicate 4

description:
ko_10.CEL
Gene expression data from lung tissue of Ifitm1-deficient mice


title: 8.1 ug/L PVP coated AgNP, exposure 3, rep.3

description: LC25 PVP coated AgNP exposure


title: Cp70sps 0

description: replicate 1

tag: cell line


title: 3.5 ug/L citrate coated AgNP, exposure 3, rep.4

description: LC25 citrate coated AgNP exposure

source_name: citrate coated AgNP exposed, 24-h, whole organism


title: 8.1 ug/L PVP coated AgNP, exposure 3, rep.6

description: LC25 PVP coated AgNP exposure


title: 3.5 ug/L citrate coated AgNP, exposure 3, rep.5

description: LC25 citrate coated AgNP exposure


title: 3.5 ug/L citrate coated AgNP, exposure 3, rep.6

description: LC25 citrate coated AgNP exposure


title: 3.5 ug/L citrate coated AgNP, exposure 3, rep.3

description: LC25 citrate coated AgNP exposure


title: 3.5 ug/L citrate coated AgNP, exposure 3, rep.2

description: LC25 citrate coated AgNP exposure


title: unexposed control, exposure 3, rep.5

description: unexposed control for AgNP high concentration exposures

source_name: unexposed, 24-h, whole organism


title: 8.1 ug/L PVP coated AgNP, exposure 3, rep.2

description: LC25 PVP coated AgNP exposure


title: unexposed control, exposure 3, rep.4


title: 8.1 ug/L PVP coated AgNP, exposure 3, rep.1

description: LC25 PVP coated AgNP exposure


title: 3.5 ug/L citrate coated AgNP, exposure 3, rep.1

description: LC25 citrate coated AgNP exposure


title: Cp70sps 2

description: replicate 1

tag: cell type


title: unexposed control, exposure 3, rep.6


title: Ifitm1-deficient lung tissue, biological replicate 5

description:
ko_11.CEL
Gene expression data from lung tissue of Ifitm1-deficient mice

tag: strain


title: Ifitm1-deficient lung tissue, biological replicate 1

description:
ko_04.CEL
Gene expression data from lung tissue of Ifitm1-deficient mice


title: 1.0 ug/L PVP coated AgNP, exposure 2, rep.5

description: 1/10 LC50 PVP coated AgNP exposure

tag: Sex


title: unexposed control, exposure 3, rep.3


title: unexposed control, exposure 3, rep.2


title: 1.0 ug/L PVP coated AgNP, exposure 2, rep.6

description: 1/10 LC50 PVP coated AgNP exposure


title: unexposed control, exposure 3, rep.1


title: 1.0 ug/L PVP coated AgNP, exposure 2, rep.4

description: 1/10 LC50 PVP coated AgNP exposure


title: Ifitm1-deficient lung tissue, biological replicate 2

description:
ko_05.CEL
Gene expression data from lung tissue of Ifitm1-deficient mice


title: 1.0 ug/L PVP coated AgNP, exposure 2, rep.3

description: 1/10 LC50 PVP coated AgNP exposure


title: 1.0 ug/L PVP coated AgNP, exposure 2, rep.2

description: 1/10 LC50 PVP coated AgNP exposure


title: 0.43 ug/L citrate coated AgNP, exposure 2, rep.3

description: 1/10 LC50 citrate coated AgNP exposure


title: 1.0 ug/L PVP coated AgNP, exposure 2, rep.1

description: 1/10 LC50 PVP coated AgNP exposure


title: 0.43 ug/L citrate coated AgNP, exposure 2, rep.5

description: 1/10 LC50 citrate coated AgNP exposure


title: 0.43 ug/L citrate coated AgNP, exposure 2, rep.6

description: 1/10 LC50 citrate coated AgNP exposure


title: 0.43 ug/L citrate coated AgNP, exposure 2, rep.4

description: 1/10 LC50 citrate coated AgNP exposure


title: 0.43 ug/L citrate coated AgNP, exposure 2, rep.1

description: 1/10 LC50 citrate coated AgNP exposure


title: unexposed control, exposure 2, rep.5

description: unexposed control for AgNP low concentration exposures


title: unexposed control, exposure 2, rep.6


title: unexposed control, exposure 2, rep.3


title: unexposed control, exposure 2, rep.4


title: unexposed control, exposure 2, rep.2


title: 0.32 ug/L AgNO3, exposure 1, rep.6

description: high concentrations AgNO3 exposure

source_name: AgNO3 exposed, 24-h, whole animal


title: 0.32 ug/L AgNO3, exposure 1, rep.4

description: high concentrations AgNO3 exposure


title: 0.32 ug/L AgNO3, exposure 1, rep.5

description: high concentrations AgNO3 exposure


title: 4210902

type: genomic

description: pooled DNA from 19 patient's tissues

hyb_protocol: The labeled MeDIP DNA was precipitated with 0.1 volume 5M NaCl and 1 volume isopropanol, and hybridized in 45 ul of buffer containing 20% formamide, 1.2 M betaine, 0.1 ug/ul herring sperm DNA and 10 ug of human COT1 DNA (Invitrogen). Arrays were hybridized in Maui hybridization stations for 16-18 h at 42C, and then washed in 42C 0.2% SDS/0.2x SSC, room temperature 0.2x SSC, and 0.05x SSC. Hybridization buffers and washes were completed using manufacturer's protocols (http://www.nimblegen.com/products/lit/lit.html)

scan_protocol: Arrays were scanned on an Axon 4000B scanner per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

data_processing: Arrays were processed using Nimblegen's standard protocol for Nimblescan 2.4 ChIP data extraction.

molecule: genomic DNA

source_name: Input DNA from normal pools DNA

label_protocol: 1 µg MeDIP DNA was directly labeled by Klenow (New England Biolabs) random priming with Cy3 nonamers (MeDIP DNA isolated from normal rabbit IgG-immunoprecipitated cells) per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

extract_protocol: Using DNA Mini Kit extract tissue DNA

value: femal cervical normal scraping cells

source_name: MeDIP DNA from normal pools DNA


title: 0.32 ug/L AgNO3, exposure 1, rep.2

description: high concentrations AgNO3 exposure


title: 4343002

description: pooled DNA from 38 patient's tissues

source_name: Input DNA from squamous carcinoma pools DNA

value: femal cervical tumor tissue

source_name: MeDIP DNA from squamous carcinoma pools DNA


title: 0.43 ug/L citrate coated AgNP, exposure 2, rep.2

description: 1/10 LC50 citrate coated AgNP exposure


title: unexposed control, exposure 2, rep.1


title: 4212202

description: pooled DNA from 19 patient's tissues

source_name: Input DNA from adenocarcinoma pools DNA

source_name: MeDIP DNA from adenocarcinoma pools DNA


title: 4209502

description: pooled DNA from 19 patient's tissues


title: 0.32 ug/L AgNO3, exposure 1, rep.3

description: high concentrations AgNO3 exposure


title: 0.16 ug/L AgNO3, exposure 1, rep.6

description: mid-level concentration AgNO3 exposure


title: 0.32 ug/L AgNO3, exposure 1, rep.1

description: high concentrations AgNO3 exposure


title: 0.16 ug/L AgNO3, exposure 1, rep.4

description: mid-level concentration AgNO3 exposure


title: 0.16 ug/L AgNO3, exposure 1, rep.3

description: mid-level concentration AgNO3 exposure


title: 0.16 ug/L AgNO3, exposure 1, rep.5

description: mid-level concentration AgNO3 exposure


title: 4155502

description: pooled DNA from 19 patient's tissues


title: 0.08 ug/L AgNO3, exposure 1, rep.5

description: low concentration (1/10 LC50) AgNO3 exposure


title: 4272702

description: pooled DNA from 38 patient's tissues


title: 0.16 ug/L AgNO3, exposure 1, rep.1

description: mid-level concentration AgNO3 exposure


title: 0.08 ug/L AgNO3, exposure 1, rep.6


title: unexposed,exposure 1, rep.1

description: unexposed control for AgNO3 exposures


title: 0.16 ug/L AgNO3, exposure 1, rep.2

description: mid-level concentration AgNO3 exposure


title: 0.08 ug/L AgNO3, exposure 1, rep.4


title: unexposed,exposure 1, rep.2

description: unexposed control for AgNO3 exposures


title: unexposed,exposure 1, rep.4

description: unexposed control for AgNO3 exposures


title: unexposed,exposure 1, rep.6

description: unexposed control for AgNO3 exposures


title: unexposed,exposure 1, rep.3

description: unexposed control for AgNO3 exposures


title: 0.08 ug/L AgNO3, exposure 1, rep.3


title: 0.08 ug/L AgNO3, exposure 1, rep.1


title: unexposed,exposure 1, rep.5

description: unexposed control for AgNO3 exposures


title: CGH ZK2_vs_BYZ1

city: Hangzhou

first: Daoqiong

last: Zheng

state: Zhejiang

address: 866 Yuhangtang Road

department: Institute of Microbiology

institute: College of Life Sciences, Zhejiang University

hyb_protocol: Samples were labeled with Cy5 (BYZ1) or Cy3 (YJS329 and ZK2) and then hybridized to two S. cerevisiae 385k CGH Whole-Genome Tiling arrays (NimbleGen).

scan_protocol: Axon GenePix 4000B microarray scanner (Axon, USA) was used to scan the microarrays.

data_processing: Raw data were extracted as pair files by NimbleScan software. Log2-ratio data were calculated and normalized by spatial correction and qspline fit normalization.

organism: Saccharomyces cerevisiae

label_protocol: Genomic DNA was extracted and sheared into the DNA fragments with the length of 200–1000 bp before dye labeling.

extract_protocol: Total genomic DNA from yeast cells was isolated with the Yeast DNA kit (OMEGA, CA, USA).

tag: application

value: bioethanol strain

value: BYZ1 (MATa/MATα his3Δ1/his3Δ1 leu2Δ0/leu2Δ0 lys2Δ0/+ met15Δ0/+ ura3Δ0/ura3Δ0)

value: laboratory strain (S288c background)


title: Schu 120h Spl

status: Public on Aug 04 2012

city: Fort Collins

first: Luke

last: Kingry

state: CO

address: 2025 IDRC at Foothills Campus Delivery

institute: Colorado State University

description:
Samples were enriched for bacterial mRNA by depletion of host polyA and ribosomal RNA.
This Sample represents 3 hybridizations: slide 2, slide 35, and slide 65.

hyb_protocol: Dye-coupled cDNA was combined with yeast tRNA (10mg/mL) and hybridization buffer (formamide, 20XSSC and 10%SDS), and heated (95C 5min). Single channel (Cy3) hybridization was carried out in triplicate for each sample.

scan_protocol: Data were generated by the GenePix Pro 4000B scanner and GenePix Pro software.

data_processing: Signal-to-noise (SNR) ratios were averaged and used to determine genes that were active in the mouse spleen. Features without bad flags and with an average SNR greater than 2 were considered expressed in the mouse spleen. Data was normalized by global mean normalization and averaged among the three arrays. All normalization was done using Microsoft Excel.

organism: Francisella tularensis subsp. tularensis SCHU S4

source_name: F. tularensis from infected mouse spleen 120 hr post-infection

label_protocol: Bacterial mRNAs were converted to cDNA using random hexamer primers and Arrayscript (Invitrogen) reverse transcriptase in the presence of Cy3-coupled UTPs. Reactions were incubated at 42C for 30 minutes, treated with RNAse A at 37C for 30 minutes. cDNAs were purified using the Qiagen PCR purification kit.

growth_protocol: Mice were infected i.n. with F. tularensis Schu4 and disseminated to the spleen 120 hours post infection. Spleens were harvested 120 hours post-infection. Bacteria were growing within the host spleen.

extract_protocol: RNA was stabilized and recovered from mouse organs by the addition of TRIzol reagent and organic partitioning. Total RNA was extracted from the TRIzol by the addition of chloroform (1:1) to achieve a bi-phase separation, then precipitated by the addition of isopropanol and subjected to DNase treatment, and purified via precipitation in NH4OAc. Total RNA was depleted of host polyA RNA and ribosomal RNA using hybridization probes coupled to magnetic beads, magnets were used to pull down beads. The resulting sample was enriched for bacterial mRNA.

value: Schu 4

tag: host

value: C57BL/6 mouse spleen

tag: time post-infection

value: 120 hours


title: 0.08 ug/L AgNO3, exposure 1, rep.2


title: CD4Tcells_activated_62A_0.25_rep3

city: LA JOLLA

first: Jason

last: Greenbaum

address: 9420 Athena Circle

department: Bioinformatics Core Facility

institute: LIAI

hyb_protocol: The resulting cRNAs (two independent data sets for each sample type) were hybridized to Mouse 430 2.0 Arrays (Affymetrix) according to the manufacturer's protocol.

scan_protocol: The initial reads were processed through Affymetrix software to obtain raw .cel files.

data_processing: The .cel files were processed using cCHIP (v.2010.01), using invariant-set normalization.

label_protocol: The amplified RNA was subsequently labeled with the BioArray High Yield RNA Transcription Labeling Kit (Enzo Diagnostics) and purified with the RNeasy Mini Kit (Qiagen).

growth_protocol: CD4+T cells were isolated from 2D2 TCR transgenic mice and activated with plate bound anti-CD3 and anti-CD28 antibodies under Th1 conditions in the presence of Control-768 or I-BET-762 compounds. 48 hours after initial activation, the cells were removed from the anti-CD3 and anti-CD28 coated plates and expanded for an additional 2 days.

extract_protocol: RNA was extracted from resting cells or from cells restimulated with plate-bound anti-CD3 and anti-CD28 for 4 hours. RNA was extracted using the RNeasy Kit (Qiagen) and amplified for two rounds using the MessageAmp amplified RNA kit (Ambion).

treatment_protocol: CD4+T cells were grown in the presense of one of three molecules (DMSO, Control-768, I-BET-762 at 0.25 uM or 0.5uM)

tag: strain background

tag: genotype/variation

value: 2D2 TCR transgenic

value: CD4+ T cells

tag: state

value: activated

tag: grown in the presence of


title: CD4Tcells_resting_62A_0.5_rep3

value: resting

value: I-BET-762 at 0.5 uM


title: CD4Tcells_activated_62A_0.5_rep3


title: CD4Tcells_activated_68A_rep3


title: CD4Tcells_activated_DMSO_rep3

value: DMSO


title: CD4Tcells_resting_68A_rep3


title: CD4Tcells_resting_62A_0.25_rep3


title: CD4Tcells_resting_DMSO_rep2


title: CD4Tcells_resting_62A_0.25_rep2


title: CD4Tcells_activated_68A_rep2


title: CD4Tcells_resting_DMSO_rep3


title: CD4Tcells_activated_68A_rep1


title: CD4Tcells_activated_62A_0.25_rep1


title: CD4Tcells_resting_62A_0.25_rep1


title: CD4Tcells_activated_DMSO_rep2


title: CD4Tcells_resting_DMSO_rep1


title: CD4Tcells_activated_62A_0.25_rep2


title: CD4Tcells_activated_62A_0.5_rep2


title: CD4Tcells_resting_62A_0.5_rep1


title: CD4Tcells_resting_68A_rep2


title: CD4Tcells_resting_68A_rep1


title: CD4Tcells_activated_DMSO_rep1


title: Spinal cord_wild type_advanced

city: Nagoya

first: Makoto

last: Minamiyama

address: 65 Tsurumai-Cho, Showa-Ku

department: Neurology

country: Japan

institute: Nagoya University Graduate School of Medicine

description: WA

hyb_protocol: The hybridization process was performed by TAKARA BIO (Otsu, Japan). Affymetrix GeneChip® Expression Analysis Technical Manual With Specific Protocols for Using the GeneChip® Hybridization, Wash, and Stain Kit

scan_protocol: The scanning process was performed by TAKARA BIO (Otsu, Japan). Affymetrix® GeneChip® Scanner 3000 with GCOS software (v1.1.1) according to manufactuer's protocol (Affymetrix GeneChip® Expression Analysis Technical Manual With Specific Protocols for Using the GeneChip® Hybridization, Wash, and Stain Kit).

data_processing: The probe sets were extracted by the present detection call (Algorithm: ExpressionStat 5.0). The signals were normalized by the trimmed mean method, and significantly different probe sets (p<0.005) were identified among the strains of mice and stages with a two-way repeated ANOVA.

source_name: Wild type mouse spinal cord in advanced disease stage

label_protocol: The labelling process was performed by TAKARA BIO (Otsu, Japan). Affymetrix GeneChip® Expression Analysis Technical Manual With Specific Protocols for Using the GeneChip® Hybridization, Wash, and Stain Kit.

growth_protocol: These mice were fed under 12L12D at 25℃ condition.

extract_protocol: RNA from the total spinal cord, excluding the dorsal root ganglia, was isolated from three mice of each genotype at each stage using Trizol reagent (Invitrogen, Carlsbad, CA) according to the manufacturer’s specifications. The RNA samples were purified over RNeasy columns (Qiagen, Germantown, MA).

tag: gender

value: male

tag: genotype/varation

value: wild-type littermates of the AR-97Q mice (C57BL/6)

value: 13-15 weeks (advanced stage)

tag: tisue

value: spinal cord without DRG (pool of three mice)


title: CD4Tcells_activated_62A_0.5_rep1


title: Spinal cord_wild type_before-onset

description: WP

source_name: Wild type mouse spinal cord before onset

tag: age

value: 7-9 weeks (before-onset stage)


title: Spinal cord_wild type_early

description: WE

source_name: Wild type mouse spinal cord in early disease stage

value: 10-12 weeks (early stage)


title: CD4Tcells_resting_62A_0.5_rep2


title: Spinal cord_97Q_advanced_rep3

source_name: AR-97Q mouse spinal cord at advanced disease stage

value: transgenic mice carrying a full-length human AR with 97 CAGs (AR-97Q)

value: spinal cord without DRG


title: Spinal cord_97Q_advanced_rep2


title: Spinal cord_97Q_advanced_rep1


title: Spinal cord_97Q_Early_rep3

source_name: AR-97Q mouse spinal cord at early disease stage


title: Spinal cord_97Q_Early_rep1


title: Spinal cord_97Q_Early_rep2


title: Spinal cord_97Q_before-onset_rep3

source_name: AR-97Q mouse spinal cord before onset


title: Spinal cord_97Q_before-onset_rep2


title: 200mg/kg-jejunum-rat1

city: North Chicago

first: Rita

last: Ciurlionis

state: IL

address: 1 North Waukegan Road

institute: Abbvie

description: Gene expression data from jejunum of rats treated for 5 days orally with A-998679 at 200 mg/kg/day

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Rat 230_2 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G3000.

data_processing: Log intensity and p values generated in Rosetta Resolver (version 7.2) based on imported Affymetrix .cel files with mean scaling (controls and flagged spots excluded, trim percentage of '10.0') and standard (untransformed) detrending algorithm for non-linearity correction (max bins = '40'; trim percentage = '20.0'). Fold change; all gene expression changes with fold change at least +/-1.5 and p<0.05 in at least one sample; changes not meeting these parameters are considered unchanged (FC=1).

organism: Rattus norvegicus

source_name: jejunum

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

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

treatment_protocol: jejunum from vehicle and compound treated rats was flash frozen in LN2 at necropsy

tag: tissue

value: jejunum

value: Sprague Dawley

tag: weight

tag: treatment


title: 200mg/kg-jejunum-rat2

value: treated for 5 days orally with A-998679 at 200 mg/kg/day


title: 100mg/kg-jejunum-rat3

description: Gene expression data from jejunum of rats treated for 5 days orally with A-998679 at 100 mg/kg/day


title: 100mg/kg-jejunum-rat2

value: treated for 5 days orally with A-998679 at 100 mg/kg/day


title: Spinal cord_97Q_before-onset_rep1


title: Spinal cord_24Q_advanced_rep3

source_name: AR-24Q mouse spinal cord at advanced disease stage

value: transgenic mice bearing a wild-type allele of AR with 24 CAGs (AR-24Q)


title: Spinal cord_24Q_advanced_rep1


title: Spinal cord_24Q_advanced_rep2


title: vehicle-jejunum-rat2

description: Gene expression data from jejunum of rats treated for 5 day orally with 0.2% HPMC at 10 ml/kg/day


title: 30mg/kg-jejunum-rat1

description: Gene expression data from jejunum of rats treated for 5 days orally with A-998679 at 30 mg/kg/day


title: 30mg/kg-jejunum-rat2

value: treated for 5 days orally with A-998679 at 30 mg/kg/day


title: Spinal cord_24Q_Early_rep2

source_name: AR-24Q mouse spinal cord at early disease stage


title: vehicle-jejunum-rat3

value: treated for 5 day orally with 0.2% HPMC at 10 ml/kg/day


title: vehicle-jejunum-rat1


title: Spinal cord_24Q_Early_rep3


title: 2hr LPS exposure replicate2 vs 0hr untreatedpool

status: Public on Aug 03 2012

city: Rockville

first: Bryan

last: Frank

state: MD

address: 9704 Medical Center Drive

department: Dept of Infectious Diseases

institute: The J. Craig Venter Institute

hyb_protocol: Labeled cDNA was hybridized to the Agilent arrays according to the Agilent protocol.

scan_protocol: Hybridizations were scanned on the Axon 4000B scanner with GenePix Pro software.

data_processing: Intensity values were extracted using Feature Extraction 9.5.3.1 from Agilent and then normalized and analyzed using MIDAS and MeV from the TM4 Suite.

source_name: RAW 264.7 cell line

label_protocol: A total of 2 ug of RNA in a mixture containing 6 ug of random hexamers, 0.01 M dithiothreitol, an aminoallyl-deoxynucleoside triphosphate mixture containing 25 mM each dATP, dCTP, and dGTP, 15 mM dTTP, and 10 mM amini-allyl dUTP (aa-dUTP), reaction buffer, and 400 units of SuperScript III reverse transcriptase at 42C overnight. The RNA template then was hydrolyzed by adding NaOH and EDTA to a final concentration of 0.2 and 0.1 M, respectively, and incubating at 65C for 15 min. Unincorporated aa-UTP was removed with a MinElute column. The probe was eluted with a phosphate elution buffer (4 mM KPO4, pH 8.5, in ultrapure water), dried and resuspended in 0.1 M sodium carbonate buffer (ph 9.0). To couple the amino-allyl cDNA with fluorescent labels, normal human serum-Cy3 or normal human serum-Cy5 was added at room temperature for 1 hour. Uncoupled label was removed using the Qiagen MinElute columns.

growth_protocol: RAW 264.7 cells were grown in DMEM supplemented with 10% FBS.

extract_protocol: Cells were washed twice with PBS and then RNA was harvested according to the TriZol protocol.

treatment_protocol: Cells were treated with either flagellin or LPS for 1, 2, 4, or 24 hours.

tag: cell line

value: 2hr LPS exposure


title: Spinal cord_24Q_before-onset_rep3

source_name: AR-24Q mouse spinal cord before onset


title: 24hr flagellin exposure replicate2 vs 0hr untreatedpool

value: 24hr flagellin exposure


title: 2hr LPS exposure replicate1 vs 0hr untreatedpool


title: 4hr LPS exposure replicate1 vs 0hr untreatedpool

value: 4hr LPS exposure


title: 24hr LPS exposure replicate2 vs 0hr untreatedpool

value: 24hr LPS exposure


title: Spinal cord_24Q_before-onset_rep1

value: male


title: Spinal cord_24Q_Early_rep1


title: 100mg/kg-jejunum-rat1

tag: strain


title: 24hr LPS exposure replicate1 vs 0hr untreatedpool


title: SAMPLE 112_miRNA_Normal [FF]

city: Rochester

first: Jin Sung

last: Jang

state: MN

address: 200 First St SW

institute: Mayo Clinic

description: SAMPLE 112

hyb_protocol: Fluorescently labelled cDNA PCR products were hybridized to the Illumina Sentrix BeadChip according to the manufacturer's protocol

scan_protocol: Scanned using the Illumina Bead Array Reader

data_processing: The data were normalized using quantile normalization with BeadStudio software. The data were normalised using quantile normalisation with IlluminaGUI in R

label_protocol: Biotinylated cDNA were prepared from 100-200ng total RNA using the DASL Assay (cDNA-mediated annealing, selection, extension and ligation)

extract_protocol: RNA was extracted using the miRNeasy kit (Qiagen Inc, Valencia, California, USA) using the manufacturer’s protocols. Quality control was performed with Agilent Bioanalyser.

tag: tissue origin

value: uninvolved lung

tag: sample type

value: fresh-frozen (FF) normal tissue


title: 4hr LPS exposure replicate2 vs 0hr untreatedpool


title: 1hr LPS exposure replicate1 vs 0hr untreatedpool

value: 1hr LPS exposure


title: 24hr flagellin exposure replicate1 vs 0hr untreatedpool


title: SAMPLE 111_miRNA_Normal [FF]

description: SAMPLE 111


title: 4hr flagellin exposure replicate1 vs 0hr untreatedpool

value: 4hr flagellin exposure


title: SAMPLE 110_miRNA_Normal [FF]

description: SAMPLE 110


title: Spinal cord_24Q_before-onset_rep2

value: 7-9 weeks (before-onset stage)

value: spinal cord without DRG


title: 1hr flagellin exposure replicate3 vs 0hr untreatedpool

value: 1hr flagellin exposure


title: SAMPLE 108_miRNA_Normal [FF]

description: SAMPLE 108


title: SAMPLE 109_miRNA_Normal [FF]

description: SAMPLE 109


title: 2hr flagellin exposure replicate1 vs 0hr untreatedpool

value: 2hr flagellin exposure


title: SAMPLE 107_miRNA_Normal [FF]

description: SAMPLE 107


title: SAMPLE 105_miRNA_Normal [FF]

description: SAMPLE 105


title: 1hr LPS exposure replicate2 vs 0hr untreatedpool


title: SAMPLE 102_miRNA_Normal [FF]

description: SAMPLE 102


title: SAMPLE 106_miRNA_Normal [FF]

description: SAMPLE 106


title: SAMPLE 103_miRNA_Normal [FF]

description: SAMPLE 103


title: SAMPLE 104_miRNA_Normal [FF]

description: SAMPLE 104


title: SAMPLE 101_miRNA_Normal [FF]

description: SAMPLE 101


title: 4hr flagellin exposure replicate2 vs 0hr untreatedpool


title: SAMPLE 100_miRNA_Normal [FF]

description: SAMPLE 100


title: 1hr flagellin exposure replicate2 vs 0hr untreatedpool


title: SAMPLE 95_miRNA_Normal [FF]

description: SAMPLE 95


title: SAMPLE 99_miRNA_Normal [FF]

description: SAMPLE 99


title: SAMPLE 97_miRNA_Normal [FF]

description: SAMPLE 97


title: SAMPLE 94_miRNA_Normal [FF]

description: SAMPLE 94


title: SAMPLE 90_miRNA_Normal [FF]

description: SAMPLE 90


title: SAMPLE 89_miRNA_Tumor [FF]

description: SAMPLE 89

value: lung adenocarcinoma

tag: cancer type

value: non-small-cell lung cancer (NSCLC)

value: fresh-frozen (FF) tumor tissue


title: SAMPLE 88_miRNA_Tumor [FF]

description: SAMPLE 88


title: SAMPLE 91_miRNA_Normal [FF]

description: SAMPLE 91


title: SAMPLE 92_miRNA_Normal [FF]

description: SAMPLE 92


title: SAMPLE 85_miRNA_Tumor [FF]

description: SAMPLE 85


title: SAMPLE 83_miRNA_Tumor [FF]

description: SAMPLE 83


title: SAMPLE 87_miRNA_Tumor [FF]

description: SAMPLE 87


title: SAMPLE 82_miRNA_Tumor [FF]

description: SAMPLE 82


title: SAMPLE 86_miRNA_Tumor [FF]

description: SAMPLE 86


title: SAMPLE 80_miRNA_Tumor [FF]

description: SAMPLE 80


title: SAMPLE 81_miRNA_Tumor [FF]

description: SAMPLE 81


title: SAMPLE 93_miRNA_Normal [FF]

description: SAMPLE 93


title: SAMPLE 98_miRNA_Normal [FF]

description: SAMPLE 98


title: SAMPLE 73_miRNA_Tumor [FF]

description: SAMPLE 73


title: SAMPLE 75_miRNA_Tumor [FF]

description: SAMPLE 75


title: SAMPLE 77_miRNA_Tumor [FF]

description: SAMPLE 77


title: SAMPLE 76_miRNA_Tumor [FF]

description: SAMPLE 76


title: SAMPLE 74_miRNA_Tumor [FF]

description: SAMPLE 74


title: SAMPLE 78_miRNA_Tumor [FF]

description: SAMPLE 78


title: SAMPLE 84_miRNA_Tumor [FF]

description: SAMPLE 84


title: SAMPLE 71_miRNA_Tumor [FF]

description: SAMPLE 71


title: SAMPLE 70_miRNA_Tumor [FF]

description: SAMPLE 70


title: SAMPLE 68_miRNA_Tumor [FF]

description: SAMPLE 68


title: SAMPLE 79_miRNA_Tumor [FF]

description: SAMPLE 79


title: SAMPLE 67_miRNA_Tumor [FF]

description: SAMPLE 67


title: SAMPLE 69_miRNA_Tumor [FF]

description: SAMPLE 69


title: SAMPLE 64_miRNA_Normal [FF]

description: SAMPLE 64


title: SAMPLE 62_miRNA_Normal [FF]

description: SAMPLE 62


title: SAMPLE 72_miRNA_Tumor [FF]

description: SAMPLE 72


title: SAMPLE 57_miRNA_Normal [FF]

description: SAMPLE 57


title: SAMPLE 63_miRNA_Normal [FF]

description: SAMPLE 63


title: SAMPLE 59_miRNA_Normal [FF]

description: SAMPLE 59


title: SAMPLE 58_miRNA_Normal [FF]

description: SAMPLE 58


title: SAMPLE 60_miRNA_Normal [FF]

description: SAMPLE 60


title: SAMPLE 65_miRNA_Normal [FF]

description: SAMPLE 65


title: SAMPLE 66_miRNA_Normal [FF]

description: SAMPLE 66


title: SAMPLE 55_miRNA_Normal [FF]

description: SAMPLE 55


title: SAMPLE 48_miRNA_Tumor [FF]

description: SAMPLE 48


title: SAMPLE 56_miRNA_Normal [FF]

description: SAMPLE 56


title: SAMPLE 46_miRNA_Tumor [FF]

description: SAMPLE 46


title: SAMPLE 49_miRNA_Tumor [FF]

description: SAMPLE 49


title: SAMPLE 47_miRNA_Tumor [FF]

description: SAMPLE 47


title: SAMPLE 53_miRNA_Normal [FF]

description: SAMPLE 53


title: SAMPLE 45_miRNA_Tumor [FF]

description: SAMPLE 45


title: SAMPLE 52_miRNA_Normal [FF]

description: SAMPLE 52


title: SAMPLE 51_miRNA_Tumor [FF]

description: SAMPLE 51


title: SAMPLE 43_miRNA_Tumor [FF]

description: SAMPLE 43


title: SAMPLE 61_miRNA_Normal [FF]

description: SAMPLE 61


title: SAMPLE 54_miRNA_Normal [FF]

description: SAMPLE 54


title: SAMPLE 44_miRNA_Tumor [FF]

description: SAMPLE 44


title: SAMPLE 42_miRNA_Tumor [FF]

description: SAMPLE 42


title: SAMPLE 50_miRNA_Tumor [FF]

description: SAMPLE 50


title: SAMPLE 38_miRNA_Tumor [FF]

description: SAMPLE 38


title: SAMPLE 39_miRNA_Tumor [FF]

description: SAMPLE 39


title: SAMPLE 41_miRNA_Tumor [FF]

description: SAMPLE 41


title: SAMPLE 37_miRNA_Tumor [FF]

description: SAMPLE 37


title: SAMPLE 40_miRNA_Tumor [FF]

description: SAMPLE 40


title: SAMPLE 35_miRNA_Tumor [FF]

description: SAMPLE 35


title: SAMPLE 34_miRNA_Tumor [FF]

description: SAMPLE 34


title: SAMPLE 36_miRNA_Tumor [FF]

description: SAMPLE 36


title: SAMPLE 32_miRNA_Tumor [FF]

description: SAMPLE 32


title: SAMPLE 31_miRNA_Normal [FF]

description: SAMPLE 31


title: SAMPLE 28_miRNA_Normal [FF]

description: SAMPLE 28


title: SAMPLE 30_miRNA_Normal [FF]

description: SAMPLE 30


title: SAMPLE 27_miRNA_Normal [FF]

description: SAMPLE 27


title: SAMPLE 26_miRNA_Normal [FF]

description: SAMPLE 26


title: SAMPLE 24_miRNA_Normal [FF]

description: SAMPLE 24